Yingkai Zhang Assistant 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: yingkai.zhang@nyu.edu Phone:  212-998-7882 Lab Homepage:  http://www.nyu.edu/projects/yzhang

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.

Select Publications:

C. Xiao and Y. Zhang, J. Chem. Phys., 127, 124102 (2007).
Design-Atom Approach for the QM/MM Covalent Boundary: A Design-Carbon Atom with Five Valence Electrons.

C. Xiao and Y. Zhang, J. Phys. Chem. B ,  111, 6229-6235 (2007).
Catalytic Mechanism and Metal Specificity of Bacterial Peptide Deformylase: a Density Functional Theory QM/MM Study.

 L. Wang, X. Yu, P. Hu, S. Broyde and Y. Zhang, J. Am. Chem. Soc. , 129, 4731-4737 (2007).
A Water-mediated and Substrate-assisted Catalytic Mechanism for Sulfolobus solfataricus  DNA Polymerase IV

S. Wang, P. Hu and Y. Zhang, J. Phys. Chem. B , 111, 3758-3764 (2007).
Ab initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Enzyme Catalysis:
The Case of Histone Lysine Methyltransferase SET7/9

C. Corminboeuf, P. Hu, M. E. Tuckerman and Y. Zhang, J. Am. Chem. Soc. (Communication) , 128, 4530-4531 (2006).
Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein

 P. Hu and Y. Zhang, J. Am. Chem. Soc. ,  128, 1272-1278  (2006).
 Catalytic Mechanism and Product Specificity of the Histone Lysine Methyltransferase SET7/9.  An  ab initio QM/MM-FE Study with Multiple Initial Structures.

Y. Zhang,  Theor. Chem. Acc. , Special Issue of ``New Perspectives in Theoretical Chemistry'' , 116, 43-50 (2006).
Pseudobond ab initio QM/MM approach and its Applications to Enzyme Reactions.

Y. Zhang,  J. Chem. Phys.,  122, 024114 (2005).
Improved Pseudobonds for Combined ab initio Quantum Mechanical/Molecular Mechanical (QM/MM) Methods.

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)