Georgia Institute of TechnologyCSSB
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Dr. Rigoberto Hernandez

Associate Professor

School of Chemisty and Biochemisty

member
Dr. Rigoberto Hernandez

    Contact information:
  • School of Chemisty and Biochemisty
  • 770 State Street
  • Boggs, Room 3-15
  • Atlanta, GA 30332, Mail Code: 0400
  • Tel: 404-894-0594
  • Fax: 404-894-7452
  • Email:

Research Interests

Protein Folding and Ligand Binding. Minimalist lattice and off-lattice models provide insight into the folding behavior of proteins without suffering high computational costs. Monte Carlo simulations of designed minimalist proteins are studied to provide an understanding of the connection between protein structure and dynamics. This, in turn, is being used to analyze the behavior of all-atom dynamics in small peptides. In addition, computational techniques useful for analyzing and predicting a binding partner to a particular agent are being developed.

Far-From-Equilibrium Chemistry: Swelling and Driven Colloids. Despite the many successes of statistical mechanics in describing equilibrium and near-equilibrium behavior, truly nonequilibrium chemical dynamics remain poorly characterized by theory or computation. For example, suspensions of driven colloids-with a shape that changes in size or orientation-lead to macroscopic materials with emergent properties and complex solubility. Such systems are not presently well understood because they involve several disparate time and length scales, but are increasingly being explored experimentally using optical microscopy on various nanoparticle suspensions. Our group is studying these systems using both molecular dynamics simulations and reduced-dimensional representations.

Far-From-Equilibrium Chemistry: Controlling Diffusion on Surfaces. Can one control the motion of metal atoms "surfing" on a metallic surface and then anchor them at desired locations? Yes; an STM tip can literally be used to move atoms one at a time. But if you wish to move many atoms, all with atomic precision, to create a nanodevice, such a technique might be painfully slow. Instead, we are pursuing an approach to modify surface properties from a distance and thereby encourage the diffusion of the absorbed molecules into desired patterns.

Publications
Faculty Page
Research Group
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Selected Publications

A. V. Popov, J. Melvin, and R. Hernandez; "Dynamics of swelling/ contracting hard spheres surmised by an irreversible Langevin equation," J. Phys. Chem. A, 110, 1635-1644 (2006). (In the William L. Hase Festschrift issue.) (doi:10.1021/jp054241a).
T. Bartsch, T. Uzer and R. Hernandez; "Stochastic transition states: Reaction geometry amidst noise," J. Chem. Phys., 123, 204102, (2005).
M. Vogt and R. Hernandez; "An idealized model for nonequilibrium dynamics in molecular systems," J. Chem. Phys., 123, 144109, (2005).
T. Bartsch, R. Hernandez, and T. Uzer; "The transition state in a noisy environment," Phys. Rev. Let., 95, 058301 (2005).
J. M. Moix and R. Hernandez; "Dissipating the Langevin equation in the presence of an external stochastic potential," J. Chem. Phys., 122, 114111 (2005).
E. Hershkovitz and R. Hernandez; "Chemical reaction dynamics within anisotropic solvents in time-dependent fields," J. Chem. Phys. 122, 014509 (2005).
J. M. Moix, T. D. Shepherd, and R. Hernandez; "A phenomenological model for surface diffusion: diffusive dynamics across incoherent stochastic aperiodic potentials," J. Phys. Chem. B, 108, 19476-19482 (2004).
C. R. Locker and R. Hernandez, "Folding behavior of model proteins with weak energetic frustration," J. Chem. Phys., 120, 11292-11303 (2004).
C.-S. Liu, R. Hernandez, and G. B. Schuster; "The mechanism for radical cation transport in duplex DNA oligonucleotides," J. Am. Chem. Soc. 126, 2877-2884 (2004).
E. F. Valeev, W. D. Allen, R. Hernandez, C. D. Sherrill, H. F. Schaeffer III; "On the accuracy of orbital expansion methods: Explicit effects of k-functions on atomic and molecular energies," J. Chem. Phys., 118, 8594-8610 (2003).
T. D. Shepherd and R. Hernandez; "An optimized mean first passage time approach to obtaining rates in activated processes," J. Chem. Phys., 117, 9227-9233 (2002).
P. Doruker, R. L. Jernigan, I. Navizet and R. Hernandez; "The important fluctuation dynamics of large protein structures are preserved upon renormalization," Int. J. Quant. Chem., 90, 822-837 (2002).
T. D. Shepherd and R. Hernandez; "Activated dynamics across aperiodic stochastic potentials," J. Phys. Chem. B 106, 8176-8181 (2002).
M. T. Vogt and R. Hernandez; "A three-dimensional polymer growth model," J. Chem. Phys., 116, 10485-10491 (2002).
T. D. Shepherd and R. Hernandez; "Chemical reaction dynamics with stochastic potentials beyond the high-friction limit," J. Chem. Phys., 115, 2430-2438 (2001).
C. R. Locker and R. Hernandez; "A minimalist model protein with multiple folding funnels," Proc. Natl. Acad. Sci. USA, 98, 9074-9079 (2001).
M. T. Vogt and R. Hernandez; "A two-dimensional polymer growth model," J. Chem. Phys., 115, 1575-1585 (2001).
E. Hershkovitz and R. Hernandez; "Fast numerical integrator for stochastic differential equations with nonstationary multiplicative noise," J. Phys. Chem. A 105, 2687-2693 (2001). (In the William H. Miller Festschrift issue.)