Welcome to Xuhui Huang's Homepage

Xuhui Huang

SimBios Center
Department of Bioengineering
Stanford University
318 Campus Drive, Mail Code 5448
Stanford, CA 94305

[Education] [Teaching] [Research Experience] [ Publications] [Fellowship & Awards ] [ Presentations ] [ Program Committees ] [ Editorial Activities ][ CV (PDF) ]

This page was last updated on September 09, 2009

Education

09/2008-present, Research Associate,
Department of Bioengineering , Stanford University
Research Advisor: Professor Michael Levitt and Professor Vijay Pande
08/2006-09/2008, Distinguished Postdoctoral Scholar,
SimBios Center , Stanford University
Research Advisor: Professor Michael Levitt and Professor Vijay Pande
02/2004-07/2006, PhD in Chemical Physics
Chemistry Department, Columbia University
Research Advisor: Professor Bruce Berne
02/2004-05/2006, Master of Philosophy,
Chemistry Department, Columbia University.
09/2001-02/2004, Master of Arts, GPA 4.1/4.0
Chemistry Department, Columbia University.
09/1997 – 06/2001, Bachelor of Science (Graduate with Honor)
Department of Chemical Physics
University of Science and Technology of China (USTC)

Teaching Experience

Fall 2002, Teaching Assistant
Statistical Thermodynamics (with Prof. Philip Pechukas)
Columbia University, Chemistry Department
Spring, 2002, Spring, 2003 Teaching Assistant
General Chemistry Lab
Chemistry Department, Columbia University.

Research Experience

· Sep 2008 – Present, Research Associate
Aug 2006 – Sep 2008, Distinguished Postdoctoral Scholar
Simbios Center , Stanford University
Advisors: Professor Michael Levitt and Professor Vijay S. Pande

My current research focuses on understanding the thermodynamics and kinetics of the folding of proteins and small RNA molecules using all-atom simulations with explicit solvent. To obtain converged sampling I have implemented generalized ensemble algorithms such as Replica Exchange, and Simulated Tempering on the Folding@home distributed computing environment. I have developed a more efficient scheme to determine weights for Simulated Tempering simulations and novel algorithms for the construction of Markov State Models (MSM) to study kinetics. Other projects I am working on include (1) developing a multi-scale knowledge based potential for RNA structure refinement and molecular dynamics simulations, and (2) applying computational tools to elucidate the fundamental mechanism of RNA transcription.

Dec 01 – July 06, Research Assistant
Chemistry Dept, Columbia University.stant
Advisor: Prof. Bruce J. Berne

My graduate research was mainly focused on understanding the hydrophobic effect in protein folding. We studied the hydrophobic interactions and “dewetting” phenomena by using the molecular dynamics simulations for systems ranging from nano-size hydrophobic plates to proteins. nano-size hydrophobic plates to proteins. nano-size hydrophobic plates to proteins. The other projects I have worked on include the development of the Hydrophobic-Aided replicate exchange method (HAREM) to enhance sampling, water dynamics in the solvation shell of a two-domain protein, and molecular dynamics studies of a Green Chemistry process --- the extraction of organic compounds by using supercritical CO₂ from room temperature ionic liquids.

Fellowships and Awards

CCG Excellence Award, American Chemical Society, Division of COMP. (Atlanta, 2006)
Faculty Fellowship, Columbia University (2001-2003, 2004-2006)
Blanche R. and David Kasindorf Fellowship in Physical Chemistry (2003-2004)
Scholarships for excellent students, USTC (2000)
Duohui He Fellowship, USTC (1998)
Zhongzhi Zhang Fellowship, USTC (1997)

Publications

Huang, X., Yao Y., Sun J., Bowman G.R.,Guibas L., and Carlsson G.. and Pande V.S. "Constructing Multi-resolution Markov State Models(MSMs) to elucidate RNA hairping folding mechanisms", The Pacific Symposium on Biocomputing 2010, Submitted
Sun J, Yao Y, Huang, X, Pande V.S., Carlsson G. and Guibas L., "A Fast Geometric Clustering Method on Conformation Space of Biomolecules", J. Phys. Chem. B., Submitted, (2009)
Young T., Hua L., Huang, X., Abel R., Friesner R., Berne B.J., "Dewetting Transitions in Protein Cavities", Proteins., Submitted, (2009)
Huang, X., Bowman, G. R., Bacallado, S., and Pande, V. S. “Rapid Equilibrium Sampling Initiated from Non-equilibrium Data.” Proc. Nat. Acad. Sci. U.S.A., In Press, (2009)
Bowman, G. R., Huang, X. and Pande, V. S. “Using generalized ensemble simulations and Markov state models to identify conformational states.” Methods, In Press, (2009) PMID 19410002
Wang D, Bushnell D.A., Huang, X, Westover K.D., Levitt M, and Kornberg R.D. “Structural Basis of Backtracked RNA Polymerase II Ternary Complex” , Science, 324, 1203-1206, (2009)
Kelley, N., Huang, X, Tam, S., Spiess C., Frydman, J., Pande, V. S. “The Predicted Structure of the Headpiece of the Huntingtin Protein and its Implications on Huntingtin Aggregation.” J. Mol. Bio., 338, 919-927, (2009)
Yao Y, Sun J, Huang, X, Bowman G.R., Lesnik M, Singh G, Pande V.S., Guibas L, and Carlsson G. “Topological Methods for Exploratory Pathway Analysis of Complex Biomolecular Systems”, J. Chem. Phys., 130, 144115, (2009)
Bowman G.R., Huang, X, Yao Y, Sun J, Carlsson G, Guibas L., Pande V.S. “Structural Insight into RNA Hairpin Folding Intermediates.” J. Am. Chem. Soc., 130, 9676–9678, (2008)
Huang, X., Bowman, G. R., and Pande, V. S. “Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.” J. Chem. Phys. 128, 205106, (2008)
Hu, Z., Huang, X., Annapureddy H.V.R.,and Margulis C.J. “Molecular Dynamics Study of the Temperature-Dependent Optical Kerr Effect Spectra and Intermolecular Dynamics of Room Temperature Ionic Liquid 1-Methoxyethylpyridinium Dicyanoamide”, J. Phys. Chem. B, 112 (26), 7837–7849, (2008)
Huang, X., Hagen, M., Kim, B., Friesner, R.A., Zhou, R and Berne, B.J. “Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems” J. Phys. Chem. B. 111, 5405-5410, (2007)
Hua, L., Huang, X., Liu, P., Zhou, R. and Berne, B.J. “Nanoscale Dewetting Transition in Protein Complex Folding.” J. Phys. Chem. B. 111, 9069-9077, (2007)
Liu, P., Huang, X., Zhou, R., Berne, B.J. “Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent.” J. Phys. Chem. B 110, 19018-19022, (2006)
Hua, L., Huang X., Zhou, R., and Berne, B.J., “Dynamics of water confined in the interdomain region of a multidomain protein”, J. Phys. Chem. B., 110, 8, 3704-3711 (2006).
Huang, X., Margulis, C.J., Li, Y. and Berne, B.J.,“Why is the Partial Molar Volume of CO2 So Small When Dissolved in a Room Temperature Ionic Liquid? Structure and Dynamics of CO2 Dissolved in [Bmim+] [PF6-].”, J. Am. Chem. Soc., 127, 50, 17842-17851 (2005).
Liu, P., Huang, X., Zhou, R., Berne, B.J., “Observation of a dewetting transition in the collapse of the melittin tetramer”, Nature, 437, 159-162 (2005).
Huang, X., Zhou, R. and Berne, B.J., “Drying and Hydrophobic Collapse of Paraffin Plated”, J. Phys. Chem. B, 109, 3546-3552 (2005).
Zhou, R., Huang, X., Margulis, C.J., and Berne, B.J., “Hydrophobic Collapse in Multi-domain Protein Folding”, Science, 305, 1605-1609 (2004).
Huang, X., Margulis, C.J., Berne, B.J. “Comment on "Do molecules as small as neopentane induce a hydrophobic response similar to that of large hydrophobic surfaces?" - Reply ” J. Phys. Chem. B 108 (26): 9373-9374,(2004)
Huang, X., Margulis C.J., and Berne, B.J., “Dewetting-induced collapse of hydrophobic particles”, Proc. Nat. Acad. Sci., 100, 21, 11953-11958 (2003).
Huang, X., Margulis, C.J., and Berne, B.J., “Do Molecules as Small as Neopentane Induce a Hydrophobic Response Similar to That of Large Hydrophobic Surfaces?” J. Phys. Chem. B, 107, 42, 11742-11748 (2003).

Presentations

Invited talks:

USA-Mexico Workshop in Biological Chemistry, Mexico City, Mexico, March 2009
Departmental Seminar, Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO, March 9, 2009
Computational Molecular Biophysics Seminar, Department of Biochemistry and Molecular Biophysics, University of Tennessee, Knoxville, TN, Feb 25, 2009
Theoretical Chemistry Seminar, Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, Feb 16, 2009
Departmental Colloquium, Department of Physics, Chinese University of Hong Kong, Hong Kong, Feb 6, 2009
Departmental Seminar, Department of Physics, Chinese University of Hong Kong, Hong Kong, Feb 5, 2009
Physical Chemistry Seminar, Department of Chemistry, Syracus University, Syracus, NY, Jan 29, 2009
Biophysics and Biophysical Chemistry Seminar, School of Medicine, Johns Hopkins University, Jan 21, 2009
Physical Chemistry Seminar, Department of Chemistry, Wayne State University, Detroit, MI, Jan 12, 2009
Theoretical Chemistry Seminar, Department of Chemistry, University of California, Merced, Merced, CA, Dec 12, 2008
Departmental Seminar, Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, Nov 24, 2008
All Hands Meeting (AHM) for the NIH Roadmap National Centers for Biomedical Computing (NCBC), Bethesda , Maryland , Aug 2008.
Telluride Science Research Center workshop Algorithmic Development on Enhanced Sampling, Telluride, CO, July 2008.
Simbios Seminar, NIH center for Biomedical Computation at Stanford University. Stanford, CA, May 2008.
235^th ACS National Meeting, New Orleans, LA, April 2008
Simbios Seminar, NIH center for Biomedical Computation at Stanford University. Stanford, CA, May 2007.

Contributed talks:

Bay Area RNA Meeting, San Francisco, CA, Jun 2008
235^thACS National Meeting, New Orleans, Apr 2008.

Seleted Poster presentations:

Huang, X., Bowman, G. R., Bacallado, S., and Pande, V. S. “Adaptive Seeding Method”. Molecular Kinetics 2009 , Berlin, Germany, May 2009
Sun J, Huang X, Yao Y, Pande V.S., Carlsson G. and Guibas L. "A Well-controlled Fast Clustering Method on Conformation Space of Biomolecules", BCATS, 2008, Stanford, CA, Oct 2008.
Huang X, Wang D, Weiss D, Bushnell DA, Kornberg RD, Levitt M, “Computational Studies to Elucidate the Role of a Critical Histidine Residue in Transcription Elongation”, 2008 Transcriptional Regulation by Chromatin and RNA Polymerase II, Lake Tahoe, CA, Oct, 2008
Huang, X., Bowman, G.R., Pande, V.S. "Convergence of folding free energy landscapes via application of enhanced sampling methods", Gordon Research Conference on Protein Folding Dynamics, Ventura, CA, Jan 2008
Huang, X., “Exploring the folding free energy landscape of a helical peptide via serial replica exchange method”, BCATS, 2006, Stanford, CA, Oct 2006.
Huang, X., Li Y., Margulis, C.J., Berne, B.J.“A molecular dynamics simulation study of structure and dynamics of CO2 dissolved in a room temperature ionic liquid”, 231^st ACS National Meeting, Atlanta, GA, March 2006
Huang, X., Liu, P, Zhou, R, Berne, B.J.,“Hydrophobic-aided replica exchange: An efficient algorithm for sampling biological systems in explicit solvent”, 231^st ACS National Meeting, Atlanta, GA, March 2006. (CCG Excellence Award Winner Poster)
Huang, X., “Drying and hydrophobic collapse of nanoscale plates and protein complexes.” Simbios Special Seminar, NIH center for Biomedical Computation at Stanford University. Stanford, CA, Oct 2005.
Huang, X., Margulis, C.J., Zhou, R, Berne, B.J., “Drying and hydrophobic collapse in the multi-domain protein and protein oligomers”, 230^th ACS National Meeting, Washington, DC, August 2005.

Program Committees

Organize committee. 9^th Annual Symposium of Biomedical Computing at Stanford, Stanford, CA, Oct, 2008
Session co-chair. Multi-resolution Modeling of Biological Macromolecules Session, Pacific Symposium on Biocomputin, Big Island, Hawaii, Jan, 2010

Editorial Activities

Server as the reviewer for:

Journal of Molecular Biology
Nucleic Acid Research
Plos Computational Biology
RNA

CV (PDF)

Available here