Monte Carlo programs

Figure 4. The most CPU time-consuming portion of the scalar version of the Monte Carlo program for the evaluation of chain partitioning between the bulk solution and a cylindrical pore, in the scalar form (left) and the explicitly vectorized form (right).

K. Coutinho and S. Canuto, DLCE A General Monte Carlo Program for Liquid Simulation, University of Sao Paulo, 2000. 

Ramella- Roman JC, Prahl SA, Jacques SL. Three Monte Carlo programs of polarized light transport into scattering media part I. Optics Express 2005, 13, 4420-4438. 

K. Coutinho, S. Canuto, DICE A general Monte Carlo program for liquid simulation (University of Sao Paulo, Brazil (, 2000)... 

Through molecular simplification, Norte et al determined that the presence of the flexible side chain was essential for the cytotoxic activity. It was further postulated that the conformation of the C14-C19 side chain was at least partially responsible for the variation in biological responses among the analogues. In order to verify this hypothesis, the stable conformations for all the compounds were determined using calculations that involved a multiconformer search using the Monte Carlo program in Macromodel and MM2 force fields [18]. 

M. McGrath, J. Siepmann, l.-F. W. Kuo, C. J. Mundy, J. VandeVondele, M. Sprik, J. Hutter, F. Mohamed, M. Krack, and M. Parrinello (2005) Toward a Monte Carlo program for simulating vapor-liquid phase equilibria from first principles. Comp. Phys. Comm. 169, p. 289... 

These equations show how a mmmm sequence in polystyrene can be converted into a mrrm sequence by a simple epimerization event. Should the configuration of the fourth carbon from the left in the last structure also be altered, a rmrm pentad would result. Thus, by a series of epimerization steps it is possible to change isotactic polystyrene gradually into a polymer that exhibits the same NMR spectra as the polystyrene that was prepared by free radical polymerization(17-19). A Monte Carlo program has... 

Monte Carlo Simulations. The epimerization reaction was simulated using the Monte Carlo program we described earlier(17). A 5000 element array was allocated to store information about the configurations of monomer units at various positions in a 5000 unit polymer chain. The positions were indexed in such a way that the polymer could be considered cyclic. This was done to avoid end group effects. The configurations (R or S) at individual sites were indicated by 0 or 1 values. The polymer chain was made isotactic by giving all elements of the array initial values of 0. 

A Monte Carlo program was used to deduce AHads of -75 kJ/mol with a 68% confidence interval for BhOsCl, the most probable oxychloride imder these conditions. The values for the Tc and Re oxychlorides studied imder the same conditions are -51 kJ/mol and -61 kJ/mol, respectively. Thus, BhOsCl shows a stronger adsorption interaction with the chlorinated quartz surface than either of TcOsCl or ReOsCl, and is more similar to Re than to Tc. The obtained AHads are in very good agreement with the calculations described above [144]. Thus, a volatility sequence of TCO3CI > ReOsCl > BhOsCl was observed in agreement... 

A Monte Carlo program based on a microscopic model of the adsorption process was used to deduce an adsorption enthalpy of -75 kJ mol 1 with a 68% confidence interval of -66 to -81 kJ mol 1 for BI1O3CI, predicted to be the most probable oxychloride under these conditions. The values for Tc and Re were -51 and -61 kJ mol-1, respectively. These results were in agreement with the calculations (Pershina and Bastug, 2000) that predicted a volatility sequence for the... 

Ro C-U, Osan J, Szaloki I, de Hoog J, Worobiec A, Van Grieken R (2003) A Monte Carlo program for quantitative electron-induced X-ray analysis of individual particles. Anal Chem 75 851-859... 

This is not a very convenient form for a Monte Carlo program therefore, unless an analytical solution is possible, special techniques are adopted. 

Several workers have attempted to evaluate the exact Ewald pair potential directly in the Monte Carlo program. The practicality of this approach clearly depends on a judicious choice of both the convergence parameter w and the number of terms to be included in each of the two series. The value w = in (B6) leads to equal asymptotic rates of convergence for the two series but it is far from obvious that this would be the most efficient choice. In fact, the most satisfactory algorithm of this type takes w 5 with this choice only the large spherically synunetric term in the summation over real lattice vectors needs to be included (i.e., A = 0 if r is determined by the minimum image distance convention). The summation over reciprocal lattice vectors now becomes very slowly convergent, with terms up to = 14 (125... 

To understand the overall conformation of a large molecule, also called the macroconformation, one can use computers and simulate the molecule with a Monte Carlo program. Figure 1.38 illustrates the Monte Carlo technique [9]. First, one chooses a lattice for the generation of the macromolecule. Figure 1.39 illustrates a two-dimensional square lattice with coordination number (CN) four. Then one places the first atom somewhere on the lattice. This leaves four choices for the placement of the second atom (wn = 4). Choosing one of these four possibilities leads to three as the number of choices for the third and most subsequent atoms, as shown in the figure. 

A Monte Carlo program runs a large number of iterations that represents a potential real event of transmission along the food pathway. A random sample is drawn form each of the probabUity distributions used as input for the model parameters. The simulation result is a fiecpiency distribution of the output of interest which provide not only extreme values but also the most hkely outcome based on the combinations of input probabUity values that could occur that allows us to evaluate probabilities of events, which is derived in this case combining the F(LM , T) and A(x, F) models for each stage. 

Joubert HD, Swart HC, Terblans JJ (2004) Monte-Carlo program for simulating segregation and diffusion utilizing chemical potential calculations. Surf Interface Anal 36(11) 1441-1448... 

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