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

Research Experiences

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 Science

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 simulation (Towhee).
• 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 2^nd 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.

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Presentations

• 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, MI, 2010.
• 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.

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Journal Publications

• 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.

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Book Chapter

• Liqun Zhang , Sabine Bouguet-Bonnet, Matthias Buck, “Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase–Protein Interactions”, Allostery Methods in Molecular Biology, 2012, Volume 796, Part 3, 235- 259, DOI: 10.1007/978-1-61779-334-9_13.