Atomistic Monte Carlo method

When chromophores are covalently coupled in super/supramolecular objects (such as multichromo-phore-containing dendrimers), Monte Carlo-molecular dynamic calculations must be modified to take into account the restrictions on motion associated with covalent bond potentials. To accurately account for covalent bond potentials, atomistic Monte Carlo methods are required [68]. However because of the large number of atoms involved, fiilly atomistic calculations would be prohibitively time-consuming... 

In addition to the MD method, a wealth of Monte Carlo methods is used also at the atomistic level [6]. They use essentially the same models, force fields, for polymers. Their main advantage, however, is that by introduction of clever moves one can beat the slow physical dynamics of the systems and can run through phase space much faster than by MD. These methods are still in their infancy, but will certainly become more important. 

Method for the Atomistic Monte Carlo Simulation of Polydisperse Polymer Melts. 

Directed Bridging Methods for Fast Atomistic Monte Carlo Simulations of Bulk Polymers. 

Lyubartsev has also developed a multiscale parameterisation method that has been used to systematically build a CG model of a DMPC bilayer. Lyubartsev uses an inverse Monte Carlo method to generate the CG parameters from an underlying atomistic simulation. The atomistic simulation trajectory is analysed to generate the radial distribution functions (RDFs) for the CG bead model. These RDFs can be converted into pairwise interaction potentials between the beads. The... 

Robinson and Dalton use Monte Carlo statistical mechanics to explore concentration and shape dependencies of the chromophores. Monte Carlo methods provide valuable information about the distribution of a collection of chromophores but are not able to provide atomistic information about the systems. The Monte Carlo simulations performed by Robinson and Dalton employ an array of point dipoles on a periodic lattice with the given parameters for the shape of the chromophores and the chromophore spacing adjustable to achieve the desired chromophore concentration. The model system consisted of 1000 chromophores on a body-centered cubic... 

The best-known physically robust method for calculating the conformational properties of polymer chains is Rory s rotational isomeric state (RIS) theory. RIS has been applied to many polymers over several decades. See Honeycutt [12] for a concise recent review. However, there are technical difficulties preventing the routine and easy application of RIS in a reliable manner to polymers with complex repeat unit structures, and especially to polymers containing rings along the chain backbone. As techniques for the atomistic simulation of polymers have evolved, the calculation of conformational properties by atomistic simulations has become an attractive and increasingly feasible alternative. The RIS Metropolis Monte Carlo method of Honeycutt [13] (see Bicerano et al [14,15] for some applications) enables the direct estimation of Coo, lp and Rg via atomistic simulations. It also calculates a value for [r ] indirectly, as a "derived" property, in terms of the properties which it estimates directly. These calculated values are useful as semi-quantitative predictors of the actual [rj] of a polymer, subject to the limitation that they only take the effects of intrinsic chain stiffness into account but neglect the possible (and often relatively secondary) effects of the polymer-solvent interactions. 

Thermodynamic properties of a system can also be obtained from the atomistic considerations. Molecular dynamics or Monte Carlo methods have been successfully used to smdy polymers. The success stems from the fact that many properties can be projected from dynamics of relatively simple, oligomeric models. Unfortunately, miscibility strongly depends on the molecular weight and so far it cannot be examined by these methods. 

Modeling and simulation involves theoretical analysis of processing, characterization, and performance behavior using phenomenological, atomistic, molecular dynamics, and Monte Carlo methods, among others, and comparisons with experimental results. 

Science is in incessant evolution it grows with more precise theories and better instrumentation. The thermodynamic theories of polymers and polymeric systems move toward atomistic considerations for isomeric species modeled mathematically by molecular dynamics or Monte Carlo methods. At the same time good mean-field theories remain valid and useful—they must be remembered not only for the historical evolution of human knowledge, but also for the very practical reason of applicability, usefulness, and as tools for the understanding of material behavior. 

In order to fully account for finite surface mobilities and the heterogeneous surface structure, we have to employ a stochastic description of the surface processes. The kinetic Monte Carlo method enables the incorporation of structural details at an atomistic level. This method has been apphed successfully in the field of heterogeneous (electro-) catalysis [59 1,65] and is further discussed in the chapter by Phil Ross in this book. In the model, hexagonal grids represent catalyst particles. The active sites are randomly distributed on the grid. Adsorbates are considered to bind to on-top sites. The first reaction method was used [66,67]. 

Pant, P. V. K., and Theodorou, D. N., 1995. Variable connectivity method for the atomistic Monte Carlo simulation of polydisperse polymer melts. Macromolecules, 28(21) 7224-7234. 

Uhlherr, A., Leak, S. J., Adam, N. E., Nybei, P. E., Doxastakis, M., Mayrantzas, V. G., and Theodorou, D. N., 2002. Large scale atomistic polymer simulations using Monte Carlo methods for parallel vector processors, Comput. Phys. Commun., 144(l) l-22. 

Dimers of series I have been simulated using the methods and parameters described for the trimers, except for the conformational terms. Distributions of r and ip appropriate to confer on the simulated dimers conformational characteristics similar to those of dimers of series I with n = 6 and n = 7 have been obtadned by analyzing the results of atomistic Monte Carlo calculations for the molecular fragments... 

A new molecular simulation technique is developed to solve the perturbation equations for a multicomponent, isothermal stured-tank adsorber under equilibrium controlled conditions. The method is a hybrid between die Gibbs ensemble and Grand Canonical Monte Carlo methods, coupled to macroscopic material balances. The bulk and adsorbed phases are simulated as two separate boxes, but the former is not actually modelled. To the best of our knowledge, this is the first attempt to predict the macroscopic behavior of an adsorption process from knowledge of the intermolecular forces by combining atomistic and continuum modelling into a single computational tool. 

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