Darrin M. York, Ph.D.
Affiliations: | Rutgers University, New Brunswick, New Brunswick, NJ, United States |
Area:
Theoretical ChemistryWebsite:
http://theory.rutgers.edu/~york/Google:
"Darrin York"Mean distance: 7.81
Parents
Sign in to add mentor| Lee G. Pedersen | grad student | 1993 | UNC Chapel Hill | |
| (Molecular dynamics simulations of HIV-1 protease) | ||||
| Weitao Yang | post-doc | 1993-1996 | Duke | |
| (NSF postdoctoral fellow) | ||||
| Martin Karplus | post-doc | 1997-1998 | Université Louis Pasteur, Strasbourg | |
| (prior year PD @Harvard U) | ||||
Children
Sign in to add trainee| George M. Giambasu | grad student | ||
| Ming Huang | grad student | ||
| Adam Moser | grad student | Loras College | |
| Yang (Jana) Khandogin | grad student | 2003 | UMN |
| Jana Shen | grad student | 1999-2003 | UMN |
| Timothy J. Giese | grad student | 2005 | UMN |
| Brent A. Gregersen | grad student | 2005 | UMN |
| Evelyn A. Mayaan | grad student | 2005 | UMN |
| Kevin Range | grad student | 1999-2005 | UMN |
| George M. Giambasu | grad student | 2010 | UMN |
| Haoyuan Chen | grad student | 2011-2016 | Rutgers, New Brunswick |
| Jinzhe Zeng | grad student | 2019-2025 | Rutgers, New Brunswick |
| Kin-Yiu Wong | post-doc | 2010-2012 | Hong Kong Baptist University |
| Xiao Li | post-doc | 2018-2021 | Rutgers, New Brunswick |
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Publications
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| Zeng J, Zhang D, Peng A, et al. (2025) DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials. Journal of Chemical Theory and Computation |
| Zeng J, Giese TJ, Götz AW, et al. (2025) The QDπ dataset, training data for drug-like molecules and biopolymer fragments and their interactions. Scientific Data. 12: 693 |
| Zeng J, Giese TJ, Zhang D, et al. (2025) DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials. Journal of Chemical Information and Modeling |
| Wilson TJ, McCarthy E, Ekesan Ş, et al. (2024) The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme. Acs Catalysis. 14: 15294-15305 |
| Tsai HC, Xu J, Guo Z, et al. (2024) Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. Journal of Chemical Information and Modeling |
| Giese TJ, Zeng J, Lerew L, et al. (2024) Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The Journal of Physical Chemistry. B |
| Tao Y, Giese TJ, York DM. (2024) Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials. Molecules (Basel, Switzerland). 29 |
| Tao Y, Giese TJ, Ekesan Ş, et al. (2024) Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials. The Journal of Chemical Physics. 160 |
| Zhang S, Giese TJ, Lee TS, et al. (2024) Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of Chemical Theory and Computation |
| Giese TJ, Ekesan Ş, McCarthy E, et al. (2024) Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of Chemical Theory and Computation |