Computational Physical Chemistry
Computer simulations is a powerful tool in exploring microscopic details of physical and chemical phenomena. Sizes of systems that are investigated range from clusters to bulk systems. We focus on application of Molecular Dynamics and Monte Carlo techniques to study activated processes in solutions. These are modeled on atomic scale using different levels of description in order to capture features defining the properties of the systems.
Phase transitions and chemical reactions in solution
Molecular modelling tutorial
Thu, 11/11/2010 - 09:02 — Styliani ConstasA live debian system could be installed onto a memory key. Please, provide me with a key and I 'll burn a copy for you. Booting from the memory key you can make few runs without modifying your computer or installing additional software. Otherwise check www.gromacs.org and install Gromacs on your computer.
In the home directory of the default user styliani you can find an example of MD run using Gromacs package.
Open a terminal window.
~$ cd teaching
Teaching
Thu, 09/16/2010 - 17:23 — Styliani ConstasSuggested 4490 projects for 2010/11
Molecular simulations of the dynamics of charged macromolecules Additional info
CHEM 4444a "Computer Simulations in Chemistry" Fall
Tue, 09/14/2010 - 22:08 — Styliani ConstasTHE UNIVERSITY OF WESTERN ONTARIO
DEPARTMENT OF CHEMISTRY
CHEMISTRY 4444A/B-FALL 2010
CHEM 4444a-Computer Simulations in Chemistry
Submitting jobs on the cluster
Sun, 12/20/2009 - 05:18 — Styliani ConstasJob Submission
To submit a 4 processor job on the cluster run the following command
qsub -N jobname -pe openmpi 4 submit_gromacs.bash
where submit_gromacs.bash is the following file in your work directory
Zhang Hui is leaving for an academic position in China
Sat, 11/28/2009 - 03:43 — Styliani Constas
Jun Chung, Daniella Mei, Styliani Constas, Serge Ayissi and Zhang Hui
Molecular simulations of the conformational behavior of 1-chloropropane adsorbed in Faujasite-type zeolite. 4490 project, 2009
Wed, 08/26/2009 - 15:20 — Styliani ConstasThe increased awareness of the environmental hazards of chlorinated halocarbons (CHCs) has led to the development of new separation and catalytic conversion processes of CHCs. Faujasite zeolite is the most widely used material in separation processes in petroleum industry and is a candidate for the catalytic decomposition of CHCs. In this project molecular simulations will be performed by inserting molecules of 1-chloropropane in the Faujasite zeolite matrix.
Molecular simulations of diffusion in zeolites. 4490 project, 2009
Wed, 08/26/2009 - 15:17 — Styliani ConstasDiffusion of aromatic compounds in zeolites is significant in petrochemical industry since zeolites are used as catalysts in petrochemical processes. The diffusion in zeolites is also a challenging problem in simulations. The zeolite that will be studied is composed out of oxygen and silicon atoms and it is penetrated by zig-zag and straight channels that intersect. Diffusion takes place along these channels. The challenge in simulations arises from the fact that the free energy profile of the diffusion process along the channels involves several barriers.
Estimation of free energies of binding and changes in conformation by molecular simulations. 4490 project, 2009
Wed, 08/26/2009 - 15:14 — Styliani ConstasThe free energy of binding of two molecules is defined as the free energy difference between these molecules in the bound and the free, unbound state. This quantity can be determined experimentally through the measurement of binding constants using for instance BIAcore or microcalorimetry techniques. In simulations several schemes that involve statistical mechanics and reaction paths have been devised in order to compute free energy differences. In this project a student will study the tricks of free energy perturbation methods and will apply them in a simple model of protein and ligand.
