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Edit PDF files

Convert a batch of files to PDF

libreoffice --headless --convert-to pdf *.ppt --outdir PDF

Edit PDF files to rearrange pages

apt-get install pdfmod
pdfmod

To convert few files from svg to png

for name in *.svg
do
inkscape --export-area-page -z --export-background="white" --export-png=${name/%svg/png} $name
done

Release Mechanisms of Poly(ethylene glycol) Macroions from Aqueous Charged Nanodroplets

Jun Kyung Chung and Styliani Consta* Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7 J. Phys. Chem. B, 2012, 116 (19), pp 5777–5785

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

Zhang Hui is leaving for an academic position in China

Group photo

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

The 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

Diffusion 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

The 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.

Molecular simulations of the disintegration of charged droplets in the presence of macromolecules. 4490 project, 2009

Highly charged liquid droplets that contain solvent and excess of ions of the same sign are ubiquitous in aerosol and atmospheric chemistry, electrospray methods, as well as in technologies such as inkjet-printing and air-purification processes. In analytical chemistry techniques, electrospray methods are coupled to mass spectrometry (ESMS). Electrospray mass spectrometry is often used for the detection of macromolecules such as polypeptides or proteins in solution.

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

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