Welcome to the home page for the Cheatham lab at the University of Utah.

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Thomas E. Cheatham, III Assistant Professor Departments of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry College of Pharmacy Adjunct Assistant Professor Department of Bioengineering Henry Eyring Center for Theoretical Chemistry Center for High Performance Computing University of Utah 30 South 2000 East, Room 201 Salt Lake City, Utah 84112-5820 (801) 587-9652 FAX: (801) 585-9119 tec3@utah.edu Offices: BPRB 295

The research in our lab involves the development and application of molecular dynamics and free energy simulation methodologies (with AMBER, CHARMM, NAMD, and other programs) to biomolecular systems in their native environments. Until recently, this has focused heavily on the reliable representation of small nucleic acid duplexes in solution. Now we are begining to also look at other systems including larger DNA and RNA models, proteins, and polymeric micelle systems with a keen focus on both assessing and validating the simulation results and exposing and overcoming limitations in the methods and force fields. In addition to continued development of ptraj (see the software link) for analysis of MD trajectories, we are exploring methods to mine more information from the simulation data and means to more broadly disseminate the MD results.

Research in the lab is currently funded by various research grants, including:

• NIH RO1-GM081411-01A1 (2/01/08-1/31/13) "Biomolecular simulation for the end-stage refinement of nucleic acid structure".
      PI: Cheatham.

  This core R-01 funding supports research into the development of better force fields for simulation of RNA, attempts various means to assess and validate the performance of MD simulation as applied to RNA, and seeks to explore means to more broadly disseminate MD simulation data. Here is the link to the NIH CRISP abstract.

• NIH R01-GM079383-01A1 (9/28/07-8/31/12) "AMBER force field consortium: A coherent biomolecular simulation platform."
      PI: Y. Duan (UC Davis)
      Co-PIs: Cheatham, C. Simmerling (Stony Brook U), R. Luo (UC Irvine), P. Cieplak (Burnham Inst), and J. Wang.

  The consortium aims to improve the AMBER force fields; our role focuses on polarizable force fields for nucleic acids. Here is the link to the NIH CRISP abstract.

• Office of Naval Research N00014-05-1-0457 (4/01/05-9/30/09) "A new research tool for the computer simulation of chemical dynamics in complex systems.".
      PI: G. Voth
      Co-PIs: Cheatham, Case (Scripps), Miller (Berkeley), and Schlegel (Wayne State U).

  Cheatham consults related to AMBER application and development of chemical reaction capabilities.

• NSF Cyberinfrastructure partnership, LRAC MCA01S027 (yearly) "Insight into biomolecular structure, dynamics, interactions and energetics from simulation".
      PI: Cheatham.

  This is a large allocation of resources on the NSF supercomputer centers to support research in the Cheatham lab.

If you are trying to reach me, my office is in the Biopolymers building, BPRB 295A, on the Health Sciences Campus.