Prediction of sound velocity and compressibility via molecular simulation at fixed entropy

A molecular-level simulation route is proposed to compute the isentropic thermodynamic properties in a fluid system by Monte Carlo simulation at fixed entropy. The method involves computation of the pressure response of a system to an infinitesimal change in system density by introduction of a single molecule, while retaining the system volume as well as the absolute molar entropy. The probability for accepting a change in temperature during the Monte Carlo moves was weighted against the argument proposed by Smith et al. [W.R. Smith, M. Lísal, I. Nezbeda, Chem. Phys. Lett. 426 (2006) 436–440]. Application to fluid argon has confirmed superior accuracy for the technique within the gas state to yield results within 1.2% of the measured values for the range of thermodynamic conditions investigated.     

MCDOCK: A Monte Carlo simulation approach to the molecular docking problem

Prediction of the binding mode of a ligand (a drug molecule) to its macromolecular receptor, or molecular docking, is an important problem in rational drug design. We have developed a new docking method in which a non-conventional Monte Carlo (MC) simulation technique is employed. A computer program, MCDOCK, was developed to carry out the molecular docking operation automatically. The current version of the MCDOCK program (version 1.0) allows for the full flexibility of ligands in the docking calculations. The scoring function used in MCDOCK is the sum of the interaction energy between the ligand and its receptor, and the conformational energy of the ligand. To validate the MCDOCK method, 19 small ligands, the binding modes of which had been determined experimentally using X-ray diffraction, were docked into their receptor binding sites. To produce statistically significant results, 20 MCDOCK runs were performed for each protein–ligand complex. It was found that a significant percentage of these MCDOCK runs converge to the experimentally observed binding mode. The root-mean-square (rms) of all non-hydrogen atoms of the ligand between the predicted and experimental binding modes ranges from 0.25 to 1.84 Å for these 19 cases. The computational time for each run on an SGI Indigo2/R10000 varies from less than 1 min to 15 min, depending upon the size and the flexibility of the ligands. Thus MCDOCK may be used to predict the precise binding mode of ligands in lead optimization and to discover novel lead compounds through structure-based database searching.     

Algorithm and application of Monte Carlo simulation for multi-dispersive copolymerization system

A Monte Carlo algorithm has been established for multi-dispersive copolymerization system, based on the experimental data of copolymer molecular weight and dispersion via GPC measurement. The program simulates the insertion of every monomer unit and records the structure and microscopical sequence of every chain in various lengths. It has been applied successfully for the ring-opening copolymerization of 2,2-dimethyltrimethylene carbonate (DTC) with δ-caprolactone (δ-CL). The simulation coincides with the experimental results and provides microscopical data of triad fractions, lengths of homopolymer segments, etc., which are difficult to obtain by experiments. The algorithm presents also a uniform frame for copolymerization studies under other complicated mechanisms.     

Monte Carlo simulation of polarizable systems: Early rejection scheme for improving the performance of adiabatic nuclear and electronic sampling Monte Carlo simulations

An early rejection scheme for trial moves in adiabatic nuclear and electronic sampling Monte Carlo simulation (ANES-MC) of polarizable intermolecular potential models is presented. The proposed algorithm is based on Swendsen–Wang filter functions for prediction of success or failure of trial moves in Monte Carlo simulations. The goal was to reduce the amount of calculations involved in ANES-MC electronic moves, by foreseeing the success of an attempt before making those moves. The new method was employed in Gibbs ensemble Monte Carlo (GEMC) simulations of the polarizable simple point charge-fluctuating charge (SPC-FQ) model of water. The overall improvement in GEMC depends on the number of swap attempts (transfer molecules between phases) in one Monte Carlo cycle. The proposed method allows this number to increase, enhancing the chemical potential equalization. For a system with 300 SPC-FQ water molecules, for example, the fractions of early rejected transfers were about 0.9998 and 0.9994 at 373 and 423 K, respectively. This means that the transfer moves consume only a very small part of the overall computing effort, making GEMC almost equivalent to a simulation in the canonical ensemble.     

Positron backscattering from an Al target: analytical calculation and Monte Carlo simulation

Positron backscattering coefficients are analytically calculated and numerically simulated for an Al target in the positron energy range 0.50–4 keV and for incident angles between 0° and 80° . The differential elastic scattering cross section has been obtained using the Bentabet and Bouarissa approximation (Phys. Lett. 2006; A 355: 390). Both the analytical and simulated results show good agreement with the experiment and previous theoretical work. Copyright © 2007 John Wiley & Sons, Ltd.     

Monte Carlo simulation on layered polymeric films

Thin films of polymer blends composed of alternating copolymer, diblock copolymer and/or homopolymer are studied using Monte Carlo simulation. A multilayer morphology is observed in the film, that is, the blended polymers assemble into individual domains arranged from interior to the surfaces of the film. The coexisting components residing throughout the neighboring domains in the film make no distinguishable interface between any neighboring domains. By this means, it forms a vertical composition gradient in the polymeric film. Being different from layer-by-layer deposition of polyelectrolyte or hydrogen bonding approach etc., the layered structure in this study is formed by polymer blending in one step. Alternating copolymers are found to be essential components to form vertical composition gradient （layered structure） in thin films.     

A Monte Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z form

Summary Monte Carlo computer simulation is described for the hexamer d(CGCGCG) in the Z form together with 910 water molecules at an environmental density of 1 gm/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the non-bonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordination numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove, the minor groove, and the sugar-phosphate backbone were examined, and the probabilities of occurrence for one- and two-water bridges in the simulation were enumerated. The results are compared with observations of crystallographic ordered water sites from the X-ray diffraction studies.     

Monte Carlo simulation of the structure of mono- and bidisperse polyethylene nanocomposites

The structure of bidisperse polyethylene(PE) nanocomposite mixtures of 50:50(by mole) of long and short chains of C160H322/C80H162 and C160H322/C40H82 filled with spherical nanoparticles were investigated by a coarse-grained, on lattice Monte Carlo method using rotational isomeric state theory for short-range and Lennard-Jones for long-range energetic interactions. Simulations were performed to evaluate the effect of wall-to-wall distance between fillers(D), polymer-filler interaction(w) and polydispersity(number of short chains in the mixture) on the behavior of the long PE chains. The results indicate that long chain conformation statistics remain Gaussian regardless of the effects of confinement, interaction strength and polydispersity. The various long PE subchain structures(bridges, dangling ends, trains, and loops) are influenced strongly by confinement whereas monomer-filler interaction and polydispersity did not have any impact. In addition, the average number of subchain segments per filler in bidisperse PE nanocomposites decreased by about 50% compared to the nanocomposite system with monodisperse PE chains. The presence of short PE chains in the polymer matrix leads to a reduction of the repeat unit density of long PE chains at the interface suggesting that the interface is preferentially populated by short chains.     

Protection of nano-powders by adsorbed surfactants: A Monte Carlo study

The production of high-performance ceramics requires the protection of powder particles against chemical reactions. Hydrolysis and oxidation of nanoscaled non-oxidic powders can be impeded by a coating consisting of a dense adsorbed layer of amphiphilic molecules. Using Monte Carlo simulations for a coarse grained model the adsorption equilibrium of differently shaped amphiphiles in apolar and polar solvents is investigated. For estimating the protection capability of the adsorbed surfactant film in aqueous environment we study the diffusion of small hydrophilic particles through the adsorbed surfactant film. The surfactants considered as coating agents differ in the number of hydrocarbon tails. It is found that amphiphiles with a single hydrocarbon tail or at most two branches are more suitable to protect particle surfaces than amphiphiles with three or four branches, although the adsorption energy of amphiphiles with many branches is higher.     

Monte Carlo simulation of miscibility of polymer blends with repulsive interactions: effect of chain structure

The effects of the chain structure and the intramolecular interaction energy of an A/B copolymer on the miscibility of the binary blends of the copolymer and homopolymer C have been studied by means of a Monte Carlo simulation. In the system, the interactions between segments A, B and C are more repulsive than those between themselves. In order to study the effect of the chain structure of the A/B copolymer on the miscibility, the alternating, random and block copolymers were introduced in the simulations, respectively. The simulation results show that the miscibility of the binary blends strongly depends on the intramolecular interaction energy () between segments A and B within the A/B copolymers. The higher the repulsive interaction energy, the more miscible the A/B copolymer and homopolymer C are. For the diblock copolymer/homopolymer blends, they tend to form micro phase domains. However, the phase domains become so small that the blend can be considered as a homogeneous phase for the alternating copolymer/homopolymer blends. Furthermore, the investigation of the average end-to-end distance () in different systems indicates that the copolymer chains tend to coil with the decrease of whereas the of the homopolymer chains depends on the chain structure of the copolymers. As for the system containing the alternating or the random copolymers, the homopolymer chains also tend to coil with the decrease of . However, for the systems including the block copolymers, there is a slight difference in the of the homopolymer chains with the variation of .     

A comprehensive Monte Carlo simulation of styrene atom transfer radical polymerization

<正>An optimized and high-performance Monte Carlo simulation is developed to take thorough account of four different cases of termination in styrene ATRP.According to the simulation results,the bimolecular termination rate constant sharply drops throughout the polymerization when either chain-length dependency of termination rate constant,gel effect,or both together is applied to the simulation.In addition,as expected,the initiator is quickly decomposed at the early stages of the polymerization.The concentration of the catalyst in lower oxidation state decreases at first and then plateaus at higher conversion;furthermore,the steady concentration of M_t~nY/L in the polymerization is the highest when the chain-length-dependent diffusion-controlled termination rate constant is employed in the simulation.The rates of deactivation and chain end degradation reactions are also smaller in this case.Therefore,the fraction of dormant chains is higher throughout the reaction and consequently the portion of dead polymers decreases.Besides,molecular weight increases linearly with conversion;however,when neither gel effect nor chain-length dependency of termination rate constant is considered,the molecular weight deviates from linearity at the end of the reaction.The peak of chain length distribution shifts toward higher molecular weight too during the reaction.Finally,the molecular weight distribution broadens at higher conversion;however, the chain length distribution of polymers produced under conditions of applying chain-length-dependent diffusion-controlled termination rate constant is narrower.     

Monte Carlo方法在高分子科学中的应用

介绍了Monte Carlo方法的历史及其特点,并描述了它在现代高分子科学研究中的广泛应用情况,并对其前景作了一些展望。     

Cassandra: An open source Monte Carlo package for molecular simulation

Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc.     

Monte Carlo simulation of polymer analogous reaction in confined conditions: effects of ordering

The influence of energetic parameters of the interchain homo- and heterocontacts on a local ordering of Bernoullian copolymers has been studied using Monte Carlo simulations and probabilistic analysis. The results of both methods are in a good agreement. Then simple Monte Carlo procedure was employed to study the ordering in products of a polymeranalogous reaction with accelerating effect of neighboring groups. When the reaction with intra- and interchain acceleration and local ordering proceed simultaneously in confined conditions, the ordering might affect the process so that the formation of certain nano-structures (in particular, not trivial strip-like ones) is possible.     

Efficient implementation of periodic boundary conditions in Monte Carlo simulation

Determination of the shortest distances between particles is one of the most time-consuming parts of molecular simulation by the Monte Carlo method. In this work, we demonstrate that the use of signed-integer storage of coordinates in a scaled box allows one to skip multiple conditional statements in realization of periodic boundary conditions in cubic and rectangular boxes, which, in turn, increases the performance. Performance of the improved procedure was tested in NVT Monte Carlo simulations for liquid krypton and water. © 2018 Wiley Periodicals, Inc.     

Monte Carlo simulation of phase separation kinetics in a concentrated polymer solution

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Monte Carlo simulation of AB diblock copolymer between surface and substrate and comparison of experimental results

The morphologies of AB diblock copolymer film between the substrate and surface were investigated via Monte Carlo simulations on simple cubic lattices. The morphological dependence of the diblock copolymer thin film on the thickness, as well as the composition and interactive intensity has been mainly studied. With the increase of A‐segments fraction, various microdomain morphologies including regular parallel stripe‐like, mesh‐like, and normal lamella near the region of the surface were generated in this work. The morphology of thin films of asymmetric diblock copolymer was found to form cylinders in a bulk system when L_z was equal to 30. The morphologies of PS‐b‐PDMS diblock copolymer films have been studied via atomic force microscopy (AFM) and transition electron microscopy (TEM) measurements. The surface morphology of the PS‐b‐PDMS copolymer thin film shows a mesh‐like microphase separated structure, and PDMS continuous phase protruded on the PS dispersed phase. The surface composition of PS‐b‐PDMS copolymer thin films was measured by means of X‐ray photoelectron spectroscopy (XPS) and ATR‐IR. The comparison results show that the experimental observations are in good agreement with the simulation results. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1835–1845, 2006     

Grafting of maleic anhydride onto linear polyethylene: A Monte Carlo study

Monte Carlo simulation was used to study the graft of maleic anhydride (MAH) onto linear polyethylene (PE‐g‐MAH) initiated by dicumyl peroxide (DCP). Simulation results revealed that major MAH monomers attached onto PE chains as branched graft at higher MAH content. However, at extremely low MAH content, the fraction of bridged graft was very close to that of branched graft. This conclusion was somewhat different from the conventional viewpoint, namely, the fraction of bridged graft was always much lower than that of branched graft under any condition. Moreover, the results indicated that the grafting degree increased almost linearly to MAH and DCP concentrations. On the other hand, it was found that the amount of grafted MAH dropped sharply with increasing the length of grafted MAH, indicating that MAH monomers were mainly attached onto the PE chain as single MAH groups or very short oligomers. With respect to the crosslink of PE, the results showed that the fraction of PE‐(MAH)_n‐PE crosslink structure increased continuously, and hence the fraction of PE‐PE crosslink decreased with increasing MAH concentration. Finally, quantitative relationship among number average molecular weight of the PE, MAH, and DCP contents was given. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5714–5724, 2004     

Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study

In the spirit of Gillespie’s stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.