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] [ Publications] [Fellowship & Awards ] [ Presentations ] [ Program Committees ] [ CV (PDF) ]

Education

08/2006-present, 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

· Aug 2006 – Present, Distinguished Postdoctoral Scholar
Simbios Center, Stanford University
Advisor: Professor Michael Levitt and Professor Vijay S. Pande

My research is focused on understanding folding of proteins and small RNA molecules using all-atom simulations in the explicit solvent. Generalized ensemble algorithms such as Replica exchange, and simulated tempering are used to enhance sampling. The other projects I am working on include developing an all-atom knowledge based RNA potential to help RNA tertiary structure prediction, and simulating RNA Polymerase II transcription elongation complex.

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. 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

Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ., Pande VS. “Structural Insight into RNA Hairpin Folding Intermediates.” J. Am. Chem. Soc., ja8032857, ASAP article, (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).
Kelley, N., Huang X, Tamm, 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, (Submitted), (2008)
Huang X., Ensign D, Bowman GR, and Pande V.S.,“On the convergence of generalized ensemble and canonical ensemble simulations to equilibrium” (In preparation), (2008)
Bernauer, J., Huang X., Bacallado, B. and Levitt, M. “A Multi-Scale Knowledge Based Potential for RNA structure refinement and Molecular Dynamics Simulaitons” (In Preparation), (2008)

Selected

Presentations

Huang, X., “On the Convergence of Generalized Ensemble Enhanced Sampling Algorithms ”, Telluride Science Research Center workshop Algorithmic Development on Enhanced Sampling, Telluride, CO, July 2008.
Huang, X., “Computational Studies of RNA Hairpin Folding”, Bay Area RNA Meeting, San Francisco, CA, Jun 2008
Huang, X., “Computational Studies to Elucidate the Fundamental Mechanism of RNA Transcription”, Simbios Seminar, NIH center for Biomedical Computation at Stanford University. Stanford, CA, May 2008.
Huang, X., Pande, V.S., Bowman, G.R.,“Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment”, 235^thACS National Meeting, New Orleans, Apr 2008.
Huang, X., “Exploring free energy landscapes of RNA folding by all-atom simulations using Replica Exchange Sampling Method”, Simbios Seminar, NIH center for Biomedical Computation at Stanford University. Stanford, CA, May 2007.
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

CV (PDF)

Available here