arXiv subjects

Edward Lyman

Publications and source records attributed to Edward Lyman.

9 recordsLinked to original sources

arXiv2016

Molecular Dynamics simulations and Kelvin Probe Force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures

The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.

cond-mat.soft↗

arXiv2007

Annealed importance sampling of dileucine peptide

Annealed importance sampling is a means to assign equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol. The weights may then be used to calculate equilibrium averages, and also serve as an ``adiabatic signature'' of the chosen cooling schedule. In this paper we demonstrate the method on the 50-atom dileucine peptide, showing that equilibrium distributions are attained for manageable cooling schedules. For this system, as naively implemented here, the method is modestly more efficient than constant temperature simulation. However, the method is worth considering whenever any simulated heating or cooling is performed (as is often done at the beginning of a simulation project, or during an NMR structure calculation), as it is simple to implement and requires minimal additional CPU expense. Furthermore, the naive implementation presented here can be improved.

q-bio.BM↗

arXiv2007

The structural de-correlation time: A robust statistical measure of convergence of biomolecular simulations

Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of trajectories has remained difficult to assess. Such assessment is critical not only for establishing the relevance of any individual simulation but also in the extremely active field of developing computational methods. Here we map the trajectory assessment problem onto a simple statistical calculation of the ``effective sample size'' - i.e., the number of statistically independent configurations. The mapping is achieved by asking the question, ``How much time must elapse between snapshots included in a sample for that sample to exhibit the statistical properties expected for independent and identically distributed configurations?'' The resulting ``structural de-correlation time'' is robustly calculated using exact properties deduced from our previously developed ``structural histograms,'' without any fitting parameters. We show the method is equally and directly applicable to toy models, peptides, and a 72-residue protein model. Variants of our approach can readily be applied to a wide range of physical and chemical systems.

q-bio.QM↗

arXiv2006

Ensemble based convergence assessment of biomolecular trajectories

Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different conformers; insufficient convergence translates into systematic errors. Here we present a simple method to self-consistently assess the convergence of a simulation. Standard clustering methods first generate a set of reference structures to any desired precision. The trajectory is then classified by proximity to the reference structures, yielding a one-dimensional histogram of structurally distinct populations. Comparing ensembles of different trajectories (or different parts of the same trajectory) built with the same reference structures provides a sensitive, quantitative measure of convergence. Please note: this is a preliminary manuscript, and should be read as such. Comments are most welcome, especially regarding pertinent prior work.

physics.bio-ph↗

arXiv2006

Resolution exchange simulation with incremental coarsening

We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally applicable incremental coarsening procedure and apply the algorithm to a larger peptide, met-enkephalin. In addition, we demonstrate a combination of resolution and temperature exchange, in which the coarser simulations are also at elevated temperatures. Both simulations are implemented in a ``top-down'' mode, to allow efficient allocation of CPU time among the different replicas.

physics.bio-ph↗

arXiv2006

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the literature. Mainly, we wish to call attention to limits on the maximum speed-up to be expected from temperature-based methods, and also note the need for careful quantification of sampling efficiency. Because potentially lengthy studies may be necessary to address these issues, we felt it would be useful to bring them to the attention of the broader community. Here \emph{we are strictly concerned with canonical sampling at a fixed temperature,} and \emph{not} with conformational search.

physics.bio-ph↗

arXiv2005

Resolution exchange simulation

We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models. Such ``resolution exchange'' can be applied to molecular systems or spin systems. The second extension is to ``pseudo-exchange'' simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduces the need for overlap between levels. Pseudo exchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.

q-bio.BM↗

arXiv2005

Steady States of a Nonequilibrium Lattice Gas

We present a Monte Carlo study of a lattice gas driven out of equilibrium by a local hopping bias. Sites can be empty or occupied by one of two types of particles, which are distinguished by their response to the hopping bias. All particles interact via excluded volume and a nearest-neighbor attractive force. The main result is a phase diagram with three phases: a homogeneous phase, and two distinct ordered phases. Continuous boundaries separate the homogeneous phase from the ordered phases, and a first-order line separates the two ordered phases. The three lines merge in a nonequilibrium bicritical point.

cond-mat.stat-mech↗

arXiv2003

A nonequilibrium lattice gas of two species: Monte Carlo investigations

We present the phase diagram of a far from equilibrium system, mapped by Monte Carlo simulation. The model is a lattice gas of two species of particles and holes. The two species are biased to hop in opposite directions and interact via excluded volume and nearest neighbor attractions. Three phases are found as a function of temperature and charge density.

cond-mat.stat-mech↗