[Postdoc] A postdoctoral position in computational molecular biology at UCSD

**haichit** · #1 (**permalink**) 06-14-2010

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Article:
Postdoctoral Research Scholar
University of California
Campus: San Diego

Academic Department/Research Unit:
San Diego Supercomputer Center

Research Discipline:
Computational Molecular Biology/Chemistry, High Performance Computing

Description:
A postdoctoral position in computational molecular biology is available immediately within the group of Prof Ross Walker at the San Diego Supercomputer Center. This will involve close collaboration with researchers at UCSD, Cornell, University of Michigan and the National Renewable Energy Laboratory to carry out research in the field of algorithm and method development for Molecular Dynamics Simulations.

The research focus of the group is advanced Molecular Dynamics (MD) simulations and related method development. It includes the development of efficient algorithms for accurate and parallel computation of classical and hybrid quantum mechanical/molecular mechanical (QM/MM) MD simulations; comprehensive force field development for simulation of complex phospholipid membranes; improved sampling techniques for classical and QM/MM MD simulations; GPU acceleration of MD simulations; the development of novel approaches for analysis of large scale and long time length MD simulation trajectories; approaches to parallel post-processing and on the fly MD analysis; the use of MD simulation techniques for studying protein reactivity including elucidation of the activation pathways and, specific to this project, studies of cellulose degrading enzymes for use in bio-fuel production.

The successful candidate will interact with the developers of the AMBER and CHARMM software packages to develop improved techniques for modeling enzymes involved in cellulose degradation although the techniques developed will be of general benefit to all MD researchers. This work will include the development, optimization and validation of highly scalable algorithms and software addressing complex MD simulation techniques that go beyond the traditional explicit solvent PME approaches that most parallel MD packages currently implement. This will include development for both traditional highly parallel architectures and also emerging technologies such as GPUs and other accelerator technologies. While the focus will mostly be on classical MD techniques there is opportunity, for a candidate with additional QM/MM experience to spend a portion of their time working on extending the QM/MM functionality of the AMBER software. The incumbent will have access to SDSC, DOE and NSF supercomputer resources including some of the world's most powerful machines. Occasional travel may be required including visits to the collaborating sites approximately 2 to 3 times per year and presentation of results at scientific conferences.

Skills and Knowledge Required:
The applicant should have, or expect to shortly receive, a Ph.D. in Computational Biology, Computational Chemistry, Computational Life Sciences or relevant disciplines as well as research experience in computational molecular biology, and strong computer programming skills, including Fortran 95 and C/C++ and knowledge of molecular biology, protein structure and molecular dynamics. Applicants with Ph.D.'s in Computer Science backgrounds will also be considered if they have experience in molecular dynamics simulations or related disciplines. Experience in high performance computing, molecular dynamics and parallel (MPI) or GPU programming (CUDA) is also extremely desirable. Applicants should enjoy working on challenging and exciting projects together with a team of international experts.

Location:
Nestled along the Pacific Ocean on 1,200 acres of coastal woodland, with year round summer, just steps from the beach and minutes from beautiful downtown La Jolla, UC San Diego is a preeminent university in the country providing an excellent environment for research in computational biology, computer science, biochemistry, bioengineering, medicine, as well as interdisciplinary research. The successful candidate will reside in the new building of San Diego Supercomputer Center on the main campus of UCSD.

Salary/Stipend Information:
Commensurate with NIH Guidelines.

Benefits:
This position qualifies for Full Postdoctoral Benefits - see [Only registered and activated users can see links. ] for further information.

Procedure to Apply:
Interested individuals should e-mail their curriculum vitae, a cover letter stating research interests and career goals and the names, telephone numbers, and e-mail addresses of three references to Prof. Ross C. Walker at rcw_at_sdsc.edu.

Position Closing Date:
Open Until Filled.

Appointment Length/Period:
Initial appointment for one year, with the possibility of renewals.

For more information or to apply, please contact:
Ross C. Walker, Phd
rcw_at_sdsc.edu
Telephone: (858) 822-0854