Computational Modelling Group

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• Syma Khalid

Research

The systems and synthetic biology modelling group, headed by Dr Syma Khalid is based in the Chemical Biology sub-section of the School of Chemistry, University of Southampton. Our research involves the application of computational techniques to the study of large biological molecules and systems including bacterial outer membrane proteins and nucleic acids. One of our key areas of research involves applying the knowledge gained from studying biological systems to aid the design of synthetic systems for applications in bionanotechnology. We are particularly interested in developing methods to bridge the gap between traditional biomolecular simulation and systems biology.

We have strong links with experimental groups in physical biology, biochemistry, chemical biology and structural biology

Current Projects

Bacterial Outer Membrane Proteins

Stochastic Sensors

Stochastic biosensors are built around a membrane containing a cylindrically shaped protein (usually a bacterial outer membrane protein). A voltage applied across the membrane generates an ionic current that pulls charged analyte molecules through the pore. As the analyte molecule is pulled through the nanopore, it blocks the current by a characteristic amount, thus leaving a trace of itself. The characteristic decrease in the current arising from differences in their chemical properties allows discrimination between different analyte molecules. We are undertaking simulation studies of bacterial proteins and model nanopores based on proteins, to aid the development of robust and efficient biosensors suitable for the detection of a variety of analytes. This project is funded through a BBSRC CASE award with Oxford Nanopore Technologies as the industrial partner.

Linking Structure to Function

We are interested in the link between the structure of bacterial outer membrane proteins (OMPs) and their function. To this end we have studied the conformational dynamics and interactions with membranes of a variety of OMPs.

DNA-lipid interactions

The E.coli membrane: towards a systems description This project includes the OMSys collaboration with Prof Mark Sansom's group, Oxford

The cohesin hinge region Collaborative project with Professor Kim Nasmyth's group, Oxford

Research Interests

Life sciences simulation: Bioinformatics, Biomolecular Organisation, Biomolecular simulations, Microbiology, Nanoscale Assemblies, Structural biology, Systems biology

Physical Systems and Engineering simulation: Biomechanics, Elasticity, Structural dynamics

Algorithms and computational methods: FFT, Molecular Dynamics, Molecular Mechanics

Visualisation and data handling methods: Database

Simulation software: Gromacs

Visualisation and data handling software: Gnuplot, MS Office Access, VMD, Xmgrace

Software Engineering Tools: CVS, Emacs

Programming languages and libraries: C, Fortran, Perl, Python, Tcl

Computational platforms: HECToR, HPCx, Iridis, Linux, Mac OS X

Transdisciplinary tags: Complex Systems, Computer Science, e-Research, HPC, Scientific Computing, Visualisation

Syma's team members

James Graham Postgraduate Research Student, Electronics and Computer Science (FPAS)

Jamie Parkin Postgraduate Research Student, Chemistry (FNES)

Ric Gillams Postgraduate Research Student, Chemistry (FNES)

Andrew Guy Postgraduate Research Student, Chemistry (FNES)

Josephine Corsi Alumnus, University of Southampton

Joint projects with...

Philip Williamson Senior Research Fellow, Biological Sciences (FNES)

Research Groups

Projects

Gallery