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2020 – today
- 2023
[j17]Lauren Winkler
, Thomas E. Cheatham:
Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. J. Chem. Inf. Model. 63(8): 2505-2511 (2023)- [j16]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, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.:
AmberTools. J. Chem. Inf. Model. 63(20): 6183-6191 (2023) - [c21]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:
Professionalization of Research Computing and Data: An Expanded Agenda. PEARC 2023: 129-136 - 2022
- [c20]Thomas J. Hacker, Preston M. Smith, Dana Brunson, Lisa Arafune, Thomas E. Cheatham, Ewa Deelman:
Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community✱. PEARC 2022: 26:1-26:7 - 2021
- [j15]Patrick Schmitz, Scott Yockel, Claire Mizumoto, Thomas E. Cheatham, Dana Brunson:
Advancing the Workforce That Supports Computationally and Data Intensive Research. Comput. Sci. Eng. 23(5): 19-27 (2021) - [c19]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, John Goodhue, James Griffioen, Abigail Hyde, Douglas M. Jennewein, Shelley Knuth, B. J. Lougee, Timothy Middelkoop, Sasmita Mohapatra, Sia Najafi, Kaylea Nelson, Lisa Perez, Bruce Segee, Julia Sheats, Andrew H. Sherman, Christopher Simmons, Ermal Toto, Scott Valcourt, Lucas Varella, Ralph Zottola:
The Connect.Cyberinfrastructure Portal. PEARC 2021: 51:1-51:4 - 2020
- [c18]Patrick Schmitz, Dana Brunson, Gail Krovitz, Thomas E. Cheatham, Claire Mizumoto:
Leveraging a research computing and data capabilities model for strategic decision-making. PEARC Companion 2020: 12:1 - [c17]Patrick Schmitz, Claire Mizumoto, John Hicks, Dana Brunson, Gail Krovitz, James B. Bottum, Joel Cutcher-Gershenfeld, Karen Wetzel, Thomas E. Cheatham:
A Research Computing and Data Capabilities Model for Strategic Decision-Making. PEARC 2020: 77-84 - [c16]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:
Fostering Collaboration Among Organizations in the Research Computing and Data Ecosystem. PEARC 2020: 393-401
2010 – 2019
- 2019
- [c15]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:
Assessment of financial returns on investments in cyberinfrastructure facilities: A survey of current methods. PEARC 2019: 33:1-33:8 - [c14]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, Andrew M. Johnson, Becky Yeager:
Improving regional cyberinfrastructure services through collaboration: Cyberteam for the Rocky Mountain Advanced Computing Consortium. PEARC 2019: 41:1-41:4 - 2018
- [j14]Daniel R. Roe, Thomas E. Cheatham III:
Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. J. Comput. Chem. 39(25): 2110-2117 (2018) - [c13]Ioannis Paraskevakos, André Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha:
Task-parallel Analysis of Molecular Dynamics Trajectories. ICPP 2018: 49:1-49:10 - 2017
- [j13]Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka:
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model. 57(2): 275-287 (2017) - [c12]Amit Roy, Daniel R. Roe, Mary W. Hall, Thomas E. Cheatham:
Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ. LCPC 2017: 26-35 - 2016
- [j12]Zahra Heidari, Daniel R. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi, Thomas E. Cheatham III:
Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations. J. Chem. Inf. Model. 56(7): 1282-1291 (2016) - 2015
- [j11]Thomas E. Cheatham III, Daniel R. Roe:
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis. Comput. Sci. Eng. 17(2): 30-39 (2015) - 2014
- [j10]Julien C. Thibault, Daniel R. Roe, Julio C. Facelli, Thomas E. Cheatham III:
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. J. Cheminformatics 6(1): 4 (2014) - [j9]Niel M. Henriksen, Hamed S. Hayatshahi, Darrell R. Davis, Thomas E. Cheatham III:
Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations. J. Chem. Inf. Model. 54(6): 1758-1772 (2014) - [j8]Julien C. Thibault, Thomas E. Cheatham III, Julio C. Facelli:
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings. J. Chem. Inf. Model. 54(6): 1810-1819 (2014) - 2013
- [j7]Julien C. Thibault, Julio C. Facelli, Thomas E. Cheatham III:
iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. J. Chem. Inf. Model. 53(3): 726-736 (2013) - 2012
- [j6]Kiumars Shahrokh, Anita M. Orendt, Garold S. Yost, Thomas E. Cheatham III:
Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. J. Comput. Chem. 33(2): 119-133 (2012) - 2011
- [c11]Niel M. Henriksen, Thomas E. Cheatham III:
RNA structure refinement and force field evaluation using molecular dynamics simulations. TG 2011: 3:1
2000 – 2009
- 2006
- [j5]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, Yong Kim, Suengkeol Choe, Jihoon Choi, Thomas E. Cheatham III, Julio C. Facelli:
Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. J. Chem. Inf. Model. 46(3): 971-984 (2006) - 2005
- [j4]David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods:
The Amber biomolecular simulation programs. J. Comput. Chem. 26(16): 1668-1688 (2005)
1990 – 1999
- 1998
- [j3]Stephen C. Harvey, Robert K.-Z. Tan, Thomas E. Cheatham III:
The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comput. Chem. 19(7): 726-740 (1998) - 1997
- [j2]Michael F. Crowley, Thomas A. Darden, Thomas E. Cheatham III, David W. Deerfield II:
Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program. J. Supercomput. 11(3): 255-278 (1997) - [c10]Thomas A. Darden, Lee G. Pedersen, Abdulnour Y. Toukmaji, Michael F. Crowley, Thomas E. Cheatham:
Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations. PP 1997 - 1995
- [c9]Thomas E. Cheatham, Amr F. Fahmy, Dan C. Stefanescu, Leslie G. Valiant:
Bulk synchronous parallel computing-a paradigm for transportable software. HICSS (2) 1995: 268-275 - [c8]Thomas E. Cheatham, Amr F. Fahmy, Dan C. Stefanescu:
General Purpose Optimization Technology. LCPC 1995: 422-433 - 1994
- [c7]Thomas E. Cheatham, Haiming Gao, Dan C. Stefanescu:
A Suite of Analysis Tools Based on a General Purpose Abstract Interpreter. CC 1994: 188-202 - [c6]Thomas E. Cheatham, Amr F. Fahmy, Dan C. Stefanescu:
H-BSP - A General Purpose Parallel Computing Environment. IFIP Congress (1) 1994: 515-520 - [c5]Thomas E. Cheatham, Amr F. Fahmy, Dan C. Stefanescu:
Supporting multiple evolving compilers. SEKE 1994: 241-248 - 1993
- [c4]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, Dennis Gannon, Tomasz Haupt, Carl Kesselman, Charles Koelbel, Wei Li, Monica S. Lam, Thomas J. LeBlanc, Jim Openshaw, David A. Padua, Constantine D. Polychronopoulos, Joel H. Saltz, Alan Sussman, Gil Weigand, Katherine A. Yelick:
Common runtime support for high-performance parallel languages. SC 1993: 752-757 - 1992
- [c3]Thomas E. Cheatham, Dan C. Stefanescu:
A Suite of Optimizers Based on Abstract Interpretation. PEPM 1992: 75-81 - 1991
- [c2]Azer Bestavros, Thomas E. Cheatham:
Efficient Execution of Homogeneous Tasks with Unequal Run Times on the Connection Machine. ICPP (3) 1991: 304-305 - 1990
- [c1]Azer Bestavros, Thomas E. Cheatham, Dan C. Stefanescu:
Parallel bin packing using first fit and k-delayed best-fit heuristics. SPDP 1990: 501-504
1960 – 1969
- 1966
- [j1]Thomas E. Cheatham:
Compiling techniques. Commun. ACM 9(7): 481 (1966)
Coauthor Index
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