Ph.D., Chemical Engineering 12/2007
University of Rhode Island Kingston, Rhode Island, USA
Advisor: Michael L. Greenfield
Thesis title: “Physical and Mechanical Properties of Model Asphalt Systems Calculated
Using Molecular Simulation”
M.S.,B. S., Chemical Engineering Zhejiang University Hangzhou, China
Tennessee Technological University,Cookeville, TN Chemical Engineering
Assistant Professor 08/15-present
- Perform CHARMM and NAMD molecular dynamics simulations to investigate the structure,
dynamics and functional properties of Human Beta Defensin type 3 interaction with
EphA2 & EphrinA1 complex.
- Perform Monte Carlo and LAMMPS molecular dynamics simulations to understand the Processing-Structural-Performance
Relationship in Asphalt Mix Technology
Case Western Reserve University, Cleveland, OH School of Medicine
Postdoc Research Associate 07/09-02/15
- Perform CHARMM and NAMD molecular dynamics simulations to investigate the structure,
dynamics and functional properties of human beta defensin type 3 interaction with
C C chemokine receptors: CXCR4, CCR2b.
- Investigate the structure and dynamics of the complexes between transmembrane protein
plexin and Rho family GTPases using both CHARMM and NAMD molecular dynamics simulations,
and docking programs: HADDOCK, Rosettadock, XPLOR-NIH.
- Work on plexin transmembrane monomer/dimmer/trimer in lipid bilayers by performing
CHARMM, NAMD, and Anton molecular dynamics simulations to understand the relationships
among plexin dynamics, structure, and functional mechanism.
- Perform microsecond-long molecular dynamics simulations on EphA2-SHIP2 SAM:SAM heterodimer
to investigate its dynamics and structure properties, and the diverse functional mechanism.
Case Western Reserve University, Cleveland, OH Chemical Engineering and Geological
Postdoc Research Scholar 01/08- 06/09
- Performed Ab Initio VASP simulation on silicate melts and minerals with/without a
noble gas；analyzed sitting and dynamic properties of noble gas in silicate melts and
minerals at different temperature and pressure conditions.
- Calculated thermodynamic properties of binary silica joins using both first principles
and empirical molecular dynamics simulations; Analyzed factors influencing neutral
species and charged small particles transport behavior inside silica melts; investigated
isotopes transport behavior in silicate.
University of Rhode Island, Kingston, RI Chemical Engineering
Graduate Assistant 09/03-12/07
- Worked on Linux system and multiple CPU platforms; implemented molecular simulation
source code using Fortran; extended atom-based OPLS-aa force field in Monte Carlo
- Created model asphalt mixtures for molecular simulation input; performed molecular
simulation on original and polymer modified asphalt system using parallel molecular
dynamics (Lammps) and Monte Carlo (Towhee) methods. Calculated transport properties
by relaxation autocorrelation function analysis; calculated density, heat capacity,
isothermal compressibility and expansion coefficient of pure compounds and mixtures;
analyzed molecular orientation, radial distribution function and solubility parameters
of molecules in the system.
Awards and Fellowships
- Poster presentation 2nd place, 2014 Annual Retreat Poster Award, Department of Physiology and Biophysics, 2014.
- Ruth Kirschstein NRSA Postdoc Fellowship , NIH, 2012-2014.
- Travel awards to attend the Biophysics Society meeting, sponsored by the Education, Minority Affairs, and Professional Opportunities for
Women Committees. February, 15-19, San Francisco, California, 2014 .
- Travel awards to attend the Expanding Cross-Disciplinary Dialogue workshop, sponsored by NSF, April, Arlington, VA, 2012.
- Travel awards to attend the Engaging Difference: Diverse Women in STEM Building Careers,
Creating Alliances workshop, University of Virginia in Charlottesville, VA, 2011.
- Travel awards to present seminar at Computational Biophysics to Systems Biology (CBSB10)
Workshop , Traverse City, MI, 2010.
- Postdoc Travel awards for National Summit on Gender and Postdoctorate , sponsored by NAP and NSF, March, Philadelphia, PA, 2010.
- Excellence in Doctoral Research in the Area of Science, Technology, Engineering and
Mathematics , University of Rhode Island, 2008.
- New England Institute of Chemists Graduate Student Award , American Institute of Chemists, 2006-2007.
- Liqun Zhang, Matthias Buck, “Investigation on the Interaction between Plexin
Intracellular Plus Transmembrane Domains with GTPases and with the Lipid Bilayer Using
All-atom Molecular Dynamics Simulations”, Biophysical Society. Baltimore, MD, 2015.
- Liqun Zhang, Matthias Buck, “Structure and dynamic properties analysis of plexin-B1
Rho-GTPase binding domain as a monomer and dimer”, ACS, Dallas,TX, 2014.
- Liqun Zhang, Matthias Buck, “Structure and Dynamics of the Plexin-B1 Transmembrane
Receptor bound to GTPases” Biophysical Society. San Francisco, CA, 2014.
- Liqun Zhang, Matthias Buck, “Investigation of the Structure and Dynamics of Heterodimeric
Sam-Sam complexes using Microsecond Molecular Dynamics Simulations”. Biophysical Society,
Philadelphia, PA, 2013.
- Liqun Zhang, Alexander Sodt, Rick Venable, Richard W. Pastor, Matthias Buck, “Molecular
dynamics prediction and refinement of transmembrane helix dimers”, Biophysical Society,
San Diego, CA, 2012.
- Liqun Zhang, James Van Orman, Daniel Lacks, “Molecular dynamics investigation of MgO-CaO-SiO2
melts: influence of pressure and composition on density and transport properties”,
Amer. Chem. Soc., Boston, MA, 2010.
- Liqun Zhang, Matthias Buck, “Differential dynamics coupling of plexin GTPase complexes
in MD Simulations”, ACS, Boston, MA, 2010.
- Liqun Zhang, Matthias Buck, “Molecular dynamics simulations of the plexin Trans- and
Juxta-membrane region in a DPPC lipid bilayer: application of the primary hydration
shell model”, Computational Biophysics to Systems Biology Workshop, Traverse city,
- Liqun Zhang, Daniel J. Lacks, James Van Orman, “Investigation on transport properties
of generic species in silicate melts using molecular simulations”. Midwest Thermodynamics
and Statistical Mechanics Conference, Detroit, MI, 2009.
- Liqun Zhang, Daniel J. Lacks, James Van Orman, “First principles simulations of noble
gases dissolved in liquid silica”, AIChE, 2008, Philadelphia, PA.
- Liqun Zhang, “Structure and Freezing of MgSiO3 Liquid in Earth’s Lower Mantle”, Science
and Nature club, 2008, Case Western Reserve University, Cleveland, OH.
- Liqun Zhang, Michael L. Greenfield, “Viscosity calculation in model asphalt system”,
AIChE, 2006, San Francisco, CA.
- Liqun Zhang, Michael L. Greenfield. “Orientation calculation for model asphalt mixture
using molecular simulation”, AIChE, 2005, Cincinnati, OH.
- Liqun Zhang, Michael L. Greenfield, “Research on asphalt using molecular simulation”,
2005, University of Rhode Island, Kingston
- Liqun Zhang, Michael L. Greenfield, “Developing model asphalt systems using molecular
simulation”, AIChE, 2004, Austin, TX.
- Liqun Zhang, Susmita Borthakur, Matthias Buck “Molecular Simulations of a Dynamic Protein Complex:
Role of Polar Interactions and Solvent in the Process of Protein Dissociation”, Biophysical Journal. 110, 877–886. 2016.
- Liqun Zhang, Anton Polyanski and Matthias Buck, “Modeling Transmembrane Domain Dimers/Trimers
of Plexin Receptors: Implications for Mechanisms of Signal Transmission across the
Membrane”, PLOS ONE., 10(4):e0121513. 2015.
- Liqun Zhang, Thomas Centa, Matthias Buck “Structure and Dynamics Analysis on Plexin-B1 Rho-GTPase
Binding Domain Monomer and Dimer”, J. Phys. Chem. B. 118(26):7302-11, 2014.
- Liqun Zhang, Matthias Buck “Molecular Simulations of a Dynamic Protein Complex: Role of Salt-Bridges
and Polar Interactions in Configurational Transitions”. Journal of Biophysics . 105(10), 2421-2417, 2013.
- Mirco Zerbetto, Ross Anderson, Sabine Bouguet-Bonnet, Mariano Rech, Liqun Zhang, Eva Meirovitch, Antonino Polimeno, Matthias Buck,”Analysis of 15N-1H NMR relaxation
in proteins by a combined experimental and molecular dynamics simulation approach:
Picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the
dimeric state”, J. Chem. Phys. B, 117(1), 174-184, 2013.
- Liqun Zhang, Alexander Sodt, Rick M.Venable, Richard W. Pastor, Matthias Buck, “Prediction and
Refinement of ErbB1/B2 and EphA1 Transmembrane Dimers from Microsecond MD Simulations”, Proteins. 81(3), 365-76. 2013.
- Gaurav Goel, Liqun Zhang , Daniel J. Lacks, James A. Van Orman, “Isotope fractionation by diffusion in silicate
melts: Insights from Molecular dynamics simulations”, Geochim. Cosmochim. Acta , 93, 205-213. 2012.
- HyeongJu Lee, Prasanta K. Hota, Preeti Chugha, Hui Miao, Liqun Zhang, SoonJeung Kim, Rebecca S. Alviani, Lukas Stetzig, Bing-Cheng Wang, B, Matthias Buck
“Refined NMR structure of a heterodimeric SAM:SAM complex. Characterization and manipulation
of the EphA2 interface leads to new cellular functions of SHIP2.” Structure, 20, 41-55, 2012.
- Liqun Zhang, “Thermodynamic properties calculation for MgO-SiO2 liquids using both empirical
and first-principle molecular simulations”, Physical Chemistry Chemical Physics , 13, 21009-21015, 2011.
- Mehdi Bagheri Hamaneh+, Liqun Zhang+, Matthias Buck, “A direct coupling between global and internal motions in a single
domain protein? A molecular dynamics investigation of extreme case scenarios”, Biophysical Journal, 101, 196-204, 2011 (+ shared first authorship).
- Liqun Zhang, James Van Orman, Daniel J. Lacks, “Molecular dynamics investigation of liquid MgO-CaO-SiO2
as a function of composition and pressure”, Chemical Geology, 275, 50-57, 2010.
- Liqun Zhang, Michael L. Greenfield, “Rotational relaxation time of individual compounds from
simulations of molecular asphalt models”, Journal of Chemical Physics, 132,184502, 2010.
- Liqun Zhang, James Van Orman, Daniel J. Lacks, “The influence of atomic size and charge of dissolved
species on the diffusivity and viscosity of silicate melts”, American Mineralogist Letter , 94, 1735-1738, 2009.
- Liqun Zhang, Daniel J. Lacks, James Van Orman, “Diffusivity calculation on noble gas silica systems
using first principles molecular simulations”, Molecular Simulation, 35, 942-952, 2009.
- Liqun Zhang, Daniel J. Lacks, James Van Orman, “Effective radii of noble gas atoms in silicates
from first principles molecular simulation”, American Mineralogist, 94, 600608, 2009.
- Liqun Zhang, Michael L. Greenfield, “Polymer modification effects to model asphalt systems”, Energy & Fuels ,22(5), 3363-3375. 2008.
- Liqun Zhang, Michael L. Greenfield, “Relaxation time, diffusion, and viscosity analysis of model
asphalt systems using molecular simulation”, Journal of Chemical Physics, 127, 194502, 2007.
- Liqun Zhang, Michael L.Greenfield, “Analyzing properties of model asphalts using molecular simulation”,
Energy & Fuels, 21, 1712-1716, 2007.
- Liqun Zhang, Michael L.Greenfield, “Molecular orientation in model asphalts using molecular simulation”,
Energy & Fuels, 21, 1102-1111, 2007.
- Liqun Zhang, Bo Lu, Zhirong Cheng, “Study on mechanism and kinetics of oxidizing reaction of
pinane to hydroperoxide”, Chemical Reaction Engineering and Technology, 18, 225-230, 2002.