Yingkai Zhang

Professor of Chemistry
B.S. Nanjing University; Ph.D. Duke University; Postdoctoral research at Howard Hughes Medical Institute, University of California at San Diego

Email:
Phone: 212-998-7882
Office: Silver Center, 100 Washington Square East, Room 1001N
Lab Homepage

Areas of Research/Interest
Theoretical and Computational Chemistry: combined ab initio quantum mechanical and molecular mechanical methods, computer simulations, with applications to chemical reactions and molecular recognitions in biological systems.

Research Description
We are interested in the development and application of cutting-edge computational and theoretical methods to understand the inner workings of important biological processes. Due to the complexity of biomolecular systems, the computational methods that we develop and utilize are multiscale in nature, ranging from electronic level description of crucial chemical bonds to coarse-grained approaches for large scale motions and interactions. For the methodology development, we focus on ab initio QM/MM methods, efficient sampling approaches and multiscale simulation methods. For biomolecular simulations, we are currently interested in investigating enzyme mechanism, catalysis and regulation; histone modifications and recognition; and membrane enzymes.

PublicationsQ. Wu, P. W. Ayers and Y. Zhang, J. Chem. Phys., 131, 164112 (2009).
Density-based energy decomposition analysis for intermolecular interactions with variationally determined
intermediate state energies

Z. Lu, J. Lai, Y. Zhang, J. Am. Chem. Soc. , 131, 14928-14931 (2009).
Importance of Charge Independent Effects in Readout the Trimethyllysine Mark by HP1 Chromodomain.

H. Zheng, S. Wang and  Y. Zhang, J. Comput. Chem., 30, 2706-2711 (2009).
Increasing the Time Step with Mass Scaling in Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations

Z. Ke, Y. Zhou, P. Hu, S. Wang, D. Xie and Y. Zhang, J. Phys. Chem. B, 113, 12750-12758, (2009). ( Cover)
Active Site Cysteine Is Protonated in the PAD4 Michaelis Complex: Evidence from Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations

L. Wang,  S. Broyde and Y. Zhang,  J. Mol. Biol.,  389, 787-796 (2009).
Polymerase-tailored Variations in the Water-Mediated and Substrate-Assisted Mechanism for Nucleotidyl Transfer: Insights from a Study of T7 DNA Polymerase

P. Hu, S. Wang and Y. Zhang, J. Am. Chem. Soc. , 130, 16721-16728 (2008).
A Highly Dissociative and Concerted Mechanism for the Nicotinamide Cleavage Reaction in Sir2Tm Enzyme Suggested by ab initio QM/MM Molecular Dynamics Simulations

Z. Lu and Y. Zhang,  J. Chem. Theory Comp., 4, 1237-1248 (2008).
Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions

H. Zheng and Y. Zhang,  J. Chem. Phys. ,128, 204106 (2008).
Determination of Free Energy Profiles by Repository Based Adaptive Umbrella Sampling: Bridging Nonequilibrium and Quasiequilibrium Simulations

P. Hu, S. Wang and Y. Zhang, J. Am. Chem. Soc. , 130, 3806-3813 (2008).
How do SET-domain Protein Lysine Methyltransferases Achieve the Methylation State Specificity ? Revisited by ab initio QM/MM Molecular Dynamics Simulations.

Fellowships/Honors
National Science Foundation Career Award (2005), James D. Watson Young Investigator Award (2005), Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences (2006)

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