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List of works by Rigoberto Hernandez

A minimalist model protein with multiple folding funnels

scientific article

A spectroscopic and computational exploration of the cybotactic region of gas-expanded liquids: methanol and acetone

scientific article

Ab initio calculation of anharmonic constants for a transition state, with application to semiclassical transition state tunneling probabilities

article

Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y.

scientific article

Adaptive steered molecular dynamics: validation of the selection criterion and benchmarking energetics in vacuum

scientific article published in June 2012

An idealized model for nonequilibrium dynamics in molecular systems

scientific article published in October 2005

Biological Responses to Engineered Nanomaterials: Needs for the Next Decade

scientific article

Chemical dynamics between wells across a time-dependent barrier: Self-similarity in the Lagrangian descriptor and reactive basins

scientific article published in August 2017

Chemical reaction dynamics within anisotropic solvents in time-dependent fields

scientific article published in January 2005

Chemical reactions induced by oscillating external fields in weak thermal environments. ⬇️

scientific article published in February 2015

Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields ⬇️

scientific article published in July 2014

Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents

scientific article published on 13 May 2015

De novo identification of binding sequences for antibody replacement molecules

scientific article

Deconstructing field-induced ketene isomerization through Lagrangian descriptors

scientific article published on 01 February 2016

Defects in Self-Assembled Monolayers on Nanoparticles Prompt Phospholipid Extraction and Bilayer-Curvature-Dependent Deformations

scientific article published on 23 October 2019

Density, Structure, and Stability of Citrate3– and H2citrate– on Bare and Coated Gold Nanoparticles

article

Detailed study of the direct numerical observation of the Kramers turnover in the LiNC⇌LiCN isomerization rate

scientific article published on 01 November 2012

Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics

scientific article published on 10 March 2016

Diffusion of a spherical probe through static nematogens: effect of increasing geometric anisotropy and long-range structure

scientific article published on 27 December 2011

Diffusional effects on the reversible excited-state proton transfer. From experiments to Brownian dynamics simulations

scientific article published on 14 July 2011

Dissipating the Langevin equation in the presence of an external stochastic potential

scientific article published in March 2005

Dynamical simulation of dipolar Janus colloids: dynamical properties

scientific article published on 01 May 2013

Dynamical simulation of dipolar Janus colloids: equilibrium structure and thermodynamics

scientific article published on 01 July 2012

Dynamical simulation of electrostatic striped colloidal particles

scientific article published on 01 January 2014

Dynamics of swelling/contracting hard spheres surmised by an irreversible Langevin equation

scientific article published in February 2006

Effective surface coverage of coarse-grained soft matter.

scientific article published on 4 August 2014

Effects of solute structure on local solvation and solvent interactions: results from UV/vis spectroscopy and molecular dynamics simulations

scientific article published in November 2008

Erratum: "Quantum and quasi-classical collisional dynamics of O2-Ar at high temperatures" [J. Chem. Phys. 144, 234311 (2016)].

scientific article published in December 2016

Femtosecond-Laser Desorption of H2 (D2) from Ru(0001): Quantum and Classical Approaches

scientific article published on 9 April 2009

Folding behavior of model proteins with weak energetic frustration

scientific article published on 15 June 2004

Identifying reaction pathways in phase space via asymptotic trajectories

scientific article published on 28 April 2020

Identifying reactive trajectories using a moving transition state.

scientific article published in June 2006

Influence of external driving on decays in the geometry of the LiCN isomerization

scientific article published on 01 August 2020

Invariant Manifolds and Rate Constants in Driven Chemical Reactions

scientific article published on 20 February 2019

Ionic Environment Affects Bacterial Lipopolysaccharide Packing and Function

scientific article published on 12 March 2020

Lagrangian Descriptors of Thermalized Transition States on Time-Varying Energy Surfaces

scientific article published on 29 September 2015

Lagrangian descriptors in dissipative systems

scientific article published on 21 June 2016

Lagrangian descriptors of driven chemical reaction manifolds

scientific article published on 31 August 2017

Limits on the transition to Gaussian orthogonal ensemble behavior: Saturated radiationless transitions between strongly coupled potential surfaces

scientific article published on 01 November 1989

Lipid Corona Formation from Nanoparticle Interactions with Bilayers

scientific article published in November 2018

Mechanism for radical cation transport in duplex DNA oligonucleotides.

scientific article published in March 2004

Molecular Dynamics Simulations of Solvation and Solvent Reorganization Dynamics in CO2-Expanded Methanol and Acetone

scientific article published on 01 February 2009

Molecular dynamics simulation of the cybotactic region in gas-expanded methanol-carbon dioxide and acetone-carbon dioxide mixtures

scientific article published in November 2006

Momentum and velocity autocorrelation functions of a diatomic molecule are not necessarily proportional to each other

scientific article published on 7 September 2007

Multiple branched adaptive steered molecular dynamics

scientific article published in August 2014

Mutational Analysis of Neuropeptide Y Reveals Unusual Thermal Stability Linked to Higher-Order Self-Association.

scientific article published on 21 February 2018

Neural network approach for the dynamics on the normally hyperbolic invariant manifold of periodically driven systems

scientific article published on 01 February 2020

Neural network approach to time-dependent dividing surfaces in classical reaction dynamics

scientific article published on 01 April 2018

Nonequilibrium structure in sequential assembly

scientific article published on 9 November 2015

Optimizing bags of artificial neural networks for the prediction of viability from sparse data

scientific article published on 01 August 2020

Peripheral Membrane Proteins Facilitate Nanoparticle Binding at Lipid Bilayer Interfaces

scientific article published on 30 August 2018

Persistence of transition-state structure in chemical reactions driven by fields oscillating in time. ⬇️

scientific article published on 28 April 2014

Phase-space resolved rates in driven multidimensional chemical reactions

scientific article published on 01 December 2019

Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach

scientific article published on 22 May 2019

Probing the cybotactic region in gas-expanded liquids (GXLs).

scientific article published in August 2006

Quantum and quasi-classical collisional dynamics of O2-Ar at high temperatures

scientific article published on June 2016

Solution NMR Analysis of Ligand Environment in Quaternary Ammonium-Terminated Self-Assembled Monolayers on Gold Nanoparticles: The Effect of Surface Curvature and Ligand Structure

scientific article published on 14 February 2019

Solvated molecular dynamics of LiCN isomerization: All-atom argon solvent versus a generalized Langevin bath

scientific article published on 01 January 2016

Solvent-induced acceleration of the rate of activation of a molecular reaction

scientific article published on 22 October 2008

Stochastic dynamics of penetrable rods in one dimension: Entangled dynamics and transport properties

scientific article published on 01 April 2015

Stochastic dynamics of penetrable rods in one dimension: occupied volume and spatial order.

scientific article published in June 2013

Stochastic transition states: reaction geometry amidst noise

scientific article published on 01 November 2005

Structure of a tractable stochastic mimic of soft particles

scientific article published on 17 June 2014

Surface Coating Structure and its Interaction with Cytochrome c in EG6 Coated Nanoparticles Varies with Surface Curvature

scientific article published on 17 April 2020

Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies

scientific article published on 7 July 2016

Temperature-driven irreversible generalized Langevin equation can capture the nonequilibrium dynamics of two dissipated coupled oscillators

scientific article published on 30 September 2013

The role of the CN vibration in the activated dynamics of LiNC<−>LiCN isomerization in an argon solvent at high temperatures

scientific article published on 01 August 2014

Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations

scientific article published on 24 October 2012

Transition state geometry of driven chemical reactions on time-dependent double-well potentials.

scientific article published on 15 June 2016

Transition state in a noisy environment.

scientific article published on 25 July 2005

Transition state theory characterizes thin film macrospin dynamics driven by an oscillatory magnetic field: Inertial effects

scientific article published in 2022

Transition state theory for activated systems with driven anharmonic barriers

scientific article

Transition state theory for solvated reactions beyond recrossing-free dividing surfaces. ⬇️

scientific article published on 6 June 2016

Transition-state theory rate calculations with a recrossing-free moving dividing surface.

scientific article published on 13 October 2007

Uncovering the Geometry of Barrierless Reactions Using Lagrangian Descriptors

scientific article published on 2 November 2015

Using an environmentally-relevant panel of Gram-negative bacteria to assess the toxicity of polyallylamine hydrochloride-wrapped gold nanoparticles

article

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