二维三角格子上高分子动态 Monte Carlo模拟的协同运动算法

在动态Monte Carlo模拟的协同运动算法中,几个相邻的链节可以同时运动,这可以理解为高分子链中张力的作用引起的协同运动。将这一算法用于二维三角格子模型上RW链和SAW链的模拟。结果表明RW链的动力学行为符合Rouse理论,说明说明该算法可以用于高分子动力学研究,其优点是不需要使用键长涨落模型。     

Monte Carlo studies on the deformation behaviour of glassy model systems

We present an alternative methodology for the investigation of deformation properties of polymer glasses. The calculation of the stress–strain relation in simple extension is performed in the framework of a highly flexible lattice Monte Carlo algorithm. In contrast to other studies, this method enables the dynamic and temperature-dependent deformation analysis of an actual multichain system. The most characteristic properties of polymer systems, namely, excluded volume of effective monomers, non-crossability and finite extensibility of the chains as well as van der Waals attraction and the local chain stiffening with decreasing temperature are rigorously accounted for during the dynamics. The simulated stress–strain relations qualitatively agree with experimental findings. Analysis of the structure reveals pronounced non-affine and inhomogeneous deformation behaviour.     

Self-assembly on multiple length scales: a Monte Carlo algorithm with data augmentation

We present a Monte Carlo algorithm that allows simulations where portions of the system of variable size are moved. The algorithm requires the definition of an augmented space that contains information on the bonding between components of the system and is updated as the simulation proceeds. With this method it is possible to incorporate, within the same simulation, processes involving motion of smaller and larger portions of a given system. The algorithm is presented in general terms and illustrated for a simple one-dimensional lattice model.     

Monte Carlo modelling of the polymer glass transition

We are proposing a lattice model with chemical input for the computer modelling of the polymer glass transition. The chemical input information is obtained by a coarse graining procedure applied to a microscopic model with full chemical detail. We use this information on Bisphenol-A-Polycarbonate to predict it's Vogel-Fulcher temperature out of a dynamic Monte Carlo Simulation. The microscopic structure of the lattice model is that of a genuine amorphous material, and the structural relaxation obeys the time temperature superposition.     

Coarse-grained nonequilibrium approach to the molecular modeling of permeation through microporous membranes

We present a modeling technique that combines a statistical-mechanical coarse-graining scheme with a nonequilibrium molecular simulation algorithm to provide an efficient simulation of steady-state permeation across a microporous material. The coarse-graining scheme is based on the mapping of an atomistic model to a lattice using multidimensional free-energy and transition-state calculations. The nonequilibrium simulation algorithm is a stochastic, lattice version of the recently developed atomistic dual-control-volume grand canonical molecular dynamics. We demonstrate the approach on a model of methane permeating through a bulk portion of siliceous zeolite ZK4 at 300 K under imposed fugacity differences. We predict the coarse-grained (cage-level) density profiles and observe the development of nonlinearities as the magnitude of the fugacity difference is increased. From the net flux of methane we also predict a mean permeability coefficient under the various conditions. The simulation results are obtained over time scales on the order of microseconds and length scales on the order of dozens of nanometers.     

Lennard-Jones团簇最低能量构型的预测

针对Lennard-Jones(LJ)团簇的结构优化问题,在前人工作的基础上,提出了一个新的无偏优化算法,即DLS-TPIO(dynamic lattice searching method with two-phase local searchand interior operation)算法.对LJ2-650,LJ660,LJ665-680这666个实例进行了优化计算.为其中每个实例所找到的构型其势能均达到了剑桥团簇数据库中公布的最好记录.对LJ533与LJ536这两个算例,所达到的势能则优于先前的最好记录.在DLS-TPIO算法中,采用了内部操作,两阶段局部搜索方法以及动态格点搜索方法.在优化的前一阶段,内部操作将若干能量较高的表面原子移入团簇的内部,从而降低团簇的能量,并使其构型逐渐地变为有序.与此同时,两阶段局部搜索方法指导搜索进入更有希望的构型区域.这种做法显著地提高了算法的成功率.在优化的后一阶段,借用动态格点搜索方法对团簇表面原子的位置作进一步优化,以再一次降低团簇的能量.另外,为识别二十面体构型的中心原子,本文给出了一个简单的新方法.相比于文献中一些著名的无偏优化算法,DLS-TPIO算法具...     

Relaxation of flexible chains in dilute and non‐dilute systems. Dynamic Monte Carlo results for linear and star chains

A dynamic Monte Carlo algorithm is employed to investigate the dynamics of flexible linear and star chains on a cubic lattice at different concentrations. Some results for similar systems are also obtained with an off‐lattice algorithm. Diffusion coefficient, relaxation times and mean size data are combined into friction‐independent ratios in good agreement with the theoretical predictions from the Rouse theory. The relaxation times and amplitudes corresponding to the Rouse normal modes are analyzed in terms of their variation with the mode order. The end‐to‐end vector correlation times obtained from the simulations for linear chains are compared with the theoretical expression obtained from the Rouse theory. Deviations from this theory are observed for the contribution of the different modes in the non‐dilute systems. Finally, the time correlation function corresponding to a subchain's end‐to‐end vector is investigated. The results also show deviations from the Rouse theory, which are in qualitative agreement with the features observed in data from dielectric relaxation experiments of block copolymers.     

Search strategies in structural bioinformatics

Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.     

Structure,spectroscopy and electronic properties of neutral lattice-like (MgO) n clusters: a study based on a blending of DFT with stochastic algorithms inspired by natural processes

In this article, we explore the feasibility of using stochastic optimization techniques, which are inspired by natural processes, namely simulated annealing (SA) and genetic algorithm (GA) in association with DFT, to find out the global minimum structures of (MgO) _n clusters with n being in the range of 2–15. To check whether the structures are indeed the correct ones, we proceed to do several property calculations like IR-spectroscopic modes, vertical excitation energy, cluster-formation energy, vertical ionization potential, the HOMO–LUMO gap as well as polarizability and hyperpolarizability—both static and dynamic. We emphasize on the point that an initial determination of structure using SA/GA leads to very quick relaxation to structures which are very close to the structures predicted from quantum chemical calculations done from the outsets like DFT. The general pattern of these systems to form beautiful three-dimensional lattice networks is also evident from our study.     

The simulation of the three-dimensional lattice hydrophobic-polar protein folding

One of the most prominent problems in computational biology is to predict the natural conformation of a protein from its amino acid sequence. This paper focuses on the three-dimensional hydrophobic-polar (HP) lattice model of this problem. The modified elastic net (EN) algorithm is applied to solve this nonlinear programming hard problem. The lattice partition strategy and two local search methods (LS(1) and LS(2)) are proposed to improve the performance of the modified EN algorithm. The computation and analysis of 12 HP standard benchmark instances are also involved in this paper. The results indicate that the hybrid of modified EN algorithm, lattice partition strategy, and local search methods has a greater tendency to form a globular state than genetic algorithm does. The results of noncompact model are more natural in comparison with that of compact model.     

Static and dynamic structures of spherical nonionic surfactant micelles during the disorder-order transition

We have investigated the static and dynamic structures of nonionic surfactant micelles, a C(12)E(8)/water binary system, during the disorder-order transition using small angle x-ray scattering, static light scattering, and dynamic light scattering techniques. In the disordered phase, the micelles have spherical shape and intermicellar interactions are governed by the hard core and weak long ranged attractive potentials. With increase of the micellar concentration, the disordered micelles transform to the three characteristic ordered micellar phases, a hexagonally close packed lattice, a body centered cubic lattice, and an A15 lattice having area-minimizing structure. The stability of these phases is well explained by balance of a close packing rule and a minimal-area rule proposed by Ziherl and Kamien [Phys. Rev. Lett. 85, 3528 (2000)]. The role of hydrodynamic interactions in surfactant micellar solutions was compared with that in hard sphere colloidal particle suspensions.     

Influence of lattice dynamics on charge transport in the dianthra[2,3-b:2',3'-f]-thieno[3,2-b]thiophene organic crystals from a theoretical study

The influence of lattice dynamics on carrier mobility has received much attention in organic crystalline semiconductors, because the molecular components are held together by weak interactions and the transfer integrals between neighboring molecular orbitals are extremely sensitive to small nuclear displacements. Recently, it has been shown that the dynamic disorder has little effect on hole mobility in the ab plane of pentacene, but a reasonable explanation is absent for such a puzzle. To better understand the effect of lattice vibrations on carrier transport, a further study is required for other organic materials. In this work, a mixed molecular dynamic and quantum-chemical methodology is used to assess the effect of nuclear dynamics on hole mobility in the dianthra[2,3-b:2',3'-f]-thieno[3,2-b]thiophene (DATT) crystals which exhibit high air stability with the hole mobility as large as that in rubrene-based devices. It is found that the lattice vibrations lead to an increasing encumbrance for hole transport in the ab plane of the DATT crystals as the temperature increases. By comparing the crystal structures of DATT and pentacene, the reduced hole mobility in DATT is attributed to the unsymmetric arrays of nearest-neighboring molecular dimers in the ab plane, because the electronic coupling exhibits unbalanced thermal fluctuations for the nearest-neighboring dimers which then induces a stronger oscillation for carriers along the directions with asymmetric packing. To further relate the dynamic disorder with hole transport, the variations of anisotropic mobilities are also analyzed. As a result, the negligible effect of lattice dynamics on the hole mobility in pentacene is explained by the centrosymmetric molecular packing of the nearest-neighboring molecular pairs in the ab plane.     

Monte Carlo simulations of star‐branched polymers in a network of obstacles

A simple model of branched polymers in space confined between two parallel plates is developed. Star‐branched polymer molecules are built on a simple cubic lattice with excluded volume and no attractive interactions. A single star molecule is immersed in a network of irregularly dispersed linear rod‐like obstacles. The classical Monte Carlo Metropolis sampling algorithm is employed in the simulation. The aim of this study is to determine the effects of changes in dynamic properties of the star‐branched polymer as functions of the length of the molecule and the concentration of obstacles. Also the mechanism of motion of the polymer is discussed.     

On the construction of self-avoiding chains

In this article an algorithm to generate self-avoiding chains fitting a predefined lattice is described. The lattice has to fulfill some mild conditions but can be one, two, or many dimensional. The chains are random in the sense that they are calculated in such a way that every chain fitting the lattice has the same chance to be constructed.     

Tilting operator for phospholipidic molecular domains at the liquid–gas interface

We derive a coordinate independent operator expression for the tilting operator of molecular domains at the liquid–gas interface. The domains are made up of phospholipidic molecules modeled as spherocylinders. The molecules of the domain are oriented parallel to each other. The centers of symmetry of the molecules form a lattice. The tilting operator keeps track of the deformations suffered by this lattice as the domain molecules are tilted relative to the normal to the interface. The results obtained are important for dynamic calculations of inclination dependent collective film characteristics, as in the simulation of surface density versus surface pressure curves in a Langmuir film. The tilting operation can be decomposed into three separate simple operations: a global rotation, a local oblique realignment, and a global vertical translation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Improving the Wang-Landau algorithm for polymers and proteins

The 1/t Wang-Landau algorithm is tested on simple models of polymers and proteins. It is found that this method resolves the problem of the saturation of the error present in the original algorithm for lattice polymers. However, for lattice proteins, which have a rough energy landscape with an unknown energy minimum, it is found that the density of states does not converge in all runs. A new variant of the Wang-Landau algorithm that appears to solve this problem is described and tested. In the new variant, the optimum modification factor is calculated in the same straightforward way throughout the simulation. There is only one free parameter for which a value of unity appears to give near optimal convergence for all run lengths for lattice homopolymers when pull moves are used. For lattice proteins, a much smaller value of the parameter is needed to ensure rapid convergence of the density of states for energies discovered late in the simulation, which unfortunately results in poor convergence early on in the run.     

Magnetic field induced assembly of highly ordered two-dimensional particle arrays

Suspended magnetic beads are exposed to an external homogeneous magnetic field which rotates around the axis perpendicular to the field direction. Because of dipolar interactions, magnetic beads assemble in highly ordered two-dimensional hexagonal arrays perpendicular to the rotation axis. By continuous provision of the particle concentration, the growth modes of two-dimensional particle clusters and monolayers are observed. The structure of the resulting assembled objects is analyzed for different field frequencies and particle concentrations. We identify dynamic processes which enhance stability and reduce lattice distortions and, thus, allow for the application of these particle agglomerations as dynamic components in lab-on-a-chip technologies.