Fall 2010 PHYS 170a – UNIVERSITY PHYSICS FOR THE LIFE SCIENCES – SGJM, August 30 Draft 1.

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PHYS 170 Syllabus, etc.
Yale University Department of Physics

The electronic version of this document (which is available in the PHYS 170 Resources on classesv2) contains a
number of important links which you can go to by clicking them.

What is “University Physics for the Life Sciences”?

Two recent reports, Bio 2010 (actually published by the National Academy’s Press in 2003), and “Scientific Foun-
dations for Future Physicians”, published by the American Association of Medical Colleges (AAMC) and the
Howard Hughes Medical Institute (HHMI) Scientific Foundation in 2009, have pointed out the increasing impor-
tance of quantitative skills for students who are planning biomedical careers. These are just the sorts of skills that
are traditionally acquired in physics classes, and the physics faculty who teach those classes, including myself,
like to say that “physics teaches students how to think”. Unfortunately, the selection of topics presented in intro-
ductory physics classes often owes more to tradition than to a consideration of what might be most relevant for
biology and medicine.
PHYS 170/171 is the Yale Physics department’s response to the issues highlighted in these reports. The goal of
PHYS 170/171 is to teach introductory physics for life science and pre-medical students in way that is actually
relevant for biology. Thus, in addition to covering the basics – force, energy, momentum, kinematics, Hooke’s
Law, electrostatics, Ohm’s Law, etc. – PHYS 170/171 will emphasize such topics as probability distributions,
diffusion, kinetic theory, microfluidics, DNA elasticity, etc. – topics that are actually important in biology!! – and
eschew topics such as rolling motion down inclined planes, special relativity, and gyroscopes – that really are not,
even though many of these topics are indeed fascinating in their own right. Nevertheless, an important aspect of
PHYS 170/171 is that it does serve as a route into the Physics major (or a Physics–Biology double major).
To acquire the skills we are talking about, no matter what the slant, requires practice, just as becoming skillful
in anything requires practice. As I am writing this, the 2010 Soccer World Cup has just concluded. Maybe you
watched some of the matches? You may learn how to play soccer a little by watching (certainly not the England
team, but maybe Spain), but to become a significantly improved soccer player requires that you practice kicking a
ball around on the field. In PHYS 170/171 you will practice quantitative skills in the time-honored fashion, namely
by doing Physics problem sets. Following unanimous advice from colleagues in medicine and the life sciences,
PHYS 170/171 will be a calculus-based course, that will stress basic science. However, as described below, we
are not in Kansas anymore...

What is physics?

The point of view, we will take in PHYS 170/171, is that the essential aspect of physics is that it constitutes a
mathematical description of the natural world, irrespective of whether the topic of interest is planetary motion or
cellular motion. The approach that physicists take in trying to gain insight into any system of interest is, first,
to abstract and simplify the system of interest as much as possible, but not more than necessary to retain the
features that are essential for an understanding of the phenomenon of interest.
Thus, for example, astrophysicists like to envision the Sun, Earth and planets as point particles when they dis-
cuss planetary motion, even though our presence in this room shows that this is certainly not precisely correct.
Nevertheless, this approximation permits many accurate predictons to be made about planetary motions within
the solar system, and so on.

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With an appropriate abstraction in hand, i.e. a model, physicists then invoke basic principles to create a mathe-
matical description, which is then solved to explain and ultimately predict the behavior of the system of interest.
When this is successful, it is a beautiful thing to put a theoretical curve through a set of experimental data.
What do I mean by a prediction? An example of a quantitative prediction might be the answer to the following
question: How effective do you expect an angioplasty procedure to be, in terms of increased blood flow, if the
procedure in question opens a patient’s partially occluded artery by increasing its interior radius by 20%? What’s
your prediction?

a. Blood flow increases by about 20%.

b. Blood flow increases by about 40%.

c. Blood flow approximately doubles.

“Models” in physics

As illustrated in this figure, in PHYS170/171, we may have occasion to represent DNA as a sequence, or as a
binding site, or as a charged rod, or as an elastic rod, or as a random walk, depending on what we are interested
in. Similarly, we may have occasion to represent a bacterium as a receptor array, as a hydrodynamic object, as
a random walk, or as an information processing network – as illustrated in this figure, or a solution in one of the
several different ways illustrated in this figure. Each one of these is a useful model for understanding a particular
aspect of the behavior of DNA, bacteria, or solutions, respectively.
Molecular biology text books and research papers are full of cartoons representing how biology happens. These
sorts of cartoons are indeed a strong statement by their authors concerning which features of a particular prob-
lem are important. Beyond the cartoons, however, the POV of PHYS 170/171 is that for many phenomena a
deeper understanding demands that the cartoons be represented mathematically, and the corresponding equa-
tions solved.

Goals
In order to have a number of definite goals in view from the start of the course, and to thereby motivate the
complete set of topics, that we will cover, the following is a list of some of phenomena that you will understand (in
some approximation) by the end of the year.
In the first semester:

• Force generation by actin polymerization and the physical basis of cell motility, as shown in this movie
Sometimes this mechanism is nefariously exploited by bacteria, such as listeria. (PHYS 170a).

• Microfluidic flow in vascular systems, for example fluid flow in the heart of a zebrafish embryo and in mi-
crofluidic devices for biomedical research. (PHYS 170a)

• Bacterial locomotion. The bacterial flagellar motor rotates, giving rise to a torque and a corresponding force,
that drives the bacteria along. (PHYS 170a)

• DNA elasticity and DNA packing in chromatin via histones, in sperm via protamines, and in viruses (bacte-
riophage). (PHYS 170a).

In the second semester:

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 • DNA force-versus-extension curve (PHYS 171b).

• Super-resolution microscopy. This is a new way of obtaining very high resolution microscope images. (PHYS
171b).

• The λ-switch, which is an example of feedback, control, and non-linearity. (PHYS 171b).

• The propagation of electrical signals along nerve cells (axons). (PHYS 171b).

• Electrostatic screening. (PHYS 171b).

Each one of these topics is biology or is biologically relevant, but in every case physics permits a new and
predictive understanding. For example, physics permits us to determine how does the velocity of a cell’s motion
depend on actin concentration and how does the velocity of a cell’s motion depend on load, i.e. if there’s an
obstacle that effectively pushes back on the cell with a force F , how is the cell’s velocity changed?

Why we study what we study

To achieve an understanding of these and other topics will involve the synthesis of a whole bunch of intercon-
nected ideas, that perhaps can best be appreciated via a diagram of the sort shown below (Fig. 1), which serves
to help to motivate why we will study the complete list of topics that we will study. This figure is one way to
represent syllabus for PHYS 170/171. Arrows represent intellectual connections.

To give one example of how apparently unconnected topics are actually connected: Early on we will cover “kine-
matics”, which is the motion of a particle subject to a constant acceleration. (If you had physics in high school, you
will have seen this material before.) Beyond the obvious, namely that this will permit us to understand the motion
of a particle subject to a constant acceleration, what we will learn concerning kinematics, when put together with
what we will learn about random walks, will be the starting point for a discussion of “kinetic theory”, which will lead
us to an understanding (a) of the connection between molecular diffusion and friction, and hence the physical
basis for electrophoretic separation, which is a key technique in modern molecular biology and (b) of viscosity,
which is an essential determinant of fluid flow through our own vascular system. More generally, kinematics will
allow us to appreciate the role of calculus in a simple physical setting, which will prove invaluable time and time
again, both in PHYS 170/171 and beyond.

Actually, my favorite example on this figure is the close connection between steady-state diffusion and electro-
statics, which are both described by the same equation, namely that belonging to Laplace. It follows that, if we
understand one, we understand the other “for free”, as we’ll see. Physicists love such analogies.

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PHYS 170a Syllabus and Approximate Timetable
• Week 1 – Sept. 1, 3: Introduction to PHYS 170/171. Vectors. Kinematics. Position, velocity, and acceleration.
Rate of change of a vector.

• Week 2 – Sept. 6, 8, 10: Rate of change in chemical reactions. Detailed balance. Force and Newton’s Laws.
Free body diagrams.

• Week 3 – Sept. 13, 15, 17: Terminal velocity. Momentum. Friction. Circular motion. Torque. Fundamental
forces. Fields.

• Week 4 – Sept. 20, 22, 24: Probability. Binomial distribution. Poisson distribution. Counting photons and
other events. Radioactive decay and other decays.

• Week 5 – Sept. 27, 29, Oct. 1: Random walks. Diffusion. Einstein relation. Electrophoresis. Centrifugation
and atmospheric density. Polymer conformations.

• Week 6 –
Oct. 4: Midterm Quiz 1, covering the material of Weeks 1–5.
Oct. 6, 8: Energy. Potential energy. Kinetic energy. Heat. Work. Hooke’s Law. Gravitational potential energy.
Electrostatic potential energy.

• Week 7 – Oct. 11, 13, 15: Steady-state diffusion and Poisson’s equation. Current and flux. “Ohm’s Law”.
Analogy between steady-state diffusion and electrostatics.

• Week 8 – Oct 18, 20, 22: Viscosity. Momentum transport. Reynolds number. Fluid flows. Microfluidics.
Vascular systems. Bacterial locomotion.

• Week 9 – Oct. 25, 27, 29: Biological filaments. DNA/actin elasticity. Surface tension. Surfactants and
premature babies’ lungs.

• Week 10 –
Nov. 1: Midterm Quiz 2, covering the material of Weeks 6–9
Nov. 3: Guest lecturer: Dr. Michael Choma 11:35-11:55 am, taking about microfluidic vascular systems.
Ideal gases and the ideal gas law. Temperature. Osmotic pressure.
Nov. 5: Atmospheric density re-visited. Microstates. Boltzmann factor.

• Week 11 – Nov 8, 10, 12: Monte Carlo simulations. Thermal ratchets. Heat engines.

• Week 12 – Nov 15, 17, 19: Actin polymerization. Force generation by actin polymerization. Entropy. Ther-
modynamics.

• Thanksgiving week. Whew!

• Week 13 –
Nov. 29: Guest lecturer: Prof. Tom Pollard, Dean of the Graduate School, 11:35 -11:55 am, talking about
actin.
Simple harmonic motion.
Dec. 1, 3: Damped SHM. Underdamped, critically damped, and overdamped SHM. Driven SHM. Q-factor of
a resonator. Coupled oscillators and normal modes.

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On-line lectures
There is a beautiful set of introductory physics lectures, delivered by my esteemed colleague Prof. Shankar for
PHYS 200, on-line at http://oyc.yale.edu/physics/fundamentals-of-physics/content/class-sessions.
Although this is PHYS 170 and Shankar is lecturing PHYS 200, in fact, his lectures have considerable over-
lap with the topics we will cover in PHYS 170, which I will point out on a case-by-case basis.

Mathematics in PHYS 170/171

Concerning the mathematics and the calculus, in particular, that will be used in PHYS 170/171, we will try to keep
it as simple as possible, but no simpler than needed. In this context, I will shamelessly quote what Shankar, says
concerning mathematics and calculus: “You may be in danger of learning something!” Thus, the philosophy of
PHYS 170/171 is that mathematics is an indispensible tool that we will not shy away from.
Similarly, a saw is an indispensible tool for a carpenter. Now, when building a deck, a carpenter could use a hand
saw, but it’s much faster and easier to use a power tool. In PHYS 170/171, we encourage the use of power tools
for mathematics. Specifically, we will encourage you to exploit Wolfram Alpha, which is a tremendous resource
for doing mathematics. Thus, if you are asked in PHYS 170/171 to solve a differential equation, you will be asked
to do it using Wolfram Alpha.

Memorizing equations in PHYS 170/171

Please do not think that physics is about memorizing equations. It is not. Now, there are some memorable
equations – the basics – that are so important and/or occur so frequently in introductory physics that it’s difficult
not to remember them, and life is just faster if you do remember them. I will tell you any such equations that I
think you should commit to memory, e.g. F = ma.
However, there’s not enough room in my head, at least, for all the equations we’ll encounter in PHYS 170/171.
So rather than memorizing equations, your goal for PHYS 170/171 should be to understand how to set about
deriving the equation(s) that you need in any particular circumstances from the basics.
It is important that you understand (1) that it is possible to construct a mathematical description of the natural
world, including the biological world, and (2) how to go about doing that, i.e. how to create a model, both for
examples, presented in PHYS 170/171, but also in examples that you may encounter beyond PHYS 170/171,
and (3) how to go about elucidating the model you have built, i.e. what does it mean – both the equations and
their solutions.

Computer simulations
Computer simulations constitute an essential component of how scientific research is now carried out. This is
increasingly true in the life sciences. To introduce you to this aspect of the scientific endeavor, we will ask you to
download a number of simulations, written in Mathematica, and run them yourself using Mathematica Player or
Mathematica, itself, which is available from Yale ITS. No prior knowledge of Mathematica is assumed or required,
and Mathematica Player is freely available for download.

Textbooks
Unfortunately, there’s no single textbook that covers all of the material of PHYS 170a. Therefore, we have three
required books:

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 • “Physics”, Fifth Edition, by Halliday, Resnick and Krane.
• “Reasoning about Luck: Probability and its Uses in Physics” by Vinay Ambegaokar.
• “Random Walks in Biology” by Howard Berg. This book is also available electronically from the Yale Library

Not required for the class, but useful for mathematics is

• ”Basic Training in Mathematics: A Fitness Program for Science Students” by R. Shankar.

What is missing from PHYS 170?

What is missing from PHYS 170, that you would see in a class such as PHYS 180 or PHYS 200?
• An in-depth discussion of momentum conservation and rocket motion.
• An in-depth discussion of rotational motion, including elliptical planetary motion, angular momentum, gyro-
scopes.
• All discussion of Special Relativity.

How then can you become a physics major, or a physics–biology double major, if these topics are not covered in
PHYS 170? Well, it’s the nature of all physics programs, including Yale’s, to cover similar material in successive
classes at a progressively more sophisticated level. So physics majors who have taken PHYS 170 will encounter
the missing topics in PHYS 401. Of course, there will be extra effort required then to catch up, but it will be
possible.

What is included in PHYS 170, that you won’t see in PHYS 180?
• Treatment of probability and its role in numerous phenomena.
• Treatment of random walks and diffusion, which are essential processes in biology.
• Treatment of low Reynolds number fluid flow, which is highly relevant to fluid phenomena occuring on mi-
crosopic length scales, such as bacterial locomotion.
• Treatment and discussion of the Boltzmann factor, which is the basis for understanding thermodynamics.
• Treatment of thermal ratchets which is highly relevant to the Second Law of Themodynamics and to molecular
motors and force generation by actin polmerization.

Administrative details
Switching from PHYS 180 to PHYS 170, and vice versa
The last date that students will be permitted to switch from PHYS 180 to PHYS 170 is October 11, shortly after
the first midterm in both PHYS 170 and PHYS 180.

TAs
The Head TA for PHYS 170 is Stephen Eckel. For administrative issues, please see Stephen.
The other TAs for this class are Alexander Cerjan, Peter Koo, Lawrence Lee, and Andrew Mack.

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Discussion sections
The TAs will run discussion sections on Tuesday evenings. You must sign up for a particular session and TA. The
Tuesday evening session will focus on Homework problems, and provide additional material that I didn’t have time
to cover fully in lecture.
Alex, Andrew, and Peter will hold their sections at 7-8pm on Tuesdays.
Lawrence and Stephen will hold their sections at 8-9pm on Tuesdays.
Attendance at the discussion sections is not mandatory. However, it will be possible to get extra points towards
your homework grade, based on your participation in discussion sections (and the help sessions), at the TA’s
discretion. In other words, not coming to recitation won’t hurt if you are doing fine with the homework without
coming, but if you find aspects of the homework difficult, participating in recitation will both help with the problems
and likely get you ”bonus” points.

Help sessions
In addition to the discussion sections there will be help sessions that will run 7-10pm on Sundays and 8-10pm
on Mondays. The Sunday evening help session will focus on a review of the previous week’s material, as it might
come up on Monday’s 10-minute in-class quiz.
If you have questions, the help sessions are an important opportunity to have the TAs answer them for you.

Office hours
The instructor and TA have office hours:
Simon: before class on Friday. Also, feel free to e-mail anytime.
Andrew and Peter: 10:30am-11:30, Thursdays in SPL29. Stephen: 3:30-4:30pm, Thursdays in the Sloane Third
Floor Lounge. Lawrence: 10:00am-11:00am, Thursdays in JWG 511.

Homework assignments
Homework assignments – problem sets, reading assignments, etc. – will be assigned weekly on Wednesdays,
with the problem sets due immediately before class on the Wednesday of the following week. You are encouraged
to discuss the homework problems with your class colleagues, and/or the TAs, but the solutions to every problem,
you must write up yourself.
Please be aware that the reading assignments are an essential component of the homework that you will be
expected to have done prior to the next week’s lectures and Monday quiz.

Homework grading
Solutions will be posted on classesv2 soon after the homeworks are due. To be fair to everyone, no late home-
works will be accepted for grading under any circumstances. If you need to miss doing a homework for a real
reason, please discuss the issue with me ahead of time, and we’ll work something out.
You must do all assigned problems. Of these, a limited number (typically 3) will be graded, selected after the
homework has been handed in. The reason for this procedure is to free up resources so that TAs can be
available to lead discussion sections, which is a more useful way to employ them in PHYS 170/171 than grading.
Your overall score on the graded homework problems will contribute 15% to your overall grade.

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Weekly Quizzes
To give you further confidence that you are keeping up with the material, every Monday, there will be a short (10
minute) in-class quiz on the previous week’s material. Don’t be late!! These quizzes will constitute 15% of your
final grade. No electronic devices of any kind are permitted. No collaboration of any kind in quizzes is permitted.
Any collaboration in quizzes will be considered to be a case of academic dishonesty, and as the Handbook notes,
For the sake of consistency, impartiality, fairness, and due process in treating cases of academic dishonesty, it is
essential that all such cases be referred to the Executive Committee rather than being settled privately between
instructor and student.

Midterm Quizzes
There will be two in-classes quizzes (midterms). The first midterm will be held on Monday, October 4. The second
will be on Monday, November 1. Each midterm will contribute 20% to your final grade. No electronic devices of
any kind are permitted. No collaboration of any kind in the midterms is permitted. Please contact the Instructor
immediately if these dates present a problem.

Final Exam
There will be a 3 hour final exam, worth 30% of the overall grade. The final exam will cover subject matter from
the entire semester. No electronic devices of any kind are permitted in the final. No collaboration of any kind in
the final exam is permitted. As per usual at Yale, you will have 3.5 hours to do this exam.

Final grade
Reiterating: the final grade for PHYS 170 will be based on the following percentages: 15% for the homework,
15% for the weekly quizzes, 30% for the final exam, 20% for each of the two midterms.
However, if you score higher on the final exam than on this weighted sum of your performance across the
semester, your grade will be based entirely on the final exam. Of course, not doing the required work throughout
the semester and relying on your final exam performance is a recipe for disaster, and is strongly discouraged.
The idea here is that if you do ace the final, we should not hold a weak performance early in the semester against
you, because you have demonstrated mastery of the material at the end, and who could ask for more?

Cell phone usage

Please turn off all cell phones in lectures and in the discussion sections.