Grading

25%-quiz 1 25% quiz 2 50% final exam

Format
~8 MCQs ~4 Assays with calculations Open book

Agenda
Jan 16 --- Lecture 1 ( Cell, bacterial, and biomolecule) Jan 23 --- Lecture 2 (statistics and Diffusion) Jan 30 --- Break (Chinese new year) Feb 6 --- Lecture 3 (Thermodynamics and Chemical reaction) Feb 13 --- No class Feb 20 --- Lecture 4 (Characterization technologies) Feb 27 --- Exam I (open book) Mar 6 --- Recess week Mar 13 --- Guest lecture 1 (optical imaging strategies) Dr. Audrey Shi (Leica) Mar 20 --- Guest lecture 2 (MRI for biology/physiology) Prof. ShaoYing Huang (SUTD) Mar 27 --- Guest lecture 3 (cell-cell/substrate interaction) Dr. Nils Gauthier (NUS) Apr 3 --- Guest lecture 4 (development of electron microscope for studying plasmid, protein, and cell) Prof. Utkur Mirsaidov (NUS) Apr 10 Exam II (open book) Apr 17 Overview

What are we made of?

We are mostly made of water (H2O): 75%

C very versatile: everything made of: Nucleic acids, Proteins, Lipids (fat), Carbohydrates. O bonding, proteins, fats, nucleic acids N proteins, genetic material Ca, P bones

Biophysics
Biophysics is a bridge between biology and physics

Biophysics Applications
Biomolecular interaction analysis membrane protein and lipid studies Drug discovery and development (protein-small molecular interaction) Protein-metal ion interaction Biomolecular structure and stability Protein crystallography studies

Two areas of BioPhysics

Model Development What it means (lectures 2-3) Method Development New techniques to see better

Model Development
Statistics Random Walks, Friction and Diffusion
Thermodynamics Chemical reaction and biological machines

Statistics

Probability in Science
You can NOT tell the exact state of each gas molecular in the room; BUT you can measure the precise probability distribution of gas molecules

0.259X60=

 For the babies distribution, find the variance of x

What is the probability of getting a 6 with a dice plus getting head with a coin?
What is the probability of getting a 6 with a dice plus getting a 1 with another dice?

Integral of P(r) from R0 to infinite

Low-density gases obey a universal law

The number of gas molecules in a box at atmospheric pressure is proportional to its volume. (VN) Further, p*V=N*kB*T (Ideal gas law)
1. kB is Boltzmann constant and is 1.38*E(-21) joules per degree 2. T is absolute temperature. (t+273C) 3. At room temperature (22C), kB*T equals 4.1E(-21)J or 4.1pN*nm

Compared mgh and 3/2KT

What about a dirt particle with 1.25E(-10)kg?

Partition Function for 2-state system

- 1 E1 - o Eo e -E1/kT P E1 = -E o /kT e +e -E1/kT

Simple case: Ball in gravitational field. Thermal fluctuations, finite probability of being at height, h.

E = ??

E = mgh Eo h = 0 E1 h =(mg)(h meter)

P(h) P(0)

e-mgh/kT =

As ball gets smaller, probability gets smaller / larger ? Ball the size of O2? Why can you breathe standing up?

What is 1/e height for O2?

For O2, 1/e height is ~10 km ~height of Mt. Everest. (10 kM is death zone)

Random Walks, Friction and Diffusion

http://youtu.be/STLAJH7_zkY
1. Why does the dye spread through the solution? 2. Why does the diffusion take a random/unpredicted path? 3. Why is the diffusion quicker at higher temperature?

http://youtu.be/cDcprgWiQEY

Probability for getting back to the starting point

L=1; R=-1

To return to the starting point, the head has to be same as the tail
M0=possible combinations M=total way of flip coming out

P=M0/M

HT or TH HHTT or TTHH HTHT or THTH THHT or HTTH

http://www.math-prof.com/Prob/Prob_Ch_05.asp https://www.khanacademy.org/math/probability/probability-and-combinatoricstopic/probability_combinatorics/v/probability-using-combinations

Probability using Combinations

Total number of way all the flip can come out

5000 heads out of 10000

The exclamation point denotes the Factorial function

Factorial function is a non-negative integer n, denoted by n!, is the product of all positive integers less than or equal to n

4!=4X3X2X1=24
0!=1 N!=(n-1)!Xn

Displacement and diffusion law

RRR RRL RLR LRR LRL LLR RLL LLL

When L=1cm

The diffusion law is model independent

Key: image the bin to be very narrow; the difference between a function, line N(x), at two nearby points is L times the derivative of N

Key: the development of the density wont depend on how big the box is; the important thing is the number per unit area of a

1. J measures the net number of particles moving from left to right;

2. A net drift to the right ensures, tending to even out the distribution, or make it more uniform. 3. If there is structure in the original distribution, Ficks law says that diffusion will tend to erase it. 4. Diffusion constant D enters the formula because morerapidly diffusing particles will erase their order fast

B: partition coefficient of solute in oil versus water D: diffusion constant in oil

Constant I=J*4r^2

More than diffusion

++ + + + +

http://youtu.be/Md0PtdRxXvw http://youtu.be/Ya-jpBgzcc8
112

113

Adapted from Nernst relation

C(z): profile of particles density

114

Scale height

115

1g/ml

Not a stable suspension

116

Scale height also depends on the acceleration constant

Comparable with z and cause a significant difference between Cx and C0

117

Sedimentation equilibrium in centrifuge

118

Or sedimentation coefficient

119

-1

49

120

P=0.57

Log-log plot of diffusion constant D of polymethyl methacrylate in acetone as a function of the polymers molar mass M.

121

Log-log plot of sedimentation coefficients of polymethyl methacrylate in acetone as a function of the polymers molar mass M.
122

http://youtu.be/_dbnH-BBSNo

123

Pushed to right

Fixed

Definition of laminar flow

124

Any fluid obeying is called a Newtonian fluid.

125

Characteristics of Newtonian Fluid

1. Obey
= 0

2. Completely characterized by its viscosity and mass density;

3. Isotropic (the same in every direction)

126

127

128

http://youtu.be/fma5WBl90Sw

129

Now we want to compare ftotal with ffrict If one is much bigger than another, we could drop the smaller on in Newton law

130

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139

Calculate travel distance

140

141

Cilia motion is periodic but not reciprocal

142

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