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Physics & Astronomy

Materials Simulation Group

Biophysics: The physics of life

Learning objectives

By the end of the course, the student will be able to:

  • Recognize the basic physical principles behind cellular processes (how things happen to just what things happen)
  • Explore and explain life processes (and other physical processes) using the concept of free energy
  • Recognize and understand the interplay between heat and work in the processes of life
  • Have an intuitive understanding of the role of entropy, especially in life processes
  • Understand the relationship between free energy and entropy and how the former takes into account the latter and mimics physical intuition

Syllabus

click here

Schedule

Week
Date

Quiz
HW
prob.
Reading/ Discussion
Topic
Sol.
Quiz

Week
Date

HW
prob.
Reading/ Discussion
Topic
Sol.

01
Aug. 30

01   To the Student (preface), 1.1--1.4     08
Oct. 20
  No class, Exam 1 (chaps. 1--6)
Testing center, Oct 20--24
 
01
Sep. 1
02 1.3, 1.4, 1.6, 1.7

1.5, 2.1--2.3 (you can "skim" 2.2 and 2.3)
Cool video of cellular process

01 16 09
Oct. 25
 

8.1--8.2 Chemical potential and chemical reactions
Chemical potential demo (Mathematica)

 
02
Sep. 6
03 HW #2 3.1--3.2, skim 3.3 02 17 09
Oct. 27
HW #14 8.3--8.4 Disassociation and self-assembly 14
02
Sep. 8
04 3.2, 3.3, 3.4 4.1--4.2 Friction, dissipation, and random walks in time. 03 18 10
Nov. 1
  8.6 Self assembly in cells  
03
Sep. 13
05   4.3 Random walks in space (rather than time)   19

10
Nov. 3

HW #15 10.1--10.2.2 Mechanical machines (also read the first two paragraphs of Chap. 9) 15
03
Sep. 15
06 HW #4

4.4--4.5 Diffusion
Walker_Strategy1, Walker_Strategy2, hw05_01, hw05_03
Try this in Mathematica: Graphics3D[{Red, Thin,
Line[Accumulate[RandomReal[{-1, 1}, {5000, 3}]]]}]

04 20 11
Nov. 8
HW #16 10.2.3--10.3.3 Molecular implementation of mechanical principles 16
04
Sep. 20
07 HW #5 4.6 Biological applications of diffusion and random walks 05 21 11
Nov. 10
  10.3.3--10.4.2 Enzymes and machines  
04
Sep. 22
08 HW #6 5.1--5.2 Friction in fluids, low Reynolds numbers 06 22
12
Nov. 15
HW #17 10.4.3--10.5 Kinesin 17
05
Sep. 27
09 HW #7 5.3 Biological applications of viscous liquids 07 23
12
Nov. 17
HW #18 10.5 Kinesin again 18
05
Sep. 29
10 HW #8 6.1--6.2 Disorder and Entropy 08  
13
Nov. 22
  Friday instruction
(No class)
 
06
Oct. 4
11 HW #9 6.3 & 6.4 Temperature and the second law 09  
13
Nov. 24
  Thanksgiving Holiday  
06
Oct. 6
12 HW #10 6.5 Open systems 10 24
14
Nov. 29
HW #19 11.1--11.2.1Electro osmotic effects 19
07
Oct. 11
13 HW #11

6.6 Microscopic systems (6.7 is interesting if you have time. It's short.)

kBT = 3;
DeltaE = 4;
state = Table[
 If[RandomReal[] < 1/(1 + Exp[DeltaE/kBT]), 1, 2], {i, 1, 
 100}];
ListPlot[state, PlotRange -> {.7, 2.1}]
11 25
14
Dec. 1
HW #20 11.2.2--11.3.1 Ohmic conductance and active pumping  
07
Oct. 13
14 HW #12 7.1--7.3 Entropic forces, osmosis 12 26
15
Dec. 6
HW #21 9.1--9.1.3, 9.4 Cooperativity (how transitions become "sharp")  
08
Oct. 18
15 HW #13 7.4--7.5 How stereospecificity arises, properties of water 13 27
15
Dec. 8
Concept Map activity 11.3.2--11.4 Chemiosmosis and the flagellar motor  
Final Project due on last day of finals week
 

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