Monte Carlo liquid water simulation with four-body interactions included

A four-body interaction potential for water molecules is derived. The new terms are combined with previously developed two- and three-body potential terms and applied in a Metropolis—Monte Carlo simulation at 298 K for an (N, V, T) ensemble with 512 water molecules. Improvements, relative to the results using only two-body, or two- and three-body interactions, are reported for the correlation function g(OO), for the X-ray and neutron-beam scattering intensities, and for the enthalpy.     

Plastic and glassy crystalline states of methane: A Monte Carlo simulation study

A Monte Carlo simulation study has been carried out on the glassy crystalline phases of methane obtained by annealing or quenching the plastic (orientationally disordered) phase. Different cooling rates lead to different states of the glass. Temperature variation of the reorientational parameter suggests the presence of a transition between the plastic and glassy crystalline phases.     

Monte Carlo simulation of liquid hydroxylamine using ab initio intermolecular potential functions

A potential model for intermolecular interactions between hydroxylamine (NH₂OH) molecules based on ab initio quantum mechanical calculations is reviewed and critically assessed by analyzing results from a Monte Carlo simulation of liquid hydroxylamine. The liquid structure is studied in detail using radial, energy, and angular distribution functions, coordination numbers, and their distribution. Results indicate a large first solvation shell (5.3 Å), which contains 13 molecules, out of which only 4 are truly bonded by nonlinear, low-energy hydrogen bonds. These are of either the OH…O or the OH…N type, as NH…O and NH…N linear bonds are considerably suppressed, and no cyclic dimers are found. The dependence of the structural and physical properties on the simulation characteristics has also been investigated.     

Reverse Monte Carlo and Voronoi-Delaunay simulation and structure analysis for liquid metals

This paper discusses the applicability of the integrated reverse Monte Carlo and Voronoi-Delaunay approach to local structure analysis and medium-scale structure determination of liquid metals. The advantages of this approach are shown: generation of 3D structural models using experimental diffraction data and subsequent structure determination by atomic coordinate analysis.Original Russian Text Copyright © 2004 by A. S. Roik, V. P. Kazimirov, and V. E. SokolskiiTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 683–691, July–August, 2004.This revised version was published online in April 2005 with a corrected cover date.     

Monte Carlo simulation of DNA electrophoresis

This paper describes an attempt to study the electrophoresis mobility of a DNA molecule in a gel by means of a Monte Carlo simulation. We find that the electrophoresis mobility mu can be well described by the empirical equation mu v kappa 1/N + kappa 2E2 with N being the number of monomers of the model chain and E being the applied field. For small E the data can merge into the linear response result mu = kappa 1/N. The paper also discusses necessary extensions of the present approach.     

Monte Carlo simulation of polymer welding

Monte Carlo Modelling of random polymer chains, course grained onto a cubic F lattice, provides the ability to monitor the long range relaxation processes and the dynamic parameters of chains up to 400 units long. The model, described and verified by Haire et al. (Haire KR, Carver TJ, Windle AH. A Monte Carlo model for dense polymer systems and its interlocking with molecular dynamics simulation. Computational and Theoretical Polymer Science 2000; in press), is here applied to the study of molecular parameters in the vicinity of different types of surface and also to the process of polymer welding, whereby adhesion between two adjacent surfaces is achieved by the interpenetration of chains which are across the surface.The model demonstrates that a surface distorts the conformation of chains adjacent to it to give an oblate molecular envelope, that the concentration of vacant sites and chain ends increases near to the surface and that the density of points representing the centres of mass of the chains increases in the sub-surface regions. These results confirm earlier predictions and provide additional confidence in the model.Modelling of the welding process leads to the parameter intrinsic weld time, t_w, which is the time from initial perfect contact of the surfaces to the achievement of a weld within which the chain conformation is indistinguishable from the bulk. After the initial period in which the mating surfaces roughen, the welding proceeds according to the t^1/4 law predicted by reptation theory. The time to a given level of interdiffusion across the boundary is proportional to the chain length l, a comparatively weak dependence, while t_w is proportional to l³, a strong dependence. This is the same dependence on length as for the relaxation time of the chain end-to-end vectors. In fact, the agreement between the relaxation time, measured on the model of the bulk, and t_w is surprisingly close, at least for the monodisperse polymers investigated here.     

Monte Carlo simulation of polymer adsorption

We developed and employed the incremental gauge cell method to calculate the chemical potential (and thus free energies) of long, flexible homopolymer chains of Lennard-Jones beads with harmonic bonds. The free energy of these chains was calculated with respect to three external conditions: in the zero-density bulk limit, confined in a spherical pore with hard walls, and confined in a spherical pore with attractive pores, the latter case being an analog of adsorption. Using the incremental gauge cell method, we calculated the incremental chemical potential of free polymer chains before and after the globual-random coil transitions. We also found that chains confined in attractive pores exhibit behaviors typical of low temperature physisorption isotherms, such as layering followed by capillary condensation.     

Monte Carlo simulation of osmotic equilibria

We present a Metropolis Monte Carlo simulation algorithm for the Tpπ-ensemble, where T is the temperature, p is the overall external pressure, and π is the osmotic pressure across the membrane. The algorithm, which can be applied to small molecules or sorption of small molecules in polymer networks, is tested for the case of Lennard-Jones interactions.     

Order-parameter-based Monte Carlo simulation of crystallization

A Monte Carlo simulation method is presented for simulation of phase transitions, with emphasis on the study of crystallization. The method relies on a random walk in order parameter Phi(q(N)) space to calculate a free energy profile between the two coexisting phases. The energy and volume data generated over the course of the simulation are subsequently reweighed to identify the precise conditions for phase coexistence. The usefulness of the method is demonstrated in the context of crystallization of a purely repulsive Lennard-Jones system. A systematic analysis of precritical and critical nuclei as a function of supercooling reveals a gradual change from a bcc to a fcc structure inside the crystalline nucleus as it grows at large degrees of supercooling. The method is generally applicable and is expected to find applications in systems for which two or more coexisting phases can be distinguished through one or more order parameters.     

Monte Carlo simulation of hard spheroids

We present Monte Carlo simulations of the equation of state and radial distribution function for a model fluid composed of hard spheroids.     

Monte Carlo simulation of block copolymers

Monte Carlo simulations deal with crudely simplified but well-defined models and have the advantage that they treat the statistical thermodynamics of the considered model exactly (apart from statistical errors and problems due to finite size effects). Therefore, these simulations are well suited to test various approximate theories of block copolymer ordering, e.g. the self-consistent field theory. Recent examples of this approach include the study of block copolymer ordering at melt surfaces and confinement effects in thin films, adsorption of block copolymers at interfaces of unmixed homopolymer blends, the phase behavior of ternary mixtures of two homopolymers and their block copolymer, and micelle formation in selective solvents.     

Collective-variable Monte Carlo simulation of DNA

Monte Carlo simulations have been carried out on DNA oligomers using an internal coordinate model associated with a pseudorotational representation of sugar repuckering. It is shown that when this model is combined with the scaled collective variable approach of Noguti and Go, much more efficient simulations are obtained than with simple single variable steps. Application of this method to a DNA oligomer containing a recognition site for the TATA-box binding protein leads to striking similarities with results recently obtained from a 1-ns molecular dynamics simulation using explicit solvent and counterions. In particular, large amplitude bending fluctuations are observed directed toward the major groove. Conformational analysis of the Monte Carlo simulation shows clear base sequence effects on conformational fluctuations and also that the DNA energy hypersurface, like that of proteins, is complex with many local, conformational substates. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2001–2011, 1997     

Monte Carlo simulation of liquid Br2: Test of an effective hamiltoniain

Monte Carlo simulations for the structure of a fluid of molecules interacting with a pair potential having one Lennard- Jones center plus a quadrupole interaction is reported. The numerical experiments are compared with an approximation method previously suggested and with experimental results for the liquid Br₂ structure. This effective pair potential turns out to be unable to reproduce the Br₂ structure while the approximation method is only useful for quadrupole moments less than 1.2 × 10^?40 C m².     

Model liquid crystalline dimers in a slit pore: Monte Carlo simulation study

ABSTRACT

In this work, we present results from (isobaric–isothermal) Monte Carlo Simulation studies of liquid crystalline dimer systems confined in a slit pore. Liquid crystalline dimer systems of various spacer numbers have been considered. Surface-induced conformational and alignment properties of these systems at different pressures under homeotropic anchoring condition have been investigated. We have used easily manageable coarse grained force fields to model both monomer–monomer and monomer–substrate interaction potentials. According to the simulated result, the anchoring of dimers to the surface and orientation of mesogenic units with respect to the surface normal seem to depend on the spacer number for messogen attractive confinement. Dimers with lower spacer number are able be adsorbed to the surface and most of their mesogens are oriented along the surface normal even at lower pressure. Those with larger spacer number are distributed throughout the volume at lower pressure. In the case of mesogen repulsive confinement, most of the dimers are adsorbed to the surface and most mesogens are randomly oriented at low pressure. As the pressure gets higher, the adsorption and orientability increase depending on the type of confinement and spacer number. As a result, clear submolecular partitioning and smectic A like structure have been identified.     

A Monte Carlo study of liquid benzene

A Monte Carlo study for liquid benzene, where the pair potential is described as a sum of Lennard-Jones (12, 6) interactions acting between six equivalent centres of each molecule, has been carried out. The potential parameters have been chosen in such a way that the internal energy and virial pressure were in agreement with the experimental values. The liquid structure has been examined in detail by computing several distribution functions: the radial, the angular correlations and the radial-angular distribution between molecular planes.     

Monte Carlo simulation of catalytic CO oxidation

A simple Monte Carlo model of the CO oxidation on a single-crystal catalyst surface is presented. The simulation model considers the following elementary reaction steps:

1. (1) chemisorption of a CO molecule, its surface migration and possible desorption

2. (2) physisorption of an O₂ molecule to a precursor state and its subsequent dissociative chemisorption

3. (3) activated reaction of adsorbed O and CO (the Langmuir - Hinshelwood reaction mechanism), formation of CO₂ and its rapid desorption.

The changes in the activation energy of reaction and in the adsorption energy of CO resulting from the interactions between adsorbed species are also considered. The model makes possible to monitor temperature programmed reaction spectra or reaction spectra obtained during changes of the ratio of the partial pressures of CO and O₂. The results of simulations for a Pd(111) single-crystal plane are compared with experiment.     

Monte Carlo simulation studies of polymer systems

Polymers molecules in solution or melt are more or less flexible and continuously change their shape and size. Thus, characteristic properties of the system fluctuate around statistical mean values which are dependent on the concentration of the solution, on the quality of the solvent used, and on the specific structure of the molecules, e.g. linear or star-branched. The most direct approach to these quantities on a molecular level are computer simulations. Due to restrictions of computer power fully atomistic simulations of macromolecules are presently still at the beginning but several arguments justify the use of simplified models. The most efficient way dealing with polymer systems are Monte Carlo simulations based on lattice chains, at least as long as static properties are of interest only. In the present paper a short introduction to the field is given and selected examples are presented in order to demonstrate the usefulness of these methods.     

Monte Carlo simulation of pulsed laser polymerization

Pulsed laser polymerization (PLP) has been simulated using a Monte Carlo procedure. From the results of numerous simulations it has been shown that the molecular weight distribution (MWD) consists primarily of two superimposed distributions. One distribution, a relatively broad background, represents the termination reactions during the dark period; the other, a rather sharply peaked distribution, represents the termination reactions occurring as a consequence of the large number of small radicals produced during the laser pulse. The postulate that the inflection point on the sharp peak can be used to calculate that the propagation rate constant was tested and found to be accurate to within 3%. The relative position of the broad and sharp distributions on the chain length scale determines the qualitative appearance of the overall MWD and is in turn governed by the rate of photoinitiation and the relative values of termination and propagation rate constants. This explains the qualitatively different shapes of MWD which have been experimentally observed. Finally, it is shown that the occurrence of chain length dependent termination reactions precludes the use of an analytical expression to deduce quantitative or qualitative information about the termination reaction from PLP data.     

Monte Carlo simulation study of droplet nucleation

A new rigorous Monte Carlo simulation approach is employed to study nucleation barriers for droplets in Lennard-Jones fluid. Using the gauge cell method we generate the excess isotherm of critical clusters in the size range from two to six molecular diameters. The ghost field method is employed to compute the cluster free energy and the nucleation barrier with desired precision of (1-2)kT. Based on quantitative results obtained by Monte Carlo simulations, we access the limits of applicability of the capillarity approximation of the classical nucleation theory and the Tolman equation. We show that the capillarity approximation corrected for vapor nonideality and liquid compressibility provides a reasonable assessment for the size of critical clusters in Lennard-Jones fluid; however, its accuracy is not sufficient to predict the nucleation barriers for making practical estimates of the rate of nucleation. The established dependence of the droplet surface tension on the droplet size cannot be approximated by the Tolman equation for small droplets of radius less than four molecular diameters. We confirm the conclusion of ten Wolde and Frenkel [J. Chem. Phys. 109, 9901 (1998)] that integration of the normal component of the Irving-Kirkwood pressure tensor severely underestimates the nucleation barriers for small clusters.