Monte Carlo method applications

Baptista, A.M. Martel, P.J. Soares, C.M., Simulation of electron-proton coupling with a Monte-Carlo method application to cytochrome C3 using continuum electrostatics, Biophys. J. 1999, 76, 2978-2998... 

D. R. Ripoll, M. J. Vasquez, and H. A. Scheraga, Biopolymers, 31, 319 (1991). The Electrostatically Driven Monte Carlo Method Application to Conformational Analysis of Decaglycine. 

P. Beroza, D. R. Fredkin, M. Y. Okamura, and G. Feher, Proc. Natl. Acad. Sci. U.S.A., 88, 5804 (1991). Protonation of Interacting Residues in a Protein by a Monte Carlo Method Application to Lysozyme and the Photosynthetic Reaction Center of Rhodobacter sphaeroides. 

Beroza, R, Fredkin, D.R., Okamura, M.Y., Feher, G. Protonation of interacting residues in a protein by a Monte Carlo method Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA 1991, 88, 5804-8. 

In 1998. Andrec and Prestegard- measured the coupling constants in antiphase patterns. They introduced a variant using a Metropolis-Hasting Monte Carlo method. Application to the measurement of coupling constants smaller than linewidth is shown to be applicable to simulations and experimental data stemming from INADEQUATE experiments. 

Conformational Sampling with Poisson-Boltzmann Forces and a Stochastic Dynamics Monte Carlo Method Application to Alanine Dipeptide. 

Salsburg Z W, Jacobson J D, Fickett W and Wood W W 1959 Application of the Monte Carlo method to the lattice gas model. Two dimensional triangular lattice J. Chem. Phys. 30 65-72... 

Binder K (ed) 1987 Application of the Monte Carlo Method in Statistical Physics (Topics in Current Physics, vol 36) (Berlin Springer)... 

The basic scheme of this algorithm is similar to cell-to-cell mapping techniques [14] but differs substantially In one important aspect If applied to larger problems, a direct cell-to-cell approach quickly leads to tremendous computational effort. Only a proper exploitation of the multi-level structure of the subdivision algorithm (also for the eigenvalue problem) may allow for application to molecules of real chemical interest. But even this more sophisticated approach suffers from combinatorial explosion already for moderate size molecules. In a next stage of development [19] this restriction will be circumvented using certain hybrid Monte-Carlo methods. 

Applications of the Configurational Bias Monte Carlo Method... 

Monte Carlo search methods are stochastic techniques based on the use of random numbers and probability statistics to sample conformational space. The name Monte Carlo was originally coined by Metropolis and Ulam [4] during the Manhattan Project of World War II because of the similarity of this simulation technique to games of chance. Today a variety of Monte Carlo (MC) simulation methods are routinely used in diverse fields such as atmospheric studies, nuclear physics, traffic flow, and, of course, biochemistry and biophysics. In this section we focus on the application of the Monte Carlo method for... 

K. Binder, ed. Applications of Monte Carlo Methods in Statistical Physics. Berlin Springer, 1984. 

C. C. Battaille, D. J. Srolvitz, J. E. Butler. A kinetic Monte Carlo method for the atomic-scale simulation of chemical vapor deposition application to diamond. J App Phys 52 6293, 1997. 

Levesque D, Weis JJ, Hansen JP (1984) In Binder K (ed) Topics in current physics 36 -applications of the Monte Carlo method in statistical physics, chap 2. Springer, Berlin Heidelberg New York... 

Applications of Monte Carlo Methods to Sequence Distributions in Polymers... 

In tfiis chapter we address first the electrochemical application of the more familiar method of molecular (or atom) dynamics, and later turn to consider Monte Carlo methods, in each case giving a short introduction that should motivate the reader to pursue reading more specific works. Although the present research field is relatively new, the investigations are already too extensive to review in detail in a single chapter. For this reason, we discuss here the more extended research branches in the field and present a few representative examples. The application of simulations applied to nanostructuring problems is discussed in Chapter 36 liquid-liquid interfaces have been addressed by I. Benjamin (1997). 

Frenkel, D. Ladd, A. J. C., New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fee and hep phases of hard spheres, J. Chem. Phys. 1984, Si, 3188-3193... 

Tsai, C.J. Jordan, K.D., Use of the histogram and jump-walking methods for overcoming slow barrier crossing behavior in Monte Carlo simulations applications to the phase transitions in the (Ar)i3 and (FbOjs clusters, J. Chem. Phys. 1993, 99, 6957... 

Hukushima, K. Nemoto, K., Exchange Monte Carlo method and application to spin glass simulations, J. Phys. Soc. Jpn. 1996, 65, 1604—1608... 

Binder, K., Applications of Monte Carlo methods to statistical physics, Rep. Prog. Phys. 1997, 60, 487-559... 

Kristof, T. Liszi, J., Application of a new Gibbs ensemble Monte Carlo method to site-site interaction model fluids, Mol. Phys. 1997, 90, 1031-1034... 

Valleau, J. P., Thermodynamic scaling methods in Monte Carlo and their application to phase equilibria, Monte Carlo Methods Chem. Phys. 1999,105, 369-404... 

Monte Carlo calculations have been carried out to simulate the spin transition behaviour in both mono- and dinuclear systems [197]. The stepwise transition in [Fe(2-pic)3]Cl2-EtOH as well as its modification by metal dilution and application of pressure have been similarly modelled by considering short- and long-range interactions [52, 198, 199]. An additional study of the effect of metal dilution was successfully simulated with the Monte Carlo treatment considering direct and indirect inter-molecular interactions [200]. A very recent report deals with the application of the Monte Carlo method to mimic short- and long-range interactions in cooperative photo-induced LS—>HS conversion phenomena in two- and three-dimensional systems [201],... 

This criterion requires a search through a nonconvex multidimensional conformation space that contains an immense number of minima. Optimization techniques that have been applied to the problem include Monte Carlo methods, simulated annealing, genetic methods, and stochastic search, among others. For reviews of the application of various optimization methods refer to Pardalos et al. (1996), Vasquez et al. (1994), or Schlick et al. (1999). 

Up to this point and in the following sections and as long as the contrary is not specified, all the discussion will refer to the study of closed, isothermal systems (N,V,T). Though in the applications of Monte Carlo method to the study of solutions... 

The main drawback with the application of Monte Carlo method in this ensemble lies in the fact that, due to the perturbation [34] that must be applied to the volume, it takes approximately 15% more of computing time than in the canonical (N,V,T) ensemble. Another possible problem is that some interaction potentials may lead to unreasonable densities in the calculation. 

Vandermonde matrices often arise when reconstructing PDFs from their moments, and efficient numerical methods exist for solving (B.51) (Press et al. 1992). Although Vandermonde matrices are notoriously ill-conditioned for large Ne, this will usually not be a problem in applications of the DQMOM-IEM model since it is most attractive (relative to Monte-Carlo methods) when Ne is small. 

B. Application of the Monte Carlo Method to a Continuous, Elevated Line Source... 

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