Rigoberto Hernandez

Gompf Family Professor of Chemistry

Mergenthaler 121
410-516-4018
r.hernandez@jhu.edu
Curriculum Vitae
Personal Website
Group/Lab Website

Biography
Research
Teaching
Publications

Dr. Rigoberto Hernandez is the Gompf Family Professor in the Department of Chemistry at the Johns Hopkins University as of July 1, 2016, and remains as the Director of the Open Chemistry Collaborative in Diversity Equity (OXIDE) since 2011. Before Hopkins, he was a Professor in the School of Chemistry and Biochemistry at Georgia Tech, and Co-Director of the Center for Computational Molecular Science and Technology he co-founded. He holds a B.S.E. in Chemical Engineering and Mathematics from Princeton University (1989), and a Ph.D. in Chemistry from the University of California, Berkeley (1993). (Hernandez was born in Güinez, Havana, Cuba but was raised and educated in the United States of America since he was in primary school. He is a U.S. citizen by birthright.)

Dr. Hernandez is the recipient of a National Science Foundation (NSF) CAREER Award (1997), Research Corporation Cottrell Scholar Award (1999) , the Alfred P. Sloan Fellow Award (2000), a Humboldt Research Fellowship (2006-07), the ACS Award for Encouraging Disadvantaged Students into Careers in the Chemical Sciences (2014), the CCR Diversity Award (2015), and the RCSA Transformative Research and Exceptional Education (TREE) Award (2016). He is a Fellow of the American Association for the Advancement of Science (AAAS, 2004), the American Chemical Society (ACS, 2010), and the American Physical Society (APS, 2011). In 2015-2016, he was a Phi Beta Kappa Visiting Scholar. At Georgia Tech, he served as the first Blanchard Assistant Professor of Chemistry (1999-2001), the first Goizueta Foundation Junior Rotating Faculty Chair (2002-07) and a Vasser Woolley Faculty Fellow (2011-13). His recent board memberships include the National Academies Panel within the Army Research Laboratory Technical Assessment Board (2005-2011), the National Academies Board on Chemical Sciences and Technology (2007-2010), the Telluride Summer Research Conference Board of Directors (2007-09), the NIH Study Section on Molecular Structure and Function B (MSFB, 2009-2013), the Research Corporation Cottrell Scholars Advisory Committee (member 2011-15, and chair 2016-17), the DOE Committee of Visitors (Division of Chemical Sciences, Geosciences and Bio-sciences, 2014) and the American Chemical Society Board of Directors (2014-2019).

Dr.Hernandez's research programs are currently funded by the National Science Foundation and other agencies. The OXIDE effort is cofunded by the NSF, DOE and NIH.

Dr. Hernandez’s research area can be broadly classified as the theoretical and computational chemistry of systems far from equilibrium. This includes a focus on microscopic reaction dynamics and their effects on macroscopic chemical reaction rates in arbitrary solvent environments. His current projects involve questions pertaining to the diffusion of mesogens in colloidal suspensions and liquid crystals, the structure and dynamics of assemblies of Janus and other patchy particles, fundamental advances in transition state theory, the role of molecular reactions in nonequilibrium air and the dynamics of protein folding and rearrangement.

AS.030.114 - Freshman Seminar: The Making of a Chemist (Fall 2016)

Credits: 3.00

Meetings: M 1:30PM - 4:00PM

Students will be introduced to professional culture and practice in academic and industrial chemical research laboratories. Through reading and analysis of a few series of seminal papers from the 1800's to the present leading to Nobel Prizes in Chemistry or Physics, students will learn how scientific inquiry and writing has evolved over time. Through discussion and practice, students will learn how to communicate chemistry in social media, scientific publications, scientific talks, and public lectures.

    1. Q. Cui, R. Hernandez, S. E. Mason, T. Frauenheim, J. A. Pedersen, and F. Geiger, "Mini-review. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies," J. Phys. Chem. B 120, 7297 (2016). (doi:10.1021/acs.jpcb.6b03976)

    2. J. T. Buchman, M. J. Gallagher, C.-T. Yang, X. Zhang, M. O. P. Krause, R. Hernandez, G. Orr, "Research highlights: examining the effect of shape on nanoparticle interactions with organisms," Environ. Sci.: Nano 3, 696 (2016). (doi:10.1039/c6en90015a)

    3. A. Junginger and R. Hernandez, "Lagrangian descriptors in dissipative systems," Phys. Chem. Chem. Phys. 18, 30282 (2016). (In the themed issue on "Insights from advanced methods in molecular dynamics.") (doi:10.1039/C6CP02532C)

    4. A. Junginger, G. T. Craven, F. Revuelta, T. Bartsch, F. Borondo, R. M. Benito and R. Hernandez, "Transition state geometry of driven chemical reactions on time-dependent double-well potentials," Phys. Chem. Chem. Phys. 18,30270 (2016). (In the themed issue on "Insights from advanced methods in molecular dynamics.") (doi:10.1039/C6CP02519F)

    5. I. S. Ulusoy, D. A. Andrienko, I. D. Boyd and R. Hernandez, "Quantum and quasi-classical collisional dynamics of O2-Ar at high temperatures," J. Chem. Phys. 144, 234311 (2016). (doi:10.1063/1.4954041, JCP URL)

    6. F. Revuelta, Thomas Bartsch, P. L. Garcia-Muller, R. Hernandez, R. M. Benito and F. Borondo, "Chemical reactions induced by oscillating external fields in weak thermal environments," Phys. Rev. E 93, 062304 (2016). (doi:10.1103/PhysRevE.93.062304)

    7. H. R. Bureau, E. Hershkovits, S. Quirk and R. Hernandez, "Determining the energetics of small β-sheet peptides using Adaptive Steered Molecular Dynamics," J. Chem. Theory Comput 12, 2028 (2016). doi:10.1021/acs.jctc.5b01110R. Hernandez, "Academic Leadership 101", C&EN 94:10, 47 (March 7, 2016). Hyperlink to C&EN

    8. G. T. Craven and R. Hernandez, "Deconstructing field-induced ketene isomerization through Lagrangian descriptors," Phys. Chem. Chem. Phys. 18, 4008 (2016). (doi:10.1039/C5CP06624G)

    9. A. Junginger, P. L. Garcia Muller, F. Borondo, R. M. Benito and R. Hernandez, "Solvated molecular dynamics of LiCN isomerizaion: All-atom argon solvent versus a generalized Langevin bath," J. Chem. Phys. 144, 024104 (2016). (doi:10.1063/1.4939480)

    10. A. Junginger and R. Hernandez, "Uncovering the geometry of barrierless reactions using Lagrangian descriptors," J. Phys. Chem. B,120, 1720 (2016). (In the Bruce C. Garrett Festschrift issue, March 2, 2016.) (doi:10.1021/acs.jpcb.5b09003)

    11. K. Solntsev, A. Popov, V. Solovyeva, S. Abou Al-Ainain, Y. Ilitchev, R. Hernandez and M. Kuzmin, "Kinetics of intra- and intermolecular excited-state proton transfer of ω-(2-hydroxynaphthyl-1)-decanoic acid in homogeneous and micellar solutions,"Methods Appl. Fluoresc. 4, 014001 (2016). (doi:10.1088/2050-6120/4/1/014001)

    12. A. V. Popov, G. T. Craven, and R. Hernandez, "Nonequilibrium structure in sequential assembly," Phys. Rev. E 92, 052108 (2015). (doi:10.1103/PhysRevE.92.052108)

    13. G. T. Craven and R. Hernandez, "Lagrangian descriptors of thermalized transition states on time-varying energy surfaces," Phys. Rev. Let. 115, 148301 (2015). (doi: 10.1103/PhysRevLett.115.148301)R. Hernandez, "The Private Sector’s Role In Chemistry’s Future," C&EN 93:37, 33 (September 21, 2015). Hyperlink to C&ENR. Hernandez, "Diversity in Academia: Solutions To Get There," C&EN 93:33, 40 (August 24, 2015). Hyperlink to C&EN

    14. C. Murphy, A. Vartanian, F. Geiger, R. Hamers, J. Pedersen, Q. Cui, C. Haynes, E. Carlson, R. Hernandez, R. Klaper, G. Orr, Z. Rosenzweig, "Biological Responses to Engineered Nanomaterials: Needs for the Next Decade," ACS Central Science 1, 117 (2015). (OpenAccess Direct Link, doi:10.1021/acscentsci.5b00182)

    15. H. R. Bureau, D. Merz Jr., E. Hershkovits, S. Quirk and Rigoberto Hernandez, "Constrained unfolding of a helical peptide: Implicit versus Explicit Solvents," PLoS ONE 10, e0127034 (2015). (doi: 10.1371/journal.pone.0127034, OA data is also available through SMARTech)

    16. G. T. Craven, A. V. Popov, and R. Hernandez, "Stochastic dynamics of penetrable rods in one dimension: Entangled dynamics and transport properties," J. Chem. Phys. 142, 154906 (2015). (doi: 10.1063/1.4918370)

    17. G. T. Craven, T. Bartsch and R. Hernandez, "Chemical reactions induced by oscillating external fields in weak thermal environments,"J. Chem. Phys. 142, 074108 (2015). (doi: 10.1063/1.4907590)

    18. P. L. Garcia Muller, R. Hernandez, R. M. Benito and F. Borondo, "The role of the CN vibration in the activated dynamics of LiNC → LiCN isomerization in argon-solvent at high temperatures," J. Chem. Phys. 141, 074312 (2014). (doi: 10.1063/1.4892921)

    19. R. Hernandez and S. Watt in "A top-down approach for diversity and inclusion in chemistry departments," Careers, Entrepreneurship, and Diversity: Challenges and Opportunities in the Global Chemistry Enterprise, ACS Symposium Series 1169, edited by H. N. Cheng, S. Shah, and M. L. Wu, Chapter. 19, pp. 207-224 (American Chemical Society, Washington DC, 2014). (ISBN13: 9780841229709, eISBN: 9780841229716, doi: 10.1021/bk-2014-1169.ch019)

    20. G. T. Craven, A. V. Popov, and R. Hernandez, "Effective surface coverage of coarse grained soft matter," J. Phys. Chem. B 118, 14092 (2014). (In the Spectroscopy of Nano- and Biomaterials Special Issue, doi: 10.1021/jp505207h)

    21. G. Ozer, T. Keyes, S. Quirk and R. Hernandez, "Multiple branched adaptive steered molecular dynamics," J. Chem. Phys. 141, 064101 (2014). (doi: 10.1063/1.4891807)

    22. G. T. Craven, T. Bartsch and R. Hernandez, "Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields," J. Chem. Phys. 141, 041106 (2014). (Communication:doi:10.1063/1.4891471)

    23. I. S. Ulusoy and R. Hernandez, "Revisiting roaming trajectories in ketene isomerization at higher dimensionality," Theoretical Chemistry Accounts 133, 1528 (2014). (In the Greg Ezra Festschrift issue, doi:10.1007/s00214-014-1528-z)

    24. R. Hernandez and A. V. Popov, "Molecular dynamics out of equilibrium: Mechanics and measurables," WIREs Comput. Mol. Sci., 4, 541-561 (2014). (doi:10.1002/wcms.1190)R. Hernandez, "Advancing The Chemical Sciences Through Diversity," C&EN 92:28, 45 (July 14, 2014). Hyperlink to C&EN

    25. G. T. Craven, A. V. Popov, and R. Hernandez, "Structure of a tractable stochastic mimic of soft particles," Soft Matter, 10, 5350-5361 (2014). (doi:10.1039/C4SM00751D)

    26. G. T. Craven, T. Bartsch and R. Hernandez, "Persistence of transition state structure in chemical reactions driven by fields oscillating in time," Phys. Rev. E. 89, 040801(R) (2014). (Rapid Communication: doi:10.1103/PhysRevE.89.040801 / PRE Link)R. Hernandez, "Mentoring new faculty---It really works!," C&EN 92:12, 36 (March 24, 2014). Hyperlink to C&EN cover

    27. M. C. Hagy and R. Hernandez, "Dynamical simulation of electrostatic striped colloidal particles," J. Chem. Phys. 140, 034701 (2014). (doi:10.1063/1.4859855)

    28. I. S. Ulusoy, J. F. Stanton and R. Hernandez, "Correction to `Effects of roaming trajectories on the transition state theory rates of a reduced-dimensional model of ketene isomerization'," J. Phys. Chem. A, 117, 10567-10568 (2013). (doi:10.1021/jp408997z)

    29. A. V. Popov and R. Hernandez, "Temperature-driven irreversible generalized Langevin equation can capture the nonequilibrium dynamics of two dissipated coupled oscillators," Phys. Rev. E, 88, 032145 (2013). (doi:10.1103/PhysRevE.88.032145)

    30. I. S. Ulusoy, J. F. Stanton and R. Hernandez, "Effects of roaming trajectories on the transition state theory rates of a reduced-dimensional model of ketene isomerization," J. Phys. Chem. A 117, 7553-7560 (2013). (In the Joel Bowman Festschrift issue.) (doi:10.1021/jp402322h)

    31. G. T. Craven, A. V. Popov and R. Hernandez, "Stochastic dynamics of penetrable rods in one dimension: Occupied volume and spatial order," J. Chem. Phys. 138, 244901 (2013). (doi:10.1063/1.4810807)

    32. M. C. Hagy and R. Hernandez, "Dynamical simulation of dipolar Janus colloids: Dynamical properties," J. Chem. Phys. 138, 184903 (2013). (doi:10.1063/1.4803864)

    33. P. L. García-Müller, R. Hernandez, R. M. Benito and F. Borondo, "Detailed study of the direct numerical observation of the Kramers turnover in the LiNC→LiCN isomerization rate," J. Chem. Phys. 137, 204301 (2012). (doi:10.1063/1.4766257)

    34. G. Ozer, S. Quirk and R. Hernandez, "Thermodynamics of decaalanine stretching in water obtained by adaptive steered molecular dynamics simulations," J. Chem. Theory Comput. 8, 4837-4844 (2012). (doi:10.1021/ct300709u)

    35. M. C. Hagy and R. Hernandez, "Dynamical Simulation of Dipolar Janus Colloids: Equilibrium Structure and Thermodynamics," J. Chem. Phys. 137, 044505 (2012). (doi:10.1063/1.4737432)

    36. G. Ozer, S. Quirk and R. Hernandez, "Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum," J. Chem. Phys. 136, 215104 (2012). (doi:10.1063/1.4725183)
      Selected for the June 15, 2012 issue of the Virtual Journal of Biological Physics Research.

    37. coverfull2012 cover jpcb A. K. Tucker and R. Hernandez, "Diffusion of a spherical probe through static nematogens: Effect of increasing geometric anisotropy and long-range structure," J. Phys. Chem. B 116, 1328-1334 (2012). (doi:10.1021/jp207346j)

    38. A. V. Popov, E.-A. Gould, M. A. Salvitti, R. Hernandez and K. M. Solntsev, "Diffusional effects on the reversible excited-state proton transfer. From experiments to Brownian dynamics simulations,"Phys. Chem. Chem. Phys. 13, 14914-14927 (2011). (doi:10.1039/C1CP20952C)

    39. A. K. Tucker and R. Hernandez, "Absence of enhanced diffusion in the dynamics of a thick needle through three-dimensional fixed point scatterers," J. Phys. Chem. B 115, 4412-4418 (2011). (doi:10.1021/jp201867f)

    40. A. V. Popov, D. Viehman and R. Hernandez, "Nonequilibrium heat flows through a nanorod sliding across a surface." J. Chem. Phys.134, 104703:1-12 (2011). (doi:10.1063/1.3561296)
      Selected for the March 21, 2011 issue of the Virtual Journal of Nanoscale Science & Technology.

    41. G. Ozer, E. Valeev, S. Quirk and R. Hernandez; "Adaptive steered molecular dynamics of the long-distance unfolding of Neuropeptide Y," J. Chem. Theory Comput., 6, 3026-3038 (2010). (doi:10.1021/ct100320g)

    42. A. K. Tucker and R. Hernandez, "Observation of a Trapping Transition in the Diffusion of a Thick Needle through Fixed Point Scatterers," J. Phys. Chem. A 114, 9628-9634 (2010). (In the Reinhard Schinke Festschrift issue.) (doi:10.1021/jp100111y)

    43. CoverChemPhys R. Hernandez, T. Bartsch and T. Uzer, "Transition state theory in liquids beyond planar dividing surfaces," Chem. Phys.370, 270-276 (2010). (In the Eli Pollak Festschrift issue, and featured on the cover.) (doi:10.1016/j.chemphys.2010.01.016)

  1. P. Saalfrank, T. Klamroth, T. Vazhappilly and R. Hernandez, "Theory of femtochemistry at metal surfaces: Associative molecular photodesorption as a case study," in Dynamics at solid state surfaces and interfaces, Part IIi: Current Developments, edited by U. Bovensiepen, H. Petek, and M. Wolf (Wiley-VCH, 2010). ISBN-10: 3-527-40938-6 Wiley-VCH link

  2. 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.

  3. 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)

  4. 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)

  5. 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)

  6. 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)

  7. 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)

  8. 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)

  9. 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)

  10. T. Bartsch, J. M. Moix, R. Hernandez, S. Kawai, and T. Uzer, "Time-dependent transition state theory," Adv. Chem. Phys. 140, 191-238 (2008). (doi:10.1002/9780470371572.ch4, ISBN: 978-0-470-22688-9)

  11. 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)

  12. 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)

  13. J. M. Moix, R. Hernandez, and E. Pollak, "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)

  14. 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)

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

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. 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)
  21. 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)
  22. 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)
  23. T. Bartsch, R. Hernandez, and T. Uzer; "Transition state in a noisy environment," Phys. Rev. Let. 95, 058301 (2005). (cond-mat/0506231, doi:10.1103/PhysRevLett.95.058301)
  24. 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)
  25. 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)
  26. 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)
  27. 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)
  28. C.-S. Liu, R. Hernandez, and G. B. Schuster; "Mechanism for radical cation transport in duplex DNA oligonucleotides," J. Am. Chem. Soc. 126, 2877-2884 (2004). (doi:10.1021/ja0378254)
  29. 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)
  30. 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)
  31. P. Doruker, R. L. Jernigan, I. Navizet and R. Hernandez; "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)
  32. 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)
  33. M. T. Vogt and R. Hernandez; "A three-dimensional polymer growth model," J. Chem. Phys. 116, 10485-10491 (2002). (doi:10.1063/1.1477455)
  34. 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)
  35. 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)
  36. M. T. Vogt and R. Hernandez; "A two-dimensional polymer growth model," J. Chem. Phys. 115, 1575-1585 (2001). (doi:10.1063/1.1380709)
  37. 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)
  38. 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)
  39. 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)
  40. 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)
  41. 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)
  42. 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)
  43. 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)
  44. 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)
  45. R. Hernandez and E. Pollak; "Reduced-dimensional semiclassical reaction rate theory for dissipative systems," unpublished notes.
  46. 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)
  47. 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)
  48. 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)
  49. 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)
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