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Star-shaped droplets

Droplets subject to electric fields may obtain spectacular morphologies. Starting from the seminal works of Rayleigh (1882), Zeleny (1917) and G. I. Taylor (1964), the behaviour of droplets in an electric field continues to fascinate scientists due to their numerous applications. Charged droplets are often generated by electrospray ionization methods. We have found by molecular simulations that when a nano-drop comprising a single spherical central ion and dielectric solvent is charged above a well-defined threshold, it acquires a stable star morphology [S.

Modeling the stability of non-covalent protein complexes and assemblies

Protein-protein interactions (PPIs) play a pivotal role in all biological processes, including signal transduction, enzymatic catalysis as well as the formation of protein quaternary structures.


Mechanisms of Phase Transformations of TiO2 Nanotubes and Nanorods

Andrei Buin, Styliani Consta*, and Tsun-Kong Sham
Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
J. Phys. Chem. C, 2011, 115 (45), pp 22257–22264

Submitting jobs on the theory cluster

Job 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

Molecular modelling tutorial

A 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 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

Files in the example directory

CHEM 9444a-Computer Simulations in Chemistry


CHEM 9444a-Computer Simulations in Chemistry

Rare event dynamics and reaction rates

Many processes in chemical and biological systems such as chemical reactions, conformational changes of macromolecules, nucleation processes in solution or in other condensed phases take place by infrequent fluctuations of the locations of the molecules in the solvent and the reactive system. Capturing these special fluctuations that finally determine the mechanism and rate of the process is a challenging problem in computations. This problem lies at the heart of chemistry.

Render a molecule from command line using VMD

export name="1hjm"
export tachyon="/usr/local/lib/vmd/tachyon_LINUX"

Create script using VMD

The result


Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry.... if mathematical analysis should ever hold a prominent place in chemistry, an aberration which is happily almost impossible, it would occasion a rapid and widespread degeneration of that science.

Auguste Comte, Cours de philosophie positive, 1830

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