Rigoberto Hernandez Associate Professor Office: MSE 2100L Phone: 404-894-0594 Fax: 404-894-7452 E-mail Rigoberto Hernandez Research Group Web site

B.S.E., Princeton University, 1989; Ph.D., University of California at Berkeley, 1993; Postdoctoral Fellow, The Weizmann Institute of Science, 1994; Postdoctoral Fellow, University of Pennsylvania, 1996

Humboldt Research Fellow (2006-2007); Goizueta Foundation Jr. Professor (2002-2007); Alfred P. Sloan Fellow (2000); Research Corporation Cottrell Scholar (1999); Sigma Xi Young Faculty Award (GT-1999); Blanchard Assistant Professor of Chemistry (1999-2001); and NSF CAREER Award (1997-2002). He was elected as fellow of the American Association of Arts and Science, the AAAS, in 2004.

Research Interests

Nonstationary Stochastic Dynamics. A new approach to understanding nonstationary processes has recently been developed through the use of the so-called irreversible generalized Langevin equation (iGLE). The iGLE model can accommodate nonstationary changes in temperature and the friction strength of the environment. These changes may be coupled to macroscopic averages of the environment as induced by the collective motion of many equivalent tagged particles. As these environments may not be identical, the WiGLE model has also been developed, and it accounts for heterogeneous environments, each of which is coupled to a set of neighbors. Possible applications of these models include the chemical reaction dynamics of thermosetting polymers and living polymers, and the folding dynamics of proteins.

Polymerization Dynamics. Existing theories of polymers are often aimed at the characterization of the final product and often omit treatment of the reaction dynamics in which the viscosity self-consistently affects the reaction process. For example, the polymerizations may end not because the reactants have been depleted, but because of diffusional quenching due to the dramatic change in viscosity with the polymerization. To better understand this question, two different approaches are being developed: a generalization of the bond-percolation model to provide a system in which the growth may be observed within a Monte Carlo simulation, and a non-stationary dissipative model to provide real time information. Ultimately, these models will be used within interactive programs for the design and characterization of polymeric materials with specified time-dependent material properties.

Protein Folding. Minimalist lattice and off-lattice models provide rich insight characterizing the universal behavior of protein folding without suffering high computational costs. Monte Carlo simulations of designed minimalist proteins are being analyzed through novel projections to provide a better understanding of the connection between structure and protein dynamics.

Representative Publications

T. Bartsch, J. M. Moix, R. Hernandez, S. Kawai, and T. Uzer, "Time- dependent transition state theory," Adv. Chem. Phys. 140, XXX (2008), in press.

J. L. Gohres, C. L. Kitchens, J. P. Hallett, A. V. Popov, R. Hernandez, C. L. Liotta, and C. A. Eckert; "A spectroscopic and computational exploration of the cybotactic region of gas-expanded liquids: Methanol and acetone," J. Phys. Chem. B 112, XXXX (2008), in press. (doi:10.1021/jp077552p)

T. Bartsch, T. Uzer, J. M. Moix, and R. Hernandez, "Transition state theory rate calculations with a recrossing-free moving dividing surface," J. Phys. Chem. B 112, 206-212 (2008). (In the James T. Hynes Festschrift issue.) doi:10.1021/jp0755600)

J. M. Moix, R. Hernandez, and E. Pollak, "The momentum and velocity autocorrelation functions of a diatomic molecule are not necessarily proportional to each other," J. Phys. Chem. B 112, 213-218 (2008). (In the James T. Hynes Festschrift issue.) (doi:10.1021/jp0730951)

J. M. Moix and R. Hernandez, "The role of long-time correlation in dissipative adsorbate dynamics on metal surfaces," Ann. Rep. Comp. Chem. 3, 137-151 (2007). (doi:10.1016/S1574-1400(07)03008-3).

A. V. Popov and R. Hernandez, "The ontology of temperature in nonequilibrium systems," J. Chem. Phys., 126, 244506 (2007). (doi:10.1063/1.2743032, arXiv:0705.0745)

C. L. Shukla, J. P. Hallet, A. V. Popov, R. Hernandez, C. L. Liotta, and C. A. Eckert; "Molecular Dynamics Simulation of the Cybotactic Region in Gas-Expanded Methanol-Carbon Dioxide and Acetone-Carbon Dioxide Mixtures," J. Phys. Chem. B 110, 24101-24111 (2006). (doi:10.1021/jp0648947)

S. Zhong, J. M. Moix, S. Quirk, and R. Hernandez; "Dihedral-angle information entropy as a gauge of secondary structure propensity," Biophys. J. 91, 4014-4023 (2006). (doi:10.1529/biophysj.106.089243)

J. P. Hallett, Christopher L. Kitchens, R. Hernandez, C. Liotta, and Charles Eckert, "Probing the Cybotactic Region in Gas-Expanded Liquids (GXLs)," Acc. Chem. Res., 39, 531 (2006). (doi:10.1021/ar0501424, ACR abstract)

T. Bartsch, T. Uzer, J. M. Moix and R. Hernandez; "Identifying reactive trajectories using a moving transition state," J. Chem. Phys. 124, 244310 (2006). (cond-mat/0604640, doi:10.1063/1.2206587)

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.)