Compiling techniques. - Thomas E. Cheatham (Commun. ACM, 1966)

Parallel bin packing using first fit and k-delayed best-fit heuristics. - Azer Bestavros; Thomas E. Cheatham; Dan C. Stefanescu (SPDP, 1990)

Efficient Execution of Homogeneous Tasks with Unequal Run Times on the Connection Machine. - Azer Bestavros; Thomas E. Cheatham (ICPP (3), 1991)

A Suite of Optimizers Based on Abstract Interpretation. - Thomas E. Cheatham; Dan C. Stefanescu (PEPM, 1992)

Common runtime support for high-performance parallel languages. - Geoffrey C. Fox; Sanjay Ranka; Michael L. Scott; Allen D. Malony; James C. Browne; Marina C. Chen; Alok N. Choudhary; Thomas E. Cheatham; Janice E. Cuny; Rudolf Eigenmann; Amr F. Fahmy; Ian T. Foster; et al. (SC, 1993)

A Suite of Analysis Tools Based on a General Purpose Abstract Interpreter. - Thomas E. Cheatham; Haiming Gao; Dan C. Stefanescu (CC, 1994)

H-BSP - A General Purpose Parallel Computing Environment. - Thomas E. Cheatham; Amr F. Fahmy; Dan C. Stefanescu (IFIP Congress (1), 1994)

Supporting multiple evolving compilers. - Thomas E. Cheatham; Amr F. Fahmy; Dan C. Stefanescu (SEKE, 1994)

Bulk synchronous parallel computing-a paradigm for transportable software. - Thomas E. Cheatham; Amr F. Fahmy; Dan C. Stefanescu; Leslie G. Valiant (HICSS (2), 1995)

General Purpose Optimization Technology. - Thomas E. Cheatham; Amr F. Fahmy; Dan C. Stefanescu (LCPC, 1995)

Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations. - Thomas A. Darden; Lee G. Pedersen; Abdulnour Y. Toukmaji; Michael F. Crowley; Thomas E. Cheatham (PP, 1997)

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program. - Michael F. Crowley; Thomas A. Darden; Thomas E. Cheatham III; David W. Deerfield II (J. Supercomput., 1997)

The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. - Stephen C. Harvey; Robert K.-Z. Tan; Thomas E. Cheatham III (J. Comput. Chem., 1998)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. - Thanh N. Truong; Manohar Nayak; Hung H. Huynh; Tom Cook; Priya Mahajan; Le-Thuy T. Tran; Jannu Bharath; Shrish Jain; Ha B. Pham; Chaiwoot Boonyasiriwat; Nhat Nguyen; Evan Andersen; et al. (J. Chem. Inf. Model., 2006)

RNA structure refinement and force field evaluation using molecular dynamics simulations. - Niel M. Henriksen; Thomas E. Cheatham III (TG, 2011)

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. - Kiumars Shahrokh; Anita M. Orendt; Garold S. Yost; Thomas E. Cheatham III (J. Comput. Chem., 2012)

iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. - Julien C. Thibault; Julio C. Facelli; Thomas E. Cheatham III (J. Chem. Inf. Model., 2013)

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. - Julien C. Thibault; Daniel R. Roe; Julio C. Facelli; Thomas E. Cheatham III (J. Cheminformatics, 2014)

Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations. - Niel M. Henriksen; Hamed S. Hayatshahi; Darrell R. Davis; Thomas E. Cheatham III (J. Chem. Inf. Model., 2014)

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings. - Julien C. Thibault; Thomas E. Cheatham III; Julio C. Facelli (J. Chem. Inf. Model., 2014)

The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis. - Thomas E. Cheatham III; Daniel R. Roe (Comput. Sci. Eng., 2015)

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations. - Zahra Heidari; Daniel R. Roe; Rodrigo Galindo-Murillo; Jahan B. Ghasemi; Thomas E. Cheatham III (J. Chem. Inf. Model., 2016)

Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ. - Amit Roy; Daniel R. Roe; Mary W. Hall; Thomas E. Cheatham (LCPC, 2017)

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. - Marie Zgarbová; Petr Jurecka; Filip Lankas; Thomas E. Cheatham III; Jirí Sponer; Michal Otyepka (J. Chem. Inf. Model., 2017)

Task-parallel Analysis of Molecular Dynamics Trajectories. - Ioannis Paraskevakos; André Luckow; Mahzad Khoshlessan; George Chantzialexiou; Thomas E. Cheatham; Oliver Beckstein; Geoffrey C. Fox; Shantenu Jha (ICPP, 2018)

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. - Daniel R. Roe; Thomas E. Cheatham III (J. Comput. Chem., 2018)

Improving regional cyberinfrastructure services through collaboration: Cyberteam for the Rocky Mountain Advanced Computing Consortium. - Andrew J. Monaghan; Brett Milash; Tobin Magle; Thomas Hauser; Thomas E. Cheatham; Patrick J. Burns; Shelley Knuth; Anita M. Orendt; Suzi White; Dawn Paschal; Howard Jay Siegel; Timothy Kaiser; et al. (PEARC, 2019)

Assessment of financial returns on investments in cyberinfrastructure facilities: A survey of current methods. - Craig A. Stewart; David Y. Hancock; Julie Wernert; Thomas R. Furlani; David Lifka; Alan Sill; Nicholas Berente; Donald F. McMullen; Thomas E. Cheatham; Amy W. Apon; Ron Payne; Shawn D. Slavin (PEARC, 2019)

Fostering Collaboration Among Organizations in the Research Computing and Data Ecosystem. - Sharon Broude Geva; Dana Brunson; Thomas E. Cheatham III; James Deaton; James Griffioen; Curtis W. Hillegas; Douglas M. Jennewein; Gail Krovitz; Tobin Magle; Patrick Schmitz; Karen Tomko; James C. Wilgenbusch (PEARC, 2020)

Leveraging a research computing and data capabilities model for strategic decision-making. - Patrick Schmitz; Dana Brunson; Gail Krovitz; Thomas E. Cheatham; Claire Mizumoto (PEARC Companion, 2020)

A Research Computing and Data Capabilities Model for Strategic Decision-Making. - Patrick Schmitz; Claire Mizumoto; John Hicks; Dana Brunson; Gail Krovitz; James B. Bottum; Joel Cutcher-Gershenfeld; Karen Wetzel; Thomas E. Cheatham (PEARC, 2020)

The Connect.Cyberinfrastructure Portal. - Julie Ma; Sarah Akbar; Torey Battelle; Kevin L. Brandt; Eric Brown; Dana Brunson; Dhruva Chakravorty; Thomas E. Cheatham; Bhushan Chitre; Adrian Del Maestro; Andrea Elledge; Vikram Gazula; et al. (PEARC, 2021)

Advancing the Workforce That Supports Computationally and Data Intensive Research. - Patrick Schmitz; Scott Yockel; Claire Mizumoto; Thomas E. Cheatham; Dana Brunson (Comput. Sci. Eng., 2021)

Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community✱. - Thomas J. Hacker; Preston M. Smith; Dana Brunson; Lisa Arafune; Thomas E. Cheatham; Ewa Deelman (PEARC, 2022)

Professionalization of Research Computing and Data: An Expanded Agenda. - Joel Cutcher-Gershenfeld; Torey Battelle; Dana Brunson; Thomas E. Cheatham; Jacob Fosso-Tande; Douglas M. Jennewein; Julie Ma; Lauren A. Michael; Timothy Middelkoop; Henry Neeman; Patrick Schmitz (PEARC, 2023)

Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. - Lauren Winkler; Thomas E. Cheatham (J. Chem. Inf. Model., 2023)

AmberTools. - David A. Case; Hasan Metin Aktulga; Kellon Belfon; David S. Cerutti; G. Andrés Cisneros; Vinícius Wilian D. Cruzeiro; Negin Forouzesh; Timothy J. Giese; Andreas W. Götz; Holger Gohlke; Saeed Izadi; Koushik Kasavajhala; et al. (J. Chem. Inf. Model., 2023)

Recent Developments in Amber Biomolecular Simulations. - David A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambasu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai-Sung Lee; et al. (J. Chem. Inf. Model., 2025)