Transition Path Sampling Study of the Local Molecular Structure in the Aqueous Solvation of Sodium Chloride

Abstract

The aqueous solvation of sodium chloride has been investigated using the recently introduced technique of the transition path sampling. We performed a series of Monte Carlo simulations for each element of an ensemble of chains of states. The evolution of the local solvent structure during the dissociation process has been observed. The incoming of a couple of waters to the first coordination shell is responsible for the structural changes which allow the dissociation occur: waters which leave the second coordination shell produce voids and a local molecular reorganization in order to allocate the dissociated ion pair.     

Test of the Inverse Monte Carlo Method for the Calculation of Interatomic Potential Energies in Atomic Liquids

Abstract

The principle purpose of this paper is to demonstrate the use of the Inverse Monte Carlo technique for calculating pair interaction energies in monoatomic liquids from a given equilibrium property. This method is based on the mathematical relation between transition probability and pair potential given by the fundamental equation of the “importance sampling” Monte Carlo method. In order to have well defined conditions for the test of the Inverse Monte Carlo method a Metropolis Monte Carlo simulation of a Lennard Jones liquid is carried out to give the equilibrium pair correlation function determined by the assumed potential. Because an equilibrium configuration is prerequisite for an Inverse Monte Carlo simulation a model system is generated reproducing the pair correlation function, which has been calculated by the Metropolis Monte Carlo simulation and therefore representing the system in thermal equilibrium. This configuration is used to simulate virtual atom displacements. The resulting changes in atom distribution for each single simulation step are inserted in a set of non-linear equations defining the transition probability for the virtual change of configuration. The solution of the set of equations for pair interaction energies yields the Lennard Jones potential by which the equilibrium configuration has been determined.     

Monte Carlo Comparison of Multiple Comparison Procedures

Seven procedures of multiple comparisons: Tukey, Scheffé, Bonferroni, Studentized Maximum Modulus, Duncan, Newman-Keuls and F are compared with respect to the probability of the correct decision. Monte Carlo simulation shows that there is no the best procedure. AMS 1985 Subject Classification: 62 J 15.     

Phylogenetic tree construction using sequential stochastic approximation Monte Carlo

Monte Carlo methods have received much attention recently in the literature of phylogenetic tree construction. However, they often suffer from two difficulties, the curse of dimensionality and the local-trap problem. The former one is due to that the number of possible phylogenetic trees increases at a super-exponential rate as the number of taxa increases. The latter one is due to that the phylogenetic tree has often a rugged energy landscape. In this paper, we propose a new phylogenetic tree construction method, which attempts to alleviate these two difficulties simultaneously by making use of the sequential structure of phylogenetic trees in conjunction with stochastic approximation Monte Carlo (SAMC) simulations. The use of the sequential structure of the problem provides substantial help to reduce the curse of dimensionality in simulations, and SAMC effectively prevents the system from getting trapped in local energy minima. The new method is compared with a variety of existing Bayesian and non-Bayesian methods on simulated and real datasets. Numerical results are in favor of the new method in terms of quality of the resulting phylogenetic trees.     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.     

Investigation of the Air Separation Properties of Zeolites Types A,X and Y by Monte Carlo Simulations

Abstract

The air separation properties of zeolite types A, X, and Y have been studied using grand canonical Monte Carlo simulations of nitrogen, oxygen, and argon adsorbed in these zeolite lattices. Nitrogen is adsorbed preferentially due to the quadrupole-ion electrostatic interactions with the extra framework cations. The localization of adsorption sites for nitrogen near cations and the more diffuse distributions of oxygen and argon within zeolite cavities are clearly illustrated. Predicted nitrogen/oxygen selectivity for 5A from simulations is in good agreement with that determined experimentally. The effect of the calcium-sodium ion exchange on the predicted nitrogen/oxygen selectivity is examined, and is shown to be sensitive to the magnitude of the charges assigned to the extra framework cations.     

小鼠大脑纹状体诱发多巴胺信号分析——Monte Carlo模拟

突触前释放的多巴胺以容积式释放（volume transmission）来传递多巴胺信号,而碳纤电极（carbon fiber electrode,CFE）所记录的胞外电化学信号是大量多巴胺分子氧化电流的平均统计结果。这些特征为使用Monte Carlo方法来直观而细致地描述多巴胺在胞外“自由行走”的行为提供了可能。作者尝试使用Monte Carlo建模的方法来研究动作电位（AP）刺激的频率对纹状体内多巴胺浓度（[DA]）变化的影响。结果显示,与实验记录多巴胺信号相比,在生理强度（低频≤20 Hz,或≤12个 APs高频 80 Hz）刺激模式下,基于单一囊泡库的突触模型可以较好地模拟实验结果。此外,作者还分析了大脑神经网络结构等对实验数据的影响。研究说明,Monte Carlo模拟为研究大脑内多巴胺信号的产生机制提供了一种有效的辅助研究方法。     

Basic statistics and variational concepts behind the reverse Monte Carlo technique

We revise the statistical foundations of the reverse Monte Carlo (RMC) technique by constructing the associated functional of a variational principle which incorporates, without any ad hoc assumptions, the inherent errors accompanying the simulation and the experimental data. We propose a Bayesian criteria for acceptance/rejection of configurations, in terms of the variations of the functional. The loss function and variational functional minimization approaches are compared.     

A Monte Carlo scheme based on mid-density in a hysteresis loop to determine equilibrium phase transition

A new and simple method to determine equilibrium phase transition in adsorption systems exhibiting a hysteresis loop is presented as an alternative to methods such as multiple histogram reweighting, gauge cell method and thermodynamic integration. This method is based on the NVT-grand canonical Monte Carlo mid-density scheme to determine the coexistence chemical potential and coexistence densities of an adsorption system. We illustrate this new scheme with argon and methane adsorption in a number of model solids having slit and cylindrical pores. This method does not have a strong basis on thermodynamic ground, but it does provide a simple heuristic approach that is simpler to understand physically.     

Bias in Markov models of disease

We examine bias in Markov models of diseases, including both chronic and infectious diseases. We consider two common types of Markov disease models: ones where disease progression changes by severity of disease, and ones where progression of disease changes in time or by age. We find sufficient conditions for bias to exist in models with aggregated transition probabilities when compared to models with state/time dependent transition probabilities. We also find that when aggregating data to compute transition probabilities, bias increases with the degree of data aggregation. We illustrate by examining bias in Markov models of Hepatitis C, Alzheimer’s disease, and lung cancer using medical data and find that the bias is significant depending on the method used to aggregate the data. A key implication is that by not incorporating state/time dependent transition probabilities, studies that use Markov models of diseases may be significantly overestimating or underestimating disease progression. This could potentially result in incorrect recommendations from cost-effectiveness studies and incorrect disease burden forecasts.