This page will contain links to a variety of information meant to supplement the lectures, including the slides used in class and links to other sites with related information.

Lecture 1, 22 August

Lecture 2, 24 August

Lecture 3, 26 August

Lecture 4, 29 August

Lecture 5, 31 August

Lecture 6, 2 September

Lecture 7, 7 September

Lecture 8, 9 September

  • The Binomial Probability Distribution Function and Expected Values
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Lecture 9, 12 September

Lecture 10, 14 September

Lecture 11, 16 September

  • Two-dimensional Random Walks - Part 2
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    Note: Someone pointed out an error in the originally posted slides for this lecture. The error, in the second line of the equations on slide 7, has been corrected.
  • Logo Resources
    • The version of Logo that I used in class is called ACSLogo and is only available for Mac OS X. It can be downloaded at no costs from: http://www.alancsmith.co.uk/logo/release.html
      ACSLogo is nice for quick demonstrations like the one that I did in class, but it has some limitations.

    • To the extent that there is a "standard" version of the Logo computer language it is UCBLogo, developed by Brian Harvey at UC Berkeley. It is available as free software for Macs, Windows an Unix from: https://people.eecs.berkeley.edu/~bh/logo
      UCBLogo has not been updated in some time, and even when it was being actively developed the user interface was bare bones. But, the internals probably represent the most solid version of Logo available.
      Harvey is also the author of a three volume set of books, titled "Computer Science Logo Style," from the MIT Press and also available for free download as pdf files his web page https://people.eecs.berkeley.edu/~bh/

    • FMSLogo, http://fmslogo.sourceforge.net, incorporates the core of UCBLogo into a graphical user environment for Windows. I am not aware of any comparable version for Macs or Linux.

    • The Logo Foundation, http://el.media.mit.edu/logo-foundation/, at MIT, continues work in the spirit of Logo, including a new language, Scratch, which is designed to introduce computer programming to kids in a fun and engaging way.

Lecture 12, 19 September

  • Two-dimensional Random Walks - Part 3
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    Two-dimensional Random Walks - Part 2

Lecture 13, 21 September

  • A Bit More on Random Walks and the Gaussian Probability Distribution Functions
    Download slides

Lecture 14, 23 Septemberg

Lecture 15, 26 September

  • A Bit More on the Statistics of Experimentl Measurements
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  • The download includes a few slides that we didn't get to today. These concern another statistic calculated from experimental data, the standard error of the mean (SEM). This statistic is used to estimate the precision or reliabilitiy of the mean, as opposed to the precision of individual measurements, which is estimated by the sample standard deviation, s. The two statistics are ofen confused and, thereby, misused. A short discussion of this issue can be found in:
    Altman, D. G. & Bland, J. M. (2005). Standard deviations and standard errors. BMJ , 331, 903.
    http://dx.doi.org/10.1136/bmj.331.7521.903

Lecture 16, 28 September

Lecture 17, 30 September

Lecture 18, 3 October

  • More on Diffusion and Introduction to Kinetic Energy
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  • Mathematica simulation of diffusion from a sharp boundary.
    This is a "computable document format" file and can be viewed interactively using the free Wolfram CDF player, downloadable from here.

Lecture 19, 5 October

Lecture 20, 17 October

  • More on Diffusion at the Molecular Level, in Liquids and Gasses
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Lecture 21, 19 October

  • A Plant Faces Diffusion
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  • For more information about the water flow in plants, see the web page of Prof. John Sperry, at the University of Utah.

Lecture 22, 21 October

Lecture 23, 24 October/h3>

  • More on Bacterial Chemotaxis and an Introduction to the Section on Thermodynamics
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Lecture 24, 26 October

Lecture 25, 28 October

Lecture 26, 31 October

  • Thermodynamics, Part 3: The Statistical Definition of Entropy and the Second Law
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Lecture 27, 2 November

Lecture 28, 4 November

  • Thermodynamics, Part 5: Chemical Thermodynamics, the Equilibrium Constant and ΔG.
    Download slides

Lecture 29, 7 November

Lecture 30, 9 November

  • A Bit More on Enzymatic Coupling, and Properties of Water
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Lecture 31, 11 November

Lecture 32, 14 November

  • Review of Quiz 3 and Introduction to Lipids and Membranes
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  • Additional notes on thermodynamics.
    From discussions in class, I now realize that I was unclear about some aspects of the thermodynamic functions, ΔH and ΔG, and downright wrong in a few! I have written some supplementary notes to help clarify these points.
    Please let me know if you have questions! I need to know when things are not clear.

Lecture 33, 16 November

  • More on Lipids and Membranes: Bilayer Permeability and the Origins of Life
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Lectures 34 and 35, 18 and 21 November

Lecture 36, 23 November

  • More on Protein Folding and Introduction to Molecular Motors
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Lecture 37, 28 November

Lecture 38, 30 November

Lecture 39, 2 December

Lectures 40 and 41, Monday, 5 December and Wednesday, 7 December

  • Rotary Motors: ATPsynthase and the Bacterial Flagellar Motor
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