Monte Carlo tests

A. Milchev, K. Binder. A polymer chain between two parallel repulsive walls A Monte Carlo test of scaling behavior. Europ Phys J B 3 411-4 4, 1998. 

Scaling in Semidilute Polymer Solutions A Monte Carlo Test. 

K. Binder and E. Luijten (2001) Monte Carlo tests of renormalization-group predictions for critical phenomena in Ising models. Phys. Rep. 344, pp. 179-253... 

Blumberg, R.L., Shlifer, G., and Stanley, H.E. Monte Carlo tests of universality in a correlated-site percolation problem, /. Phys. A Math. Gen., 13, L147,1980. 

Monte Carlo Tests of Flory-Huggins Theory and Comparison... 

The observed and expected counts are given as well as the standard deviation (sd) of the expected counts determined from 30 Monte Carlo tests. The z-value is defined as (observed-expected)/(sd expected). Trimers are only listed if their z-values were >= 4.00 or <= -4.00. 

G. W. Milligan, Multivariate Behav. Res., 16,379 (1981). A Review of Monte Carlo Tests of Cluster Analysis. 

Here the right-hand side of the equation is simply the thermodynamic factor which hence should be linear in the variable Nx- The Monte Carlo test of eq. (7.41) revealed a rather pronounced curvature of this ratio Ant(x)/Ant(x = 0) as function of x, however also the short chains accessible (N = 10,20, and 40, respectively) did not conform to the expected scaling in terms of the variable Nx- This problem certainly deserves further study, however, since the chain lengths used are very short, and there are also possible systematic errors in principle, one should deduce Ant(x) from interdiffusion of layers which differ in their concentrations 4 A, A only a Uttle (rather than having = 0,4>A /i i A + = 1, as done in the avail-... 

O. Dillmann, W. Janke, M. Mueller, K. Binder, A Monte Carlo test of the Fisher-Nakanishi-scaling theory for the capillary condensation critical point, J. Chem. Rhys. 114 (2001) 5853-5862. 

We tested our recipe on many trial densities by Monte Carlo simulation, c. g., on the normal mixture tajrget densities of Jones et al. [14]. Examples of pair potentials U r) = Wy q r)) reconstructed in this way are given in Figure 3. 

RipoU D R and H A Scheraga 1988. On the Multiple-Mirumum Problem in the Conformational Anal of Polypeptides. II. An Electrostatistically Driven Monte Carlo Method Tests on Poly(L-Alani Biopolymers 27 1283-1303. 

The tests in the two previous paragraphs are often used because they are easy to perform. They are, however, limited due to their neglect of intermolecular interactions. Testing the effect of intennolecular interactions requires much more intensive simulations. These would be simulations of the bulk materials, which include many polymer strands and often periodic boundary conditions. Such a bulk system can then be simulated with molecular dynamics, Monte Carlo, or simulated annealing methods to examine the tendency to form crystalline phases. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

With the Monte Carlo method, the sample is taken to be a cubic lattice consisting of 70 x 70 x 70 sites with intersite distance of 0.6 nm. By applying a periodic boundary condition, an effective sample size up to 8000 sites (equivalent to 4.8-p.m long) can be generated in the field direction (37,39). Carrier transport is simulated by a random walk in the test system under the action of a bias field. The simulation results successfully explain many of the experimental findings, notably the field and temperature dependence of hole mobilities (37,39). 

To test the results of the chemical potential evaluation, the grand canonical ensemble Monte Carlo simulation of the bulk associating fluid has also been performed. The algorithm of this simulation was identical to that described in Ref. 172. All the calculations have been performed for states far from the liquid-gas coexistence curve [173]. 

In this situation computer simulation is useful, since the conditions of the simulation can be chosen such that full equihbrium is established, and one can test the theoretical concepts more stringently than by experiment. Also, it is possible to deal with ideal and perfectly flat surfaces, very suitable for testing the general mechanisms alluded to above, and to disregard in a first step all the complications that real substrate surfaces have (corrugation on the atomistic scale, roughness on the mesoscopic scale, surface steps, adsorbed impurities, etc.). Of course, it may be desirable to add such complications at a later stage, but this will not be considered here. In fact, computer simulations, i.e., molecular dynamics (MD) and Monte Carlo (MC) calculations, have been extensively used to study both static and dynamic properties [11] in particular, structural properties at interfaces have been considered in detail [12]. 

For this expression to be valid, in cell A components 1 and 2 must be identical in all respects, so it is a rather special case of an ideal mixture. They are however, allowed to interact differently with the membrane, as described above, xa is the mole fraction of the solute in cell A, while p and p are the number densities of cells A and B respectively. The method was extensively tested against both Monte Carlo and equations of state for LJ particles, and the values of the chemical potential were found to be satisfactory. The method can also be extended to mixtures [29] by making... 

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

Purpose Generate data sets using mixed deterministic/stochastic models with N = 1. .. 1000. These data sets can be used to test programs or to do Monte Carlo studies. Five different models are predefined sine wave, saw tooth, base line, GC-peaks, and step functions. Data file SIMl.dat was... 

Monte Carlo simulations of transport by electrophoresis have also been performed. Recent simulations by Slater and Gno [356] have tested the fnndamental assumption nsed in electrophoresis given by Eq. (91). Using Monte Carlo simnlations in a two-dimensional... 

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