Publication List

Rigoberto Hernandez
NOTEs:


  1. A. V. Popov and R. Hernandez, "Diffusion in a nonequilibrium binary mixture of hard spheres swelling at different rates ", J. Chem. Phys. 131, 024503 (2009). (doi:10.1063/1.3168405)
    Selected for the July 27, 2009 issue of the Virtual Journal of Nanoscale Science & Technology.

  2. T. Vazhappilly, T. Klamroth, P. Saalfrank, and R. Hernandez, "Femtosecond-laser desorption of H2 (D2) from Ru(0001): Quantum and classical approaches," J. Phys. Chem. C 113, 7790-7801 (2009). (doi:10.1021/jp810709k)

  3. S. Quirk, S. Zhong, and R. Hernandez, "De novo identification of binding sequences for antibody replacement molecules," Proteins: Struct. Func. Bioinfo. 76, 693-705 (2009). (doi:10.1002/prot.22382)

  4. J. L. Gohres, A. V. Popov, R. Hernandez, C. L. Liotta, and C. A. Eckert; "Molecular dynamics simulations of solvation and solvent reorganization dynamics in CO2-expanded methanol and acetone," J. Chem. Theory Comput., 5, 267-275 (2009). (doi:10.1021/ct800353s)

  5. J. L. Gohres, R. Hernandez, C. L. Liotta, and C. A. Eckert; "Viewing the cybotactic structure of gas-expanded liquids," in Gas-Expanded Liquids and Near-Critical Media: Green Chemistry and Engineering, ACS Symposium Series No. 1006, edited by K. W. Hutchenson, A. M. Scurto, and B. Subramaniam (American Chemical Society: Washington, D.C., 2009), Chapter 4, pp. 81-94. (doi:10.1021/bk-2009-1006.ch004)

  6. P. L. García-Müller, F. Borondo, R. Hernandez and R. M. Benito, "Solvent-induced acceleration in an activated molecular reaction," Phys. Rev. Let. 101, 178302 (2008). (doi:10.1103/PhysRevLett.101.178302)

  7. J. L. Gohres, C. L. Shukla, A. V. Popov, R. Hernandez, C. L. Liotta, and C. A. Eckert; "Effects of Solute Structure on Local Solvation and Solvent Interactions: Results from UV/Vis Spectroscopy and Molecular Dynamics Simulations," J. Phys. Chem. B 112, 14993-14998 (2008). (doi:10.1021/jp806135s)

  8. Y. Qin, A. V. Popov, and R. Hernandez, "Stochastic models for polymerization reactions under nonequilibrium conditions," Ann. Rep. Comp. Chem. 4, 173-199 (2008). (doi:10.1016/S1574-1400(08)00010-8)

  9. T. Bartsch, J. M. Moix, R. Hernandez, S. Kawai, and T. Uzer, "Time-dependent transition state theory," Adv. Chem. Phys. 140, 191-238 (2008). ISBN: 978-0-470-22688-9

  10. 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, 4666-4673 (2008). (doi:10.1021/jp077552p)

  11. 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)

  12. 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)

  13. 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)

  14. 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)

  15. C. L. Shukla, J. P. Hallett, 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)

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. T. Bartsch, T.Uzer and R. Hernandez; "Stochastic transition states: Reaction geometry amidst noise," J. Chem. Phys. 123, 204102 (2005). (cond-mat/0509425, doi:10.1063/1.2109827)

  21. M. Vogt and R. Hernandez; "An idealized model for nonequilibrium dynamics in molecular systems," J. Chem. Phys. 123, 144109 (2005). (cond-mat/0501328, doi:10.1063/1.2052594)

  22. T. Bartsch, R. Hernandez, and T. Uzer; "The transition state in a noisy environment," Phys. Rev. Let. 95, 058301 (2005). (cond-mat/0506231, doi:10.1103/PhysRevLett.95.058301)

  23. J. M. Moix and R. Hernandez; "Dissipating the Langevin equation in the presence of an external stochastic potential," J. Chem. Phys. 122, 114111 (2005). (cond-mat/0501327, doi:10.1063/1.1870875)

  24. E. Hershkovitz and R. Hernandez; "Chemical reaction dynamics within anisotropic solvents in time-dependent fields," J. Chem. Phys. 122, 014509 (2005). (cond-mat/0501434, doi:10.1063/1.1829252)

  25. 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). (doi:10.1021/jp046629w)

  26. C. R. Locker and R. Hernandez, "Folding behavior of model proteins with weak energetic frustration," J. Chem. Phys. 120, 11292-11303 (2004). (doi:10.1063/1.1751394)

  27. 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). (doi:10.1021/ja0378254)

  28. 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). (doi:10.1063/1.1566744)

  29. 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). (doi:10.1063/1.1516590)

  30. 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). (In the Per-Olov Lowdin Festschrift issue.) (doi:10.1002/qua.955)

  31. T. D. Shepherd and R. Hernandez; "Activated dynamics across aperiodic stochastic potentials," J. Phys. Chem. B 106, 8176-8181 (2002). (In the John C. Tully Festschrift issue.) (doi:10.1021/jp020620h)

  32. M. T. Vogt and R. Hernandez; "A three-dimensional polymer growth model," J. Chem. Phys. 116, 10485-10491 (2002). (doi:10.1063/1.1477455)

  33. T. D. Shepherd and R. Hernandez; "Chemical reaction dynamics with stochastic potentials beyond the high-friction limit," J. Chem. Phys. 115, 2430-2438 (2001). (doi:10.1063/1.1386422)

  34. C. R. Locker and R. Hernandez; "A minimalist model protein with multiple folding funnels," Proc. Natl. Acad. Sci. USA 98, 9074-9079 (2001). (doi:10.1073/pnas.161438898)

  35. M. T. Vogt and R. Hernandez; "A two-dimensional polymer growth model," J. Chem. Phys. 115, 1575-1585 (2001). (doi:10.1063/1.1380709)

  36. 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.) (doi:10.1021/jp0037044)

  37. R. Hernandez and F. L. Somer; "Nonstationary stochastic dynamics and applications to chemical physics," in Theoretical Methods in Condensed Phase Chemistry, edited by S. Schwartz (Kluwer Academic, The Netherlands, 2000). (doi:10.1007/0-306-46949-9_4)

  38. F. L. Somer and R. Hernandez; "Stochastic dynamics in irreversible nonequilibrium environments. 4. Self-consistent coupling in heterogeneous environments," J. Phys. Chem. B 104, 3456 (2000). (doi:10.1021/jp9928762)

  39. F. L. Somer and R. Hernandez; "Stochastic dynamics in irreversible nonequilibrium environments. 3. Temperature-ramped chemical kinetics," J. Phys. Chem. A 103, 11004 (1999). (doi:10.1021/jp9915836)

  40. R. Hernandez; "The projection of a mechanical system onto the irreversible generalized Langevin equation (iGLE)," J. Chem. Phys. 111, 7701 (1999). (abstract, doi:10.1063/1.480160)

  41. R. Hernandez and F. L. Somer; "Stochastic dynamics in irreversible nonequilibrium environments. 2. A model for thermosetting polymerization," J. Phys. Chem. B 103, 1070 (1999). (abstract, doi:10.1021/jp9836269)

  42. R. Hernandez and F. L. Somer; "Stochastic dynamics in irreversible nonequilibrium environments. 1. The Fluctuation-Dissipation Relation," J. Phys. Chem. B 103, 1064 (1999). (abstract, doi:10.1021/jp983625g)

  43. R. Hernandez and G. A. Voth; "Quantum time correlation functions and classical coherence," Chem. Phys. 233, 243-255 (1998). (doi:10.1016/S0301-0104(98)00027-5 )

  44. R. Hernandez and E. Pollak; "Reduced-dimensional semiclassical reaction rate theory for dissipative systems," unpublished notes.

  45. R. Hernandez, J. Cao and G. A. Voth; "On the Feynman path centroid density as a phase space distribution in quantum statistical mechanics, " J. Chem. Phys. 103, 5018 (1995). (HTML, doi:10.1063/1.470588)

  46. R. Hernandez; "A combined use of perturbation theory and diagonalization: application to bound energy levels and semiclassical rate theory," J. Chem. Phys. 101, 9534 (1994). (HTML, doi:10.1063/1.467985)

  47. R. Hernandez and W. H. Miller, "Semiclassical transition state theory - a new perspective," Chem. Phys. Lett. 214, 129 (1993). (HTML, doi:10.1016/0009-2614(93)90071-8)

  48. R. Hernandez, W. H. Miller, C. B. Moore and W. F. Polik; "A random matrix / transition state theory for the probability distribution of state-specific unimolecular decay rates: generalization to include total angular momentum conservation and other dynamical symmetries," J. Chem. Phys. 99, 950 (1993). (HTML, doi:10.1063/1.465360)

  49. M. J. Cohen, N. C. Handy, R. Hernandez and W. H. Miller; "Cumulative reaction probabilities for H+H2→H2+H from a knowledge of the anharmonic force field," Chem. Phys. Lett. 192, 407 (1992). (doi:10.1016/0009-2614(92)85491-R)

  50. W. H. Miller, R. Hernandez, C. B. Moore and W. F. Polik; "A transition state theory-based statistical distribution of unimolecular decay rates, with application to unimolecular decomposition of formaldehyde," J. Chem. Phys. 93, 5657 (1990). (doi:10.1063/1.459636)

  51. W. H. Miller, R. Hernandez, N. C. Handy, D. Jayatilaka and A. Willetts; "Ab initio calculation of anharmonic constants for a transition state, with application to semiclassical transition state tunneling probabilities," Chem. Phys. Lett. 172, 62 (1990). (doi:10.1016/0009-2614(90)87217-F)

  52. S. L. Coy, R. Hernandez and K. K. Lehmann; "Limits on the transition to Gaussian orthogonal ensemble behavior: Saturated radiationless transitions between strongly coupled potential surfaces," Phys. Rev. A 40, 5935 (1989). (doi:10.1103/PhysRevA.40.5935)