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In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2-3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard- Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent. [ABSTRACT FROM AUTHOR]

The microscopic structure of fluids of simple spheres is well known. However, the constituents of most real-life fluids are non-spherical, leading to a coupling between the rotational and translational degrees of freedom. The structure of simple dense fluids of spheroids - ellipsoids of revolution - was only recently determined by direct experimental techniques [A. P. Cohen, E. Janai, E. Mogilko, A. B. Schofield, and E. Sloutskin, Phys. Rev. Lett. 107, 238301 (2011)]. Using confocal microscopy, it was demonstrated that the structure of these simple fluids cannot be described by hard particle models based on the widely used Percus-Yevick approximation. In this paper, we describe a new protocol for determining the shape of the experimental spheroids, which allows us to expand our previous microscopy measurements of these fluids. To avoid the approximations in the theoretical approach, we have also used molecular dynamics simulations to reproduce the experimental radial distribution functions g(r) and estimate the contribution of charge effects to the interactions. Accounting for these charge effects within the Percus-Yevick framework leads to similar agreement with the experiment. [ABSTRACT FROM AUTHOR]

In order to interpret measured intensity autocorrelation functions obtained in evanescent wave scattering, their initial decay rates have been analyzed recently [P. Holmqvist, J. K. G. Dhont, and P. R. Lang, Phys. Rev. E 74, 021402 (2006); B. Cichocki, E. Wajnryb, J. Blawzdziewicz, J. K. G. Dhont, and P. R. Lang, J. Chem. Phys. 132, 074704 (2010); J. W. Swan and J. F. Brady, ibid. 135, 014701 (2011)]. A theoretical analysis of the longer time dependence of evanescent wave autocorrelation functions, beyond the initial decay, is still lacking. In this paper we present such an analysis for very dilute suspensions of spherical colloids. We present simulation results, a comparison to cumulant expansions, and experiments. An efficient simulation method is developed which takes advantage of the particular mathematical structure of the time-evolution equation of the probability density function of the position coordinate of the colloidal sphere. The computer simulation results are compared with analytic, first and second order cumulant expansions. The only available analytical result for the full time dependence of evanescent wave autocorrelation functions [K. H. Lan, N. Ostrowsky, and D. Sornette, Phys. Rev. Lett. 57, 17 (1986)], that neglects hydrodynamic interactions between the colloidal spheres and the wall, is shown to be quite inaccurate. Experimental results are presented and compared to the simulations and cumulant expansions. [ABSTRACT FROM AUTHOR]

In biochemical reaction systems dominated by delays, the simulation speed of the stochastic simulation algorithm depends on the size of the wait queue. As a result, it is important to control the size of the wait queue to improve the efficiency of the simulation. An improved accelerated delay stochastic simulation algorithm for biochemical reaction systems with delays, termed the improved delay-leaping algorithm, is proposed in this paper. The update method for the wait queue is effective in reducing the size of the queue as well as shortening the storage and access time, thereby accelerating the simulation speed. Numerical simulation on two examples indicates that this method not only obtains a more significant efficiency compared with the existing methods, but also can be widely applied in biochemical reaction systems with delays. [ABSTRACT FROM AUTHOR]

The hydrodynamic interaction is an essential effect to consider in Brownian dynamics simulations of polymer and nanoparticle dilute solutions. Several mathematical approaches can be used to build Brownian dynamics algorithms with hydrodynamic interaction, the most common of them being the exact but time demanding Cholesky decomposition and the Chebyshev polynomial expansion. Recently, Geyer and Winter [J. Chem. Phys. 130, 1149051 (2009)] have proposed a new approximation to treat the hydrodynamic interaction that seems quite efficient and is increasingly used. So far, a systematic comparison among those approaches has not been clearly made. In this paper, several features and the efficiency of typical implementations of those approaches are evaluated by using bead-and-spring chain models. The different sensitivity to the bead overlap detected for the different implementations may be of interest to select the suitable algorithm for a given simulation. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared, , was found to scale as N4/5 for an intermediate regime and N2/3 for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are 'surface beads' interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the next paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204905 (2011)]. Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ∼ N-2.4 scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension , neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η0 ∼ N1.4 ± 0.2 which is much weaker than the N3.4 behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)]. [ABSTRACT FROM AUTHOR]

Tau leaping methods enable efficient simulation of discrete stochastic chemical systems. Stiff stochastic systems are particularly challenging since implicit methods, which are good for stiffness, result in noninteger states. The occurrence of negative states is also a common problem in tau leaping. In this paper, we introduce the implicit Minkowski-Weyl tau (IMW-τ) methods. Two updating schemes of the IMW-τ methods are presented: implicit Minkowski-Weyl sequential (IMW-S) and implicit Minkowski-Weyl parallel (IMW-P). The main desirable feature of these methods is that they are designed for stiff stochastic systems with molecular copy numbers ranging from small to large and that they produce integer states without rounding. This is accomplished by the use of a split step where the first part is implicit and computes the mean update while the second part is explicit and generates a random update with the mean computed in the first part. We illustrate the IMW-S and IMW-P methods by some numerical examples, and compare them with existing tau methods. For most cases, the IMW-S and IMW-P methods perform favorably. [ABSTRACT FROM AUTHOR]

A comparative study of the dynamics of the electron beam-plasma system in two spatial dimensions is carried out by means of particle-in-cell (PIC) simulation and quasilinear theory. In the literature, the beam-plasma instability is usually studied with one-dimensional assumption. Among the few works that include higher-dimensional effects are two- and three-dimensional quasilinear theory and two-dimensional PIC simulations. However, no efforts were made to compare the theory and simulation side by side. The present paper carries out a detailed comparative study of two-dimensional simulation and quasilinear theory. It is found that the quasilinear theory quite adequately accounts for most important features associated with the simulation result. For instance, the particle diffusion time scale, the maximum wave intensity, dynamical development of the electron distribution function, and the change in the wave spectrum all agree quantitatively. However, certain nonlinear effects such as the Langmuir condensation phenomenon are not reproduced by the quasilinear theory. Nevertheless, the present paper verifies that the simple quasilinear theory is quite effective for the study of beam-plasma instability for the present choice of parameters. [ABSTRACT FROM AUTHOR]

The experimental study on the expanding plasma movement of low-density gold foam (~1% solid density) irradiated by a high power laser is reported in this paper. Experiments were conducted using the SG-III prototype laser. Compared to solid gold with 19.3 g/cc density, the velocities of X-ray emission fronts moving off the wall are much smaller for gold foam with 0.3 g/cc density. Theoretical analysis and MULTI 1D simulation results also show less plasma blow-off, and that the density contour movement velocities of gold foam are smaller than those of solid gold, agreeing with experimental results. These results indicate that foam walls have advantages in symmetry control and lowering plasma fill when used in ignition hohlraum. [ABSTRACT FROM AUTHOR]

This paper presents simulations of isolated 3D filaments in a slab geometry obtained using a newly developed 3D reduced fluid code, written using the BOUT++ framework. First, systematic scans were performed to investigate how the dynamics of a filament are affected by its amplitude, perpendicular size, and parallel extent. The perpendicular size of the filament was found to have a strong influence on its motions, as it determined the relative importance of parallel currents to polarization and viscous currents, whilst drift-wave instabilities were observed if the initial amplitude of the blob was increased sufficiently. Next, the 3D simulations were compared to 2D simulations using different parallel closures; namely, the sheath dissipation closure, which neglects parallel gradients, and the vorticity advection closure, which neglects the influence of parallel currents. The vorticity advection closure was found to not replicate the 3D perpendicular dynamics and overestimated the initial radial acceleration of all the filaments studied. In contrast, a more satisfactory comparison with the sheath dissipation closure was obtained, even in the presence of significant parallel gradients, where the closure is no longer valid. Specifically, it captured the contrasting dynamics of filaments with different perpendicular sizes that were observed in the 3D simulations which the vorticity advection closure failed to replicate. However, neither closure successfully replicated the Boltzmann spinning effects nor the associated poloidal drift of the blob that was observed in the 3D simulations. Although the sheath dissipation closure was concluded to be more successful in replicating the 3D dynamics, it is emphasized that the vorticity advection closure may still be relevant for situations where the parallel current is inhibited from closing through the sheath due to effects such as strong magnetic shear around X points or increased resistivity near the targets. [ABSTRACT FROM AUTHOR]

A novel ultra-high pressure device, multilayer stagger-split die, has been constructed based on the principle of 'dividing dies before cracking.' Multilayer stagger-split die includes an encircling ring and multilayer assemblages, and the mating surfaces of the multilayer assemblages are mutually staggered between adjacent layers. In this paper, we investigated the stressing features of this structure through finite element techniques, and the results were compared with those of the belt type die and single split die. The contrast experiments were also carried out to test the bearing pressure performance of multilayer stagger-split die. It is concluded that the stress distributions are reasonable and the materials are utilized effectively for multilayer stagger-split die. And experiments indicate that the multilayer stagger-split die can bear the greatest pressure. [ABSTRACT FROM AUTHOR]

In this paper, we compare two recent models [N. A. Yampolsky and N. J. Fisch, Phys. Plasmas 16, 072104 (2009); D. Bénisti, D. J. Strozzi, L. Gremillet, and O. Morice, Phys. Rev. Lett. 103, 155002 (2009)] introduced to predict the nonlinear growth of stimulated Raman scattering in the kinetic regime, and providing moreover a nonlinear description of the collisionless, Landau-like, damping rate of the driven electron plasma wave. We first recall the general theoretical framework common to these two models, based on the derivation of the imaginary part of the electron susceptibility, χi, and then discuss in detail why the two approaches differ. By comparing the theoretical predictions for χi to those derived from test particle or Vlasov simulations, we moreover discuss the range of validity of the two models. [ABSTRACT FROM AUTHOR]

This paper deals with a two-dimensional simulation of electric wakefields generated by two color laser pulses propagating in homogeneous plasma, using VORPAL simulation code. The laser pulses are assumed to have a frequency difference equal to the plasma frequency. Simulation studies are performed for two similarly as well as oppositely polarized laser pulses and the respective amplitudes of the generated longitudinal wakefields for the two cases are compared. Enhancement of wake amplitude for the latter case is reported. This simulation study validates the analytical results presented by Jha et al. [Phys. Plasmas 20, 053102 (2013)]. [ABSTRACT FROM AUTHOR]

A direct Density Modulation Cathode (DMC) in magnetron is proposed in this paper. By removing the velocity modulation process, electron spokes corresponding to the dominant operating mode can be quickly formed when the DMC is used. Based on theoretical analysis, particle-in-cell simulations and experimental investigations are carried out for demonstration. The final results show that compared with conventional solid cathode and transparent cathode, the DMC can increase 68% and even 146% of relative microwave widths, respectively. [ABSTRACT FROM AUTHOR]

This paper compares two continuously tunable systems for time-resolved spectroscopy of diffusive media based on a supercontinuum laser source. Two approaches for spectral selection are considered relying either on a dispersive prism or on a commercial acoustic-optic tunable filter (AOTF) device. The comparison was performed first in terms of extracted power and spectral response function, then in terms of distortions introduced in the retrieved absorption and scattering spectra. Simulations and experiments on diffusive phantoms confirmed that, besides narrower FWHM in the AOTF bandpass, the prism solution is superior with respect to the distortions produced on the recovered spectra. [ABSTRACT FROM AUTHOR]

A positive slope in a velocity distribution function perpendicular to the ambient magnetic field, such as due to a loss cone or ring velocity distribution, can become a free energy source for the excitation of various plasma waves. Since there exists no analytic expression for integrals of Maxwellian ring velocity distribution functions, their linear properties have previously been studied using several approximations or modeled distributions. In this paper, a numerical method for analyzing the linear dispersion relation for Maxwellian ring-beam velocity distributions is developed. The obtained linear properties are confirmed by direct comparison with full particle simulation results. [ABSTRACT FROM AUTHOR]