个人简介

B.S., UNC Chapel Hill, 1989 Ph.D., UNC Chapel Hill, 1993 (Lee G. Pedersen) Awards & Honors NSF Fellow in Computational Science and Engineering, Duke University 1993-1996 (Weitao Yang) NIH Fellow, Harvard University, 1996-1997 (Martin Karplus) European Molecular Biology Organization (EMBO) Fellow Universite Louis Pasteur, Strasbourg, FRANCE 1997-1998 (Martin Karplus)

研究领域

Biophysical Chemistry/Physical Chemistry

The development and application of multi-scale quantum methods for simulations of biological reactions. Research Summary The York Group research involves the development and application of multi-scale quantum methods for simulations of biological reactions. These methods involve the integration of linear-scaling electronic structure, polarizable force field, generalized solvent boundary and new-generation molecular simulation techniques that work together synchronously to study the detailed mechanisms of RNA catalysis.

近期论文

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Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ models commonly used in biomolecular simulations Maria T. Panteva, George M. Giambasu, Darrin M. York J. Comput. Chem., (2015) , DOI: 10.1002/jcc.23881 Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations Thakshila Dissanayake, Jason M. Swails, Michael E. Harris, Adrian E. Roitberg, Darrin M. York Biochem., (2015) 54, 1307-1313, DOI: 10.1021/bi5012833 Multiscale methods for computational RNA enzymology Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambasu, Tai-Sung Lee, Darrin M. York Methods Enzymol., (2015) 14, 335-374, DOI: 10.1016/bs.mie.2014.10.064 Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects Haoyuan Chen, Joseph A. Piccirilli, Michael E. Harris, Darrin M. York, Biochim. Biophys. Acta, In Press , Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field Timothy J. Giese, Maria T. Panteva, Haoyuan Chen, Darrin M. York J. Chem. Theory Comput., (2015) 11, 451-461, DOI: 10.1021/ct500799g Multipolar Ewald Methods. I. Theory, Accuracy, and Performance Timothy J. Giese, Maria T. Panteva, Haoyuan Chen, Darrin M. York J. Chem. Theory Comput., (2015) 11, 436-450, DOI: 10.1021/ct5007983 Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM Brian K. Radak, Tai-Sung Lee, Michael E. Harris, Darrin M. York RNA, Submitted Nucleic acid reactivity: challenges for next-generation semiempirical quantum models Ming Huang, Timothy J. Giese, Darrin M. York J. Comput. Chem., Submitted , Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations Brian K. Radak, Melissa Romanus, Tai-Sung Lee, Haoyuan Chen, Ming Huang, Antons Treikalis, Vivekanandan Balasubramanian, Shantenu Jha, Darrin M. York J. Chem. Theory Comput., (2015) 11, 373-377, DOI: 10.1021/ct500776j Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin George M. Giambasu, Darrin M. York, David A. Case RNA, In Press , Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions Haoyuan Chen, Timothy J. Giese, Ming Huang, Kin-Yiu Wong, Michael E. Harris, Darrin M. York Chem. Eur. J., (2014) 20, 1-9, DOI: 10.1002/chem.201403862 Recent advances toward a general purpose linear-scaling quantum force field Timothy J. Giese, Ming Huang, Haoyuan Chen, Darrin M. York Acc. Chem. Res., (2014) 47, 2812–2820, DOI: 10.1021/ar500103g Linear Free Energy Relationships in RNA Transesterification: Theoretical Models to Aid Experimental Interpretations Ming Huang, Darrin M. York Phys. Chem. Chem. Phys., (2014) 16, 15846-15855, DOI: 10.1039/C4CP01050G Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation Daniel L. Kellerman, Darrin M. York, Joseph A. Piccirilli, Michael E. Harris Curr. Opin. Chem. Biol., (2014) 21C, 96-102, DOI: 10.1016/j.cbpa.2014.06.010. Ab Initio Path-Integral Calculations of Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models Kin-Yiu Wong, Yuqing Xu, Darrin M. York J. Comput. Chem., (2014) 35, 1302-1316, DOI: 10.1002/jcc.23628 Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field Anna Pabis, Inacrist Geronimo, Darrin M. York, Piotr Paneth J. Chem. Theory Comput., (2014) 10, 2246-2254, DOI: 10.1021/ct500205z Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path Hugh Heldenbrand, Pawel Janowski, George M. Giambasu, Timothy J. Giese, Joseph Wedekind, Darrin M. York J. Am. Chem. Soc., (2014) 136, 7789-7792, DOI: 10.1021/ja500180q Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods Ming Huang, Timothy J. Giese, Tai-Sung Lee, Darrin M. York J. Chem. Theory Comput., (2014) 10, 1538–1545, DOI: 10.1021/ct401013s Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions Timothy J. Giese, Haoyuan Chen, Ming Huang, Darrin M. York J. Chem. Theory Comput., (2014) 10, 1086–1098, DOI: 10.1021/ct401035t Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation Jason M. Swails, Darrin M. York, Adrian E. Roitberg J. Chem. Theory Comput., (2014) 10, 1341–1352, DOI: 10.1021/ct401042b