Monte Carlo Simulation of Binary Gas Adsorption in Zeolite Cavities

Abstract

Grand canonical Monte Carlo simulations have been performed for binary adsorption of Lennard-Jones molecules with point multipole moments in zeolite cavities of type X. Fluid-solid electrostatic interactions were taken into account. Phase diagrams and total coverage were calculated for three binaries and compared with experimental measurements. MC simulations gave good agreement with experiment for two mixtures (C₂H₄-CO₂ and CO₂-CH₄) but there were discrepancies between simulation and experiment for the system i-C₄H₁₀-C₂H₄. The dependence of excess Gibbs free energy on the composition and pressure was studied. Negative deviations from ideality are due to energetic heterogeneity and size effects. Unlike liquid-vapor equilibrium, deviations from the Lorentz-Berthelot mixing rules for the adsorbates have little effect upon the phase behavior. Density distributions show that the components compete for the high energy sites inside the cavity; depending on its relative strength of adsorption, one component may be excluded from such positions (CH₄ in CO₂-CH₄), or the two species may share sites inside the cavity (C₂H₄-CO₂).     

Adsorption and diffusion of CO2 and CH4 in covalent organic frameworks: an MC/MD simulation study

Covalent organic frameworks (COFs) are a promising gas separation material which have been developed recently. In this work, we have used grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations to investigate the adsorption and diffusion properties of CO₂ and CH₄ in five recent synthesised COF materials. We have also considered the properties of amino-modified COFs by adding –NH₂ group to the five COFs. The adsorption isotherm, adsorption/diffusion selectivity, self/transport diffusion coefficients have been examined and discussed. All of the five COFs exhibit promising adsorption selectivity which is higher than common nanoporous materials. An S-shaped adsorption isotherm can be found for CO₂ instead of CH₄ adsorption. The introduction of –NH₂ group is effective at low pressure region (<200?kPa). The diffusion coefficients are similar for TS-COFs but increase with the pore size for PI-COFs, and the diffusion coefficients seem less dependent on the –NH₂ groups.     

Adsorption of Binary Mixtures in a Zeolite Micropore

Abstract

We investigate the selective adsorption of xenon, argon, and methane in zeolite NaA by applying the grand canonical ensemble Monte Carlo simulation technique to an adsorbed binary mixture and to two reference systems: i) an adsorbed single component system and ii) a bulk mixture. We define and calculate selectivities and excess densities due to i) mixing and ii) adsorption in terms of differences between the binary adsorbed system and these reference systems. We observe that xenon selectively adsorbs in both xenon-argon and xenon-methane mixtures at low chemical potential (low pressure) due to its greater energetic interaction with the zeolite. However, a reversal in selectivity occurs at higher chemical potential in both of these mixtures. This is due in large part to the greater efficiency in which the smaller component “packs” in the pore as compared to the bulk. We show that the crossover in selectivity occurs at a lower chemical potential for a mixture where one component can occupy regions of the porespace inaccessible to the other. We suggest that this crossover in selectivity may be a general feature of microporous adsorption.     

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.     

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.     

Barrier height of free energy on confined polymer translocation through a short nano-channel

The translocation of a confined polymer chain through a nano-channel has been simulated by using two-dimensional bond fluctuation model (BFM) with Monte Carlo dynamics. It is found that the trapping time for the polymer chain to overcome the free energy barrier during the translocation, tautrap, depends exponentially on the chain length N and the channel length M, respectively. The results suggest that the barrier height of free energy depends linearly on N and M, which is different from that predicted for the Gaussian chain.     

Parameterization of Coulomb interaction in three-dimensional periodic systems

A simple method is proposed to calculate Coulomb interactions in three-dimensional periodic cubic systems. It is based on the parameterization of the interaction on polynomials and rational functions. The parameterized functions are compared to tabulation methods, to the Ewald calculations and cubic harmonic function fits found in the literature. Our parameterizations are computationally more efficient than, the use of tabulations at all cases and seem to be more efficient than the cubic harmonic parameterizations in the case of simultaneous potential energy and force calculations. In comparison to the Ewald method, it is feasible to use the parameterizations on small systems and on systems, where pair-wise additive short-range interactions are dominant. One also may prefer the parameterizations to the Ewald method for large systems, if limited accuracy is needed. The embedding of the method into existing molecular dynamics and Monte Carlo simulation codes is very simple. The presented investigation contains some numerical experimental data to support the correct theoretical partition of potential energy in periodic systems, as well.     

Multiple time step diffusive Langevin dynamics for proteins

We present an algorithm for simulating the long time scale dynamics of proteins and other macromolecules. Our method applies the concept of multiple time step integration to the diffusive Langevin equation, in which short time scale dynamics are replaced by friction and noise. The macromolecular force field is represented at atomic resolution. Slow motions are modeled by constrained Langevin dynamics with very large time steps, while faster degrees of freedom are kept in local thermal equilibrium. In the limit of a sufficiently large molecule, our algorithm is shown to reduce the CPU time required by two orders of magnitude. We test the algorithm on two systems, alanine dipeptide and bovine pancreatic trypsin inhibitor (BPTI), and find that it accurately calculates a variety of equilibrium and dynamical properties. In the case of BPTI, the CPU time required is reduced by nearly a factor of 60 compared to a conventional, unconstrained Langevin simulation using the same force field. Proteins 30:215–227, 1998. © 1998 Wiley-Liss, Inc.     

Monte Carlo simulations in the isothermal-isobaric ensemble: use of a ‘shell’ particle for simulating polyatomic fluids

The recent reformulation of the isothermal-isobaric ensemble requires the use of a ‘shell’ particle to define uniquely the volume of the system, thereby avoiding the redundant counting of configurations. A previous modification of the Monte Carlo method, in which trial moves are generated and accepted consistent with the correct constant pressure partition function, is extended here to the case of polyatomic fluids. With a ‘shell’ molecule, either the centre of mass of the molecule or the location of any one of the atoms within the molecule can be chosen to define the system volume. Ensemble averages obtained with the use of the shell molecule differ from ensemble averages determined with the old (i.e. no shell particle) Monte Carlo algorithm, specifically for small system sizes, although both sets of averages become equal, as they must, in the thermodynamic limit. Monte Carlo simulations in the constant pressure ensemble for various Lennard-Jones polyatomic fluids, both for pure component and binary mixtures, demonstrate these differences for small systems. For mixtures, Monte Carlo simulations may include attempted identity swaps for the shell molecule, as the choice of which component serves as the shell molecule is arbitrary when periodic boundary conditions are applied.     

Study of Liquid Dimethyl Sulfoxide by Computer Simulation

The paper reports Monte Carlo and molecular dynamicsresults for pure liquid dimethyl sulfoxide (DMSO) at298 K and 1 atm. The classical 6–12 Lennard–Jones plusCoulomb pairwise potential was used to calculateintermolecular interaction energy. Potentialparameters for the liquid were optimized in this work.Some thermodynamic and dynamical properties obtained,such as heat of vaporization, density and diffusioncoefficient, are in good agreement with theexperimental values. The present model is comparedwith other models for DMSO reported previously. It isshown to be an improvement over earlier potentials.The structure factors and the radial distributionfunctions (rdf), are compared with experimentalresults for the liquid. The analysis shows that thestructure of DMSO is not completely understood yet anddeserves deeper investigation. The geometry of thedimer that corresponds to the rdf plots obtained, isreported. The results suggest that the dipole momentof this dimer plays an important role in the structureof the liquid.     

基于EM算法的遗传重组率估计方法

EM算法是在不完全信息资料下实现参数极大似然估计的一种通用方法．本文导出了双位点不同标记类型,包括共显性-共显性,共显性-显性和显性-显性3种模式下,估计遗传重组率的EM算法,以及获得重组率抽样方差的Bootstrap方法;并将之推广到部分个体缺失标记基因型(未检测到电泳谱带)下的重组率估计．通过大量Monte Carlo模拟研究发现: (1)连锁紧密时,样本容量对重组率的估计影响不大;连锁松散时,需要较大样本容量才可检测到连锁以及实现重组率的较精确估计．(2)用包含缺失标记的所有个体估计重组率比仅用其中的非缺失标记个体估计更准确,且可显著提高连锁检测的统计功效．     

The effects of structural parameters of zeolite on the adsorption of hydrogen: a molecular simulation study

The adsorption isotherm of hydrogen in zeolites FAU, LTA, KFI, RWY, RHO and TSC has been simulated employing grand canonical Monte Carlo procedure for a temperature range of 77 to 95 K and different pressures. The effects of structural composition, unit cell volume, framework density and specific surface area of zeolite on hydrogen adsorption in zeolites were investigated. The results clearly show that the adsorption of hydrogen in zeolites with the same silica density is a function of oxygen density at low pressures, and it is approximately the same at intermediate pressures. Nevertheless, at high pressures, the adsorption of hydrogen is a function of pore diameter for zeolites with same silica density. The effect of specific surface area on the adsorption isotherm of hydrogen on zeolites with approximately the same specific surface area is significant at low and high pressures. The results clearly indicate that the adsorption of hydrogen in RWY zeolite has maximum value at 77 K and at high pressures. The optimum condition of pressure for hydrogen adsorption isotherm in RWY zeolite is determined to be 600 bar. At a temperature of 77 K and a pressure of 600 bar, the adsorption of hydrogen in RWY zeolite is 6.93 wt %.     

The structure of polymer chains in confinement. A Monte Carlo study

A coarse-grained model of polymer star chains confined in two parallel impenetrable surfaces, which were attractive for polymer beads was studied. The flexible homopolymer chains were built of united atoms whose positions in space were restricted to vertices of a simple cubic lattice. The chains were modeled in good solvent conditions and, thus, there were no long-range specific interactions between polymer beads—only the excluded volume was present. The influence of the polymer density and the distances between the confining surfaces on the properties of star-branched polymers was studied. It is shown that the chains adsorbed on one surface could change their position so that they swap between both surfaces with frequency depending on the size of the slit and on the density of the system only. The increase of the polymer density diminished the frequency of jumps and caused that chains became only partially adsorbed. The analysis of structural elements of chains showed that the increase of the density of the system leads to increase of the number of bridges connecting the two adsorbing surfaces, thus, the frequency of jumps between them decreases.     

Influence of substrate pattern on the adsorption of HP lattice proteins

With the highly simplified hydrophobic-polar model representation of a protein, we can study essential qualitative physics without an unnecessarily large computational overhead. Using Wang-Landau sampling in conjunction with a set of efficient Monte Carlo trial moves, we studied the adsorption of short HP lattice proteins on various simple patterned substrates and in particular for checkered patterned surfaces. A set of single-site mutated HP proteins is used to investigate the role of hydrophobicity of a protein chain and surface pattern for substrates with various pattern cell sizes relative to the protein’s native configuration. For most cases, we found that the adsorption transition occurs at a lower temperature, while the hydrophobic core formation is less affected. The flattening procedure after the HP protein is adsorbed is more sensitive to the change in surface patterns and single-site mutations. These observations stay valid for both strongly and weakly attractive surfaces.     

Molecular Modelling of The Mechanism of Action of Organic Clay-Swelling Inhibitors

Abstract

It is well known that the sodium smectite class of clays swells macroscopically in contact with water, whereas under normal conditions the potassium form does not. In recent work using molecular simulation methods, we have provided a quantitative explanation both for the swelling behaviour of sodium smectite clays and the lack of swelling of potassium smectites [1]. In the present paper, we apply similar modelling methods to study the mechanism of inhibition of clay-swelling by a range of organic molecules.

Experimentally, it is known that polyalkylene glycols (polyethers) of intermediate to high relative molecular mass are effective inhibitors of smectite clay swelling. We use a range of atomistic simulation techniques, including Monte Carlo and molecular dynamics, to investigate the interactions between a selection of these compounds, water, and a model smectite clay mineral. These interactions occur by means of organised intercalation of water and organic molecules within the galleries between individual clay layers.

The atomic interaction potentials deployed in this work are not as highly optimised as those used in our clay-cation-water work [1]. Nevertheless, our simulations yield trends and results that are in qualitative and sometimes semi-quantitative agreement with experimental findings on similiar (but not identical) systems. The internal energy of adsorption of simple polyethers per unit mass on the model clay is not significantly different from that for water adsorption; our Monte Carlo studies indicate that entropy is the driving force for the sorption of the simpler organic molecules inside the clay layers: a single long chain polyethylene glycol can displace a large number of water molecules, each of whose translational entropy is greatly enhanced when outside the clay. Hydrophobically modified polyalkylene glycols also enjoy significant van der Waals interactions within the layers which they form within the clay galleries.

In conjunction with experimental studies, our work furnishes valuable insights into the relative effectiveness of the compounds considered and reveals the generic features that high performance clay-swelling inhibitors should possess. For optimal inhibitory activity, these compounds should be reasonably long chain linear organic molecules with localised hydrophobic and hydrophilic regions along the chain. On intercalation of these molecules within the clay layers, the hydrophobic regions provide an effective seal against ingress of water, while the hydrophilic ones enhance the binding of the sodium cations to the clay surface, preventing their hydration and the ensuing clay swelling.     

Stochastic simulation of actin dynamics reveals the role of annealing and fragmentation

Recent observations of F-actin dynamics call for theoretical models to interpret and understand the quantitative data. A number of existing models rely on simplifications and do not take into account F-actin fragmentation and annealing. We use Gillespie's algorithm for stochastic simulations of the F-actin dynamics including fragmentation and annealing. The simulations vividly illustrate that fragmentation and annealing have little influence on the shape of the polymerization curve and on nucleotide profiles within filaments but drastically affect the F-actin length distribution, making it exponential. We find that recent surprising measurements of high length diffusivity at the critical concentration cannot be explained by fragmentation and annealing events unless both fragmentation rates and frequency of undetected fragmentation and annealing events are greater than previously thought. The simulations compare well with experimentally measured actin polymerization data and lend additional support to a number of existing theoretical models.     

生物可降解聚合物纳米粒给药载体

生物可降解聚合物纳米粒用于给药载体具有广阔的前景。本文综述了生物可降解聚合物纳米粒给药载体领域的最新进展 :包括纳米粒表面修饰特性、药物释放、载多肽和蛋白质等生物大分子药物传输中的潜在应用。     

Dosimetry of small photon fields in the presence of bone heterogeneity using MAGIC polymer gel,Gafchromic film,and Monte Carlo simulation

BackgroundThe presence of heterogeneity within the radiation field increases the challenges of small field dosimetry. In this study, the performance of MAGIC polymer gel was evaluated in the dosimetry of small fields beyond bone heterogeneity.Materials and methodsCircular field sizes of 5, 10, 20 and 30 mm were used and Polytetrafluoroethylene with density of 2.2 g/cm³ was used as the bone equivalent material. The PDD curves, beam profiles, and penumbra widths were measured using MAGIC polymer gel, EBT2 film, and Monte Carlo simulation.ResultsThe maximum differences between MAGIC and EBT2 are 6.1, 4.7, 2.4, and 2.2 for PDD curves at 5, 10, 20, and 30 mm circular fields, respectively. The dose differences and distance to agreement between MAGIC and MC were within 1.89%/0.46 mm, 1.66%/0.43 mm, 1.28%/0.77 mm, and 1.31%/0.81 mm for beam profile values behind bone heterogeneity at 5, 10, 20, and 30 mm field sizes, respectively.ConclusionThe results presented that the MAGIC polymer gel dosimeter is a proper instrument for dosimetry beyond high density heterogeneity.