December222012
Cut-away through a vesicle containing E.coli outer membrane proteins. This coarse-grained, solvated system is composed of over 1 million particles. It has been studied by MD simulations using the GROMACS simulation package on the IridisIII HPC resource at the University of Southampton

Cut-away through a vesicle containing E.coli outer membrane proteins. This coarse-grained, solvated system is composed of over 1 million particles. It has been studied by MD simulations using the GROMACS simulation package on the IridisIII HPC resource at the University of Southampton

vesicle GROMACS molecular dynamics simulation MARTINI coarse-grain iridisIII southampton computing HPC 

November132012
ssDNA in a simplified nanopore based on the alpha hemolysin barrel. Biophys J. 2012 Sep 5;103(5):1028-36. Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for sequencing; a Molecular Dynamics Simulation Study. Guy AT, Piggot TJ, Khalid S.

ssDNA in a simplified nanopore based on the alpha hemolysin barrel.

Biophys J. 2012 Sep 5;103(5):1028-36.
Single-Stranded DNA within Nanopores:
Conformational Dynamics and Implications for sequencing; a Molecular Dynamics Simulation Study.
Guy AT, Piggot TJ, Khalid S.

DNA nanopore biotechnology nanotechnology molecular dynamics simulation biophysical journal sequencing 

September62012
FecA protein from the outer membrane of E.coli, embedded in an asymmetric model of the outer membrane environment. Soon to be published in Piggot, Holdbrook and Khalid, BBA Biomembranes, 2012. 

FecA protein from the outer membrane of E.coli, embedded in an asymmetric model of the outer membrane environment. Soon to be published in Piggot, Holdbrook and Khalid, BBA Biomembranes, 2012. 

protein membrane simulation model outer LPS lipids phospholipids TonB E.coli FecA transporeter 

July112012

This movie shows the top view of a melittin (venom from honey bees) tetramer embedded in a POPE lipid bilayer. 

melittin simulation molecular dynamics peptide antimicrobial membrane lipids 

June102012

CECAM meeting on Free Energy Calculations

Free energy calculations: From theory to applications

June 4, 2012 to June 8, 2012

Location : Ecole des Ponts, Champs-sur-Marne, France.

http://www.cecam.org/workshop-695.html

This workshop featured talks from a combination of  established high profile speakers as well as younger researchers.

A number of themes arose from this workshop, the overarching one being that there is still no ‘best way’ to calculate free energies from molecular simulations. Workshops like this, are essential in facilitating discussion and disseminating the latest findings. Given  that new methods are being developed and refined, disseminating the latest progress in a timely fashion is of utmost importance. 

A very useful resource from Michael Shirts’ lab:

http://www.alchemistry.org/wiki/index.php?title=Main_Page

free energy simulation molecular dynamics monte carlo delta G 

May242012

Prestigious PhD studentships available

4-year studentships are available to work in Dr Syma Khalid’s group the Institute for Complex Systems Simulation Doctoral Training Centre at the University of Southampton.

For details see:

http://www.icss.soton.ac.uk/programme/index.html

Please send informa enquiries to Dr Syma Khalid via email : S.Khalid@soton.ac.uk

PhD studentship funding science complexity simulation 

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