This page will contain links to a variety of information meant to supplement the lectures. The material will include notes that I will try to make available before the lectures and the slides used in class, which I will post after the class sessions. As appropriate, I will also post linkst to to other sites with related information.
The notes provided here are a work in progress. They are intended to provide a guide to the material covered in class, and, in some cases, go into greater depth than we are able to in class. For quizzes and exams, you will only be responsible for what is actually covered in class, but reading the additional material may still be helpful in gaining a deeper understanding.
The notes are organized into chapters representing the major topics to be covered during the semester. Unfortunately, they were not all ready for the beginning of the semester, but they will be added to as the semester progresses.
Lecture Slides and Other Items
Lecture 4, 28 August
- A Bit More on Units and Moving on to Brownian Motion and Probability.
YouTube movie of Brownian motion
Computer demonstration of Einstein model of Brownian motion
During class, a sharp-eyed student caught an error on slide 8. At the top of that slide, I had written, in reference to the bacterial cell:
Volume = 1.6x10-12 L
But, on a previous slide, I had written: Volume = 1.6x10-12 mL
The correct volume is 1.6x10-12 mL = 1.6x10-15 L
This is the value that I used further down on the slide, to get the answer that the cell contains approximately 100 H+ ions.
This was a big relief, because I have been getting 100 ions as the answer to this question for many years!
I apologize for the confusion, and the slide has been corrected.
Lecture 5, 30 August
- Introduction to Probability
Two recommended books on probability:
Lecture 8, 8 September
- Plinko Probabilities, Part III: Binomial Coefficients and the Binomial Distribution Function
Lecture 9, 11 September
- Random Variables, the Expected Value and Introduction to Random Walks
Lecture 10, 13 September
- Random Walks in One Dimension
- Logo Resources
In class, I did a computer demonstration using turtle graphics to show the dynamics of a random walk. The idea of turtle graphics was popularized through the Logo computer language, which was developed as an educational tool for children in the 1960s. There is still significant interest in Logo, and the following are some links to currently available versions. Turtle graphics has also been incorporated in other computer languages, including Python, which I used for the demonstration. Still, one of the Logo versions listed below may be the easiest way for a programming novice to play with turtle graphics and get an introduction to programming.
- 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.
- ACSLogo has a nice graphical interface and is useful for quick demonstrations. But it does have some limitaions and is only available for Mac OS X.
It can be downloaded at no costs from: http://www.alancsmith.co.uk/logo/
- 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 11, 15 September 2017
Lecture 12, 18 September
- Moreo on Two-dimensional Random Walks and the
Gaussian Probability Distribution Function
Lecture 13, 20 September
- Gaussian Distributions of Random Walk End Points and a Random Walk to Error Analysis
Lecture 16, 27 September
- Diffusion: Fick's Second Law
- Simulation of Diffusion. The animated simulation of diffustion from a sharp bounddary that I showed in class was created in Mathematica, a computer program with a wide range of powerful tools for mathematics. Although Mathematica is quie expensive, the file for the simulation can be opened and used with a free player program avalialble from the makers of Mathematica, Wolfram Research.
The simulation file can be downloaded here.
The player program can be downloaded from: http://www.wolfram.com/cdf-player/
Lecture 17, 29 September
- Review of Quiz 2 and More on Diffusion from a Sharp Boundary
Lecture 19, 3 October
- More on Diffusion at the Molecular Level and the Nature of Liquids and Gasses
Lecture 20, 16 October
- Calculting Diffusion Coefficients, Diffusion in Gasses and CO2 Diffusion into Plants
Lecture 21, 18 October
- A Plant Faces Diffusion and Introduction to Bacterial Chemotaxis
- For more information about the water flow in plants, see the web page of Prof. John Sperry, at the University of Utah.
Lecture 27, 1 November
- Thermodynamics: Enthalpy, Gibbs Free Energy and Equilibrium Constants
Lecture 28, 6 November
- Thermodynamics: Gibbs Free Energy, Equilibrium Constants and the
Entropy Change for a Bimolecular Reaction
Lecture 34, 20 November
- A Bit More on Membranes and Introduction to Protein Folding and Unfolding
Lecture 38, 1 December
- Molecular Motors, Part III:
Actin, Myosin and Mircrotubule Motors