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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)
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