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Re: Mathematica materials for Chemistry

• To: mathgroup at christensen.cybernetics.net
• Subject: [mg221] Re: [mg212] Mathematica materials for Chemistry
• From: Gene C Van Nostern <gene>
• Date: Wed, 23 Nov 1994 11:08:16 -0600

> Dear MathGroup, 
> 
> can I make a general request for information on the 
> whereabouts and what-abouts of Mathematica Notebooks
> and packages related to chemistry. 
> 
> A chemist colleague says that he found loads of stuff
> on the Maple archive, and very little at MathSource.
> I'm sure there must be more things around - can anyone
> tell us where it is?
> 
> Regards, Phillip Kent.
> 
> ----------------------------------+----------------------------
>  Dr Phillip Kent                  | Email: p.kent at ic.ac.uk 
>  Transitional Mathematics Project | 
>  Mathematics Department           | Tel: +44 (0)71 59 48503 
>  Imperial College                 | Fax: +44 (0)71 59 48517   
>  180 Queen's Gate                 |   
>  London SW7 2BZ                   | Project World-Wide-Web at: 
>  United Kingdom.                  | http://othello.ma.ic.ac.uk
> ----------------------------------+----------------------------

Hello Dr Kent,

A search of MathSource for "chemistry" revealed the items listed below.
I hope this is helpful.

Kind regards,
Gene.

Gene C. Van Nostern
MathSource Administrator
Wolfram Research, Inc.

---< Begin "chemistry" search results >---

0202-420: The Joule-Thomson Coefficient for a Square Well Gas (August 1991)
          Author: M. Hanson
          Mathematica notebook demonstrating the solution of the
          Joule-Thomson coefficient for argon.

          0011:  Joule-Thomson.ma Mathematica notebook (August 1991; 34
                 kilobytes)

          0022:  argboft.list data file for notebook (August 1991; 1
                 kilobyte)

          0033:  argmujt.list data file for notebook (August 1991; 1
                 kilobyte)


0200-316: Crystal Structure Graphics (August 1991)
          Author: Wolfram Research
          Produces a nice picture of the crystal structure of diamond.

          0011:  CrystalStructure.m Mathematica package (August 1991; 4
                 kilobytes)


0202-431: Gases (August 1991)
          Author: Mervin P. Hanson
          A Mathematica notebook presenting five problems dealing with the
          behavior of a gas under varying conditions.

          0011:  Gases.ma Mathematica notebook (August 1991; 15 kilobytes)

          0022:  B-VT-Kr data file for Gases.ma (August 1991; 1 kilobyte)


0206-211: MDNewton Version 0.2 (March 2, 1994)
          Author: Kazume Nishidate
          This is a Mathematica package for the two-dimensional classical
          molecular dynamics calculuation of the Lenerd-Jones potential
          system.

          0011:  MDNewton.m Mathematica package (March 2, 1994; 5 kilobytes)

          0022:  MDNewton.ma example notebook with graphics (March 2, 1994;
                 51 kilobytes)


0206-198: Activity Coefficients Package (February 22, 1994)
          Author: Arnd Roth
          This package provides experimental data on the mean activity
          coefficient in water at 25 degrees celsius for some common
          electrolytes, as well as functions for fitting an extended
          Debye-Hueckel model to these data, yielding expressions for the
          activity coefficient as a function of ionic strength or
          concentration. The fitting functions also work on experimental 
          data supplied by the user.

          0011:  ActivityCoefficients.m Mathematica package (February 21,
                 1994; 32 kilobytes)

          0022:  ACManual.ma example notebooks (February 21, 1994; 62
                 kilobytes)


0205-164: Molecular Graphics Package 1.0 (June 15, 1993)
          Author: David Nordfors
          The package provides routines for plotting molecules and molecular
          displacements, for example, vibrational modes, in three 
          dimensions.  Bonds may be generated automatically. Some commands:
          DrawNuclei, DrawBonds, DrawMolecule, DrawVectors, DrawDistortion.

          0011:  MolecularGraphics.m Mathematica package (June 1, 1993; 14
                 kilobytes)

          0022:  DemoMolecularGraphics.m Demonstration package (June 15,
                 1993; 3 kilobytes)


0203-207: Literature Survey of Mathematica (January 7, 1994)
          Author: Brian L. Evans
          A partial index of articles relating to or citing Mathematica. 
          Compiled by Brian Evans of the Georgia Institute of Technology,
          this  reference covers many areas of interest from artificial
          intelligence to geophysics to symbolic mathematics.

          0011:  LitSurvey.txt Plain text survey file  (January 7, 1994; 61
                 kilobytes)

          0022:  LitSurvey.ma Mathematica notebook survey file (January 7,
                 1994; 77 kilobytes)


0205-344: Perturbation Theory Package 1.0 (July 20, 1993)
          Author: David Nordfors
          The package provides routines for first- and second-order
          Rayleigh-Schroedinger perturbation theory in a matrix hamiltonian
          formalism, i.e., first and second order corrections to eigenvalues
          and eigenvectors of a matrix when a small perturbation is added to
          the matrix.

          0011:  PerturbationTheory.m Mathematica package (July 20, 1993; 4
                 kilobytes)


0205-197: Automata (February 3, 1994)
          Author: Klaus Sutner
          A Mathematica package that generates and manipulates finite state
          machines and their syntactic semigroups.

          0011:  README.txt Author notes and information (January 31, 1994;
                 10 kilobytes)

          0022:  aut.info Plain-text documentation file (January 31, 1994; 
                 22 kilobytes)

          0033:  automata.tar.Z Unix compressed tar archive (January 31,
                 1994; 320 kilobytes)

          0044:  automata.sit.hqx Macintosh binhexed stuffit archive 
                 (January 31, 1994; 497 kilobytes)

          0055:  automata.zip PK-Zip archive (January 31, 1994; 256
                 kilobytes)


0206-020: Pseudo-Random Pulse Sequencing (January 4, 1994)
          Author: Erik Jensen
          The package PseudoRandom.m defines a few routines that are useful
          for working with pseudorandom sequences.  These sequences (also
          called Maximum Length PseudoRandon Sequences or MLPRS's) have been
          used in optimizing time-of-flight spectroscopies in the physical
          sciences (neutron beam and molecular beam scattering). 

          0011:  PseudoRandom.m Mathematica package (December 1, 1993; 9
                 kilobytes)

          0022:  PRSequenceTest.ma Mathematica notebook (December 1, 1993; 
                 18 kilobytes)


0200-833: Physical Constants (March 14, 1994)
          Author: Wolfram Research
          Within this package are numerous physical constants. Once loaded,
          name of the constant can be used directly, rather than having to
          replace the variable with the constant value at some point. This
          package defines everything from the mass of a proton to the age of
          the universe.

          0011:  PhysicalConstants.m Mathematica package (August 1993; 3
                 kilobytes)

          0022:  Documentation.txt Plain-txt documentation (February 1994; 4
                 kilobytes)

          0033:  SampleInput.txt Sample input lines from
                 Miscellaneous`PhysicalConstants` (February 1994; 1 
                 kilobyte)


0202-059: Gallium Arsenide Crystal Graphics (February 1992)
          Author: Alastair McLean
          Renders the GaAs(110) surface within Mathematica.  It is similar 
          to the CrystalStructure.m package, which is a representation of 
          the diamond lattice.  These packages were partly inspired by the
          clarity with which CrystalStructure.m renders the diamond lattice,
          when the final output is generated PostScript, and the  desire to
          rotate the crystal structure and view it from different angles to
          look for symmetry planes, etc. Basically these models are
          alternatives to ball-and-stick type models. 

          0011:  GaAsNotebook.ma Mathematica notebook (February 1992; 73
                 kilobytes)

          0022:  GaAs1.m Mathematica package (February 1992; 2 kilobytes)

          0033:  GaAs2.m Mathematica package (February 1992; 3 kilobytes)

          0044:  GaAs3.m Mathematica package (February 1992; 4 kilobytes)

          0055:  GaAs4.m Mathematica package (February 1992; 4 kilobytes)

          0066:  GaAs5.m Mathematica package (February 1992; 6 kilobytes)

          0077:  GaAs6.m Mathematica package (February 1992; 6 kilobytes)

          0088:  GaAs7.m Mathematica package (February 1992; 6 kilobytes)

          0099:  GaAs-README.txt documentation (February 1992; 5 kilobytes)


0206-648: Movies of Molecular Model Vibrations (May 10, 1994)
          Author: W. Martin McClain
          Normal modes of molecular vibration lie at the heart of
          understanding the absorption of infrared light by molecules. These 
          notebooks were developed to accompany an undergraduate laboratory
          experiment.  Students spend one week using the infrared
          spectrometer, and two weeks understanding the theory, as presented
          in the notebooks.  The molecular model is a spring-and-ball model,
          and it uses only Hooke's Law for the springs and Newton's Third 
          Law for the balls.  The problem is transformed to an eigenproblem,
          solved, and the solution is transformed back to the 
          spring-and-ball space.  It is then easy to produce a movie of the
          molecular motion, starting from any desired initial conditions.  
          We show pseudorotation of a ring molecule, a motion that cannot be
          foreseen intuitively. 1994 Mathematica Developer Conference,
          Champaign, Illinois.

          0011:  1-TriangleNormalModes.ma Mathematica notebook (April 29,
                 1994; 225 kilobytes)

          0022:  2-TriangleMovies.ma Mathematica notebook (April 29, 1994; 
                 61 kilobytes)


0204-657: Schroedinger's Equation (March 1993)
          Author: Terry Robb
          Schroedinger's equation is numerically solved by calling an
          external subroutine from within Mathematica. By importing the
          Fortran subroutine (named SCHROED, which implements a
          Crank-Nicholson scheme) using InterCall, it is possible to do
          various experiments -- for example shooting a wave-packet at a
          potential barrier and watching an animation of the packet being
          mostly reflected but also partially tunnelling through the wall.
          The potential function V[x,t], required by the Fortran SCHROED
          routine, can be written as a Mathematica function which gives a 
          lot of flexibility for interactive experimentation. This notebook
          demonstrates one such experiment.

          0011:  schroed.ma Mathematica notebook (March 1993; 792 kilobytes)


0202-622: Lie Symmetries (March 1993)
          Author: Gerd Baumann
          The purpose of this program is to derive the determining equations
          for Lie-point symmetries. The determining equations are derived in
          a form simplified as far as possible. The program allows an
          automatic solution of the determining equations by using a
          polynomial ansatz in the dependent and independent variables. If
          the infinitesimals (symmetries) of the symmetry transformation is
          known, a classification of the related Lie-algebra is possible. 
          The Lie-algebra is directly related to the symmetry group of the
          equations that can be used to construct an explicit solution of 
          the equations of motion considered. Lie's symmetry method is 
          usable to construct solutions for linear and especially for
          nonlinear systems of differential equations. The program also
          provides a classification of the Lie-algebra by derived algebras.

          0011:  lie.m Mathematica package (March 1993; 68 kilobytes)

          0022:  Documentation.ps PostScript documentation for lie.m (March
                 1993; 373 kilobytes)


0203-397: Crystal Animations Resulting from Molecular Dynamics Calculations
          (July 1992)
          Author: Kazume Nishidate
          Mathematica gives us a very useful and simple way to visualize
          Molecular Dynamics (MD) simulations.  Mathematica is used to
          animate the motion of ions from the results of MD calculations
          produced by the ANRZR2 and MXDORTO programs, written by K.
          Nishidate and K.  Kawamura, respectively.  These notebooks allow 
          us to "look" at the dynamic motion of ions within a crystal from
          the results of MD calculation. There are many advantages to using
          Mathematica to analyze the MD simlation. For example, we can 
          easily view not only the animation of crystals, but also the
          graphics of trajectory of atoms over the MD simulation. Utilizing
          the graphics object  in animation notebooks, stereoscopic views 
          and projections of crystals can also be obtained .

          0011:  README.txt Author's notes  (July 1992; 5 kilobytes)

          0022:  NaCl.ma Mathematica notebook (July 1992; 72 kilobytes)

          0033:  KCl.ma Mathematica notebook (July 1992; 72 kilobytes)

          0044:  MgF2.ma Mathematica notebook (July 1992; 117 kilobytes)

          0055:  CaF2.ma Mathematica notebook (July 1992; 68 kilobytes)

          0066:  Perovskite.ma Mathematica notebook (July 1992; 75 
                 kilobytes)

          0077:  Quartz.ma Mathematica notebook (July 1992; 32 kilobytes)

          0088:  QuartzProjection.ma Mathematica notebook (July 1992; 32
                 kilobytes)

          0099:  QuartzStero.ma Mathematica notebook (July 1992; 27
                 kilobytes)


0206-031: Linear Lattice-Ligand Binding Notebooks (February 18, 1994)
          Author: Alan R. Wolfe
          These Mathematica notebooks calculate and plot data for the 
          binding of ligands to an infinite linear lattice.  Binding site
          overlap and cooperative interactions between adjacent bound 
          ligands are taken into account.  This is a mathematical model for
          non-sequence-selective binding of proteins and other small
          molecules (ligands) to a linear macromolecule such as DNA (the
          lattice).  The method is based on the treatment given in Wolfe, A.
          R. and Meehan, T. (1992) Journal of Molecular Biology 223,
          1063-1087.

          0011:  README.txt Plain-text documentation for all notebooks
                 (January 7, 1994; 10 kilobytes)

          0022:  README.ma Mathematica notebook documentation for all
                 notebooks (January 7, 1994; 13 kilobytes)

          0033:  Sym-Initialization.ma Mathematica notebook documentation 
                 for all notebooks (January 7, 1994; 22 kilobytes)

          0044:  Sym-CPNESP.ma Mathematica notebook documentation for all
                 notebooks (January 7, 1994; 6 kilobytes)

          0055:  Sym-cluster.ma Mathematica notebook documentation for all
                 notebooks (January 7, 1994; 8 kilobytes)

          0066:  Iso-Initialization.ma Mathematica notebook documentation 
                 for all notebooks (January 7, 1994; 44 kilobytes)

          0077:  Iso-cluster-CPNESP.ma Mathematica notebook documentation 
                 for all notebooks (January 7, 1994; 13 kilobytes)

          0088:  2Lig-Initialization.ma Mathematica notebook documentation
                 for all notebooks (January 7, 1994; 38 kilobytes)

          0099:  2Lig-CPNESP.ma Mathematica notebook documentation for all
                 notebooks (January 7, 1994; 12 kilobytes)

          0101:  Ani-Initialization.ma Mathematica notebook documentation 
                 for all notebooks (January 7, 1994; 103 kilobytes)

          0112:  Ani-cluster-CPNESP.ma Mathematica notebook documentation 
                 for all notebooks (January 7, 1994; 15 kilobytes)


0205-782: ChannelKinetics: Packages for Modeling Ion Channel Kinetics
          (941024)
          Author: Arnd Roth
          The ChannelKinetics packages implement parts of "Relaxation and
          fluctuations of membrane currents that flow through drug-operated
          channels" by D. Colquhoun and A.G. Hawkes, Proc.  R. Soc. Lond. B
          199, 231-262 (1977). Assuming a discrete state, continuous time
          Markov model for the behavior of ligand-gated ion channels, and
          given the transition rate constants between these states, the time
          evolution of their occupancy can be computed. This occupancy is
          then used to predict observables like the mean transmembrane
          current and its coefficient of variation. ColquhounHawkes.m
          numerically integrates the occupancy equation, which allows for
          arbitrary transmitter concentration functions of time. 
          ColquhounHawkesMC.m performs a Monte Carlo simulation of the
          channel state transitions. In order to be fast, it uses some C
          routines via MathLink.

          0011:  README.txt Introduction and file descriptions (930419; 3
                 kilobytes)

          0022:  Manual.ma Documentation notebook, read this first (930419;
                 659 kilobytes)

          0033:  DiagramToQMatrix.m Builds the transition rate matrix
                 (921201; 6 kilobytes)

          0044:  ColquhounHawkes.m Numerically solves the occupancy ODE
                 (930201; 10 kilobytes)

          0055:  ColquhounHawkesMC.m Package for Monte Carlo simulation
                 (930201; 33 kilobytes)

          0066:  chmc.tm MathLink templates and C routines for MC sim.
                 (930201; 33 kilobytes)

          0077:  NeuronInterface.m Package for data transfer (930419; 5
                 kilobytes)

          0088:  Talk.ma Mathematica notebook reprinted from the 1994
                 European Mathematica Conference, Oxford (940920; 691
                 kilobytes)


0200-787: Chemical Elements (August 1991)
          Author: Wolfram Research
          This includes a listing of all elements and important  related 
          data including atomic weight, boiling point,  melting point, heat
          of fusion and vaporization, density,  etc.  In addition to this,
          one can find the specific electronic structure of any element.

          0011:  ChemicalElements.m Mathematica package (August 1991; 65
                 kilobytes)

          0022:  Documentation.txt Plain-text documentation (June 1992; 5
                 kilobytes)

          0033:  SampleInput.txt Sample input lines from
                 Miscellaneous`ChemicalElements` (June 1992; 1 kilobyte)


0200-855: SI Units and Conversions (October 1991)
          Author: Wolfram Research
          This primarily deals with unit conversions and definitions.  
          Included are prefixes, electrical units, angles,  amounts of
          substances, acceleration due to gravity,  magnetic units, and 
          units of length, information, time,  mass, force, inverse length,
          volume, viscosity, types of  luminous energy and intensity,
          radiation, power, area,  pressure, energy, frequency, and speed.

          0011:  Units.m Mathematica package (October 1991; 21 kilobytes)

          0022:  SIUnits.m Mathematica package (October 1991; 2 kilobytes)

          0033:  Documentation.txt Plain-txt documentation (June 1992; 6
                 kilobytes)

          0044:  SampleInput.txt Sample input lines from 
                 Miscellaneous`Units` (June 1992; 1 kilobyte)