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<h2>
Course Instructor: <a href="http://www.rpgroup.caltech.edu/people/phillips.html">Rob
Phillips</a><br>
</h2>

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<h4>
[
<a href="#ann">Announcements</a> |
<a href="#cla">Course Information</a> |
<a href="#book">Textbooks</a> |
<a href="#hw">Homework</a> |
<a href="#links">Useful Links</a> |
<a href="#lectures">Lecture Notes</a> |
<!-- <a href="#abs">Poster Abstracts</a> | -->
<a href="#con">Contact Information</a>
]
</h4>
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<img  src="soap_bubble.png" alt="picture" width="300">
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<h4>
Interface of soap bubbles.  
<br>

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<!-- Announcements -->
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<hr>
<h3><a name="ann">Announcements</a></h3>
<ul>
<li> <b>Office hours:</b> Wednesday and Thursday 3-5pm, 155 Broad
</ul>

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<!-- Course Information -->
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<hr>
<h3><a name="cla">Course Information</a></h3>
<ul>
<li><a href="CourseInfo_2006.pdf">Course Outline (pdf)</a>
<li><b>Lecture Schedule:</b> Thursday -- 8:30 am to 10:25 am and Friday -- 11:00am to 11:55am, 104 Watson
</ul>

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<!-- Textbooks -->
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<hr>
<h3><a name="book">Textbooks</a></h3>
<ul>
<!-- <li><b>Physical Biology of the Cell</b><br>
by Phillips, Kondev and Theriot<br>
<a href="./protected/pboc">Click here to download book chapters</a><br>
<br> -->

<li><b>Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology</b><br>
by Sarina Bromberg, Ken A. Dill
</ul>

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<!-- Homework -->
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<hr>
<h3><a name ="hw">Homework</a></h3>
<ul>

<!--============ Homework #1 =============-->

<li><b>HW 1 (<a href="./hw/APH105c_HW1_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps1.pdf" name="hw1soln">solutions</a>)</b><br>
<br>

<!--============ Homework #2 =============-->

<li><b>HW 2 (<a href="./hw/APH105c_HW2_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps2.pdf" name="hw2soln">solutions</a>)</b><br><br>

Related articles
<ul>
<li><a href="./articles/Klein_Einstein.pdf">Martin J. Klein</a>; <u>Thermodynamics in Einstein's Thought</u>, Science, New Series, Vol. 157, No. 3788, Aug. 4 1967, pp. 509-516.<br>
<br>
<li><a href="./articles/Pais.pdf">Pais, A. </a>; <u>Einstein and the Quantum-Theory</u>, Reviews of Modern Physics,   Vol. 51, 1979, pp. 863-913.<br>
<i><b>"These articles describe the huge importance that Einstein attached to the use of fluctuations as a tool for
discovering new physics. Indeed, his use of fluctuations figured into his analysis of specific heats, the wave-particle duality, the existence of atoms, etc. "</b></i>
</ul>
<br>

<!--============ Homework #3 =============-->

<li><b>HW 3 (<a href="./hw/APH105c_HW3_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps3.pdf" name="hw3soln">solutions</a>)</b><br><br>
Related articles
<ul>
<li><a href="./hw/Changeux1965.pdf">Jean-Pierre Changeux</a>; <u>The Control of Biochemical Reactions</u>.<br>
<br>
<li><a href="./hw/HemoMyoglobin.xls">Problem 1(d) data </a>.
<i><b>"Data related to Problem 1: The Hemoglobin Story"</b></i>
</ul>
<br>


<!--============ Homework #4 =============-->

<li><b>HW 4 (<a href="./hw/APH105c_HW4_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps4.pdf" name="hw4soln">solutions</a>)</b><br>

<br>

<!--============ Homework #5 =============-->

<li><b>HW 5 (<a href="./hw/APH105c_HW5_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps5.pdf" name="hw5soln">solutions</a>)</b><br><br>
Related articles
<ul>
<li><a href="./hw/majumbar2001.pdf">Wu et al.</a>; <u>Bioassay of prostate-specific antigen (PSA) using microcantilevers</u>, Nature Biotechnology, Vol. 19, 2001, pp. 856-860.<br>
<i><b>"Article related to Problem 3 of this homework"</b></i>
</ul>

<br>

<!--============ Homework #6 =============-->

<li><b>HW 6 (<a href="./hw/APH105c_HW6_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps6.pdf" name="hw6soln">solutions</a>)</b><br>

<br>

<!--============ Homework #7 =============-->

<li><b>HW 7 (<a href="./hw/APH105c_HW7_2006.pdf">problems</a>, <a href="./hw/solutions/aph105ps7.pdf" name="hw7soln">solutions</a>)</b><br>

<br>
Related articles
<ul>
<li><a href="./hw/bessel.xls">Problem 2(b) data </a>.
<i><b>"This excel file contains the first 40 zeros of J_1(x)"</b></i>
</ul>
<br>

<br>

</ul>
 <!-- homework list -->

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<!-- Useful Links -->
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<hr>
<h3><a name ="links">Useful Links</a></h3>
<!-- <ul>
<li> <a href="http://www.imb-jena.de/IMAGE_AA.html">Amino acid data</a>
<li> <a href="http://www.pdb.org/">The Protein Databank (PDB)</a>
<li><a href="http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html">Compilation of genome sizes</a>
<li><b>Molecule Viewers</b>
<ul>
<li><a href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a>
<li><a href="http://www.umass.edu/microbio/rasmol/">Rasmol</a>
<li><a href="http://www.expasy.org/spdbv/">DeepView</a>
</ul>
<li><a href="http://www.uni-mainz.de/FB/Medizin/Anatomie/workshop/EM/EMAtlas.html">Electron Microscope Atlas</a>
<li><a href="http://www.med.uiuc.edu/histo/small/atlas/index.htm">Internet Atlas of Histology</a><br>
<i>"This site provides images of cells and tissues"</i>
<li><a href="http://www.itg.uiuc.edu/technology/atlas/">A Web Atlas of Cellular Structures</a><br>
<i>"This is a web-based atlas of confocal microscopy images of cells and organelles."</i>
<li><b>Important Model Organisms</b>
<ul>
<li><a href="http://www.nih.gov/science/models">NIH - Model Organisms for Biomedical Research</a>
<li><a href="http://www.dictybase.org/">Dictyostelium - dictyBase</a>
<li><a href="http://www.wormbase.org/">C. elegans - WormBase</a>
<li><a href="http://www.flybase.org/">Drosophila - FlyBase</a>
</ul>
<li><a href="http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi"><i>E. coli</i> statistics</a><br>
<i>"This website gives some of the vital statistics for <i>E. coli</i>."</i>
</ul> -->

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<!-- Lecture Notes -->
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<hr>
<h3><a name ="lectures">Lecture Notes</a></h3>
<ul>


<!--============ Lecture #1 =============-->

<li><b>Lecture #1 (<a href="./lectures/APh105_Lecture1.ppt">ppt</a>, <a href="./lectures/APh105_Lecture1.pdf">pdf</a>) (3/30/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="http://nobelprize.org/physics/laureates/1965/feynman-lecture.html">R.P. Feynman</a>; <u>http://nobelprize.org/physics/laureates/1965/feynman-lecture.html </u> and <u> R.P. Feynman in Nobel Lectures in Physics: 1901-1995</u>, World Scientific, Singapore, 1998<br>
<i><b>"Feynman's Nobel Prize Lecture: In Feynman's lecture he has important comments on the virtue of multiple formulations for a given problem. In the setting of this course, this is relevant to our treatment of statistical mechanics from the information theory perspective."</b></i><br><br>

<li><a href="./articles/Jaynes1957.pdf">E. T. Jaynes</a>; <u>Information Theory and Statistical Mechanics</u>, Phys. Rev., May 15, 1957; Vol.106,  No.4<br>
<i><b>"This article ushered in the use of Shannon's information entropy as a basis for doing statistical mechanics."</b></i><br>
<br>

<li><a href="./articles/PrentissBoltzmann2.pdf">J. J. Prentiss</a>; <u>Thank You, Boltzmann, That Your Constant Is So Small</u>, The Physics Teacher, Oct 1996; Vol.34<br>
<i><b>"This article is akin to George Gamow's books about Mr. Tompkins in Wonderland. The basic idea is to examine how the world would look if Boltzmann's constant had a very different value"</b></i><br>
</ul>
<br>

<!--============ Lecture #2 =============-->

<li><b>Lecture #2 (3/31/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/Jaynes_brandeis.pdf">E. T. Jaynes</a>; <u>Information Theory and Statistical Mechanics</u>, Statistical Physics, K. Ford (ed.), Benjamin, New York, p. 181</u>, <br>
<i><b>"This is the paper where I first learned of the use of maximum entropy methods to treat the problem of the dishonest die. The paper is full of other fun and interesting ideas."</b></i><br>
<br>

<li>
<i><b>"My favorite treatment of the use of Lagrange multipliers is in the wonderful book by Cornelius Lanczos entitled <u>'The Variational Principles of Mechanics'</u>. Pgs. 43-48 have a beautiful discussion of Lagrange multipliers."</b></i><br>
<br>
</ul>

<!--============ Lecture #3 =============-->

<li><b>Lecture #3 (4/6/06)</b><br>
<br>

Suggested reading<br>
<br>
<!--============ Lecture #4 =============-->

<li><b>Lecture #4 (<a href="./lectures/HbLecture.ppt">ppt</a>, <a href="./lectures/HbLecture.pdf">pdf</a>) (4/7/06)</b><br>
<br>

Suggested reading<br>
<br>
<!--============ Lecture #5 =============-->

<li><b>Lecture #5 (4/13/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/Klotz2003.pdf">Irving M. Klotz</a>; <u>Hemoglobin-oxygen equilibria: retrospective and phenomenological perspective</u>, Biophysical Chemistry, 2003, Vol. 100, pp. 123-129</u>, <br>
<i><b>"The first few pages of this article provide a useful and brief overview of thinking on hemoglobin.  Note that in Table 1 the units should be mmHg^-1.  I don't know what to say about the stuff near the end of the article."
</b></i><br>
<br>
<li><a href="./articles/AnimalPhys.jpeg">Hill, Wyse, Anderson</a>; <u>Animal Physiology</u>, Sinauer Associates, Inc. Publishers, Sunderland, MA; Chapter 22,  p. 588<br>
<i><b>"This is one of the pages of interest from the book that was passed around during class."</b></i><br>
<br>
</ul>

<!--============ Lecture #6 =============-->

<li><b>Lecture #6 (4/14/06)</b><br>
<br>

Suggested reading<br>
<br>

<!--============ Lecture #7 =============-->

<li><b>Lecture #7 (4/20/06)</b><br>
<br>

Suggested reading<br>
<br>

<!--============ Lecture #8 =============-->

<li><b>Lecture #8 (4/21/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/Schweber1986.pdf">Schweber, Silvan</a>; <u>Feynman and the visualization of space-time processes</u>, Reviews of Modern Physics, 1986, Vol. 58, No. 2, pp. 449-511</u>, <br>
<br>
</ul>

<!--============ Lecture #9 =============-->

<li><b>Lecture #9 (4/27/06)</b><br>
<br>

Suggested reading<br>
<br>

<!--============ Lecture #10 =============-->

<li><b>Lecture #10 (4/28/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/Asakura2.pdf">Asakura, Oosawa</a>; <u>Interactions between Particles Suspended in Solutions of Macromolecules</u>, Journal of Polymer Science, 1958, Vol. 33, pp. 183-192</u>, <br>
<i><b>"The work of Oosawa and Asakura introduced the idea of excluded volume forces."
</b></i><br>
<br>
<li><a href="./articles/Yodh2001.pdf">Yodh et al.</a>; <u>Entropically driven self-assembly and interaction in suspension</u>,  Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 359, No. 1782, May 15 2001, pp. 921-937</u>, <br>
<i><b>"This paper gives an impression of the experimental situation on excluded volume forces."
</b></i><br>
<br>

</ul>

<!--============ Lecture #11 =============-->

<li><b>Lecture #11 (5/4/06)</b><br>
<br>

Suggested reading<br>
<br>

<!--============ Lecture #12 =============-->

<li><b>Lecture #12 (5/5/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/Srolovitz.pdf">D. J. Srolovitz</a>; <u>On the Stability of Surfaces of Stressed Solids</u>, Acta Metallurgica, 1989, Vol. 37, No. 2, pp. 621-625</u>, <br>
<i><b>"This paper introduced the idea of sinusoidal instabilities in thin films as a competition between bulk and surface energies."</b></i><br>
<br>

<li><a href="./articles/tersoff.pdf">J. Tersoff, R. M. Tromp</a>; <u>Shape Transition in Growth of Strained Islands: Spontaneous Formation of Quantum Wires</u>, Physical Review Letters, Vol. 70, No. 18, 3 May 1993, pp. 2782-2786</u>, <br>
<i><b>"This paper shows how to apply ideas similar to those we discussed for
sinusoidal instabilities to the development
of islands on surfaces."</b></i><br>
<br>

<li><a href="./lectures/Lecture12.pdf">L. B. Freund and S. Suresh</a>; <u>Thin Film Materials: Stress, Defect Formation and Surface Evolution</u>, Cambridge University Press, 2003, Ch. 8, pp. 573-579, 632-633, <br>
<i><b>"This file contains the pictures and calculation on epitaxial growth presented during lecture."</b></i><br>
<br>
</ul>

<!--============ Lecture #13 =============-->

<li><b>Lecture #13 (5/11/06)</b><br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/ElowitzLeibler.pdf">M. Elowitz et al.</a>; <u>Protein Mobility in the Cytoplasm of Escherichia coli</u>, Journal of Bacteriology, Jan. 1999, Vol. 181, No. 1, pp. 197-203</u>, <br>
<i><b>"This paper illustrates the use of FRAP for looking at
diffusion within E. coli cells.  The one-dimensional nature of this
problem is relevant to the FRAP problem
you will work out on HW7."</b></i><br>
<br>

<li><a href="./articles/WebbElson.pdf">D. Axelrod, D. E. Koppel, J. Schlessinger, E. Elson, W. W. Webb</a>; <u>Mobility Measurement by Analysis of Fluorescence Photobleaching Recovery Kinetics</u>, Biophysical Journal, 1976, Vol. 16, pp. 1055-1069, <br>
<i><b>"This is one of the papers that founded the use of FRAP."</b></i><br>
<br>

</ul>

<!--============ Lecture #14 =============-->

<li><b>Lecture #14 (5/12/06)</b><br>
<br>

Suggested reading<br>
<br>

Suggested reading<br>
<ul>
<li><a href="./articles/milvia's_lab_notebook.pdf">Paul B. Laub</a>; <u>The Black Box, or the Significance of r = (Et^2/p)^0.2 </u>, 7 May 2004, pp. 1-27</u>, <br>
<i><b>"I have not yet read this, but it claims to be a fictionalized account of how GI Taylor estimated
the yield of the first atomic bomb by inspecting photographs on the cover of Life Magazine."</b></i><br>
<br>

<li><a href="./articles/Langevin1908.pdf">Don S. Lemons and Anthony Gythiel</a>; <u>Paul Langevin's 1908 paper "On the Theory of Brownian Motion"</u>, American Journal of Physics, 1997, Vol. 11, pp. 1079-1081, <br>
<i><b>"This is the 1908 paper from Langevin which tackled the theory of Brownian motion from the perspective of what are now called Langevin
equations"</b></i><br>
<br>

</ul>


</ul>

 <!-- lecture list -->


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<!-- Contact Information -->
<!--=====================-->

<hr>
<h3><a name="con">Contact Information</a></h3>
<ul>
<li><a href="http://www.rpgroup.caltech.edu/people/phillips.html">Rob Phillips</a><br>
159 Broad<br>
x3374<br>
phillips AT pboc.caltech.edu<br>
<br>
<li><b>David Van Valen</b><br>
155 Broad<br>
x5876<br>
vanvalen AT caltech.edu<br>
<br>
<li><b>Frosso Seitaridou</b><br>
071 Broad<br>
x5761<br>
frosso AT caltech.edu<br>
</ul>

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