Publications

Journal Articles

 
91. Lin, H.; Zhang, Y.; Pezeshki, S.; Duster, A. W.; Wang, B.; Wu, X.-P.; Zheng, S.-W. Gagliardi, L.; Truhlar, D. G. "QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations," Comput. Phys. Commun. 2023, 295, 108987.
 
90. Chon, N. L.; Schultz, N. J.; Zheng, H.; Lin, H. "Anion pathways in the NarK nitrate/nitrite exchanger," J. Chem. Inf. Model. 2023, 63, 5142-5152.
 
89. Yan, S.; Wang, B.; Lin, H. "Tracking the delocalized proton in concerted proton transfer in bulk water," J. Chem. Theory Comput. 2023, 19, 448-459.
 
88. Talachutla, S.; Bhat, S.; Duster, A. W.; Lin, H. "Improved indicator algorithms for tracking a hydrated proton as a local structural defect in Grotthuss diffusion in aqueous solutions," Chem. Phys. Lett. 2021, 784, 139121.
 
87. Mato, J.; Duster, A. W.; Guidez, E. B.; Lin, H. "Adaptive-partitioning multilayer dynamics simulations: 1. On-the-fly switch between two quantum levels of theory," J. Chem. Theory Comput. 2021, 17, 5456-5465.
 
86. Alnaas, A. A.; Watson-Siriboe, A.; Tran, S.; Negussie, M.; Henderson, J. A.; Osterberg, J. R.; Chon, N. L.; Harrott, B. M.; Oviedo, J.; Lyakhova, T.; Michel, C.; Reisdorph, N.; Reisdorph, R.; Shearn, C. T.; Lin, H.; Knight, J. D. "Multivalent lipid targeting by the calcium-independent C2A domain of synaptotagmin-like protein 4/ granuphilin," J. Biol. Chem. 2021, 296, 100159.
 
85. Chon, N. L.; Duster, A. W.; Aydintug, B. O.; Lin, H. "Anion pathways in CLCF fluoride/proton antiporters," Chem. Phys. Lett. 2021, 762, 138123.
 
84. Duster, A. W.; Lin, H. "Riding elevators into and out of cells," eLife 2020, 9, e62925.
 
83. Duster, A. W.; Lin, H. "Tracking proton transfer through titratable amino acid side chains in adaptive QM/MM simulations," J. Chem. Theory Comput. 2019, 15, 5794-5809.
 
82. 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," J. Chem. Theory Comput. 2019, 15, 892-905.
 
 
80. 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." J. Gen. Physiol. 2018,150, 783-807.
 
79. 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," Front. Chem. 2018, 6, 62/1-16.
 
78. Bendahmane, M.; Bohannon, K. P.; Rao, T. C.; Schmidtke, M. C.; Bradberry, M. M.; Abbineni, P.; Chon, N. L.; Tran, S.; Lin, H.; Chapman, E. R.; Knight, J. D.; Anantharam, A. "The synaptotagmin C2B domain calcium-binding loops modulate the rate of fusion pore expansion." Mol. Biol. Cell  2018, 29, 834-845.
 
 
76. 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 Interdiscip. Rev. Comput. Mol. Sci. 2017, 7, e1310-n/a.
 
75. Addassi, M.; Schreyer, L.; Johannesson, B.; Lin, H. "Pore-scale modeling of vapor transport in partially saturated capillary tube with variable area using chemical potential." Water Resour. Res. 2016, 52, 7023-7035.
 
74. 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.” Biochemistry, 2015, 54, 5696-5711.
 
73. Osterberg, J. R.; Chon, N. L.; Boo, A.; Maynard, F. A.; Lin, H.; Knight, J. D. “Membrane docking of synaptotagmin 7 C2A domain: 1. EPR measurements show contributions from two membrane binding loops.” Biochemistry, 2015, 54, 5684–5695.
 
72. Pezeshki, S.; Lin, H. “Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water.” J. Chem. Theory Comput. 2015, 11, 2398-2411.
 
71. Pezeshki, S.; Davis, C.; Heyden, A.; Lin, H. “Adaptive-partitioning QM/MM dynamics simulations: 3. Solvent molecules entering and leaving protein binding sites.” J. Chem. Theory Comput. 2014, 10, 4765-4776.
 
 
69. Pezeshki, S.; Lin, H. “Recent developments in QM/MM methods towards open-boundary multi-scale simulations.” Mol. Simul. 2014, 41, 168-189.
 
68. Damrauer, R.; Lin, H.; Damrauer, N. H. “Computational studies of carbodiimide rings.” J. Org. Chem. 2014, 79, 3781-3788.
 
67. Chon, N. L.; Lee, S.-H.; Lin, H. “A theoretical study of temperature dependence of cluster formation from sulfuric acid and ammonia.” Chem. Phys. 2014, 433, 60-66.
 
66. Church, J.; Pezeshki, P.; Davis, C.; Lin, H. “Charge transfer and polarization for chloride ions bound in CLC transport proteins: Natural bond orbital and energy decomposition analyses.” J. Phys. Chem. B. 2013, 117, 16029-16043.
 
65. Wu, X.; Thiel, W.; Pezeshki, S.; Lin, H. “Specific reaction path Hamiltonian for proton transfer in water: Re-parameterized semi-empirical methods.” J. Chem. Theory Comput. 2013, 9, 2672-2686.
 
 
63. Smith, M.; Lin, H. “Charge delocalization upon chloride ion binding in CLC chloride ion channels/transporters.” Chem. Phys. Lett, 2011, 502, 112-117.
 
62. 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.
 
 
 
59. Zhang, Y.; Morisetti, P.; Kim, J.; Smith, L., Lin, H. “Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4.” Theor. Chem. Acc. 2008, 121, 313-319.
 
 
 
 
55. Lin, H.; Truhlar, D. G.; “QM/MM: What have we learned, where are we, and where do we go from here?” Theor. Chem. Acc. 2007, 117, 185-199. [Invited keynote presentation at the 10th Electronic Computational Chemistry Conference (ECCC10)]
 
 
53. Lin, H.; Zhao, Y.; Tischchenko, O.; Truhlar, D. G.; “Multi-configuration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations.” J. Chem. Theor. Comput.2006, 2, 1237-1254.
 
 
51. Yurchenko, S. N.; Zheng, J. J.; Lin, H.;Jensen, P.; Thiel, W.; “Potential energy surface for the electronic ground state of NH3 calculated ab initio up to 20,000 cm-1 above equilibrium.” J. Chem. Phys. 2005, 123, 134308/1-14.
 
50. Lin, H.; Truhlar, D. G.; “Redistributed charge and dipole schemes for combined quantum-mechanical and molecule mechanical calculations.” J. Phys. Chem. A 2005, 109, 3991-4004.
 
49. Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G.; “Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change.” J. Am. Chem. Soc. 2005, 127, 2830-2831.
 
48. Yurchenko, S. N.; Carvajal, M.; Lin, H.; Zheng, J.; Thiel, W.; Jensen, P.; “Dipole moment and intensities in the electronic ground state of NH3: bridging the gap between ab initio theory and spectroscopic experiment.” J. Chem. Phys. 2005, 122, 104317/1-14.
 
47. Yurchenko, S. N.; Carvajal, M.; Jensen, P.; Lin, H.; Zheng, J.; Thiel, W.; “Rotation-vibration motion of pyramidal XY3 molecules described in the Eckart frame: theory and application to NH3.” Mol. Phys. 2005, 103, 359-378.
 
46. Lin, H.; Schoeneboom, J. C.; Cohen, S.; Shaik, S.; Thiel, W.; “QM/MM study of the product-enzyme complex in P450cam catalysis.” J. Phys. Chem. B 2004, 108, 10083-10088.
 
45. Lin, H.; Pu, J.; Albu, T. V.; Truhlar, D. G. "Efficient molecular mechanics for chemical reactions: multi-configuration molecular mechanics using partial electronic structure Hessians," J. Phys. Chem. A 2004, 108, 4112-4124.
 
44. Schoeneboom, J. C.; Cohen, S.; Lin, H.; Shaik, S.; Thiel, W. "QM/MM investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism." J. Am. Chem. Soc. 2004, 126, 4017-4034.
 
43. Lin, H.; Thiel, W.; Yurchenko, S. N.; Carvajal, M.; Jensen, P. "Vibrational energies for NH3 based on high level ab initio potential energy surfaces," J. Chem. Phys. 2002, 117, 11265-11276.
 
42. Schoeneboom, J. C.; Lin, H.; Reuter, N.; Thiel, W.; Cohen, S.; Ogliaro, F.; Shaik, S. "The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical / molecular mechanical (QM/MM) calculations." J. Am. Chem. Soc. 2002, 124, 8142-8151.
 
 
40. He, S. G. Liu, A. W.; Lin, H.; Zheng, J. J.; Hu, S. M.; Hao, L. Y.; Zhu, Q. S. "Stretching vibrational band intensities of XH4 molecules employing four-dimensional ab initio (X = C and Sn) and effective (X = C and Si) dipole moment surfaces," J. Chem. Phys. 2002, 117, 10073-10080.
 
39. He, S. G.; Lin, H.; Buerger, H.; Thiel, W.; Ding, Y.; Zhu, Q. S. "Calculation of the Si-H stretching-bending overtones in SiHCl3 employing ab initio potential energy and dipole moment surfaces," J. Chem. Phys. 2002, 116, 105-111.
 
38. Hu, S. M.; Ulenikov, O. N.; Bekhtereva, E. S.; Onopenko, G. A.; He, S. G.; Lin, H.; Cheng, J. X.; Zhu, Q. S. "High resolution Fourier-transform intra-cavity laser absorption spectroscopy of D2O in the region of the 4nu1 + nu3 band," J. Mol. Spectrosc. 2002, 212, 89-95.
 
37. He, S. G.; Lin, H.; Thiel, W.; Zhu, Q. S. "Four-dimensional dipole moment surfaces and local mode vibrational band intensities of GeH4," Chem. Phys.Lett. 2001, 349, 131-136.
 
36. Lin, H.; He, S.G.; Wang, X.G.; Yuan, L. F.; Buerger, H.; D′Eu, J.-F.; Reuter, N.; Thiel, W. "The vibrational overtones of SiH4 isotopomers: experimental wavenumbers, assignment, ab initio dipole moment surfaces, and intensities," Phys. Chem. Chem. Phys. 2001, 3, 3506-3517.
 
35. Lin, H.; Buerger, H.; Mkadmi, E. B.; He, S. G.; Yuan, L. F.; Breidung, J.; Thiel, W.; Huet, T. R.; Demaison, J. "The Si-H stretching-bending overtone polyads of SiHF3: assignments, band intensities, internal coordinate force field, and ab initio dipole moment surfaces," J. Chem. Phys. 2001, 115, 1378-1391.
 
34. Lin, H.; Buerger, H.; He, S. G.; Yuan, L. F.; Breidung, J.; Thiel, W. "Overtones of the Si-H stretching-bending polyad in SiHD3: internal coordinate force field, ab initio dipole moment surfaces, and band intensities," J. Phys. Chem. A 2001, 105, 6065-6072.
 
 
 
31. He, S. G.; Zheng, J. J.; Hu, S. M.; Lin, H.; Ding, Y.; Wang, X. H.; Zhu, Q. S. "The stretching vibrational overtone spectra of PH3: local mode vibrational analysis, dipole moment surfaces from density functional theory and band intensities," J. Chem. Phys. 2001, 114, 7018-7026.
 
30. Zheng, J. J.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; He, S. G.; Wang, X. H.; Hu, S. M.; Lin, H.; Zhu, Q. S. "Study of the vibration-rotation bands belonging to the nu1 + nu2/2 + nu3 = 3.5 polyad of the D2O molecule," Mol. Phys.2001, 99, 931-937.
 
29. Lin, H.; Yuan, L. F.; He, S. G.; Wang, X. G.; Zhu, Q. S. "The ab initio calculated dipole moment surface and overtone relative intensities of CH chromophore in CHCl3," J. Chem. Phys. 2000, 112, 7484-7489.
 
28. Lin, H.; Yuan, L. F.; He, S. G.; Wang, X. G. "Calculating relative intensities for CH stretching polyads of CHI3 with ab initio dipole moment surface," Chem. Phys. Lett. 2000, 332, 569-575.
 
27. Hou, J. G.; Yang, J. L.; Wang, H. Q.; Li, Q. X.; Zeng, C. G.; Lin, H.; Chen, D. M.; Zhu, Q. S. "Comment on 'Identifying molecular orientation of individual C60 molecules on Si(111)-(7x7) surfaces' - Hou et al. reply." Phys. Rev. Lett. 2000, 85, 2654-2654.
 
26. Wang, X. H.; Lin, H.; Chen, X. Y.; Wang, X. G.; Wang, D.; Deng, K.; Zhu, Q. S. "Coriolis interaction parameters of the (n100;F2) states of GeH4," Mol. Phys. 2000, 98, 1409-1413.
 
25. Cheng, J. X.; Lin, H.; Hu, S. M.; He, S. G.; Zhu, Q. S.; Kachanov, A. A. "Infrared intra-cavity laser absorption spectroscopy with a continuous-scan Fourier transform interferometer," Appl. Opt. 2000, 39, 2221-2229.
 
24. Chen, X. Y.; Lin, H.; Wang, D.; Wang, X. G.; Zhu, Q. S. "Spectroscopic study of local mode (4000) overtone of GeH4," J. Mol. Struct. 2000, 517, 41-51.
 
23. Hu, S. M.; Lin, H.; Cheng, J. X.; He, S. G.; Zhu, Q. S.; Kachanov, A. A. "High sensitivity and high resolution Fourier-transform intra-cavity laser absorption spectroscopy (FT-ICLAS)," Proceedings of SPIE, 2000, 4063, 264-268.
 
22. He, S. G.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; Wang, X. H.; Hu, S. M.; Lin, H.; Zhu, Q. S. "High resolution Fourier transform spectrum of the D2O molecule in the region of the second triad of the interacting vibrational states," J. Mol. Spectrosc. 2000, 200, 34-39.
 
21 Wang, X. H.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; He, S. G.; Hu, S. M.; Lin, H.; Zhu, Q. S. "High resolution study of the first Hexade of the D2O." J. Mol. Spectrosc. 2000, 200, 25-33.
 
20. Hu, S. M.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; Wang, X. H.; He, S. G.; Lin, H.; Zhu, Q. S. "High-resolution study of strongly interacting vibrational bands of HDO in the region 7600 - 8100 cm−1," J. Mol. Spectrosc. 2000, 203, 228-234.
 
19. Ulenikov, O. N.; He, S. G.; Onopenko, G. A.; Behtereva, E. S.; Wang, X. H.; Hu, S. M.; Lin, H.; Zhu, Q. S. "High resolution study of the nu1 + n2/2 + n3 = 3 polyad of strongly interacting vibrational bands of D2O," J. Mol. Spectrosc.2000, 204, 216-225.
 
18. Lin, H.; Wang, D.; Yuan, L. F.; Zhu, Q. S. "Nonlinearity of the dipole moment surface and intensities anomaly of CHCl3," Chinese Phys. Lett. 2000, 17, 13-15.
 
17. Lin, H.; Ulenikov, O. N.; Olechnovitch, I.; Wang, D.; Chen, X. Y.; Hao, L. Y.; Zhu, Q. S. "Local mode spectroscopic study of the AsH3 molecule: The perturbed (500) local mode overtone," Chinese Phys. 2000, 9, 113-118.
 
16. Hu, S. M.; He, S. G.; Lin, H.; Cheng, J. X.; Wang, X. H.; Zheng, J. J.; Cheng, G. S.; Zhu, Q. S. "High-resolution Fourier transform intra-cavity laser absorption spectroscopy: method and application," Acta Physica Sinica, Chinese Phys. Soc. 2000, 49, 1435-1440.
 
15. Chen, X. Y.; Lin, H.; Wang, D. Zhu, Q. S. "False Lines due to folding in Fourier transform spectroscopy," Chinese J. Chem. Phys. 2000, 13, 129-134.
 
14. Hou, J. G.; Yang, J. L.; Wang, H. Q.; Li, Q. X.; Zeng, C. G.; Lin, H.; Chen, D. M.; Zhu, Q. S. "Identifying molecular orientation of individual C60 molecules on Si(111)-(7x7) surfaces," Phys. Rev. Lett. 1999, 83, 3001-3004.
 
13. Lin, H.; Yuan, L. F.; Zhu, Q. S. "Local mode overtone intensities of SiH4 and GeH4 by bond dipole model with ab initio calculated dipole moment surface," Chem. Phys. Lett. 1999, 308, 137-142.
 
12. Hu, S. M.; Lin, H.; He, S. G.; Cheng, J. X.; Zhu, Q. S. "Fourier-transform intra-cavity absorption spectroscopy of HOD v(OD) = 5 overtone," Phys. Chem. Chem. Phys. 1999, 1, 3727-3730.
 
11. Zhou, Z. Y.; Zhu, Q. S.; Lin, H. "High-resolution spectroscopic study of H280Se in the v(stretch) = 5 and 6 local-mode pairs states," Mol. Phys. 1999, 97, 503-510.
 
10. Deng, K.; Wang, X. G.; Lin, H.; Wang, D.; Zhu, Q. S. "High resolution spectroscopic study of CH3D in the region of 5900 - 6100 cm−1," Mol. Phys. 1999, 97, 787-796.
 
9. Wang, D.; Lin, H, Wang, X. G.; Zhu, Q. S. "High resolution spectroscopic study of arsine in the region 6000 - 6500 cm−1," Spectrochim. Acta A 1999, 55, 109-119.
 
8. Lin, H.; Wang, D.; Chen, X. Y.; Wang, X. G.; Zhou, Z. P.; Zhu, Q. S. "Absorption intensity of stretching vibration states of silane and germane," J. Mol. Spectrosc.1998, 192, 249-256.
 
7. Yang, S. F.; Lin, H.; Wang, D.; Zhu, Q. S. "High resolution vibration-rotation spectra of arsine local mode (110 A1/E) band," J. Chem. Soc. Faraday Trans. 1998, 94, 1397-1402.
 
6. Ulenikov, O. N.; Onopenko, G. A.; Lin, H.; Zhang, J.; Zhou, Z. Y.; Zhu, Q. S.; Tolchenov, R. N. "Joint rotational analysis of twenty four bands of the H280Se molecule," J. Mol. Spectrosc. 1998, 189, 29-39.
 
5. Cheng, J. X.; Wang, X. G.; Lin, H.; Zhu, Q. S. "The high resolution spectrum of AsH3 (400) local mode state: symmetry reduction and rotational re-quantization," Spectrochim. Acta A 1998, 54, 1947-1960.
 
4. Lin, H.; Wang, X. G.; Yang, S. F.; Hu, S. M.; Zhu, Q. S. "Study of an intra-cavity laser absorption spectrometry incorporated with the Fourier transform spectrometry," Chinese J. Laser A 1998, 25, 1008-1012.
 
3. Cheng, J. X.; Xu, R. X.; Shi, Q.; Lin, H.; Zhu, Q. S. "Selective bond-breaking in a polyatomic molecule," Chinese J. Chem. Phys. 1998, 11, 516-520.
 
2. Lin, H.; Ulenikov, O. N, Yurchinko, S.; Wang, X. G.; Zhu, Q. S. "High-resolution spectroscopic study of the local mode (310) combination band system of AsH3," J. Mol. Spectrosc.1997, 187, 89-96.
 
1. Cheng, J. X.; Wang, X. G.; Lin, H.; Zhu, Q. S. "Symmetry reduction and rotational re-quantization of symmetric top molecules at the local mode limit," Chinese Phys. Lett.1997, 14, 656-659.

 

Book

Lin, H. "QM/MM Methods," In ACS in Focus series, 2024, eISBN ‍9780841299504, DOI: 10.1021/acsinfocus.7e7030.

 

Invited Book Chapters

5. Duster, A.; Garza, C.; Lin, H. "Adaptive partitioning QM/MM dynamics simulations for substrate uptake, product release, and solvent exchange," In Voth, G. A. ed. Computational Approaches for Studying Enzyme Mechanism, or the "Methods in Enzymology" series, 2016, pp 342-358, published by Elsevier: Cambridge, MA. DOI: 10.1016/bs.mie.2016.05.019

4. Pezeshki, S., Lin, H. "Recent developments in adaptive QM/MM," In Rivail, J.-L.; Ruiz-Lopez M.; Assfeld, X. eds. Quantum Modeling of Complex Molecular Systems, or the "Challenges and Advances in Computational Chemistry and Physics" series, 2015, published by Springer Nature: New York, NY, pp 93-114, DOI:10.1007/978-3-319-21626-3_3

3. Dahlke, E. E.; Leverentz, H. R.; Lin, H.; Truhlar, D. G. "Electrostatically embedded many-body expansion for large systems," In Manby, F. ed. Accurate Condensed-Phase Electronic Structure Theory, or the ″Computation in Chemistry″ series, edited by Gill, P., 2010, 105-127, published by CRC Press, Taylor and Francis:Boca Raton, FL.

2. Yurchenko, S. N.; Zheng, J. J.; Thiel, W.; Carvajal, M.; Lin, H.; Jensen, P. "Theoretical quantitative spectroscopy: Computer simulation of molecular spectra," In Perrin, A. et al.(eds.), Remote sensing of the atmosphere for environmental security. 2006, 171-183, published by Springer: Dordrecht, NL.

1. Yurchenko, S. N.; Thiel, W.; Carvajal, M.; Lin, H.; Jensen, P. "Rotation-vibration motion of pyramidal XY3 molecules described in the Eckart frame: the calculation of intensities with application to NH3," Adv. Quantum Chem. 2005, 48, 209-238.

 

Conference/Seminar Contributions

Oral Seminar Presentations:

63. Guidez, E.; Tran, A.; Lin, H. "Development of multilayer adaptive partitioning methods for molecule/ion transport," in Fall 2023 ACS national meeting in San Francisco, CA, Aug. 13-17, 2023 . (Invited Talk)

62. Lin, H. "Recent development in adaptive-partitioning QM/MM for the simulations of ion transport," Symposium “Award for Computers in Chemical and Pharmaceutical Research 2023 in Honor of Jiali Gao” in Spring 2023 ACS national meeting in Indianapolis, IN, Mar. 26-30, 2023 . (Invited Talk)

61. Guidez, E.; Tran, A.; Lin, H. "Development of adaptive partitioning multilayer methods for accurate and efficient dynamic simulations," Symposium “QM/QM and embedding models” in Spring 2023 ACS national meeting in Indianapolis, IN, Mar. 26-30, 2023 . (Invited Talk)

60. Schultz, N. J.; Lin, H. "Pore arginine in cross-membrane transport of nitrate/nitrite by the NarK antiporter from E. coli," 2022 Colorado Single Molecule and Membrane Meeting (CSMMM), Denver, CO, Dec. 9, 2022 . (Contributed Talk)

59. Lin, H. "Adaptive multiscale simulations for diffusive systems," Seminar at the Computational Redox Catalysis Group at Huazhong University of Science and Technology, Wuhan, China, Sept. 20, 2022. (Invited Virtual Talk)

58. Guidez, E.; Mato, J.; Duster, A.W.; Lin, H. "Development of adaptive partitioning multilayer methods for accurate QM/MM dynamic simulations," 12th Triennial Congress of the World Association of Theoretcial and Computational Chemists (WATOC 2022) at Vancouver, BC, Canada, Jul. 3-8, 2022. (Invited Talk)

57. Lin, H. "Adaptive multiscale simulations: QM/MM and beyond," Seminar at Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry (FTCC) at Xiamen University, Xiamen, China, Sept. 28, 2021. (Invited Talk)

56. Lin, H. "Molecular transport by adaptive-partitioning QM/MM simulations," Seminar at School of Medicine, Virginia Commonwealth University, Richmond, VA, Mar. 4, 2021. (Invited Talk)

55. Chon, N. L.; Tran, S.; Miller, C. S.; Lin, H.; Knight, J. D. "Mapping electrostatic protein-membrane interactions of Slp-4 C2 domain using molecular phylogenetic analysis and structure prediction," 2020 ACS virtual Rocky Mountain Regional Meeting, Nov. 13, 2020. (Contributed Talk)

54. Lin, H. "Adaptive multiscale simulations for ion transport," Departmental Seminar at the Department of Chemistry, CU-Denver, Denver, CO, Nov. 13, 2020. (Invited Talk)

53. Duster, A.; Lin, H. "Machine-learning-enhanced adaptive-partitioning multiscale simulations," 2020 Rocky Mountain Advanced Computing Consortium Symposium, Boulder, CO, May 21, 2020. (Invited Talk)

52. Duster, A.; Lin, H.; "Simulations of ion solvation and transfer by adaptive-partitioning QM/MM dynamics,"10th Congress of International Society of Theoretical Chemical Physics (ISTCP-X), Tromso, Norway, Jul. 11-19, 2019. (Invited Talk)

51. Lin, H.; "Tracking proton traveling through titratable amino acid side chains in adaptive QM/MM simulations," Seminar at the Physics Department, Free University of Berlin, Berlin, Germany, Jul. 10, 2019. (Invited Talk)

50. Duster, A.; Lin, H.; " Adaptive QM/MM dynamics simulations of proton transfer through biological channels," 2019 Beijing Symposium of “Electronic Structure and Dynamics of Complex Systems,” Beijing, China, Apr. 25-28, 2019. (Invited Talk)

49. Lin, H.; " Proton transfer through biological channels," Seminar in Institute of Chemistry, Chinese Academic of Sciences, Beijing, China, Apr 28, 2019. (Invited Talk)

48. Lin, H. "Proton transfer by adaptive QM/MM," 2018 Telluride Workshop "Proton Transfer in Biology", Telluride, CO, Jul. 9-13, 2018. (Invited Talk)

47. Lin, H. "Towards Open-Boundary QM/MM," Seminar at Molecular Sciences Software Institute (MolSSI) & Virginia Tech, Blacksburg, VA, Mar. 14, 2018. (Invited Talk)

46. Bendahmane M.; Bohannon K; Rao T.; Schmidtke M. W.; Abbineni P.; Ranski A.; Bradberry M.; Tran S.; Chon N. L.; Knight J.; Lin H.; Chapman E. R.; Anantharam A. "The synaptotagmin calcium-binding loops modulate the rate of fusion pore expansion," 2018 Annual Meeting of Biophysical Society, San Francisco, CA.  Feb. 17-21, 2018. (Invited Talk)

45. Lin, H. "Computer Simulations of Membrane Proteins," Biology Department Seminar, University of Colorado Denver, Denver, CO, Feb. 16, 2018. (Invited Talk)

44. Chon, N. L.; Tran, S.; Knight, J.; Lin, H. Calcium Binding to C2B domains of Synaptotagmin 1, Synaptotagmin 7, and chimeric Synaptotagmin 1/7: A Computational Study," 2017 American Chemical Society Rocky Mountian Regional Meeting, Loveland, CO, Oct. 25-28, 2017. (Contributed Talk)

43. Wang, C.-H.; Duster, A. W.; Zarecki, M. G.; Lin, H. Non-Equilibrium Dynamics of Chloride Transport through the E. coli Cl-/H+ antiporter. 2017 American Chemical Society Rocky Mountian Regional Meeting, Loveland, CO, Oct. 25-28, 2017. (Contributed Talk)

42. Lin, H.; Adaptive-Partitioning for Dynamics Simulations. 252nd American Chemical Society National Meeting, Philadelphia, PA, Aug. 21-25, 2016. (Invited Talk)

41. Lin, H.; Adaptive Multiscale Modeling of Proton Transport. Telluride Workshop: Proton Transfer in Biology, Telluride, CO, Jul. 12-16, 2016. (Invited Talk)

40. Lin, H.; Adaptive Multiscale Modeling of Solvation and Transport. Inorganic Chemistry Group Seminar, University of Utrecht, Netherlands, Jun. 15, 2016. (Invited Talk)

39. Lin, H.; Adaptive QM/MM Scheme for Simulations of Ion Solvation and Transport. Theoretical Chemistry Group Seminar, Max-Planck Institute for Carbon Research, Muelheim an der Ruhr, Germany, Jun. 13, 2016. (Invited Talk)

38. Lin, H.; Multiscale Modeling of Ion Solvation and Transport. Chemistry Department Seminar, University of Bergen, Bergen, Norway, Jun. 9, 2016. (Invited Talk)

37. Lin, H.; Ion Solvation by QM/MM: Flexible Boundary and Adaptive Partitioning. Physical Chemistry Seminar, Purdue University, West Lafatyette, IN, Oct 21, 2015. (Invited Talk)

36. Lin, H.; Chemical Insights for Biological Phenomena by Computer Modeling and Simulations. Seminar in the STEM/Pre-Health Preview Day, University of Colorado Denver, Oct. 16, 2015. (Invited Talk)

35. Lin, H.; Simulations of Membrane Proteins. Seminar in the Structural Biology and Biochemistry Program, University of Colorado Denver Anschutz Medical Campus, Denver, CO, Sep. 9, 2015. (Invited Talk)

34. Lin, H.; Unconventional QM/MM: Flexible-boundary and Adaptive-Partition. Seminar in Institute of Chemistry, Chinese Academic of Sciences, Beijing, China, June 10, 2015. (Invited Talk)

33. Pezeshki, S.; Lin, H.; Adaptive-partitioning QM/MM dynamics simulations of proton transfer, 249th American Chemical Society National Meeting, Denver, CO, Mar. 22-25, 2015. (Contributed Talk)

32. Pezeshki, S.; Lin, H.; Molecular dynamics by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems. 249th American Chemical Society National Meeting, Denver, CO, Mar. 22-25, 2015. (Contributed Talk)

31. Lin, H.; Chemical Insights for Biological Phenomena by Computer Modeling and Simulations. Seminar in the Chemistry Department, Metro State University of Colorado, Apr. 18, 2014. (Invited Talk)

30. Lin, H.; Toward the Open-Boundary QM/MM Dynamics Simulations. DFT-based Multi-layer Methods workshop, Lorentz Center, University of Leiden, Leiden, the Netherlands, Aug. 19-23, 2013. (Invited Talk)

29. Lin, H.; Toward the Next Generation QM/MM: Partial Charge Transfer and Adaptive Partition. Physical Chemistry Seminar in the Chemistry Department, University of Colorado at Boulder, Apr. 5, 2013. (Invited Talk)

28. Lin, H.; Open-boundary QM/MM: Partial Charge Transfer and Adaptive Partition. Seminar in the Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, the Netherlands, Oct. 30, 2012. (Invited Talk)

27. Lin, H.; Multiscale and Multilevel Simulations of Biological Systems. Seminar in the Chemistry Department, Jacobs University Bremen, Germany, Oct. 24, 2012. (Invited Talk)

26. Lin, H.; Beyond Conventional QM/MM: Potential & Dynamics. Seminar in the Chemistry Department, University of Stuttgart, Germany, Oct. 16, 2012. (Invited Talk)

25. Lin, H.; Unconventional QM/MM: Flexible boundary and Adaptive Partition. Theoretical Chemistry Group Seminar, Max-Planck Institute for Carbon Research, Muelheim an der Ruhr, Germany, Oct. 4, 2012. (Invited Talk)

24. Lin, H.; Multiscale and Multilevel Modeling and Simulations in the Condensed Phase. Seminar in the Chemistry Department, University of Bergen, Norway, Sept. 26, 2012. (Invited Talk)

23. Pezeshki, S.; Lin, H.; Sodium Ion Translocation through the Gramicidin A Channel by QM/MM Simulations. ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012 (Contributed Talk)

22. Pezeshki, S.; Lin, H.; Adaptive-Partitioning QM/MM Simulations of Proton Hopping between Hydronium Ion and Water Molecules. ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012 (Contributed Talk)

21. Lin, H.; Multi-scale and Multi-level Modeling for Condensed-Phase. Invited Leader of Discussion, Gordon Conference of Computational Chemistry 2012, Mountain Snow, VA, Jul. 22-27, 2012

20. Lin, H.; QM/MM: An Efficient Computational Tool for Studying Enzymatic Reactions. Seminar at the National Renewable Energy Laboratory, Golden, CO, Mar. 1, 2012 (Invited Talk)

19. Lin, H.; Molecular Dynamics Simulations of Biomolecules by Open-boundary QM/MM. Seminar at the Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, Nov. 9-11, 2011 (Invited Talk)

18. Pezeshki, S.; Lin, H.; Open-boundary QM/MM for Enzyme Simulations. Symposium of Computational Enzymology: From Mechanistic Understanding to Inhibitor and Biocatalyst Design at the 43rd IUPAC World Chemistry Congress (IUPAC 2011), San Juan, Puerto Rico, Jul 31 - Aug 5, 2011 (Invited Talk)

17. Pezeshki, S.; Lin, H.; Multiscale Simulations by Open-boundary QM/MM. Symposium of New Frontier of Combined Quantum Mechanical Molecular Mechanical Methods: Theory and Applications in Chemistry and Biology in the 42nd ACS Central Regional Meeting at Indianapolis, IN, Jun. 8-10, 2011 (Invited Talk)

16. Lin, H.; Multiscale Simulations of Large-Size Reactive Systems by Combining Quantum Mechanics and Molecular Mechanics. Physical Chemistry Seminar in the Chemistry Department, Colorado State University, May. 6, 2011 (Invited Talk)

15. Lin, H.; Multiscale simulations of large-size reactive systems by combining quantum mechanics and molecular mechanics. Computational Chemistry Group Seminar at the Institute of Chemistry, Chinese Academic of Sciences, Beijing, China, June 1, 2010. (Invited Talk)

14. Lin, H.; Multiscale simulations of large-size reactive systems by combining quantum mechanics and molecular mechanics. Group Seminar at the Institute of Intelligent Machines, Chinese Academic of Sciences, Hefei, China, May 31, 2010. (Invited Talk)

13. Lin, H.; Multiscale simulations of large-size reactive systems by combining quantum mechanics and molecular mechanics. Group Seminar at the Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China, May 27, 2010. (Invited Talk)

12. Lin, H.; Testosterone hydroxylation by cytochrome P450 3A4. Computational Chemistry Program Seminar at the Chemistry Department, Xiamen University, Xiamen, China, May 26, 2010. (Invited Talk)

11. Lin, H.; Flexible-boundary QM/MM: Partial charge transfer between the QM and MM subsystems. Computational Chemistry Group Seminar at the University of Minnesota, Minneapolis, MN, May 18-22, 2009. (Invited Talk)

10. Lin, H. Flexible-boundary QM/MM: Adaptive partition and partial charge transfer between QM and MM subsystems. Quantum Theory Project Seminar, University of Florida, Gainesville, FL, April 15-17, 2008. (Invited Talk)

9. Lin, H.: Understand biochemical processes at the atomic level. Program in Biomolecular Structure Seminar, School of Medicine, University of Colorado Denver, Denver, CO, October 5, 2007. (Invited Talk)

8. Lin, H.; Zhang, Y.; Truhlar, D. G.: Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined QM/MM calculations. 234st ACS National Meeting, 2007, Boston, MA, August 19 - 23, 2007. (Contributed Talk)

7. Lin, H.; Truhlar, D. G.: Toward more realistic simulations for large-size reactive systems by combining quantum mechanics and molecular mechanics. NWChem Meeting 2007, Richland, WA, January 25-26, 2007. (Invited Talk)

6. Truhlar, D. G.; Zhao, Y.; Schultz, N.; Cramer, C.; Kelly1, C.; Chamberlin, A.; Tischchenko, O.; Lin, H.: Density Functional Calculations. AIChE 2006 Annual Meeting, San Francisco, CA, November 11-17, 2006. (Invited Talk)

5. Lin, H.; Zhao, Y.; Truhlar, D. G. (2006): Multi-configuration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations. 231st ACS National Meeting, 2006, Atlanta, GA, March 26 - 30, 2006. (Contributed Talk)

4. Lin, H.: An accurate and efficient computational tool for understanding enzymatic reactions. Center for Computational Mathematics Seminar, Department of Mathematics, University of Colorado Denver, Denver, CO, February 27, 2006. (Invited Talk)

3. Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G. (2004): Carbon-13 kinetic isotope effects of importance to atmospheric science and their temperature dependences. 228th ACS National Meeting, 2004, Philadelphia, PA, August 21 - 26, 2004. (Contributed Talk)

2. Lin, H. "Overtone intensities of Si-H stretching-bending polyads of SiHD3 and SiHF3," SPHERS Network Meeting, Uhldingen-Muehlhofen, Germany, May 27 - 29, 2001. (Contributed Talk)

1. Lin, H. "Overtone intensities of XH (X = C and Si) chromophores in some small molecules," Workshop on Reductions of the Rovibrational Hamiltonian, Oberwolfach, Germany, September 28 - October 1, 2000. (Contributed Talk)

Posters/Book-Abstracts:

108. Nguyen, J.; Chon, N. L.; Lin, H. “Developing an atomistic model for the E318Q mutant for CLCF F-/H+ antiporter,” Poster at the 2023 ACS Rocky Mountain Regional Meeting, Laramie, WY, Sep. 15-17, 2023.

107. Wooten, E.; Chon, N. L.; Lin, H. “Sialin: A proton/sialic acid co-transporter,” Poster at the 2023 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 28, 2023.

106. Schultz, N. J.; Chon, N. L.; Lin, H. “The QM/MM simulations of the NarK antiporter from E. coli,” Poster at the 2023 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 28, 2023.

105. Nguyen, J.; Chon, N. L.; Lin, H. “Construction of an atomistic model for the E318Q mutant for CLCF F–/H+ antiporter” Poster at the 2023 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 28, 2023.

104. Schultz, N.; Chon, N. L.; Lin, H. “Molecular dynamics and quantum chemistry study of the NarK antiporter from E. coli,” Poster at the 2022 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 29, 2022.

103. Chon, N. L.; Tran, S.; Miller, C. S.; Lin, H.; Knight, J. D. “Using protein structure prediction with molecular phylogenetic analysis to understand membrane interactions in synaptotagmin-like proteins,” Poster at the 2022 Biophysical Society Conference, San Francisco, CA, Feb. 19-23, 2022.

102. Beaven, A.; Chon, N. L.; Lin, H.; Knight, J. D.; Sodt, A. “Simulating membrane reshaping proteins on fusion/fission pores,” Poster at the 2022 Biophysical Society Conference, San Francisco, CA, Feb. 19-23, 2022.

101. Knodle, S.; Bhat, S.; Talachutla, S.; Duster, A.; Lin, H. “Construction of atomistic CLCF F–/H+ antiporter models in physiological environment,” Poster at the 2021 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 30, 2021.

100. Bhat, S.; Talachutla, S.; Duster, A.; Lin, H. “Tracking proton in aqueous solutions during dynamics simulations: Improved algorithms,” Poster at the 2021 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 30, 2021.

99. Oviedo, J.; Kovacevic, T.; Vugmeyster, L.; Lin, H. “Hydrophobic core folding properties of the villin headpiece HP36 protein subdomain,” Poster at the 2021 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 30, 2021.

98. Chon, N. L.; Tran, S.; Miller, C. S.; Lin, H.; Knight, J. D. “Structure prediction and molecular phylogenetics analysis of membrane interactions in synaptotagmin-like proteins,” Poster at the 2021 Biophysical Society Conference (virtual), Feb. 22-26, 2021.

97. Stone, B.; Duster, A. W.; Bennett, A.; Ramsey, I. S.; Lin, H. “Exploring the proton-transfer mechanism in Hv1 by multi-scale simulations,” Poster at the 2021 Biophysical Society Conference (virtual), Feb. 22-26, 2021.

96. Kovacevic, T.; Oviedo, J.; Vugmeyster, L.; Lin, H. “Probing the dynamics of the villin headpiece protein’s subdomain HP-36,” Poster at the 2020 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 29, 2020.

95. Bhat, S.; Talachutla, S.; Lin, H. “Tracking the excess proton in proton transfer between water and titratable amino acid side chains,” Poster at the 2020 Research and Creative Activities Symposium, University of Colorado Denver, Denver, CO, Apr. 29, 2020.

94. Duster, A. W.; Lin, H. “Tracking proton transfer through amino acids in adaptive QM/MM simulations,” Poster at the 2020 Biophysical Society Annual Meeting, San Diego, CA, Feb. 15-19, 2020.

93. Oviedo, J.; Kovacevic, T.; Vugmeyster, L.; Lin, H. “Molecular dynamics of villin headpiece-36 under different hydration levels,” Poster at the 2020 Biophysical Society Annual Meeting, San Diego, CA, Feb. 15-19, 2020.

92. Chon, N. L.; Tran, S.; Miller, C. S.; Lin, H.; Knight, J. “Using high-throughput structure prediction and evolutionary alignment to map electrostatic protein-membrane interactions,” Poster at the 2020 Biophysical Society Annual Meeting, San Diego, CA, Feb. 15-19, 2020.

91. Negussie, M.; Tran, S.; Chon, N. L.; Oviedo, J.; Alnaas, A.; Knight, J.; Lin, H. “Membrane interaction of synaptotagmin-like protein 4: simulations of mutant C2A domains,” Poster at the 2020 Biophysical Society Annual Meeting, San Diego, CA, Feb. 15-19, 2020.

90. Aydintug, B.; Duster, A. W.; Lin, H. “Proton transport through E. coli CLC chloride/proton antiporter in the presence of bound fluoride,” Poster at the 2020 Biophysical Society Annual Meeting, San Diego, CA, Feb. 15-19, 2020.

89. Negussie, M. Tran, S.; Chon, N. L.; Oviedo, J.; Alnaas, A.; Knight, J.; Lin, H. "Electrostatic membrane interaction of synaptotagmin-like protein 4: Simulations of mutant C2A domains,” Poster at the 2020 Colorado Single Molecules and Membranes Meeting, Denver, CO, Jan. 10, 2020.

88. Negussie, M. Tran, S.; Chon, N. L.; Oviedo, J.; Alnaas, A.; Lin, H.; Knight, J. "Synaptotagmin-like protein 4: Membrane binding simulations of single and triple mutants,” Poster at the 2019 Rocky Mountain Membrane Trafficking Meeting, Denver, CO, Aug 18, 2019.

87. Duster, A. W.; Lin, H. “ Neural-network corrections to semi-empirical quantum chemistry methods for accurate descriptions of proton transfer reactions ,” Poster and Talk at the 2019 Rocky Mountain Advanced Computing Consortium Symposium Denver, CO, May 22-24, 2019.

86. Kovacevic, T.; Lin, H. “ Investigating the dynamics of F58 within HP36 via umbrella sampling: A computational analysis,” Poster and Talk at the 2019 Rocky Mountain Advanced Computing Consortium Symposium Denver, CO, May 22-24, 2019.

85. Bhat, S.; Talachutla, S.; Lin, H. “ Quantitative assessment of equilibration in molecular dynamics simulations,” Poster and Talk at the 2019 Rocky Mountain Advanced Computing Consortium Symposium Denver, CO, May 22-24, 2019.

84. Deyanova, J.; Duster, A.; Lin, H. “ A Protocol of model construction for polymer electrolyte systems in advanced computer simulation,” Poster at the 22nd Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2019.

83. Aydintug, B.; Duster, A.; Negussie, M.; Garza, C.; Lin, H. “ Proton transport in E. coli CLC transport protein by adaptive QM/MM dynamics simulations,” Poster at the 22nd Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2019.

82. Kovacevic, T.; Vugmeyster, L.; Lin, H. “ Probing the dynamics of the villin headpiece protein’s subdomain HP-36,” Poster at the 22nd Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2019.

81. Tran, S. M.; Negussie, M.; Knight, J.; Lin, H. “ Molecular simulations of granuphilin binding to charged membrane,” Poster at the 22nd Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2019.

80. Negussie, M.; Tran, S. M.; Chon, N. L.; Knight, J.; Lin, H. “ Membrane binding of synaptotagmin-like protein 4: Insight from molecular dynamics simulation with strategically mutated C2A domains,” Poster at the 22nd Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2019.

79. Chon, N. L.; Zheng, H.; Lin, H. “A computational study of the essential transmembrane protein Nark as nitrate/nitrite exchanger,” Poster at the 2019 Biophysical Society Annual Meeting, Baltimore, MD, Mar. 2-6, 2019.

78. Alnaas, A.; Oviedo, J.; Watson-Siriboe, A.; Tran, S.; Negussie, M.; Lin, H.; Knight, J. “Membrane binding by synaptotagmin-like protein 4: site-directed mutagenesis of the lipid interaction surface,” Poster at the 2019 Biophysical Society Annual Meeting, Baltimore, MD, Mar. 2-6, 2019.

77. Negussie, M.; Tran, S.; Chon, N.; Knight, J. K.; Lin, H. “Membrane Binding of Synaptotagmin-like Protein 4: Insight from Molecular Dynamics Simulation of two Mutants,” Poster at the 2019 Biophysical Society Annual Meeting, Baltimore, MD, Mar. 2-6, 2019.

76. Aydintug, B.; Duster, A.; Negussie, M.; Garza, C.; Lin, H.  “Proton Transport in E. coli CLC Transport Protein by Adaptive QM/MM Calculations,” Poster at the 2018 Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) National Conference, San Antonio, TX, Oct. 11-13, 2018.

75. Kovacevic, T.; Miller, D.; Vugmeyster, L.; Crowley, M.; Lin, H.  “A Computational Study of the Villin Headpiece Subdomain HP-36,” Poster at the 2018 Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) National Conference, San Antonio, TX, Oct. 11-13, 2018.

74. Chon, N. L.; Anantharam, A.; Knight, J.; Lin, H. "Wild-type and Chimeric C2B Domains of Synaptotagmin 1 and Synaptotagmin 7: Comparison of Computational and Experimental Studies,” Poster at the 2018 Rocky Mountain Membrane Trafficking Meeting, Aurora, CO, Aug 17, 2018.

73. Deyanova, J.; Duster, A.; Lin, H. "Molecular Dynamics Simulation of Lithium Ion Transfer through EC and EMC Electrolyte Batteries,” Poster at the 21st Research and Creative Activities Symposium, University of Colorado Denver, Apr. 27, 2018.

72. Aydintug, B.; Duster, A.; Negussie, M.; Garza, C.; Lin, H. "Proton Transport in E. coli CLC Transport Protein by Combined QM/MM Calculations,” Poster at the 21st Research and Creative Activities Symposium, University of Colorado Denver, Apr. 27, 2018.

71. Chon, N. L.; Tran, S.; Knight, J.; Lin, H. "Structural Features for Synaptotagmin 1 and Synaptotagmin 7: A Computational Study on the Wild-type and Chimeric C2B Domains,” Poster at the 21st Research and Creative Activities Symposium, University of Colorado Denver, Apr. 27, 2018.

70. Kovacevic, T.; Miller, D.; Vugmeyster, L.; Crowley, M.; Lin, H. "A Computational Study of the Villin Headpiece Subdomain HP-36,” Poster at the 21st Research and Creative Activities Symposium, University of Colorado Denver, Apr. 27, 2018.

69. Tran, S. M.; Negussie, M.; Chon, N. L.; Henderson, J.; Knight, J.; Lin, H. “Essential Membrane Docking Regions in Granuphilin C2A,” Poster at the 21st Research and Creative Activities Symposium, University of Colorado Denver, Apr. 27, 2018.

68. Tran, S. M.; Negussie, M.; Chon, N. L.; Henderson, J.; Knight, J.; Lin, H. “Regions of granuphilin C2A domain involved in membrane docking,” 2018 Colorado Single Molecules and Membranes Meeting, Denver, CO, Jan. 12, 2018. 

67. Aydintug, B.; Garza, C.; Duster, A.; Lin, H. Molecular Dynamics Simulations of CLC Proton/Chloride Antiporter. Poster at the 2016 Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) National Conference, Salt Lake City, UT, Oct. 19-21, 2017.

66. Wang, C.-H.; Lin, H. Energetic and structural properties of liquid water by Hamiltonian permuted adaptive-partitioning QM/MM simulation. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

65. Duster, A. W.; Lin, H. Implementation of a NAMD/QMMM interface. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

64. Garza, C.; Duster, A. W.; Lin, H. Adaptive-partitioning QM/MM study of proton transport through EcCLC. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

63. Zarecki, M.; Wang, C.-H.; Lin, H. Computational study of chloride transport through the E. coli Cl–/H+ antiporter. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

62. Chon, N. L.; Shin, E.; Lin, H. Computational study in CtBP1 protein towards inhibitor design. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

61. Miller, D.; Duster, A. W.; Lin, H. Proton uptake and transfer by the M2 channel in influenza A virus. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

60. Tran, S.; Chon, N. L.; Henderson, J. A.; Knight, J.; Lin, H. Binding sites of granuphilin C2A with negatively charged lipids. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

59. Spotts, T.; Watson-Siriboe, A.; Henderson, J. A.; Lin, H.; Knight, J. Quantitative measurements of SLP-2 C2A’s unusual Ca2+-inhibited membrane binding. Poster at the 20th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 28, 2017.

58. Schreyer, L.; Addassi, M.; Johannesson, B.; Lin, H. Modeling vapor transport through partially saturated porous media at the pore scale using chemical potential. Poster at the fall 2016 American Geophysical Union Meeting, San Francisco, CA, Dec. 11-18, 2016.

57. Lin, H. On the mysterious proton transfer through CLC antiporters. Poster at the 2016 Dreyfus Foundation Teacher-Scholar Symposium: Research Frontiers in the Chemical Sceinces, New York, NY, Oct. 28, 2016.

56. Garza, C.; Duster, A.; Lin, H. QM/MM molecular dynamics simulations of proton transfer in EcCLC chloride/proton antiporter. Poster at the 2016 Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) National Conference, Long Beach, CA, Oct. 13-15, 2016.

55. Chon, N.; Shin, E.; Lin, H. A computational study of CtBP1-peptide complex. Poster at the 19th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2016.

54. Duster, A.; Lin, H. Parallel adaptive-partitioning algorithms for multiscale molecular dynamics simulations. Poster at the 19th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2016.

53. Garza, C.; Duster, A.; Lin, H. Combined QM/MM dynamics simulations of proton transfer in E. coli CLC chloride ion transport proteins. Poster at the 19th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2016.

52. Zarecki, M.; Wang, H.; Lin, H. A molecular dynamics study of the effects of protein thermal fluctuations on electron transfer within the photosynthetic reaction center of the bacterium Rhodopseudomonas viridis. Poster at the 19th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2016.

51. Henderson, J.; Merrill, D.; Chon, N.; Shin, E.; knight, J.; Lin, H. Binding of granuphilin C2A domain to memberane by molecular simulations. Poster at the 19th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2016.

50. Miller, D.; Duster, A.; Garza, C.; Lin, H. Proton transfer via Grotthuss shuttling mechanism through carbon nanotube. Poster at the 19th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 29, 2016.

49. Waston-Siriboe A.; Henderson, J.; Osterberg, J. R.; Giardina, D. T.; DeLima, M.; Line, H.; Knight, J.  Multivalent membrane lipid targeting by the calcium-independent C2A domain of granuphilin: Evidence from computation and experiment. Poster at the 60th Annual Meeting of Biophysical Society, Los Angeles, CA, Feb. 27-Mar. 2, 2016.

48. Garza, C.; Duster, A.; Davis, C.; Lin, H. Combined QM/MM dynamics simulations of proton transfer in E. Coli CLC chloride/proton antiporter. Poster at the 60th Annual Meeting of Biophysical Society, Los Angeles, CA, Feb. 27-Mar. 2, 2016.

47. Chon, N. L.; Henderson, J.; Osterberg, J. R.; Khan, H.; Reuter, N.; Knight, J.; Lin, H. Ca2+-induced membrane associations of synaptotagmin 1 and 7: Insights from molecular dynamics simulations. Poster at the 2015 Butcher Symposium, Westminster, CO, Nov. 6, 2015.

46. Pezeshki, S.; Duster, A.; Lin, H. Molecular dynamics simulations of proton hopping by adaptive-partitioning QM/MM. Poster at the 15th International Congress of Quantum Chemistry (ICQC), Beijing, China, Jun. 8-13, 2015.

45. Duster, A.; Lin, H. Parameterization of semiempirical methods to reproduce proton transfer to and from glutamic and aspartic amino acids. Poster at the 18th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 17, 2015.

44. Chon, N. L.; Henderson, J.; Osterberg, J. R.; Khan, H.; Reuter, N.; Knight, J.; Lin, H. Ca2+-induced membrane associations of synaptotagmin 1 and 7 C2A domains: Molecular dynamics simulations. Poster at the 18th Research and Creative Activities Symposium, University of Colorado Denver, Apr. 17, 2015.

43. Davis, C.; Pezeshki, S.; Garza, C.; Lin, H. Combined QM/MM study of the translocation of chloride ions through Escherichia coli chloride ion transporters. Poster at the 2014 Research and Creative Activities Symposium, University of Colorado Denver, Apr. 17, 2015

42. Chon, N. L.; Henderson, J.; Knight, J.; Lin, H. Comparisons of synaptotagmin 1 and synaptotagmin 7 C2A domains in membrane associations by molecular dynamic simulations. Poster at the 249th American Chemical Society National Meeting, Denver, CO, Mar. 22-25, 2015.

41. Davis, C.; Pezeshki, S.; Garza, C.; Lin, H. Study of the translocation of chloride ions through Escherichia coli transporters using the combined QM/MM method. Poster at the 249th American Chemical Society National Meeting, Denver, CO, Mar. 22-25, 2015.

40. Boo, A.; Osterberg, J. R.; Maynard, F.; Chon, N. L.; Lin, H.; Knight, J. Docking model of synaptotagmin 7 C2A via electron paramagnetic response. Poster & Talk at the 249th American Chemical Society National Meeting, Denver, CO, Mar. 22-25, 2015

39. Davis, C.; Pezeshki, S.; Garza, C.; Lin, H. Combined QM/MM study of the translocation of chloride ions through Escherichia coli chloride ion transporters. Poster at the 2015 Annual Meeting of Biophysical Society, Baltimore, MD, Feb. 7-11, 2015

38. Chon, N. L.; Henderson, J.; Osterberg, J. R.; Khan, H.; Reuter, N.; Knight, J.; Lin, H. Membrane association of synaptotagmin 7 C2A domain by molecular dynamics simulations. Poster at the 2015 Annual Meeting of Biophysical Society, Baltimore, MD, Feb. 7-11, 2015

37. Davis, C.; Pezeshki, S.; Lin, H. Will charge delocalization of chloride ions offset the need for large-scale conformational changes of the ClC protein in ion translocation? Poster at the 2014 Research and Creative Activities Symposium, UC-Denver, Apr. 25, 2014

36. Henderson, J.; Chon, N. L.; Knight, J.; Lin, H. Associations of the C2A domains of synaptotagmins 1 and 7 with membranes by molecular dynamics simulations. Poster at the 2014 Research and Creative Activities Symposium, UC-Denver, Apr. 25, 2014.

35. Chon, N. L.; Lee, S.; Lin, H. A theoretical study of temperature dependence of cluster formation from sulfuric acid and ammonia. Poster at the 2014 Research and Creative Activities Symposium, UC- Denver, Apr. 25, 2014.

34. Davis, C.; Pezeshki, S.; Lin, H. Steered molecular dynamics simulations of Escherichia coli ClC chloride ion transporter.Poster at the 2013 Gamma Sigma Epsilon National Chemistry Honor Society's Biennial Convention, Frostburg, MD, Oct. 11-13, 2013.

33. Chon, N. L.; Lee, S.; Lin, H. A density functional theory study of temperature dependence of cluster formation from sulfuric acid and ammonia. Poster at the 2013 American Geophysical Union Meeting, San Francisco, CA, Dec. 9-13, 2013.

32. Tyk, L.; Johnson-Sasso, C.; Julian, L.; Lin, H. Structure-based design of small molecule inhibitors of Mcl-1 protein. Poster at the 2013 Research and Creative Activities Symposium, University of Colorado Denver, Apr. 19, 2013.

31. Chon, N. L.; Kim, E.; Pezeshki, S.; Reed, S. M.; Lin, H. Interactions between the human C-Reactive Protein and lipid-coated nanoparticles. Poster at the 2013 Research and Creative Activities Symposium, University of Colorado Denver, Apr. 19, 2013.

30. Church, J.; Pezeshki, S.; Lin, H. Interactions between chloride ions and amino acids. Poster at the ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012

29. Chon, N. L.; Lee, S.; Lin, H. Binding energy of ammonia-sulfuric acid clusters in atmospheric nucleation. Poster at the ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012

28. Chon, N. L.; Kim, E.; Pezeshki, S.; Reed, S.; Lin, H. Interactions between the human C-reactive protein and lipid-coated nanoparticles. Poster at the ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012

27. Tyk, L.; Johnson-Sasso, C.; Julian, L.; Lin, H. Structure-based design of small molecule inhibitors of Mcl-1 protein. Poster at the ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012

26. Davis, C.; Pezeshki, S.; Lin, H. Molecular dynamics simulations of Escherichia coli CLC chloride ion transporters with different protonation states of critical residues. Poster at the ACS Rocky Mountain Regional Meeting, Westminster, CO, Oct. 17-20, 2012

25. Chon, N.; Kim, E. ; Lin, H.; Molecular dynamics simulations of the human C-reactive protein. Poster at the 15th Annual Research and Creative Activities Symposium, UC-Denver, April 27, 2012.

24. Pezeshki, S.; Lin, H. Steered molecular simulations by adaptive partitioning QM/MM. Poster at the 242nd ACS National Meeting, Denver, CO, Aug. 28-Sept. 1, 2011

23. Smith, M.; Lin, H. Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters.Poster at the 242nd ACS National Meeting, Denver, CO, Aug. 28-Sept. 1, 2011

22. Zhang, Y.; Lin, H. Partial charge transfer across the QM/MM boundary: Flexible-boundary QM/MM calculations.Poster at the 241st ACS National Meeting, Anaheim, CA, Mar. 26-31, 2011

21. Smith, M.; Lin, H. Quantum effect can be important to chloride ion channel/transporter mechanism: A computational study.14th Annual Research and Creative Activities Symposium, UC-Denver, May 15, 2011 (Oral Presentation)

20. Kim, K.; Lin, H. Computational study of gold-thiol complexes and their implication on nanotoxicity.Poster at the 14th Annual Research and Creative Activities Symposium, UC-Denver, May 15, 2011

19. Zhang, Y.; Lin, H.; Partial charge transfer across the QM/MM boundary: Flexible-boundary QM/MM calculations. International Symposium on Theoretical and Computational Chemistry, Muelheim an der Ruhr, Germany, February 28 - March 2, 2010. (Poster)

18. Zhang, Y.; Lin, H.; Quantum tunneling in testosterone 6β-hydroxylation by cytochrome P450. International Symposium on Theoretical and Computational Chemistry, Muelheim an der Ruhr, Germany, February 28 - March 2, 2010. (Poster)

17. Zhang, Y.; Lin, H. Flexible-boundary QM/MM: Partial charge transfer between the QM and MM subsystems. IMA Annual Program Year Workshop: Molecular Simulations: Algorithms, Analysis, and Applications, Minneapolis, MN, May 18-22, 2009 (Poster)

16. Levy, J.; Ader, L.; Lin, H. Theoretical modeling of binding affinity of alcohol with odorant-binding protein. 12th Annual Research Creative Activities Symposium, University of Colorado Denver, Denver, CO, April 25, 2009. (Poster)

15. Zhang, Y.; Lin, H. Flexible-boundary QM/MM: Partial charge transfer between the QM and MM subsystems. IWoM3 2009 - International Workshop on Multiscale Materials Modeling, Berlin, Germany, March 10 - 13, 2009 (Poster)

14. Morisetti, P.; Lin, H. Computational study of metformin binding to insulin receptor. 1st Annual STEMapalooza, Denver, Oct. 24-25, 2008. (Poster)

13. Morisetti, P.; Lin, H. Anti-diabetes drug metformin binding to activated insulin receptor. 11th Annual Research Creative Activities Symposium, University of Colorado Denver, Denver, CO, April 11, 2008. (Poster)

12. Kim, J.; Morisetti, P.; Lin, H.; Docking testosterone in the active site of cytochrome P450 3A4: Simulations suggest protein conformational changes are critical to substrate binding.

Rocky Mountain Regional Meeting, Denver, CO, August 29 - September 1, 2007 (Poster)

11. Zhang, Y. Lin, H.; Hydrogen abstraction of testosterone by cytochrome P450 3A4: A computational investigation. Rocky Mountain Regional Meeting, Denver, CO, August 29-September 1, 2007 (Poster)

10. Yurchenko, S. N.; Carvajal, M.; Jensen, P.; Lin, H.; Thiel, W.; Vibrational energies of the ammonia molecule and its isotopomers calculated from high level ab initio surfaces. 17th International Conference on High Resolution Molecular Spectroscopy, Prague, Czech Republic, 2002 (Oral)

9. Carvajal, M.; Yurchenko, S. N.; Jensen, P.; Lin, H.; Thiel, W.; Analysis of the ammonia molecule in the MORBID approach based on high level ab initio surfaces. 5th Iberian Joint Meeting on Atomic and Molecular Physics, 2002 (Poster)

8. Schoeneboom, J. C.; Lin, H.; Reuter, N.; Thiel, W.; Cohen, S.; Ogliaro, F.; Shaik, S. Study of cytochrome P450 enzymes by combined quantum mechanical / molecular mechanical (QM/MM) calculations. 6th World Congress of Theoretically Oriented Chemists, Lugano, Switzerland, 2002 (Poster)

7. Hu, S. M.; Lin, H.; Cheng, J. X.; He, S. G.; Zheng, J. J.; Zhu, Q. S.; Bekhtreva, E. S.; Ulenikov, O. N.; Fourier-transform intra-cavity laser absorption spectroscopy study of the D2O molecule in the region of the 4nu1 + n3 band. 17th Colloquium on High Resolution Molecular Spectroscopy, Nijmegen, the Netherlands, 2001 (Poster)

6. Lin, H.; He, S. G.; Wang, X. G.; Yuan, L. F.; Buerger, H.; D'Eu, J.-F.; Reuter, N.; Thiel, W.; The vibrational overtones of SiH4 isotopomers. 17th Colloquium on High Resolution Molecular Spectroscopy, Nijmegen, the Netherlands, 2001 (Poster).

5. Lin, H.; Yuan, L. F.; Zhu, Q. S. Calculation of the local mode overtone intensities of silane and germane using four-dimensional dipole moment surfaces obtained from ab initio calculations. 16th International Conference on High Resolution Molecular Spectroscopy, Prague, Czech Republic, 2000 (Poster)

4. Hu, S. M.; Lin, H.; He, S. G.; Wang, X. H.; Zheng, J. J.; Zhu, Q. S.; Kachanov, A. A. Measurement of integrated line intensities by Fourier transform intra-cavity laser absorption spectroscopy (FT-ICLAS). 16th International Conference on High Resolution Molecular Spectroscopy, Prague, Czech Republic, 2000 (Poster)

3. Bekhtereva, E. S.; Ulenikov, O. N.; Onopenko, G. A.; Hu, S. M.; He, S. G.; Wang, X. H.; Lin, H.; Zhu, Q. S. High resolution analysis of the v = 3 and v = 3.5 (v = nu1 + n2 / 2 + n3) polyads of the D2O molecule. 16th International Conference on High Resolution Molecular Spectroscopy, Prague, Czech Republic, 2000 (Poster)

2. Ulenikov, O. N.; Onopenko, G. A.; Bekhtereva, E. S.; Hu, S. M.; He, S. G.; Wang, X. H.; Lin, H.; Zhu, Q. S. High resolution study of strongly interacted vibrational bands of HDO in the region of 7600 - 8100 cm-1. 16th International Conference on High Resolution Molecular Spectroscopy, Prague, Czech Republic, 2000 (Poster)

1. Hu, S. M.; Lin, H.; Cheng, J. X.; He, S. G.; Zhu, Q. S.; Kachanov, A. A. High sensitivity and high resolution Fourier-transform intra-cavity laser absorption spectroscopy (FT-ICLAS). XIII International Symposium and School on High Resolution Molecular Spectroscopy (HighRus-99), Tomosk, Russia, 1999 (Poster)

 

Dissertations

Dissertation for Ph. D. Degree:

The intensities of the local mode overtones of the XH4type molecules and Fourier transform intra-cavity laser absorption spectroscopy. (University of Science and Technology of China, Hefei, May, 1998)

Dissertation for M. S. Degree:

A multi-task 100 MHz sampling-rate logic analyzer. (University of Science and Technology of China, Hefei, July, 1995)

 

Computational Programs

5. QMMM

Hai Lin, Yang Zhang, Soroosh Pezeshki, Adam Duster

Department of Chemistry, 
University of Colorado Denver, Denver, CO 80217, USA

Bo Wang, Xin-Ping Wu, Shi-Wen Zheng, Laura Gagliardi, and Donald G. Truhlar 
Department of Chemistry and Supercomputing Institute, 
University of Minnesota, Minneapolis, MN 55455-0431, USA

4. EquCheck

Shamik Bhat, Sahitya Talachuntla, and Hai Lin
Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA
 

3. MBPAC

Hannah Leverentz, Erin Dahlke, Hai Lin, Bo Wang, Jeremy Tempkin, Helena Qi, and Donald G. Truhlar

Department of Chemistry and Supercomputing Institute, 
University of Minnesota, Minneapolis, MN 55455-0431, USA

2. MCSI (MC-TINKER)

Oksana Tishchenko, Masahiro Higashi, Titus V. Albu, Jose C. Corchado, Yongho Kim, Jordi Villa, Jinhua Xing, Hai Lin, and Donald G. Truhlar

Department of Chemistry and Supercomputing Institute, 
University of Minnesota, Minneapolis, MN 55455-0431, USA

1. MC-TINKERATE

Titus V. Albu, Oksana Tishchenko, Jose C. Corchado, Yongho Kim, Jordi Villa, Jinhua Xing, Hai Lin, Masahiro Higashi, and Donald G. Truhlar

Department of Chemistry and Supercomputing Institute, 
University of Minnesota, Minneapolis, MN 55455-0431, USA

Dr. Hai Lin

Dr. Hai Lin profile photograph

Professor, Chemistry Department, 
University of Colorado Denver,
SI 4126B, Campus Mail 194,
PO Box 173364, Denver, CO 80217

Phone: +1-303-315-7656
Fax: +1-303-556-4776  
E-mail

ORCID • Google Scholar • Researcher ID

Interested students are very welcomed to contact me via my email about research projects and research positions.

By the way, I found this interesting link.