The extension of coordination number model by using the local composition theory: mixtures

The extension of a new coordination number model to mixture is presented in this work. Extended model agrees well with the Monte Carlo (MC) simulation results for square-well (SW) mixture fluids and shows better results compared with other models. To test our model, we compare the compressibility factors from various models for SW fluids at different λ values and for SW fluid mixtures at λ=1.5. Although our model is obtained by fitting simulation data at λ=1.5, it shows better results for the different λ values than other coordination number model. Compared with the compressibility factors of various binary mixtures of SW fluids calculated from other models, this model presents better results. Because our model considers the temperature dependency importantly by using the total site number, it predicts coordination number and compressibility factor well in the wide temperature range and enables one to derive an equation of state (EOS) through integration of the coordination number equation.     

Excess energy and equation of state of fluids with hard-core potential models from a second-order Monte Carlo perturbation theory

Monte Carlo simulations in the NVT ensemble of the reference hard-sphere fluid have been performed to obtain the “exact” first- and second-order terms in the inverse temperature expansion of the free energy of fluids with hard-core potentials. The results have been used to obtain parametrizations of the free energy of fluids with Sutherland potentials with variable range as well as for a fluid with a hard-core Lennard–Jones potential. The results for the excess energy and the equation of state are compared with simulation data available in the literature for these fluids.     

About the numerical pitfalls characteristic for SAFT EOS models

This study demonstrates that SAFT EOS models might exhibit the practically unrealistic and even non-physical predictions due to the two factors, namely the temperature dependencies of a segment packing fraction and the very high-polynomial orders by volume. The first factor is responsible for predicting the negative values of the heat capacities at very high pressures and the intersections of isotherms at high densities. The very high-polynomial orders of several SAFT EOS models result in prediction of the additional stable unrealistic critical points and the pertinent fictive phase equilibria. It is demonstrated that the unrealistic phase splits might present the globally stable states established by the models, while the VLE matching the experimental data might be in fact metastable. In addition, the excessive complexity of certain SAFT models might result in wrong prediction of auxiliary thermodynamic properties of the experimentally available fluid phases. The undesired predictions discussed in the present study arise queries regarding the robustness and the over-all physical validity of the models under consideration in their present forms. This study discusses the ways of removing the numerical pitfalls.     

A Monte Carlo study of the coil-to-globule transition of model polymer chains near an attractive surface

When a polymer chain in solution interacts with an atomically smooth solid substrate, its conformational properties are strongly modified and deviate substantially from those of chains in bulk. In this work, the interplay of two competing transitions that affect the conformations of polymer chains near an energetically attractive surface is studied by means of Monte Carlo simulations on a cubic lattice. The transition from an extended to a compact conformation of a polymer chain near an attractive wall, as solubility deteriorates, exhibits characteristics akin to the “coil-to-globule” transition in bulk. An effective θ-temperature is determined. Its role as the transition point is confirmed in a variety of ways. The nature of the coil-to-compact transition is not qualitatively different from that in the bulk. Adsorbed polymer chains may assume “globular” or “pancake” configurations depending on the competition among adsorption strength, cohesive energy, and entropy. In a very relevant range of conditions, the dependence of the adsorbate thickness on chain-length is intermediate between that of 3-d (“semidroplets”) and 2-d (“pancake”) objects. The focus of this study is on rather long polymer chains. Several crucial features of the transitions of the adsorbed chains are N-dependent and various aspects of the adsorption and “dissolution” process are manifested clearly only at the “long chain” limit. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 2462–2476, 2009     

Assessing the coefficient of variations of chemical data using bootstrap method

The coefficient of variation is frequently used in the comparison and precision of results with different scales. This work examines the comparison of the coefficient of variation without any assumptions about the underlying distribution. A family of tests based on the bootstrap method is proposed, and its properties are illustrated using Monte Carlo simulations. The proposed method is applied to chemical experiments with iid and non‐iid observations. Copyright © 2011 John Wiley & Sons, Ltd.     

A lattice-gas model for halide adsorption on single-crystal electrodes

A lattice-gas model is described for the adsorption of halides on single-crystal electrodes. The lateral interactions between the adsorbed halides include a short-range nearest-neighbor interaction and a long-range electrostatic interaction. By Monte Carlo simulations the model is used to fit the experimental isotherm of bromide adsorption on Ag(100), giving information about the relative importance of the long-range and short-range interactions. The model reproduces the order–disorder transition observed experimentally, and the way in which the long-ranged interactions influence the properties of this phase transition is discussed. The Monte Carlo simulations are also compared to analytical mean-field and quasi-chemical approximations to the isotherm. Finally, the kinetics of the disorder–order transition are studied by dynamic Monte Carlo simulations, and some results on isotherms and ordered phases on (110) and (111) surfaces are described.     

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of For-Ala(2)-NH(2) in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for For-Gly(10)-NH(2) and For-Ala(10)-NH(2) showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (E(TOTAL)) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the E(SAAP) term) may play definitive roles on the topologies of protein secondary structures.     

A new cubic equation of state for simple fluids: pure and mixture

A two-parameter cubic equation of state is developed. Both parameters are taken temperature dependent. Methods are also suggested to calculate the attraction parameter and the co-volume parameter of this new equation of state. For calculating the thermodynamic properties of a pure compound, this equation of state requires the critical temperature, the critical pressure and the Pitzer’s acentric factor of the component. Using this equation of state, the vapor pressure of pure compounds, especially near the critical point, and the bubble point pressure of binary mixtures are calculated accurately. The saturated liquid density of pure compounds and binary mixtures are also calculated quite accurately. The average of absolute deviations of the predicted vapor pressure, vapor volume and saturated liquid density of pure compounds are 1.18, 1.77 and 2.42%, respectively. Comparisons with other cubic equations of state for predicting some thermodynamic properties including second virial coefficients and thermal properties are given. Moreover, the capability of this equation of state for predicting the molar heat capacity of gases at constant pressure and the sound velocity in gases are also illustrated.     

蒙特卡罗法估算真实溶液的无限稀释活度系数

在无限稀释活度系数实验测定、模型预测等方面的研究工作不断深入的同时，基干系统的微观分子结构信息通过计算机分子模拟方法来求取无限稀释活度系数的研究也更多地开展起来［‘，’］．但是鉴于摘类热力学性质，如自由能、化学位等的特殊性，开展的模拟工作总的说来是初步的·许多方法复杂，实现的难度较大，而研究的系统技多地针对于模型流体混合物（modelfluidrn－ixtures）．本文是蒙特卡罗法估算真实溶液的无限稀释活度系数的一个尝试，研究对象选取298．15K温度条件下甲醇的水溶液·1原理对于一个NTV系综，化学位定义为可以将UN－…     

Cooperativity in the Conformational Rearrangements of Polymer Chain Segments as Seen by Bond Fluctuation Model

The kinetics of structural relaxation was simulated using the bond fluctuation model. Annealing of the system in the glassy state produces a clearly nonexponential decrease in the energy in a certain temperature interval. At lower temperatures, the decrease in energy takes place by successive small steps, due to the change of the energy of individual polymer chains that modify their conformation into small neighbourhoods. This cooperativity is behind the nonexponential behaviour shown by structural relaxation at higher temperatures. A second order Markov chain is able to reproduce the nonexponentiality with quite good agreement with the bond fluctuation simulated curves. Cooperativity comes from the fact that the transition probability of a polymer chain between two energy levels depends on the history of previous transitions that took place in its neighbourhood.

     

Calculating thermodynamic properties from perturbation theory: II. An analytic representation for the square-well chain fluid

An analytic representation of thermodynamic properties of the freely jointed square-well chain fluid is developed based on the thermodynamic perturbation theory of Barker–Henderson, Zhang and Weitheim. By using a real function expression for the radial distribution function and incorporating structural information for square-well monomer of TPT1 model, an analytic expression for the Helmholtz energy of square-well chain fluid is expanded from Zhang’s analytic expressions for thermodynamic properties of square-well monomer. The expression leads to good predictions of the compressibility factor, residual internal energy and constant-volume heat capacity for 4-mer, 8-mer and 16-mer square-well fluids when compared with the Monte Carlo (MC) simulation results. The incorporating structural information for square-well dimer of TPT-D model is also calculated. To obtain the constant-volume heat capacity needed, NVT MC simulations were performed.     

On the computation of the fundamental derivative of gas dynamics using equations of state

The value of the fundamental derivative of gas dynamics, Γ$\mathrm{\Gamma }$, is a quantitative measure of the variation of the speed of sound with respect to density in isentropic transformations, such as those occurring, for example, in gas-dynamic nozzles. The accurate computation of its value, which is a constant for a perfect gas, is key to the understanding of real-gas flows occurring in a thermodynamic region where the polytropic ideal gas law does not hold. The fundamental derivative of gas dynamics is a secondary thermodynamic property and so far, no experiments have been conducted with the aim of measuring its value. Several studies document the estimation of Γ$\mathrm{\Gamma }$ for fluids composed of complex molecules using mainly simple thermodynamic equations of state, e.g., that of Van der Waals. A review of these studies has revealed that the calculated values of Γ$\mathrm{\Gamma }$ are affected by large uncertainties; these uncertainties are due to the functional form of the adopted equations and because of uncertainties in the available fluid property data on which these equations were fitted. In this work, the fundamental derivative of gas dynamics of molecularly simple fluids is computed with the aid of, among other models, modern reference equations of state. The accuracy of these computations has been assessed. Reference thermodynamic models however, are not available for molecularly complex fluids; some of these molecularly complex fluids are the substances of interest in studies on the so-called nonclassical gas dynamics. Therefore, results of the computation of Γ$\mathrm{\Gamma }$ for few, molecularly simple hydrocarbons, like methane, ethane, etc., are used as a benchmark against which the performance of simpler equations of state, can be assessed. For the selected substances, the Peng–Robinson, Stryjek–Vera modified, cubic equation of state yields good results for Γ$\mathrm{\Gamma }$-predictions, while the modern multiparameter technical equations of state, e.g., the one in the Span–Wagner functional form, are preferable, provided that enough accurate thermodynamic data are available. Another notable result of this study, is that Γ$\mathrm{\Gamma }$ for a fluid composed of complex molecules is less affected by the inaccuracy of _Cv$C_v$-information (_Cv$C_v$ is the isochoric heat capacity), if compared to the estimation of Γ$\mathrm{\Gamma }$ for simple molecules. Inspection of the results of the calculation of Γ$\mathrm{\Gamma }$ in the proximity of the critical point confirms that analytical equations of state fail to predict the correct physical behavior, even if they include terms which allow for the correct estimation of thermodynamic properties.     

A+B2表面催化反应相变及自振荡的蒙特卡罗模拟

用MonteCarlo法研究了脱附和E－R机理对不可逆催化氧化反应A＋1／2B2→AB的相交和自振荡的影响、结果表明，（1）催化剂表面A的脱附使ZGB模型中的一级相变点消失，但对二级相交点的影响很小；当有E－R机理参与时，二级相交点消失，且E－R过程的几率对一级相交点的影响较大；当A的脱附和E－R过程同时起作用时，上述反应不存在相交（2）在ZGB模型中的二级相变点附近，反应速率随时间的变化具有明显的振荡现象，在其它位置主要表现为噪音。引入A的脱附后在二级相交点附近明显的自振荡现象依然存在；当E-R过程起作用时，随着二级相交点的消失，明显的振荡现象亦随之消失．（3）A的脱附和E－R过程对上述反应相变的影响与A的表面扩散对相变的影响有着本质的区别，因为后者只能改变相变点的位置而不能改变相变点的存在状况．     

A new formulation of the predictive NRTL-PR model in terms of kij mixing rules. Extension of the group contributions for the modeling of hydrocarbons in the presence of associating compounds

A generalized NRTL model was previously proposed for the modeling of non ideal systems and was extended to the prediction of phase equilibria under pressure according to the cubic NRTL-PR EoS. In this work, the model is reformulated with a predictive k_ij temperature and composition dependent mixing rule and new interaction parameters are proposed between permanent gases, ethane and nitrogen with hydrocarbons, ethane with water and ethylene glycol. Results obtained for excess enthalpies, liquid-vapor and liquid-liquid equilibria are compared with those provided by the literature models, such as VTPR, PPR78, CPA and SRKm. A wide variety of mixtures formed by very asymmetric compounds, such as hydrocarbons, water and ethylene glycols are considered and special attention is paid to the evolution of k_ij with respect to mole fractions and temperature.     

A model for charge transport in semicrystalline polymer thin films

A model for simulating the charge transport properties of semicrystalline polymer (SCrP) using Monte Carlo simulation is reinvented. The model is validated by reproducing the experimentally observed field and temperature dependence of mobility in Poly(3‐hexylthiophene‐2,5‐diyl) (P3HT) thin films. This study also provides a new physical insight to the origin of much debated negative field dependence of mobility (NFDM) observed at low electric field strengths in P3HT thin films. The observed NFDM, which is not explainable with the mechanisms proposed earlier, is attributed to the weak dependence of transit time on the applied electric field strengths. In the semicrystalline films, the charge transport takes place mostly through the crystalline regions, in which the charge transport is weakly dependent on the strength of the applied electric field. In addition, a possible explanation for the origin of Arrhenius temperature dependence of mobility (lnμ ∝ 1/T) commonly observed in SCrP thin films is also proposed. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 137–141     

Modeling the phase equilibria of hydrogen sulfide and carbon dioxide in mixture with hydrocarbons and water using the PCP-SAFT equation of state

The perturbed-chain polar statistical associating fluid theory (PCP-SAFT) equation of state is applied to correlate phase equilibria for mixtures of hydrogen sulfide (H₂S) and carbon dioxide (CO₂) with alkanes, with aromatics, and with water over wide temperature and pressure ranges. The binary mixtures of H₂S–methane and CO₂–methane are studied in detail including vapor–liquid, liquid–liquid and fluid–solid phase equilibria. Very satisfying results were obtained for the binary mixtures as well as for the ternary mixture of H₂S–CO₂–methane using the (constant) interaction parameters of the binary pairs.     

KoBra: A rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings

We present a new method for calculating the diffusion tensor for the systems of sorbates inside nanoporous materials at different loadings by just using transition rate constants. In addition, a user-friendly program with graphical user interface has been developed and is freely provided to be used ( https://sourceforge.net/projects/kobra/ ). It needs from the user just to provide the values of the unit cell lengths and angles, the transition rate constants for each sorbate, and any spatial constraint between these sorbates. This program is shown to be about 30 times faster than kinetic Monte Carlo method. Application of the method to the problem of diffusion of aromatics in silicalite-1 at different loadings is presented too. © 2019 Wiley Periodicals, Inc.     

Computation of some thermodynamic properties of nitrogen using a new intermolecular potential from molecular dynamics simulation

A new pair-potential energy function of nitrogen has been determined via the inversion of reduced viscosity collision integrals and fitted to obtain an analytical potential form. The pair-potential reproduces the second virial coefficient, viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor of nitrogen in a good accordance with experimental data over wide ranges of temperatures and densities. We have also performed the molecular dynamics simulation to obtain pressure, internal energy, heat capacity at constant volume, and self-diffusion coefficient of nitrogen at different temperatures and densities using our calculated pair-potential and some other potentials. The molecular dynamics of the nitrogen molecules has been also used to determine nitrogen equation of state in two (low and high) pressure ranges. Our results are in a good agreement with experiment and literature values.