arXiv subjects

Thomas B. Woolf

Publications and source records attributed to Thomas B. Woolf.

10 recordsLinked to original sources

arXiv2011

Order parameter prediction from molecular dynamics simulations in proteins

A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that may dramatically enhance sampling of intermediate states.

physics.bio-ph↗

arXiv2004

Folding is Not Required for Bilayer Insertion: Replica Exchange Simulations of an a-Helical Peptide with an Explicit Lipid Bilayer

We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the DPPC bilayer and its folding into an a-helix with a trans-bilayer orientation. We observe that the insertion of the peptide into the DPPC bilayer precedes secondary structure formation. Although the peptide has some propensity to form a partially helical structure in the interfacial region of the DPPC/water system, this state is not a productive intermediate but rather an off-pathway trap for WALP-16 insertion. Equilibrium simulations show that the observed insertion/folding pathway mirrors the potential of mean force (PMF). Calculation of the enthalpic and entropic contributions to this PMF show that the surface bound conformation of WALP-16 is significantly lower in energy than other conformations, and that the insertion of WALP-16 into the bilayer without regular secondary structure is enthalpically unfavorable by 5-10 kcal/mol/residue. The observed insertion/folding pathway disagrees with the dominant conceptual model, which is that a surface bound helix is an obligatory intermediate for the insertion of a-helical peptides into lipid bilayers. In our simulations, the observed insertion/folding pathway is favored because of a large (> 100 kcal/mol) increase in system entropy that occurs when the unstructured WALP-16 peptide enters the lipid bilayer interior. The insertion/folding pathway that is lowest in free energy depends sensitively on the near cancellation of large enthalpic and entropic terms. This suggests that intrinsic membrane peptides may have a diversity of insertion/folding behaviors depending on the exact system of peptide and lipid under consideration.

q-bio.BM↗

arXiv2004

Stochastic dynamics and the dynamic phase transition in thin ferromagnetic films

The dynamic phase behavior of a classical Heisenberg spin system with a bilinear exchange anisotropy in a planar thin film geometry has been investigated by Monte Carlo simulations using different forms for the stochastic dynamics. In simulations of the dynamic phase transition (DPT) in films subject to a pulsed oscillatory external field with competing surface fields, both Glauber and Metropolis dynamics show a continuous DPT. Furthermore the field amplitude dependence of the DPT is qualitatively similar for both Glauber and Metropolis dynamics. However, the temperature dependence of the DPT is markedly different with the DPT being much sharper for Glauber dynamics. The difference arises from a decoupling of the surface and bulk responses of the film near the dynamic phase transition with Metropolis dynamics that is not evident for Glauber dynamics.

cond-mat.stat-mech↗

arXiv2003

Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities

Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the availability of only a finite number of data values, N. In previous work, we outlined the fundamental statistical description of this ``finite-sampling error.'' We now give a more complete presentation of (i) rigorous general bounds on the free energy and other nonlinear averages, which underscore the universality of the phenomenon; (ii) asymptotic N->infinity expansions of the average behavior of the finite-sampling error in Delta-F estimates; (iii) illustrative examples of large-N behavior, both in free-energy and other calculations; and (iv) the universal, large-N relation between the average finite-sampling error and the fluctuation in the error. An explicit role is played by Levy and Gaussian limiting distributions.

physics.comp-ph↗

arXiv2002

Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm

We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of rapidly determining multiple pathways between known states. Monotonic progress toward the target state is not required. The soft-ratcheting algorithm is applied to an all-atom model of alanine dipeptide, whose unbiased trajectories are assumed to follow overdamped Langevin dynamics. All possible pathways on the two-dimensional dihedral surface are determined. The associated probability scores, though not optimally distributed at present, may provide a mechanism for estimating reaction rates.

physics.chem-ph↗

arXiv2002

Dependence of Sidechain Rotamer Preference on Backbone Conformation: Relative Free Energy Calculations for Valine and Leucine

Three dimensional relative free energy calculations are used to directly calculate the dependence of the preferred sidechain rotamers for valine and leucine on the conformation of the backbone. Specifically, umbrella restrained molecular dynamics calculations are used to sample all of Ramachandran space for chi values surrounding the common rotameric states of leucine and valine. Relative free enegy slices were calculated from the biased trajectories using the weighted histogram analysis method (WHAM). The slices were connected together by another set of slices perpendicular to Ramachandran space to determine the favored rotamer for a given backbone conformation. The calculated preferences are quite similar to those seen in the backbone-dependent rotamer library of Dunbrack and Karplus, despite the fact that the current calculations neglect the effects of neighboring residues. It appears likely that these calculations could be extended to calculate the optimal sidechain conformation for a peptide with known backbone conformation in the context of structure refinement and prediction

cond-mat.soft↗

arXiv2002

Theory of Systematic Computational Error in Free Energy Differences

Systematic inaccuracy is inherent in any computational estimate of a non-linear average, due to the availability of only a finite number of data values, N. Free energy differences (DF) between two states or systems are critically important examples of such averages in physical, chemical and biological settings. Previous work has demonstrated, empirically, that the ``finite-sampling error'' can be very large -- many times kT -- in DF estimates for simple molecular systems. Here, we present a theoretical description of the inaccuracy, including the exact solution of a sample problem, the precise asymptotic behavior in terms of 1/N for large N, the identification of universal law, and numerical illustrations. The theory relies on corrections to the central and other limit theorems, and thus a role is played by stable (Levy) probability distributions.

physics.comp-ph↗

arXiv2001

Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System

We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results suggest that extrapolation can greatly reduce the systematic error in DF estimated from a small number of very fast switches. Our extrapolation procedure uses block-averages of finite-data estimates, and appears to be particularly useful for broad, non-Gaussian distributions of data which produce substantial systematic errors with insufficient data. In every tested case, the extrapolative results were better than direct estimates.

physics.chem-ph↗

arXiv2001

Transition Events in Butane Simulations: Similarities Across Models

From a variety of long simulations of all-atom butane using both stochastic and fully-solved molecular dynamics, we have uncovered striking generic behavior which also occurs in one-dimensional systems. We find an apparently universal distribution of transition event durations, as well as a characteristic speed profile along the reaction coordinate. An approximate analytic distribution of event durations, derived from a one-dimensional model, correctly predicts the asymptotic behavior of the universal distribution for both short and long durations.

physics.chem-ph↗

arXiv2000

Efficient Dynamic Importance Sampling of Rare Events in One Dimension

Exploiting stochastic path integral theory, we obtain \emph{by simulation} substantial gains in efficiency for the computation of reaction rates in one-dimensional, bistable, overdamped stochastic systems. Using a well-defined measure of efficiency, we compare implementations of ``Dynamic Importance Sampling'' (DIMS) methods to unbiased simulation. The best DIMS algorithms are shown to increase efficiency by factors of approximately 20 for a $5 k_B T$ barrier height and 300 for $9 k_B T$, compared to unbiased simulation. The gains result from close emulation of natural (unbiased), instanton-like crossing events with artificially decreased waiting times between events that are corrected for in rate calculations. The artificial crossing events are generated using the closed-form solution to the most probable crossing event described by the Onsager-Machlup action. While the best biasing methods require the second derivative of the potential (resulting from the ``Jacobian'' term in the action, which is discussed at length), algorithms employing solely the first derivative do nearly as well. We discuss the importance of one-dimensional models to larger systems, and suggest extensions to higher-dimensional systems.

physics.comp-ph↗