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Dr. Hai Lin 

Professor, Chemistry Department

Dr. Hai Lin

Dr. Hai Lin 
Professor, Chemistry Department, 
University of Colorado Denver,
SI 4126B, Campus Mail 194,

PO Box 173364, Denver, CO 80217

Tel: +1-303-315-7656  Fax: +1-303-556-4776  



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Researcher ID:

Prof. Hai Lin's Group of Computational Chemistry


Curriculum vitae




BSc. Eng.

Computer Science

University of Science and Technology of China


M. S.


University of Science and Technology of China


Ph. D.


University of Science and Technology of China


Positions and Appointments



Professor, University of Colorado Denver

Associate Professor,  University of Colorado Denver


Assistant Professor, University of Colorado Denver


Minnesota Supercomputing Institute Research Scholar, University of Minnesota


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


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


Alexander von Humboldt Fellow, University-Wuppertal, Germany


Assistant Professor, University of Science and Technology of China



  • Cottrell Plus SEED (Singular Exceptional Endeavors of Discovery) Awards, Research Corporation for Science Advancement (2018)
  • Dean’s Master’s Student Mentoring Award, University of Colorado Denver Graduate School (2018)
  • Cottrell Scholar, Research Corporation for Science Advancement (2015, for PUI class 2006)
  • Henry Dreyfus Teacher-Scholar Award, Camille & Henry Dreyfus Foundation (2014)
  • Research Corporation for Science Advancement Cottrell College Science Multi-Investigator Award (2013)
  • Alexander von Humboldt Alumni Research Fellowship (2012)
  • National Science Foundation CAREER Award (2010)
  • Excellence in Research & Creative Work Award (2007), College of Liberal Arts and Sciences, University of Colorado Denver
  • Research Corporation Cottrell College Science Award (2006)
  • Minnesota Supercomputing Institute Research Scholarship (2003)
  • Max-Planck Postdoctoral Research Fellowship (2001-2003, Germany)
  • Alexander von Humboldt Research Fellowship (1999, Germany)
  • Excellent Prize of President Scholarship of Chinese Academy of Sciences (1998, China)



Multiscale Modeling of Chemical Processes in Complex Environments

Chemistry is very much about recombining atoms into new molecules through breaking old bonds and forming new bonds. How does this happen in complex environments, such as one inside a protein that is solvated in aqueous solution or trapped in cell membrane? The marriage of modern quantum mechanics and classical Newtonian mechanics has led to novel computational techniques that allow us to understand chemical reactions in great detail at the very fundamental atomistic level…

A short video about Prof. Lin talking about multiscale modeling and simulation published by the Dreyfus Foundation

More details about our work in multiscale modeling and simulations of chemical reactions in complex environment

Method Development

1.       Molecular dynamics by open-boundary quantum-mechanics/molecular-mechanics (QM/MM)

2.       Electrostatically embedded many-body expansion of potentials

Codes Coauthored

If you are interested in using these free programs, please visit the code websites or email Hai Lin (

1.       QMMM (for QM/MM single-point calculations, energy minimizations, and dynamic simulations using advanced and unique algorithms such as flexible-boundary embedding and adpative partitioning, which allow on-the-fly exchanges of partial charges and matters, respectively, across the QM/MM boundary)

2.       EquCheck (for rigourous statistical analysis on whether equilibrium has been achieved for a given time series recorded in dynamics simulations).

3.       MBPAC (for single-point calculations of molecular clusters using the electrostatically-embedded many-body potential)

4.       MCSI (for multi-configurational molecular-mechanics calculations that constructs empirical semi-global reactive potential surfaces based on Shepard's interpolation)

5.       MC-Tinkerate (for reaction rate calculations by variational transition state theory with multi-dimensional tunneling based on the reactive potential generated through multi-configurational molecular mechanics)  


1.       Chloride and proton transferred by CLC chloride ion transport proteins

2.       Association of synaptotagmin C2 domains with membranes

3.       Cytochrome P450 enzymes: substrate docking and oxidizations

4.       Cluster formation and dynamics of ammonia and sulfuric acids


More about Research  

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

  1. Duster, A. W.; Lin, H. "Tracking proton transfer through titratable amino acid side chains in adaptive QM/MM simulations," Journal of Chemical Theory and Computation, 2019, 15, 5794-5809.text
  2. Duster, A. W.; *Garza, C. M.; *Aydintug, B. O.; *Negussie, M. B.; Lin, H. "Adaptive QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel," Journal of Chemical Theory and Computation, 2019, 15, 892-905.text
  3. Duster, A. W.; Wang, C.-H.; Lin, H. "Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes," Molecules, 2018, 23, 2170.text
  4. Macdougall, D. D.; Lin, Z.; *Chon, N. L.; Jackman, S.; Lin, H.; Knight, J. D.; Anantharam, A. "The high-affinity calcium sensor synaptotagmin-7 serves multiple roles in regulated exocytosis ," Journal of General Physiology, 2018, 150, 783-807.text
  5. Wang, C.-H.; Duster, A. W.; *Aydintug, B. O.; *Zarecki, M. G.; Lin, H. "Chloride ion transport by the E. coli CLC Cl-/H+ antiporter: A combined quantum-mechanical and molecular-mechanical study," Frontiers in Chemistry 2018, 6, 62/1-16.text
  6. *Duster, A.; Lin, H. "Restrained proton indicator in combined quantum-mechanics/molecular-mechanics dynamics simulations of proton transfer through a carbon nanotube" Journal of Physical Chemistry B 2017, 121, 8585-8592. DOI:10.1021/acs.jpcb.7b06657text
  7. *Duster, A.; Wang, C.-H.; *Garza, C.; *Miller, D.; Lin, H. "Adaptive QM/MM: Where are we, what have we learned, and where will we go from here?" Wiley Interdisciplinary Reviews: Computational Molecular Science, 2017, 7, e1310.text
  8. *Chon, N. L.; Osterberg, J. R.; *Henderson, J.; Khan, H.; Reuter, N.; Knight, J. D.; Lin, H. "Membrane docking of synaptotagmin-7 C2A domain: 2. Computations reveal interplay between electrostatic and hydrophobic contributions." Biochemistry2015, 54, 5696-5711. text
  9. Pezeshki, S.; Lin, H. "Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water." Journal of Chemical Theory and Computation201511, 2398-2411. text
  10. Pezeshki, S.; *Davis, C.; Heyden, A.; Lin, H. "Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Solvent Molecules Entering and Leaving Protein Binding Sites." Journal of Chemical Theory and Computation2014, 10,4765-4776. text
  11. 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, 35, 1778-1788. text
  12. Pezeshki, S.; Lin, H. "Recent developments in QM/MM methods towards open-boundary multi-scale simulations." Molecular Simulations 2014, 41, 168-189. text
  13. *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. text
  14. *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. text
  15. 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 Computation2013, 9, 2672-2686. text
  16. 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 Computation2011, 7, 3625-3634. text
  17. *Smith, M.; Lin, H. "Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters." Chemical Physics Letters2011, 502, 112-117. text
  18. *Ader, L.; Jones, D. N. M.; Lin, H"Alcohol binding to the odorant binding protein LUSH: Multiple factors affecting binding affinities." Biochemistry2010, 49, 6136-6142. text
  19. 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. text
  20. 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. text
  21. 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. text
  22. 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. text

Computational program packages (co-authored) QMMMMBPACMCSI (formerly MC-TINKER)MC-TINKERATE

Full List of Publications  

Research Supports

  1. Research Corporation for Science Advancement (PI, 2018-2020) "Combining Artificial Neural Networks and Quantum Chemistry for Simulations of Proton Transfer through Channels and Transporters," Grant No. 25793, $50,000.
  2. National Science Foundation (PI, 2016-2019) "Adaptive QM/MM Methods for Proton Transfer in Complex Environments," Grant No. CHE-1564349, $405,000.
  3. NERSC (PI, 2015-2018) "Ion Solvation and Transport in complex Environments by Advanced Quantum-Mechanics/Molecular-Mechanics," Grant No. m2495. CPU time service units: 50,000 for 2015; 284,000 for 2016, 150,000 for 2017, 80,000 for 2018.
  4. XSEDE (PI, 2014-2018"Multiscale Simulations of Membrane Proteins," Grant No. 140070 (annually renewed). CPU time service units (estimated value): 1,181,576 (~$40,893) for 2014; 2,188,235 (original 1,738,235 + supplment 450,000, ~$60,172) for 2015; 1,830,286 (1,330,286 + 500,000, ~$46,050) for 2016; 3,100,315 (~110,735) for 2017; 2,412,878 (~36,578) for 2019.
  5. Camille & Henry Dreyfus Foundation (PI, 2014-2019) "Open-Boundary QM/MM Methods for Multiscale Modeling and Simulations of Chemical Reactions in Complex Environments," Grant No. TH-14-028, $60,000
  6. 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
  7. XSEDE (PI, 2013-2014) "Multiscale Simulations of Chloride Transport Proteins," Grant No. 130090. CPU time 170,000 (150,000 original + 20,000 supplemnet) service units.
  8. National Renewal Energy Laboratory (PI, Subcontract 2013) "Catalytic Conversion of Biomass," $35,065
  9. National Science Foundation (PI, 2009-2014) "CAREER: Multiscale Simulations of Chloride Transport Proteins by CombinedQuantum and Classic Mechanical Approaches," Grant No. CHE-0952337, $625,000
  10. 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.
  11. 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.
  12. National Science Foundation (Senior Personnel, 2008) "MRI-Consortium: Acquisition of a Supercomputer by the Front Range Computing Consortium," $3,995,000.
  13. 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
  14. 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 ( for research projects and research positions.


By the way, I found this interesting link:


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