Now showing items 1-20 of 22

    • Accurate modeling of noise in quantum error correcting circuits 

      Gutierrez Arguedas, Mauricio (Georgia Institute of Technology, 2015-11-16)
      A universal, scalable quantum computer will require the use of quantum error correction in order to achieve fault tolerance. The assessment and comparison of error-correcting strategies is performed by classical simulation. ...
    • Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum 

      Ozer, Gungor; Quirk, Stephen; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2012-06)
      The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered ...
    • Chemical reaction dynamics within anisotropic solvents in time-dependent fields 

      Hershkovits, Eli; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2004-12)
      The dynamics of low-dimensional Brownian particles coupled to time-dependent driven anisotropic heavy particles (mesogens) in a uniform bath (solvent) have been described through the use of a variant of the stochastic ...
    • The Classroom [Spring 2005] 

      Llewellyn, Donna C.; Hernandez, Rigoberto; Stein, John; Brown, Jennie N. (Jennifer Nicole); Kingsley, Gordon; Loss, Michael; Gable, Amanda C.; Folwer, Debra (Georgia Institute of Technology, 2005)
      In this issue: Teaching First Year Students; Mentoring One Freshman at a Time; The Classroom Interview: John Stein; My First Semester at Tech: Four Freshman Share Their Journals; In the CETL Library; The Classroom Interview: ...
    • Constrained unfolding of a helical peptide: Implicit versus solvents dataset 

      Bureau, Hailey R.; Merz, Dale R. Jr; Hershkovits, Eli; Hernandez, Rigoberto; Quirk, Stephen (Georgia Institute of Technology, 2015)
      Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive ...
    • Diffusion in a nonequilibrium binary mixture of hard spheres swelling at different rates 

      Popov, Alexander V.; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2009-07)
      The nonequilibrium dynamics of a probe in a driven binary mixture of effective hard-sphere particles has been measured computationally in molecular dynamics simulations so as to obtain a better understanding of the energy ...
    • Dihedral-angle information entropy as a gauge of secondary structure propensity 

      Zhong, Shi; Moix, Jeremy M.; Quirk, Stephen; Hernandez, Rigoberto (Georgia Institute of TechnologyBiophysical Society, 2006-12)
      Protein structural information can be uncovered using an information-theory-based entropy and auxiliary functions by taking advantage of high-quality correlation plots between the dihedral angles around a residue and those ...
    • Dissipating the Langevin equation in the presence of an external stochastic potential 

      Moix, Jeremy M.; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2005-03)
      In the Langevin formalism, the delicate balance maintained between the fluctuations in the system and their corresponding dissipation may be upset by the presence of a secondary, space-dependent stochastic force, particularly ...
    • Dynamical simulation of structured colloidal particles 

      Hagy, Matthew Canby (Georgia Institute of Technology, 2013-11-06)
      In this thesis, computer simulations are used to study the properties of new colloidal systems with structured interactions. These are pair interactions that include both attraction and repulsion. Structured colloids differ ...
    • Exploring complex interactions within microgels and microgel assemblies 

      Herman, Emily Sue (Georgia Institute of Technology, 2014-08-08)
      Hydrogels are water-swellable cross-linked polymeric networks that are capable of incorporating a variety of functionalities and responsivities. The stable colloidal form of a hydrogel is known as a microgel and ranges ...
    • Folding behavior of model proteins with weak energetic frustration 

      Locker, C. Rebecca; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2004-06)
      The native structure of fast-folding proteins, albeit a deep local free-energy minimum, may involve a relatively small energetic penalty due to nonoptimal, though favorable, contacts between amino acid residues. The weak ...
    • Gas-expanded liquids: synergism of experimental and computational determinations of local structure 

      Eckert, Charles A.; Liotta, Charles L.; Hernandez, Rigoberto (Georgia Institute of Technology, 2009-06-22)
    • An idealized model for nonequilibrium dynamics in molecular systems 

      Vogt, Marc; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2005-10)
      The nonequilibrium dynamics of highly nonlinear and multidimensional systems can give rise to emergent chemical behavior which can often be tracked using low-dimensional order parameters such as a reaction path. Such ...
    • Identifying reactive trajectories using a moving transition state 

      Bartsch, Thomas; Uzer, Turgay; Moix, Jeremy M.; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2006-06)
      A time-dependent no-recrossing dividing surface is shown to lead to a new criterion for identifying reactive trajectories well before they are evolved to infinite time. Numerical dynamics simulations of a dissipative ...
    • Materials and methods for atomistic characterization of emergent nanoporous adsorbents 

      Camp, Jeffrey S. (Georgia Institute of Technology, 2016-07-08)
      Metal organic frameworks (MOFs) are an emerging class of nanoporous materials that have shown promise in applications including gas storage, separations, and catalysis. The complexity and diversity of MOF chemical space ...
    • Minimalist theory for mesoscale reaction dynamics 

      Craven, Galen Thomas (Georgia Institute of Technology, 2014-11-13)
      The prediction of an atomistic system's macroscopic observables from microscopic physical characteristics is often intractable, either by theory or computation, due to the intrinsic complexity of the underlying dynamical ...
    • Nonequilibrium heat flows through a nanorod sliding across a surface 

      Popov, Alexander V.; Viehman, Douglas C.; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2011-03)
      The temperature-ramped irreversible Langevin equation [A. V. Popov and R. Hernandez, J. Chem. Phys. 134, 244506 (2007)] has been seen to describe the nonequilibrium atomic oscillations of a nanorod dragged across a surface. ...
    • On the accuracy limits of orbital expansion methods: Explicit effects of k-functions on atomic and molecular energies 

      Valeev, Edward F.; Allen, Wesley D.; Hernandez, Rigoberto; Sherrill, C. David; Schaefer, Henry F. (Georgia Institute of TechnologyAmerican Institute of Physics, 2003-05)
      For selected first- and second-row atoms, correlation-optimized Gaussian k functions have been determined and used in the construction of septuple-ζ basis sets for the correlation-consistent cc-pVXZ and aug-cc-pVXZ series. ...
    • Ontology of temperature in nonequilibrium systems 

      Popov, Alexander V.; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2007-06)
      The laws of thermodynamics provide a clear concept of the temperature for an equilibrium system in the continuum limit. Meanwhile, the equipartition theorem allows one to make a connection between the ensemble average of ...
    • Stochastic transition states: Reaction geometry amidst noise 

      Bartsch, Thomas; Uzer, Turgay; Hernandez, Rigoberto (Georgia Institute of TechnologyAmerican Institute of Physics, 2005-11)
      Classical transition state theory (TST) is the cornerstone of reaction-rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive ...