[BiO BB] 2 Postdoctoral positions in computational biophysics and bioinformatics

Dr. Dennis R. Livesay drlivesay at csupomona.edu
Fri Dec 16 15:33:23 EST 2005

(2) Postdoctoral Research Associate Positions
Computational Biophysics, Biophysical Chemistry, Bioinformatics

Applications are invited for two postdoctoral Research Associate positions starting in March 2006. A challenge of biophysics is to understand protein folding, stability, flexibility, and function in terms of structure and solvent/thermodynamic conditions. This project builds upon prior success of using graph-rigidity algorithms to identify flexible and rigid regions in proteins, and development of the Distance Constraint Model (DCM). The DCM is based on the hypothesis that network rigidity is an underlying mechanism for enthalpy-entropy compensation, yielding an algorithm to account for non-additivity in free energy decompositions. A prototype DCM will be extended to include explicit modeling of essential enthalpy-entropy compensation mechanisms that include: hydration, hydrophobic and electrostatic interactions, and residue-specific component enthalpy and entropy parameterization. These improvements will enable us to predict protein stability in mixed solvent conditions, including heat and cold denaturation. There are three distinct project goals. Goal (i): Development and release of a fast computational tool that harmoniously quantifies stability and flexibility in practical computing times. Goal (ii): To construct a publicly accessible QSFR database providing users access to protein stability and flexibility data in conjunction with user-friendly analysis tools to investigate Quantified Stability/Flexibility Relationships. Goal (iii): Application of the DCM to investigate protein flexibility and stability. For example, the local-details of protein flexibility can be quantified to identify correlated atomic motions, important for induced fit and allosteric conformational changes, at a given thermodynamic condition. Moreover, this software tool will be used to elucidate evolutionarily conserved QSFR within protein families and superfamilies.

We are looking for highly motivated candidates with a Ph.D. in Biophysics, Physical Chemistry, Physics, Computer Science, or related discipline. Candidates should have prior experience in the area of Computational Biophysics and/or Bioinformatics. The successful candidates must have demonstrated ability to conduct research independently, and ability to work in an interdisciplinary environment that requires team effort. Prior postdoctoral experience is desirable. The pay scale will be based on standard NIH rates, commensurate with experience. Both candidates must have strong skills and a record of accomplishment in C/C++ programming. Knowledge of UNIX/LINUX operating systems is essential. Both Research Associates will routinely work with high performance (grid and cluster) computing at the operational and algorithmic levels. They will be working closely with one another, Dr. Donald J. Jacobs (DJJ) at the University of North Carolina at Charlotte, Dr. Dennis R. Livesay (DRL) at Cal Poly Pomona, students and collaborators. One Associate will reside in the group of DJJ with emphasis on biophysical modeling. The candidate interested in this position must have a strong background in statistical mechanics and chemical thermodynamics. The other Associate will reside in the group of DRL with emphasis on Computational Biology as it pertains to protein modeling. The candidate interested in this position must have experience with database design, MySQL and CGI programming. Knowledge of basic sequence and structure analysis techniques is essential. Impressive computing resources are available at both sites for both Associates.   

Further information can be obtained at www.physics.uncc.edu/PhysStaff/djacobs/djacobs.html or by e-mail to DJJ (djacobs1 at email.uncc.edu) and at http://www.csupomona.edu/~drlivesay or by e-mail to DRL (drlivesay at csupomona.edu). Applicants interested in biophysical modeling should send a curriculum vitae, graduate transcripts, a research statement, and arrange for three letters of reference to be sent to Prof. Donald J. Jacobs, Dept. of Physics and Optical Science, UNC Charlotte, 9201 University City Blvd., Charlotte, NC 28223. Applicants interested in computational biology should send their materials to Prof. Dennis R. Livesay, Dept. of Chemistry, Cal Poly Pomona, 3801 W. Temple Ave, Pomona, CA 91768. Both positions are supported by the recently funded NIH project entitled “Predicting Protein Stability and Flexibility.” Full consideration will be to applications received before February 12, 2006. UNC Charlotte and Cal Poly Pomona are EOE/AA employers. 

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