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We propose the extension of the test-area methodology, originally proposed to evaluate the surface tension of planar fluid-fluid interfaces along a computer simulation in the canonical ensemble, to deal with the solid-fluid interfacial tension of systems adsorbed on slitlike pores using the grand canonical ensemble. In order to check the adequacy of the proposed extension, we apply the method for determining the density profiles and interfacial tension of spherical molecules adsorbed in slitlike pore with different pore sizes and solid-fluid dispersive energy parameters along the same simulation. We also calculate the solid-fluid interfacial tension using the original test-area method in the canonical ensemble. Agreement between the results obtained from both methods indicate that both methods are fully equivalent. The advantage of the new methodology is that allows to calculate simultaneously the density profiles and the amount of molecules adsorbed onto a slitlike pore, as well as the solid- fluid interfacial tension. This ensures that the chemical potential at which all properties are evaluated during the simulation is exactly the same since simulations can be performed in the grand canonical ensemble, mimicking the conditions at which the adsorption experiments are most usually carried out in the laboratory., The authors would like to acknowledge helpful discussions with B. Mendiboure. This work was supported by Ministerio de Ciencia e Innovación (MICINN, Spain) through Grant Nos. FIS2010-14866, FIS2009-07923, and FPU Ref. AP2007-02172 (J.M.M.). Further financial support from Proyecto de Excelencia from Junta de Andalucía (Grant No. P07-FQM02884) and Universidad de Huelva are also acknowledged.

A molecular simulation method is proposed for the evaluation of the equilibrium density of a pure fluid given the temperature, volume, and chemical potential. In this sense, the technique is formulated in the grand canonical ensemble. However, it does not employ true particle insertion and deletion steps as part of the simulation algorithm; instead, the volume fluctuates in a fashion that brings the density to the appropriate value. The chemical potential must be evaluated by some means to guide convergence of the density, but there is little restriction on the manner in which this is done. The technique is demonstrated through application to the hard sphere model. Simple Widom insertion is used to evaluate the chemical potential, yet the proposed technique converges significantly more quickly than the usual grand canonical Monte Carlo when applied at high density. The method is perhaps most appropriately viewed not as pure molecular simulation, but as a hybrid of a simulation and a numerical technique. I...

We present an approach to incorporate the effect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a specifically tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational efficacy and mode selectivity of vibrationally stimulated reactions can then be quantified in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We first validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the effect of vibrational excitation on a symmetric SN2 reaction and radical addition on CO2.

The exhaust gases, including SO2, NH3, H2S, NO2, NO, and CO, are principal air pollutants due to their severe harms to the ecological environment. Zeolites have been considered as good absorbent candidates to capture the six exhaust gases. In this work, we performed grand canonical ensemble Monte Carlo (GCMC) simulations to examine the capability of 95 kinds of all-silica zeolites in the removal of the six toxic gases, and to predict the adsorption isotherms of the six gases on all the zeolites. The simulation results showed that, H2S, NO, NO2, CO and NH3 are well-captured by zeolite structures with accessible surface area of 1600–1800 m2·g− 1 and pore diameter of 0.6–0.7 nm, such as AFY and PAU, while SO2 is well-adsorbed by zeolites containing larger accessible surface area (1700–2700 m2·g− 1) and pore diameter (0.7–1.4 nm) at room temperature and an atmospheric pressure. However, at saturated adsorption, zeolites RWY, IRR, JSR, TSC, and ITT are found to exhibit better abilities to capture these gases. Our study provides useful computational insights in choosing and designing zeolite structures with high performance to remove toxic gases for air purification, thereby facilitating the development and application of exhaust gas-processing technology in green industry.

Azeotropes have been studied for decades due to the challenges they impose on separation processes but fundamental understanding at the molecular level remains limited. Although molecular simulation has demonstrated its capability of predicting mixture vapor–liquid equilibrium (VLE) behaviors, including azeotropes, its potential for mechanistic investigation has not been fully exploited. In this study, we use the united atom transferable potentials for phase equilibria (TraPPE-UA) force field to model the ethanol/benzene mixture, which displays a positive azeotrope. Gibbs ensemble Monte Carlo (GEMC) simulation is performed to predict the VLE phase diagram, including an azeotrope point. The results accurately agree with experimental measurements. We argue that the molecular mechanism of azeotrope formation cannot be fully understood by studying the mixture liquid-state stability at the azeotrope point alone. Rather, azeotrope occurrence is only a reflection of the changing relative volatility between the two components over a much wider composition range. A thermodynamic criterion is thus proposed on the basis of the comparison of partial excess Gibbs energy between the components. In the ethanol/benzene system, molecular energetics shows that with increasing ethanol mole fraction, its volatility initially decreases but later plateaus, while benzene volatility is initially nearly constant and only starts to decrease when its mole fraction is low. Analysis of the mixture liquid structure, including a detailed investigation of ethanol hydrogen-bonding configurations at different composition levels, reveals the underlying molecular mechanism for the changing volatilities responsible for the azeotrope. Natural Sciences and Engineering Research Council (NSERC) of Canada (RGPIN-4903-2014); National Natural Science Foundation of China (NFSC; No. 21878219); China Scholarship Council (CSC; No. 201500090106).

Novel gas adsorption properties by room-temperature ionic liquids (ILs) confined in carbon nanotube (CNT) bundles were ascertained using grand canonical ensemble Monte Carlo (GCMC) simulations in which the adsorption and separation of CO2 from CO2/N2 mixtures. The introduction of ILs into the CNT channels significantly enhances the adsorption of CO2, while it is not sensitive to N2 adsorption. This is due to the strong interaction between specific ILs in the CNTs and CO2 molecules. The presence of water showed a significant impact on the adsorption capacity of CO2 as well.

Monocomponent adsorption of hydrogen sulfide and multicomponent adsorption with CO2 and CH4 mixtures were predicted in two samples of commercial activated carbons. We perform Monte Carlo calculations in the grand canonical ensemble in representative slit-pores of each carbon material and proposed a new energy parameter for H2S-carbon interaction from experimental adsorption heat in selected activated carbons. Further analysis of adsorption in representative pores demonstrated the importance of ultramicropores in H2S retention and a cooperative effect of CO2 molecules favoring H2S adsorption. To the best of our knowledge this is the first time that a method based on molecular simulation is proposed to predict H2S adsorption on carbon. This study contributes to a better understanding of the role of pore size distribution and adsorption regimes in carbon materials.

In this work, Monte Carlo simulation of CO2, N2, and CH4 adsorption on zeolite 13X is carried out in grand canonical ensemble. FAU framework was used to reproduce the structure of zeolite 13X. Univ...

Studies of the importance of shape considering both adsorption molecule and pore geometry were performed by Monte Carlo simulation in grand canonical ensemble (GCMC) for activated carbons (AC). The effects on adsorption capacity and isosteric heat were investigated in different pore sizes using a pseudo-sphere model and a multi-site potential (elongated shape) on triangular-shaped pore. The triangular geometry was considered as a need to allow for the simultaneous interaction of an adsorbed molecule with three graphite walls to account for the high values observed in the isosteric heat of adsorption at low pressures. Kernels of adsorption isotherms were generated by GCMC for different pore sizes considering two potential models for the determination of pore size distribution that allows for the characterization of various micro and mesoporous solids. We propose using a mixed geometry model (slit-triangular) and an elongated molecule potential to characterize activated carbons. The model is used to characterize a family of AC samples both texturally and energetically. The isosteric heat of adsorption was determined from the experimental isotherm by Monte Carlo simulation and the results were contrasted with experimental data obtaining a good agreement. In addition, the work reports the interesting result on the need to use multi-atom potential (together with the mixed model) to predict heat of adsorption values of the order of those reported experimentally. Fil: Delgado Mons, Rodrigo Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; Argentina Fil: Cornette, Valeria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; Argentina Fil: Toso, Juan Pablo. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Departamento de Física; Argentina Fil: Soares Maia, Debora Aline. Universidade Estadual do Ceará; Brasil Fil: López, Raúl Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; Argentina

Generalized-ensemble algorithms are powerful techniques for investigating biomolecules such as protein, DNA, lipid membrane, and glycan. The generalized-ensemble algorithms were originally developed in the canonical ensemble. On the other hand, not only temperature but also pressure is controlled in experiments. Additionally, pressure is used as perturbation to study relationship between function and structure of biomolecules. For this reason, it is important to perform efficient conformation sampling based on the isothermal-isobaric ensemble. In this article, we review a series of the generalized-ensemble algorithms in the isothermal-isobaric ensemble: multibaric-multithermal, pressure- and temperature-simulated tempering, replica-exchange, and replica-permutation methods. These methods achieve more efficient simulation than the conventional isothermal-isobaric simulation. Furthermore, the isothermal-isobaric generalized-ensemble simulation samples conformations of biomolecules from wider range of temperature and pressure. Thus, we can estimate physical quantities more accurately at any temperature and pressure values. The applications to the biomolecular system are also presented.

The accurate description of the behavior of fluids in nanoporous materials is of great importance for numerous industrial applications. Recently, a new approach was reported to calculate the pressure of nanoconfined fluids. In this approach, two different pressures are defined to take into account the smallness of the system: the so-called differential and the integral pressures. Here, the effect of several factors contributing to the confinement of fluids in nanopores are investigated using the definitions of the differential and integral pressures. Monte Carlo (MC) simulations are performed in a variation of the Gibbs ensemble to study the effect of the pore geometry, fluid-wall interactions, and differential pressure of the bulk fluid phase. It is shown that the differential and integral pressure are different for small pores and become equal as the pore size increases. The ratio of the driving forces for mass transport in the bulk and in the confined fluid is also studied. It is found that, for small pore sizes (i.e., &lt, 5 &sigma, fluid ), the ratio of the two driving forces considerably deviates from 1.

Typical experimental setups for molecular systems must deal with a certain coupling to the external environment, that is, the system is open and exchanges mass, momentum, and energy with its surroundings. Instead, standard molecular simulations are mostly performed using periodic boundary conditions with a constant number of molecules. In this review, we summarize major development of simulation methodologies, which, contrary to standard techniques, open up the boundaries of a molecular system and allow for exchange of energy and matter with the environment, in and out of equilibrium. In particular, we construct the review around the open boundary simulation approaches based on the Adaptive Resolution Scheme (AdResS), which seamlessly couples different levels of resolution in molecular simulations. Ideas and theoretical concepts used in its development lie at the crossroad of different fields and disciplines and open many different directions for future developments in molecular simulation. We examine progress related to theoretical as well as novel modeling approaches bridging length scales from quantum to the continuum description and report on their application in various molecular systems. The outlook of the review is dedicated to the perspective of how to further incorporate rigorous theoretical approaches such as the Bergmann–Lebowitz and Emch–Sewell models into the molecular simulation algorithms and stimulate further development of open boundary simulation methods and their application.

We have published vapor liquid equilibrium data (VLE) for the binary mixture of CO2 + R-1234ze(E) (trans-1,3,3,3-tetrafluoroprop-1-ene) in International Journal of Refrigeration, Volume 98, February 2019, Pages 362-371. In this paper, we presented Gibbs Ensemble Monte Carlo simulation data performed at 293.15 K and 353.02 K. It just so happened that there was a mistake in one of the initial configurations at 353.02 K and the results were not correct. We present here corrected MC values and we compare the results with Peng Robinson EoS calculation and REFPROP predictions.

In this work, we present improved estimates of the critical temperature (Tc), critical density (ρc), critical pressure (Pc), and critical compressibility factor (Zc) for n-alkanes with chain lengths as large as C48. These are obtained for several different force field models with Gibbs ensemble Monte Carlo simulations. We implement a recently proposed data analysis method designed to reduce the uncertainty in Tc, ρc, Pc, and Zc when predicted with molecular simulation. The results show a large reduction in the uncertainties compared to the simulation literature with the greatest reduction found for ρc, Pc, and Zc. Previously, even the most computationally intensive molecular simulation studies have not been able to elucidate the n-alkane Pc trend with respect to larger carbon numbers. The results of this study are significant because the uncertainty in Pc is small enough to discern between conflicting experimental data sets and prediction models for large n-alkanes. Furthermore, the results for Tc resolve...

Made available in DSpace on 2020-12-10T17:32:35Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-05-15 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) FAPESB (Bahia State Research Support Foundation)/SECTI, Bahia, Brazil Some ethanolamine or hydroxylammonium based ionic liquids have shown great potential in CO2 separation processes. However, not much is known about the influence of water on the CO2 solubility of these liquids. In this paper, we study the high-pressure ternary liquid-vapor phase equilibria. The systems were composed of carbon dioxide, water, and an alkanolamine based IL: N-methyl-2-hydroxyethylammonium propionate [m-2HEA] [Pr]. We studied systems whose water contents varied from 6.7% to 52.5%, temperatures from 313 K to 353 K, and pressures from 0.6 MPa up to 22 MPa.The phase equilibria experiments showed that the amount of ionic liquid in the mixture controls the solubilization of CO2 and is not significantly affected by changes in the water content within the studied range. These data were simulated from a molecular point of view using the Gibbs ensemble Monte Carlo method. A force field was estimated to describe the Ionic Liquid (IL) density at a wide range of water content values using the isothermal-isobaric Monte Carlo (NPT-MC). The calculated densities presented a good agreement with experimental data, indicating that the proposed force field parameters are suitable to describe the densities of the IL mixtures and, therefore, can be used to simulate the ternary phase equilibria. The software package CassandraV1.2 was employed to simulate the ternary phase equilibria, resulting in reasonably low deviations when compared to the experimental data. However, the predicted solubility of carbon dioxide in N-methyl-2-hydroxyethylammonium propionate [m-2HEA][Pr] was slightly higher when compared with the experimental values. (C) 2020 Elsevier B.V. All rights reserved. Univ Fed Bahia, Chem Engn Grad Program, Polytech Sch, Salvador, BA, Brazil Univ Fed Uberlandia, Sch Chem Engn, Uberlandia, MG, Brazil Univ Estadual Maringa, Chem Engn Dept, Maringa, PR, Brazil Sao Paulo State Univ, Campus Sao Joao Boa Vista, Sao Joao Da Boa Vista, SP, Brazil Univ Sao Paulo, Chem Engn, Sao Paulo, SP, Brazil Sao Paulo State Univ, Campus Sao Joao Boa Vista, Sao Joao Da Boa Vista, SP, Brazil CNPq: PQ 306640/2016-3 CNPq: 452003/2019-9 CAPES: PDSE-88881.132805/2016-01 FAPEMIG: APQ-03452-17 FAPESB (Bahia State Research Support Foundation)/SECTI, Bahia, Brazil: APP0075/2016

The applicability of the Wolf method for calculating electrostatic interactions is verified for simulating vapor-liquid equilibria of hydrogen sulfide, methanol, and carbon dioxide. Densities, chemical potentials, and critical properties are obtained with Monte Carlo simulations using the Continuous Fractional Component version of the Gibbs Ensemble. Saturated vapor pressures are obtained from NPT simulations. Excellent agreement is found between simulation results and data from literature (simulations using the Ewald summation). It is also shown how to choose the optimal parameters for the Wolf method. Even though the Wolf method requires a large simulation box in the gas phase, due to the lack of screening of electrostatics, one can consider the Wolf method as a suitable alternative to the Ewald summation in VLE calculations.

A new molecular simulation method is proposed to solve the governing equations for a multicomponent, isothermal stirred-tank adsorber under equilibrium controlled conditions. The technique is formulated in the Gibbs ensemble, but is more appropriately viewed as a hybrid of a molecular simulation and continuum modeling. For the general case of an arbitrary multicomponent mixture, the total number of molecules of each species is allowed to fluctuate so that the ensemble average satisfies the macroscopic material balances to the adsorber. It is shown that if an analytical equation of state for the fluid phase is known, the simulation procedure can be considerably simplified and acquires many characteristics of a Monte Carlo simulation conducted in the grand canonical ensemble. The technique is thoroughly validated and its usefulness is demonstrated through application to a gas separation problem encompassing the major steps of practical value to batch adsorption processes.

This paper introduces an efficient technique to generate new molecular simulation Markov chains for different temperature and density conditions, which allow for rapid extrapolation of canonical ensemble averages at a range of temperatures and densities different from the original conditions where a single simulation is conducted. Obtained information from the original simulation are reweighted and even reconstructed in order to extrapolate our knowledge to the new conditions. Our technique allows not only the extrapolation to a new temperature or density, but also the double extrapolation to both new temperature and density. The method was implemented for Lennard-Jones fluid with structureless particles in single-gas phase region. Extrapolation behaviors as functions of extrapolation ranges were studied. Limits of extrapolation ranges showed a remarkable capability especially along isochors where only reweighting is required. Various factors that could affect the limits of extrapolation ranges were investigated and compared. In particular, these limits were shown to be sensitive to the number of particles used and starting point where the simulation was originally conducted.

The adsorption and separation of natural gas in the ordered mesoporous carbon material CMK-3 was investigated by molecular simulation and adsorption theory.Grand canonical ensemble Monte Carlo(GCMC) simulations show that a maximum excess uptake of 10.07 and 14.85 mmol·g-1 is obtained at the optimum temperature and pressure of 208 K,4 MPa for CH4 and 298 K,6 MPa for CO2 adsorption,respectively.Based on the dual-site Langmuir-Freundlich(DSLF) model,ideal adsorption solution theory(IAST) was used to predict the adsorption and separation of binary mixtures.The adsorption selectivity of [SCO2/CH4] is approximately the same as that of [SCH4/N2],with a value of about 3 at 298 K and 4 MPa while the highest CO2 selectivity of 7.5 was found in the N2-CO2 system under the same conditions.This indicates that the CMK-3 material is a promising candidate for natural gas separation.

The interfacial interaction between asphalt binder and mineral aggregate makes different components have different diffusion behavior. It influences the performance of interface and consequently that of the mix. In this research, the models of four asphalt components (asphaltene, resin, aromatics and saturate) and five minerals were constructed individually, and then the Al2O3-asphalt interface model was constructed by adding the asphalt layer and mineral layer together. The interfacial behavior at molecular scale was simulated by setting boundary conditions, optimizing the structure and canonical ensemble. The mean square displacement (MSD) and diffusion coefficient of particles were selected as indicators to study the diffusion of asphalt components on the surface of Al2O3. The results show that when the temperature was 65 °C, asphalt binder showed more viscosity, the diffusion speed of asphalt components ranked according to their molecular mass, which was saturate > aromatics > resin > asphaltene. At 25 °C and 165 °C, the resin had the fastest diffusion speed, which was nearly twice of asphaltene. The interaction between asphalt components and Al2O3 mineral surface can make the diffusion of asphalt components independent on temperature.

Vapour–liquid equilibrium (VLE) and volumetric data of multicomponent mixtures are extremely important for natural gas production and processing, but it is time consuming and challenging to experimentally obtain these properties. An alternative tool is provided by means of molecular simulation. Here, Monte Carlo (MC) simulations in the Gibbs ensemble are used to compute the VLE of multicomponent natural gas mixtures. Two multicomponent systems, one containing a mixture of six components ((Formula presented.), (Formula presented.), (Formula presented.), (Formula presented.)S, (Formula presented.)(Formula presented.) and (Formula presented.)(Formula presented.)), and the other containing a mixture of nine components ((Formula presented.), (Formula presented.), (Formula presented.), (Formula presented.)S, (Formula presented.)(Formula presented.), (Formula presented.)(Formula presented.), (Formula presented.)(Formula presented.), (Formula presented.)(Formula presented.) and (Formula presented.)(Formula presented.)) are simulated. The computed VLE from the MC simulations is in good agreement with available experimental data and the GERG-2008 equation of state modelling. The results show that molecular simulation can be used to predict properties of multicomponent systems relevant for the natural gas industry. Guidelines are provided to setup Gibbs ensemble simulations for multicomponent systems, which is a challenging task due to the increased number of degrees of freedom.

This chapter gives an introduction to the theoretical framework of molecular simulation studies provided by statistical mechanics Molecular simulations are aimed at predicting macroscopic thermophysical properties based on the behavior of the particles contained in the system. The detailed configuration of the system on the molecular level is called a microstate, and statistical mechanics is the theoretical framework that allows for determining macroscopic properties from studying the properties of the microstate.

Reverse nonequilibrium molecular dynamics in the canonical ensemble and coupled–decoupled configurational-bias Monte Carlo simulations in the Gibbs ensemble were used to predict the low-shear rate Newtonian viscosities and vapor–liquid coexistence curves for 1,2-butanediol, 1,3-butanediol, 1,4-butanediol, 2-methyl-1,3-propanediol, and 1,2,4-butanetriol modeled with the transferable potentials for phase equilibria-united atom (TraPPE-UA) force field. Comparison with available experimental data demonstrates that the TraPPE-UA force field yields very good predictions of the viscosities and vapor–liquid coexistence curves. A detailed analysis of liquid structure and hydrogen bonding is provided.

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte-Carlo/molecular dynamics (MD) simulations in the grand-canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand-canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand-canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand-canonical scheme is only minimal.

International audience; The adsorption of pure methane in activated carbon Ecosorb was studied by combining grand canonical ensemble Monte Carlo molecular simulations and an experimental approach based on a gravimetric device. Experimental and calculated adsorption isotherms of methane were determined in supercritical conditions at 303.15 and 353.15 K and pressures up to 10 MPa. The comparison between both experimental and estimated data proves the consistency of the methodology used in this work, starting from the characterization of the porous media in terms of pore size distribution, the determination of the experimental adsorption isotherms, and the final estimation of computational results through estimated isotherms determination. Moreover, additional differential enthalpy of adsorption calculations were compared with experimental values obtained by means of a manometric/calorimetric technique. The good agreement shows the strength and the originality of this paper by combining experimental and computational homemade results allowing a complete characterization of the activated carbon substrate and its methane storage capacity

We report a coarse-grained molecular dynamics simulation study of a bundle of parallelactin filaments under supercritical conditions pressing against a loaded mobile wall using aparticle-based approach where each particle represents an actin unit. The filaments are graftedto a fixed wall at one end and are reactive at the other end, where they can perform singlemonomer (de)polymerization steps and push on a mobile obstacle. We simulate a reactive grandcanonical ensemble in a box of fixed transverse area A, with a fixed number of grafted filaments Nf ,at temperature T and monomer chemical potential μ1. For a single filament case (Nf=1) and fora bundle of Nf = 8 filaments, we analyze the structural and dynamical properties at equilibriumwhere the external load compensates the average force exerted by the bundle. The dynamics of thebundle-moving-wall unit are characteristic of an over-damped Brownian oscillator in agreementwith recent in vitro experiments by an optical trap setup. We analyze the influence of thepressing wall on the kinetic rates of (de)polymerization events for the filaments. Both static anddynamic results compare reasonably well with recent theoretical treatments of the same system.Thus, we consider the proposed model as a good tool to investigate the properties of a bundle ofliving filaments., SCOPUS: ar.j, info:eu-repo/semantics/published

A generalized methodology for statistical analogues of derivatives of the fundamental equation of state in the microcanonical and canonical ensembles is suggested. Those analogues include rigorous measuring prescriptions for any thermodynamic property in molecular NVE and NVT simulation. In particular, optimal data sets for exhaustive thermodynamic data correlation become rigorously accessible.

In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential. We analyze the behavior of the confined system for several supercritical temperatures as a function of variation of molecular parameters: potential range λ, bulk densities ρb*, pore width H, cutoff range interaction rc*, and range of the potential and depth of the particle-wall (λw, ew*). Additionally, we include predictions for liquid-vapor coexistence of bulk associative particles and how their critical properties are modified by the presence of associative sites in the molecule. The molecular simulation data presented in this work are of prime importance to the development of theoretical approaches for inhomogeneous fluids as classical density functional theory. The simulation results presented here are resourceful for predicting adsorption isotherms of real associating fluids such as water.

Histogram reweighting offers a powerful means for extending the information obtained from Monte Carlo simulations to different thermodynamic states. With only a few simulations the entire vapor–liquid coexistence region of a pure fluid can be investigated. We have developed a histogram reweighting method for the isothermal–isobaric (NPT) ensemble and compared it to a method in the grand-canonical ensemble. Results are presented for a Lennard–Jones fluid and a fully flexible SPC water model with and without long-range interactions. For the Lennard–Jones fluid both ensembles give equivalent coexistent densities. The agreement for the screened water potential (i.e., no long-range interactions) is also satisfactory. The full water model was analyzed via reweighting of NPT-ensemble histograms and was found to agree with data obtained for the SPC water model in the Gibbs ensemble. The NPT histogram reweighting method is demonstrated to be an effective tool for examining phase equilibria and may have great utility in situations for which grand-canonical simulations are difficult.

The thermodynamic properties of the triangular-well fluid with a well range of up to twice the hard sphere diameter were studied by means of a new developed equation of state and molecular simulation. This EoS is based on the perturbation theory of Barker and Henderson with the first and second-order perturbation terms evaluated by molecular simulation and then a fit with a simple function based on the radial distribution function of the reference fluid. The thermodynamic properties for the triangular-well fluid were also obtained directly by Gibbs ensemble and NPT Monte Carlo simulations. Good agreement is observed between the proposed EoS and the molecular simulation results. A model for the triangular-well solid is also presented; this has been used to calculate the solid–liquid transition line. Very good agreement is obtained with previously report values for this line and for the triple point temperature and pressure.

The NpT - Gibbs ensemble Monte Carlo computer simulation method was applied to predict the vapour-liquid equilibrium (VLE) behavior of the binary systems ethane + pentane at 277.55 K and 310.95 K, ethane + hexane at 298.15 K, propane + methanol at 313.15 K and propane + ethanol at 325.15 K and 425.15 K. The optimized potentials for the liquid simulating (OPLS) model were used to describe the interactions of alkanes and alcohols. The simulated VLE predictions are compared with experimental data available for the pressure and phase composition of the analyzed binary systems. The agreement between the experimental data and the simulation results is found to be generally good, although slightly better for system in which both components were nonpolar.

In this paper, we derived the potential parameters for three toxic gases, hydrogen sulfide, phosgene and nitrous oxide, modeled by the effective Stockmayer potential model proposed by Gao et al. [Fluid Phase Equilib. 137 (1997) 87]. The vapor–liquid equilibria (VLE) of these substances have been extensively investigated over a wide range of temperatures by the Gibbs ensemble Monte Carlo (GEMC) technique. The simulated saturated densities and pressures are in good agreement with experimental data. The critical properties obtained by regression of the simulated data also agree well with the experimental values. The present work demonstrates that the effective Stockmayer potential can describe well the toxic gases concerned.

The Gibbs ensemble algorithm is implemented to determine the vapour–liquid and liquid–liquid phase coexistence of dilute ternary fluid mixtures interacting via a Lennard–Jones potential. Calculations are reported for mixtures with a third component characterised by different intermolecular potential energy parameters. Comparison with binary mixture data indicates that the choice of energy parameter for the third component affects the composition range of vapour–liquid substantially. The addition of a third component lowers the energy of liquid phase while slightly increasing the energy of the vapour phase.

The shear viscosities of n-decane and 4-propylheptane have been calculated over a range of densities. Equilibrium molecular dynamics simulations were carried out in the canonical ensemble for an empirical force field using the united-atom representation. Quantitative agreement is obtained with the experimental shear viscosities and the pressure−viscosity coefficient.

The Gibbs ensemble algorithm is implemented to determine the liquid–liquid phase coexistence of binary fluid mixtures interacting via a two-body Lennard–Jones+three-body Axilrod–Teller potential. The contributions of both two-body and three-body interactions are calculated exactly. The addition of the Axilrod–Teller term can affect liquid–liquid miscibility substantially. In particular, Axilrod–Teller interactions have a large effect on the densities of the coexisting liquid phases.

A molecular simulation methodology with the algorithm usually used in equation of state calculations for phase equilibrium is applied to calculations for vapor–liquid equilibria of Lennard–Jones binary mixtures. This method can determine a phase equilibrium of pure substances or multicomponent mixtures by performing a single simulation, and any kinds of methods to determine chemical potentials can be used. The calculations for vapor–liquid equilibria are performed by simulation, with results in agreement with those by a Gibbs ensemble method except near critical points for the mixtures. Good reproducibility of the simulation results by the proposed method is obtained.

The connection between molecular force fields and equations of state (EoS) is typically established at the level of predicted quantities, e.g., by comparing simulation data and EoS data. In this paper we show how an EoS can be used to extract the density of states (Omega) of a system thus establishing a deeper connection between EoSs and statistical thermodynamics. We also show how such an EoS Omega can be used to aid molecular simulation methods designed to map out Omega (like the multicanonical approach). Central to the implementation of these ideas is the fact that the configurational Omega is related to thermodynamic properties accessible by an EoS via Boltzmann's equation. Sample calculations are presented for the Omega relevant to isothermal-isobaric and grand canonical ensemble simulations using the hard-sphere system and the Lennard-Jones system as model fluids, and the Carnahan-Starling EoS and a cubic EoS, respectively, as thermodynamic models.