Biomedical subjects

Rigoberto Hernandez

Publications and source records attributed to Rigoberto Hernandez.

12 recordsLinked to original sources

PubMed2006

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

Local solvation and transport effects in gas-expanded liquids (GXLs) are reported based on molecular simulation. GXLs were found to exhibit local density enhancements similar to those seen in supercritical fluids, although less dramatic. This approach was used as an alternative to a multiphase atomistic model for these mixtures by utilizing experimental results to describe the necessary fixed conditions for a locally (quasi-) stable molecular dynamics model of the (single) GXL phase. The local anisotropic pair correlation function, orientational correlation functions, and diffusion rates are reported for two systems: CO2-expanded methanol and CO2-expanded acetone at 298 K and pressures up to 6 MPa.

Acetone↗

PubMed2006

Dihedral-angle information entropy as a gauge of secondary structure propensity.

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 between sequential residues. A standard information entropy for a primary sequence has been defined using the values of the probabilities of the most likely dihedral angles along the sequence. The distribution of entropy differences relative to the standard for each protein in a reference set--a sublibrary of the Protein Data Bank at the 90% sequence redundancy level--appears to be nearly Gaussian. It gives rise to an auxiliary checking function whose value signals the extent to which the dihedral angle propensities differ from typical structures. Such deviations can arise either because of incorrect dihedral angle assignments or secondary structural propensities that are atypical of the structures in the reference set. This auxiliary checking function can be readily calculated at the public website, (http://www.d2check.gatech.edu). Its utility is demonstrated here in an analysis displaying differences between experimentally and theoretically derived structures, and in the analysis of structures derived by homology modeling. A comparison of the new measure, D(2)Check, to other checking functions based on backbone conformation-namely, PROCHECK and WHAT_CHECK--is also provided.

Algorithms↗

PubMed2006

Identifying reactive trajectories using a moving transition state.

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 anharmonic two-dimensional system confirm the efficiency of this approach. The results are compared to the standard fixed transition state dividing surface that is well-known to suffer from recrossings and therefore requires trajectories to be evolved over a long time interval before they can reliably be classified as reactive or nonreactive. The moving dividing surface can be used to identify reactive trajectories in harmonic or moderately anharmonic systems with considerably lower numerical effort or even without any simulation at all.

Algorithms↗

PubMed2006

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

The diffusion of molecules through uniform homogeneous materials can readily be described by Brownian motion or generalizations thereof. The further generalization of these models to describe molecular diffusion through heterogeneous and nonstationary solvents is much less understood. Phenomenological nonstationary generalizations of the generalized Langevin equation (GLE) have earlier been developed satisfying the fluctuation-dissipation relationship in quasi-equilibrium limits while exhibiting somewhat complex behavior away from equilibrium. This reduced-dimensional representation should be capable of describing the diffusion of a particle through a colloidal suspension whose average particle size is tuned by an external driving force such as pH. A simple particle model of such a process involves the motion of a hard-sphere particle in an explicit environment of swelling hard spheres. The velocity autocorrelation functions observed in a large number of simulations of the particle model under various swelling rates agree precisely with those of a single form of the nonstationary phenomenological model. Though this procedure is not an explicit projection of the mechanical system onto the nonstationary GLE, it does show that the latter correctly describes the dynamics of the projected coordinate--namely, diffusion of the solute--under nonequilibrium conditions. Both nonequilibrium solvent models lead to behavior reminiscent of beta-relaxation processes at packing fractions substantially below that of the glass transition.

Algorithms↗

PubMed2006

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

Gas-expanded liquids (GXLs) are a new and benign class of liquid solvents, which may offer many advantages for separations, reactions, and advanced materials. GXLs are intermediate in properties between normal liquids and supercritical fluids, both in solvating power and in transport properties. Other advantages include benign nature, low operating pressures, and highly tunable properties by simple pressure variations. The chemical community has only just begun to exploit the advantages of these GXLs for industrial applications. This Account focuses on the synergism of experimental techniques with theoretical modeling resulting in a powerful combination for exploring chemical structure and transport in the cybotactic region of GXLs (at the nanometer lengthscale).

Journal Article↗

PubMed2005

Stochastic transition states: reaction geometry amidst noise.

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 trajectories must cross. In order not to overestimate the reaction rate, the dynamics must be free of recrossings of the dividing surface. This no-recrossing rule is difficult (and sometimes impossible) to enforce, however, when a chemical reaction takes place in a fluctuating environment such as a liquid. High-accuracy approximations to the rate are well known when the solvent forces are treated using stochastic representations, though again, exact no-recrossing surfaces have not been available. To generalize the exact limit of TST to reactive systems driven by noise, we introduce a time-dependent dividing surface that is stochastically moving in phase space, such that it is crossed once and only once by each transition path.

Journal Article↗

PubMed2005

An idealized model for nonequilibrium dynamics in molecular systems.

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 behavior cannot be readily surmised by stationary projected stochastic representations such as those described by the Langevin equation or the generalized Langevin equation (GLE). The irreversible generalized Langevin equation (iGLE) contains a nonstationary friction kernel that in certain limits reduces to the GLE with space-dependent friction. For more general forms of the friction kernel, the iGLE was previously shown to be the projection of a mechanical system with a time-dependent Hamiltonian [R. Hernandez, J. Chem. Phys. 110, 7701 (1999)]. In the present work, the corresponding open Hamiltonian system is shown to be amenable to numerical integration despite the presence of a nonlocal term. Simulations of this mechanical system further confirm that the time dependence of the observed total energy and the correlations of the solvent force are in precise agreement with the projected iGLE. This extended nonstationary Hamiltonian is thus amenable to the study of nonequilibrium bounds and fluctuation theorems.

Journal Article↗

PubMed2005

Transition state in a noisy environment.

Transition state theory overestimates reaction rates in solution because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a time-dependent dividing surface free of such recrossings in the presence of noise. The no-recrossing limit of transition state theory thus becomes generally available for the description of reactions in a fluctuating environment.

Algorithms↗

PubMed2005

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

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 in the low-friction regime. In prior work, the latter was dissipated self-consistently through an additional uniform (mean-field) friction [T. Shepherd and R. Hernandez, J. Chem. Phys. 115, 2430 (2001).] An alternative approach to ensure that equipartition is satisfied relies on the use of a space-dependent friction while ignoring nonlocal correlations. The approach is evaluated with respect to its ability to maintain constant temperature for two simple one-dimensional, stochastic potentials of mean force wherein the friction can be evaluated explicitly when there is no memory in the barriers. The use of a space-dependent friction is capable of providing qualitatively similar results to those obtained previously, but in extreme cases deviations from equipartition may be observed due to the neglect of the memory effects present in the stochastic potentials.

Journal Article↗

PubMed2005

Chemical reaction dynamics within anisotropic solvents in time-dependent fields.

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 Langevin equation. The rotational motion of the mesogens is assumed to follow the motion of an external driving field in the linear response limit. Reaction dynamics have also been probed using a two-state model for the Brownian particles. Analytical expressions for diffusion and reaction rates have been developed and are found to be in good agreement with numerical calculations. When the external field driving the mesogens is held at constant rotational frequency, the model for reaction dynamics predicts that the applied field frequency can be used to control the product composition.

Anisotropy↗

PubMed2004

Folding behavior of model proteins with weak energetic frustration.

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 energetic frustration that such contacts represent varies among different proteins and may account for folding behavior not seen in unfrustrated models. Minimalist model proteins with heterogeneous contacts--as represented by lattice heteropolymers consisting of three types of monomers--also give rise to weak energetic frustration in their corresponding native structures, and the present study of their equilibrium and nonequilibrium properties reveals some of the breadth in their behavior. In order to capture this range within a detailed study of only a few proteins, four candidate protein structures (with their cognate sequences) have been selected according to a figure of merit called the winding index--a characteristic of the number of turns the protein winds about an axis. The temperature-dependent heat capacities reveal a high-temperature collapse transition, and an infrequently observed low-temperature rearrangement transition that arises because of the presence of weak energetic frustration. Simulation results motivate the definition of a new measure of folding affinity as a sequence-dependent free energy--a function of both a reduced stability gap and high accessibility to non-native structures--that correlates strongly with folding rates.

Amino Acid Sequence↗

PubMed2004

Mechanism for radical cation transport in duplex DNA oligonucleotides.

We investigated the photoinduced one-electron oxidation of a series of DNA oligomers having a covalently linked anthraquinone group (AQ) and containing [(A)(n)GG](m) or [(T)(n)GG](m) segments. These oligomers have m GG steps, where m = 4 or 6, separated by (A)(n) or (T)(n) segments, where n = 1-7 for the (A)(n) set and 1-5 for the (T)(n) set. Irradiation with UV light that is absorbed by the AQ causes injection of a radical cation into the DNA. The radical cation migrates through the DNA, causing chemical reaction, primarily at GG steps, that leads to strand cleavage after piperidine treatment. The uniform, systematic structure of the DNA oligonucleotides investigated permits the numerical solution of a kinetic scheme that models these reactions. This analysis yields two rate constants, k(hop), for hopping of the radical cation from one site to adjacent sites, and k(trap), for irreversible reaction of the radical cation with H(2)O or O(2). Analysis of these findings indicates that radical cation hopping in these duplex DNA oligomers is a process that occurs on a microsecond time scale. The value of k(hop) depends on the number of base pairs in the (A)(n) and (T)(n) segments in a systematic way. We interpret these results in terms of a thermally activated adiabatic mechanism for radical cation hopping that we identify as phonon-assisted polaron hopping.

Cations↗