Zhiwei Liu PhD
Zhiwei Liu PhD
Associate Director, West Center for Computational Chemistry and Drug Design
Assistant Professor of Chemistry
B. S. in Chemistry, Peking University
M. S. in Physical Chemistry, Peking University
Ph. D. in Computational Chemistry, Emory University
- Use computational methods to study chemical, biological and biomimetic systems
- Quantum mechanical and Density Functional Theory (DFT) methods
- All-atom molecular dynamics simulations utilizing molecular mechanics force fields
- Coarse grain molecular dynamics simulations
My research focuses on using computational methods to study chemical, biological and biomimetic systems to gain molecular insights into mechanisms of chemical reactions, biological and biomedical functions. Computational methods ranges from high level quantum mechanics (QM or ab initio) methods, Density Functional Theory (DFT), to molecular dynamics (MD) simulations using molecular mechanics (MM) force fields, to coarse grain (CG) molecular dynamics simulations using models and parameters developed in house and by our collaborators.
One research area I am involved in is the development of internal force field parameters for Coarse Grain (CG) molecular dynamics simulations of proteins, as well as protein/membrane systems. CG molecular dynamics method uses CG models that are reduced representations of all atom models. We lump together multiple atoms into a single site. The major advantage of the CG model is that the computational demands are approximately four orders of magnitude less than the all-atom models, at the expense of some atomistic details. Accordingly, this has opened the door for the study of biological events of interests such as signal transduction through transmembrane proteins.
Another research area involves computer-aided design of functional foldamers that are either mimicking the structures of naturally occurring biological polymers or exhibiting therapeutic functions. In this research, we utilize and improve existing molecular mechanics force fields so that molecular dynamics simulations can be used for the accurate prediction of secondary structures of foldamers in solutions.
Selected Scholarly Activity
Abramyan, A. M., Liu, Z., Pophristic, V. Mechanistic and Dynamic Insights into Ligand Encapsulation by Helical Arylamide Foldamers. Phys. Chem. Chem. Phys. 2014, 16, 20406-20409.
Nguyen, T. H. T., Liu, Z., Moore,P. B. Molecular Dynamics Simulations of Homo-oligomeric Bundles Embedded within a Lipid Bilayer. Biophys. J. 2013, 105, 1569-1580.
Galan, J. F., Tang, C. N., Chakrabarty, S., Liu, Z., Moyna, G., Pophristic, V. Conformational preferences of furan- and thiophene-based arylamides: a combined computational and experimental study. Phys. Chem. Chem. Phys. 2013, 15, 11883-11892.
Liu, Z., Teslja, A., Pophristic, V. An ab initio molecular orbital study of intramolecular hydrogen bonding in ortho-substituted arylamides: implications for the parameterization of molecular mechanics force fields. J. Comp. Chem. 2011, 32, 1846-1858.
Liu, Z., Ensing, B., Moore, P. B., Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (Φ - Ψ) space. J. Chem. Theory Comput. 2011, 7(2), 402-419.
Liu, Z., Remsing, R. C., Liu, D., Moyna, G., Pophristic, V., Hydrogen Bonding in ortho-substituted Arylamides: The Influence of Protic Solvents. J. Phys. Chem. B 2009, 113, 7041-7044.
Galan, J. F., Brown, J., Wildin, J., Liu, Z., Liu, D., Moyna, G., Pophristic, V., Intramolecular Hydrogen Bonding in ortho-substituted Arylamide Oligomers: A Computational and Experimental study of ortho-fluoro and ortho-chloro N-methylbenzamides. J. Phys. Chem. B 2009, 113, 12809-12815.
Remsing, R. C., Liu, Z., Sergey, I., Moyna, G., Solvation and Aggregation of N,N’-dialkylimidazolium ionic liquids: A multinuclear NMR spectroscopy and molecular dynamics simulation study. J. Phys. Chem. B 2008, 112, 7363-7369.
Meek, P. J., Liu, Z., Tian, L., Wang, C. Y., Welsh, W. J., Zauhar, R. J., Shape Signatures: Speeding up Computer Aided Drug Discovery. Drug Discovery Today 2008, 11 (19-20), 895-904.
Ensing, B., De Vivo, M., Liu, Z., Moore, P. B., Klein, M. L., Metadynamics as a Tool for Exploring Free Energy Landscape of Chemical Reactions. Acc. Chem. Res. 2006, 39(2), 73-81.
Liu, Z., Torrent, M., Morokuma, K., A Molecular Orbital Study of Zn(II)-Catalyzed Alternating Copolymerization of Carbon Dioxide and Epoxide. Organometallics, 2002, 21, 1056-1071.
|Office location:||Griffith Hall, Room 258B|
|Mailing address:||Department of Chemistry and Biochemistry|
University of Sciences
600 South 43rd Street
Philadelphia, PA 19104-4495
z [dot] liu [at] usciences [dot] edu