Garland Science - Taylor and Francis Group.Physical Biology of the Cell.
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Mathematica® & Matlab® Codes


The Computational Exploration sidebars in the book feature simple computer analyses to solve problems that would otherwise be inaccessible. Matlab and Mathematica code related to most of the Computational Explorations is provided here for further computation, visualization, and analysis. For a selection of figures and end-of-chapter problems, many algebraic steps were performed or confirmed with a very powerful computational tool known as Mathematica. In addition, we have often used Mathematica to construct figures, such as the vector fields associated with phase portraits.

(TIP: To save the files directly to your computer right-click or alt-click and select 'save target as' or 'save link as' then select a location on your desktop to save the file. Otherwise you may be prompted to open the file first then save to your local computer.)

Getting Started
Matlab Resources
Zip file. Matlab Tutorial (Zip file archive)
Zip file. Harvard "Boot Camp in Quantitative Methods" Website. Tutorial courtesy of Mike Springer, Hao Yuan Kueh, Zeba Wunderlich and Andy Hilfinger.

Chapter 2
Computational Explorations
Zip file. Sizing Up E. coli (Zip file archive)
Zip file. Counting mRNA and Proteins by Dilution (Zipped Matlab file)

Chapter 3
Computational Explorations
Zip file. Timing E. coli (Zip file archive)
Zip file. Growth Curves and the Logistic Equation (Zipped Matlab file)

Chapter 5
Computational Exploration
Zip file. Determining the Spring Constant of an Optical Trap (Zip file archive)

Chapter 7
Computational Exploration
Zip file. Determining Ion Channel Open Probability by Thresholding (Zip file archive)

Chapter 17
Computational Exploration
Zip file. Numerical Solution of the Cable Equation (Zipped Matlab file)

Chapter 18
Computational Exploration
Zip file. Electrons in a Well of Finite Depth (Zipped Mathematica file)
Figure
Zip file. Figure 18.48 (Zipped Mathematica file)
Problem
Zip file. Problem 18.7 (Zipped Mathematica file)

Chapter 19
Computational Explorations
Zip file. Extracting Level of Gene Expression from Microscopy Images (Zip file archive)
Zip file. The Gillespie Algorithm and Stochastic Models of Gene Regulation (Zipped Matlab file)

Chapter 20
Computational Exploration
Zip file. Scaling of Morphogen Gradients (Zip file archive)

Chapter 21
Computational Exploration
Zip file. Searching the E.coli Genome for Binding Sites (Zip file archive)

 

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