Lei Huang

Lei Huang

Research Associate

HPC Applications Group


Lei Huang joined TACC in 2014 and he is a research associate in TACC's High Performance Computing group. His current research focuses on algorithm development, implementation, validation and performance optimization involved in molecular dynamics software on modern HPC architectures.

Lei earned his PhD in computational chemistry from UT Austin, then have worked as a postdoctoral fellow at Harvard University and a research assistant professor at University of Chicago. He has worked on diverse projects spanning from material science to biophysics. He is a developer for widely used modeling/simulation software including CHARMM and NAMD. He also developed a web server, GAAMP, which can automatically parameterize a small compound with ab initio calculations.

Areas of Research


Large scale high performance computing

Parallel algorithm and programming

Code optimization

Molecular mechanics models development

Selected Publications

Jiang W, Phillips J, Huang L, Fajer M, Meng Y, Gumbart J, Luo Y, Schulten K and Roux B, Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput Phys Commu 185 (3): 908 2014.
Huang L and Benoit Roux, Automated force field parameterization for non-polarizable and polarizable atomic models based on ab initio target data, J Chem Theory Comput 9 (8): 3543 2013.
Huang L and Shakhnovich EI, Is there an en-route intermediate for the folding of cold shock proteins?, Protein Sci 21(5): 677 2012.
Huang L and Makarov DE, The rate constant of polymer reversal inside a pore, J Chem Phys 128(11): 114903 2008.
Huang L and Makarov DE, Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains, J Phys Chem A 111 (41): 10338 2007.
Huang L and Makarov DE, On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data, J Chem Phys 124 (6): Art. No. 064108 2006.
Huang L, Kirmizialtin S and Makarov DE, Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore, J Chem Phys 123 (12): Art. No. 124903 2005.
He XH, Huang L, Liang HJ and Pan CY, Localizations of junction points of ABC 3-miktoarm star terpolymers, J Chem Phys 118 (21): 9861 2003.


Ph.D., Computational Chemistry,
University of Texas at Austin

M.S., Polymer Physics
University of Science and Technology of China

B.E., Polymer Physics
University of Science and Technology of China

Memberships/Professional Affiliations

American Physical Society (APS)