Sei sulla pagina 1di 113
StudentStudent Student -- - FacultyFaculty Faculty ProgramsPrograms Programs 2015 Abstract Book
StudentStudent Student -- - FacultyFaculty Faculty ProgramsPrograms Programs 2015 Abstract Book

StudentStudentStudent---FacultyFacultyFaculty ProgramsProgramsPrograms 2015 Abstract Book


2015 Abstract Book

This document contains the abstracts of the research projects conducted by students in all programs coordinated by Caltech’s Student-Faculty Programs Office for the summer of 2015.

Table of Contents

Summer Undergraduate Research Fellowships (SURF)


WAVE Undergraduate Research Fellowships


Amgen Scholars Program


Laser Interferometer Gravitational-Wave Observatory (LIGO)



Reference Frames Employed by Neuronal Populations in the Posterior Parietal Cortex of Humans Minaam Abbas Mentors: Richard A. Andersen and Tyson Aflalo

A brain machine interface (BMI) works by decoding the intentions of the user from patterns of neural activity. In

this study, we seek to understand the reference frame of intention signals in the posterior parietal cortex of a tetraplegic human participating in a BMI clinical study e.g. whether intention signals are represented with respect

to where the subject is looking, the current location of the effector, or the body or world.

Neural population activity was recorded from an electrode array implanted in the PPC of a tetraplegic subject during a modified delayed reach task. We instructed different gaze and starting effector positions to understand how these factors influenced neural firing for intended reaches. Analysis was performed on single units as well as on the whole neural population recorded. We found that both the initial hand and eye positions affect intention decoding during reaches providing evidence that understanding neural reference frames is critical for optimizing BMI performance. Preliminary results suggest that individual neurons can code reach intentions in a variety of reference frames providing a rich set of intention related activity. The results help identify the regions of the brain important for spatial transformations underlying movements. Additionally, the findings provide critical information about how future decoding algorithms should interpret signals when used in a BMI.

Inner Core Translation and True Polar Wander Jacob Abrahams Mentors: David Stevenson and Hao Cao

Recent seismological observations point to asymmetric seismic velocity distribution in the Earth's inner core, which has the potential to cause long term East-West asymmetry observed in the Earth's magnetic field. Data from the MESSENGER spacecraft show that Mercury's magnetic field is strongly asymmetric in the North-South direction yet lacks East-West asymmetry. Current understanding of the Earth's inner core's asymmetry, in particular the inner core translation scenario, tend to favor the asymmetry in the direction normal to the spin axis when the heat transfer efficiency is isotropic near the inner core boundary. \newline

Here we explore the density distributions and moments of inertia (MoI) of a translating planetary inner core. In particular, we focus on the relative magnitude of the inner core's polar moment of inertia and equatorial moment of inertia. We find that in an East-West translating inner core, there is about 10\% probability that the equatorial moment of inertia can becomes larger than the polar moment of inertia. True polar wander of an internally driven translating inner core would then rotate an originally East-West translation into a North-South translation. We propose that a North-South translating inner core could produce a magnetic field which qualitatively resembles that of Mercury's, given that the inner core is viscous enough and can true polar wander. In addition, the high likelihood of the translation direction establishing a maximum moment of inertia normal to itself likely explains Earth's equatorially aligned translation.

Graphical User Interface (GUI) for MacroDFT and Parallel Computing Oreoluwa Adesina Mentors: Kaushik Bhattacharya, Mauricio Ponga, and Dingyi Sun

Bhattacharya’s group developed a software called MacroDFT. This is a large-scale Density Functional Theory (DFT) software that requires input from its user. But unfortunately, this software did not have a graphical user interface to accept the user’s data, and this proved a drawback in the user experience. The aim of my project was to create

a graphical user interface which is able to collect user input for the code. Using the Python programming language,

a graphical user interface (GUI) was designed and after a few weeks, the GUI became a complete standalone windows application which solved the problem that slowed down the progress of MacroDFT.

In addition to this project, I worked on another project with the aim of reducing the amount of time computers spend in performing work assigned to them. Using MATLAB, I performed simulations which tested different algorithms. This project I still a work in progress but the intention is to obtain the most efficient algorithm which simultaneously saves the most time, and then apply it to computers and get work done quicker and better.

Global Analysis of Rotational Spectra of the Ground State and Excited Torsional State of Propylene Oxide Avinash Agrawal Mentors: Geoff Blake, Ian Finneran, and Jacob Good

This paper analyses the spectra of Propylene Oxide with special attention to the splitting caused by the methyl group internal rotation. This molecule is important as it a candidate for first chiral molecule found outside our solar system. Previous data are used alongside more accurate data collected in the Blake lab from 8 - 18 GHz to refine the values of the inertial parameters, the internal rotation barrier height, and the rotational distortion constants. Multiple programs are used for ab initio calculations and experimental data fitting such as SPFIT, XIAM, and


Gaussian 09. Ab initio calculations indicate that the barrier height is 915 cm -1 and the rotational constants are A: 18094, B: 6719, C: 5990, all in MHz. Subsequent work will include the use of lab data as well as previous data to modify the ab initio calculations and to fit ground state and excited torsional states.

Frustrated Lewis Pairs as a Route for N 2 Reduction by H 2 Saaket Agrawal Mentors: Jonas C. Peters, Jonathan Rittle, Miles W. Johnson, and Sidney E. Creutz

The reduction of nitrogen (N 2 ) to ammonia (NH 3 ) is an important transformation relevant to life. Our group has previously synthesized tripodal iron complexes that can catalytically reduce N 2 to NH 3 . Unfortunately, these transformations require the use of a very high energy reducing mixture of KC 8 and HBAr F 4 , limiting the system’s practicality. A sustainable route for the reduction of N 2 to NH 3 with a homogenous catalyst will use a much cheaper and easy to access reductant, such as hydrogen gas (H 2 ). Frustrated Lewis pairs (FLPs), sets of Lewis acids and bases that remain unquenched due to steric encumbrance, have been shown to be a promising route for activation of H 2 . Herein, we present progress towards the utilization of the FLP concept to activate H 2 for the reduction of N 2 to NH 3 on our previously reported tripodal iron complexes. Studies are ongoing.

Observation and Reactivity Studies of a Rh I Intermediate in H 2 Evolution Catalysis Luis M. Aguirre Quintana Mentors: Harry B. Gray, James D. Blakemore, Jay R. Winkler, and Bruce S. Brunschwig

Understanding mechanisms of hydrogen evolution is important for improving catalysts that generate clean fuels. Catalysts often operate via unknown mechanism(s) due to the difficulty of observing or isolating key intermediates in the 2e /2H + reduction process. For our study, we prepared a family of Rh I complexes bearing the pentamethylcyclopentadienyl (η 5 -Cp*) ligand in addition to derivatives of 4,4´-bipyridyl or 1,10-phenanthroline (bound in the κ 2 mode). Under carefully chosen conditions, these compounds formed intermediate species that suggest a previously unknown mechanism of H 2 evolution. This intermediate complex could be isolated in a MeCN solution, and even as a solid, making it amenable to further mechanistic investigations. The intermediate species were analyzed by mass spectrometry, 1 H NMR, and 2 H NMR (NMR is nuclear magnetic resonance spectroscopy). Results will be discussed concerning the properties and reactivity of these active intermediates.

Rapid Prototyping of Moderate Complexity Biomolecular Circuits: Bistable Switch Enrique Amaya Mentors: Richard Murray, Clare Hayes, and Vipul Singhal

Synthetic biologists adapt engineering principles to biological systems by developing robust and standardized modules in order to design complex biomolecular circuits. These are used to program cells with desired functions that attempt to address societal challenges such as deadly diseases and damaged environments. However implementing a complex biocircuit in vivo is a laborious process as there are long steps between DNA assembly, transformation, growing and selecting cultures. This can be addressed by using modeling and prototyping to predict what conditions are required for proper performance. In this project our prototyping device was an E.coli based cell-free expression system called TX-TL (translation-transcription). With this tool we prototyped several sets of repression systems, including the promoters pLac and pTet, the repressor proteins LacI and TetR and the inducers IPTG and aTc. The data obtained was used for parameter estimation using a TX-TL simulation environment in MATLAB and the lsqcurvefit method. As a final step we plan to build a bistable switch, first simulating the circuit in silico and then comparing its behavior in the TX-TL expression system to find out if our modeling toolbox reliably predicts biocircuits performance.

Self-Assembly of Large Structures in Space Using Lagrangian Mechanics Carmen Amo Alonso Mentor: Michael Ortiz

In-orbit assembly of structures is a costly and time-consuming task at present. The approach carried out in this research relies on the invariance of the Lagrange mechanics equations under change of time sign. With this strategy, the most natural self-assembly mechanisms are easily found, which allows an innovative and efficient way of self-assembly that has not been studied before. The work focuses on the dissolution of a rotating structure in a spiral shape composed by discrete units held together. The structure increases its angular velocity until the peripheral units start to detach as an effect of the centrifugal acceleration. As the structure losses mass, its angular velocity increases, so it can result in the complete dissolution of the spiral. For this to happen the rate of emission needs to be stable, what can be reached by imposing the laws of conservation and some design requirements. Just by changing the sign of time, the way to provide the discrete components and the appropriate geometry of the structure in order to assure the continuous assembly is reached.


Practical Implementation of Interference Alignment for Cellular Networks Alexander Anemogiannis Mentor: Babak Hassibi

Many researchers have proposed various approaches to Interference Alignment (IA), a way of mitigating the effects of interference in multi-user networks, but these approaches tend to take place in ideal settings somewhat removed from practice. We present a practical approach that uses minimal channel state information and encourages fairness among users. Rather than relying on full channel knowledge, we focus on the topology of the network and represent channels between users with one bit to distinguish between strongly interfering users and weakly interfering users that can be ignored. Given the topology, we use an alternating minimization between precoding filters at the transmitters and receiver shaping filters at the receivers to isolate desired signals from strong interferers. Maximizing the sumrate of the users leads to better individual rates for users with favorable channel states at the expense of users with poor channel states. In order to encourage fair individual rates, we instead maximize the minimum user rate, which is a quasi-convex problem that can be solved using the bisection method.

Development and Characterization of a Josephson Parametric Amplifier for Study of Near Ground State Quantum Systems Alexander V. Anferov Mentors: Oskar Painter and Johannes Fink

Measurements of solid-state quantum systems at or near the quantum ground state need to be preceded by amplification, since the energies of signals of interest in the microwave range are too small for conventional detection. Interest in high fidelity measurements of individual photons, which are easily overpowered by amplification noise, call for robust, high accuracy amplification systems with detection thresholds approaching the quantum limit. Recent advances in very low noise signal amplification devices have focused on parametric amplifiers, which offer a very high signal to noise ratio over a very narrow band of frequencies. In order to maximize the tunability and dynamic range of operation, we develop a Josephson Parametric amplifier, which uses an array of superconducting quantum interference devices (SQUIDs) composed of superconducting Josephson junctions to provide additional tunability and the necessary nonlinearity for parametric amplification. This work details the modeling, development and full characterization of a microwave range Josephson Junction Parametric amplifier in terms of its frequency tunability, Josephson junction characteristics, drive power regimes, signal amplification regimes, and gain performance.

Luminescent Ruthenium Probes for DNA Mismatches Sarah Antilla Mentors: Jacqueline Barton and Adam Boynton

The development of cancer diagnostics and treatments is a growing area of research. The accumulation of DNA mismatches is associated with several forms of cancer, and we are interested in designing ruthenium complexes to function as diagnostic probes for mismatches. The complex [Ru(bpy) 2 dppz] 2+ (bpy= 2,2’-bipyridine; dppz = dipyrido[3,2-a:2’,3’-c]phenazine) is a DNA “light switch” because it does not luminesce in aqueous solution but does luminesce when bound to DNA. Although this complex does luminescence more brightly in the presence of mismatched DNA relative to well-matched DNA, it is not mismatch-specific. We are aiming to achieve mismatch specificity by synthesizing [Ru(L) 2 dppz] 2+ derivatives bearing more sterically expansive ancillary ligands (L) to discriminate against binding to well-matched sites. We characterize these complexes via mass spectrometry, NMR, and UV-Visible spectroscopy, and use luminescence spectroscopy to measure their emission intensity in the presence of well-matched and mismatched DNA. We have synthesized two complexes, [Ru(Me 4 phen) 2 dppz] 2+ and [Ru(Me 2 bpy) 2 dppz] 2+ , which bear methyl substituents on their ancillary ligands. Compared to their respective parent [Ru(phen) 2 dppz] 2+ and [Ru(bpy) 2 dppz] 2+ complexes, these new methyl derivatives exhibit significantly greater luminescence in the presence of mismatched DNA relative to well-matched DNA, suggesting that they may be used as novel probes for DNA mismatches.

Lepidoptera Identification via Pose-Normalization and Convolutional Neural Networks Richard J. Antonello Mentors: Pietro Perona and Steve Branson


major goal of computer vision research has been to provide efficient and accurate algorithms for the automation


subcategory recognition. We propose a generalized methodology for the full implementation of fine-grained

classifiers for biological organisms, which we apply to a Lepidoptera test domain. After dataset collection, we use crowdsourcing tools to fully annotate the collected images. Utilizing redundant annotation of images, we obtain ground truth annotations for our dataset. With these ground truth annotations, we normalize the images from our dataset into several standardized poses, which we use as feature vectors to train and finetune on VGGNet, a state- of-the-art deep neural network architecture. In addition to our CNN methodology, we also explore and implement an alternative technique, based on adaptive kernel density estimation, for the training of a probability map of species likelihood given geographic sighting data.


Designing Biomolecular Temperature Sensors Divyansh Apurva Mentors: Richard Murray, Shaunak Sen, and Dan Siegal-Gaskins

RNA Thermometers are temperature-sensing elements present in mRNA in an organism that have a property of changing their secondary structures in response to temperature changes. Their location in the 5’-UTR regions genes enable them to regulate gene expression with shifts in temperature. Previously, frameworks for designing simple synthetic RNATs with different temperature profiles have been reported and a toolbox of RNA thermometers based on that framework has been constructed. However, the behaviour of the RNA thermometers in live cells and in cell free systems has not yet been fully analysed and understood. To address this issue, we aim to standardize and characterize changes in expression for various RNA Thermometers with temperature. With this characterization and tuning as a basis, a temperature-regulated synthetic biomolecular gene expression circuit will be produced. The results should present a huge library of temperature-dependent RNA Thermometers which can be used to increase robustness or sensitivity of bio-molecular circuits.

Virtual Proof of Position of a Living Organism Fabio Kenji Arai Mentors: Changhuei Yang and Roarke Horstmeyer

A virtual proof of reality is a new cryptography protocol that goes beyond classical security keys and utilizes more

general physical statements. In this approach, the statement to be proved is whether an organism is dead or alive. In order to do this, a living organism is confined inside a box made of a scattering material. When illuminate by a coherent light source, this box will create a unique random pattern (a speckle pattern), which may be detected by

a camera. This speckle pattern depends upon the position of the living organism. By recording speckle patterns

specific to certain positions, it is possible to prove to a verifier that the organism moved, and therefore it is alive.

We have shown the feasibility of this approach using a drosophila melanogaster as our living organism. These results along with previous work on different approaches shows promise for this new protocol, increasing its viability for practical applications.

Reciprocity Laws on Arithmetic Surfaces Diana Alexandra Ardelean Mentor: Xinwen Zhu

An arithmetic surface is a two dimensional scheme of finite type over the ring of integers. It could be an algebraic surface over a finite field, or an integral model of an algebraic curve over a number field. We investigate the possibility of introducing new symbols for arithmetic two-dimensional local fields, such as (()) and use them to prove various reciprocity laws for arithmetic surfaces. Our study will start from the perspective of describing a central extension of × by fields such as × and using it to obtain the tame symbol as the commutator of the lifting of two elements from × to this central extension.

Computational Discovery of Binding Poses for Beta-Ionone to hOR5A1 Naveen Arunachalam Mentor: William A. Goddard, III

Understanding the mechanism of olfaction in humans is a difficult process due to the computational complexity of predicting structures for human olfactory receptors (hORs). However, methods previously developed by the Goddard group have made the problem computationally feasible through GEnSeMBLE, a suite of structure prediction methods for G-protein coupled receptors (GPCRs). Using GEnSeMBLE, we have found three low-energy structures for hOR5A1 based on homology to hOR5BC, hOR2J3, and hOR7D4. Using the structures, we have found three energetically favorable docking poses for beta-Ionone (a typical ligand for hOR5A1). Further analysis of the results will involve molecular dynamics simulations at 6000 K near the binding site to assess the validity of the discovered poses.

Lightweight, Adaptable Manipulator for Aerial Door-Opening Rescue Robot Sarah Keiko Asano Mentor: Hideyuki Tsukagoshi

My research was to design a 3 degrees-of-freedom, lightweight, doorknob-grasping manipulator actuated and powered by pressured plastic tubes. This allows more ways of manipulating objects for the operator or program controlling the finger, but specifically allows a door-opening aerial robot to securely grasp the two main types of doorknobs, as well as a variety of other objects. The optimum actuation sequences are determined by testing the security of the manipulator's grip, and an method to grasp arbitrary graspable objects using this manipulator is proposed.


Protein-Catalyzed Capture Agents Targeting Misfolded Superoxide Dismutase 1 Beatriz Atsavapranee Mentors: James Heath and David Bunck

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects motor neurons in the brain and spinal cord. Familial ALS can be caused by mutant isoforms of superoxide dismutase 1 (SOD1) that lead the protein to misfold and adopt toxic conformations. Over 180 mutations in SOD1 are linked to the disease, making it a challenging therapeutic target. The objective of this project is to develop protein-catalyzed capture (PCC) agents that target SOD1 mutants. We used an epitope-targeted screen to identify oligopeptides that bind regions of the protein destabilized upon mutation and an internal fragment revealed upon misfolding. We anticipate that the PCC agents against the internal fragment and precleared against the electrostatic loop will bind misfolded SOD1 selectively, while the PCC agents against the electrostatic loop will detect folded SOD1. This will allow us to discriminate between the folded and misfolded species. Screens against one external epitope yielded several hits whose ability to recognize SOD1 is under investigation. Ultimately, these ligands might be used to mitigate aggregation of mutant isoforms and treat ALS.

Genes of Trunk Neural Crest Pathways Caroline Atyeo Mentors: Marianne Bronner and Christina Murko

Neural crest cells are a multipotent, migratory set of cells that arise in the primitive neural system during embryogenesis. The cells of the trunk neural crest migrate in two pathways, and the specialization of these cells correlates with their migratory pathways. The dorsolateral pathway gives rise to pigment cells, whereas the ventromedial pathway forms neurons and glia of the peripheral nervous system. The question of whether the differentiation of these cells is predetermined or dependent upon their final destination still remains. To address this problem, we aimed to determine what genes govern the different migratory patterns and cell lineages of cells in the trunk of the neural crest in chicken embryos. Based on a transcriptome analysis, we used in situ hybridization and immunochemistry on candidate neural crest genes to validate the transcriptional profiles of ventrally migrating neural crest cells. With this knowledge, the relationship between cell migration and cell lineage in trunk neural crest cells can begin to be uncovered.

A Versatile Framework Integrating Machine Learning With PSTREAMS Streaming Data Library Rahul Bachal Mentor: Mani Chandy

With the increasing prevalence of the Internet of Things in our daily lives, real-time analysis of streaming data is becoming an exciting and growing field. The PSTREAMS package enables a novice programmer to quickly and easily apply vanilla functions to streaming data in Python without prior knowledge of the streaming architecture. The goal of this project was to extend the PSTREAMS package to provide a framework for applying machine learning algorithms to windows over streaming data. Steps taken to design and implement such a framework include the development of an underlying abstraction to enable plug-and-play support for any machine learning algorithm along with a small library of tailored incremental ML algorithms boasting increased efficiency over vanilla batch algorithms. Enhancements such as built-in outlier and change detection were also researched and implemented. The results show that this framework significantly reduces development time and program runtime with the use of provided incremental algorithms. This framework has been tested extensively in the Caltech Community Seismic Network to predict offsets between local and NTP server clock time to accurately timestamp sensor events. The power and versatility of this framework highlights its scalability and potential use in any scenario.

Optomechanical Modeling and Signal Processing for Analysis of Novel Implantable Interocular Pressure Sensor to Monitor Medical Condition of Glaucoma Patients Ashwin Balakrishna Mentors: Hyuck Choo and Jeong Oen Lee

Glaucoma is one of the leading causes of blindness in the world and still has no cure, making it important to develop methods to consistently and accurately measure interocular pressure to monitor the state of glaucoma patients. The idea here is to design, build, and evaluate an optomechanical pressure sensor that is implanted into the eye of glaucoma patients. Light is shone into the eye and based on an optical model, the air gap between the sensor and the eye can be determined. Then the difference between the initial expected air gap and that after the deformation of the sensor from eye pressure can be used to determine the interocular pressure using mechanical modeling of the sensor deformation. Several sensors have been fabricated, each of which were subjected to different pressures. Then the appropriate reflection measurements were performed. An analytical model was then synthesized to simulate theoretical reflection data given a certain interocular pressure. Finally, a variety of signal processing techniques were employed to compare the experimental results to theory. Further measurements and analysis were performed with sensors implanted into a rabbit eyeball. The experimental results matched up quite well with the theoretical predictions, demonstrating the success of the sensor.


UV Slope Measurements of 10 High Redshift Sub-Millimeter Galaxies Ivana Barisic Mentor: Peter Lawrence Capak

We present high-resolution Hubble Space Telescope Wide Field Camera 3 Infrared (HST WFC-3 IR) images of 10 normal galaxies at z5-6 with dust continuum and C[II] dynamical measurements from ALMA (Capak et al. 2015). These new data enable much more accurate measurements of the rest-frame ultra-violet (UV) spectral slope (β) than were possible in the original analysis. Specifically the new data will reduce the systematic effects in measurements due to the low signal-to-noise ground based data used in the previous analysis and allow us to explore reddening gradients and positional offsets between the sources of the UV and FIR emission. We will also be able to explore the link between the rest-frame UV morphology and the dynamics of the galaxies.

Time-Based Vertex Reconstruction in the Compact Muon Solenoid Ben Bartlett Mentors: Maria Spiropulu, Adi Bornheim, and Lindsey Gray

The Phase-II upgrades to the Large Hadron Collider will introduce a variety of new measurement devices to the CMS, including the High-Granularity Calorimeter (HGCAL). The increase in luminosity from these LHC upgrades will also have the undesired side effect of vastly increasing pileup to a level at which the current machine learning vertex selection algorithms will cease to be effective. This will necessitate the development of further vertex reconstruction (vertexing) algorithms. Using high precision timing measurements from simulated events in the HGCAL, we design a vertexing algorithm that requires only the spatiotemporal arrival coordinates to reconstruct the interaction vertex of a collision with sub-millimeter resolution. We also analyse how particle energy and simulated time smearing affect this resolution and we apply this algorithm to more complex data sets, such as Hγγ, jets, and high-pileup events. For these, we implement a set of secondary algorithms and filters to remove poorly-reconstructed events, account for premature interactions, and resolve reconstruction ambiguity.

Numerical Simulation of Atmospheric Photochemistry in a Laminar-Flow Tube Reactor Michael Bauer Mentors: John H. Seinfeld and Matthew Coggon

The climatological impact and chemical characteristics of atmospheric aerosols remain very uncertain. The latest step in this field is the experimental use of UV-lit gas-phase tube reactors to simulate days to weeks of atmospheric photochemistry. These reactors have typically been modeled as plug-flow reactors. We have constructed a more detailed model to describe the new laminar-flow tube reactor constructed by the Seinfeld Group. This model assumes radial symmetry and takes into account the non-uniform velocity distribution in the tube’s flow. However, it ignores gas-phase diffusion since preliminary simulations indicated that it may not have a large effect. A numerical simulation of this model was constructed to consider the steady-state addition of an arbitrary number of reactants. Starting with a list of reactions and reaction rate constants, this simulation can generate an estimate of species concentrations for each species everywhere in the reactor. It does this by repeatedly solving an N-dimensional ODE for different reactor streamlines using backward differentiation formulae and Newton iteration. This allows for the simulation of very large and very stiff kinetic systems within the reactor. Experimental evaluation of the model’s accuracy is necessary. Diffusion may also be considered in the future.

C-H Amination of Tetrahydroisoquinoline Katherine Bay Mentors: Brian Stoltz and Seojung Han

Cyanocycline A is a member of the tetrahydroisoquinoline (THIQ) alkaloids, a class of natural products that display potent biological activity as antitumor antibiotics. Isolated from the fermentation broth of Streptomyces flavogriseus, cyanocycline A is a potent, broad-spectrum cytotoxin effective against mammalian and bacterial cells. We envisioned a total synthesis of cyanocycline A involving late-stage C–H activation as a key step. The chemistry of C–H amination offers powerful methodology for the synthesis of amine-derived materials through intramolecular C–H oxidation. Progress was made towards producing a benzo-fused oxathiazinane heterocycle from an ortho- substituted phenolic sulfamate through C–H amination using a Rhodium-tetracarboxylate catalyst. The preparation of this novel substrate contributes to the total synthesis of Cyanocycline A.

Self-Replication of One-Dimensional Colloidal Structures Through Shape Complementarity Joseph Berleant Mentors: Sharon Glotzer, Pablo Damasceno, and Erik Winfree

Self-replication is an essential feature of many fascinating natural phenomena, such as the replication of DNA strands during cell division. In synthetic materials, self-replication is important in part because it is expected to be a useful route to the scalable design of materials for complex structural assembly. Simulated self-replication of colloidal structures has been moderately successful by relying on a set of highly specific attractive forces to control interactions between particles; however, the ability to create such forces between particles at the nano and


colloidal scales has proven challenging. We propose and test an alternative approach to self-replication that utilizes particle shape to confer binding specificity comparable to that achieved with multiple attractive forces. In this scheme, a single attractive force promotes nonspecific binding between particles while shape complementarity ensures that only desired bonds form. Self-replication is enabled through a temperature cycle that facilitates each successive step of the replication process (Figure 1). System simulations demonstrate self-replication of a strand of particles with some error in the replicated strand lengths. By varying properties of the temperature cycle, strands of a particular length may be selected, making this type of scheme potentially useful in a mutation-selection scheme for materials design.

useful in a mutation-selection scheme for materials design. Figure 1: A single replication cycle involves a

Figure 1: A single replication cycle involves a cooling phase followed by a heating phase. During the cooling step, monomers bind to the template strand, and at the end any adjacent monomers on a strand are bonded to create a new strand. During the heating step, the two strands separate to serve as templates during the next replication cycle.

Quantum Walk Frameworks and Quantum Speedup of Markov Mixing Jeremy D. Bernstein Mentors: Thomas Vidick and Stacey Jeffery

Algorithms based on random walks have a wide applicability: from problems in theoretical Computer Science to Google's PageRank algorithm. We investigate two frameworks for quantising algorithms on reversible Markov chains that confer polynomial speedup over the classical counterparts. The MNRS framework is based on the spectral properties of Markov chains, and the Belovs framework is based on the electric network interpretation.

In an effort to unify the frameworks, we rediscover a quantum algorithm for sampling from the stationary distributions of ergodic, reversible Markov chains due to Wocjan and Abeyesinghe. The algorithm makes use of phase estimation on the Szegedy walk operator to implement a reflection in the stationary distribution à la MNRS. The complexity is asymptotically better in the size of the spectral gap than both the classical power method and a quantum algorithm using adiabatic state generation due to Aharonov and Ta-Shma. We use this algorithm to compare the power of the Belovs and MNRS frameworks.

High Strain-Rate Dynamic Behavior of Magnesium and AZ31B Moriah Bischann Mentors: Guruswami Ravichandran and Owen T. Kingstedt

Magnesium’s implementation as a light weight structural material has lagged because its hexagonal-close-packed (HCP) crystal structure leads to complex deformation response. Within this work we examine the high strain-rate (10 2 to 10 3 s -1 ) dynamic response using the split-Hopkinson pressure bar. Experiments were conducted using specialized striker bars to promote a constant strain-rate, strain-rate increment, or strain-rate decrement during a single loading event. Thermo-mechanically processed magnesium (Mg) and Mg alloy AZ31B were examined along various loading directions to explore the strain-rate sensitivity of the different deformation mechanisms, such as deformation twinning or basal slip, which occur under a prescribed loading condition. The results of these experiments capture the anisotropic material response of Mg and AZ31B with respect to loading orientation.

Magnetic Field Profile of a Third-Scale Model for the nEDM Experiment Aritra Biswas Mentors: Bradley Filippone and Simon Slutsky

Discovery of an electric dipole moment in neutrons (nEDM) would be a novel instance of CP violation, with implications for extending the Standard Model and potentially helping explain matter-antimatter asymmetry. Experiments using shifts in polarized neutron spin-precession frequency to measure the nEDM are prone to a geometric phase (GP) effect, caused by gradients of the magnetic field, that can create a false signal. Preventing the GP effect requires precise engineering to create a space-uniform magnetic field. We present a third-scale prototype of a shielded magnet suitable for a more precise nEDM measurement, with improvements over earlier models. The field is produced by a cos θ coil wound with superconducting (SC) wire. Two cylindrical shields made


of ferromagnetic Metglas and SC lead surround the magnet; the lead shield is closed on top and bottom with SC

lead endcaps. An aluminum shell surrounds these components and serves as a vacuum chamber, cooling its interior to 4 K such that the coil wire and lead shield become SC. A cavity in this shell serves as a warm bore, allowing a magnetic probe to explore the field around fiducial volumes which will be used to measure the nEDM in the full-scale experiment. A magnetic field profile of components of this prototype is presented.

Exploring the Reactivity of Diazo Compounds: Discovery of a Novel Rhodium-Catalysed Cyclopropenation of Diazooxindole and Identification of an Exceptionally Simple System for the Oxidation of Aryl Diazoacetates to α-Ketoesters Peter Bolgar Mentors: Brian M. Stoltz and Nicholas O’Connor

A novel, highly strained, cyclopropene-containing spirooxindole has been synthesised by the insertion of a rhodium

carbenoid derived from N-methyl-3-diazooxindole into the π-bond of a terminal alkyne. This reaction provides a new entry into the spirooxindole class of molecules, which often have important biological functions. We also present a systematic study of the oxidation of electron rich aryl diazoacetates to α-ketoesters by warming in dry DMSO. The use of cheap and environmentally friendly DMSO provides a major advantage over methods using expensive and toxic metal catalysts. Furthermore, the mild nature of DMSO makes this method compatible with a variety of common functional groups susceptible to oxidation under other conditions.

groups susceptible to oxidation under other conditions. Three-Dimensional Microstructures as Effectively Transparent

Three-Dimensional Microstructures as Effectively Transparent Front Contacts for Solar Cells Aleca Borsuk Mentors: Harry Atwater and Rebecca Saive

For solar cells to achieve optimal photovoltaic performance, front contacts—electrodes at the surface of the solar cell—must offer excellent electrical conductance and optical transmission. At present, however, front contacts do not deliver on all criteria—e.g. metal grids shadow otherwise active surfaces, while transparent conducting oxides absorb photons. In the present work, a novel front contact architecture is realized—namely, three-dimensional (3-D) microstructured fingers that are highly conductive and effectively transparent. Here, fine metal grids with 3.0 µm finger width and 40 µm periodicity were first defined lithographically. These were superimposed with pyramidal structures with >45 degree angles, which re-direct incident light to the active surface of the solar cell. Pyramids were written with the Nanoscribe direct laser writing system, in which high intensity laser pulses induce polymerization of photoresist at nanoscale volumes. To achieve efficient re-direction of light, 3-D surfaces were selectively coated with a metal film using directional deposition. Spatially resolved laser beam induced current measurements (LBIC) show that 3-D contact patterning leads to significantly improved photocurrent as compared with planar contacts. Current-voltage (IV) curve characterization of 3-D contacts additionally indicates enhanced absolute current and increased efficiencies in state-of-the-art solar cells.

Using Textured Silicon as an Antireflective Treatment for Microwave Lenses Arjun Bose Mentors: Sunil Golwala and Simon Radford

Since modern astrophysics requires much larger millimeter and submillimeter detector arrays than ever before, previous antireflection (AR) treatments, such as grooved designs and laminated plastic coatings, are begin presenting deficiencies. These deficiencies include distortions from inability to effectively vary the index of refraction or deformities from thermal contraction and expansion, and noise from the absorbing and re-emitting light. An option with fewer drawbacks may be to create an antireflection treatment with layers of silicon with various holed patterns in order to create a gradient index (GRIN) coating, which would solve the previously mentioned issues for the millimeter and submillimeter spectrum.

Engineering Prolyl tRNA Synthetase for Accommodation of Non-Canonical Amino Acids Mary Boyajian Mentors: David Tirrell, Katherine Yan Fang, and Seth Lieblich

Current methods of engineering recombinant proteins primarily involve the replacement of one canonical amino acid with another; however, for certain proteins of heavy research and commercial interest, all reasonable canonical mutations have been extensively explored. Diabetics is a disease that affects millions in the world; it is the result of an inability to produce or respond to insulin. As a result, insulin has been the subject of intensive engineering efforts for decades. Few, if any further, engineering opportunities remain undiscovered using canonical amino acids; however, the replacement of canonical amino acids (cAAs) with non-canonical amino acids (ncAAs) is relatively new and opens new unexplored chemical space wherein beneficial engineering via mutations is possible.


Previous research in the field has demonstrated that hundreds of ncAAs can be incorporated into newly synthesized proteins by bacterial and mammalian cells. These ncAAs have unique side chains and can introduce novel chemical, physical, and biological changes that cannot be achieved with the natural cAAs. Aminoacyl-tRNA synthetases (aaRSs) are responsible for catalyzing the specific ligation of amino acids to their cognate tRNAs; in most cells, there are at least 20 aaRSs, one for each natural amino acid. While some ncAAs are promiscuously charged to tRNA by aaRSs, most ncAAs require a mutant aaRS to enable protein translation. Insulin has a single proline in its mature form: B28; this position is known to be critical for controlling insulin oligomer states and has served as the most important site of alteration and modification in new biologic drugs. In this project, certain mutations will be made to the prolyl tRNA synthetase (ProRS) to accommodate the different side chains on ncAAs in order to explore new protein sequence space for the engineering of improved insulin variants.

Spectroscopic Quantification of Structurally-Bound Water in Pyroxenes and Olivines, With Applications to Meteorites Alec Brenner Mentor: George Rossman

I present polarized near-infrared absorption spectra of several mineral species extracted from meteorites. I place emphasis on absorption features associated with O-H stretching (peaks near wavenumbers of ~3500-3300 cm -1 ), which I use as proxies for the presence of structurally-bound water (or OH - ). The meteorites treated in this analysis include the Fukang pallasite (a stony-iron cumulate originating from the core-mantle boundary of a protoplanet), the Esquel pallasite (of similar origin), and ALH84001 (a shergottite of Martian crustal igneous origin). In the cases of both pallasites, the mineral species I analyze for O-H content is forsterite (Mg 2 SiO 4 , the magnesic olivine), and I compare these spectra to existing IR spectra of terrestrial forsterite. For ALH84001, the analytical material is the orthopyroxene cumulate that dominates the meteorite’s composition (~97 vol%). Additionally, I compare the O-H region spectra of the ALH84001 orthopyroxene to existing spectra of terrestrial enstatite (Mg 2 Si 2 O 6 , the magnesic and most common orthopyroxene), as well as new IR spectra of wollastonite (CaSiO 3 , a calcic pyroxenoid) and spodumene (LiAl(SiO 3 ) 2 , the lithic clinopyroxene).

Non-Linear Entropy Inequalities for 2D Conformal Field Theories Emory Brown Mentors: John Preskill and Ning Bao

Significant work has gone into determining the minimal set of entropy inequalities to determine the holographic entropy cone. It was previously shown that there must exist at least one non-linear entropy inequality when describing states on a 2D conformal field theory. We report on five sets of these non-linear inequalities. We also present an equality obtained by application of a hyperbolic extension of Ptolemy's theorem to a 2D conformal field theory.

Single Molecule Investigation of Phage-Mediated Gene Transfer in E. coli Robin Brown Mentors: Rob Phillips and Griffin Chure

With an estimated global population of 10 31 , bacteriophages (viruses that infect bacteria) are the most numerous biological entities. Despite their abundance, much about their basic biology as well as their influence on microbial communities remains unknown. In a process called transduction, a bacteriophage accidentally packs segments of the host bacteria’s genome instead of viral DNA in its capsid and donates it to the recipient. The Phillips lab has previously designed and implemented a system using recognition sites and fluorophores to visualize the spatial distribution and movement of DNA within the cell. We modified this system to track phage infection with the intention of comparing transduction frequency to infection frequency. Due to the low frequency of transduction, this system seems to be impractical for the study of transduction. However, I was able to observed infected cells lyse and infect neighboring cells. As a result, this system seems to work well to track phage infection and propagation through populations of E. coli. For example, we will be able to time how long it takes an infected cell to lyse, and then how long it takes neighboring cells to become infected. Furthermore, we can the range of phage infection from the location of the lysed cell.

Modeling Turbulent Buoyant Flows From Direct Numerical Simulation Data Sets Nicholas A. Buoniconti IV Mentors: Guillaume Blanquart and Julien Claret

Turbulent Buoyant Flows (TBF) occur when discontinuities are generated in a fluid’s flow regime due to a variance in the densities of fluid particles in that flow. TBFs are present in a multitude of natural and engineering phenomenon. Understanding these flows is a fundamental problem that we have not yet solved. Herein we evaluate a variety of data sets developed from Direct Numerical Simulations (DNS) with a Matlab code framework. The findings include a relation for the dependence of velocity on density, a model of the effect of partial buoyancy on turbulent flow behavior, and an understanding of the effect of energy dissipation rates on flow velocities. The results supported existing theories for turbulent behaviors found in the literature. Additionally the different


components contributing to the flows turbulence were successfully separated and modeled. In the future this research can be utilized to ease the computing cost of TBF simulations. Additionally the insight gained from the results will be important in supporting theories of the TBF behavioral framework and continuing the understand of the effects of density variance on TBF.

Investigating a Potential Role for Karyopherin-α in the Assembly of the Nuclear Pore Complex Nina Butkovich Mentors: André Hoelz and George Mobbs

The nuclear pore complex (NPC) is an essential, massive macromolecular structure composed of approximately 30

different proteins known as nucleoporins, providing the sole gateway between the nucleus and cytoplasm in eukaryotic cells. While significant regions of its architecture have recently been resolved, the NPCs assembly is not well characterized. Karyopherin-α, a nuclear transport factor, has been shown to interact with several nucleoporins and is hypothesized to play a role in the assembly and oligomerization of the NPCs distinctive ring like structures. To further study its role in assembly, we have investigated how Karyopherin-α interacts with Nup53, a flexible linker which interacts with a wide array of nucleoporins, and Nup133, the base of the coat nucleoporin complex. We have successfully expressed, purified and crystallized Karyopherin-α with a short peptide corresponding to the minimal binding region of Nup53. We have also identified a minimal Karyopherin-α binding region in Nup133 through testing various truncated constructs using size-exclusion chromatography. This work shows that Karyopherin-α forms physiologically significant interactions with two crucial nucleoporins, which opens the door for

a larger role in NPC assembly.

Designing an in vitro Translation System and Engineering Methane Monooxygenases Slava Butkovich Mentors: Steve Mayo and Alex Nisthal

Molecular engineering is a powerful tool that can be used to improve many aspects of life. In this research, two separate projects utilizing molecular engineering are pursued. One project involves creating an in vitro translation system, using RNA to synthesize protein instead of starting with DNA. By modifying tRNA synthetases in this system, tRNA could be made to accept different amino acids than usual; a successful system could be used to better incorporate unnatural amino acids in proteins. Current work strives to show that this theoretical system can be implemented. Another project involves discovering methods of more efficiently turning methane into methanol. Methane is readily available but relatively difficult to transport, while methanol is easier to transport. Thus, expanded use of this conversion could reduce waste and help to prevent the buildup of carbon dioxide in the atmosphere. Methane monooxygenases are proteins naturally found in methanotrophic bacteria that can perform this conversion under ambient conditions. Current work involves engineering methane monooxygenases and developing a folded protein screen in bacteria and yeast. Further research will be able to better implement the proposed in vitro translation system and to improve engineered methane monooxygenases for more efficient conversion of methane to methanol.

Structural and Functional Characterization of the Interaction of mRNA Export Factor Gle1 With Cytoplasmic Filament Protein yNup42/hNupl2 at the NPC Sarah Cai Mentors: André Hoelz and Daniel Lin

The mRNA export factor Gle1 is an essential nucleoporin that functions in the export of poly(A)+ mRNA through the nuclear pore complex (NPC). Mutations in Gle1 can result in defects in mRNA export— amyotrophic lateral sclerosis (ALS) is linked to a mutation removing the Nupl2 binding domain on Gle1. Gle1 has two known binding partners, one of which is the cytoplasmic filament protein hNupl2 (yNup42 in S. cerevisiae). A minimal binding construct was determined, expressed in E. coli, and purified. We solved the atomic structure of the yGle1-yNup42 complex, refined to 1.75 resolution. The structure reveals several key residues that mediate the interaction, and experiments are being done in vivo with S. cerevisiae using mutants to validate the structure and to study NPC localization patterns of yGle1 and yNup42. The homologous human complex (hGle1-hNupl2) has been purified and

is in the process of screening for crystallization conditions. Understanding the atomic structure of these interactions

can be applied toward the study of diseases such as ALS that result from mRNA export defects.

Increasing the Resolution of N-Body Cosmological Simulations Chris Cannella Mentors: Andrew Benson and George Djorgovski

A method for inserting Monte-Carlo derived branches into the dark matter halo merger trees produced by N-Body

simulations (such as those from the Millennium Run) is created and tested. Such a method allows the artificial increase in the resolution of merger trees generated by N-Body simulations, allowing accurate modelling of galactic formation and evolution based on N-Body simulations.


The Effects of Accretion on the Age Spreads of Young Stars Lyra Cao Mentor: Lynne Hillenbrand

Stars are thought to form from an initial period of “hot” spherical accretion that accounts for most of the mass, followed by “cold” disk accretion that occurs throughout a significant portion of the star’s early evolution. Since accretion histories are unknown for individual stars, the effect of the accretion is to produce an error on stellar parameters, including luminosity, radius, and age. Recent studies have shown that these errors due to cold accretion are systematic and large for low-mass stars, producing older ages and smaller radii than expected (Baraffe et al. 2009). However, a detailed study of accretion on higher mass stars has not been done. Theoretical and observational arguments suggest that rapid accretion, suitable for high-mass stars, is likely to be hot rather than cold (Hartmann et al. 2011). To treat high-mass star formation correctly, we develop routines to perform episodic hot accretion in the Modules for Experiments in Stellar Astrophysics (MESA). We present the correct treatment of protostellar accretion, with plausible accretion histories, on stars ranging from 0.1 to 8 solar masses.

Toward the Synthesis of a High-Valent Terminal Mn(IV)-Oxo Motif Supported by a Tripodal Trimanganese Framework as a Model for the Oxygen-Evolving Complex of Photosystem II Kurtis Carsch Mentors: Theodor Agapie and Graham de Ruiter

A series of homometallic, tetramanganese clusters of structures [LMn 3 (PhPz) 3 OMn][OTf] x (x = 0, 1, 2; PhPz = 3-

phenylpyrazolate) and [LMn 3 (F 2 PhPz) 3 OMn][OTf] x (x = 1, 2; F 2 PhPz = 3-(2,6-difluorophenyl)-pyrazolate) were synthesized to provide insight into the O–O bond coupling mechanism accomplished by the oxygen-evolving complex (OEC) of photosystem II. The rational, stepwise synthesis of [LMn 3 (PhPz) 3 OMn][OTf] 2 (3) was accomplished starting from precursor LMn 3 (OAc) 3 (1). Cyclic voltammetry of 3 revealed two reversible redox waves corresponding to [Mn II 4 ] 0 /[Mn II 3 Mn III ] 1+ (-1.66 V) and [Mn II 3 Mn III ] 1+ /[Mn II 2 Mn III 2 ] 2+ (-0.66 V) oxidation and reduction events. [LMn 3 (PhPz) 3 OMn][OTf] (4) was obtained upon reduction of 3 via cobaltocene (CoCp 2 ). Both 3 and 4 are further characterized by single-crystal X-ray diffraction, supporting the respective oxidation state assignments as [Mn II 2 Mn III 2 ] 2+ and [Mn II 3 Mn III ] 1+ . Treatment of 3 and 4 with oxygen-atom transfer reagents iodosobenzene (PhIO) and TBAIO 4 suggest intramolecular C–H hydroxylation of the adjacent phenyl motif to yield [LMn 3 (PhPz) 2 (OPhPz)OMn][OTf] 2 (5). A similar reaction with [LMn 3 (F 2 PhPz) 3 OMn][OTf] 2 (7) and PhIO – or TBAIO 4 – suggests C–F activation of the difluorophenyl pyrazolate motif, accompanied by coordination of F - onto unreacted starting material with subsequent one-electron disproportionation to yield [LMn 3 (F 2 PhPz) 2 (OFPhPz)OMn][OTf] 2 (8) and [LMn 3 (F 2 PhPz) 3 OMnF][OTf] 2 (9). Both C–H and C–F activation via addition of PhIO are examined via independent synthesis routes employing substituted pyrazolate scaffolds as well as addition of XeF 2 for 9. Computational studies based on density functional theory (DFT) are provided to address the observed reactivity with PhIO. Efforts to access more electron-deficient configurations relevant to the OEC are further discussed.

Investigating the Role of Magnetite in Cryopreservation Thomas Chaffee Mentor: Joseph Kirschvink

Recent technological advances have utilized alternating magnetic and electric fields in freezers that are able to supercool food and keep it almost perfectly preserved. The mechanism by which this supercooling is enabled has not yet been discovered, but there are indications that biologically precipitated magnetite plays a key role in ice crystal nucleation. Our proposed mechanism is that the alternating magnetic field causes magnetite crystals in the food to oscillate, preventing damaging ice crystals from forming, keeping the cells better preserved than in traditional freezing. Our goal is to investigate the magnetite content of fruits and vegetables, to determine the importance of magnetite crystal content to this freezing technology.

Study of the CMS ECAL Calibration and Timing Performance With π 0 Decays at 13 TeV Kai Chang Mentors: Maria Spiropulu, Adi Bornheim, and Emanuele Di Marco

The CMS ECAL is capable measuring the energy of high energy photons with a precision of about 1% and their time of arrival in the detector with a precision of around 100 ps. The calibration of the detector in situ with neutral pion decays into two photons is a crucial step to achieve the energy resolution performance. To date the timing response is calibrated with generic calorimeter clusters which have the characteristics of electromagnetic interactions. One important systematic effect limiting the timing performance is the radiation induced transparency change of the crystals. This modifies the optical path of the scintillation photons in the crystals which changes the time response. In this project the measurement of the crystal transparency will be used to study this dependency

an derive a correction for the timing measurement. The π 0 calibration sample and analysis framework will serve as

a clean benchmark sample to test the corrections.


Engineering Nucleic Acid Probes for Delivery, Localization, and Branch Migration in Mammalian Cell Culture Ann Chen Mentors: Niles Pierce and Mikhail Hanewich-Hollatz

Because of the predictability of Watson-Crick binding thermodynamics in nucleic acids and the potential to interface with existing nucleic acid pathways, nucleic acid nanotechnology has the potential to be a powerful tool for the development of novel techniques in biology. The engineering of nucleic acid mechanisms, a biochemical interaction of nucleic acid species that produces a unique output, allows for a range of programmable behaviors. Such engineered systems are ideal for conditional gene regulation - the control of the expression of genes either in a test tube or within a living cell - because they can generate biologically functioning species conditionally through interactions with endogenous nucleic acid species. In this study, we characterize nucleic acid mechanisms, designed using NUPACK (Nucleic Acid Package), that have inputs of arbitrary sequence and are designed to produce biologically functional outputs in mammalian cells. To validate these mechanisms, microinjection assays are used to study localization of fluorescently-labeled species. We deliver a pre-defined volume of prepared solution to HEK 293 cells at a relevant working condition. After injection, GFP and DsRed expressions are monitored to determine cellular behavior. We provide a characterization of GFP knockdown by the conditionally generated output upon microinjection of small conditional RNAs (scRNAs) into HEK 293 cells containing the target DsRed input. After validation of a particular nucleic acid mechanism via microinjection assays, additional mechanisms can be designed and characterized.

Establishing Methods of Transgenesis in the Nematode Bursaphelenchus okinawaensis Anthony Chen Mentors: Paul Sternberg and Ryoji Shinya

The fungal-feeding hermaphroditic nematode Bursaphelenchus okinawaensis is an emerging laboratory model useful for understanding the characteristics and disease mechanisms of various types of parasitic nematodes. Recently, Dr. Shinya and I developed a forward genetics system in B. okinawaensis and successfully generated a large number of mutants. Therefore, the establishment of reverse genetics and transgenic tools are needed to accelerate the genetic study of B. okinawaensis. This research attempts to establish a reliable method of transgenesis for the nematode B. okinawaensis by using microinjection, microparticle bombardment, and CRISPR- Cas9, all of which have been used extensively in C. elegans study as well as in other organisms. Establishing a method of transgenesis would allow for deeper understanding of the genetic processes present in the nematode. Because some groups of parasitic nematodes currently negatively affecting agriculture and public health are very similar to B. okinawaensis, this new information about B. okinawaensis should also be very useful in developing genetic methods for them.

Characterization, Simulation, and Optimization for III-V Solar Cell Contact Grids Kevin C. Chen Mentors: Harry A. Atwater and Cristofer A. Flowers

High material quality, high performance III-V solar cells are particularly attractive solar energy converters for concentrating and spectrum splitting photovoltaic systems. To achieve high efficiency power production, it is especially important to optimize the metal contact grid at the front of the cell. The goal is to minimize power losses by finding a balance between resistive loss in conduction and amount of light reflected away from the cell on sparse metal contact features. The circular transfer length method was employed to extract sheet resistance and contact resistivity of III-V materials. These data enable accurate prediction of cell electrical performance using HSPICE simulations, and genetic algorithmic approach will offer insights on the ideal geometry of the front metal contact for maximum power conversion efficiency.

Data-Matching Algorithms for Fabry-Perot Intraocular Pressure Sensors Oliver W. Chen Mentors: Hyuck Choo and Jeong Oen Lee

Glaucoma is a leading cause of blindness, affecting an estimated 4 million Americans and 70 million individuals globally. The Choo lab has developed a highly miniaturized IOP monitoring system using a nanophotonics-based implantable IOP sensor with remote optical readout that can be adapted for both patient and research use. However, data collection of IOP using such a micro-sensor results in a burdensome amount of background spectra mixed in with a few useful sensor-generated spectra. We created a data extraction algorithm based on the optical properties of the Fabry-Perot cavity of the sensor to separate the background spectra from the sensor spectra. Subsequently, we generated a data-matching algorithm to choose the best fitting theoretical spectra for each experimental spectrum. With these two algorithms, we calculated the IOP exerted on the sensor in optical test bench, ex vivo, and in vivo settings.


Engineering Protein Matrices for Production of β-Like Cells for Treatment of Type 1 Diabetes Desnor Chigumba Mentors: David A. Tirrell and Mark T. Kozlowski

Type 1 diabetes is a chronic condition in which patients cannot produce their own insulin. Previous studies have shown that it is possible to manipulate post-natal progenitor cells to differentiate directly into β-cells for transplantation by using laminin and methylcellulose to provide the appropriate biochemical and mechanical cues respectively. By using engineered protein hydrogels with an encoded laminin sequence and leucine zippers, we can make a material that provides both cues. As the cell culture is 3-dimensional, this would enable us to suspend the cells in solution. Our primary objective was to produce a hydrogel which would be soluble at 37°C. Previous protein constructs were not soluble and we suspect this was because they had low LCSTs. Therefore, we altered the sequence to increase solubility. We cloned a PC 10 -lam-C 10 P protein where the C domain is hydrophilic and does not have an LCST. PE 6 -lam-E 6 P, PE 6 -trunc lam-E 6 P and PE 6 -lam-E 6 P C3A were also constructed as modifications of a previous elastin PEP construct. All constructs were soluble and MALDI-TOF MS suggests we obtained our protein of interest. All constructs are sent to City of Hope Hospital for cell culture studies.

Developing Nickel Inverse Opal Cathodes for Lithium Air Batteries Evelyn S. Chin Mentors: Julia R. Greer and Dylan D. Tozier

Lithium air batteries have an energy density up to 10 times greater than that of lithium ion batteries. This property makes Li-air battery systems very desirable, however there are many challenges to making these systems. Recent research has focused on the use of carbon based cathodes because carbon provides a high surface area ideal for maximizing battery chemistry. However, these cathodes lead to unwanted byproducts which hinder the ability to recharge these batteries. Metals with nanoporous structures can be used to prevent production of these byproducts as they can both catalyze the reaction and provide the desired high surface area. In this study, nickel inverse opal structures were synthesized by electroplating nickel through self-assembled polystyrene opal structures. The inverse opal structures were then tested in a molten salt battery system.

Tools for Developing Apps for the Internet of Things Wonwoo Cho Mentors: K. Mani Chandy and Julian Bunn

Basic part of Internet of Things (IoT) includes sensors, processors, and codes. We develop a framework that could be applied to IoT, and it should be easily handled by novice users. The framework is based on several sensors, Arduino, Raspberry Pi, and python codes running on Raspberry Pi. One of popular programming languages for developing IoT applications is python. Using python, novice programmers write a standard non-stream codes. For wrapping the non-stream function codes to generate streams, we used a python package called PStreams which enables working with streams. Testing with several kinds of sensors and connection types, we developed a basic example platform that can read sensor data, and generate data streams for application. We can expect novice users and programmers can develop their own useful streaming system based on our platform. Also it could be applied to further related area like Machine learning, and visual UI.

Numerical Analysis of Thermocapillary Patterning of Polymer Films Dahan Choi Mentors: Sandra M. Troian and Chengzhe Zhou

Thermocapillary forces are believed to be a dominant cause of spontaneous growth of nanopillars from molten polymer nanofilms subject to a transverse thermal gradient. According to this mechanism, the difference in polymer film thickness causes disturbances in film surface temperature, which results in the rearrangement of film material towards colder regions. We examine the highly nonlinear equation governing the evolution of the film height under thermocapillary forces. Linear stability analysis was used to model a flat film perturbed by a small amount, and to calculate dispersion relation between the growth rate and the wavenumber of the perturbation. Several different initial film configurations were numerically simulated. Results yielded a nearly perfect match between LSA and numerical computations for early times, but failed to capture the long term behavior of the instability. Subsequent work will be aimed at understanding this long term behavior of the instability.

Localization of Photoactive Rubpy Label by Strategic Labeling of CssII Scorpion Toxin Nelson Chou Mentors: Robert Grubbs and Melanie Pribisco

Visual impairment due to incurable retinal degenerative diseases such as retinal pigmentosa and age-related macular degeneration is characterized by the loss and damage of photoreceptors, which in turn leads to degeneration of the visual field. However, vision can be restored by bypassing damaged photoreceptors and activating surviving retinal ganglion cells. Previous studies have shown RubpyC17 inserts evenly into a cell membrane. Upon illumination, Rubpy is excited to Rubpy* which can reduce or oxidize the redox active molecules


around the ion-gated channel, causing a buildup of negative charge leading to action potential firing and transmittance of light information to the brain. Such method, though useful, has no inherent targeting, therefore may require higher doses of toxic ruthenium than necessary. We hope to localize this phenomenon by tagging the Rubpy label to CssII, a 66-amino acid peptide that binds with nanomolar affinity to Na v 1.6 ion-gated channels of concentrated near ganglion cells. To form full-length CssII, three fragments must be synthesized and joined by native chemical ligation. We propose to label the native His 50 residue of CssII with Rubpy. If the binding affinity is retained, the Rubpy label will be localized and oriented such that, upon illumination, localization of accumulation of negative charge so that action potential firing can be induced efficiently. Recently, we also identified a new 31 amino acid fragment that contains important binding sites of CssII as well as the His 50 residue and may provide a more efficient route to targeted delivery of the molecular artificial retina.

Machine-Readable Protocols and Rapid-Prototyping for Synthetic Biology Research Ahammad Rafsan Chowdhury Mentors: Richard M. Murray, Scott C. Livingston, and Sean R. Sanchez

Natural biological systems have always been challenging to manipulate. In recent years advancement has been made in synthetic biology to encourage an engineering approach. A central concern of synthetic biology is predictable engineering of chemical processes within cells, which requires repeatable experiments. The aim of this project is to develop a machine-readable format for protocols. Focus is placed on the construction of liquid handling robots that automate parts of a protocol in a wet lab. A prototype robot made of acrylic plastic has been devised. The robot is designed in SOLIDWORKS. Tools such as laser cutter, water jet, lathe and milling machine are used to construct the robot. The robot is capable of movement in three-dimensional axis using stepper motors and timing belts. Work needs to be undertaken to create the mechanism that can be attached to the robot with the capability to pipette liquid.

Designing a Thermal Management System for Electric Vehicle Performance Edward Chu Mentor: Guillaume Blanquart

My project seeks to address the issue of thermal management and cooling of the various components of electric vehicles, or EVs. This is an important issue; although electric vehicles have come quite a long way in the past decade, with corporations such as Tesla leading the way, they are not quite up to par with conventional vehicles in terms of both performance and cost. Range, refueling time, and cost are simply not up to par with consumer expectations. This is partly due to suboptimal temperature management of various EV components. My project seeks to improve the cooling system of EVs with a potentially novel design. We will use a variety of methods and materials to keep an electric vehicle’s components each running at the temperature for maximum efficiency. To achieve this end, we first started with some thermal analysis simulations in SolidWorks, to model how the heat would flow and distribute in models of the battery pack, motor, and motor controller. Using that data, and data gathered from actual experimentation on the CSVC electric vehicle, an optimal design will be apparent. Improving the thermal management system of electric vehicles will make them much more viable in the consumer market, helping to battle against pollution and climate change.

Nanoindentation Characterization of Acrylic-Zinc Oxide Systems as Model Artists’ Paints Ya Lun Chuan Mentors: Katherine T. Faber and Matthew T. Johnson

In order to better preserve paintings that are important to our cultural heritage, conservation scientists are looking to characterize paint systems. Because it takes up to decades for paint to cure, it is important for conservation scientists and conservators to understand how these paint systems change mechanically as they cure. In this project, model paints of acrylic binders and zinc oxide pigments are produced and characterized as a function of pigment concentration with acrylic systems were compared to a fast drying alkyd binder. As the paints were set to cure in a dark, dry environment at room temperature, increases in the hardness and elastic modulus were observed for all pigment fractions. Scanning electron microscope images show that the pigment particle sizes are small relative to the indentation impression, proving that the indentation data are sampling both binder and pigments. Similar future experiments can be conducted on different binders, pigments, and pigment percentages.

Beltrami Differentials and the Gauss-Bonnet Theorem for Noncommutative Two Tori John Michael Clark Mentor: Farzad Fathizadeh

The Gauss-Bonnet theorem for surfaces serves as the prime example of a novel connection between geometry and topology. There is a spectral formulation of the theorem that has stimulated the investigation of its analog in noncommutative geometry. The theorem has been proved for translation-invariant conformal structures on the noncommutative two torus (T θ 2 ) that are associated with arbitrary complex numbers in the Poincaré half-plane. We study the analog of the Gauss-Bonnet theorem and develop an understanding of the local differential geometry of T θ 2 equipped with metrics that belong to general conformal structures introduced by Beltrami differentials. We


introduce a complex structure on T θ 2 and go on to compute its scalar curvature using the noncommutative pseudodifferential calculus to follow the heat kernel method for computing the heat coefficients of elliptic differential operators. We then investigate whether the scalar curvature vanishes under the volume form, namely whether the analog of the Gauss-Bonnet theorem holds.

Focused Ultrasound Induces Currents Across the Cell Membrane of Xenopus laevis Oocytes Jonathan R. Clements Mentors: Mikhail Shapiro and Jérôme Lacroix

It has been shown that focused ultrasound (FUS) can induce neuromodulation in the brain. In my experiments I tested the hypothesis that this phenomenon is caused by the opening of mechanosensitive ion channels (MS channels) in neurons. This would be caused by the mechanical pressure of FUS creating a membrane stretch which opens the channels. To model a neuron, we used Xenopus laevis oocytes, which express various endogenous MS channels. We used a two-electrode voltage clamp to detect any currents generated across the membrane of the oocytes and subjected them to FUS. At first, we were unable to induce a current, so we attempted to increase the effect of FUS on the membrane by subjecting the oocytes to various treatments, but instead found that, interestingly, only a narrow range of FUS frequencies are sufficient to induce a current, which can at times be as large as 2 μA. The nature of the current and its mechanism are still under investigation.

Incorporating Realistic Feedback From Super Massive Black Holes in Simulations of Galaxy Formation Matthew J. Colbrook Mentors: Phil Hopkins and Xiangcheng Ma

Supermassive black holes (SMBHs) are found at the centre of massive galaxies. One of the ways these SMBHs interact with their host galaxies is through energy and momentum delivered through relativistic, high energy particle “jets.” This may give rise to many interesting observed relations between black hole and galaxy properties, and may also play an important role in star formation within massive galaxies. To model feedback better, we need to better understand some fundamental processes that are not well-studied, among which is the problem of metal diffusion, important in galactic chemical evolution, cooling etc. The interstellar medium is mostly supersonically turbulent and current literature sub-grid models of diffusion are generally over-simplified, producing unrealistic results in cosmological simulations. We ran numerical simulations in GIZMO, a magneto-hydrodynamics and gravity code on a periodic turbulent box in two and three dimensions. We found that the tracer was well modelled by a diffusion type equation with a diffusivity dependent on the wave number in Fourier space. Physically this corresponds to eddies of different length scales. Scalings were found to agree well with Burgers’ model of shock driven turbulence. Finally, in the coming weeks we hope to extend this analysis to a galactic disk where shearing becomes important dynamically.

Implicit Bias and Social Decision Making in Autism Spectrum Disorder Caitlin Cooper Mentors: Ralph Adolphs and Damian Alexander Stanley

Trust is indispensable to forming relationships, and is influenced by implicit social biases of which we are often unaware, such as racial bias. Individuals with Autism Spectrum Disorder (ASD) are known to have atypical social processing, however, previous work from our lab shows that their implicit social biases remain intact. We investigated whether implicit social biases in ASD maintain their influence over social behavior. Data from 200 neurotypical participants was collected online using MTurk. Each participant completed two economic games, where they viewed faces of many different partners and made economic decisions that reflect trust and altruism, and a task in which they explicitly rated the trustworthiness of many faces. They then completed an implicit association test (IAT) and finally various questionnaires designed to measure traits associated with ASD as well as explicit race bias. Consistent with previous findings, we found individuals’ race disparity in trustworthiness ratings correlated with their implicit race bias. Interestingly this was not the case for the economic games. We are in the process of collecting data from ASD participants and matched controls as well as probing whether ASD traits in the general population account for variation in the association between trust and implicit race bias.

Wing Threats Are Sufficient to Establish Dominance in Drosophila melanogaster Alberto Corona Mentors: David J. Anderson and Brian Duistermars

Animals from flies to humans express extremely complex aggressive social behaviors that have been studied for many years. However, aggressive behaviors remain poorly understood. It is essential to understand the neural circuitry controlling innate behaviors, such as aggression, to further investigate psychiatric disorders in humans. We have recently isolated a small set of neurons that when activated or silenced, promote or abolish, respectively, a single aggressive behavior in Drosophila, the wing threat. During an aggressive encounter, a wing threat consists of raising one or two wings upward at a 45-90°. In this project, we investigated whether wing threats are sufficient


for dominance formation using artificial activation of identified wing threat cells. To study this behavior, and despite its variability, we utilized a semi-automated classifier to accurately score wing threats contained in large datasets. Measuring the relative level of aggression between a pair of flies and relative territoriality, we conclude that wing threats are sufficient to establish dominance in conspecific interactions in Drosophila melanogaster.

Nondestructive Mapping of Hybrid Rocket Fuel Grains Adrian Costantino Mentors: Brian Cantwell and Sergio Pellegrino

The regression rates of solid fuels used in hybrid rocket motors are a critical parameter in the design and development of hybrid propulsion systems. Currently, it is difficult to measure fuel geometries accurately, thus causing difficulties in accurately describing regression rates, especially for smaller scale systems. Nondestructive techniques can solve this problem, as it is not necessary to get tooling into the ports. An apparatus that maps the fuel grain employing an immersed ultrasound transducer has been manufactured; its results will be the primary focus of this study. The full geometry of the fuel grains can be generated pre and post fire, which may lead to greater understanding of the way hybrid rocket fuels burn. Furthermore, previously undetectable defects, such as cracks and voids, may be identified. The generated data can further validate proposed analytical solutions (Cantwell, 2014) to the regression rate equations (Marxman and Gilbert, 1963) associated with hybrid rocket propulsion systems.

Innovative Design and Construction of 3D Architecture Si/Li 2 S Batteries Melissa Cronin Mentors: Morteza Gharib, Isabelle Darolles, and Azin Fahimi

Since 1990, lithium ion batteries have ruled the portable devices industry. However, they have major drawbacks such as their flammable electrolyte, degenerative effects, and low storage capacity. A safer battery with greater storage capacity is needed for the upcoming market of next generation smartphones, electric vehicles, and smart grid technology. Two materials, silicon and lithium sulfide, are promising candidates as electrodes for a new lithium ion battery - which will have more than three times the specific energy of current lithium ion batteries. Certain drawbacks have made the use of these electrode materials impractical, however the Gharib lab has designed a new battery that allows the use of these electrodes. Through the use of 3D architecture, a carbon nanotube scaffold, and a solid electrolyte, silicon and lithium sulfide's drawbacks are negated. We seek to build a prototype battery to begin testing, and have made progress towards its completion. Both electrodes have been tested in coin cells in a half cell configuration with the ARBIN cycling machine. The carbon nanotube lattice is grown with a Lindburg/Blue furnace, with carbon nanotubes being grown successfully on a metal current collector over 1mm high. Experiments are currently ongoing as to maximize the height of the grown carbon nanotubes, and to scale the carbon nanotube up to a larger furnace. A prototype is currently in development and is expected to be done by the end of the summer.

Testing for Paleomagnetic Wobble in Upper Cretaceous Strata Marco Cruz-Heredia Mentors: Joseph Kirschvink and Ross Mitchell

A new form of TPW that occurs on a short (1Myr) time frame is being investigated through the study of the characteristic remanent magnetization (ChRM) of paleomagnetic samples from the late Cretaceous period (chrons C33-34). To resolve the ChRM, an initial measurement of the natural remanent magnetization (NRM) is made followed by liquid nitrogen cooling and subsequent NRM measurement. The samples are then demagnetized using three successive decaying alternating magnetic fields with increasing strength and an NRM measurement at each step. Finally, the samples are heated at increasing temperatures until the NRM vanishes. The NRM measurements at the highest temperatures should form a vector that represents the ChRM and can be used to find the direction of the ambient field, and thus the location of the magnetic north pole, at the moment of lithification. Paleomagnetic data from the Scaglia Rossa formation in Furlo, Italy have provided very well behaved vectors that clearly show the magnetic reversal at the start of chron C34N. This data, along with data from several locations in California, can be further analyzed for evidence of the hypothesized 1Myr TPW phenomenon. Sufficient evidence must be found in order to measure the statistical significance of our findings.

Orbital Period Determination of Cataclysmic Variables Using Photometric Survey Data Daniel Cushey Mentors: Thomas Prince and Ashish Mahabal

Cataclysmic variable stars are characterized by their short outbursts in luminosity, followed by periods of quiescence during which many systems demonstrate a periodic luminosity. Cataclysmic variable periodicity is of great interest due to the distribution of periods among the population which shows a distinct period minimum at 77 minutes and a gap from two to three hours in which very few systems are found. A Python pipeline was developed to search for periodicity in cataclysmic variable systems taken from literature and five online databases using photometric data from the Palomar Transient Factory and the Catalina Real Time Survey. The pipeline implements


preconditioning steps to remove extraneous data before a Lomb Scargle method is used to find candidate periods for each system. Candidate periods were inspected using folded light curves displayed through an original HTML interface that included multiple added functionalities to improve efficiency and accuracy. Follow up observations were performed on selected candidate periodic systems using the Palomar 60” telescope. Further photometric and spectroscopic observations and data analysis will be performed to confirm periods in candidate systems and further study eclipsing or interesting sources for possible publication.

Optimizing Wireless Energy Transmitter Bailey Da Costa Mentors: Ali Hajimiri and Florian Bohn

Currently, designers of portable devices must strike a balance between device size and battery lifetime, or, in other words, portability and convenience. This trade-off can be solved using wireless power transmission. By merely being in a room with a wireless power transmitter, a laptop or phone can charge automatically. As part of previous research efforts, Professor Hajimiri’s Caltech High-Speed Integrated Circuits (CHIC) group has created an array of PCBs that are able to charge devices up to 15 ft away. However, the PCBs that make up the transmitter array have a low frequency, overheating issues, and a significant amount of jitter, all of which decrease power transmission efficiency. The objective of my summer undergraduate research fellowship is to test, develop, and assemble a new transmitter board that operates at a higher frequency with less jitter. The new boards have updated amplifiers and a flip chip design which should significantly decrease jitter and overheating.

A Homology Modeling Protocol to Predict Non-Native Intermediate States in the Cotranslational Protein Folding Pathway Collin Davda Mentors: Thomas Miller and Reid Van Lehn

Cotranslational folding is the process by which some proteins fold into tertiary structure while still being translated by the ribosome. A subset of proteins that fold cotranslationally fold into metastable, non-native conformations while they are still partially translated. These intermediate states must be reversed or bypassed for the fully translated sequence to fold into its native conformation, possibly due to interactions with chaperone proteins or other ribosome-associated complexes. Previously, identifying proteins that encounter metastable intermediate states while folding cotranslationally has proven computationally expensive, limiting these studies to peptide chains of less than 100 residues and small sample sizes. We present a high-throughput, computationally inexpensive method for prediction of proteins that reach metastable, non-native intermediate states in the cotranslational folding pathway. The protocol uses homology modeling to predict structures for partial sequences truncated at intervals of 9 amino acids from the N-terminus, analogous to protein translation. This efficient protocol allows for rapid screening of large numbers of cytosolic proteins to identify sequences that warrant treatment with a higher level of theory. The method may also enable the identification of general sequence or structural features shared by this set of proteins that could provide physical insight into the cotranslational folding process.

Modification of Morpholine and Piperazine Rings in Pharmaceuticals Ryan Dempsey Mentors: Brian Stoltz and Alexander Sun

Linezolid is a synthetic antibiotic used for the treatment of infections from Gram-positive bacteria that are antibiotic resistant. It is used as a last resort when other treatments like penicillin are ineffective. The morpholine ring is present in many popular pharmaceuticals that are currently on the market. The enantioselective Tsuji reaction developed in the Stoltz laboratory can be used to functionalize morpholine rings to modify these drugs. Using this technique, among others, we synthesized functionalized variants of the morpholine ring. We are hoping to reduce side effects of these drugs and/or increase their efficacy. For example, in Linezolid, we hope to eliminate relatively common side effects of nausea, headache, and diarrhea or to make the drug metabolize more slowly so that it only needs to be taken once a day instead of the current dosage of twice a day. We plan to determine if any of the modified drugs’ chemical properties were enhanced by the functionalized through examination through molecular docking software and by involving the biologists at the City of Hope.

Observations of Shock Structure in High Void Fraction Multiphase Flow Using X-Ray Densitometry Nishant Desai Mentors: Steven Ceccio and Melany Hunt

Gas-water mixtures have previously been shown to achieve a minimum speed of sound at a void fraction of 50% and low mixture pressures. In this study, we designed a blowdown tunnel and gas injection system to produce bubbly flow and achieve Mach numbers up to 6 in a square test section. The bubbly flow was achieved by injecting gas into the water flow upstream of the test section. The test section static pressure and inflow velocity were controlled by manipulating the relative pressures of the reservoir and drain tanks. A pressure reduction allowed for low sound speed and thus made it feasible to achieve our desired Mach numbers. After construction, a deflection wedge will be placed in the tunnel to produce an observable shock. High-speed video, pressure transducers, and X-


ray densitometry will be used to measure mixture pressures, bubble and liquid speeds, and actual void fraction of the flow. These modern imaging capabilities will provide a novel look at shock structure and possibly shock- boundary layer interactions in multiphase flows.

Targeting Terphenyl Diphosphine Molybdenum Compounds Bearing Metal-Ligand Multiple Bonds Bogdan Alexandru Dimitriu Mentors: Theodor Agapie and Joshua Buss

Molybdenum complexes featuring metal-ligand multiple bonds are utilized as model complexes for metalloenzyme active sites and reactive metal surfaces and have been shown to act as efficient catalysts for proton reduction, dinitrogen fixation, carbon monoxide reductive coupling, and alkyne metathesis. We present the synthesis and characterization of a series of molybdenum compounds supported by a para-terphenyl ligand framework en route to an unprecedented molybdenum hydride hydrosulfide complex. Hoping to access higher oxidation state molybdenum complexes, bearing Mo–S multiple bonds, a related meta-substituted bis(2- (diisopropylphosphino)phenyl) phenol ligand was prepared. A tri-carbonyl molybdenum complex supported by the potassium phenolate was synthesized and its solid state structure was determined via single-crystal X-ray diffraction. The reactivity of the newly generated compound was further investigated with the aim of establishing molybdenum-arene interactions and ultimately forming sulfur ligated molybdenum complexes. In addition, an anthracene-supported phosphide chloride group transfer reagent was synthesized and subsequently used in an attempt to generate molybdenum-phosphide moieties on these ligand platforms.

The Optimization of ARPES Resolution Based on Space Charge Effect Weiyi (Sophie) Ding Mentor: David Hsieh

The resolution of ARPES (Angle-resolved photoemission spectroscopy) has been improved greatly over the years. The space charge effect, which is caused the Coulomb force between photoelectrons, leads to the broadening and shift in Fermi level. This is one of the major causes of the loss of resolution in ARPES. In my project, I am going to explore space charge effect in terms of laser intensity and beam size. In general, low intensity and large beam size can provide higher resolution. In this process, I am going to measure the beam size using knife-edge methods, build a variable attenuator using half-wave plate and polarizer to tune the output power, and fit the data to a Fermi-Dirac function to calculate the band broadening and shift.

Combining Experimental and Computational Approaches to Observing Photoactivator Chemistry in Atmospheric Aerosols Kayané K. Dingilian Mentors: V. Faye McNeill and Richard C. Flagan

Secondary organic aerosols (SOA) form in the atmosphere when inorganic aerosols interact with volatile organic compounds (VOC) in the aqueous phase. Light-absorbing organic molecules are a common substituent of atmospheric aerosols, and there is evidence that aerosol formation may be driven by light-absorbing organics.

These molecules, known as photoactivators (PA), can lead to direct organic molecule oxidation in the formation of aerosols. Methods of this project consisted of a combination of experimental and computational experiments as follows. Experiments were done with a reaction chamber emulating conditions in the atmosphere with UV light.

A solution of the inorganic aerosol seed and photosensitizer were passed through an atomizer and differential

mobility analyzer (DMA) to generate and size-selected aerosol particles. This stream was added to a humidified

nitrogen flow and a stream containing a PA and run through the chamber. The reaction chamber operated at continuous flow steady-state. The exiting particles were characterized. Quantum chemical calculations were performed on a series of molecules proposed to be candidate PAs to observe their highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels. Results have shown the emergence of possible PA candidates, including 4-hydroxy-3-nitrobenzoic acid, which is more effective than 4-imidazole carboxaldehyde, an established photoactivator. These conclusions can be verified through computational experiments with higher levels of theory.

Finding the Resonant Frequency of the Zwicky Transient Facility (ZTF) Telescope Joe Donermeyer Mentors: Richard Dekany and Roger Smith

The goal of this project is to ensure that the Zwicky Transient Facility (ZTF) telescope’s shutters will not open with

a frequency that resonates with the telescope. Excessive vibration of the telescope will affect the image quality. I

used a linear motor to model the opening of the shutters. To test the effect on image quality, I set the telescope to focus on specific stars and then slowly moved the telescope, taking images every 15 ms. During this time, the motor oscillated while attached to the telescope. Using a program to find out how much the image of a specific star


shifted from its expected location in each time step, I determined how the profile affected the image. I ran profiles at a range of frequencies to find which ones would affect the telescope the most. 2.5 Hz, 4.5 Hz, and 5.5 Hz were the frequencies that stood out as having the largest effect on the image quality. This information will prevent us from attaching shutters to the telescope that detract from its image quality.

Dissecting the Neural Circuitry of Aggression in Drosophila melanogaster Rebecca Du Mentors: David J. Anderson and Eric Hoopfer

Understanding the neurobiology of emotion requires knowledge of how the brain controls emotional behaviors such as aggression, courtship and fear. Recent work with Drosophila melanogaster has shown that it is possible to isolate the neural populations that are responsible for these complex social behaviors and map their connectivity, thereby providing valuable insight into the neural circuitry controlling them. This SURF project seeks to use quantitative behavioral assays to isolate small neuronal populations that are responsible for male aggressive behaviors in Drosophila. Specifically, we will test 20 GAL4 lines—driver lines that express in specific subsets of neurons in the brain—which are known to promote various aggressive behaviors such as wing threat, lunging and tussling when neurons are temperature-activated. To do so, we separate the GAL4 gene into its two functional domains, the DNA-binding domain (DBD) and the transcription-activation domain (AD), and target them with different promoters. We can then cross each of the 20 DBD lines to each of the 20 AD (transcription-activation domain) lines, and only neurons in which both halves of the GAL4 gene are expressed will be able to be activated. Preliminary tests of a small subset of the 400 potential split-GAL4 combinations have identified 4 lines which exhibit significantly higher frequencies of lunging than the negative control, and 3 lines which show higher frequencies of wing extension than the negative control. The next set of experiments to conduct will be to cross these 7 lines to each of the 20 AD lines in order to further narrow down the neural population underlying these particular aggressive behaviors. If behavioral analysis of any of these intersections produces the expected aggression phenotype, it will also be dissected in order to image the labeled neurons with the end goal of identifying the specific neural populations underlying various aggressive behaviors, and understanding the neural circuitry underlying this emotional behavior.

Investigating Multi-Epoch Spectral Variability in Quasars Alison Dugas Mentor: Matthew J. Graham

Various astrophysical processes can only be studied in the time domain, including the accretion of matter into black holes. Quasars vary in time at all wavelengths and are believed to be caused by supermassive black holes. The Catalina Real-time Transient Survey (CRTS) is the largest currently-operating open transient survey, and it has light curves for about 340,000 spectroscopically-confirmed quasars. The Sloan Digital Sky Survey (SDSS) has as many as three spectra for each of these objects, taken across about ten years. The aim of this project is to identify quasars with unusual spectra and highly variable light curves and investigate whether their spectra have also changed throughout time. We have developed a way to identify statistically deviant light curves, and have used this to find quasars that display variability both spectroscopically and in brightness.

Development of Criteria for the Analysis of Bimodal Distributions in Stochastic Biochemical Reaction Networks Cody Dunn Mentors: Richard Murray, Ania Baetica, and Vipul Singhal

Gene expression is a naturally random process. Experiments in synthetic biology have shown stochastic behavior to interfere with mRNA and protein levels in engineered biocircuits. We can use stochastic models to help engineer biocircuits. In this research, we analyze stochastic effects in the negative autoregulation reaction network using the stochastic modeling framework of the chemical master equation. Negative autoregulation is the process by which a gene self-regulates; the proteins produced by that gene repress the creation of more proteins. The chemical master equation describes how probability distributions of molecule species in a reaction network evolve as a function of time. We are especially interested in determining the influence of reaction rates on the modality of the steady state probability distributions. We developed criteria and implemented them in MATLAB to test whether negative autoregulation’s free protein distributions were unimodal or bimodal and then attempted to find sets of parameter values that produce bimodal stationary distributions. Our results may help forward experimental design by offering information on the correct regions of parameter values for the desired modality of the distribution. We plan to use the criteria for bimodality that we developed to analyze other biochemical reaction networks displaying the property of bimodality.


Vernacular Music in Medieval England and Its Relationship to Modern Music Matthew Edwards Mentor: Jennifer Jahner

The study of medieval vernacular music—Middle English lyrics and songs—is problematic due to a frequent lack of descriptive musical notation for the lyrics, if any notation exists at all, and also due to the scarce quantity of such lyrics. Many facets of medieval music composition and performance remain unknown or debated, which prevents us from knowing how accurate our recreation of medieval songs are, the circumstances under which songs were composed or performed, and who would have composed or performed them, amongst other things. London, British Library, MS Harley 2253 contains one of the most important collections of unnotated Middle English lyrics, but we don’t know for certain what the manuscript’s purpose was. The Harley manuscript offers an essential source of information, and various collections of musically notated Middle English lyrics provide additional information about notation and transmission. In learning about medieval song, there’s a very limited supply of historical evidence, and so while we may never know the melodies for many songs, working backwards from more recent music and its performance, composition, and transmission could teach us more about medieval music. So, I plan to compare various aspects of medieval and modern music, using selected songs and lyrics.

The Effects of Bursty Star Formation Histories on Population Gradients, Stellar Kinematics, Gas Distributions, and Dark Matter Profiles in Simulated Dwarf Galaxies Kareem J. El-Badry Mentor: Philip F. Hopkins

We use the FIRE suite of cosmological zoom-in simulations to study the role of stellar feedback in regulating the evolution of dwarf galaxies. Our sample consists of 10 isolated galaxies with stellar masses between 10 4 and 10 11 and halo masses between 10 9 and 10 12 . The FIRE simulations use explicit models of the multi-phase ISM and state-of-the-art treatments of star formation and stellar feedback derived directly from stellar evolution models, with zero tunable parameters. They are run with sufficiently high force and mass resolution to resolve galactic structures on the scale of giant molecular clouds in a cosmological setting. We demonstrate that the dynamical and morphological properties of dwarf galaxies are highly dependent on changes in the star formation rate on timescales of only 100 Myr. Rapid gas outflows following bursts of star formation lead to a periodically time-varying potential, temporarily quenching star formation, driving short-timescale stellar migration, and placing stars on highly radial orbits. The gravitational pull from outflowing gas also causes significant short-timescale variation in the central dark matter density, which continues to oscillate after the star formation rate has stabilized. We find that these effects are strongest in galaxies with halo masses near 10 11 , likely because star formation is inefficient at lower masses, while at higher masses, galactic potential wells are deep enough to retain cold gas during starbursts.

A High-Order Method for Wave Propagation in 3D Dielectric Waveguides of Arbitrary Transverse Shape John R. Emmons Mentors: Oscar Bruno and Emmanuel Garza

Dielectric waveguides play essential roles in fiber optic devices, wireless communication, and other specialized electronics. However, modelling the propagation of electromagnetic fields in dielectric waveguides of arbitrary shape presents several challenges. In particular, the mode spectrum consists of a discrete and continuous set of eigenfunctions and the continuous modes requires special treatment to avoid low order convergence. Previous works do not fully address this challenge or ignore it altogether, limiting their use to simplified cases and making them unsuitable for physically realistic simulations.

We present progress on a general, high-order numerical method for simulating dielectric waveguides with complex 3D geometries requiring only modest computational resources (a single workstation). The method is based on first expanding fields into the modes of the waveguide, then propagating each mode independently. We characterize the continuous spectrum of radiation modes and make progress toward a general prescription for its discretization. Using this approach, we can compute a highly accurate expansion of an arbitrary field into the modes of the waveguide, including discrete and continuous modes, yielding a more general technique for high precision dielectric waveguide simulations.

Formal Synthesis of Switching Protocols for Estimation and Control of Aircraft Electric Power Systems Charlie Erwall Mentors: Richard M. Murray, Benson Christalin, and Scott C. Livingston

Aircraft electric power systems (EPS) are growing in size and complexity as more mechanical, pneumatic and hydraulic systems are being replaced by electrical subsystems. These electrical systems are equipped with contactors that can reroute the circuits in case of component failure. The growing complexity of aircraft EPS increases the need for automatically generated protocols for controlling contactors, since current hand-practice design becomes less viable for larger systems. In this project formal specifications of safety and fundamental requirements for aircraft EPS are proposed. A Python script which automatically generates a protocol describing


safe, allowable control actions based on these specifications is developed and such a protocol is verified on an aircraft EPS testbed. Implementation of these control protocols rely on the ability to estimate the state of components, since the amount of sensors in the system is limited. This process of estimation can benefit from contactor switching, but is restricted by the same requirements as the control. Thus, implementation of an estimation algorithm subject to those constraints is also explored. Lastly, joint execution of estimation and control protocols is explored and discussed.

Progress Towards the Total Synthesis of Eucomic Acid Benzi Estipona Mentors: Brian Mark Stoltz and Beau Pritchett

Eucomic acid is a naturally occurring compound derived from the genus Vanda. Eucomic acid has recently been shown to serve as a global stimulus of cytochrome c oxidase in the body. This function has been directly linked with attenuating the cell aging process as well as serving as a preventative measure towards cancer. Herein, we utilize synthetic methodologies pioneered by the Stoltz group, namely, the asymmetric allylic alkylation of dioxanone substrates, to achieve a total synthesis from commercially available cyclohexanone dimethyl ketal to access enantioenriched alpha-hydroxy methyl esters, which serves as the basic framework for many biologically active compounds including eucomic acid. Currently, we have been successful in synthesizing the dimethyl ester intermediate leaving only saponification of the diester to yield the natural product.

Development of an SFC-ESI-MS System for Online Observation of Prebiotic Chemical Reaction Products in Supercritical Carbon Dioxide via Mass Spectrometry Jieyuan (Jenny) Fan Mentors: Jesse L. Beauchamp, Daniel A. Thomas, and Kathleen T. Upton

Beyond well-known applications to “green chemistry,” supercritical carbon dioxide (scCO 2 ) provides a unique opportunity to investigate chemical reactivity in an environment that differs from water and organic solvents. Hypothesized to be present in the subsurface of several planets, both within and beyond our solar system, scCO 2 is therefore an intriguing medium in which to explore prebiotic chemistry and the possibility that it may have supported non-aqueous life. The motivation in studying prebiotic chemistry in scCO 2 is two-fold: in addition to the possibility that it may have contributed to the emergence of life on earth, it will help to inform the search for life on other planets. To examine reactions in scCO 2 , a high-pressure reactor coupled to a mass spectrometer has been developed. The system comprises a high pressure pump to generate scCO 2 , a reaction vessel enclosed in a temperature-controlled oven, and a modified ESI source that interfaces the high-pressure system with a Thermo Scientific LTQ-XL ion trap mass spectrometer for real time online monitoring of reactants and products. Diagnostic testing with caffeine and other molecules known to be soluble in scCO 2 has been performed, and studies of chemical reactivity, including the synthesis of amino acids and peptides from simple precursors, are underway.

Spectral Action for Bianchi-Type IX Minisuperspace Wentao Fan Mentor: Farzad Fathizadeh

We carry out a detailed study of the Seeley-de Witt coefficients appearing in the asymptotic expansion of the spectral action for the Dirac operator acting on sections of the spin-bundle over the Bianchi-type IX minisuperspace. The first three coefficients are calculated by expanding the heat kernel and applying parametric pseudodifferential calculus. We have also developed an efficient general method for computing the Seeley de-Witt coefficients associated with an elliptic positive operator on a compact manifold, which is based on making use of Wodzicki's noncommutative residue. The results derived from both methods are compared to confirm the validity of the new approach. In addition to being remarkably efficient, after taking advantage of the SU(2) symmetry of the Bianchi-type IX metric, this method yields an elegant proof of a rationality result. That is, we show that a general term in the spectral action for Bianchi-type IX metric is expressed by a several variable polynomial with rational coefficients evaluated on the cosmic evolution factors 1 (), 2 (), 3 () and their higher time derivatives of a certain order. An especially interesting family of metrics called Bianchi IX gravitational instantons, which, after a correct choice of a conformal factor, form a family of self-dual Einstein metrics, are then considered and the rationality result is extended to this case. Considering the latter and the fact that there is a parametrization of Bianchi IX gravitational instatons in terms of theta functions with characteristics, arithmetic and modular properties of their spectral action and their relation with modular forms are studied in detail.

Optimal Trajectory Generation Under Environmental Uncertainties Using Signal Temporal Logic Specifications Nuno Ferreira Duarte Mentors: Richard Murray and Samira Farahani

Signal Temporal Logic (STL) has successfully been used for specifying a wide range of behaviors for systems and environments. Previous works using Linear Temporal Logic (LTL) have synthesized controllers when specifying properties of discrete time signals but are incapable of handling continuous signals with time dependency, in


particular, when optimizing trajectories under environmental uncertainties, such as static or dynamical obstacles, known and unknown obstacles. To address these issues, we use STL and our aim is to design a reactive strategy and trajectory planning for a surveillance mission in a partially known environment; the autonomous vehicle will satisfy tasks such as periodically monitoring areas, path planning, staying safe, and avoiding obstacles while the position of some of them is not known a priori. We also compare the performance of the obtained controller with the one obtained using LTL language.

Developing a Search for Dark Matter Direct Production Using Razor Variables in Proton-Proton Collisions at 13 TeV Jared Filseth Mentors: Harvey Newman, Maria Spiropulu, Cristian Peña, and Javier Duarte

Dark matter makes up 27% of the mass-energy budget of the universe, but still remains elusive today. In recent years, searches for dark matter production in proton-proton (pp) collisions have been carried out up to a center of momentum energy of 8 TeV. This project involves improving and reengineering the analysis methods used on 8 TeV data, so that they can be applied to new 13 TeV data. These methods involve looking at razor variables, which are used to quantify the imbalance in transverse momenta in each collision. In order to update these methods, I have been measuring quantities such as the trigger and lepton efficiencies for simulated events as well as Compact Muon Solenoid (CMS) data. Further studies would involve finishing the search, using these methods, once a sufficient integrated luminosity has been recorded.

Written Roles: Female Letter Writing in Romantic England Jennifer Frazin Mentor: Kevin Gilmartin

In 18th and 19th century England, written correspondence provided the average female with a means to extend herself beyond the domestic sphere of her own home, but did this extension entail greater independence? In order to answer this question, this project turns to 18th century letter writing manuals, episodes of correspondence in three Jane Austen novels, and Mary Shelley’s Frankenstein, as well as a collection of published letters by Mary Wollstonecraft. Analyses of these works and related scholarship serve to place the Romantic woman in relation to her world and, in so doing, pose several other key questions. What was the Romantic woman’s role, and how did letter writing reflect, change, and/or solidify this position? What can we learn about expectations for female behavior from letter writing manuals or episodes of correspondence in novels? How might these examples compare to published collections of letters? As might be expected, answers to these questions are anything but black-and- white. My analysis demonstrates how the female letter writer can be viewed both as oppressed, by her limited means of representation, and liberated by the opportunity to transcend private domestic life. Analytical recognition of this ambiguity paves the way for future literary and historical analysis of this topic.

Investigation of the Role of Treslin in DNA Replication in Xenopus Egg Extracts Ángel Gálvez Merchán Mentor: William G. Dunphy

Once every cell cycle, genetic material duplicates in an accurate process called DNA Replication. In eukaryotic organisms, replication involves the ordered recruitment of conserved proteins on replication origins. This assembly culminates with the activation of the replicative helicase, which unwinds the double strand and gives rise to the onset of DNA replication. However, despite its great importance, our knowledge on this process in vertebrates is limited. In this project, we aimed to improve the current understanding of DNA replication onset using Xenopus laevis egg extracts as a model system. Performing immunodepletions, we removed essential origin proteins such as Treslin, RecQ4 and TopBP1. Subsequent chromatin-binding assays allowed us to develop spatial-temporal models on proteins’ behavior at replication origins. Additionally, time course origin-binding experiments of crucial players were performed in untreated and drug-treated conditions, giving us insights into the complex dynamics of the process. These results led us to contemplate a potential extra role of one of the proteins in the intra-S phase checkpoint, although additional experiments need to be carried out to confirm this. In conclusion, this project has shed some light on the poorly understood DNA replication onset, and might have unveiled a new role of one of its players as a safeguard of genomic stability.

Multiplexed Cell Sorting Based Upon Relative Quantitation of Endogenous mRNA Targets by in situ Hybridization Chain Reaction Siva Gangavarapu Mentors: Niles Pierce and Aneesh Acharya

Hybridization chain reaction (HCR) has been recently developed as an alternative method of signal amplification for in situ hybridization systems. It can also be applied to cell sorting using genetic markers present in various cell types. This project aims to demonstrate HCR as an effective system for studying endogenous mRNA targets and isolating and sorting cells. We picked targets picked from four different tissue types: retinal g protein coupled


receptor from the retina, surfactant protein A1 from the lung, albumin from the liver, and chymotripsinogen B1 from the pancreas. Results have demonstrated both very high signal from targeting the surfactant protein in lung tissue and low background signal. By performing redundancy studies using multiple probe sets, probe signal in all samples could be increased by eliminating poorly performing probes. Moreover, we will be able to demonstrate relative quantitation between HCR signal and mRNA concentration. After demonstrating high presence of a target in the intended tissue type and low presence in the other tissue types by observing signal-to-background ratios, we can conclude that HCR can be used to isolate and sort cells from heterogeneous tissue samples using mRNA targets.

Determining Survey Completeness for Friends of Hot Jupiters Paige Gannon Mentors: Heather Knutson and Henry Ngo

Some systems containing hot Jupiters─Jupiter mass planets orbiting extremely close to the host star─also host stellar mass companions, which may have influenced the migration of the planets. The Knutson group’s standard method for examining these systems is to use Keck’s NIRC2 camera with Keck’s adaptive optics (AO) to directly image their targets. There is an alternate survey mode, angular differential imaging (ADI), typically used with a coronagraph to occult most of the primary star’s light. It is capable of resolving fainter companions, though it takes more observational time and places a lower limit on projected separations. Through injecting synthetic companions into the target systems, I determine the expected difference in the number of companions found by the current survey mode and the ADI survey mode, and compare it with the percentage of companions missed due to their geometrical arrangement with the target stars. Through this analysis, I have also created an automatic companion detection algorithm, which should provide a useful check for manual inspection.

Analysis of Chromatin Conformation of Cis-Regulatory Modules in Drosophila melanogaster Galen Gao Mentor: Angelike Stathopoulos

Spatial and temporal control over gene expression is often mediated by sequential action of cis-regulatory modules (CRMs)—stretches of DNA usually several hundred base pairs in length near the genes they regulate. Recently, it has been hypothesized that local changes in chromatin conformation can reposition CRMs and that these shifts may cause changes in gene expression. One such gene, brinker (brk), encodes a transcription factor essential for proper Drosophila dorsal-ventral development and is controlled temporally and spatially in early development by a 5’ CRM, a 3’ CRM, and a promoter proximal element (PPE) near the brk coding region. To test the role of the relative positioning of these elements in brk expression, fluorescent probes marking the 5’ CRM, 3’ CRM, and PPE were introduced into nuclear cell cycle 14 embryos, which were then imaged via fluorescence microscopy. A spot detection algorithm employing a multi-scale Laplacian of Gaussian detector with automatic scale selection was used to detect the probes’ positions and group them into triplets corresponding to each nucleus’s conformation of 5’ CRM, 3’ CRM, and PPE components. The resulting triplets were classified into eight conformations based on their elements’ proximity to each other and then mapped back onto the embryo.

Preparation of Isoquinolines for Rapid, Convergent, and Enantioselective Access to Jorumycin Kevin Gao Mentors: Brian Stoltz and Max Klatte

Accessing diverse isoquinolines has important implications for pharmaceutical applications and natural product synthesis. These structural motifs are found in numerous potential antitumor agents among the tetrahydroisoquinoline (THIQ) alkaloid family. The Stoltz group has a longstanding interest in the total synthesis of biologically active THIQs. Recent efforts towards jorumycin have been a particular research focus. Our original synthetic strategies were built on aryne annulation. Issues with scalability, efficient material throughput, and the demethylation of key substituents in the late stages of the synthesis led us to seek alternative access to isoquinolines. In this effort, we employed a robust approach utilizing known cross-coupling methodology such as the Heck and Sonogashira reactions to generate our desired substituted isoquinolines from readily available 3,4,5-trimethyoxybenzaldehyde. Benzyl substituents were installed to enable facile deprotection. Fagnou coupling will allow access to the carbon framework of jorumycin.

Characterization of CZT and CdTe Pixel Detectors for Future Astrophysical X-Ray Missions Daniel Gawerc Mentors: Fiona Harrison, Hiro Miyasaka, and Vikram Rana

The Nuclear Spectroscopic Telescope Array, or NuSTAR, has CdZnTe (CZT) hybrid detectors in its focal plane for x-ray observation. Next generation detectors can benefit from NuSTAR analysis. High quality CZT crystal yield is low. Studying CdTe crystals is important, as they were found to have a higher yield than CZT. CdTe crystals are crucial for wider focal plane missions, where more crystals are necessary. CZT and CdTe properties have different upsides and downsides for x-ray detection. Leakage current shot noise fluctuations may be incorrectly read out as x-ray signals in the detected spectrum. It is due to an applied bias voltage and the internal resistance of the crystal


pushing a small current into the ASIC. It increases with HV, temperature, and crystal impurities. CZT was confirmed to have a constant leakage current over time. CdTe electrode contacts were compared to ascertain which exhibited the lowest leakage current. Gamma flood, or radioactive source illumination, tests are used to characterize the structure and uniformity of a crystal. 241 Am was used to characterize CZT hybrid H79 by comparing the emitted and detected spectra. Additionally, the NuSTAR laser metrology optics tracking system power decay was estimated as a function of time and intensity.

Calorimeter Photodetector Studies for the Mu2e Project Hallmann Óskar Gestsson Mentors: David Hitlin and Frank Porter

The neutrinoless decay of a muon into a monoenergetic electron is an example of a charged lepton flavor violation. The Mu2e project will study this process by trying to detect this decay with a proposed sensitivity of 6.7 10 17 . This will provide data that will show which types of new physics models are favorable. Produced muons will be captured and guided by a series of superconducting solenoids onto an aluminum stopping target. Conversion electrons will emerge from the target and enter a tracker and then a calorimeter. The calorimeter provides secondary and independent measurements of converted electron energies. It will make use of scintillating crystals and photodetectors to do these measurements. The crystal that is investigated in this paper is BaF 2 which has a fast and slow time component in the UV spectrum. The photodetector to be used must be able to work in a 1 Tesla magnetic field, have high quantum efficiency in the UV spectrum, and be able to block out the slow time component. Measurements carried out on large area avalanche photodiodes that are delta doped are presented in the paper and determined if they meet the demands of the project.

Explicit Orbit Construction for the Matsuki Correspondence for the Affine Grassmannian Iulia Gheorghita Mentor: Xinwen Zhu

For a connected reductive complex algebraic group G with Cartan involution δ, real form G_R with respect to conjugation θ, maximal compact subgroup G_c, let η be the composition of θ and δ. Let K be the fixed points of η and K_c be the maximal compact subgroup of both G_R and K. If B is the flag variety of G, G_R and K act on B with finitely many orbits. The Matsuki correspondence states that for each G_R-orbit O_R in B, there exists a unique K-orbit O_K such that their intersection is a single K_c orbit and thus, this correspondence gives an order- reversing isomorphism between G_R\B and K\B. In 2004, D. Nadler extended this correspondence to the case where B is replaced with the affine Grassmannian, Gr = G(C((t)))/G(C[[t]]), the polynomial loop group LG_R is taken instead of G_R, and K(C((t))) instead of K. We seek to explicitly describe the orbits of which D. Nadler gives a parameterization, by making use of the natural stratification of Gr.

Resonant Production of Sterile Neutrinos in the Early Universe Lauren Gilbert Mentors: George Fuller and Christian Ott

This study examines the cosmological impacts of a light resonantly produced sterile neutrino in the early universe. Such a neutrino could be produced through lepton number-driven Mikheyev-Smirnov-Wolfenstein (MSW) conversion of active neutrinos prior to big bang nucleosynthesis (BBN). During BBN, the neutron-proton ratio depends sensitively on the electron neutrino flux. If electron neutrinos are being converted to sterile neutrinos, this makes the n-p ratio a sensitive probe of possible sterile neutrinos. We therefore use experimental measurements of primordial Y p and D/H to place limits on this process.

The Effect of Chronic Nicotine Use on Neurons in the Substantia Nigra in Relation to Parkinson's Disease Heather Gold Mentors: Henry A. Lester and Beverley Henley

The chronic use of nicotine has been suggested to have a neuroprotective effect against Parkinson’s disease by the inverse association between cigarette use and Parkinson’s disease incidence. This project seeks to understand the mechanisms behind this effect and specifically study the effect of nicotine on neurons in the substantia nigra, the brain region in which neurons selectively die in Parkinson’s disease. After chronic exposure to nicotine, the transcriptome of a neuron was sequenced using single-cell RNA-sequencing, allowing data libraries to be collected on individual neurons from the heterogeneous population of the substantia nigra. After sequencing, each library was aligned against a genome, quantified, and normalized before differential analyses were performed. Data processing was performed with Tophat, Bowtie, htseq-count, and Cufflinks, as well as custom python scripts. Preliminary results indicate the suppression of neuroinflammation and cytokine signaling as possible neuroprotective mechanisms, but further testing must be conducted to verify and replicate these results with expanded datasets.


Ground Deformation in Simulated Earthquake Shaking Using Complex Fourier-Based Amplification Factors Carlos Gonzalez Mentors: Domniki Asimaki and Jian Shi

It has long been known that local site characteristics have notable effects on the ground motions caused by an

earthquake. Most modern U.S. seismic design codes for building structures account for the specific near surface response of the soil layers in the location of interest. However, the established site-classification criteria in use today do not sufficiently describe soil’s susceptibility to nonlinear ground motion. Previous work has been done validating a proposed nonlinear model's (NLHH) ability to construct the Fourier amplitude spectrum for various sites. This project seeks to collect data and perform statistical analysis on the viability and accuracy NLHH's ability to construct the Fourier phase curve. Using data from the KIK-net downhole array, we are able to compare the performance of various simulations ability to recreate a ground motion time series Fourier phase curve. Additionally, we have explored an empirical relationship between the transfer functions for Fourier amplitude and Fourier phase for linear, homogeneous, viscoelastic soil layers. Once verified, we can explore it further for more complicated soil layers with the goal of using it for post-facto broadband ground simulations to verify simulations’ ability to predict ground motion based on nonlinear site characteristics.

Mechanistic Studies on QUINAP and Its Triflate Precursor Ashay Makarand Gore Mentor: Scott Virgil

A novel method of the asymmetric synthesis of the chiral ligand QUINAP via dynamic kinetic resolution was

recently developed. This synthesis involves an isomerization process of the arylpalladium intermediate in which the isoquinoline piece can adopt two positions in relation to the naphthalene ring. Mechanistic studies to deduce the mode of isomerization of the arylpalladium intermediate and the triflate precursors via deuterium labeling and kinetic analysis were performed. Work on isolating the arylpalladium intermediate was also conducted.

A Novel Radiation Shield Design for sub-K, Angle-Resolved Photoemission Spectroscopy Arjun Goswami Mentors: David Hsieh and Tejas Deshpande

Angle-resolved photoemission spectroscopy (ARPES) is a technique that images the electronic bandstructures of solids by inducing photoemission in a sample, and analyzing the energy and momentum of the ejected photoelectrons. The Hsieh lab's laser-based ARPES system at Caltech cools down samples to sub-K temperatures under ultra-high vacuum (UHV) conditions, enabling measurements of condensed matter phenomena. Such measurements may provide insight into the existence of topological superconductors, a potential platform for low- decoherence topological quantum computation. To achieve proper measurement conditions, liquid cryogens (nitrogen and helium) are used to cool down the sample, which must be encased in radiation shields during this process. Here, a novel design for a radiation shield in the form of a machined helical spring is presented. Characteristics that are embodied in the design include UHV-compatibility, a robust thermal enclosure for the sample, and a mechanism for sample loading. Analytical techniques, as well as numerical techniques (finite element analysis) were used to quantify mechanical and thermal properties of the shield. After testing the radiation shield on the system, modifications and refinements can be recommended for optimal functionality.

Investigation of Human Magnetoreception Using Bistable Visual Illusions Mara Green Mentor: Joseph Kirschvink

It is already well documented that a wide variety of organisms sense and respond to the Earth’s magnetic field.

Examples of bacteria, invertebrates, birds, fish, reptiles, and even mammals use this magnetoreception for navigation and orientation. Since humans likely descend from a magnetoreceptive ancestor, we are investigating a possible latent magnetic sense in humans. Our experimental setup consists of a large Faraday cage in which we can precisely control the magnetic field, allowing us to expose subjects to changing fields and to try to elicit subconscious subject responses. One approach is to rotate the field in the horizontal plane and simultaneously instruct the subject to view a bistable visual illusion. This type of illusion provides sensory information which is equally likely to be interpreted in either of two ways, and which causes random perceptual switching between these two interpretations. In this case, the illusion may be interpreted as rotating either left or right. We hope to modulate subjects’ perception of this illusion using the rotation of the ambient magnetic field.


Machine-Readable Protocols and Rapid-Prototyping for Synthetic Biology Research: Implementation of a Liquid Handling Robot Carl Marcus Greiff Mentors: Richard Murray and Scott Carlton Livingston

This project is focused on creating a liquid handling robot for use in the synthetic biology lab. The goal is to improve the consistency of the TX-TL cell free expression system by reducing the potential for human error during production, and also free up time for the researchers, increasing the total research volume of the Keck synthetic biology lab. This is done by rapidly prototyping the robot while maintaining a high level of reusability and versatility. For these purposes, the project is divided into four subsections. The first is to create a Python based graphical user interface (GUI); the second is to make use of the robot operating system ROS to enable the interaction between the GUI and the controller; the third is to implement the controller and set up the sensors and motors of the robot; and the fourth is to help with the hardware design in order to ensure compatibility between the hardware and software.

Predicting the Structures of Family 2 Human Olfactory Receptors Daniel Gu Mentors: William Goddard, III, and Soo-Kyung Kim

The sense of smell is mediated in humans by the human olfactory receptors (hORs), a group of G-protein coupled receptors (GPCRs). Since these proteins do not crystallize easily, there are very few structures known for GPCRs. The overall aim of the project is to use the GEnsemble methods previously developed by the lab to predict structures and the ligand docking behaviors of these hORs. In particular, my project focused on the family 2 hORs OR11H4, OR11H7, and OR10J5 and their docking behaviors.

The Invariant Theory of the Order 3 Automorphism of so(8) Jeffrey Gu Mentor: Xinwen Zhu

The Lie algebra so(8) is unique since it is the only Lie algebra to have an order 3 automorphism. This automorphism induces a grading so(8) = g 0 +g 1 +g 2 , where g i is the eigenspace corresponding to ζ i , where ζ is a primitive 3 rd root of unity, and the set of fixed points g 0 is the g 2 Lie algebra. We seek to describe the action of g 0 on g 1 and its invariants, such as the nilpotent cone and nilpotent orbits.

Analysis of DNA Charge Transport in E. coli DNA Repair Proteins Using CRISPR Interference Stephanie Gu Mentors: Jacqueline K. Barton and Andy Zhou

Various environmental factors induce mutations within an organism’s DNA, which can result in cancer if left unchecked. An organism needs to employ DNA repair mechanisms to protect the integrity of the genome for itself and future generations. Here we constructed a CRISPR interference (CRISPRi) system to study how DNA-mediated charge transfer (CT) facilitates signaling amongst E. coli’s three DNA repair proteins: EndoIII, MutY, and UvrC. Using Gibson assembly, we constructed a CRISPRi one-plasmid system that consists of two parts: an inducible dCas9 endonuclease regulated by pBAD and a constitutively expressed single-guide RNA (sgRNA) sequence using a GAPDH promoter. Following its construction, we will conduct an in-vivo UV sensitivity assay to examine how expression levels of the three DNA repair proteins affect the cell’s ability to repair UV-induced DNA damage. We will also use atomic force microscopy (AFM) assays to measure protein redistribution on DNA with or without base pair mismatches. Cyclic voltammetry will be used to examine the repair proteins’ redox potential. These results will verify the CT-mediated mechanism for identifying DNA damage and will establish DNA CT as a method for signaling within biological chemistry.

Matching Tumor Antigens to T Cells Katherine Guo Mentors: James R. Heath and Songming Peng

Cancer immunotherapy involves stimulating the body’s immune system to fight cancer. One application of immunotherapy is adoptive cell transfer (ACT), which involves isolating T cells from patients and picking the ones that react to cancer. They then multiply the cells, stimulate them with immunotherapy drugs that ramp up T cell abilities, and inject them back in the patient. While promising, a big challenge is to broaden its reach by identifying new tumor antigens that will guide the T cells to specifically kill the cancer cells while sparing the healthy cells. Current immunotherapy methods mainly target the common antigens, however, by discovering neo-antigens specific to a person’s cancer, the ACT treatment will be more effective. With a library of potential antigens derived from tumor sequencing data, we aim to pull down single T cells with PDMS microfluidic chips, read the barcode of their associated tumor antigen through sequentially coded fluorescent dyes, and then isolate T cells that can recognize a patient’s known tumor antigens. By identifying a tumor antigen and its matched T cell receptor at the single cell level, we can pave the way for personalized cancer immunotherapy.


Using Lens Cuttings to Derive Upper Bounds for Incidence Problems Songshan (Bella) Guo Mentor: Adam Sheffer

Lens cutting is a technique used to improve by Aronov and Sharir to improve the current bound for point circle incidences involving circles of arbitrary radii in the plane. This paper used archaic partitioning techniques, so we improve their bound by using the polynomial partitioning method, which was recently developed by Guth and Katz. Other problems examined included the cutting number, or the cuts needed in order to convert an arrangement of curves to an arrangement of pseudosegments, such that there are no K 2,2 ’s, of various objects, such as ellipses, graphs of polynomials, and general polynomials.

Immobilization and Study of Fluorinated Molecular Catalysts on Graphitic Surfaces Ayush Gupta Mentors: Harry B. Gray and James D. Blakemore

Interfacing well-defined molecular catalysts with electrode surfaces is a key step toward constructing devices for selective solar-fuel production. Noncovalent interactions between fluorinated aromatic cycles and other aromatic cycles have been observed in a variety of compounds. Most notably of these is the interaction between hexafluorobenzene and benzene. We now report synthesis of a new bipyridine ligand appended with two perfluorobiphenyl groups. The ligand was synthesized by reacting 4,4′-Dimethyl-2,2′-bipyridine with lithium diisopropylamide to afford the reduced bipyridine. This was then reacted with decafluorobiphenyl to form the final compound. The ligand was then reacted with a rhodium cyclopentadiene dimer to form the proton reduction catalyst that was studied. To better study the surface-attached catalyst. A high surface-area carbon material was prepared on highly oreiented pyrolytic graphite using Ketjen black and a conductive polymer. Preliminary studies with the carbon material show a wide range of stable potentials that can be applied. Further data about the attachment and stability of the catalyst will be provided once the experiments are completed.

Estimation of Hypocenter for a Given Seismic Event Gaurav Gupta Mentors: K. Mani Chandy and Julian Bunn

The earthquake monitoring system consists of large widespread sensor network which measures the acceleration at the ground due to shaking and sends this data to a server, and various statistical algorithms are used to detect and issue warnings about the impending seismic activity. This paper contains the algorithm for detection of Hypocenter using the large amount of data streams collected by Community Seismic network (CSN) sensors during an earthquake event. The estimation of hypocenter will enable us to determine the arrival time of seismic wave using statistical models and will contribute towards development of early warnings systems for possible damage control during such an event.

High Sensitivity CMOS Potentiostat for in vivo Distributed Wireless Sensing Albert Gural Mentors: Azita Emami and Manuel Monge

Addressable Transmitters Operated as Magnetic Spins (ATOMS) are micro-scale devices capable of power harvesting and communication at magnetic field-dependent frequencies. Their locations can be discerned by applying a magnetic field gradient and communicating with them at correspondingly shifted frequencies. A potentiostat, an electrochemical sensor that measures the concentration of any given electroactive chemical analyte in solution, can be added to these devices to allow for minimally-invasive wireless implantable chips that are capable of determining the chemical constituents of the surrounding fluids. For example, by placing many potentiostat-functionalized ATOMS chips throughout the brain, global real-time dopamine recording can be achieved. We present a novel CMOS potentiostat that adheres to the power, voltage, and size constraints of ATOMS technology while still allowing for high dynamic range sensitivity and a wide redox voltage swing. The potentiostat was designed using predictive technology models of 45nm CMOS technology and operates at 1V.

On the Bounds of the Carbery Rectangle Problem Daniel Guth Mentor: Nets Katz

In attempting to extend a theorem on sublevel sets to higher dimensions, Carbery, Christ, and Wright observed that any measurable set E in the unit square in R 2 not containing the corners of an axis-parallel rectangle with area

greater than λ has measure bounded by O(� λ log( λ ) ). Under certain conditions the logarithm in this bound can be

removed, but it is an open problem whether or not this bound is sharp in the general case. We examine the geometric properties of a specific case where part of the set is E is known.



Investigating the Role of Cellulose in Morphogenesis of Arabidopsis Hypocotyls and Shoot Apical Meristem Melina Theoni Gyparaki Mentors: Elliot Meyerowitz and Arun Sampathkumar

Cellulose is synthesized at the plasma membrane by rosette-like cellulose synthase complexes (CESA). Primary cell wall formation requires CESA1, 3 and either CESA2, 5, 6 or 9, while secondary wall formation requires CESA4, 7 and 8. The deposition and guidance of the CESA complexes are mediated by the microtubule cytoskeleton. The Meyerowitz lab has shown that mechanical stress acts as an instructing signal to regulate cell wall synthesis at subcellular and tissue scales via the microtubule cytoskeleton network. However, the molecular aspects of CESA gene regulation have not been fully described with regards to mechanical forces in different tissues and cell types. Cytokinin is a hormone involved in shoot apical meristem formation among other processes. The aim of this project was to investigate the interactions between the CESA genes, the microtubule network and cytokinin and how they are all related to cellulose synthesis as well as hypocotyl and meristem development. A variety of techniques was used including In-Fusion cloning of CESA1 and CESA3 genes, next-generation in situ hybridization, imaging of cytokinin markers in hypocotyls as well as mechanical perturbation coupled with confocal microscopy. Our results demonstrate a putative interaction between cytokinin signalling, microtubules and cellulose synthase gene regulation.

Preventing Environmental Release of Genetically-Modified Gut Bacteria With a Thermally-Activated Kill Switch Gloria Ha Mentors: Mikhail Shapiro and Mohamad Abedi

The human body carries about 100 trillion microorganisms in its intestines, a number ten times greater than the total number of human cells in the body. These organisms play a major role in maintaining our health and mood, and are targeted by engineered bacteria and medicines. Unfortunately, therapeutic bacteria engineered to modify the gut microbiota are eventually excreted into the environment, where they continue to propagate. In order to design engineered gut bacteria that are incapable of spreading into the environment, we used TlpA, a coiled-coil protein found in Salmonella typhimurium, to establish heat-modulated bacteria that can survive at gut temperatures (37ºC) but not outside (25ºC). To this end, we targeted the production of D-alanine, an amino acid that is essential for cell membrane formation, and thus for bacterial growth. Alr-100, an essential gene for D- alanine production, was made dependent on TlpA binding, and auxotrophic bacteria incapable of D-alanine production were transformed with these plasmids. Future work will use the optimized constructs to design bacteria that are activated at fever temperatures (40ºC) but not at body temperature (37ºC).

Reproducibility in Cancer Biomarker Studies James Ha Mentors: Ashish Mahabal and Thomas Fuchs

The ease of use and availability of next-generation sequencing and microarray platforms has resulted in a deluge of cancer biomarker studies being published. Given the importance of the various clinical uses of cancer biomarkers, including early detection screening, the development of effective treatment regimens, and estimating patients’ prognoses, it is important to ensure that the results of biomarker studies are reproducible. Of the many levels of reproducibility that may be examined in a biological study, we elected to examine the reproducibility of figures from processed data. We addressed this reproducibility issue by building a web application that allows users to visualize their data using a variety of methods (such as principle components analysis, correlation heatmaps, and pairs plots), and download plots generated by the app.

Characterizing Entangled Strategies for Nonlocal Prover Games Nick Haliday Mentor: Thomas Vidick

The goal of this project is to broaden understanding of entangled strategies (allowing shared entangled states but no communication) for nonlocal prover-verifier games beyond the well-understood case of XOR games, either by generalizing known results or finding pathological examples. We constrain ourselves to 2-prover games with classical verifiers, and focus on the values ω c ≤ ω q ≤ ω sdp ≤ ω ns (the classical, entangled, SDP, and non-signaling values), i.e., the maximal winning probability for strategies of various sorts. We consider the last two mainly because they are computationally and analytically tractable, and provide a route toward analyzing the first two. We begin with marginal XOR games, an extension of XOR games where certain answers are more heavily weighted for particular players. We show that the “identity game,” played on a graph, always satisfies ω ns = ω c , so that entangled strategies offer no benefit over classical. This generalizes a result from the literature where the graph was the path graph. We consider k-coloring games for small k, and attempt to sharpen known bounds on the ω c -ω q gap for general games for this particular class.


Implementing Coarse-Grained Atomistics for Multi-Scale Material Modeling Andrew Han Mentors: Dennis Kochmann and Ishan Tembhekar

It is of great interest in materials science to acquire a fundamental understanding of the physics of materials across various scales, so that a bottom-up approach to engineering material properties may be possible. Most computational models which describe material phenomena are, while accurate, constrained to discrete length and time scales, and these models are not capable of predicting the cascading effects of phenomena across scales. Magnesium, a material of high interest for transportation and defense applications due to its high strength to weight ratio, is one example of a material which requires multi-scale modeling for accurate property prediction. Magnesium is inherently susceptible to the nanoscale phenomena of twinning, and modeling this behavior harmoniously with atomic scale dislocation activity is computationally expensive and difficult. A new quasi- continuum method uses coarse-grained atomistics to approach multi-scale modeling by allowing simulations with atomic resolution and finite element efficiency. This model can describe both twinning and dislocation activity in stressed Magnesium, demonstrating the model’s potential to facilitate significant progress in material property prediction and engineering.

Characterization of a Putative [4Fe-4S] Complex in UvrC by Means of X-Ray Crystallography Sirus Han Mentors: Jacqueline Barton and Rebekah Silva

DNA-mediated charge transport (DNA CT) is the fidelity-dependent ability of DNA to transfer electrons through the aromatic systems that run up the helices. It has been demonstrated via a combination of genetic and molecular assays that two proteins, Endonuclease III and MutY, participate in base excision repair, facilitated by DNA CT. Both of these proteins contain an uncommon [4Fe-4S] cluster which until recently was thought to be only structural in function. However, since these clusters are only redox active at physiological potentials when bound to DNA, it is hypothesized that they aid the repair proteins in locating damage.

The Barton Group has identified UvrC as another protein that participates in NER that may contain a [4Fe-4S] cluster. Strong evidence for the cluster’s existence in UvrC was obtained through EPR. In order to confirm the cluster’s existence, UvrC is in the process of being purified and crystallized. Once obtained, these crystals of UvrC will be subjected to X-Ray Crystallography, by which a crystal structure will be obtained.

An Investigation of Two Different Power Distribution Options for Small Fuel Cell Vehicles Jacob Harmon Mentor: Guillame Blanquart

The purpose of this investigation is to evaluate the pros and cons of two popular power distribution systems in small fuel cell vehicles. The first system, used primarily in mid-sized vehicles, powers the drive train, while sending excess power to battery and superconductor, theoretically increasing fuel cell efficiency. The second system bypasses the extra battery banks, thus being a simpler, lighter, and cheaper system that is only viable in small vehicles. Modifications to a small electric vehicle constructed by Caltech Sustainable Vehicle Club, along with manufacturer specifications of commonly used fuel cells, provide data to be used in the analysis of the two systems.

Using Machine Learning to Develop Algorithmic Trading Strategies for Stock Market Investing Christopher Hazard Mentor: Ben Gillen

Wall Street traders seek to extract information from historical market data and utilize it to identify and exploit patterns to execute profitable trades, leading to the development of a variety of forecasting and trading strategies ranging from simple methodologies to complex trading systems. Many approaches for achieving winning trading strategies have their roots in information theory, mathematical finance, stochastic modelling, and machine learning. The underlying question of this study is: Can one achieve consistent above average returns based on recent stock price movements alone, or is other information necessary to make consistent algorithmic trading strategies? This project attempts to utilize machine learning techniques in conjunction with price derived indicators taken from technical analysis to predict the future direction of stock price changes by applying them to minute by minute historical stock data. The performance of these algorithms is measured by comparing them to a benchmark “buy and hold” strategy for the same securities over the same time period. Further study will include refining the more promising machine learning derived indicators and utilizing them to create better algorithmic trading strategies.


Classifiying RR Lyrae Variable Stars Using Random Forest Kevin He Mentors: Judith G. Cohen

RR Lyrae stars are blue, variable stars that can be found in the outer halo of the Milky Way. Because of their variability and blueness, which arises from them being relatively hot stars, RR Lyraes are unique and stand out when compared to other objects. There are many advantages to classifying RR Lyraes, as they can be used as standard candles and probes of the gravity field in the outer halo of our galaxy. Previous work to identify RR Lyraes has only given a binary “yes” or “no” result, rather than a quantitative measurement. This project developed a process to determine the probability that an object is an RR Lyrae by using the random forest machine learning algorithm. Random forest, implemented in the Python programming language, takes a training sample and creates a classifier. This classifier can then quantitatively judge whether other light curves resemble RR Lyraes. Probabilities were successfully generated for a sample of 1257 potential RR Lyraes. Future work could incorporate more features such as corrections for weather, color, etc., as well as completeness corrections.

Oxygen Isotope Studies of Mineral Separates in Eucrite Meteorites Andrew Heard Mentors: Edward Stolper and Maryjo Brounce

The eucrites are basaltic meteorites belonging to the howardite, eucrite, and diogenite (HED) clan. The petrology and oxygen isotope compositions of the HEDs suggest that they derive from a common, differentiated parent body, likely asteroid 4 Vesta. Experimental work has demonstrated that eucrite compositions cluster around the 1- atmosphere olivine, pyroxene, plagioclase peritectic, leading to the hypothesis that eucrite meteorites represent low-degree partial melts from a differentiated source. However, 26 Mg excesses in HEDs indicate that the young planetary body was hot, due to decay of the extinct radionuclide 26 Al. Heating by 26 Al- 26 Mg decay may necessitate high-degree, rather than low-degree, partial melting. There has been significant work documenting HED whole rock oxygen isotope compositions, however separate mineral phases have received less attention. Oxygen isotope partitioning between minerals is temperature dependent, enabling a detailed study of thermal histories and potential means to discriminate between petrogenetic models for eucrite formation. Preliminary modelling results using parameterised partition functions, mass balance, and available published data, suggest that oxygen isotope fractionations between pyroxene and plagioclase reflect temperatures ranges of 500-1100 O C. Additional high precision laser fluorination analysis of mineral phases will illuminate the thermal history of eucrite meteorites. Data will be collected pending resolution of equipment maintenance issues.

Effects of the Rocky Mountains on Precipitation in Eastern North America Alexander Henny Mentors: Simona Bordoni and Jinqiang Chen

This paper analyzes the atmospheric flows around and east of the Rocky Mountains in the context of the moist static energy (MSE) budget. Using ERA-Interim Reanalysis data, we decompose the horizontal moist enthalpy advection, the horizontal dry enthalpy advection, and the latent energy advection into mean, transient, and stationary eddy fluxes. These terms are interpreted in the context of orography and known atmospheric processes, in order to establish why the Rockies do not induce a monsoon similar to that seen in East Asia.

Characterizing the Elemental Compositions and Temperature Structures of Brown Dwarfs and Exoplanets Erich Herzig Mentors: Heather Knutson and Björn Benneke

Spectroscopic observations of exoplanets and brown dwarfs contain crucial information about their atmospheric composition and temperature structures. In this work, I use the newly developed atmospheric retrieval framework SCARLET to recover the atmospheric properties of these objects from their thermal spectra. The framework is tested on the brown dwarf Gl570D with plans to study the atmospheres of other brown dwarfs and giant exoplanets. The results produced by running these retrievals will crucial constraints on the formation histories of giant planets and brown dwarfs as well as the chemical and physical processes in their atmospheres.

Developing an Automated Process for Quantifying Cellular Structures in Hydrogen Flames Morgan Hill Mentors: Guillame Blanquart and Jason Schlup

Our current simulations of lean hydrogen combustion show cellular instabilities, which are computationally taxing to represent. As lean hydrogen mixtures combust, the flames develop cell-like instabilities, which can potentially lead to flame extinction or blowback, where to the flame goes out or escapes to the fuel source, respectively. Understanding hydrogen flame instabilities more completely will enable these processes to be mitigated by performing accurate and computationally efficient simulations to aid the design of new burners. The lab's current simulations with hydrogen mixtures are performed at atmospheric pressure with lean equivalence ratios, indicating


a deficit of hydrogen relative to the amount that would be needed to fully combust in air. In this work, an

automated program is developed to validate the hydrogen combustion simulations. Using multiple experimental data sets collected from other researchers, an image-processing algorithm is designed and tested to both sharpen the images and detect edges between the cellular instabilities. Multiple edge detection and sharpening schemes were utilized before selecting a best performing set of parameters. Finally, once the images are processed sufficiently, cell size and shape are determined and catalogued.

Design and Growth of Broadband Anti-Reflective Coatings for III-V Photoelectrochemical Devices Alec Ho Mentors: Nate Lewis, Erik Verlage, and Stefan Omelchenko

Photoelectrochemical (PEC) devices use solar radiation to split water into molecular hydrogen and molecular oxygen for use as chemical fuels. High-efficiency III-V semiconductors such as GaAs have ideal band gaps that make them desirable for PEC cells, but are unstable in 1M KOH. TiO 2 functions as a viable protection layer that also acts as a single-layer antireflective (AR) coating. However, a thick layer of TiO 2 is needed for sufficient protection, and therefore a single-layer AR coating is non-ideal. Adding a second layer gives design flexibility to reduce reflective losses. The focus for this research is to increase the efficiency of multi-junction PEC devices by designing an optimal double-layer coating without altering the chemical stability of the oxide surface. In creating the double- layer AR coating, transparent thin films were deposited by atomic-layer deposition and radio-frequency sputtering onto GaAs and optically characterized by ellipsometry and electrochemically characterized by cyclic voltammetry and chronoamperometry. Stable samples with low refractive indices were patterned with photolithography. Thicknesses were optimized for the AM 1.5 spectrum for the ideal 1.8/1.2 eV band gaps and deposited by rf- sputtering followed by electrodeposition of nickel. SiO 2 and Y 2 O 3 are viable candidates for integration with TiO 2 in record efficiency PEC devices.

Bulk Friction Angles in Dry, Drained, and Saturated Gravel Beds Samuel Holo Mentors: Michael Lamb and Marisa Palucis

We examined the effect of capillary action and lubrication of grains on bulk friction angles through tilting chute experiments. In each experiment, we screed a bed of 5mm gravels in a 65cm x 18cm tilting chute and slowly tilted the chute until a granular avalanche occurred. We performed these experiments with a bed of dry grains and with a bed that had been submerged and subsequently drained such that no water occupied the pore space. For each of these cases, we performed experiments with 5, 10, and 15cm bed thicknesses. In the dry case, the bed failed at

~ 41º, and bed thickness did not have a significant effect on failure angle. In the drained case, friction angles

increased from 46.5º to 50.9º with increasing bed thickness. The observed increase in friction angles between the dry and drained cases suggests that addition of the water induces some sort of cohesive effect on the grains and that this effect increases with bed thickness. Ongoing work includes experiments with fully saturated beds to differentiate between capillary and lubrication effects, as well as debris flow initiation modeling at the catchment scale.

Role of Retinoic Acid Pathway on Zebrafish Enteric Nervous System Development Stephanie Hong Mentors: Marianne Bronner and Rosa Uribe

The enteric nervous system (ENS) controls the peristaltic movement of food through the gastrointestinal tract. During development, it derives from vagal neural crest cells (VNCC) that migrate into the developing gut to become a diverse class of neurons and glial cells. In avian and mouse embryos, the Retinoic Acid (RA) signaling pathway has been shown to induce migration and population growth of VNCC, improving the ability of VNCC to colonize the gut in chains. To date, there are no published functional roles for the RA pathway during zebrafish ENS development, despite its strong expression therein. Previously, our preliminary experiments showed that RA application prior to 48 hours post-fertilization (hpf) induced a greater number of NCC in the gut region than control, eventually resulting in increased enteric neuron number later in development. In order to further investigate these observations and test the hypothesis that the RA pathway plays an important functional role during ENS development, the focus has been shifted from gain of function effects of the RA pathway to the effects of loss of function. The transgenic fish line Tg(hsp70:dn-zrar-gfp) expresses a dominant-negative Retinoic Acid receptor, Raraa, fused with a GFP molecule on its C-terminal domain, the expression of which is controlled by the heat shock promoter hsp70 such that incubation of embryos at 38˚C results in its expression. Expression of this dominant negative construct attenuates RA signaling in a temporally controlled manner. Zebrafish embryos were heat shocked at 24 hours post fertilization (hpf) and assayed by in situ hybridization and immunohistochemistry for genes that mark neural crest cells or the gut environment. RA attenuation resulted in expansion of the RA pathway component aldh1a2 mRNA expression and diminishment of meis3, a downstream RA target. Furthermore, heat shocked embryos exhibited morphed and irregular patterning in the pharyngeal arches, of which NCCs are a precursor, compared to the controls at 72 hpf. Embryos were also double-heat shocked to increase the severity of RA pathway loss of function. Using phox2bb as a marker for migrating NCC in the gut, it was found that a one-time heat shock caused NCCs to migrate farther down the gut but in lower numbers, whereas the NCC migration of


double-heat shocked embryos was delayed. However, when crestin was used as a marker for all neural crest, single-heat shocked embryos displayed delayed migration compared to the controls. These loss of function results indicate that the RA pathway plays a complicated role in influencing VNCC migration into the developing gut and suggest that RA is a highly conserved signaling pathway that VNCC utilize in order to colonize the developing gut.

Engineering Conditional CRISPR Interference Andrew Hou Mentors: Niles Pierce and Mikhail Hanewich-Hollatz

CRISPR/Cas9 is a novel gene editing tool which has been repurposed for regulation of gene expression, via a guide RNA which confers sequence-specificity and a catalytically dead Cas9 endonuclease (dCas9, for short). Termed CRISPR interference (CRISPRi), dCas9 and the guide RNA form a complex which binds to and blocks transcription of a specific target gene. Using RNA design principles, we sought to re-engineer guide RNAs such that CRISPRi can be conditionally activated or inactivated by synthetic or endogenous inputs in E. coli. To this end, we demonstrated that guide RNAs can be inactivated either by binding a separately expressed antisense strand, or by self- complementarity. However, as is, the guide RNA sequence is heavily constrained. In order to obtain the programmability required for conditionality, we added extra nucleotides to the loop region found in the secondary structure of the guide RNA. We hypothesize that: (1) a guide RNA with an extended loop could be conditionally inactivated by an input strand which is antisense to the loop, and (2) a guide RNA with self-complementarity to the extended loop would be natively inactivated, and that it could be conditionally activated via toehold-mediated strand displacement.

Hardness vs. Randomness Tradeoffs for Arthur-Merlin Games in the Uniform, Extreme Low-End Setting William Hoza Mentor: Chris Umans

We investigate candidates for a polynomial-stretch hitting set generator against uniform conondeterministic circuits, with an associated commit and evaluate protocol for establishing correctness. Such a hitting set generator would imply subexponential-time nondeterministic simulations of AM in the uniform average-case setting, under the assumption that E is not contained in AM.

The Role and Expression of Myc-Nick in Migratory Neural Crest Cells Jenny Hsin Mentors: Marianne Bronner and Laura Kerosuo

The neural crest is a transient population of multipotent stem cells that form in the dorsal part of the developing neural tube. As the neural tube closes, the neural crest cells go through an epithelial to mesenchymal transition (EMT) that allows them to migrate out of the neural tube and into various target tissues in the developing embryo. Two members of the Myc transcription family, c-Myc and n-Myc, are expressed during neural crest development. In addition to Myc’s nuclear, DNA binding function, Myc can also be post-translationally cleaved into a cytoplasmic form called Myc-Nick that recruits acetylases to microtubules and therefore causes cytoskeletal rearrangement. So far, Myc-Nick expression has not been shown in vivo and the goal of this project was to examine whether neural crest cells express Myc-Nick. We also wanted to compare the expression pattern of n-Myc and c-Myc in the neural crest cells. For this approach, we cloned Flag-tagged versions of full length c-Myc and n-Myc; truncated Myc-Nick; and a mutated c-Myc called c-Myc Δ295, which cannot form Myc-Nick into a chicken expression vector. We used in ovo electroporation and immunostaining to verify whether the proteins were located either in the nucleus or the cytoplasm at various stages of neural crest development. We also used double fluorescent in situ hybridization (FISH) to efficiently compare the expression differences of n-Myc and c-Myc mRNA. Our preliminary results suggest that nuclear Myc is expressed in the neural tube prior to EMT and Myc-nick is formed in the migrating neural crest cell population. At the mRNA level, in premigratory stages, expression of n-Myc is dominant in the neural portion of the neural tube whereas c-Myc is only expressed in the dorsal neural tube where the neural crest is formed. However, both Myc family members are expressed in the migrating neural crest population after EMT. Our results suggest interesting new and separate roles for the Myc family members in the premigratory versus the migrating neural crest cell populations and function experiments to reveal this are ongoing.

Time Evolution of a Damped Quantum Oscillator Tianyi Hu Mentor: Vidar Gudmundsson

We consider the time-evolution of a damped quantum oscillator. The oscillator is weakly coupled toa thermal reservoir of high temperature. The Liouville-von Neumann equation of motion for the density operator is transformed into a master equation for the reduced density operator by tracing out the varibles of the reservior. As the system is Stark-shifted by the potential V 0 θ(t) (x/a), where θ is the Heaviside step function and a is the characteristic length of the harmonic oscillator, we can solve the time-dependent master equation by two different methods. In the first method, we use direct iteration via the Cranck-Nicholson method in the Hilbert space made from the eigenstates of the harmonic oscillator. We then calculate mean values as the trace over the density matrix


and the corresponding operator. In the second method, we first seek the steady state solution in the Liouville space and then use transformations to derive the time-evoultion without the need to numerically intergrate the equation. With these two methods, we can analyze the complex spectrum of the Liouville operator with a harmonic or anharmonic oscillator. In addition, the pumped quantum oscillator is briefly examined. We use Fortran 2008 to achieve fast parallel programs with high flexibility. The aim of the project is to test methods on a simple open quantum system that will be used on a more complex model of interacting electrons transported through a photon cavity.

Stress-Induced Alterations in Behavior Are Mediated by the Tac2 System May Hui Mentors: David Anderson and Moriel Zelikowsky

Stress is a behavioral response found in virtually all animal species. Recently, Tachykinin 2 (Tac2), which encodes the neuropeptide Neurokinin B (NKB), has been implicated in fear memory consolidation. We were interested in exploring the possibility of a larger role for Tac2 in mediating stress. In particular, we examined whether systemic and local antagonism of the NKB-specific receptor, NK3, with the drug osanetant, could alter the effects of various manipulations to induce stress. Mice were subjected to chronic stress comprised of either social isolation, restraint stress, or footshock, given daily across 14 days. Mice were then tested for stress-induced changes in behavior using a looming assay (as a measure of innate defensive behavior) and trace fear conditioning (as a measure of cognitive function and stimulus reactivity). At test, mice were treated with a systemic injection (i.p.) of osanetant or microinfusions into the dorsal-lateral striatum or the dorsal bed nucleus of the stria terminalis. We found that osanetant was able to buffer against the effects of chronic stress. Moreover, we found that systemic administration of the NK3 agonist senktide was able to induce stress-like effects in non-stressed, group-housed control mice. Collectively, our data point to a broad role for Tac2 in the regulation of chronic stress.

Bayesian Updating of Uncertain Parameter Vectors by Sampling From an Auxiliary Dynamic System Hanna Hultin Mentors: James Beck and Thomas Catanach

Bayesian updating can be used to learn uncertain model parameter vectors with sensor data from a dynamic system. A fully probabilistic Bayesian model updating approach requires the evaluation of multidimensional integrals which usually cannot be done analytically. Instead sampling based numerical methods can be used, although high-dimensional problems are still challenging for current sampling methods. The aim of this project is to examine how to use theory from stochastic dynamics to generate samples from a high-dimensional distribution efficiently. This method, which we call the Langevin Monte Carlo method, should work well in higher dimensions because the samples naturally move to areas of high probability according to the stochastic dynamics. To reduce the unproductive computational effort during the settling-in period, as short settling time and low correlation as possible is sought. In this project, the method used to reduce the settling time is by choosing the damping and temperature schedule for a virtual annealing scheme.

Modelling Anisotropic Particle Distributions for Solar Probe Plus Olivia Humes Mentors: Mark Wiedenbeck and Richard Leske

The Solar Probe Plus mission will investigate the dynamics of solar energetic particles using the High Energy Telescope and Low Energy Telescopes. Monte Carlo simulations were used in order to model the angular response of these particle detectors. Typical inferred best fit values were calculated from simulated detector counts for various combinations of parameters: magnetic field zenith angle and azimuth angle, as well as values of the first and second order anisotropies. These data will be useful for understanding the responses of the High and Low Energy Telescopes once they begin taking measurements for the Solar Probe Plus mission.

Spin Selectivity of Electron Transmission Through Solvated Double-Stranded DNA Sylvia Hürlimann Mentors: Jacqueline K. Barton and Theodore Zwang

In recent years, double stranded DNA (dsDNA) has been shown to have a large spin polarization in electron transmission that is several orders of magnitude larger than what the current theory predicts. A study of how tertiary structure affect the spin polarization of dsDNA could shed light to the biological implications of the effect and help improve the theory. Thiol labeled dsDNA was attached to gold capped nickel substrates in order to inject a current in the dsDNA and vary its spin polarization. Progress has been made towards attaching the dsDNA to nickel and investigating the effect that mismatches in dsDNA has on spin selectivity.


Engineering and Understanding Light Sensitive Proteins With Applications in Live-Cell Imaging Nicholas Hutchins Mentors: William Clemons, Jr., and Austin J. Rice

Red-fluorescent proteins (RFP’s) provide an alternative to the typical blue and green fluorescent proteins used in cellular biology. The red light used to visualize RFPs is less cytotoxic, scatters less, and avoids natural cellular autofluorescence. However, RFP’s have two disadvantages: they are typically tetrameric in their native state and they are dimmer than their green and blue counterparts. We show that RFP monomers can be created from a natively dimeric RFP without substantial loss of fluorescence using computational design coupled with directed evolution. To better understand the molecular basis of our improved RFPs, we pursue structural information through protein crystallography.

Creating a Platform Independent GUI Utilizing Bayesian Rapid Optimal Adaptive Design (BROAD) to Study Time Preference and Risky Choices Seong Bin Im Mentors: Colin F. Camerer and Romann M. Weber

Many different models have been proposed to account for time-inconsistent preferences and risky behaviors in the field of behavioral economics. Experimental comparison is essential to testing these models and their implications. However, most of the standard designs tackling such problems are not practical due intractability of these models in large design spaces. Bayesian Rapid Optimal Adaptive Design (BROAD) takes advantage of adaptively optimizing questions based on previous response of each iteration and thus allows for fast, real-time implementation with performance guarantees. In order to make such method more wide-spread and user-friendly, we create a platform independent Graphical User Interface (GUI) utilizing BROAD. As a prototype, we aim to build the interface for risky choices, such that we may generalize to fit other areas of interest such as time preference.

Engineering Chimeric Antigen Receptor T-Cells for the Treatment of HIV Erin Isaza Mentors: Pamela Bjorkman and Rachel Galimidi

Chimeric antigen receptors (CARs) are engineered receptors that graft the specificity of a monoclonal antibody onto a T-cell—the cells are removed from a patient, modified to express the desired receptors via retroviral vectors, and reintroduced into the patient. While the only previous attempt to use CAR T-cells to attack HIV proved unsuccessful, in the time since this study broadly neutralizing anti-HIV antibodies, which are able to neutralize many strains of HIV, have been discovered. We have engineered CAR T-cells expressing broadly neutralizing antibodies, which bind to and neutralize HIV with a much higher avidity and are safer than the first generation of anti-HIV CAR T-cells.

Improved State Estimation and Control of a Pioneer 3-DX for a Resilient Software Executive Riashat Islam Mentor: Richard M. Murray and Catharine L.R. McGhan

Autonomous navigation systems that can operate safely without collisions in an unknown environment with little to no human intervention can have significant applications towards space exploration missions for science discoveries. In this project, we strive to further develop the initial implementation of a resilient risk-aware software architecture that can handle uncertainty in hazardous environments. We present a framework that integrates real time planning capabilities for an autonomous robot that uses the observed maps from the environment for planning and obstacle avoidance algorithms. We propose a model that uses the Robot Operating Software (ROS) for real-time environment map generation using Hokuyo lidar sensors, and use generated maps for navigating and avoiding obstacles in an unknown environment. Furthermore, we work towards integrating simultaneous mapping and localization (SLAM) techniques for the autonomous vehicle to be able to localize itself in the unknown generated environment map. Our results suggest the integration of real time mapping capabilities into the resilient software architecture, using Hokuyo lidar sensors mounted on top of the autonomous vehicle, on both simulated and practical environments. We demonstrate results of implementation of obstacle avoidance algorithms, along with existing probabilistic planning algorithms, for safe navigation using the maps generated by the laser sensors. We also demonstrate that SLAM based techniques can be integrated into the resilient software architecture of the autonomous vehicle.

Encapsulins as Molecular Reporters for Spatiotemporal Control of Biological Systems Vasant Iyer Mentors: Mikhail G. Shapiro and Pradeep Ramesh

Continued advancement in molecular medicine and our understanding of biological systems depends on developing techniques to modulate gene expression, cell behavior, and tissue properties in a spatiotemporally specific and noninvasive manner. We aim to develop such a technique using proteins of a new class of bacterial nanoparticles called encapsulins, which natively contain guest proteins that enable bacteria to sequester iron in times of oxidative


stress. We have targeted proteins to the interior of encapsulins to create a redox-controlled environment in which magnetite particles may be nucleated upon iron supplementation, yielding T2 contrast under magnetic resonance imaging (MRI). Further work involves developing encapsulins as noninvasive agents for cellular control based on hyperthermia induced by incident radio frequency waves.

Extreme Scale Parameter Discovery Using Randomized Metric Embeddings Nauman Javed Mentors: Sumit Kumar Jha and Axel Müller

In many fields, complex computational models can exist in high dimensional parameter spaces in which conventional optimization methods are computationally infeasible. A significant reduction in the search space dimension combined with the intelligent use of probabilistic metaheuristics can drastically reduce the computational cost of many optimization problems, and would pave the way for increasingly sophisticated and informative models. We introduce a novel dimension reduction and search algorithm that logarithmically reduces a given model’s parameter space dimension via the Johnson Lindenstrauss lemma and searches for the model optimum in the lower dimensional space using simulated annealing. Once located, the global optimum is reconstructed in the original higher dimensional space by exploiting the structure preserving properties of the JL transform and simple distance geometry arguments. We implement our algorithm in CUDA C to parallelize computation and experiment with a range of computational models and initial parameter space dimensions. Our results demonstrate that the algorithm can successfully approximate the global optimum of the parameter discovery problem for a sufficiently large initial dimension. Furthermore, we demonstrate that the algorithm significantly reduces the computational cost of model optimization.

Arterial Wall Shear Stress Imaging of Flow Phantom Using 4D MRI Cynthia Jiang Mentors: Albert Hsiao, Geno Pawlak, and Steven Low

Magnetic resonance imaging (MRI) is an important modality used in the diagnosis and treatment of cardiovascular diseases, whether congenital or acquired. Until recently, planar two-dimensional MRI techniques have been predominantly used for visualization of the heart. However, four-dimensional Flow MRI, a specialized MRI sequence that allows for measurement and visualization of time-resolved three-dimensional blood flow patterns with velocity encoding, is now steadily becoming more widespread as a more comprehensive, and time-efficient method of obtaining flow and anatomic data.

Early work with 4D Flow MRI has proposed that hemodynamic flow patterns and wall shear stress may contribute to the formation and growth of ascending aortic aneurysms. Measuring and calculating the wall shear stress may be predictive of which patients eventually require surgery to repair these aneuryms. Our objective is to determine the accuracy of calculated fluid shear stress and other hemodynamic parameters from 4D Flow MRI, given limitations in its spatial and temporal resolution when used for routine clinical scanning.

Traveling Wave and Fractal Analysis of Complex Waveforms in Marangoni Driven Systems Katherine Jiang Mentor: Sandra M. Troian

The rapid spreading of an insoluble surfactant monolayer along the surface of a thin liquid film of higher surface tension is known to be driven by Marangoni stresses. These forces, which pull the monolayer and underlying liquid toward regions of higher surface tension, are proportional to the local magnitude of the surface tension gradient caused by the local concentration gradient. Previous experiments in our lab using liquid films of the order of 10 microns in thickness have verified the propagation of an outer stable circular ring behind which there often develops a bifurcating fractal front. While theoretical models predict that the ring should advance in time as t 1/4 , we consistently find higher exponents ranging from about 2/5 to 1/2. Image analysis to determine the fractal dimension of the trailer bifurcating front, using various thresholding and edge detection techniques, has revealed differences from the values obtained in conventional hydrodynamic systems. In contrast to the well-known fractal exponent of 1.67 associated with the Saffman-Taylor instability, we find values closer to 1.85. This significant difference may help elucidate the physical mechanism responsible for the fingering instability observed.

Developing Temperature-Sensitive Proteins From a Bacterial Coiled-Coil for Thermal Regulation of Genes Yiwei Jiang Mentors: Mikhail Shapiro and Dan Piraner

Thermosensitive proteins may enable selective regulation of genes with an external heat source, providing a noninvasive technique for studying gene regulation. The coiled-coil motif of the TlpA protein allows it to sense temperature shifts directly and modulate the extent of transcriptional repression by blocking its own promoter. We are harnessing this system to demonstrate temperature-dependent gene up and down-regulation in both prokaryotic and eukaryotic cells. In the most straightforward implementation of this system, we are expressing an


orange fluorescent protein gated directly by TlpA, resulting in protein production above a critical dissociation temperature. In another construct, TlpA blocks the expression of the lacI repressor, thereby allowing a Lac operator-gated promoter to drive expression of a red fluorescent protein at low temperature. At higher temperatures, the TlpA uncoils, enabling transcription of lacI repressors and down-regulating red fluorescence. Future experiments will use fluorescence measurements to observe brightness of cells transformed with the RFP plasmid co-plated with cells transformed with the orange fluorescent protein. The mammalian implementation of the TlpA system uses clustered, regularly interspaced, short palindromic repeat (CRISPR) technology to generate RNA-guided nucleases, like Cas9, with customizable specificities for genome editing. Alternatively, catalytically inactive mutants of Cas9 called dCas9 can be paired with short-guide RNAs (sgRNA) and block transcription. We are currently validating a previously published system in which dCas9 tethered to the VP64 transactivator enhances expression from a minimal CMV promoter with the appropriate upstream sgRNA binding site. Future work involves replacing upstream tandem Lac operator with the TlpA operator to enhance fluorescence above the TlpA critical temperature.

Waypoint Sequencing in a Dynamically Shadowed Environment Jonathan Joo Mentors: William Red Whittaker and Antonio Rangel

Future missions to explore planetary surfaces depend on the ability of solar-powered rovers to visit multiple waypoints in shadowy environments. The order in which these locations are visited, called the waypoint sequence, is crucial to the overall success of a mission. While efficient routes maximize the net value of visited locations, inefficient routes may waste time navigating to dead-end regions or re-routing to previously visited areas. Current studies have investigated efficient travel from one point to another in such an environment, but there does not yet exist an effective way to plan for a multiple-location mission. Furthermore, existing approaches to similar sequencing problems have never been applied to a time-variant shadowy environment such as that of the lunar poles. This paper thus describes a genetic algorithm to create efficient waypoint sequences in dynamically lit regions. The genetic algorithm greatly outperforms a brute force approach in calculation time, while generating near-optimal paths. Furthermore, this algorithm obtains significant improvements in value optimization compared to a simple greedy algorithm. Thus, this research demonstrates that a genetic approach could be utilized to effectively plan future missions for solar-powered rovers in dynamic, shadowed environments.

Discovering RNA Structural Motifs Responsible for lncRNA-Protein Interactions Rushikesh Joshi Mentors: Mitchell Guttman and Mario Blanco

It is now apparent that our genome is primarily comprised of non-coding RNAs (ncRNAs), and not protein-coding messenger RNAs. Advances in high throughput RNA sequencing have established the existence of thousands of large non-coding RNAs (lncRNAs) that are involved in diverse biological and regulatory roles.

Similar to classical ncRNAs, the function of lncRNAs depends on RNA-protein interactions. RNA structure corresponds directly to both protein-binding affinity and function. We know that lncRNAs act as flexible, modular scaffolds, and are essential for assembling protein complexes based on highly specific, discrete, protein-binding domains located within the lncRNA. We aim to characterize the RNA secondary structure motifs that are present at these protein-binding domains.

By combining high throughput sequencing techniques and in vivo application of RNA structure probing reagents, which react at the 2’-hydroxyl group of conformationally dynamic RNA nucleotides, we can determine regions of structural significance. We have been able to utilize computational methods to identify and characterize the structure of known RNAs by comparing our results to previously determined two-dimensional structures.

We plan to apply our methods on a genome-wide scale, to characterize the structure of lncRNAs. This will help us understand the structural motifs responsible for lncRNA-protein complex formation.

Predicting the Behavior of PAMAM Dendrimers in a Water, Methanol, and Sulfamethoxazole Solution Using Molecular Dynamics Simulations Sachi Kamiya Mentor: Jose Mendoza Cortes

Molecular dynamics from LAMMPS is a powerful tool to predict the atomistic behavior of materials/molecules in different environments. Additionally, the study of biocompatible materials has become a growing field in the sciences—it has become especially relevant to understand how foreign materials react and behave in the body. In this project, LAMMPS, a molecular dynamics simulation tool, is used to simulate the behavior of dendrimers, a widely studied biocompatible molecule, to understand its atomistic behavior. In order to set up the experiment, generation 3 and generation 4 polyamidoamine (PAMAM) dendrimers are placed in different simulations including a water, methanol, and drug solvent. The simulations are run in an NVT (canonical system) and NPT (isobaric system) where the system is heat up to 300K and pressure is kept constant to 1atm. The output data is then


analyzed using the radial distribution function (RDF) and velocity auto-correlation function (VAF) to understand the intermolecular behavior of the dendrimer and surrounding environment. To study spontaneity, the free energy of each system is also evaluated. Further potential research areas includes the potential of studying various other drugs using explicit solvent.

Spectral Studies of Seyfert 2 Active Galactic Nuclei From the NuSTAR Hard X-ray Observatory Nikita Kamraj Mentors: Fiona Harrison and Liz Rivers

Active Galactic Nuclei (AGN) are some of the most luminous compact objects in the universe, frequently outshining their host galaxies. Unification schemes propose that all AGN are essentially the same physical object, with the diversity of AGN classes simply arising from different orientations of the AGN with respect to the observer. This project focuses on the study of the X-ray spectral features of Seyfert 2 AGN observed with the NuSTAR telescope. The high energy X-ray focusing optics of the NuSTAR satellite have enabled AGN spectral features to be resolved to unprecedented detail, allowing tighter constraints to be placed on the geometry of the circumnuclear material. I performed data reduction and extraction processes using the NuSTAR Data Analysis software, followed by spectral modeling of the data using the XSPEC fitting tool. My investigation has focused on modeling the spectra of NGC 4388, NGC 6300, NGC 7172, NGC 1052 and IC 5063, with the results interpreted in the context of Seyfert 1/2 unification schemes.

Spatiotemporal Online Imitation Learning Andrew Kang Mentors: Yisong Yue and Hoang Le

Spatiotemporal sequence prediction is a problem of increasing interest within machine learning. The example of our focus is imitation learning for online prediction of camera planning, in which the goal is to mimic a human camera operator. However, such learning is not feasible with standard supervised learning approaches as they do not learn temporal patterns. Therefore, a promising alternate solution is the state-of-the-art approach that uses reductions with a focus on non-linear predictors. This approach is best seen in two particular algorithms, SEARN and DAGGER. However, two challenges arise in extending these algorithms to spatiotemporal sequences: each sequence can get arbitrarily large, and we are no longer working with discrete values. Thus, the algorithms must be modified to overcome these obstacles; namely, we focus on proving that the regret and loss bounds still hold when averaging between policies in the continuous setting instead of sampling in the discrete setting. That is, in this paper, we examine the theoretical guarantees we can make about an algorithm that provides minimal loss and good generalization for the camera planning prediction problem.

Band Structure Measurement of Gyroid Photonic Crystals in the Mid-Infrared Emil T. Khabiboulline Mentors: Harry A. Atwater and Siying Peng

Like electronic topological insulators, photonic topological insulators form a new class of materials with exciting properties that have implications for many areas, including photovoltaics. The topology of their band structure gives rise to propagation of light that is unidirectional, fault-tolerant, polarized, and localized to the boundary. Theory predicts that gyroid photonic crystals are photonic topological insulators. We aim to provide experimental confirmation in the mid-infrared region.

Starting with two-photon lithography to fabricate the samples in polymer, a sequence of atomic layer deposition, focused ion beam milling, plasma cleaning, and chemical vapor deposition lead to alumina structures coated with amorphous silicon. Single and double gyroid crystals, with unit cells of 5 µm organized in a 10x10x10 cube, were fabricated this way on an intrinsic silicon substrate. We build a setup to perform angle-resolved spectroscopy using a quantum cascade laser as the source of the ~8 µm beam. From measurements of reflection and transmission over a range of wavelengths and incidence angles, we construct the band structure of the photonic crystals. Theory predicts band gaps for the single gyroid and Weyl points for the double gyroid. Comparison to experiment indicates whether or not our nanofabricated gyroid structures possess a topological nature.

Engineering of Viral Vectors Selectively Expressing Cre Recombinase in Target Neural Cell Populations of Mouse Model Expressing Human Mutant Huntingtin Gene Hyun Min Kim Mentors: Viviana Gradinaru and Benjamin Deverman

Adeno-associated virus vectors are commonly used gene delivery vehicles for basic science studies and are being explored for human gene therapy. The viral capsid can be customized to create a recombinant virus expressing packaged genes and possessing transduction characteristics that enable targeting of specific regions of the brain. Cre-Recombination-based AAV Targeted Evolution (CREATE) has enabled the customization of AAV by significantly expediting the selection of viruses possessing desired characteristics. CREATE is a Cre-dependent selection system where capsids that transduce predesignated Cre + target cell types are selectively recovered. This has optimized the targeting efficiency of the AAV9, which has been demonstrated to cross the blood-brain barrier and deliver


transgenes to the CNS, resulting in the design of AAV-PHP.B. We are now enhancing the accuracy of the selection process by modifying the mutant lox sites within the capsid genome used for CREATE. Furthermore, by using AAV- PHP.B to deliver Cre regulated by promoters to neural cell populations, we are addressing questions regarding neurological disease models. By using a Cre/lox-conditional mouse model expressing the human mutant huntingtin gene (mHTT), we are seeking to identify the cell types that lead to Huntington’s disease when expressing mHTT and quantify the fraction of mHTT expressing cells that must be suppressed to ameliorate symptoms.

Three Dimensional Image Recognition in Mice Jaebin Kim Mentor: Doris Tsao and Tomo Sato

By discovering the extent to which mice are capable of perceiving and recognizing a variety of occluded objects surrounding them, and incorporating two-photon calcium imaging and electrophysiology to analyze the neuronal circuits involved in visual perception, we can not only gain a deeper understanding of neuronal functions, but also understand the mechanisms of visual perception that is conserved across species. We trained the mice to recognize various visual stimuli and recorded their rate of success in choosing the correct stimulus for a juice reward. When setups for two-photon calcium imaging and electrophysiology are installed, the mice will undergo the same experiment but instead with the partially occluded visual stimuli. This will reveal if the mice are able to recognize the occluded images, and indicate the neuronal activity and mechanism involved in three dimensional image recognition.

Single Cell RNA Imaging on a Cellphone Jinhyun Kim Mentors: Long Cai and Ahmet F. Coskun

In information-oriented society, due to high-quality specifications, phones can be utilized as microscopic imagers for biomedical applications. In this project, we demonstrate a compact home-built optical platform running on a smartphone to image and quantify RNA molecules in single cells. This cellphone based RNA imaging platform is hand-held and low-cost making it rather useful research toolset for scientists in resource poor settings. To show its proof-of-concept, we devised an optomechanical attachment that was mounted on a Samsung Galaxy S4 camera unit using a combination of 3D printed parts, an illumination source, an imaging lens, and an optical filter. We optimized the performance of this approach using a USAF chart and fluorescent microspheres with 15-micron diameter. For validation of transcript detection capability, we visualized highly expressed mRNA molecules in mammalian cells using this portable cellphone RNA imager. This platform aims to democratize systems biology particularly towards microbial diversity research.

Rotational Invariant Low-Rank Pose Estimation Joon Sik Kim Mentor: Yisong Yue

Estimating human pose from 2-D images allows to recover interesting information about the nature of human poses. Our goal is to study how human poses change when performing different activities. To do so, we try to recover basis of poses that summarizes the variability of poses in our dataset. The advantage of this representation is that we can describe the many degrees of freedom of human natural poses in a compact way, using a relatively small basis. 2-D images have the limitation that the same pose may be obtained from different 3-D poses projected from different camera angles. In this work, we address this challenge with two possible approaches based on a form of structured low-rank matrix factorization, (1) incorporate rotation invariance by learning a sequence of 2-D pose bases (one for each angle of view), (2) try to recover directly the inherently invariant 3-D pose basis. A detailed comparison of the two methods and analysis of the performances is carried out.

Optimization of Methane Monooxygenase to Convert Methane to Methanol on an Industrial Scale Lani Kim Mentors: Stephen Mayo and Alex Nisthal

Methane (CH 4 ) is the second most prevalent greenhouse gas emitted in the United States, accounting for 10% of all greenhouse gas emissions. By converting methane to methanol, the methane gas, instead of going to waste, can be used to create biofuels and other higher value chemicals. Currently, the industrial methane-to-methanol conversion process is extremely energy-intensive and environmentally unfriendly. Instead, the biological oxidation of methane to methanol using the methane monooxygenase enzyme (MMO) is a more desirable conversion process. By optimizing spmoB, an MMO variant, highly active methane-oxidizing enzymes can be created for industrial use. In order to produce large amounts of spmoB, the variant is transformed into a Pichia yeast secretion system. The effectiveness of the Pichia secretion system is then measured through absorbance and sGFP fluorescence levels.


Genetic Exploration of Conserved Unknowns in C. elegans Shawn Kim Mentors: Paul Sternberg and Ravi Nath

Caenorhabditis elegans is a multicellular organism in the phylum of Nematoda. C. elegans is made of 959 somatic cells, and has a complex developmental process, including embryogenesis, morphogenesis, and final growth to an adult. Important developmental principals are conserved from C. elegans to humans. The simple nervous system of C. elegans controls a great diversity of behaviors that can be easily quantifiable. C. elegans are estimated to have over 20,000 distinct genes. Many of these genes are orthologous with human genes, meaning that they have evolved from a common ancestral gene. Therefore, there is a high probability that orthologous genes have similar functions. Of the multitude of orthologous C. elegans genes, the Sternberg Lab has identified 1000 orthologous genes whose functions remain unknown. From this list, we identified 152 genes that are the only members of a particular undefined gene family, which means they are less likely to be genetically redundant. We noted that 30 of the 152 genes in an unknown gene family are found in neurons. Given C. elegans simple nervous system and genetic flexibility, we can identify the function of a gene by comparing the behaviors between wild-type worms to mutant worms with a null-allele. To look specifically at the effect of knocking out these genes, I have screened 19 genes of those 152 conserved unknown genes by applying tracking assay, pumping assay, avoidance assay, and aldicarb assay to the strains, each of which has knocked out one gene.

Self-Assembly, Structure, and Properties of Brush Block Copolymer Nanocomposites Shi En Kim Mentors: Robert H. Grubbs and Alice Chang

Block copolymer nanocomposites are hybrid materials that demonstrate important applications as the combination of different materials engenders novel properties not inherent in either component material. This introduces new opportunities for control in their structure and property. We incorporate nanoadditives into a brush polystyrene- block-poly(ethylene oxide) (PS-b-PEO) or brush polystyrene-block-poly(lactic acid) (PS-b-PLA) matrix. As brush block copolymers display greater rigidity and less chain entanglement than linear block copolymers, they are shown to self-assemble into unique structures with large long-range domain sizes. The brush block copolymers are synthesized by ring opening metathesis polymerization (ROMP). The nanoadditives we incorporate (linear homopolymers, compact star polymers, and tantalum oxide nanoparticles) span different length scales and functionalities. We report the self-assembled structure and optical properties of these brush block copolymer nanocomposites, toward enabling the design of novel functional materials.

Targeting lncRNAs in Pluripotency Network Using the CRISPR-Cas9 System Won Jun Kim Mentor: Barbara Wold

Long non-coding RNAs (lncRNAs) are an emerging group of RNAs that do not code for proteins and yet act as functional molecules themselves. An increasing number of lncRNAs are being identified to participate in cellular events, such as transcriptional and translation regulation, chromatin organization, and reprogramming. Despite significant research efforts to fish out novel functional lncRNAs, genetic perturbations targeting lncRNAs usually yield little success: their tendency to localize within the nucleus limits the use of genetic perturbations targeting cytoplasmic RNAs. Here we demonstrate a reliable method for gene knockout using the CRISPR-Cas9 system to delete lncRNAs in mouse embryonic stem cells (mESCs). We choose 4930444M15Rik, one of the previously identified lncRNAs that are activated during reprogramming of somatic cells. In order to test its functional role in reprogramming and pluripotency, we study the transcriptome changes after 4930444M15Rik knockout in mESCs. Our data suggest that the CRISPR-Cas9 system can efficiently and specifically delete the target lncRNA in mESC genome as we successfully isolate heterozygous mutant cell lines (single knockouts). Homozygous mutant cell lines (double knockouts) generated with this method reveal reduced viability, indicating a crucial role that 4930444M15Rik plays in mESC survival and proliferation. Further downstream cell-based assays (e.g. siRNA- mediated gene knockdown) and high-throughput transcriptome profiling studies (e.g. RNA-seq) are needed to better elucidate the exact function of 4930444M15Rik.

Neurotransmitters Modulate the Pulsation of the Jellyfish Cassiopea Young Min Kim Mentors: Paul Sternberg and Ravi Nath

Neurotransmitters and neuropeptides modulate neural circuits across the kingdom Metazoa. The effects of these neural circuit modulators have been observed and characterized in model organisms, such as Caenorhabditis elegans and Drosophila melanogaster. We investigated the effects of neuromodulators on Cnidaria, an early- branching metazoan lineage; the last common ancestor between the phyla Cnidaria and humans existed around 600 million years ago. We chose to study the cnidarian Cassiopea, which is in the class Scyphozoa, commonly known as the true jellyfish. Cassiopea, known as the upside-down jellyfish, are an ideal model organism for behavioral research in early branching lineages because they sit on their bell, which allows counting of pulsation. Taking advantage of our state-of-the-art jellyfish behavioral arenas, we can track Cassiopea pulsing behavior under


different stimuli for prolonged periods of time. We have tested numerous molecules on the jellyfish, including melatonin, serotonin, glycine, dopamine, histamine, GABA (Gamma-aminobutryic acid), epinephrine, DPCPX(an adenosine antagonist), and glutathione. Jellyfish treated with melatonin exhibited a quiescent behavior, with a reduced pulse rate; likewise, serotonin also induced behavioral quiescence, suggesting an inhibitory role of these molecules on the cnidarian nervous system. Glutathione induced an oscillation between fast and slow pulsation. Furthermore, to better understand Cassiopea pulsation, we observed the effects of temperature or salinity on this behavior. Increasing temperature directly increases pulsation behavior, and vice versa. On the other hand, while the jellyfish did not show any consistent behavior in response to high salinity, they showed drastically decreased pulsation in low salinity. Our data suggest that neuromodulation of Cassiopea provides this animal with the ability to control its pulsation rate under different environmental stimuli, which in turn also implies that neuromodulation of neural circuits has been conserved throughout the course of evolution.

Investigating BSCCO High Temperature Superconductors With Magnetometry and Annealing Gillian Kopp Mentors: Dan Dessau and Nai-Chang Yeh

Superconductors exhibit no electrical resistance and expel magnetic flux when cooled below a critical temperature, T c . High temperature superconductors can withstand higher magnetic fields than conventional superconductors, expanding their potential applications, however, the theory behind their superconducting mechanism is not well understood. My work focuses on lead-doped BSCCO samples, where the T c depends on the oxygen content and hole doping of the CuO 2 layers, which are essential to their superconducting properties. T c measurements are done with a magnetometer and lock in amplifier – a system that allows for measurement of the magnetic flux passing through the cuprate sample. T c dependence on doping and how annealing alters this has been investigated, and I have determined that by annealing in vacuum, we are able to increase the T c and keep the transition width narrow. Additionally, a monochromater spectrometer as a diagnostic tool for a mid-IR laser used for ARPES is in progress, and has involved setting up hardware, software, and optics.

X-ray Analysis of 7 Active Galactic Nuclei Peter Kosec Mentor: Fiona Harrison

We perform X-ray analysis of 7 AGNs using spectroscopic measurements from NUSTAR, SWIFT, XMM-Newton, Chandra and Suzaku satellites. The sample was initially fitted with a range of models simulating an active nucleus obscured by dusty molecular clouds, including Pexrav and MYTorus models. Subsequently, sources of interest were chosen for further analysis. ESO 383-G018 shows unexpectedly low intensity in the hard X-ray band (above 30 keV) of its spectrum, where a steep cutoff is observed. This spectral feature can be fitted with a power law with

exponential cutoff at 19,3 +8,5 5,5 keV, much lower than hundreds of keV observed in other AGNs. ESO 509-IG066 is a

galaxy pair and simultaneously an AGN pair based on the XMM data measured in 2004. However, only one source can be fitted in NUSTAR and SWIFT spectra from 2014 to high statistical accuracy. Comparing with Chandra data from 2011, we report that the second object has dimmed by a factor of 10 since 2004. Possible explanations include fading of the nucleus by decreasing the mass accretion rate or obscuration of the source by a Compton- thick molecular cloud. Further investigation in the IR band is needed to distinguish between the possibilities.

Heat Treatment Stabilization of Yttria-Stabilized Zirconia Thermal Barrier Coatings Giacomo Koszegi Mentors: Katherine T. Faber and Matthew Johnson

Thermal barrier coatings (TBCs) are commonly used to protect the blades of gas turbine engines from high operating temperatures that would otherwise result in deformation or melting. Yttria-stabilized zirconia (YSZ) is particularly well-suited as a TBC due to its thermal conductivity and coefficient of thermal expansion. When YSZ TBCs are prepared via plasma-spray physical vapor deposition, the resulting coating contains non-stoichiometric and amorphous material, both of which compromise stability during thermal cycling. The goal of this research was to use heat treatments at 350°C and 700°C for times ranging from 1-16 hours to correct stoichiometry and promote crystallization. X-ray diffraction was used to evaluate the non-stoichiometric phases before and after heating, as well as to provide a qualitative measure of amorphous content. Scanning electron microscopy was used to visualize microstructure. Similar experiments could be conducted in the future using other TBC ceramics, such as gadolinium zirconate.

Machine Learning for Fast Data Transfers at the Large Hadron Collider Nikhil Krishnan Mentors: Maria Spiropulu and Dorian Kcira

The Large Hadron Collider (LHC) is the most powerful particle collider in the world, and the Caltech Compact Muon Solenoid (CMS) group produces massive amounts of data in its experiments at the LHC. As a result, the CMS group has its own infrastructure for data transfers, implementing grid-based data analysis and global-scale networking. Because the CMS experiment generates voluminous amounts of data, there needs to be a way to improve the


current data management tools to optimize speed of transfers and facilitate fast I/O access. Machine learning offers numerous methods for such an optimization, as the field allows us to look at the present state of the network and use information about recorded transfers to predict features about future data transfers, thereby reducing the number of variables the data management tool has to consider. Using logged information from PhEDEx, the CMS data transfer system, we created a large sample matrix of data transfers, partitioned it into testing and training samples, and conducted Principal Component Analysis, a machine learning method that projects a large multivariate dataset onto the two variables that most explain variance. We also worked on constructing a deep learning neural network between various nodes of the CMS group, allowing the data management tool to learn by itself over time and optimize data transfers based on completion time.

Development of a Control System to Stabilize Magnetic Fields Outside an nEDM Detector Anita Kulkarni Mentors: Bradley Filippone and Simon Slutsky

Experiments over the past several decades have attempted to measure a neutron electric dipole moment (nEDM) with greater and greater sensitivity. The presence of a nonzero nEDM would lend support to potential explanations of matter-antimatter asymmetry, among other ramifications. A highly uniform magnetic field is required to detect a dipole moment to high precision since non-uniformities can create false signals through the geometric phase effect. The uniformity of the field inside the detector can be improved by reducing the magnitudes of magnetic field disturbances outside the detector. To do this, we program a system that controls the currents flowing to a network of six large coils (connected in pairs) around the detector in three spatial directions. The currents are programmed to generate magnetic fields that counteract external field disturbances in real time. The system implements Proportional-Integral-Derivative (PID) control of currents based on magnetic field readings from eight probes near the detector. Continuous improvements are being made in the system’s performance, and finer control could be obtained in the future by powering the six coils separately and modifying the control system accordingly.

Numerical Simulation of Phase Locked Synchronization in Coupled MEMS Oscillators With Applications to Neurocomputing Ankit Kumar Mentors: Raj Mohanty and David Hsieh

The dynamics of linearly coupled, anisochronous, self-sustaining oscillators are numerically simulated, with the aim of identifying regions of parameter space that exhibit phase locked synchronization and multistability. Robustness of synchronization in the presence of varying levels of noise is studied. The two oscillator case is extended to a linear chain and a two-dimensional grid of oscillators with nearest neighbor coupling. Pattern recognition is studied by tracking the evolution of the network towards synchronized states while iterating the initial conditions and coupling parameters. The experimental implementation of the network using self-sustaining MEMS oscillators could lead to the practical realization of neurocomputers on a scalable architecture.

Starburst: Stellar Burst Observation Program Control Software Implementation Lokbondo Kung Mentors: Anthony Readhead, Jackie Villadsen, and James Lamb

The Starburst Project aims to implement the first facility dedicated to radio observation of stellar bursts using the two 27-meter antennas located in Owens Valley Radio Observatory. Many of the projects custom built pieces of equipment require custom built software to help facilitate operations. Therefore, the implementation of data querying wrappers for embedded systems and data streaming routines for data pulling in the back-end of the antenna pipelines was crucial for the success of the project. Research into the hardware and architectural design of the software was heavily stressed to provide not only support for the project but possibilities of expansions or replications of the system. The project also involved implementation of control system software to manage and control the individual components at the front-end (receiver and related components). The new control system aims to replace an outdated legacy control system. This project will ultimately provide custom Python software for the Starburst Project that is mutable, testable, and documented.

Simulation and Characterization of Near-Subwavelength High-Refractive Index Contrast Gratings for High Efficiency Spectrum-Splitting Multijunction Photovoltaics Stephanie Kwan Mentors: Harry A. Atwater and Sunita Darbe

High-refractive index contrast gratings (HCG) are two-dimensional arrays of high-refractive index dielectric subwavelength-scale structures on the surface of a low-refractive index substrate. HCG have been shown to display near-perfect reflection over 200 nm-wide tunable bands in the near IR range under idealized condition (e.g. for normal incidence light of a given polarization). This remarkable phenomenon is attributed to Mie electromagnetic resonances and has inspired research on applications of HCG in solar energy conversion. In spectrum-splitting photovoltaics, optical elements divide white sunlight into multiple frequency bands, which are coupled into laterally separated solar cells with bandgaps tuned to best convert the target band of light. In this project, HCG are


explored as long-pass filters for the Atwater Full Spectrum team’s ultra-high efficiency spectrum-splitting photovoltaic module. Rigorous Coupled-Wave Analysis simulations are used to identify geometric parameters for TiO 2 , GaP, and a-Si HCG. In parallel, we experimentally measure the angle-dependent reflectance properties of the gratings over the visible and near IR spectrum. The long-term goal is to identify and fabricate seven high-efficiency HCG that can replace the costly and angle-sensitive Bragg reflectors currently implemented in the submodule prototype.

Progress Toward the Synthesis of Dimethyl Oxeatamide A: Synthesis of Racemic tert-ButylPyOx Netgie Laguerre Mentors: Brian M. Stoltz and Samantha Shockley

Diterpenes are a large class of natural products that display a range of biological activities that cause them to be potential pharmaceutical agents. However, the structural complexities of these natural products that commonly include all-carbon quaternary stereocenters make them formidable targets for synthetic chemists. The Stoltz group has recently developed the innovative methodology of palladium-catalyzed conjugate addition to create all-carbon quaternary stereocenters in high enantiopurity under atmospheric conditions while employing a relatively inexpensive catalyst. We propose to undertake the asymmetric synthesis of the diterpene, dimethyl oxeatamide A, utilizing palladium-catalyzed conjugate addition.

The requisite ligand for palladium-catalyzed conjugate addition chemistry, tert-ButylPyOx, requires tert-leucinol as a key intermediate in its synthesis. In order to determine the enantiomeric excess of the proposed conjugate addition reaction, racemic tert-butylPyOx is required. Since no efficient preparative methods currently exist for the racemic synthesis of tert-leucinol, we are developing a novel synthetic route to this intermediate and thus racemic tert-butylPyOx this summer.

A Numerical Analysis of Spin-Spin Coupling in Multi-Body Systems Frederick William Lake Mentor: Konstantin Batygin

Many bodies in the solar system have rotation times synchronous with their orbital periods. However, a phenomenon known as spin-orbit coupling, where a deformed moon is gravitationally torqued by its central body, permits alterations in the evolutionary process of gravitationally bound bodies, and has been fairly well studied at this point. This paper analyzes the effects of a second, related phenomenon known as spin-spin coupling, in which the spin of a central body affects the rotation rate of the secondary. A numerical integration program was written, and applied to multi-body systems such as 87 Sylvia and 216 Kleopatra to show the effects of spin-spin coupling on the systems. This program was then released publicly, as no such program is currently available for public use, allowing further study into the phenomenon.

Development of a Three Wavelength Cavity Ring-Down Instrument Karim Lakhani Mentors: Geoffrey Smith, Al Fischer, Austen Scruggs, and Mitchio Okumura

Ambient aerosols are one of the largest contributors to air pollution, and determining their optical properties allows scientists to create better models to study air pollution. However, because of their low extinctions (10 7 1 ), special techniques besides UV-Vis spectroscopy are necessary to detect them. We attempted to build a three wavelength (red, green, blue) cavity ring-down spectrometer to measure extinction by these particles. Cavity ring- down uses ultra-high reflectivity mirrors to create a large path length to detect molecules with small absorbance cross sections. This project focused on coupling the three lasers into the same cavity and interweaving them to obtain information for each wavelength at high repetition rates. I worked on setting up the spectrometer, writing the Labview program that modulated the lasers and calculated the exponential fits in real time, and calibrating the spectrometer to known gases. Future studies involve using the cavity ring-down spectrometer outside of the laboratory setting to detect ambient aerosols.

Electrochromic Inverse Opals for Smart Windows With Static and Dynamic Optical Transmittance Christian Lau Mentors: Julia Greer and Victoria Chernow

Most smart windows employ electrochromic coatings with tunable optical transmittance upon the insertion and extraction of charges. Incorporation of electrochromic coatings into windows have both reduced heat transfer into buildings and enhanced their aesthetic appearance. Nevertheless, electrochromic smart windows can be further improved by generating a photonic bandgap that continually reflects light in the near-Infrared range. Such a photonic bandgap can be generated by an array of periodically altering refractive index. Periodic inverse opal structures have been shown to produce complete photonic bandgaps in a wide range of frequencies. A number of groups have reported scalable methods for fabricating arrays of titania inverse opals. My project aims to employ these methods to produce the first smart window device with both dynamic electrochromism in the visible light spectrum and a static photonic bandgap in the near infrared range. I investigate several sol-gel methods that


employ vertical evaporative deposition, drop-casting, and doctor-blade coating to optimize the fabrication of inverse opals. Characterization of the inverse-opal morphology, chemical composition, and optical transmittance is carried out to evaluate the performance of the device. Further study is needed to determine the most scalable fabrication strategy to manufacture inverse opals for industrial production.

Ruthenium Catalysts With Chelating Fluoro-adamantyl-substituted N-Heterocyclic Carbene for Z-selective Olefin Metathesis SiiHong Lau Mentors: Robert Grubbs and Brendan Quigley

Olefin metathesis emerged as a powerful method for the construction of carbon-carbon double bonds in a wide variety of applications. However, achieving high Z-selectivity through olefin metathesis persisted as a challenge due to the thermodynamically preferred E-olefins favored by most catalysts. A series of Z-selective metathesis ruthenium catalysts with chelating fluoro-adamantyl groups has become our synthetic target in order to study how the electronic nature affects the stability, stereoselectivity, and reactivity of the catalysts. The fluoro-adamantyl amine has displayed a number of unexpected synthetic challenges, including interesting reactivity which we are trying to characterize. This resulted in us employing multiple synthetic strategies for the preparation of the catalysts.

Widefield Imaging of the Mouse Visual Cortex Minh Nhat Le Mentors: Doris Tsao and Tomo Sato

Calcium imaging using GCaMP6 mice is a promising tool to study how the mouse visual system represents surfaces and objects. Before applying this technique to these higher-order visual processes, we first performed widefield imaging to confirm that our newly assembled setup is working optimally. We performed thinned-skull surgery on 15 mice, and showed these mice a moving bar with a contrast-reversing checkerboard pattern to obtain a retinotopic map of the early visual areas. Despite a few differences, the resulting retinotopic maps closely resembled previously constructed maps from other studies, indicating the reliability of our measurements. Further improvements to our existing setup, including the implementation of eye-tracking, will be carried out before the technique can be used in future studies.

Predicting 3-Dimensional Structures and Binding Interactions of Human Olfactory Receptors Morgan Lebby Mentors: William A. Goddard, III, and Soo-Kyung Kim

G protein-coupled receptors (GPCRs) are a large family of trans-membrane proteins that mediate senses such as odor taste, vision, and pain in mammals. Olfactory receptors (ORs) represent a large subset of GPCRs, with over 400 ORs identified in humans; however, the 3-dimensional structure and binding characteristics of most ORs have not been determined. Through implementation of the GEnSeMBLE computational method, the most energetically favorable conformations of ORs OR1A2-4 and OR2W1-5 were predicted, using Monte Carlo sampling of the θ, φ, and η helical angles. These angles define the orientation of each of the seven trans-membrane helices that make up all ORs. Out of the top 25 most energetically favorable structures, three were taken through the DarwinDock method, which predicts the binding poses of the odorants that have been experimentally determined to cause GPCR activation. From the docking results, we were able to determine the key residues that are involved in odorant binding.

Expanding Fine-Grained Categorization to Novel Domains Donsuk Lee Mentors: Pietro Perona and Steve Branson

Many of the state-of-art techniques of fine-grained categorization depend upon part annotations for learning object parts that help identifying subtle differences between subordinate categories. However, the high cost of acquiring part annotations makes it challenging to expand fine-grained categorization to diverse domains. The goal of this project is to develop a scalable fine-grained visual recognition system that does not require part annotations. The system leverages the recent state-of-art technique, which generates parts using co-segmentation and alignment. We demonstrate the effectiveness of this approach by evaluating on the Stanford cars-196 dataset. The complete pipeline will be integrated into a web application where users can upload photos to retrieve relevant information. We expect the system to be easily extendable to other domains with less cost.


Designing Immersive Visual Stimuli for Human Experiments Ga Yeong Lee Mentors: Ralph Adolphs and Juri Minxha

The typical approach a scientist would use to understand brain function is to record some kind of activity (behavioral response, EEG, intracranial recordings, head tracking, eye tracking, etc.) while showing a stimulus in a controlled and structured way. In a simple experiment, this may amount to showing a single image to a subject while you record their brain activity using fMRI. This conventional approach however, rarely resembles the rich nature of our experience of the world around us. In this project, we are trying to create a platform for addressing scientific questions related to brain function, that is much more engaging in nature. We use a game engine to develop scenes (i.e. stimuli), which can be experienced by the user in a virtual reality setting. We show, using a simple exploration experiment, that users are much more engaged by this new stimulus presentation method and that the data that is collected is much more abundant and complex than what is typically collected with on-screen stimulus presentation.

Implementation of Dust Dynamics for Galaxy Formation Simulations Hyunseok Lee Mentor: Philip F. Hopkins

We study the behavior of large dust grains in turbulent molecular cloud. Interstellar dust plays a crucial role in many important processes in galaxy evolution, including conversion from neutral to molecular hydrogen and formation of low-mass stars in the early universe. While interstellar dust grains are often modeled to move with neighboring gas flow in numerical simulations, the dust grains in typical molecular cloud does not necessarily move with the gas. We therefore directly simulate dust dynamics in highly supersonic turbulent box. Under these conditions, we study how grain size and flow velocity affect local densities of dust and gas. The results exhibit dramatic fluctuations in the local dust-to-gas ratio, thereby implying large small-scale variations in abundances, dust cooling rates, and dynamics. Further researches can incorporate Lorentz forces and other physics neglected here.

Characterization of Tumor-Infiltrating T-cells With Single-Cell Barcode Chip Technology in the Context of Melanoma Therapy Jihoon Lee Mentors: James Heath and Jing Zhou

Melanoma is the most lethal of skin cancers. There are a multitude of therapies being developed to combat it, among which is the amplification of a melanoma patient’s natural immune response – tumor-infiltrating lymphocytes (TILs). TILs have the ability to attack and help destroy tumor cells due to their distinct active signaling pathways. However, often the natural response is too small for there to be effective elimination and in fact may induce tumor cell de-differentiation in order to resist the attacks. In order to detect and amplify such a population, TILs’ cell surface receptor populations may be quantified. In order to accomplish this for individual cells and many receptors efficiently, the single-cell barcode chip has been developed to assay single lymphocytes in a multiplexed manner. This investigation examines new uses of SCBC technology to characterize different aspects of tumor-infiltrating T-cells, entailing the design and construction of SCBCs in combination with a model of tumor- infiltrating T-cell clustering and signaling behavior and a SCBC analysis of melanoma cell proteomic responses to various drug and TIL therapies, with the ultimate goal of developing a more effective melanoma therapy.

Immersive and Collaborative 3D Scientific Data Visualization Joon Lee Mentors: George Djorgovski and Ciro Donalek

Scientific data sets are growing in both volume and complexity, providing novel opportunities for discovery. These massive data sets, however, are not fully exploited without tools we can use to discern the hidden patterns in the data. As a result, data visualization is becoming an increasingly indispensable part of scientific research. The Center for Data-Driven Discovery is developing a visualization program, iViz, that allows users to immerse themselves in a virtual reality containing data points which can represent numerous dimensions using position, shape, size, color, and texture. This project seeks to improve iViz through the addition of several new features. First, a spherical plot was added to make the program suitable for geographical and celestial data. Additional changes were made to make visualization and pattern recognition effortless in these spherical plots. In addition, several types of grids and planes were created to aid in data analysis. Finally, a networking framework was developed to allow for collaborative visualization through the Web.


A Partition Function Algorithm for Nucleic Acid Secondary Structure With Dangle and Coaxial Stacking

Yoon Lee Mentors: Niles Pierce and Nicholas Porubsky

We describe an algorithm for performing thermodynamic analyses of interacting nucleic acid strands. Given a nucleic acid sequence, we can calculate the partition function, which describes the statistical properties of a system in thermodynamic equilibrium, over secondary structure space with the dynamic programming paradigm. We can determine the partition function of a given sequence over all unpseudoknotted secondary structures in O(N 4 ) time, which can be reduced to O(N 3 ) complexity, where N is the length of the strand, if we simplify the loop-based free energy model. The objective of this study is to develop a partition function algorithm that rigorously incorporates the energy contributions of dangle and coaxial stacking states as they provide additional energetic stabilization for multibranch and exterior loops. We update the recursions for partition function calculation in NUPACK, a software suite for the analysis and design of nucleic acid systems, to quantify how these two factors are relevant in improving accuracy in conducting a thermodynamic analysis of a dilute solution of interacting nucleic acid strands. We use the internal validation and explicit enumeration schemes to ensure the correctness of the algorithm.

A Wavelet-Based Finite Element Approach to Atomic-Scale Mechanics

Daniel V. Leibovici Mentor: Michael Ortiz

Numerical simulations of microscopic material are often performed at an atomistic scale in order to study phenomena like crack-tip or dislocations. However due to their high computational cost, multi scaling and mesh reduction methods have become key points in computational mechanics. This research project deals with the implementation of a new method to perform mesh coarsening, based on the wavelet theory. Thanks to the properties of hierarchical refinement of the scaling functions, a lattice can be reduced or refined hierarchically on different levels of precision. The aim is to study how a phenomenon, like a wave, would propagate in uniformly fine and coarse models, and in the future in a combination of both. The study of wave-reflections between areas of different level of refinement, and the development of new integration methods to avoid them opens a broad area of research: the aim is the development of a revolutionary method of simulating molecular dynamics which would highly reduce the current computational costs.

A New High-Frequency Search for Galactic Center Millisecond Pulsars Using DSS-43

Cameron R. Lemley Mentors: Thomas A. Prince and Walid A. Majid

The primary 70-meter Deep Space Network antenna (DSS-43) in Canberra, Australia was equipped with a new high-frequency (18-28 GHz) receiver system in May 2015 for use in a search for Galactic Center (GC) millisecond pulsars. The primary motivation for this search is that a pulsar in the Galactic Center region (especially one that is gravitationally bound to the massive black hole at the GC) would provide unprecedented tests of gravity in the strong-field regime and would offer an entirely new tool for probing the characteristics of the Galactic Center region. Preparation for the GC pulsar search has involved the development of a single-pulse search pipeline that integrates tools from both Fortran and Python as well as the implementation of this pipeline on high performance CPUs. The original version of the search pipeline was developed using Vela Pulsar data from DSS-43, and a more refined version that relies upon chi-squared fitting techniques was ultimately developed using Crab Pulsar data. Future work will involve continued testing of the single-pulse search pipeline using data from the rotating radio transient (RRAT) J1819-1458 as well as the characterization of pulses from this system using high time resolution data from the new receiver system on DSS-43.

Effect of Exogenous PU.1 and PU.1-ets on Commitment and Spi1 Autoregulation in Hematopoietic Progenitor Cells Jessica D. Li Mentors: Ellen V. Rothenberg, Hao Yuan Kueh, and Jonas Ungerbäck

By the double negative (DN)2b stage of T cell development, hematopoietic progenitor cells can no longer differentiate into other cell types. Here we study PU.1, an Ets family transcription factor encoded by Spi1 that is involved in commitment. PU.1 positively regulates Spi1, so cells with high PU.1 should maintain similar expression. However, while necessary to initiate development, PU.1 levels drop sharply during the DN2b stage. To study PU.1 autoregulation change, we infected precursor cells with H2B (control), Spi1, or PU.1-ets, the PU.1 DNA binding domain, and grew them in either T cell supporting (OP9-DL1) or non-supporting (OP9-Mig) environments. We found that cells infected with PU.1 on OP9-DL1 had similar levels of endogenous PU.1-GFP and T cell development as control cells. On OP9-Mig, exogenous PU.1 impaired B cell development in favor of CD11b + cells. Adding PU.1- ets to cells biased them toward CD11b + on both environments. In samples with higher proportions of CD11b + cells, CD11b + populations with low PU.1-GFP levels not found in control samples appeared. Together, these results both


support the idea that PU.1 no longer positively autoregulates itself in T cells suggests a more complex role of PU.1, as the simple act of PU.1-ets binding to cis-regulatory elements appears to influence fate decisions. Further work will characterize the currently unknown CD11b + PU.1-GFP low+ populations and determine which genes are affected in these PU.1-ets infected cells.

Automatic Data Collection for Real-Time Usability Problem Detection in CRISIS Virtual Environments John Li Mentor: Ebba Hvannberg

Crisis training is necessary to prepare medical first responders for emergency situations. In order to train for these situations, an environment is often prepared with the appropriate props and actors. However, it takes a lot of careful planning, time, and money to set up these scenarios for the frist responders. The CRISIS project addresses this by creating virtual environments for first responders to train with, saving the time and money used to create a real-life scenario. However, virtual environments must also closely replicate real-life environments if virtual training is to be effective. Therefore, my task is to automatically detect usability problems in these virtual environments during a training scenario. In order to detect these problems, data from the environment must be undergo Complex Event Processing (CEP), which is done through the software product known as Esper and written Event Processing Language (EPL) scripts. The data from the environment must also be sent to Esper, which is done through the use of a message broker known as Apache ActiveMQ. With this architecture, we expect that our virtual reality environment will be able to detect usability problems in real-time training.

An Automated System for Geometric Differentiation of Mesh-Based Energies Kevin Li Mentors: Eitan Grinspun, Keenan Crane, and Alan Barr

We propose an automatic geometric differentiation (AGD) system that produces meaningful geometric expressions for derivatives of mesh-based quantities. Numerical evaluation of forces and gradients is a ubiquitous problem in physical simulation and geometric optimization, yet expressions quickly become cumbersome for energies involving geometric quantities associated with surface or volume meshes. Obtaining simple, meaningful expressions typically requires high-level geometric intuition that current computer algebra systems lack. Yet consistent patterns in “by- hand” derivations suggest that an intelligent AGD system may be within reach. For instance, one often infers the gradient direction by identifying the directions along which the energy remains constant, a procedure that can be performed by brute-force computation. Currently, we extend established automatic and symbolic differentiation methods to incorporate mesh-based geometric quantities as fundamental nodes in an expression tree. This extension “prunes” the tree, and facilitates the use of expert geometric knowledge during simplification as well as intelligent caching. Preliminary experiments indicate that even basic modifications to naïve automatic differentiation can yield over a 2x reduction in computational overhead; gains from modifying symbolic differentiation are expected to be strictly better. Ultimately, this tool aids rapid development of fast, reliable numerical code, allowing researchers to focus more on high-level exploration.

Audiovisual Illusory Rabbit: Perception Across Senses and Time Monica Li Mentors: Shinsuke Shimojo and Noelle Stiles

Unlike the traditional five senses, we do not have a specific sensory organ to sense time; time seems to pass fast or slow, and memories can be difficult to keep in chronological order. Furthermore, while the timing of each sense appears to be distinct, these separate sensory modalities are fused, giving rise to illusions such as the multimodal rabbit.

The audiovisual rabbit occurs when two flashes and three beeps are spaced apart spatially and temporally, with the first and third beep paired with a flash to the left then one to the right, respectivelyeach of the flashes paired with beeps flanking (in space and time) a single flash, with the standalone second beep temporally between them. The brain stitches together the impression that the two stimuli modalities are actually one in continuous movement, and thereby generatinges an illusory flash with the unpaired beep.

This rabbit is particularly interesting because the illusory flash is postdictive;, in that the brain only knows the beep-flash pairing pattern after the “illusory” flash is supposedly perceived. We have reproduced the audiovisual rabbit illusion and begun exploring changes in color and shape.

Additionally, we have found a new postdictive suppression illusion, where participants perceive three flashes with two beeps paired with the first and third flash as only two flashes.


Optimising SUSY Search at CMS With Machine Learning Techniques Yuting Li Mentors: Maria Spiropulu and Javier Duarte

The Higgs detection with its 126 GeV mass is hinting at physics beyond the standard model. We are at the stage where we are unclear as to what discovery story awaits and need to cater for an extremely small amount of signals. There have been studies demonstrating the use of supervised machine learning techniques in signal detection but supervised methods have the risks of overtraining on Monte Carlo imperfections and the difficulties of getting statistical interpretations. In this paper, the Self Organising Map (SOM) was applied as an unsupervised data-driven clustering algorithm. To tackle the problem of the lack of statistics, the Neural Autoregressive Density Estimator (NADE) was first introduced for background estimation in the cells in the SOM. Its ability to detect outliers was also investigated in this paper.

Examining the Effect of Deformation Radius on Zonal Jets Based on a Quasi-Geostrophic Model Ziwei Li Mentors: Andrew P. Ingersoll and Cheng Li

In the study of planetary atmospheres, 2D turbulence model with parameterized moist convection plays an important role in investigating the interaction between moist convection and large-scale circulation. In an earlier study, members of this group (Liming et al., 2005), used a quasi-geostrophic model to study the dynamics of Jupiter and Saturn’s atmospheres. Their results differ from others (Scott et al., 2007, Showman et al., 2006) in that the deformation radius had little impact on the width and amplitude of zonal jets. After a preliminary study, we find several unphysical treatments in the original numerical formulation that might lead to the above disagreement, including the global adjustment of the streamfunction and the boundary layer forcing method. We changed those treatments and our new model produces more reasonable results. We show that the deformation radius may indeed affect the zonal velocity profile, and at the same time, there is possible northward migration of the zonal jets, which awaits further investigation. Later on, we will keep investigating the possible effects of moist convection parameterization, spatial resolution dependence, and baroclinic stability in our newly formulated model.

The Carbery Conjecture and Related Problems David J Lichko Mentor: Majid Hadian-Jazi

Gauss's quadratic reciprocity law, which is a fundamental result in algebraic number theory, explains how quadratic polynomials decompose modulo primes. It says that the decomposition depends only on congruence conditions on the prime. In general, no such law can describe the decomposition of a cubic polynomial modulo primes. We present reciprocity laws for certain families of cubic polynomials. When the discriminant D of the polynomial is fixed, we formulate a reciprocity law in terms of congruence conditions on solutions to a finite number of quadratic forms. If the class number of Q(√-3, √D) is not divisible by 3, the law can be explicitly written in terms of the coefficients of the cubic polynomial. When the prime modulus is fixed instead, we show how the decomposition can be determined by a congruence condition on the coefficients of the polynomial. We also study the case where the splitting field of the cubic is in the Hilbert class field of Q(√D).

Fabrication of Microlens Arrays Through the MicroAngelo Technique Using Thermocapillary Forces Soon Wei Daniel Lim Mentors: Sandra M. Troian and Kevin R. Fiedler

Plano-convex microlens arrays were fabricated using the one-step MicroAngelo technique, which uses strong thermal fields to modulate forces driven by surface tension gradients on a molten polymer nanofilm interface to achieve the desired surface topology. Spatially inhomogeneous temperature gradients were achieved by varying the heights of photoresist elements on a cold plate placed above the polymer film. The fabricated arrays will implement a Shack-Hartmann wavefront sensor, and its optical quality will be compared to that of a commercially available microlens array. The experimental results thus far show that with suitable control over the thermal field, MicroAngelo has the potential to form a diverse spectrum of ultra-smooth surface topologies in a single non-contact fabrication step.

Measuring Micro-Mechanics of the Drosophila melanogaster Wing Hinge With in vivo Fluorescent Muscle Imaging Amanda Lin Mentors: Michael Dickinson and Theodore Lindsay

Although we are gaining a greater understanding of how flies use sensory signals to execute flight behaviors, the exact mechanical means controlling the wing motion remains a mystery. Previous studies have measured activity and strains of a few muscles controlling the wing-hinge; however, these studies performed under a restricted set of sensory conditions. To expand on these studies, we took advantage of transgenic Drosophila melanogaster that express fluorescent proteins and measured the strains in several identified muscles of the wing hinge. We


combined fluorescence microscopy with high-speed video and stroboscopic measurements of the steering muscles during both quiescence and visually-elicited flight maneuvers. As such, we were able to detect visually evoked changes in the strain cycles of the tergo-pleural muscles and first basalar muscle. From our analysis, we have reason to believe that the first basalar muscle is correlated with wing-stroke amplitude as, in many cases, the two occur with the same frequency. We also see that the strain of the tergo-pleural muscles are proportional to the wing-beat frequency and are important during the onset of flight. Thus, with these experimental methods, we can continue to work to understand how the steering muscles work together to control wing motion.

Analysis of K2 Light Curves and Spectral Energy Distributions to Detect Earth-Like Exoplanets Hanzhi Lin Mentors: Rachel Akeson and Erik Petigura

Since the K2 mission launched, there has been over 100,000 stars discovered, ranging from M dwarfs to red giants. Light curves of the stars display the energy flux over time, thereby allowing astronomers to identify exoplanet transits as parabolic dips. Unfortunately, different types of astronomical and arbitrary noise are prevalent in these light curves. Using Python, certain filtering functions were coded to remove the noise, thereby allowing one to easily identify transits. After pinpointing certain planet transits, the period, size, and composition of the planets could be estimated. The spectral energy distributions (SED) of the stars were also computationally analyzed to test the accuracy of certain photometric catalogs. By comparing the stars’ SED plots from all of the observational catalogs to those from reliable theoretical models, particular catalogs were revealed as flawed. After removing suspect catalogs, the stars’ temperatures, luminosity, and other physical properties were computed. With the observation of planet transits in light curves and computational calculations of the stars’ properties, exoplanets with Earth-like attributes could potentially be discovered.

Adding a Treatment for CO 2 to pMELTS Zachary Lipel Mentor: Paul Asimow

pMELTS is a software that models magmatic equilibria at high pressures. It builds upon its predecessor, MELTS, which functions similarly up to about 1 GPa, whereupon it is inaccurate. Recently, an H 2 O-CO 2 mixed fluid saturation model compatible with rhyolite-MELTS (an updated version of MELTS) was developed. We aim to apply a similar method to add a treatment for carbon dioxide to pMELTS. I organized and uploaded a collection of data containing carbonate (both liquid and solid) phases. The data define the stability fields of carbonate, multicomponent liquid carbonatite liquids, and coexisting silicate and carbonatite liquids in pressure-temperature- composition space. Using existing thermodynamic and solution models for silicate liquids at high pressure and for carbon dioxide and calcium carbonate in those liquids at low pressures, the aforementioned data should allow for the calibration of a thermodynamic model that correctly accounts for the behavior of carbon dioxide saturated melts at high pressures. We will evaluate the model by both examining energy residuals and by using forward modeling of carbonate bearing experiments to check the temperature of phase boundaries, the progression of phase proportions, and predicted phase compositions.

Semisynthesis and Analysis of AKT1 Phosphoforms Albert Liu Mentors: Philip Cole, Nam Chu, and Pamela Bjorkman

Akt1 is a protein kinase that plays an essential role in cell signaling, regulating multiple cellular processes such as apoptosis and cell proliferation. Notably, dysregulation of Akt1 signaling has been shown to lead to cancer. It has been well established that the activity of Akt1 is primarily regulated by phosphorylation at two residues: T308 and S473. Recently, two new phosphorylation sites at the C-terminus of Akt1, S477 and T479, were discovered. However, the function of these two new sites of phosphorylation has not been characterized to a large extent. By taking advantage of a natural cysteine residue within Akt1 (C460), we were able to use native chemical ligation to semisynthesize four different phosphoforms of Akt1: no phosphorylation, pS473, pS477 + pT479, and pS473 + pS477 + pT479. We are currently assaying the different phosphoforms with regard to two different activities:

ability to be activated by PDK1 (the enzyme which installs pT308), and ability to activate Akt1 substrates. By comparing the results from each of the different Akt1 phosphoforms, we hope to unravel the function of the newly discovered phosphorylation modifications. Lastly, we also hope to discover novel substrates of fully phosphorylated Akt1 by utilizing a protein microarray strategy.

Timing Resolution Studies of Hamamatsu Silicon Photomultipliers Eric Liu Mentors: Maria Spiropulu, Si Xie, Artur Apresyan, Anatoly Ronzhin, and Cristian Peña

Photodetection technology has wide application in modern scientific and commercial fields, from spectrometry to subatomic particle detection. Timing precision of detectors is critical in the performance of modern particle detectors, which calculate particle masses using strong magnetic fields and precise time-of-flight measurements. Silicon-based photodetectors are currently in use in the Large Hadron Collider (LHC), since silicon's performance


and timing precision are largely unaffected by strong magnetic fields. The current detectors have a time resolution of 200-300 ps, which is an order of magnitude too large to handle the increased collision rate of the next LHC upgrade. Sample detectors from the next generation of silicon photodetectors were tested using picosecond- duration laser pulses.

Engineering Bispecific Antibody-Like Reagents Against HIV Phillip Liu Mentors: Pamela J. Bjorkman and Rachel P. Galimidi

Despite more than three decades of effort, no effective vaccine for HIV has been developed, and AIDS remains a serious global public health issue. HIV presents numerous difficulties to researchers with its high mutation rate, glycan shielding of potential epitopes, as well as shielding constant regions of glycoproteins with highly variable regions to further protect against antibody binding. Additionally, the extremely low density of HIV envelope spikes, around 14 for every virion, results in few opportunities for inter-spike linking IgG bivalent binding, and intra-spike bivalent binding is not possible due to the structure of IgGs. Recent research has resulted in the development of protein-DNA structures where dsDNA links two Fc antibody regions. These reagents exhibit intra-spike bispecific binding. In this project, we design and engineer bispecific all-protein structures with protein linkers in place of DNA via controlled Fab-arm exchange. HIV pseudovirus neutralization assays were performed to assess the potency and breadth of the constructs. We hope to perform polyreactivity ELISA as well as additional neutralization assays to further analyze these reagents.

Integration of Behavioral Commands for Improved State Estimation and Control of Pioneer 3-DX for a Resilient Spacecraft Sandra Liu Mentors: Richard M. Murray and Catharine L. McGhan

In the upcoming years, scientists and researchers want to explore new areas in space exploration: places that are more distant, enigmatic and thus less accessible. This requires stronger and more resilient spacecraft that will be able to be risk-aware and act autonomously when commands are unable to be provided. To deal with these challenges, a Resilient Spacecraft Executive (RSE) architecture is being designed so that space robots can adapt to equipment failures, deal with different environments and make such risk-aware decisions. This project deals with developing and implementing algorithms to support the underpinnings of the RSE and vehicle objectives like obstacle avoidance and other higher-level processes. Enabling the robot to respond to autonomous commands, implementing motion constraints on vehicular movement and putting together an Inertial Measurement Suite (IMU) sensor suite that can supply more useful data will help to support future endeavors to make space vehicles more autonomous and intelligent.

Rapid Estimation of Earthquake Magnitude and Epicenter Using Ground Motion Parameters Timothy Liu Mentors: Egill Hauksson and Jennifer Andrews

Earthquake early warning systems (EEWS) are designed to provide several seconds to tens of seconds of warning that shaking from an earthquake is imminent at the user location. Such systems use a network of seismometers scattered across an area with active faults to constantly monitor and report ground motion. When an earthquake begins, algorithms must rapidly analyze ground motion data and estimate the epicenter and magnitude of the event. If an accurate estimate can be made quickly enough, an alert can be issued, possibly giving individuals crucial seconds to find shelter. EEWS are dependent on algorithms that can quickly and accurately make magnitude and epicenter estimates. One of the algorithms used by ShakeAlert, an EEWS being developed for the West Coast of the United States, is the TauC-Pd On-Site algorithm. On-Site currently uses the ground motion parameter TauC to estimate the magnitude of an event using a single station. This paper proposes an alternative method for estimating the magnitude of an event at a single station that uses the attenuation of peak displacement and peak velocity with distance from the epicenter. Results suggest that this attenuation model produces more accurate magnitude predictions than those made by using TauC. Additionally, a new method for more accurately determining the epicenter of an event based on p-wave arrival times is also proposed. Analyses of test data show that the two methods provide improved performance and robustness of the OnSite algorithm.

Investigation of the Regulation of SRP-Mediated Co-Translational Protein Targeting Yun (Demi) Liu Mentors: Shu-ou Shan and Jae Ho Lee

The signal recognition particle (SRP) provides strict coordination between protein synthesis and translocation, and the interaction between SRP and its receptor (SR) is required for the initial targeting of the ribosome-nascent chain complex (RNC) to the ER to form the ribosome/translocon junction, thereby ensuring proper biogenesis of proteins in the crowded cellular environments. We are interested in accurately describing the kinetics and thermodynamics of the interaction between SRP and SR, and testing if and how the Alu-domain communicates with the S-domain of SRP during recognition of the RNC and its targeting to SR. To examine these, we will establish Forster Resonance


Energy Transfer (FRET) assays that enable to monitor individual molecular interactions in the SRP pathway at high resolution. SR protein has been expressed and purified; human SRP54 has been labeled with a Cy3b fluorescence probe. Upon successful fluorescence labeling of SR, monitoring FRET between SRP and SR will provide insights into their interaction. Using the FRET pair of SRP9 and the RNC, the energetics of the SRP-RNC binding will be investigated to determine the mechanistic characteristics of the Alu-domain in SRP-mediated protein targeting pathway.

Random Approach For Distributed Reed-Solomon Code Construction Using Balanced Column Sparsest MDS Code Zihan Liu Mentor: Babak Hassibi

This project looks at the construction of distributed Reed-Solomon code, expecting this Reed-Solomon code's subcode to be full rank and to obtain the upper bound of at the meantime. Especially, we concentrate on the balanced column sparsest MDS code, and anticipate to randomly assign the positions of zeros in each row, or equivalently, the permutations of field elements of Reed-Solomon code columns. By revealing the generator matrix to both ends of the channel after this random construction, we could decode it efficiently.

Mechanoluminescent Inverse Opals: Design and Fabrication Peter Lommen Mentors: Julia Greer and Victoria Chernow

Photonic crystals, by virtue of their nanoscaled periodic architecture, act as natural optical bandgaps, selectively amplifying certain wavelengths of light. Photonic crystals occur naturally in nature, often in the form of opals, made of nano-sized spheres of silica (SiO 2 ) which self-assemble into a hexagonal close-packed lattice structure. The structural inverse of an opal can be created by infiltrating the gaps with a polymer mix, and then etching out the silica spheres of the original opal. These inverses, so-called “inverse opals” are studied by multiple projects undertaken by the Greer group. This project's focus is the design and fabrication of a mechanoluminescent photonic crystal, which is an elastomer-based inverse opal, functionalized with nanocrystals of metal-doped zinc sulfide, a mechanoluminescent material. When subjected to mechanical stress, the zinc sulfide particles emit light of a specific wavelength, which can then be amplified by the inverse opal's structure. After successful fabrication, the inverse opal will be optically characterized and fine-tuned for optimal performance.

Life Cycle Analysis of Electric Vehicle Systems Mark Lorden Mentor: Guillaume Blanquart

One of the most important considerations to take when planning a sustainable vehicle system is the environmental impact of the vehicle. Life cycle analysis is a method of quantifying the environmental impact of an engineering system, taking into account the power efficiency of the system, as well as the environmental impact of the materials used to construct the system. This analysis can then be used to find ways of lessening the environmental impact of the system.

In Vitro Glucose Analysis Utilizing Raman and Millimeter Wave Spectroscopy Nathan Louie Mentors: Andrei Faraon and Peter Siegel

Accurate, non-invasive methods for continuous monitoring of blood glucose levels has been a long-term goal for many healthcare researchers and companies. The current gold standard for measuring glucose involves direct sampling of the blood. This means continuous readings all over the body is not possible. By coupling the theory of transmission loss in millimeter waves as a determinate for glucose concentration and optical Raman Spectroscopy to analyze the spectral signal of the solution it is possible to determine the concentration of glucose in a solution for a period of time. The millimeter wave portion is set up with a network analyzer and waveguides to send an initial frequency through the sample. This will result in a lower frequency return. The Raman optical set up will be using an excitation source, a laser, and reading the resulting spectral signal that is reflected off the sample. The Raman spectrum of the scattered excitation coupled with the transmission loss will then be analyzed to determine and more specific result considering the signal from both techniques are fairly weak. As of now, we have only obtained results for the millimeter wave portion and, like predicted, the signal is almost the same as the original frequency. However, we do plan on moving forward to testing on rats after we complete the Raman spectroscopy of the glucose samples.


Characterization of Heavy Crude Oil Fractions by 13 C-NMR Spectroscopy Alison Lui Mentors: William Green, William Goddard, Soumya Gudiyella, and Lawrence Lai

Supercritical water (SCW) has recently been found to be an effective catalyst for the desulfurization and cracking of crude oil with less coke formation than current dry cracking methods. To better understand the role of SCW in this complex decomposition, we seek to quantify the rates of production and destruction of specific functional groups in crude oil and in the SCW reaction products. Here, we present carbon-13 nuclear magnetic resonance spectroscopy ( 13 C-NMR) as a promising method of heavy crude analysis. Unlike separation by gas or liquid chromatography, 13 C-NMR does not have restrictions on molecular weight or polarity and also provides information about the samples in terms of their functional groups. In this project, we investigated the feasibility of 13 C-NMR as a method of characterization for crude oil and determined the optimal parameters of spectra acquisition. In our heavy crude spectra, distinct aliphatic functional group peaks could be characterized; however, peaks in the aromatic and alkene regions were visible but broad and ill-defined. We remain optimistic that better definition can be achieved by increasing the number of scans taken for a single spectra and by modifying the processing parameters and conclude that 13 C-NMR still has promise as a crude oil characterization tool.

Design and Fabrication of Durable Nano Vacuum Triodes With Low Turn-On Voltages Daniil Lukin Mentors: Axel Scherer and William M. Jones

Four-terminal planar vacuum triodes with emitter-collector gaps under 10 nm were fabricated out of tungsten on sapphire. Devices display numerous desirable characteristics: maximum sustainable current of 0.5µA, modulation at 5V, gate and emitter leakage at base noise level, and no visible degradation after an hour of operation. Yield rate of 20% was obtained with our fabrication method. Vacuum triodes are expected to operate at high temperatures and high frequencies, the latter being particularly desirable for integration with on-chip photonics.

An Analysis of the Novel Cytoplasmic Streaming Patterns of Caulerpa Catherine Ma Mentors: Elliot Meyerowitz and William Gibson

It has long been accepted that unicellular organisms lack the complexity and evolutionary advantages that multicellularity entails. Caulerpa is genus of seaweeds that seems to defy this generalization. Even though members of the genus are unicellular, they possess metabolic complexity on par with that of multicellular organisms, can grow to be quite massive, and thrive in many underwater environments. Studies have shown that the cytoplasmic streaming patterns of Caulerpa are relatively distinct from those of typical multicellular plants, and we speculate that studying them can give us insight into how Caulerpa can prosper albeit its unicellularity. To determine its unique cytoplasmic contents, we cultivated Caulerpa prolifera, extracted its DNA and mRNA, and implemented many bioinformatics algorithms on the data to assemble the genome and transcriptome of the species and discern its gene expression. We also took images of C. prolifera leaf segments and utilized many image processing techniques to quantify the cytoplasmic flow patterns in the leaves of the plant. We ultimately hope to uncover cytoplasmic elements that contribute to Caulerpa’s unprecedented success in the wild, and subsequent studies of the plant will focus on how these elements can provide unicellular organisms with the survival advantages of multicellular organisms.

On-Demand Power Source for Medical Electronic Implants: Harvesting Energy From Acousto- Mechanical Vibrations of Human Vocal Cords Yuan Ma Mentor: Hyuck Choo

Microelectromechanical systems (MEMS) and microelectronics have presented a wide variety of medical applications due to the convenience of their small size and low power consumption. However, since these implantable electronic devices must be continuously running in the background, their batteries ultimately need to be replaced or recharged, a process that leads to additional invasive surgery and discomfort to patients. Therefore we will investigate and create a device that can harvest energy from the acousto-mechanical vibrations of human vocal cords. After characterizing the range of human voice frequency, we are designing and building a piezoelectric energy harvesting setup that converts the mechanical energy of vibrations from human vocal cords at resonance frequency into electrical energy. Using a system of multiple piezoelectric cantilevers placed in contact with the skin, we can generate a small amount of power from vibrations resonating throughout the skull. Our energy harvesting setup will serve as a power source to supplement or replace the batteries in implantable microelectronic sensors.


Kepler Target Analysis Through Light Curve Examination and Spectral Energy Density Modeling Mason MacDougall Mentors: Rachel Akeson and David Ciardi

Each K2 campaign carried out by the Kepler Space Telescope has continued to add to the list of exoplanet candidates found through transit detection amidst stellar light curves. The majority of such planets have been discovered using programs requiring a minimum of 3 events to confirm a periodic transit. Here, we discuss our efforts to visually identify remaining single- and double-transit events within K2 campaigns 1-3. Our goal is to analyze the light curves of the brightest 500 M-dwarfs and all stars with kepmag <10 from each of the specified campaigns in search of long-period planetary transits. We have constructed several filtering tools which have facilitated our detection of 12 candidate eclipsing binary star systems thus far. We have likewise performed stellar spectral energy density modeling for the ~100,000 K2 targets through campaign 5. Such models are used to obtain stellar parameters including surface gravity and effective temperature. Our aim for this portion of the project is to verify the accuracy of our modeling method and construct a database for our models along with stellar parameters established from these models. This database will offer a convenient location for finding the necessary stellar parameters to conduct follow-up research on potential planets.

Structural Studies of HIV-1 BG505 SOSIP.664 Trimer/8ANC195 Fab/Soluble CD4 Complexes Sumana Mahata Mentors: Pamela J. Bjorkman and Haoqing Wang

Human immunodeficiency virus type 1 (HIV-1) is a lentivirus that threatens the public health of millions worldwide. HIV-1 has been extensively studied, and its high mutation rates and glycan shielding prevents most individuals from exhibiting any neutralizing antibodies against it. Recently, a few papers have described a soluble, stable and cleaved HIV-1 gp140 trimer, known as BG505 SOSIP.664 gp140, whose structure closely resembles the native state of the HIV-1 envelope glycoprotein. 8ANC195 is a broadly neutralizing antibody (bNAb) whose target includes both the gp120 and the gp41 subunits of the HIV-1 envelope spike. We seek to investigate the structure of complexes between the antigen-binding fragment (Fab) of 8ANC195 and BG505 SOSIP.664 trimer in different conformations. We will generate and purify each component, form and purify complexes, and then collect single particle data on the complex via negative-stain single particle electron microscopy. We will then process the micrographs collected in order to determine the structure of the BG505 SOSIP.664/8ANC195/soluble CD4 complex. We hope to confirm that the neutralizing mechanism of 8ANC195 involves keeping the trimer in the closed conformation, thus preventing it from undergoing conformational changes required for membrane fusion, and to prove that 8ANC195 is able to neutralize the trimer in different conformations.

Predictors for Persistent Atrial Fibrillation Over Paroxysmal Atrial Fibrillation: A Cross-Sectional Analysis of Health eHeart Chaitanya L. Malladi Mentors: Gregory M. Marcus and Justin Bois

Numerous research studies have analyzed risk factors for atrial fibrillation—a serious heart condition that affects about one percent of the population in the United States. There are two main types of AF: persistent and paroxysmal. Quality of life for patients has been shown to be worse in those with persistent AF versus those with paroxysmal AF. Additionally, those with persistent AF are more frequently treated with procedures such as cardioversions and potentially toxic anti-arrhythmic drugs. Understanding risk factors for each type of AF may help health care providers better advise their patients on lifestyle modifications that can mitigate each risk.

Through analyzing the atrial fibrillation patient pool in UCSF’s Health eHeart study, we examined age, sex, race, hypertension, CAD, CHF, diabetes, sleep, family history, and alcohol consumption as predictors of type of AF. In a multivariable model adjusting for age, sex, race, CHF, and diabetes, we found that increasing age (OR of 1.25 per decade increase in age) is a predictor. Additionally, being male as opposed to female has an OR of 1.47. People of the Asian or Pacific Islander race have a lower risk of acquiring persistent AF (OR of 0.297) compared to whites. Lastly, congestive heart failure (CHF) is also a statistically significant predictor (OR of 1.76) of persistent AF. This result accords with previous research indicating how structural damage to the heart strongly correlates with persistent AF. Our analyses on sleep quality, alcohol consumption, hypertension, CAD, diabetes, and family history yielded no statistically significant correlations for predicting type of AF.

Fourier Transform Spectrometer System Upgrade and Complex Impedance Studies of a Semiconductor Bolometer Aashrita Mangu Mentors: Suzanne Staggs and Jamie Bock

In an effort to understand the origin of the universe by accurately imaging cosmic microwave background (CMB) radiation emitted right after the Big Bang, the Princeton experimental CMB group has been working on numerous experiments, including the current Atacama B-mode Search (ABS) and Atacama Cosmology Telescope (ACT), as well as the Multimoded Survey Experiment (MuSE) using the detector developed for the proposed Primordial


Inflation Explorer (PIXIE) satellite mission at NASA Goddard Space Flight Center (GSFC). Both multimoded optics and the Fourier Transform Spectrometer (FTS) have provided increased sensitivity for CMB polarimetry, allowing better detection and characterization of the polarization signal from an early, inflating Universe. This two part study

is the result of the coupled necessity of multimoded optics and the FTS: the objective of the first part is to develop

a new user interface (UI) for the FTS to determine bandpasses of required detectors and components by

incorporating a producer-consumer state-machine software structure; the second part is to model the frequency- dependent complex impedance and voltage responsivity of multimoded bolometers. While the updated UI will aid in more efficient data collection and control of the FTS for the user, the latter is another step in the optical testing required to further advance the MuSE and PIXIE projects and develop a better understanding of bolometer theory.

Mechanics of Peeling of Heterogeneous Medium Om Vijay Margaj Mentors: Guruswami Ravichandran and Owen Kingstedt

The measurement of interface properties between an adhesive layer and substrate can be studied through the peel test. In this study thin extensible strips of PDMS are peeled from rigid substrate. The substrate consists of patterned transparencies fixed to a rigid base. Heterogeneities are included in the systems through linear patterning of the transparency substrate by laser printing lines on transparency. The adhesion energy of the PDMS- heterogeneous substrate system is examined with respect to width and spacing of the linear patterns (i.e. 1mm, 2mm and 4mm), and orientation of the peel front with respect to the linear patterns (i.e., 0°, 22.5°, 67.5°, and 90°). During the peel test the peel front position, velocity and peel angle are monitored. It is observed that there are oscillations in the peel force, and thus the adhesion energy, when the peel front travels from a region of higher adhesion energy to a region of lower adhesion energy and vice versa.

Characterizing 7,795 Contact Binaries Using Survey Data Franklin Marsh Mentors: Thomas Prince and Ashish Mahabal

Contact Binaries are one of the most common types of eclipsing binary stars. In a contact configuration, two stars are so close together, their photospheres touch. Until recently, only a small number of these systems have been studied in detail. We aggregate data from the Catalina Real-Time Transient Survey, Palomar Transient Factory, and Sloan Digital Sky Survey for the purpose of physically characterizing a large number of contact binary systems. Our sample of nearly 8,000 systems allows the contact binaries to be studied as a population. We find that there is an overabundance of binaries with photospheric temperatures of 6200 to 7000K, which have low mass ratios. We show that starspots are the cause of the vast majority of contact binary light curve asymmetries (the O’Connell effect). Our sample is able to better define the period-temperature relationship for contact binaries, as well as provide constraints on period change rates. Our project is an example of the science that can be performed with publicly accessible survey data. In the future era of large, open access surveys, researchers will collaborate globally, vastly expanding our knowledge of eclipsing binaries and other stellar systems.

An Information-Theoretic Perspective on Fluctuation Relations in Nonequilibrium Statistical Physics Timothy Maxwell Mentors: John Preskill, Ning Bao, and Nicole Yunger Halpern

Recent advances in nonequilibrium statistical physics have given physicists powerful tools for studying systems far from equilibrium. We explored two recently discovered inequalities in nonequilibrium statistical physics: a fluctuation relation by England from 2013, and a generalization called the "Bayesian Second Law of Thermodynamics" by Bartolotta et al. in 2015. These inequalities put a lower bound on the entropy produced by a physical process. We used analytic methods to show that England's result can be derived from the Bayesian Second Law under certain assumptions. We used numeric methods to find that the Bayesian Second Law often provides a tight lower bound on the entropy produced by the physical process in question; England's result provides a looser bound than the Bayesian Second Law, but it is easier to apply. Our work will give the scientific community a better understanding of these newly discovered fluctuation relations.

Pattern Order in Photoelectrochemically Grown Se-Te Films in Response to Light Intensity and Deposition Time Richard May Mentors: Nate S. Lewis and Azhar Carim

Current photolithography faces difficulties in generating subwavelength features due to the diffraction limit and in producing intricate three-dimensional structures due to the need for multiple masking and deposition cycles. Recently, photoelectrodeposition of Se-Te semiconductor films has been shown to enable the growth of periodically patterned structures as a function of illumination conditions. Photoelectrodeposited films were generated with a series of illumination intensities (5 to 50 mW cm -2 ) as well as series of deposition times (30 to 300 s). Film morphology was assessed via scanning electron microscopy. Fourier analysis was utilized to determine the average lamellar periodicity in the resultant films as well as magnitude of the distribution of periodicities about this mean.


The lamellar periodicity was found to be independent of the illumination intensity but found to scale proportionally with the deposition time. The distribution of lamellar periods was also found to be independent of the illumination intensity but was found to tighten with increasing deposition time. Additionally, contrast thresholding of the SEMs was used to determine the average fraction of film unpatterned due to dark growth processes during the deposition. The unpatterned area was found to decrease with increasing light intensity and be mostly eliminated after a threshold intensity.

Optimizing Self Organizing Map Templates for Determining Galaxy Color Distributions and Photometric Redshifts Daniel McAndrew Mentors: Peter Capak and Daniel Masters

The elusive nature of dark matter, dark energy, and the large-scale 3-dimensional structure of the Universe remain unknown, but they are prime targets of astrophysical investigation. Upcoming weak gravitational lensing experiments from the \textit{Euclid}, \textit{WFIRST}, and other large surveys aim to map the geometry of the Universe to demystify these monumental enigmas. To do this, the astrophysics community must calibrate

photometric redshifts for $\gtrsim 10^9$ galaxies. To deal with these seemingly daunting calibrations, we consider

a machine learning technique, the self-organizing map (SOM) algorithm. The SOM is a neural network that maps

the distribution of data in a high-dimensional space onto a lower-dimensional representation. We use the SOM to characterize the empirical distribution of galaxies in color space, since a robust mapping of this distribution will help develop a color-redshift relation for calibrating photometric redshifts. To improve the performance of the SOM, we optimize a template set of galaxy spectral energy distributions (SEDs) on which to train the SOM. This is done by iteratively optimizing ``eigenspectra" obtained by using the statical method of Karhunen-Loeve (K-L)

transformations on photometric data. We also introduce an error scaling factor to our implementation of the SOM algorithm, to reduce the influence of faint objects with large photometric errors, mitigating the error and improving the smoothness of the map.

Describing the Spatial Distribution of the Urban Built Environment With Networks Sean McKenna Mentors: Steven Koonin, Kaan Ozbay, and R. Michael Alvarez

Though the population and geographic extent of cities varies greatly, some urban experiences are ubiquitous, such as crowded streets or closely-packed coffee shops. To a scientist, this suggests scaling laws inherent to urban growth. Recent work has investigated the extent to which scaling is present in cities, investigating metrics of economic growth, public safety, and infrastructure investment. This study investigates urban pedestrian networks;

it looks for scaling relationships in the spatial distribution of an urban area’s built features across its network.

Specifically, distance relationships for stores, amenities, and emergency services are presented for several United States metropolitan areas. Additionally, further characteristics of the distribution of real estate in New York City are presented. Finally, an attempt will be made to show that a marriage of the monocentric city model with standard land-developer assumptions of building characteristics can predict the geographic extent of metropolitan areas.

The Effect of Sleep on the Avoidance Response of C. elegans Katelyn McKown Mentors: Paul Sternberg and Ravi Nath

Sleep is important for survival and health, yet little is known about human sleep. Because many genes are homologous between Caenorhabditis elegans and humans, characterizing C. elegans sleep can lead to a better

understanding of the genetic basis of sleep and perhaps lead to better treatment for sleeping disorders. Stress by heat shock can induce a quiescent, sleep-like state in C. elegans. ALA, a neurosecretory cell, is necessary for this sleep-like state. Of the known characteristics of sleep, I have focused on studying the response latency of

C. elegans to 1-octanol, an aversive stimulus. To accomplish this, I have conducted avoidance assays on awake

and sleeping C. elegans. These series of experiments have allowed me to determine the dose-response curve of

C. elegans to 1-octanol. Additionally, I performed in vivo calcium imaging experiments on sensory neurons to

further study the activity of C. elegans neurons in awake and sleeping animals.

Effects of Menthol and Nicotine on the Upregulation and Stoichiometry of α6* and α4* nAChRs Emily Meany Mentors: Henry Lester and Brandon Henderson

Neuronal nicotinic acetylcholine receptors (nAChRs) are ion channels formed by pentamers of α(2-10) and β(2-4) subunits which regulate the release of acetylcholine, dopamine, and other neurotransmitters. At the level present in tobacco products, the agonist nicotine upregulates high sensitivity α4 (2 β23 and α6β2β3 nAChRs. In addition to nicotine, about 90% of cigarettes contain menthol flavorant, which has two primary stereoisomers (denoted plus and minus). As both forms are found in menthol cigarettes depending on manufacturing process, we are interested in any differences in effects between them. Neuro-2a cells and mouse brain slices were used to investigate changes in stoichiometry and upregulation due to each stereoisomer alone and in combination with nicotine. Stoichiometry


was investigated using Normalized Förster Resonance Energy Transfer (NFRET) while nAChR export to the plasma membrane, a step in upregulation, was studied with quantification of ER exit sites (ERES). Neuro-2a cells were transiently transfected with fluorescently tagged α4 subunits for NFRET and ERES experiments and mice containing fluorescent α4 (mCherry) and α6 (GFP) nAChR subunits were used for in vivo NFRET assays. We expect that the plus form of menthol will be less potent than the minus form and that menthol will upregulate the less sensitive α43 β2 (2 and α6β2(non-β3) forms, which would support previous data and could contribute to habituation and tolerance in combination with nicotine.

Examining the Transition Into Many-Body Localization in One Dimensional Quantum Spin Chains Alexander Meiburg Mentor: John Preskill and Jenia Mozgunov

We consider the Hamiltonian given by H(s) = sΣ i σ x i + (1-s) (Σ i J i σ z i σ z i+1 + Σ i h i σ z i σ z i+1 ) on a 1D quantum spin chain. The J i 's and h i 's are drawn randomly and independently from the uniform distribution on [-1,1]. At s=0, this

is a set of non-interacting spins with a x-oriented external field; at s=1, it consists entirely of z-interaction terms at

random on-site potentials. It was previously known that for intermediate s (~ 0.5) this has spin waves that propagate and non-zero heat conductivity, whereas at s=1 it enters a many-body localized phase and there are no travelling waves. We try to characterize the transition from this extended phase to localized phase through a variety of parameters about the system, including ground state energy gap, magnetic susceptibility, von Neumann entanglement, a level-clustering parameter “r”, and behavior under adiabatic evolution.

Characterization of Water-Jet Induced Gas Ionization by Optical Emission Spectroscopy Sean A. Mendoza Mentors: Mory Gharib and Francisco Pereira

A High-speed distilled water-jet, shown to generate regions of air excitation, is characterized with optical emission

spectroscopy techniques. It is determined that the excitation energy of the external charge on a neat water jet

produces an ionized region of air around the area of impingement on dielectric crystal materials. The ionized region

of air emits light spectra identical to that of an electric air corona. When air is replaced with other gases, an

equivalent ionization spectra is observed. When the gas environment is changed to a gas with a higher ionization energy however, gas ionization is instead replaced by non-ionizing gas excitation. Mechanisms of action for water-

induced air ionization are discussed.

Finding Stationary Solutions to the Chemical Master Equation by Gluing Graphs at One or Two Vertices Xianglin (Flora) Meng Mentors: Richard M. Murray, Ania A. Baetica, and Vipul Singhal

Biological systems display significant stochastic behavior at low molecular numbers, which requires stochastic modeling. The chemical master equation (CME) is a stochastic model that depicts a continuous-time Markov process whose state space comprises possible combinations of the numbers of molecules of each species. However, stationary solutions to the CME are generally unknown. Mélykúti et al. recently proposed a probability technique that derives the stationary distribution of a continuous-time Markov process whose state space can be constructed

by gluing two finite, irreducible state spaces at one or two vertices. We study the applicability of the technique to finding stationary solutions to the CME. We find the set of reactions whose stationary distributions are obtainable using the technique, which includes reactions whose state spaces are trees of trees and cycles. In addition, we propose a recursive algorithm that minimizes the computation cost when the technique is applied to closed reaction systems with three species. In particular, closed systems with three species and two reversible monomolecular reactions have state spaces that are triangular grids, and we derive explicit expressions for their stationary distributions. Knowing the stationary solution to the CME will help inform experimental design as well as the design

of distributions.

Binding Interactions of the ATP-Independent Disaggregase cpSRP43 With Its Substrate Emily Miaou Mentor: Shu-ou Shan

Membrane proteins contain hydrophobic regions that cause them to be prone to aggregation in aqueous environments, resulting in difficulties maintaining a fully-functional post-translational state as they move through aqueous cellular compartments. Novel chaperone activity has been identified in the chloroplast signal recognition particle (cpSRP), which contains a subunit cpSRP43 that has been found to be capable of preventing the substrate, light-harvesting chlorophyll-binding proteins (LHCPs), from aggregating in solution as well as resolubilizing aggregated proteins in vitro using extensive binding interactions rather than ATP. This project sought to better understand the interaction between cpSRP43 and LHCP by mapping the binding sites of LHCP on cpSRP3. Potential binding residues on cpSRP3 were identified, site-directed mutagenesis was performed to introduce single-cysteine mutations, and protein expression and purification were done to obtain the mutant chaperones. Light-scattering assays and anisotropy showed that many of the mutants had defective binding with LHCP, but a few neutral mutants were identified that will be used for future alkylation-protection experiments. Additionally, the activity of


some soft mutations may be restored by inserting the mutations into a superactive mutant, thus allowing alkylation-protection experiments to be performed on those mutations as well. Mapping the cpSRP43-LCHP interaction helps create an important model for understanding how cells process aggregation-prone membrane proteins, such as those involved in neurodegenerative diseases including Alzheimer’s, Parkinson’s, and Huntington’s.

Mechanical Behavior of Three-Dimensional Tensegrity Nanolattices Talia Minear Mentors: Julia Greer and Arturo Mateos

Tensegrity systems are lightweight structures that exhibit a high weight-to-strength ratio due to an efficient distribution of mass and force among its structural elements. Literature exists on macroscopic tensegrity systems, but very little exists on the mechanical behavior of tensegrity structures at the nanoscale. We investigate a new class of structural metamaterials composed of tensegrity architecture, which have the potential to enhance mechanical properties and simultaneously take advantage of size effects at the nanoscale. Minimal, regular, tensegrity lattices made out of polymer were fabricated using two-photon lithography and various arrangements of the lattice unit cell were fabricated. Compression experiments were performed and the mechanical properties and deformation of these nano-tensegrities were studied.

Probing Quasar Physics With Variability and Machine Learning Catalina-Ana Miritescu Mentors: Matthew Graham and George Djorgovski

Quasars are cosmic objects which have long been known to be variable sources. Their variability is being monitored by digital sky surveys, the largest open time domain survey currently operating being the Catalina Real-time Transient Survey (CRTS). A new variability-based method has been developed to analyze variable objects: the Slepian Wavelet Variance (SWV). The SWV is a statistical characterization of a large set of time series (light curves). In this project, we used SWV on a subset of CRTS data to determine the general trend of each known subtype of quasars (classes determined spectroscopically) and to identify possible outliers. From the outliers identified, we selected as objects warranting further study the ones whose light curves had unusual appearance. Using the specific behaviors for each class determined from the subset, we can extend the search for objects of interest to the whole CRTS database.

Development of Biligand Capture Agents to Target Plasmodium falciparum Histidine-Rich Protein II (PfHRP2) for Rapid Malarial Diagnosis Anvita Mishra Mentors: James Heath and JingXin Liang

Currently, malarial rapid diagnostic tests use antibodies to detect Plasmodium falciparum histidine rich protein II (PfHRP2), a biomarker for Plasmodium falciparum malarial infection. Malaria caused by this species is especially deadly and has the highest rate of fatality. However, these antibodies are too costly and too thermally and chemically unstable to be used viably in third world countries. Thus, the Heath lab is developing an antibody-free rapid diagnostic test for the diagnosing malaria by developing protein capture agents which can target the entire PfHRP2 protein.

Macrocylic peptides against distinct epitopes of PfHRP2 have been developed. Nevertheless, we are aiming to develop capture agents with higher binding affinity than the monoligands in order to develop accurate tests which have a low limit of detection. My work involves increasing the binding affinity of the capture agents by linking two PfHRP2 monoligands to create biligands. We want to test a cooperativity hypothesis to see if binding multiple sites simultaneously with an optimized linker will yield better affinity. The PfHRP2 binding affinity of the biligands was evaluated and compared to the monoligands through colorimetric enzyme-linked Immunosorbent assays (ELISAs). This report describes in detail the procedure to synthesize these biligands, along with the process to find the best biligand binders for PfHRP2.

Investigation of Neuronal Populations Controlling Thirst Jisoo Mok Mentors: Yuki Oka, Vineet Augustine, and Nikki Cruz

The fluid homeostasis is the set of processes that regulate the salt and fluid balance of the body. When this balance shifts, several regions in the circumventricular organs (CVO) of the hypothalamus are activated, and the stimulation of specific brain regions can lead to changes in drinking behavior. The Oka Lab is currently investigating the subfornical organ (SFO) and the organum vasculosum of lamina terminalis (OVLT) to discover a molecular and genetic mechanism behind this brain-body interaction that controls the fluid homeostasis and hence influences that drinking behavior. Although the Oka lab has recently demonstrated that the two regions mentioned above govern the balancing of the fluid homeostasis, it is still unclear which neuronal population is involved. The lab has been utilizing the optogenetics and immunohistochemistry to find the neurons that trigger or sense the changes in the


fluid homeostasis and to understand the genetic background. One of the neuronal markers, ER81, which could be tied with the fluid homeostasis, has been identified with the immunohistochemistry technique. Further investigation of the SFO and the OVLT and search for new neuronal markers will offer better understanding of how the mouse brain governs the drinking behavior and the fluid homeostasis.

Development of Tunable Mammalian Synthetic Transcriptional Regulators for Biomedical Applications Andrew Montequin Mentors: Ahmad Khalil and Michael Elowitz

Previous research has led to the development of a new class of synthetic transcription factors (sTFs) based on programmable zinc finger domains to precisely control gene expression and enable orthogonal recruitment of proteins to site-specific locations in the yeast genome. The goal of this project is to advance these tools and frameworks for logically controlling genes in mammalian systems for next-generation biomedical applications. To this end, we developed a catalog of synthetic mammalian regulatory elements, which we used to create novel zinc finger-based sTFs. We characterized the ability of these sTFs to regulate reporter genes driven by engineered promoters in HEK293 cells and explored transcriptional outputs for a variety of different transcriptional activation domains and DNA binding affinities, which we modulated via mutagenesis of conserved residues in the zinc finger backbone. Ongoing work is being done to engineer the conditional expression of these novel sTFs based on endogenous signals, such as hypoxia or [T-cell activation/signaling], which could hold promise for genetic tools for cell-based therapy.

Vacuum Technology for Applications in Optoelectronics and Novel Environments Aadith Moorthy Mentors: Axel Scherer and William M. Jones

Novel miniaturized vacuum triodes and vacuum-based photodetectors, both of which utilize field emission of electrons, were studied in this research work. The nano-scale vacuum triodes were fabricated using advanced lithography and their current-voltage characteristics were studied in detail, with emphasis given to their temperature variation and switching speed. The novel photodetector was proposed and analyzed computationally using the finite element method to discern suitable geometries for its most efficient function. The vacuum triodes fabricated and tested by these methods showed exponential current-voltage curves and when subject to temperature differences, showed an increase in emission with increasing temperature, as predicted by theory. They could also be switched efficiently using an oscillator circuit, showing their promise in future electronics. The photodetector computation model showed that an optimum field emission-based photodetector could be built using a slotted waveguide that had small teeth on the sides of width 60nm, height 40nm and separation 70nm. In addition, taking advantage of Surface Plasmon Polaritons (SPP) by placing small metal beads at the tips will enable efficient electron emission and subsequent photodetection. Overall, the results substantiate the promise of field emission in vacuum technologies for novel applications and environments.

Stability of the Immersed Boundary Lattice Green's Function Algorithm Ben Morley Mentors: Tim Colonius and Sebastian Liska

The Immersed Boundary Lattice Green's Function (IBLGF) algorithm is a new algorithm being developed at Caltech for simulating incompressible flow about an arbitrarily-shaped obstacle. The partial differential equations governing the flow are discretized in space to form a set differential algebraic equations (DAEs) that enforce the Navier- Stokes equations under the constraints of incompressibility and the no-slip boundary condition along the immersed surface. We show that the numerical solution of the linearization of these DAEs does not require significant additional stability conditions beyond those arising from the unconstrained equations. Using this and an analysis of the semi-discrete equations we argue that, in most situations, similar stability conditions are likely valid for the non-linear equations. The analysis presented is not specific to the IBLGF algorithm; it shows the stability of a commonly encountered class of linear DAEs in a manner that does not depend on any one choice of integration scheme, but instead applies to a range of projection based schemes.

Efficient Analysis of Sensitivity in Nucleic Acid Systems to Model Imperfections Rachael Morton Mentors: Niles Pierce and Nicholas Porubsky

The ability to program the pairing of nucleic acid bases is useful for many different applications, particularly for engineering self-assembling molecular structures and systems. Much preliminary work has been done in analyzing how nucleic acid strands interact, and in designing equilibrium base-pairing properties of an interacting nucleic acid strand complex. An algorithm for designing these latter properties has been developed. A key component of this algorithm is hierarchical ensemble decomposition: an ensemble is decomposed into “leaves”, where calculations are made, and merged upward until the original “root” level is reached. This study first involves testing the algorithm to examine how predictions alter when parameter values are perturbed. This was accomplished by perturbing random and engineered nucleotide sequences, and analyzing outlier sequences that produced results


deviating from what was expected. Next, this study investigates the effectiveness of using a less computationally intensive technique of estimating root level properties from leaf level calculations, and analyzes why certain nucleotide sequences yield incorrect predictions, and what components in the design algorithm cause this. Consistent error trends suggest a flaw in the algorithm, but show that utilizing leaf level calculations produces reliable results. Further investigations will examine possible indicators for sequences with poor leaf level calculations.

Locating Primordial Stars in the Outskirts of Nearby Dwarf Galaxies Eric Roger Moseley Mentor: Evan Kirby

The dwarf spheroidal galaxies Sextans and Ursa Minor orbit the Milky Way. Many dwarf galaxies exhibit radially decreasing gradients in their stellar metallicities. As a result, it makes sense to quantify the metallicity gradients in these galaxies and look in their outskirts for exceptionally metal-poor, primordial stars. The spectra of about 1000 stars total in the line of sight of these dwarf galaxies were analyzed for the quality of their spectra. Provided the spectra were good, we found the metallicities and heliocentric radial velocities of these stars and attempted to use these to determine their probabilities of galactic membership. In addition, if the stars lay too far from a best-fit color-magnitude isochrone, their membership probability was set to zero. For all but about a dozen stars, we have so far determined at the 99.99% significance level their galactic memberships and have found within error their metallicities. A few relatively distant and metal-poor stars had their spectra taken with the DBSP spectrograph on the Hale telescope, but this data has not been analyzed yet. More stars from the members may still be identified as good candidates for research into first generation, metal-poor stars.

Examining the Functional Differences of Drosophila FGFs Pyr and Ths by Examining in vivo Localization of Ths and Testing a TMD in Pyr Zane Murphy Mentors: Angelike Stathopoulos and Vincent Stepanik

In Drosophila, two Fibroblast Growth Factors (FGFs), Pyramus (Pyr) and Thisbe (Ths) help guide several coordinate cell migrations during embryogenesis. This includes formation and migration of the Caudal Visceral Mesoderm (CVM), a group of cells that establish the longitudinal visceral muscles. These two FGFs are closely related and overlap functionally, but are both required for efficient CVM migration. One structural difference that may contribute to this functional difference is a putative Transmembrane Domain (TMD) in amino acids 400-425 of Pyr which is not present in Ths. Using Splicing by Overlap Extension (SOE) PCR, an expression construct for a fusion protein was created from the native signal peptide of Pyr and its putative TMD ligated into fluorescent markers to test if the TMD is sufficient to localize proteins to the cell membrane in cell culture through transient transfection. To further explore the properties of Drosophila FGFs in vivo, antibody staining was performed on Drosophila embryos to visualize the localization of a mCherry-tagged Ths fusion protein under control of its endogenous regulatory sequences, as the distribution of Pyr and Ths have not yet been described. Using these data in correlation with the known localization of CVM cells could provide new insight into the role of each FGF in this process. This study also has general implications, showing that differences in evolutionary development of signaling molecules can lead to more severe functional and structural disparities.

Raman Spectroscopy of OH Vibrational Modes in Tourmaline Crystals Xinyi Nan Mentor: George R. Rossman

The OH vibrations of tourmaline were studied using polarized and unpolarized Raman spectroscopy as a potential proxy for investigation of the metal cation sites. The sample set consisted of 25 elbaites from 12 localities, 15 dravites from 11 localities, 8 liddicoatites from 3 localities, and 4 uvites, 3 schorls, 2 buergerites, 2 rossmanites, 2 foitites, 1 darrellhenryite and 1 olenite, all from different localities. Curve fitting of each polarized Raman spectrum revealed between 5 and 10 distinct bands in the region 3300 cm¹ to 3700 cm ¹. T h o u g h b an d s varied number, energy, intensity, and shape depending on the sample, consistent features were found within species for elbaite, dravite, uvite, schorl, buergerite, and foitite. Similarities were also found between elbaite and rossmanite, as well as between dravite, uvite, and schorl. The OH spectral features of buergerite and olenite were significantly less intense than those of the other species studied, indicating a rough quantitative correlation with hydrogen content. These results coupled with FE SEM analyses suggest that Raman spectroscopy of the OH region alone could be used to distinguish between some tourmaline species and give valuable insight into chemical composition.


Electrical Impedance Tomography as a Novel Method of Assessing Vulnerable Plaques Anusha Nathan Mentors: Yu-Chong Tai, Shell Zhang, and Yuan Luo

Rupture of artherosclerotic plaques is the most common mechanism through which unstable angina, acute myocardial infarction, and sudden cardiac death occur. Current methods of locating these plaques include X-ray angiography and intravascular ultrasound, both of which are expensive and lack resolution and penetration depth. Electrical impedance tomography exploits the dielectric properties of biological tissues to distinguish lipids, i.e. plaques, from other tissues in the blood vessels. Using Flexible Flat Cable, electrode rings with 32 channels were fabricated to conduct inward and outward-facing EIT in a phosphate-buffer solution and in healthy and plaque- infested pig aortas. Swisstom software was used in conjunction with MATLAB EIDORS EIT algorithms to successfully image plaque-infested, pig aortal walls. The signal-to-noise ratio of the devices was measured to determine the efficiency of this specific implementation of EIT. These ex-vivo experiments serve as prototypes for in-vivo testing using a delivery catheter to insert a similar microelectrode device into rabbits to detect plaques on their aortal walls.

Analysis of Neocortex Tissue Derived from Induced Pluripotent Stem Cells to Study Pathogenesis of Human Lissencephaly Aishwarya Nene Mentors: Arnold Kriegstein, Marina Bershteyn, and Marianne Bronner

The human cerebral cortex is an immensely complex structure whose critical functions are disrupted in developmental disorders, such as human lissencephaly. Classical lissencephaly is a rare genetic disorder characterized by a smooth cerebral surface, mental retardation, and seizures. Current understanding suggests that lissencephaly is caused by defective neuronal migration, but there has been no human model to study lissencephaly. This project uses reprogrammed induced pluripotent stem cells (iPSCs) from healthy and lissencephaly patient fibroblasts to study early cortical development using three dimensional organoid cultures. The differentiated tissue was analyzed by time-lapse imaging and immunohistochemistry (IHC) to study neuronal migration. Consistent with previous data from mouse models, lissencephaly neurons were significantly deficient in migration, validating this novel model system. Furthermore, IHC analysis was used to characterize the cleavage angles of lissencephaly ventricular neural progenitors, namely radial glia cells. These studies revealed an increase in oblique and horizontal divisions, suggesting premature neurogenesis. Results from studies on human 3-D models of lissencephaly will help elucidate disease mechanisms, which may lead to the development of new therapeutic strategies.

Gas Vesicles as Functional Ultrasonic Reporters Suchita Nety Mentors: Mikhail Shapiro and Anupama Lakshmanan

Ultrasound is a widely used non-invasive imaging modality in biomedicine, yet its high spatiotemporal resolution has not yet been fully exploited for molecular imaging due to the lack of suitable contrast agents. Gas vesicles (GVs), hollow protein-shelled nanostructures from buoyant microorganisms, have recently been identified as a new class of ultrasonic reporters, and our present goal is to engineer GVs as functional imaging agents. We aimed to enable covalent attachment of any protein of interest to the GV surface by employing the genetically-encoded SpyTag-SpyCatcher protein-tagging system. SpyTag-coated GVs were prepared and reacted with fluorescent SpyCatcher proteins in vitro. Collapse pressure assays and ultrasound imaging indicated that covalent attachment of fluorescent proteins to the GV surface did not perturb GV mechanical and acoustic properties. GV fluorescence was confirmed by fluorescence microscopy, and the degree of labeling was quantified by SDS-PAGE. Ongoing efforts are focused on co-labeling GVs with multiple proteins (i.e. targeting peptide and fluorescent protein), thus establishing GVs as functional multimodal contrast agents.

Optimizing Synthetic Capture Agent Targeting G12D Epitope of Oncoprotein KRAS Rachel Ng Mentors: James R. Heath and Ryan K. Henning

Mutations in GTPase KRAS are frequently found in human cancers. In particular, G12D is the most frequent substitution mutation that disables GTP hydrolysis in oncoprotein KRAS. The GTP-bound KRAS remains functionally active and activates cascades of intracellular pathways that propagate cancer. Here, we employed in situ click chemistry to develop cyclic protein capture agents that not only have high binding affinity and selectivity for mutant KRAS(G12D), but also are stable chemically, biochemically, and thermally. Enzyme-linked immunosorbent assays at different KRAS concentrations produced saturation curves that provide EC50, a quantification of the capture agent’s binding affinity for wild type and mutant KRAS. Further medicinal chemistry is done to optimize the capture agent’s binding. We also conducted alanine scans, which determine which amino acids are necessary for binding or changeable. Additionally, we tested fluorinations at different carbon positions in the capture agent to increase the capture agent’ binding and lipophilicity.


Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL) Phuc H.B. Nguyen Mentors: Richard Murray and Yong Y. Wu

Violacein is a violet, pyrrolidone containing compound with anti-cancer, anti-fungal, anti-viral, and anti-oxidation properties. The pigment is natively synthesized by Chromobacterium violaceum. Nevertheless, its production is too expensive due to the strain’s low productivity. Reconstructions of this pathway in heterologous hosts have been done to improve the yield. The approach, however, suffered from buildup of intermediates and byproducts due to flux imbalances. In this study, Escherichia coli Based Transcription Translation Cell-Free System (TX-TL) was employed to sample various expression levels of the violacein pathway. TX-TL enables rapid modifications and prototyping of the pathway without complicated cloning cycles. Linear DNAs of the violacein pathway’s enzymes with 100 bps protection flanking sequences were expressed in TX-TL. The products were collected in different solvents and analyzed via UV-Vis absorption and LC-MS. Violacein production at different linear DNA concentrations of each enzyme were explored. We demonstrated that the violacein metabolic pathway has been successfully reconstructed in TX-TL. Different variants of the pathway were shown to produce different colored products. Violacein synthesis was confirmed using LC-MS. Design space exploration suggested a high expression of VioC and VioD would lead to an improved violacein production level. This result can be used for the future engineering of more efficient violacein producing E.coli strain.

Ramified Coverings of the Complex Projective Line With Semisimple Galois Groups Tian Nie Mentor: Dinakar Ramakrishnan

Let 1 be the complex projective line and C a smooth projective algebraic curve. Suppose that f: C 1 is a ramified covering of 1 with ramification locus in {0,1, }. Note that the fundamental group of 1 {0,1, } is ℤ ∗ ℤ, the free group of two generators. Hence any quotient of this free group can be realized as the Galois group of some curve C. Consider the Heisenberg group which is isomorphic to the matrix subgroup of 3 (/) generated by




also interested in the cusps of .







0 and 0






1 . We studied the defining equation of a curve which has as its Galois group. We are


Thermoelectric Power Generation From Waste Heat for Wireless Aircraft Sensors Nirmal Jayaprasad Mentors: Austin Minnich and Navaneetha Ravichandran

Thermoelectric devices can recover waste heat generated in jet engines and convert them into electricity. In this project, we design and fabricate a wireless sensor prototype powered by a thermoelectric generator (TEG), which can measure temperature, pressure and air quality in aircrafts. When a temperature gradient is applied across the TEG, it generates power to charge a rechargeable Lithium-ion battery. An LTC3108 power management circuit boosts the output voltage obtained from the TEG to meet the sensor power requirements and an over-charge protection circuit protects the battery and prevents unnecessary discharge in the absence of thermal gradients. The weight and size of the prototype was minimized since they pose critical issues in aerospace applications. The final prototype works for various temperature gradients as low as 40 0 C and the TEG successfully powers the wireless sensor which transmits data wirelessly over a network connection. Hence, this TEG-powered sensor is capable of being used in commercial aircrafts at remote locations where electric power is not readily accessible.

Identifying and Characterizing TCRs From Elite Controller T Cells Won Jun Noh Mentors: David Baltimore and Alok Joglekar

Current methods of HIV therapy, such as the use of antiretroviral drugs, are insufficient in fully suppressing HIV, as improvements must be made to effectively control latently infected cells and newly created drug-resistant species. Further investigation of HIV elite controllers, a rare subpopulation of HIV-positive patients known to be able to achieve broad control over HIV without any separate treatment, may contain the key to finding a potent, long- lasting treatment for HIV infections. Recent studies on elite controllers have shown that the controller status is related to CD8+ Cytotoxic T Lymphocytes (CTLs) that are restricted by certain HLA-B alleles. Our collaborators at Bruce Walker’s laboratory have shown that certain B27-KK10-specific CTL clonotypes from elite controllers exhibit higher potencies in eliminating HIV-infected cells. Considering that the only genetic differences between these clonotypes lie in T cell receptors (TCRs), we expect that controller status is related to the TCRs. In this study, we isolate and characterize elite controller TCRs by amplifying TCRα/TCRβ transcripts from the RNA extracted from B27-KK10-specific elite controller CTLs. We tested TCR surface expression levels through flow cytometry that utilizes B27-KK10-specific tetramers. TCRs that are able to recognize B27-KK10 will be studied further to test their abilities to control HIV.


The HED Meteorite Clan: Visible-to-Near-Infrared Spectral Diversity at 81µm Spatial Resolution Geraint Northwood-Smith Mentors: Bethany Ehlmann and Abigail Fraeman

The HED meteorite clan are mafic and ultramafic igneous rocks and impact breccias, widely thought to originate from the asteroid 4 Vesta. Eucrites are surface basalts or shallow cumulate gabbros, while diogenites formed in plutons at greater depth. Howardites are a regolith breccia of eucrite, diogenite and exogenous material, possibly including olivine. In 2011 the Dawn spacecraft provided visible-to-near-infrared spectra of the Vestan surface with 70m per pixel resolution, however this resolution is insufficient to reliably extract all mineral components. In this study, a collection of HED meteorites are analysed using the Ultra-Compact Imaging Spectrometer (UCIS) at approximately 81mm per pixel resolution. Methods of hyperspectral characterisation are developed to reveal their spectral diversity at this small spatial scale and their mineralogy is interpreted. Using these methods, a variety of mineral classes has been distinguished in the samples including olivine, feldspar, multiple classes of pyroxene, and glass/melt material. Spectral variation within these classes and between lithologies has also been characterised. Results from this study will inform interpretations of Vestan surface spectra, and provide evidence regarding the cooling history of Vesta, the identification of exogenous material and its interaction with native lithologies, and specifically the proportion of olivine that is exogenous.

Genome Editing in Sea Urchins: Developing CRISPR/Cas Systems for Strongylocentrotus purpuratus Ariel Margaret O’Neill Mentors: Eric H. Davidson and Miao Cui

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins comprise an adaptive immune system first discovered in Streptococcus thermophilus. The CRISPR/Cas system allows the bacteria to edit its own genome in order to develop resistance to a virus. Researchers have harnessed the genome editing potential of CRISPR/Cas to create transgenic lines of bacteria, yeast, mice, worms, zebrafish, and human tissue. However, the technique has not yet been adapted for use in sea urchins, a key model organism for the study of gene regulatory networks. This project is part of a continuing effort to develop a reliable and efficient method of generating transgenic lines of sea urchins.

A Determination of an Explicit Set of Coset Representatives for Double Coset Spaces Involving Open-Compact Subgroups of SO 5 Tynan Ochse Mentor: Pei-Yu Tsai

The Theory of Automorphic Forms is nearly ubiquitous in modern Number Theory. Studied originally for the connection with elliptic curves, the rich interplay of mathematics that takes place did not reveal itself until the 1960s, and in particular, with the formulation of the Langlands Program. Recently, a local newform theory has been developed by Pei-Yu Tsai for Split Special Orthogonal Groups of Odd degree. In order to understand the higher order cases, one first needs to understand the rank 3 case. The purpose of this paper is to determine a set of coset representatives for SO 5 and SO 7 by first computing the corresponding root system, which then can be used to deduce the structure of the Weyl Group, W. This information is key in determining the Bruhat global decomposition for these two algebraic groups. From there, the local newform theory for SO 2n+1 is used as a guide to work out a suitable set of coset representatives for particular double coset spaces. This can then be used to study the generalized Hecke Algebra for open-compact subgroups of SO 5 and SO 7 , which in turn provides arithmetic information on the coefficients of the corresponding automorphic forms.

Immersive and Collaborative 3D Data Visualization Sunwoo Oh Mentors: George Djorgovski, Ciro Donalek, and Scott Davidoff

With massive amount of data, it is becoming more and more important to find patterns hidden in it. Data visualization is a effective way to find that pattern, which is also coherent with human intuition. However, in visualizing the data in immersive 3D environment, we use data points in different shape classes and sizes. There are many factors to consider, such as lighting, perspective, color, shape, displacement that affect the perceived size of the objects. Therefore, I tried to make a standard for objects, or functions among the shapes that indicate the equivalent size of the objects. My program is made using Unity 3D based on C#, for users to scale the size of one of given objects compared to another fixed object, both objects given randomly in color, shape, displacement. The scaling should be done using Leap Motion and Oculus VR in immersive environment, to examine the effect of being in immersive mode correctly. I also studied further about general big data analysis and data mining, since the ultimate purpose of the project is in that context.


Synthetic Studies Towards the AEF Ring System of Talatisamine Ciara Ordner Mentors: Sarah Reisman and Victor Mak

Talatisamine is a complex, hexacyclic, C19-diterpenoid alkaloid that selectively blocks potassium ion channels. Thus, it could be used as a potential treatment for Alzheimer’s disease. In addition, talatisamine, as well as other diterpenoid alkaloids, have a variety of significant biological activities. The ultimate goal of this project is to develop an efficient synthetic route to talatisamine. The first step toward this goal is to access the AEF tricycle. Studies were conducted up to an epoxyketone intermediate of the proposed AEF tricycle synthesis. The five step synthesis of an epoxyketone intermediate was carried out on both small and large scales, providing an ample amount of material to explore subsequent chemistry. This project will continue in order to construct the AEF tricycle.

Statistical Analysis of Experimental Data on Laminar Flame Speeds Jeffrey Orenstein