Thomas Cheatham III

Thomas Cheatham III is a Professor of Medicinal Chemistry in the College of Pharmacy and Adjunct Professor of Biomedical Engineering at the University of Utah, specializing in computational biomolecular simulation methodologies. His work bridges theoretical chemistry and biological applications through advanced molecular dynamics techniques.

Education:

• B.A., Middlebury College
• Ph.D., University of California, San Francisco

Research Focus: Dr. Cheatham pioneers molecular dynamics and free energy simulation methods (AMBER/CHARMM) for proteins, nucleic acids, and lipids. His group addresses critical challenges in environmental dependence of nucleic acid structure (ion/hydration effects on DNA), conformational transition pathways (e.g., B-DNA/Z-DNA junctions), and macromolecular flexibility beyond static experimental structures. Recent innovations target force field refinement for modified nucleic acids and polarizable models.

Publication Trends: Analysis of his 2023-2025 publications reveals three dominant themes: (1) Nucleic acid force field optimization (60% of recent work), particularly RNA/DNA parameterization; (2) Development of simulation infrastructure including FAIR data principles and AmberTools; (3) Application-driven studies of therapeutic targets like Bcr-Abl inhibitors. His work increasingly integrates polarizable force fields and high-performance computing.

Research Infrastructure: He leads the AMBER biomolecular simulation software development effort and maintains an active laboratory focused on methodological innovation. His group collaborates extensively with experimentalists to validate computational predictions and provides open-source tools (PTRAJ/CPPTRAJ) used globally. Current initiatives emphasize reproducibility through standardized simulation protocols and data sharing frameworks.