Atoms Molecules

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded...

The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.

EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.


Platforms: Windows, Mac, BSD, Linux

GDIS is a scientific visualization program for the display, manipulation, and analysis of isolated molecules and periodic structures. It is in development, but is nonetheless quite functional. It has the following features: * Support for many common file formats (CIF, PDB, XTL, XYZ, and many...


Platforms: *nix, C/C++, BSD

An editor for small organic molecules, written in C using gtk+. It can read and write SMILES and cml and can save to dia's file format. It is suitable for creating chemical molecule diagrams for lower level chemistry/ochem lab reports.


Platforms: Windows, Mac, Linux

The Atomic Dashboard The Atomic Dashboard is an interactive chemistry resource and learning tool developed by Bitwixt Software Systems. Used by educators, students, scientists, and the simply curious, The Atomic Dashboard features an interactive periodic table that lets you explore the chemical...


Platforms: Mac

In this submission we present the code of the Replacement Method (RM) [1-4] and Enhanced Replacement Method (ERM)[5], that were proposed some time ago by our group. Both methods produce linear regression QSPR-QSAR models that are quite close the FS (full search) ones with much less computational...


Platforms: Matlab

function [Xcoord,Ycoord,Zcoord] = fcc_cluster(L,M,a)generates coordinates of atoms inside fcc-cluster (face-centered-cubic)with cuboctatruncated shape (hovewer one can change from {111} to {110} truncation)it's arguments: L,M - parameters of cluster (L - size of the cluster,number of unit cells...


Platforms: Matlab

function [Xcoord,Ycoord,Zcoord] = bcc_cluster(L,M,a)generates coordinates of atoms inside bcc-cluster (base-centered-cubic)with cuboctatruncated shape (hovewer one can change from {111} to {110} truncation)it's arguments: L,M - parameters of cluster (L - size of the cluster,number of unit cells...


Platforms: Matlab

The file drawpdb.m is about 40 lines of code that makes a simple compact viewer of small molecules. A number of .pdb files are also included.


Platforms: Matlab

NanoVis (beta version) allows to visualize any atomistic structure by reading a user defined file. The supported formats are "gen" and "xyz". There are two display modes: normal and "spacefill". In the zip file, with the .m file, there are two examples of structure and a file containing the atoms...


Platforms: Matlab

This method computes an accurate continuous approximation of the DW-MRI signal using adaptive kernels (A. Barmpoutis et al. "Adaptive kernels for multi-fiber reconstruction", In the Proceedings of IPMI, 2009). The approximation is based on Fig. 3 of the article which shows the plot of the DW-MRI...


Platforms: Matlab

initializePhysicalConstants.m loads important physical constants into the structure CONSTS. The CONSTS structure will contain both values (accessible by CONSTS.var_name), and descriptive information (CONSTS.desc.var_name.[Name, Units, Value]).EXAMPLE USAGE: % What are the units of the unversal...


Platforms: Matlab

A Fixed-Point Iterative Schema for Error Minimization in k-Sparse DecompositionA a new algorithm to solve the sparse approximation problem over redundant dictionaries based on LiMapS, where the input signal is restricted to be a linear combination of k atoms from a fixed dictionary.


Platforms: Matlab

The fifth MATLABdlT« Programming Contest, Molecule, will run from May 16-23, 2002.The challenge is to model the structure of a molecule (which for the sake of simplicity will be limited to two dimensions). You have been given a collection of plastic connecting rods that represent the distance...


Platforms: Matlab

Is it a tumor? Magnetic Resonance Imaging (MRI) can tell. Your head is full of tiny radio transmitters (the nuclear spins of the hydrogen nuclei of your water molecules). In an MRI unit, these little radios can be made to broadcast their positions, giving a detailed picture of the inside of your...


Platforms: Mac

How did scientists figure out the structure of atoms without looking at them? Try out different models by shooting light at the atom. Check how the prediction of the model matches the experimental results. * Visualize different models of the hydrogen atom. * Explain what experimental...


Platforms: Mac

How do you know if a chemical equation is balanced? What can you change to balance an equation? Play a game to test your ideas! Sample Learning Goals * Balance a chemical equation. * Recognize that atoms are conserved in a chemical reaction. * Describe the difference between coefficients and...


Platforms: Mac

The EJS Kac Model simulates the relaxation of a gas to equilibrium by randomly selecting and then colliding gas molecules but without keeping track of the molecules' positions. As long as the collisions are consistent with spatial isotropy, the Boltzmann speed distribution will emerge. You can...


Platforms: Mac

How do greenhouse gases affect the climate? Explore the atmosphere during the ice age and today. What happens when you add clouds? Change the greenhouse gas concentration and see how the temperature changes. Then compare to the effect of glass panes. Zoom in and see how light interacts with...


Platforms: Mac