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Molecular Simulations Group at CNLS

We use molecular dynamics simulations, enhanced sampling algorithms, high performance computing and advanced data analysis methods to study molecular and biomolecular systems. The group has expertise in the simulation of materials, large biomolecular systems, including globular and membrane proteins, DNA and RNA, and molecular machines like the ribosome and the efflux pump. We have expertise in the development and applications of algorithms like accelerated molecular dynamics, coarse-grained models, and software development. Members of the group have a large number of national and international collaborators. We also have expertise in molecular simulations software development, advanced data analysis techniques, and uncertainty quantification.


Biomolecular Simulations

Gnana Gnanakaran ( web page)
Angel E Garcia ( web page)
Karisa Y Sanbonmatsu ( web page)
Michael Wall ( web page)

Accelerated Molecular Dynamics Simulations

Danny Perez ( web page)
Art Voter ( web page)

Software Development

GROMACS:
Christoph Junghans ( web page)

Coarse-Grained models

Christoph Junghans ( web page)
Cesar Lopez Bautista ( web page )

Physics Informed Machine Learning

Misha Chetkov ( web page )

Visitors

Greg A Voth (U Chicago), Ulam Scholar 2014 (web page)

Selected Publications:

  • Hansen SG, Wu HL, Burwitz BJ, Hughes CM, Hammond KB, Ventura AB, ..., Lopez CA, ..., Gnanakaran S, et al. Broadly targeted CD8+ T cell responses restricted by major histocompatibility complex E. Science. 2016.
  • Phillips JL, Gnanakaran S. A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps. Proteins. 2015;83:46-65.
  • Rosenman DJ, Wang C, Garcia AE. Characterization of Abeta Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields. J Phys Chem B. 2016;120:259-77.
  • Perez D, Uberuaga B, Voter A. The parallel replica dynamics method- Coming to age. Comp Mat Sci. 2015;100:93-103.
  • Neale C, Herce HD, Pomes R, Garcia AE. Can Specific Protein-Lipid Interactions Stabilize an Active State o the Beta 2 Adrenergic Receptor? Biophys J. 2015;109:1652-62.
  • Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, et al. Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES. Mol Cell. 2015;57:422-32.
  • Mniszewski SM, Cawkwell MJ, Wall ME, Mohd-Yusof J, Bock N, Germann TC, et al. Efficient Parallel Linear Scaling Construction of the Density Matrix for Born-Oppenheimer Molecular Dynamics. J Chem Theory Comput. 2015;11:4644-54.
  • Lopez CA, Sethi A, Goldstein B, Wilson BS, Gnanakaran S. Membrane-mediated regulation of the intrinsically disordered CD3 cytoplasmic tail of the TCR. Biophys J. 2015;108:2481-91.
  • Lopez CA, Bellesia G, Redondo A, Langan P, Chundawat SP, Dale BE, Marrink SJ and Gnanakaran S, MARTINI coarse-grained model for crystalline cellulose microfibers. J Phys Chem B. 2015;119:465-73.
  • Krafnick RC, Garcia AE. Impact of hydrodynamics on effective interactions in suspensions of active and passive matter. Phys Rev E Stat Nonlin Soft Matter Phys. 2015;91:022308.
  • Kirmizialtin S, Loerke J, Behrmann E, Spahn CM, Sanbonmatsu KY. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods Enzymol. 2015;558:497-514.
  • Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol. 2015;553:215-34.
  • Huang C, Perez D, Voter A. Hyoerdynamcis bosst factor achievable with ideal bias potential. J Chem Phys. 2015;143:074113.
  • Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci U S A. 2014;111:17887-92.
  • Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse X-ray scattering to model protein motions. Structure. 2014;22:182-4.
  • Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, ..., Gnanakaran S, et al. Improving pandemic influenza risk assessment. Elife. 2014;3:e03883.
  • Mashayak SY, Jochum MN, Koschke K, Aluru NR, Ruhle V, Junghans C. Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA. PLoS One. 2015;10:e0131754.
  • Bevc S, Junghans C, Praprotnik M. STOCK: structure mapper and online coarse-graining kit for molecular
  • simulations. J Comput Chem. 2015;36:467-77.
  • Kaushal PS, Sharma MR, Booth TM, Haque EM, Tung CS, Sanbonmatsu KY, et al. Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A. 2014;111:7284-9.
  • Huang K, Garcia AE. Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering. J Chem Theory Comput. 2014;10:4264-72.
  • Herce HD, Garcia AE, Cardoso MC. Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules. J Am Chem Soc. 2014;136:17459-67.
  • Rosenman DJ, Connors CR, Chen W, Wang C, Garcia AE. Abeta monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol. 2013;425:3338-59.
  • Junghans C, Perez D, Vogel T. Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang-Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics. J Chem Theory Comput. 2014;10:1843-7.
  • Nagarajan A, Junghans C, Matysiak S. Multiscale Simulation of Liquid Water Using a Four-to-One Mapping for Coarse-Graining. J Chem Theory Comput. 2013;9:5168-75.
  • Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013;496:469-76.
  • Gao D, Chundawat SP, Sethi A, Balan V, Gnanakaran S, Dale BE. Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis. Proc Natl Acad Sci U S A. 2013;110:10922-7.
  • Canchi DR, Garcia AE. Cosolvent effects on protein stability. Annu Rev Phys Chem. 2013;64:273-93.
  • Ganguly P, Mukherji D, Junghans C, van der Vegt NF. Kirkwood-Buff Coarse-Grained Force Fields for Aqueous Solutions. J Chem Theory Comput. 2012;8:1802-7.
  • Fritsch S, Poblete S, Junghans C, Ciccotti G, Delle Site L, Kremer K. Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. Phys Rev Lett. 2012;108:170602.
  • Whitford PC, Sanbonmatsu KY, Onuchic JN. Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys. 2012;75:076601.
  • Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, et al. Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc. 2012;134:12043-53.
  • Chen AA, Garcia AE. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations. Proc Natl Acad Sci U S A. 2012;109:E1530-9.
  • Korber B, Gnanakaran S. AIDS/HIV. Converging on an HIV vaccine. Science. 2011;333:1589-90.
  • Ratje AH, Loerke J, Mikolajka A, Brunner M, Hildebrand PW, Starosta AL, et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature. 2010;468:713-6.
  • Canchi DR, Paschek D, Garcia AE. Equilibrium study of protein denaturation by urea. J Am Chem Soc. 2010;132:2338-44.
  • Bai X, Voter A, Hoagland R, Nastasi M, Uberuaga B. Efficient emission of radiation damage bear grain boundaries via interstitial emission. Science. 2010;327:1631-4.
  • Voter A, Montalent F, FGermann T. Extending the timescale in atomistic simulation of materials. Ann Rev Mat Res. 2002;32:321-46.
  • Sorensen M, Voter A. Temperature-accelerated dynamics for simulation of infrequent events. J Chem Phys. 2000;112:9599-606.
  • Voter A. Parallel replica method for dynamics of infrequent events. J Chem Phys. 1998;106:4665-77.
  • Voter A. Hyperdynamics: Accelerated molecular dynamics of infrequent events. Phys Rev Lett. 1997;78:3908-11.
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