Yi Qin Gao

  Changjiang Professor in Chemistry

  Web site of group: /gaoyq

A. Education

• B.S. in Chemistry, Sichuan University, Chengdu, China, June 1993
• M.S. in Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China, June 1996. Advisor: Dr. Dalin Yang
• Ph.D in Chemistry, California Institute of Technology, Pasadena, California, June 2001.
  Advisor: Professor Rudolph A. Marcus
• Postdoctoral Research Fellow, California Institute of Technology, 2001- 2002 .
  Advisor: Professor Rudolph A. Marcus
• Postdoctoral Research Fellow, Harvard University , December, 2002- 2004.
  Advisor: Professor Martin Karplus

B. Positions and Honors

Positions and Employment

December, 2004-Present Assistant Professor, Department of Chemistry, Texas A&M University

Honors and Awards

• 2006 Searle Scholar
• JST Visiting Scholar, Kobe University, Japan
• 2004-2009 Camille and Henry Dreyfus New Faculty Award
• Milton and Francis Clauser Prize for the Best Doctoral Thesis, CalTech
• Herbert Newby McCoy Award
• Li Ming Scholarship, CalTech
• Chinese-American Engineers and Scientists Association Scholarship

C. Synergistic Activities and Service

• Secretary, Texas A&M local Section, American Chemical Society
• Advisory Board, Interdisciplinary Sciences
• Advisory Panel, Chinese Student Association at Texas A&M University
• Co-organizer, Annual Southwestern Theoretical Chemistry Conference
• Editorial Board, Acta Physical Chemistry
• Participant, Leadership Institute, American Chemical Society
• International Graduate Student Application Evaluation Group, Chemistry, TAMU
• Reviewed Papers for Chemical Physics Letters, Journal of Geophysical Research, Journal of American Chemical Society, Proceedings of National Academy of Sciences, U.S.A, Physical Biology, Journal of Physical Chemistry, PLOS Biology, Journal of Biomolecular Structure and Dynamics, PLOS computational Biology, Biophysical Journal, Archives of Biochemistry and Biophysics, Biochemistry, and Geophysics Letters
• Reviewed proposals for National Science Foundation, ACS-PRF, The Research Council of Hong Kong, the Science Research Foundation of France, and Chinese National Science Foundation

D. Peer-reviewed publications (in chronological order; Publications at TAMU: 21-41).

1. HeI Photoelectron Spectroscopic (PES) studies of the electronic structure of B(OCH3)3, D. X. Wang, S. Li, Y. Li, C. F. Ding, Y. Q. Gao, and W. W. Chen, Acta Phys. Chem. 12, 641 (1996).
2. HeI Photoelectron Spectroscopic (PES) studies of the electronic structure for alkyl nitrites CH3(CH2)nONO (n=0,1,2,3), D. X. Wang, S. Li, Y. Li, C. F. Ding, Y. Q. Gao, and W. W. Chen, J. Elec. Spec. 82, 19 (1996).
3. The study of the 6H-pyridine clusters, W. W. Chen, Y. Q. Gao, G. S. Wu, D. L. Yang, L. S. Sheng, G. H. Wu, W. Q. Ye, and Y. W. Zhang, Acta Phys. Chem. 12, 1067 (1996).
4. HeI Photoelectron Spectroscopic (PES) studies of the electronic structure of AL(CH3)3, In(C2H5)3, and Cd(CH3)2 compounds, D. X. Wang, S. Li, Y. Li, S. Zheng, B. Chen, C. F. Ding, and Y. Q. Gao, Chem. Phys. Lett. 260, 95 (1996).
5. Photoionization and dissociation of 4H-furan by synchrotron radiation, G. S. Wu, Y. Q. Gao, W. W. Chen, D. L. Yang, L. S. Sheng, G. H. Wu, W. Q. Ye, and Y. W. Zhang, Acta Phys. Chem. 13, 188 (1997).
6. Photoionization and dissociation of thiophene and pyridine by synchrotron radiation, G. S. Wu, W. W. Chen, Y. Q. Gao, D. L. Yang, L. S. Sheng, G. H. Wu, W. Q. Ye, and Y. W. Zhang, Chin. J. Chem. Phys. 10, 385 (1997).
7. On the theory of electron transfer at semiconductor/liquid interfaces, Y. Q. Gao, Y. Georgievskii, and R. A. Marcus, J. Chem. Phys. 112, 3358 (2000).
8. On the theory of electron transfer at semiconductor/liquid interfaces II: a free electron model, Y. Q. Gao and R. A. Marcus, J. Chem. Phys. 113, 6351 (2000).
9. The temperature dependence of electron transfer at metal and semiconductor surfaces, S. Gosavi, Y. Q. Gao and R. A. Marcus, J. Electroanal. Chem. 500, 71 (2001).
10. Pressure effect on bimolecular recombination and unimolecular dissociation, R. A. Marcus and Y. Q. Gao, J. Chem. Phys. 114, 9807 (2001).
11. Application of the z-transform to composite materials, Y. Q. Gao and R. A. Marcus, J. Chem. Phys. 115, 9929 (2001).
12. Strange and unconventional isotopic effect in ozone formation, Y. Q. Gao and R. A. Marcus, Science 293, 259 (2001).
13. On the theory of strange and unconventional isotopic effects of ozone, Y. Q. Gao and R. A. Marcus, J. Chem. Phys. 116, 137 (2002).
14. Theoretical investigation of the directional electron transfer in a small supramolecular system, Y. Q. Gao and R. A. Marcus, J. Phys. Chem. A 106, 2956 (2002).
15. Ozone isotopic effect: A detailed numerical calculation using a modified ab initio potential energy surface, Y. Q. Gao, C-W. Chen, and R. A. Marcus, J. Chem. Phys. 117, 1536-1546 (2002).
16. The missing link between thermodynamics and structure in F1-ATPase, W. Yang, Y. Q. Gao, Q. Cui, J. Ma, and M. Karplus, Proc. Natl. Acad. Sci. (USA) 100, 874-879 (2003).
17. A model for the cooperativity in the free energy transduction and kinetics in ATP hydrolysis by F1-ATPase, Y. Q. Gao, W. Yang, R. A. Marcus, and M. Karplus, Proc. Natl. Acad. Sci. (USA) 100, 11339-11345 (2003).
18. Biomolecular motors: the F1-ATPase paradigm, M. Karplus and Y. Q. Gao, Curr. Opin. Stru. Biol. 14, 250-259 (2004).
19. Protein Structural transitions and their function roles, M. Karplus, Y.Q. Gao, J.P. Ma, A. van der Vaart, and W. Yang, Phil. Trans. The Royal Society of London A- 363, 331-355 (2005).
20. The binding change mechanism of F1-ATPase revisited, Y. Q. Gao, W. Yang, and M. Karplus, Cell, 123, 195-205 (2005).
21. A simple theoretical model explains dynein’s response to external load, Y.Q. Gao, Biophys. J. 90, 811-821 (2006).
22. Thermodynamics and kinetic analysis of F1Fo-ATP synthase, Y. Q. Gao, W. Yang, and M. Karplus, in Modern computational method of biopolymers (Elsevier, 2006).
23. On the hand-over-hand mechanism of kinesin, Q. Shao and Y.Q. Gao, Proc. Natl. Acad. Sci. (USA), 103, 8072-8077 (2006).
24. On the enhanced sampling over energy barriers in molecular dynamics simulations, Y.Q. Gao and L. Yang, J. Chem. Phys. 125, 114103 (2006).
25. A kinetic model for myosin V, Y.D. Wu, Y.Q. Gao, and M. Karplus, Biochemistry, 46, 6318-6330 (2007).
26. An approximate method for the MD simulations of protein conformational changes, L. Yang and Y. Q. Gao, J. Phys. Chem. B 111, 2969-2975 (2007).
27. Application of the accelerated MD simulations to the folding of a small protein, L. Yang, M. P. Grubb, and Y. Q. Gao, J. Chem. Phys. 126, 125102 (2007).
28. A DFT study on the mechanism of phosphodiester cleavage mediated by monozinc complexes, Y. Fan and Y.Q. Gao, J. Am. Chem. Soc. 129, 895-904 (2007).
29. The effects of hydrophobic and dipole-dipole interactions on the conformational transitions between different model polypeptide structures, Y. Mu and Y. Q. Gao, J. Chem. Phys. 127, 105102 (2007).
30. Asymmetry in kinesin walking, Q. Shao and Y.Q. Gao, Biochemistry, 46, 9098-9106 (2007).
31. Selective sampling of transition paths, X. Fu, L, Yang, and Y.Q. Gao, J. Chem. Phys. 127, 154106 (2007).
32. An approximate theory for the ozone isotopic effect, Y.Q. Gao and R.A. Marcus, J. Chem. Phys. 127, 244316 (2007).
33. A molecular dynamics simulation study of ammonia transport in CPS, Y. Fan, L. Lund, L. J. Yang, F. Raushel, and Y.Q. Gao, Biochemistry, 47, 2935-2944 (2008).
34. An integrate-over-temperature approach for the enhanced sampling in molecular dynamics simulations, Y.Q. Gao, J. Chem. Phys. 128, 064105 (2008).
35. Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations, Y.Q. Gao, J. Chem. Phys. 128, 134111 (2008).
36. Enhanced sampling methods for thermodynamics and kinetics simulations, Y.Q. Gao, L.J. Yang, Y. Fan, and Q. Shao, International Review in Physical Chemistry, 27, 201-227 (2008).
37. Chemomechanical coupling of kinesin and dynein, in Proteins: Energy, Heat and Signal Flow, Taylor & Francis Group (2009).
38. Thermodynamics and folding pathways of trpzip2, L.J.Yang, Q. Shao, and Y. Q. Gao, J. Phys. Chem. B, 113, 803-808 (2009).
39. Comparison between integrated and parallel tempering methods in enhanced sampling, L.J. Yang, and Y. Q. Gao, J. Chem. Phys. 130, 124111 (2009).
40. Free energies and forces in helix–coil transition of homopolypeptides under stretching. F. C. Zegarra, G. N. Peralta, A. M. Coronado and Y. Q. Gao, Phys. Chem. Chem. Phys. 11, 4019-4024 (2009).
41. A test of implicit solvent models on the folding simulation of the GB1 peptide. Q. Shao, L. Yang, and Y. Q. Gao J. Chem. Phys. 130, 195104 (2009).
42. A combined computational and experimental studies of the ammonia transport in CPS, Y. Fan, L. Lund, Y.Q. Gao, and F. Raushel, J. Am. Chem, Soc. 131, 10211-10219 (2009).
43. On the Structure Elucidation using IMS and Molecular Dynamics, F. A. Fernandez-Lima, H. Wei, Y. Q. Gao, D. H. Russell, J. Phys. Chem. A 29, 8221-8234 (2009).
44. A simple model and assignment of the SFG spectrum for the water/air interface, Y. Fan, X. Chen. P. Cremer, and Y.Q. Gao, J. Phys. Chem. B, 113 11672-11679 (2009).

E. Presentations (Since 2005, In chronological order)

1. The rotary protein motor, Chemical Physics Seminar at Caltech, May, 10, 2005.
2. The gear mechanism of dynein, Single molecular spectrum-theory and experiments Workshop, Colorado, August, 2005.
3. Multi-time scale simulations of calmodulin, Sichuan University, Chengdu, China, December, 2005.
4. Chemomechanical coupling mechanisms of kinesin and dynein, Shenzhen Graduate School, Beijing University, China, December, 2005.
5. Enhanced sampling methods in MD simulations, Department of Physics, University of Texas at San Antonio, March, 2006.
6. Strange ozone isotopic effect, Kobe University, May, 2006.
7. Energy usage by protein motors, Institute of Technology, Kobe University, May, 2006.
8. Protein conformational changes and MD simulations, Shandong University, China, May, 2006
9. An approximate theory of unconventional ozone isotopic effect, ACS National Meeting, San Francisco, August, 2006.
10. Accelerated simulations of protein folding and conformational changes, Department of Chemistry, University of Wisconsin, September, 2006.
11. Accelerated simulations of protein motions and energy usage by motor proteins, International Symposium on Protein Conformations, Kobe, Japan, December, 2006.
12. Multi-scale simulations of protein motion, Institute of Chemical Sciences, Zhongshan University, China, December, 2006.
13. Multi-scale simulations of protein motion, Chemical Physics Seminar, Caltech, March 2007
14. Protein Motions: folding, misfolding, and aggregation, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China, May, 2007.
15. Accelerated simulations of protein folding, XingDa Lecture, Beijing University, China, May, 2007
16. Strange isotopic effects of ozone, Quantum Optics Workshop, Casper, Wyoming, July, 2007.
17. Accelerated dynamics and kinetic simulations, ACS National Meeting, Boston, August, 2007.
18. Enhanced Sampling in the energy and configuration space, Department of Bioengineering, Texas A&M University, October, 2007.
19. Enhanced sampling in the energy, configuration, and trajectory spaces, ACS Regional Meeting, Lubbock, November, 2007.
20. An integrated tempering sampling method, Telluride, Colorado, March, 2008.
21. Accelerated protein folding and aggregation simulations, Computational Biology Workshop, Texas A&M University, February, 2008.
22. Integrated tempering sampling and applications to protein folding, International conference on theoretical chemical physics, Vancouver, Canada, July, 2008.
23. Enhanced sampling in the energy, configuration, and trajectory spaces. International symposium of theoretical and computational chemistry, Shanghai, China, September, 2008.
24. A molecular assembly-line—molecular dynamics simulations of carbomoyl phosphate synthetase, University of HongKong August, 2008.
25. Integrated tempering sampling and applications to protein folding, The HongKong University of Science and Technology, August,, 2008.
26. Integrated tempering sampling and studies of water/air interface, University of Chicago, November, 2008.
27. Integrated tempering sampling and studies of water/air interface, University of Wisconsin, November, 2008.
28. Integrated tempering sampling and studies of water/air interface, University of Minnesota, November, 2008.
29. Integrated tempering sampling and studies of water/air interface, University of California, Irvine, November, 2008.
30. Integrated tempering sampling and studies of water/air interface, University of California, Santa Barbara, November, 2008.
31. Integrated tempering sampling and applications to protein aggregation, University of Texas, Austin, October, 2008.
32. Integrated tempering sampling and studies of water/air interface, California Institute of Technology, November, 2008.
33. Simulations of multi-scale motions of proteins: folding, conformational change, and aggregation. Cotton Medal Symposium, Texas A&M University, January, 2009,
34. Understanding the folding and mis-folding of polypeptides, ABCS workshop, Texas A&M University, March, 2009.
35. Sampling of protein conformations-a molecular detailed mechanism of urea denaturation, Chicago, April 23, 2009.
36. The hydrophobic and hydrogen bonding interactions in protein structure formation, The 17th Conference of the Southeast Association of Theoretical Chemistry, Durham, North Carolina, May, 2009.
37. An efficient sampling method in molecular dynamics simulations, Department of Chemistry, Nanjing University, March, 2009.
38. A molecular assembling machine made of a protein complex—cargo transport in CPS, Department of Chemistry, Nanjing University, March, 2009.
39. Integrated tempering sampling and applications to protein folding, Department of Chemistry, University of Science and Technology of China, March, 2009.
40. The hydrophobic and hydrogen bonding interactions in protein structure formation, May 5, 2009, State University of New York, Stony Brook, May, 2009.
41. Hydrophobic and hydrogen bonding interactions in protein folding, Kevli Institute of Theoretical Physics summer workshop, Beijing, China, August, 2009.