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Education

20072014

PHD, Chemistry

Stony Brook University
20022006

B.Sc, Chemistry

Hanoi College of Science

Work History

Mar 2015Present

Postdoctoral Associate

Rutgers University
  • Co-developing visualization package for Molecular Dynamics simulation (NGLView)
  • Developing Python interface for a series of programs in Amber suite
  • Exploring properties of modified DNA and RNA
  • Exploring new Generalized Born solvation models and a Python-based API for recombining Rosetta and Amber force fields for protein prediction and design

  • Improving interface between AMBER (simulation package) and Phenix (Software suite for the automated determination of macromolecular structures)
Oct 2014Feb 2015

Postdoctoral Associate

Stony Brook University
  • Developing force field for implicit solvent model
  • Implementing newly parameter-optimized implicit solvent for nucleic acid in AMBER suit program
Jan 2008Aug 2014

Research Assistant

Stony Brook University
  • Developing force field for implicit solvent model
  • Improving Generalized-Born model’s parameters for nucleic acid
  • Applying implicit solvent to study protein folding
  • Validating ff14SB force field
  • Improving Generalized-Born model’s parameters for protein
  • Improving salt bridge description for HIV-1 protease simulation
  • Testing effect of different Generalized-Born models to protein folding

Computational skills

  • Programming languages
    • Efficient: Python/Cython
    • Familiar: C/C++, Fortran, JavaScript, R
  • High Performance Computing Resources (Bluegene, Kraken, Bluewater)
  • Parallel programming experience: MPI, multiprocessing
  • Software engineering experience: git (version control) and continuous integration (very experienced)
  • AMBER, Phenix
  • Lead developer: pytraj, a Python package for data analysis for molecular dynamics simulationhttps://github.com/Amber-MD/pytraj
  • Contributing:

Publications

Google Scholar statistics: https://goo.gl/o8qVU2

  1. D.A. Case, R.M. Betz, W. Botello-Smith, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2016), AMBER 2016, University of California, San Francisco.
  2. Alexander Rose; Hai Nguyen ; David Dotson (2016). nglview v0.4. Zenodo. 10.5281/zenodo.46373
  3. H Nguyen, DR Roe, J Swails, DA Case (2016), PYTRAJ v1.0.0.dev1: Interactive data analysis for molecular dynamics simulations. http://dx.doi.org/10.5281/zenodo.44612
  4. Nguyen, H.; Pérez, A.; Bermeo, S.; Simmerling, C., Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. J Chem Theory Comput 2015. [http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00271]
  5. A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015), AMBER 2015, University of California, San Francisco. [ambermd.org/doc12/Amber15.pdf]
  6. Nguyen, H.*; Maier, J.*; Huang, H; Perrone, V; Simmerling, C., (2014) Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. Journal of the American Chemical Society (*co-1st authors) [http://pubs.acs.org/doi/pdfplus/10.1021/ja5032776]
  7. Nguyen, H.; Roe, D. R.; Simmerling, C., (2013) Improved Generalized Born Solvent Model Parameters for Protein Simulations. Journal of Chemical Theory and Computation, 9 (4), 2020-2034. [http://pubs.acs.org/doi/abs/10.1021/ct3010485]
  8. Shang, Y., Nguyen, H., Wickstrom, L., Okur, A., and Simmerling, C. (2011) Improving the description of salt bridge strength and geometry in a Generalized Born model, Journal of Molecular Graphics and Modeling 29, 676-684. [http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21168352/]

Contributed talks

  • Hai Nguyen, Pytraj, nglview: bring AmberTools to Python ecosystem, University of California, San Francisco, 03/2016.
  • Hai Nguyen, Improved generalized Born solvent model parameters for protein and nucleic acid simulations, Icahn School of Medicine at Mount Sinai, 08/2014 (invited speaker)
  • Hai Nguyen, Improved generalized Born solvent model parameters for protein and nucleic acid simulations, Memorial Sloan Kettering, 02/2014 (invited speaker)
  • Hai Nguyen, Implicit solvent developments in AMBER. AMBER developer meeting, Stony Brook University, 01/2014.
  • Hai Nguyen,  Improved Generalized Born solvent model parameters for protein and nucleic acid simulations”, Hai Nguyen, Carlos Simmerling, 244th ACS conference, Philadelphia, 08/2012.

Poster presentations

  1. Hai Nguyen, Daniel R. Roe, Jason Swails, David A. Case, "Pytraj: Interactive data analysis for molecular dynamics simulations", Biophysical Society 60th Annual Meeting, February 29, 2016.
  2. Hai Nguyen, James Maier, He Huang, Victoria Perrone, Alberto Perez, Carlos Simmerling, “Simulating protein and nucleic acid dynamics on the microsecond to millisecond timescale”, Biophysical Society 59th Annual Meeting, February 8, 2015.
  3. Hai Nguyen, James Maier, He Huang, Victoria Perrone, Alberto Perez, Carlos Simmerling, “Simulating protein and nucleic acid dynamics on the microsecond to millisecond timescale”, The New York Structural Biology Discussion Group 10th Winter Meeting, January 21, 2015.
  4. Hai Nguyen, James Maier, He Huang, Victoria Perrone, Alberto Perez, Carlos Simmerling, “Simulating protein and nucleic acid dynamics on the microsecond to millisecond timescale”, Stony Brook University Chemistry Research Day, October 31, 2014.
  5. Hai Nguyen, James Maier, He Huang, Victoria Perrone, Alberto Perez, Carlos Simmerling, “Simulating protein and nucleic acid dynamics on the microsecond to millisecond timescale”, Stony Brook University ICB&DD 8th Annual Symposium, October 9, 2014.
  6. Hai Nguyen, Daniel R. Roe, Lauren Wickstrom, Carlos Simmerling, “Improvement of an Implicit Solvent Model”, workshop "From Computational Biophysics to Systems Biology (CBSB12)", Knoxville, June 3, 2012
  7. Hai Nguyen, Daniel R. Roe, Lauren Wickstrom, Carlos Simmerling, “Improvement of an Implicit Solvent Model”, ACS conference, Boston, August 24, 2010
  8. Hai Nguyen, Daniel R. Roe, Carlos Simmerling, “An Improvement of Implicit Solvent Model”, Chemistry Research Day, Stony Brook University, November 13, 2009
  9. Hai Nguyen, Daniel R. Roe, Carlos Simmerling, “An Improvement of Implicit Solvent Model”, 3rd Annual ICB&DD Symposium, Stony Brook University, October 6, 2009
  10. Hai Nguyen, Daniel R. Roe, Carlos Simmerling, “An Improvement of Implicit Solvent Model”, Inaugural Symposium for the Laufer Center for Computational Biology and Genome Sciences, Stony Brook University, September 25, 2009

Awards

  • Rosetta CADRES GRANTS: Exploring new Generalized Born solvation models and a Python-based API for recombining Rosetta and Amber force fields for improving structure prediction and design

Aliza Rubenstein, Kristin Blacklock (PI: Sagar Khare); Hai Nguyen (PI: David Case), Rutgers University

  • Workshop "From Computational Biophysics to Systems Biology (CBSB12)" fellowship (2012)
  • Sigma Xi Award (2012)
  • Full Scholarship for Excellent Student Award, Hanoi College of Science (2002-2006)
  • Outstanding Student Award, Hanoi College of Science (2003, 2004)

Professional Organizations

Other activities

  • Presiding session "Computational Approaches to Spectroscopy Analysis", ACS Fall 2012
  • Assisting students in AMBER session in Interdisciplinary Boot Camp in Quantitative Biology, Rutgers University, January 2016

References

Dr. David A. Case

BioMaPS Institute and Dept. of Chemistry & Chemical Biology

Rutgers University

174 Frelinghuysen Road, Rm. 208b

Piscataway, NJ 08854-8087, USA

Phone:  848-445-5885

Cell:  609-751-8668

case@biomaps.rutgers.edu

http://casegroup.rutgers.edu


Dr. Carlos Simmerling

Department of Chemistry 

Stony Brook University, Stony Brook, NY 11794-3400 

Phone: 631-632-1336

carlos.simmerling@gmail.com

http://simmerlinglab.org

 

Dr. Robert C. Rizzo

Department of Applied Mathematics and Statistics 

Stony Brook University, Stony Brook, NY 11794-3600

Phone: 631-632-9340 

rizzorc@gmail.com

http://ringo.ams.sunysb.edu