Description: image024.jpgDr. Hai Lin
Associate Professor, Chemistry Department,
University of Colorado Denver,
SI 4126B, Campus Mail 194,

PO Box 173364, Denver, CO 80217

Tel: +1-303-352-3889  Fax: +1-303-556-4776 
E-mail: hai.lin@ucdenver.edu

 

(Updated 7/1/2014) (Publication Updated 7/1/2014)

 

Group website at Computational Chemistry at UC-Denver

 

Curriculum vitae

 

Education

1993

BSc. Eng.

Computer Science

University of Science and Technology of China

1995

M. S.

Physics

University of Science and Technology of China

1998

Ph. D.

Chemistry

University of Science and Technology of China

 

Positions and Appointments

2011-now

Associate Professor, University of Colorado Denver

2005-2011

Assistant Professor, University of Colorado Denver

2003-2005

Minnesota Supercomputing Institute Research Scholar, University of Minnesota

2005

Project Manager for Integrated Tools for Computational Chemical Dynamics, University of Minnesota

2001-2003

Max-Planck Postdoctoral Fellow, Max-Planck Institute for Carbon Research, Germany

2000-2001

Alexander von Humboldt Fellow, University-Wuppertal, Germany

1998-2000

Assistant Professor, University of Science and Technology of China

 

Awards/Fellowship

 

Research

Computer modeling and simulations of complex systems in chemistry, biochemistry, biophysics, and material sciences

 

Method Development

(1) Combined quantum-mechanical /molecular-mechanical (QM/MM) methods

(2) Reaction dynamics with multi-dimensional tunneling

(3) Multi-configuration molecular mechanics (MCMM)

(4) Many-body expansion for condensed-phase simulation

 

Applications

(1) Properties and functionalities of enzymes, ion channels, and protein/DNA/RNA complexes

(2) Highly accurate potentials, dipoles, spectroscopy, and dynamics for molecules and clusters

 

More about Research  

Selected Recent Peer-reviewed Articles (* indicates undergraduate or M.S. students)

1.       Pezeshki, S.; Lin, H. "Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems." Journal of Computational Chemistry 2014, in press.

2.       Pezeshki, S.; Lin, H. "Recent developments in QM/MM methods towards open-boundary multi-scale simulations." Molecular Simulations 2014, DOI:10.1080/08927022.2014.911870. (http://www.tandfonline.com/eprint/X5psF6DJNwcp7CdYDS2F/full).

3.       *Chon, N.; Lee, S.; Lin, H. "A theoretical study of temperature dependence of cluster formation from sulfuric acid and ammonia." Chemical Physics 2014, 433, 60-66.

4.       *Church, J.; Pezeshki, S.; *Davis, C.; Lin, H. "Charge transfer and polarization for chloride ions bound in clc transport proteins: natural bond orbital and energy decomposition analyses." Journal of Physical Chemistry B 2013, 117, 16029-16043.

5.       Wu, X.; Thiel, W.; Pezeshki, S.; Lin, H. "Specific Reaction Path Hamiltonian for Proton Transfer in Water: Re-parameterized Semi-empirical Methods." Journal of Chemical Theory and Computation 2013, 9, 2672-2686.

6.      Pezeshki, S.; Lin, H. "Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds." Journal of Chemical Theory and Computation, 2011, 7, 3625-3634.

7.      *Smith, M.; Lin, H. "Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters." Chemical Physics Letters, 2011, 502, 112-117.

8.      *Ader, L.; Jones, D. N. M.; Lin, H. "Alcohol binding to the odorant binding protein LUSH: Multiple factors affecting binding affinities."Biochemistry, 2010, 49, 6136-6142.

9.      Zhang, Y.; Lin, H. "Flexible-boundary QM/MM calculations: II. Partial charge transfer across the QM/MM boundary that passes through a covalent bond."Theoretical Chemistry Accounts 2010, 216, 315-322.

10.  Zhang, Y.; Lin, H. "Quantum tunneling in testosterone 6β-hydroxylation by cytochrome P450: Reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces."Journal of Physical Chemistry A 2009, 113, 11501-11508.

11.  Zhang, Y.; Lin, H. "Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems."Journal of Chemical Theory and Computation 2008, 4, 414-425.

12.  Zhang, Y.; *Morisetti, P.; *Kim, J.; *Smith, L., Lin, H. "Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4."Theoretical Chemistry Accounts 2008, 121, 313-319.

Computational program packages (co-authored) qmmm, mbpac, mc-tinker, mc-tinkerate

Full List of Publications  

Research Supports

1.       XSEDE (PI, 2014-2015) "Multiscale Simulations of Membrane Proteins," Grant No. 140070. CPU time 1,181,576 service units.

2.       Research Corporation for Science Advancement (co-PI, 2013-2015) Hydrophobic and electrostatic driving forces for protein-membrane docking: A combined experimental and computational approach, Grant No. 22399, $100,000

3.       XSEDE (PI, 2013-2014) Multiscale Simulations of Chloride Transport Proteins, Grant No. 130090. CPU time 150,000 service units.

4.       National Renewal Energy Laboratory (PI, Subcontract 2013) Catalytic Conversion of Biomass, $35,065

5.       National Science Foundation (PI, 2009-2014) "CAREER: Multiscale Simulations of Chloride Transport Proteins by Combined Quantum and Classic Mechanical Approaches," Grant No. CHE-0952337, $625,000

6.       National Science Foundation (PI, 2009) "Mathematics and Chemistry" Subcontract (NSF/1717-528-6056, $17,090) of "Institute for Mathematics and its Applications," Grant No. 9810289.

7.       William R. Wiley Environmental Molecular Sciences Laboratory (co-PI, 2009) "Computational Chemical Dynamics of Complex Systems" (Grant No. GC34900) 800,000 node-hours CPU time at the Molecular Science Computing Facility, a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory.

8.       National Science Foundation (Senior Personnel, 2008) "MRI-Consortium: Acquisition of a Supercomputer by the Front Range Computing Consortium," $3,995,000.

9.       Research Corporation (PI, 2006-2011) "Reaction mechanism and dynamics of cytochrome P2450 3A4 enzyme by combined quantum mechanical/molecular mechanical computation," Grant No. CC6725, $34,950

10.    National Natural Science Foundation of China (PI, 2000) "Study of the highly excited molecular overtones by Fourier Transform Intra-cavity Laser Absorption Spectroscopy (FT-ICLAS),"Grant No. 29903010

 

Interested students are very welcomed to contact me via email (hai.lin@ucdenver.edu) for research projects and research positions.

 

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