Succession of stacking disorder in hard-sphere crystal under gravity by Monte Carlo simulation

We have performed Monte Carlo simulations of hard spheres under gravity. Vertical boundaries are hard walls, which are well separated with each other. On the other hand, the periodic boundary condition is imposed in the horizontal direction. While we previously reported enhancement of crystallinity as well as crystallization due to gravity, we present here the results that demonstrate the succession of a defect. In case that the crystal formed at the bottom of the system includes kinds of stacking disorders for the (0 0 1) growth, twin band structure develops as mediated by a stacking disorder succeeded in the crystal formed in the fluid region which lies on the bottom crystal. In case that the stacking structure along horizontal direction changes from the (1 1 1) stacking to the (0 0 1) stacking, twin band structure in the (0 0 1) stacking region develops as succeeded in the crystal transformed. The twin band structure also becomes large with its upward growth.     

Solid-liquid phase coexistence of the Lennard-Jones system through phase-switch Monte Carlo simulation

The phase-switch Monte Carlo method of Wilding and Bruce [Phys. Rev. Lett. 85, 5138 (2000)] is extended to enable calculation of solid-liquid phase coexistence for soft potentials. The method directly accesses coexistence information about a system while avoiding simulation of the interfacial region. Order parameters are introduced that allow one to define a path that connects liquid and crystalline phases. Transition matrix methods are employed to bias the sampling such that both phases are sampled in a rapid and efficient manner. Coexistence properties are determined through an analysis of specific volume probability distributions, which are generated naturally during a biased simulation. The approach is demonstrated with the Lennard-Jones system. Finite-size effects are examined and compared to those for the hard sphere system. In addition, two techniques are considered for accounting for long-range interactions. The methodology presented here is general and therefore provides a basis for its application to other soft systems.     

Confinement effect in diffusion-controlled stepwise polymerization by Monte Carlo simulation

Diffusion-controlled stepwise polymerization of a linear polymer confined in nanoscopic slits is simulated through a Monte Carlo approach. A noticeable influence of the confinement on the kinetics is found. The confinement modifies both the spatial pair distribution function and the diffusive properties of the polymers. As a consequence, the confined system can show either faster or slower reaction kinetics with respect to the bulk system, depending on the strength of intermolecular interactions. The predicted polydispersity of the polymer is in agreement with recent theories of diffusion-controlled stepwise polymerization, and can be slightly affected by the confinement.     

Rydberg states with quantum Monte Carlo

Calculations on Rydberg states are performed using quantum Monte Carlo methods. Excitation energies and singlet-triplet splittings are calculated for two model systems, the carbon atom (3P and 1P) and carbon monoxide ((1Sigma and 3Sigma). Kohn-Sham wave functions constructed from open-shell localized Hartree-Fock orbitals are used as trial and guide functions. The fixed-node diffusion quantum Monte Carlo (FN-DMC) method depends strongly on the wave function's nodal hypersurface. Nodal artefacts are investigated for the ground state of the carbon atom. Their effect on the FN-DMC results can be analyzed quantitatively. FN-DMC leads to accurate excitation energies but to less accurate singlet-triplet splittings. Variational Monte Carlo calculations are able to reproduce the experimental results for both the excitation energies and the singlet-triplet splittings.     

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 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 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.     

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.     

Phase coexistence in heterogeneous porous media: a new extension to Gibbs ensemble Monte Carlo simulation method

The effect of confinement on phase behavior of simple fluids is still an area of intensive research. In between experiment and theory, molecular simulation is a powerful tool to study the effect of confinement in realistic porous materials, containing some disorder. Previous simulation works aiming at establishing the phase diagram of a confined Lennard-Jones-type fluid, concentrated on simple pore geometries (slits or cylinders). The development of the Gibbs ensemble Monte Carlo technique by Panagiotopoulos [Mol. Phys. 61, 813 (1987)], greatly favored the study of such simple geometries for two reasons. First, the technique is very efficient to calculate the phase diagram, since each run (at a given temperature) converges directly to an equilibrium between a gaslike and a liquidlike phase. Second, due to volume exchange procedure between the two phases, at least one invariant direction of space is required for applicability of this method, which is the case for slits or cylinders. Generally, the introduction of some disorder in such simple pores breaks the initial invariance in one of the space directions and prevents to work in the Gibbs ensemble. The simulation techniques for such disordered systems are numerous (grand canonical Monte Carlo, molecular dynamics, histogram reweighting, N-P-T+test method, Gibbs-Duhem integration procedure, etc.). However, the Gibbs ensemble technique, which gives directly the coexistence between phases, was never generalized to such systems. In this work, we focus on two weakly disordered pores for which a modified Gibbs ensemble Monte Carlo technique can be applied. One of the pores is geometrically undulated, whereas the second is cylindrical but presents a chemical variation which gives rise to a modulation of the wall potential. In the first case almost no change in the phase diagram is observed, whereas in the second strong modifications are reported.     

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     

Modified Monte Carlo simulation of adsorption in a spatially inhomogeneous porous system

A modified Monte Carlo method in conjunction with the canonical and grand canonical ensembles is proposed for simulating adsorption in spatially inhomogeneous porous systems. Unlike the traditional Monte Carlo simulation in terms of the grand canonical ensemble, the simulation for the regions of pore space having no direct communication with the bulk phase is performed in local conditions of the canonical ensemble.     

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 cavitation in pores with nonwetting defects

We investigate the onset of cavitation in a metastable fluid confined to nanoscale pores with nonwetting defects present. Using grand canonical and gauge cell mesocanonical Monte Carlo simulations, we study the degree of metastability (relative vapor pressure), at which the critical bubble forms in a spherical pore with a circular nonwetting defect. It is shown that an increase of the defect size leads to a transition from homogeneous to heterogeneous nucleation of critical bubbles formed at the defect site. In this case, the desorption process may be initiated at larger relative vapor pressures than those predicted by the theories of homogeneous cavitation.     

Monte Carlo simulation of PGNAA system for determining element content in the rock sample

The element content in rock sample can be determined by prompt gamma ray activation analysis technology. The neutron distributions under the conditions with different moderating materials, moderator size and distance from neutron source to lead-out hole were simulated using Monte Carlo method, and then the optimal structure parameters to get the highest thermal neutron flux was obtained. The PGNAA system with optimal parameters based on ²⁵²Cf neutron source was founded. In addition, the rock and element standard samples were irradiated by thermal neutron in this system. Moreover, the element content was calculated by processing gamma ray spectroscopy recorded, and it is in agreement with result of XRF method.