Biomedical subjects

Fernando A Escobedo

Publications and source records attributed to Fernando A Escobedo.

13 recordsLinked to original sources

PubMed2006

Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study.

Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular environment and might dictate whether a protein folds co-translationally or post-translationally.

Algorithms↗

PubMed2006

On the use of transition matrix methods with extended ensembles.

Different extended ensemble schemes for non-Boltzmann sampling (NBS) of a selected reaction coordinate lambda were formulated so that they employ (i) "variable" sampling window schemes (that include the "successive umbrella sampling" method) to comprehensibly explore the lambda domain and (ii) transition matrix methods to iteratively obtain the underlying free-energy eta landscape (or "importance" weights) associated with lambda. The connection between "acceptance ratio" and transition matrix methods was first established to form the basis of the approach for estimating eta(lambda). The validity and performance of the different NBS schemes were then assessed using as lambda coordinate the configurational energy of the Lennard-Jones fluid. For the cases studied, it was found that the convergence rate in the estimation of eta is little affected by the use of data from high-order transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an "elastic" window of sampling can be used to effectively enact (nonuniform) preferential sampling over the lambda domain, and how to stitch the weights from separate one-dimensional NBS runs to produce a eta surface over a two-dimensional domain.

Journal Article↗

PubMed2006

A general framework for non-Boltzmann Monte Carlo sampling.

Non-Boltzmann sampling (NBS) methods have been extensively employed in recent years, mainly due to their ability to enhance ergodicity in simulations of complex systems. In addition, they make possible reliable computation of equilibrium properties (ensemble averages, free-energy differences, and potentials of mean force) over continuous ranges of thermodynamic conditions. In this work, we put forward a general and systematic framework for NBS methods that allows a single set of equations and procedures to be applied to diverse systems. Moreover, we show how to exploit simulation data most effectively by obtaining continuous profiles of any mechanical properties, including structural quantities not directly related to the ensemble parameters. Finally, we demonstrate the usefulness of the developed formulation by applying it to spin systems, Lennard-Jones fluids, and a model protein molecule (both in isolation and in the proximity of a flat wall).

Algorithms↗

PubMed2005

A unified methodological framework for the simulation of nonisothermal ensembles.

A general framework is developed for the simulation of nonisothermal statistical-mechanical ensembles. This framework is intended to synthesize the formulation of advanced Monte Carlo simulation methods such as multihistogram reweighting, replica-exchange methods, and expanded ensemble techniques so that they can be applied to different nonisothermal ensembles. Using Lennard-Jones systems as test cases, novel implementations of these methods are demonstrated with different ensembles including the microcanonical, isobaric-isoenthalpic, and isobaric-semigrand ensembles. In particular, it is shown that the use of multiensemble methods allows the efficient simulation of microcanonical density of states, entropies, vapor-liquid and solid-liquid equilibrium for pure component systems, and fluid-phase coexistence for binary mixtures. In these applications, comparisons are also presented that highlight the advantages of the proposed multiensemble implementations over alternative methods used before.

Journal Article↗

PubMed2005

Effect of chain stiffness and entanglements on the elastic behavior of end-linked elastomers.

The effect of chain stiffness and entanglements on the elastic behavior and microscopic structure of cross-linked polymer networks was studied using Monte Carlo simulations. We investigated the behavior of entangled and entanglement-free networks at various degrees of chain stiffness and densities. Based on previous results that indicated that trapped entanglements prevent strain-induced order-disorder transitions in semiflexible chain networks, we prepared the entangled networks by end-linking the chains in very dilute conditions so as to minimize the extent of trapped entanglements. We also considered the entanglement-free case by using a "diamond" structure. We found that the presence of even a very small amount of trapped entanglements is enough to prevent a discontinuous strain-induced transition to an ordered phase. In these mildly entangled networks, a nematiclike order is eventually attained at high extensions but the elastic response remains continuous and the cross-links remain uniformly distributed through the simulation box. The entanglement-free diamond networks on the other hand show discontinuities in their stress-strain data. Networks at higher densities exhibit a more stable ordered phase and show an unusual staircaselike stress-strain curve. This is the result of a stepwise extension mechanism in which the chains form ordered domains that exclude the cross-links. Extension is achieved by increasing the number of these ordered domains in the strain direction. Cross-links aggregate in the spaces between these ordered domains and form periodic bands. Each vertical upturn in the stress-strain data corresponds to the existence of an integer number of ordered domains. This stepwise elastic behavior is found to be similar to that exhibited by some tough natural materials.

Anisotropy↗

PubMed2005

Multicanonical schemes for mapping out free-energy landscapes of single-component and multicomponent systems.

Multicanonical (MUCA) sampling is a powerful approach for simulating large domains of thermodynamic macrostate space that relies on mapping out either the density of states or a free energy of the system as a function of a suitable "order parameter." The purpose of this study is to extend and apply to more complex systems the method introduced in a previous paper [M. K. Fenwick and F. A. Escobedo, J. Chem. Phys. 120, 3066 (2004)] that uses Bennett's acceptance ratio method for estimating MUCA free energies. Four types of MUCA schemes are considered according to what order parameter is adopted and how the macrostate space is traversed: a la grand canonical ensemble, a la semigrand canonical ensemble, a la semigrand isothermal-isobaric ensemble, and a la isothermal-isobaric ensemble. Two types of systems are studied, the first is a two-component Lennard-Jones mixture that exhibits a vapor-liquid transition, and the second is a hard-cuboid containing system that exhibits an isotropic-liquid crystalline transition. These systems are simulated with different MUCA schemes and the resulting free-energy profiles are used to determine phase-coexistence conditions. For the Lennard-Jones systems, it is also demonstrated that different types of MUCA simulations can be conveniently performed over different macrostate regions and the results can be subsequently pieced together into a continuous weighting function.

Journal Article↗

PubMed2004

Stepwise elastic behavior in a model elastomer.

Monte Carlo simulations of an entanglement-free cross-linked polymer network of semiflexible chains reveal a peculiar stepwise elastic response. For increasing stress, step jumps in strain are observed that do not correlate with changes in the number of aligned chains. We show that this unusual behavior stems from the ability of the system to form multiple ordered chain domains that exclude the cross-linking species. This novel elastomer shows a toughening behavior similar to that observed in biological structural materials, such as muscle proteins and abalone shell adhesive.

Biomimetic Materials↗

PubMed2004

Liquid crystalline behavior of a semifluorinated oligomer.

Monte Carlo simulations with a coarse-grained model were performed to study the microstructure of a semifluoroalkane C20 diblock oligomer [F(CF(2))(10)(CH(2))(10)H]. The coarse-grained model adopted is based on previously reported united-atom force fields for alkanes and perfluoroalkanes and was first validated by simulating the phase behavior of a mixture of hexane and perfluorohexane. These preliminary simulations established the need of a significant correction factor in the Berthelot mixing rule between alkane and perfluoroalkane groups. Using such a force field, the semifluorinated C20 oligomer liquid was simulated using efficient Monte Carlo moves to sample different molecular arrangements and box dimensions so as to allow different layering structures to form. In qualitative agreement with experimental observations, a smectic-to-isotropic phase transition occurs as temperature is increased but the transition point and the structure of the smectic phase depend on the stiffness of the torsional potential and the model of van der Waals interactions adopted. We identify two smectic phases LC1' and LC2', whose structures do not agree with those that have been postulated before to explain x-ray diffraction data, namely, LC1 and LC2. LC1' has a layer spacing similar to LC1 but the antiparallel packing is not observed with individual chains but with groups of chains producing a checkerboard pattern. LC2' has fully microsegregated blocks such as LC2 but the alkyl tails are not fully stretched or interdigitated. Despite these inconsistencies, and considering that reported experimental data also reveal the presence of mixed phases, the simulated structures suggest other plausible ways how the semifluorinated chains could pack and microsegregate to best negotiate energetic and entropic constraints.

Journal Article↗

PubMed2004

Bridging continuum and statistical thermodynamics via equations of state and the density of states.

The connection between molecular force fields and equations of state (EoS) is typically established at the level of predicted quantities, e.g., by comparing simulation data and EoS data. In this paper we show how an EoS can be used to extract the density of states (Omega) of a system thus establishing a deeper connection between EoSs and statistical thermodynamics. We also show how such an EoS Omega can be used to aid molecular simulation methods designed to map out Omega (like the multicanonical approach). Central to the implementation of these ideas is the fact that the configurational Omega is related to thermodynamic properties accessible by an EoS via Boltzmann's equation. Sample calculations are presented for the Omega relevant to isothermal-isobaric and grand canonical ensemble simulations using the hard-sphere system and the Lennard-Jones system as model fluids, and the Carnahan-Starling EoS and a cubic EoS, respectively, as thermodynamic models.

Journal Article↗

PubMed2004

Cubatic liquid-crystalline behavior in a system of hard cuboids.

The lyotropic phase behavior of cuboidal particles was investigated via Monte Carlo simulations. Hard cubes were approximated by suitably shaped clusters of hard spheres. Changes in concentration and structure of the system were monitored as a function of osmotic pressure P* (imposed in an isobaric ensemble). As expected, an isotropic phase prevailed at low concentrations (low P*) and a crystalline phase formed at high concentrations (high P*). A third distinct phase was also observed for an intermediate range of concentrations (approximately marked by breaks in the P* versus concentration curve). The structure of this mesophase was characterized both visually and analytically by calculating radial distribution functions and order parameters. It was found that such a mesophase exhibits orientational ordering along three axes (cubatic order) but significant translational disorder, thus having a structure clearly distinct from both isotropic and crystalline phases.

Journal Article↗

PubMed2004

Influence of polymer architecture and polymer-wall interaction on the adsorption of polymers into a slit-pore.

The effects of molecular topology and polymer-surface interaction on the properties of isolated polymer chains trapped in a slit were investigated using off-lattice Monte Carlo simulations. Various methods were implemented to allow efficient simulation of molecular structure, confinement force, and free energy for a chain interacting with such "sticky" surfaces. The simulations were performed in the canonical ensemble, and the free energy was sampled via virtual slit-separation moves. Six different chain architectures were studied: linear, star-branched, dendritic, cyclic, two-node (i.e., containing two tetrafunctional intramolecular crosslinks), and six-node molecules. The first three topologies entail increasing degrees of branching, and the last three topologies entail increasing degrees of intramolecular bonding. The confinement force, monomer density profile, and conformational properties for all these systems were compared (for identical molecular weight N) and analyzed as a function of adsorption strength. The compensation point where the wall attraction counterbalances the polymer-slit exclusion effects was the focus of our study. It was found that the attractive energy at the compensation point, epsilon(c), is a weak increasing function of the chain length for excluded-volume chains. The value of epsilon(c) differs significantly for different topologies, and smaller values are associated with better-adsorbing molecules. Due to their globular shape and numerous chain ends, branched molecules (e.g., stars and dendrimers) experience a relatively small entropic penalty for adsorption at low adsorption force and moderate confinement. However, as the adsorption force increases, the more flexible linear chains reach the compensation point at a weaker attractive energy because of the ease with which monomers can be packed near the walls. In moderate to weak confinement, molecules with intramolecular cross-links, such as cyclic, two-node, and six-node molecules, always adsorb better than the other chains (with the same N). Especially at strong adsorption, two-node and six node molecules are highly localized in the region near the walls. Under strong confinement conditions, chain rigidity becomes the dominating factor and the more flexible linear chain adsorbs the best at all adsorption strengths. These results provide useful insights for controlling confinement and depletion forces of polymers with different molecular architectures in the presence of attractive polymer-surface interactions.

Adsorption↗

PubMed2004

On the use of Bennett's acceptance ratio method in multi-canonical-type simulations.

A common strategy for mapping coexistence curves is to employ multi-canonical (MUCA) sampling to simulate along a macrostate path connecting two phases. Central to this approach is the task of accurately calculating the importance weights used in the MUCA procedure, which are needed for both effective sampling and accurate determination of phase boundaries. The purpose of this study is to develop a strategy for determining the importance weights that is built upon Bennett's optimized acceptance ratio method. This approach is shown to be closely related to transition matrix schemes, and is used to compute the vapor-liquid equilibrium of a Lennard-Jones fluid and the liquid-liquid equilibrium of a n-hexane/n-perfluorohexane mixture. For the Lennard-Jones system, the importance weights as a function of the number of particles "N" (at fixed temperature and volume) are obtained by using Bennett's method to estimate free energy differences between N and N+1 particle systems over the desired range of N values. In this application, the method is found to perform slightly better than a related transition matrix scheme. For the n-hexane/n-perfluorohexane liquid mixture, the method is designed to obtain weights as a function of composition (for fixed temperature, pressure, and total number of particles); in this case, the method is found to outperform the Gibbs ensemble approach.

Journal Article↗

PubMed2003

Hybrid Monte Carlo with multidimensional replica exchanges: conformational equilibria of the hypervariable regions of a llama VHH antibody domain.

Since the structural repertoire of the hypervariable regions of human antibodies is known to be more restricted than what is implied by sequence variability, a common approach to structural prediction is to use a knowledge-based (KB) method, such as the canonical structure model (C. Chothia and A. M. Lesk, Journal of Molecular Biology, 1987, Vol. 196, pp. 901-917). However, this model is less successful when applied to camelid heavy chain antibodies. In this study, molecular simulations were used to examine the conformational equilibria of the hypervariable regions (H1, H2, and H3) of a llama heavy chain variable domain, for which KB predictions are poor. Simulations were carried out using both conventional molecular dynamics (MD) and hybrid Monte Carlo with multidimensional replica exchanges (HYMREX). The advantage of the latter method is its ability to selectively target parts of the Hamiltonian that can most readily improve sampling. A novel variant of HYMREX was implemented in which, besides the temperature, torsional interactions and the range of nonbonded interactions were varied. To compare the sampling abilities of MD and this HYMREX scheme, simulations were started from a misfolded conformational state. Overall, MD yielded final conformations more similar to the initial state, implying quasi-ergodic sampling. In contrast, HYMREX achieved more ergodic sampling, and the majority of conformations that it sampled agreed well with the known crystal structure. The HYMREX simulation results were used to help identify the chief interactions governing the conformational equilibria and to reexamine the key assumptions underlying the KB predictions. The data show that the H1 region exhibited significant conformational freedom, in support of the hypothesis that main-chain structural variability in this region could play a greater role in antigen binding in camelid antibodies than it does in normal antibodies. Key H1 residues and associated inter-loop interactions are conjectured to account for the poor KB predictions.

Amino Acid Sequence↗