Page 194 - Thermodynamics of Biochemical Reactions

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty
Copyright 0 2003 John Wiley & Sons, Inc.
ISBN 0-471-22851-6

Second Part: MathematicaR Solutions to Problems

Calculations on the thermodynamics of biochemical reactions are often very complicated because of the large num-
bers of independent variables that are involved: for example, T, pH, ionic strength, concentrations of free metal ions, and
concentrations of coenzymes. Therefore, it is necessary to use a computer with a mathematical application installed. Mathe-
matica is very convenient for these calculations, data storage, and making plots (Wolfram Research, 100 World Trade
Center, Champaign, IL 61820-7237). This part of the book provides Mathematica solutions to problems and shows how to
calculate figures and tables used in the book. Programs and all of the details involved in making these calculations are
shown. These programs can be used to make calculations at other temperatures, pHs, ionic strengths, etc.
The basic data and most of the programs are available on the web in MatlzSource at
1
http://www.mathsource.com/cgi-bin/msitem?02 1-622
BasicBiochemData2.nb is a Mathemutica notebook that contains data, programs, explanations, and examples. It can be read
using MathReader, which is free from Wolfram Research at
http://www .wolfram.com
This notebook is the first item in this part of the book. It can be downloaded into a personal computer with Matheniatica
installed and can be run by using Kernel/Evaluation/Evaluate Notebook. This brings in all the data and programs. Math-
Source also contains BasicBiochemData2.m, which is a package that contains data and programs. It can be loaded into a
Mathematica notebook by simply typing <<BasicBiochemData2' after BasicBiochemData2.m has been downloaded into
AddOnsIExtraPackages in your computer.
Many of the problems in this second part of the book require that the package has been loaded, but the command
<<BasicBiochemData2' is not included in each problem. Although the package loads programs, the programs used in
problems are usually repeated in the solutions shown here so that it is easier for the reader to see how the calculation is made.
A number of books have been written to help people get started with Mathematicu. Examples are
J. H. Noggle, Physical Chemistry Using Mathematica, HarperCollins, New York, 1996.
K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck, The Muthematica Primer, Cambridge University
Press, 1998.
C-K. Cheung, G. E. Keough, C. Landraitis, and R. H. Gross, Getting Started with Mathematica, Wiley, New York, 1998.
H. F. W. Hoft and M. H. Hoft, Computing with Mathematica, Academic Press, San Diego, 1998.
W. H. Cropper, Mathematica Computer Problems for Physical Chemistry, Springer-Verlag, New York, 1998.
R. J. Silbey and R. A. Alberty, Physical Chemistry-Solutions Manual, Wiley, 2001.
It is not necessaary to be a programmer in order to use the programs and procedures illustrated in this collection of
problems. Names, temperatures, pHs, and ionic strengths are readily changed in the solutions to problems.

Contents:
BasicBiochemData2 .nb
Solutions to Problems
Index of Mathematica Programs