Molecular Monte Carlo Simulations Research Articles

Molecular Dynamics Simulations of Molecular Diffusion Equilibrium and Breakdown Mechanism of Oil-Impregnated Pressboard with Water Impurity.

The water molecule migration and aggregation behaviors in oil-impregnated pressboard are investigated by molecular dynamics simulations in combination with Monte Carlo molecular simulation technique. The free energy and phase diagram of H2O-dodecylbenzene (DDB) and H2O-cellulose mixtures are calculated by Monte Carlo technique combined with the modified Flory-Huggins model, demonstrating that H2O molecules can hardly dissolved with infinitesimal content in cellulose system at temperature lower than 650 K, based on which the oil/cellulose layered structure with water impurity representing three-phase coexistence in oil-impregnated pressboard are modeled and performed for molecular dynamics. The molecular dynamics of H2O/DDB/cellulose three-phase mixture simulating oil-paper insulating system with H2O impurity indicates that DDB molecules can thermally intrude into the cellulose-water interface so as to separate the water phase and cellulose fiber. The first-principles electronic structure calculations for local region of H2O/DDB interface show that H2O molecules can introduce bound states to trap electrons and acquire negative charges, so that they will obtain sufficient energy from applied electric field to break DDB molecular chain by collision, which are verified by subsequent molecular dynamics simulations of H2O−/DDB interface model. The electric breakdown mechanism under higher than 100 kV/m electric field is presented based on the further first-principles calculations of the produced carbonized fragments being dissolved and diffusing in DDB phase. The resulted broken DDB fragments will introduce impurity band between valence and conduction bands of DDB system, evidently decreasing bandgap as to that of conducting materials in their existence space. The conductance channel of these carbonized DDB fragments will eventually be formed to initiate the avalanche breakdown process by the cycle-feedback of injected charge carriers with carbonized channels.

Prediction of Contact Angles and Density Profiles of Sessile Droplets Using Classical Density Functional Theory Based on the PCP-SAFT Equation of State.

This study demonstrates the capability of the density functional theory (DFT) formalism to predict contact angles and density profiles of model fluids and of real substances in good quantitative agreement with molecular simulations and experimental data. The DFT problem is written in cylindrical coordinates, and the solid-fluid interactions are defined as external potentials toward the fluid phase. Monte Carlo (MC) molecular simulations are conducted in order to assess the density profiles resulting from the Helmholtz energy functional used in the DFT formalism. Good quantitative agreement between DFT predictions and MC results for Lennard-Jones and ethane nanodroplets is observed, both for density profiles and for contact angles. That comparison suggests, first, that the Helmholtz energy functional proposed in a previous study [ Sauer , E. ; Gross , J. Ind. Eng. Chem. Res. 56 , 2017 , 4119 - 4135 ] is suitable for three-phase contact lines and, second, that Lagrange multipliers can be used to constrain the number of molecules, similar to a canonical ensemble. Experiments of sessile droplets on solid surfaces are performed to assess whether a real solid with its microscopic roughness can be described through a simple model potential. Comparison of DFT results to experimental data is done for a Teflon surface because Teflon can be regarded as a substrate exhibiting only attractive interactions of van der Waals type. It is shown that the real solid can be described as a perfectly planar solid with effective solvent-to-solid interactions, defined through a single adjustable parameter for the solid. Subsequent predictions for the contact angle of eight solvents, including polar components such as water, are found in very good agreement to experimental data using simple Berthelot-Lorentz combining rules. For the eight investigated solvents, we find mean absolute deviations of 3.77°.

Discovering privileged topologies of molecular knots with self-assembling models

Despite the several available strategies to build complex supramolecular constructs, only a handful of different molecular knots have been synthesised so far. Here, in response to the quest for further designable topologies, we use Monte Carlo sampling and molecular dynamics simulations, informed by general principles of supramolecular assembly, as a discovery tool for thermodynamically and kinetically accessible knot types made of helical templates. By combining this approach with the exhaustive enumeration of molecular braiding patterns applicable to more general template geometries, we find that only few selected shapes have the closed, symmetric and quasi-planar character typical of synthetic knots. The corresponding collection of admissible topologies is extremely restricted. It covers all known molecular knots but it especially includes a limited set of novel complex ones that have not yet been obtained experimentally, such as 10124 and 15n41185, making them privileged targets for future self-assembling experiments.

Role of Ninth Type-III Domain of Fibronectin in the Mediation of Cell-Binding Domain Adsorption on Surfaces with Different Chemistries.

The orientation and conformation of adhesive proteins after adsorption play a central role in cell-binding bioactivity. Fibronectin (Fn) holds two peptide sequences that favor cell adhesion: the Arg-Gly-Asp (RGD) loop on the tenth type-III domain (Fn-III10) and the Pro-His-Ser-Arg-Asn (PHSRN) synergy site on the ninth type-III domain (Fn-III9). Herein, adsorption of Fn fragments (Fn-III10 and Fn-III9-10) on self-assembled monolayers (SAMs) carrying various functional groups (-COOH, -NH2, -CH3, and -OH) was investigated by the Monte Carlo method and molecular dynamics simulation in order to understand its mediation effect on cell adhesion. The results demonstrated that Fn-III9 could enhance the stiffness of the Fn molecule and further fix the adsorption orientation. The RGD site of the Fn fragment appeared to be deactivated on hydrophobic surfaces (CH3-SAM) because of the binding of adjacent nonpolar residues on surfaces, whereas charged surfaces (COOH-SAM and NH2-SAM) and hydrophilic surfaces (OH-SAM) were conducive to the formation of cell-binding-favorable orientation for Fn fragments. The cell adhesion capability of Fn fragments was highly improved on positively charged surfaces (NH2-SAM) and hydrophilic surfaces because of the advantageous steric structure and orientation of both RGD and PHSRN sites. This work provides an insight into the interplay at the atomic scale between protein adsorption and surface chemistry for designing biologically responsive substrate surfaces.

Molecular simulation of volume of mixing, Helmholtz free energy of mixing and entropy of mixing in bulk fluid mixtures

ABSTRACTWe describe a kinetic Monte Carlo molecular simulation procedure to calculate the Helmholtz free energy, the entropy and the chemical potentials of all components in a bulk fluid mixture. This allows us to derive the excess properties (volume, free energy and entropy) resulting from the mixing of homogeneous fluids of pure components at constant temperature and pressure. We have chosen neon–xenon mixtures to illustrate our method because of the large difference in collision diameter and well-depth of the interaction energy. When xenon is predominant in the mixture, the volume of mixing is larger. The excess entropy of mixing correlates with the volume of mixing, since a positive excess volume enables more configurations (more possible molecular distributions). The excess thermodynamic quantities as functions of the total density were found to be insensitive to temperature. To investigate the effects of the molecular parameters, we also studied argon–nitrogen and argon–krypton mixtures. The effect of the difference in molecular parameters is in the order: argon–nitrogen < argon–krypton < neon–xenon. A large difference in the well-depth of the interaction energies results in an increase in the excess thermodynamic variables, which is in agreement with the literature McDonald IR. NpT-ensemble Monte Carlo calculations for binary liquid mixtures. Mol Phys. 1972;23(1):41–58; Singer JVL, Singer K. Monte Carlo calculation of thermodynamic properties of binary mixtures of Lennard-Jones (12-6) liquids. Mol Phys. 1972;24(2):357–390.

Gate-Opening Mechanism of Hydrophilic–Hydrophobic Metal–Organic Frameworks: Molecular Simulations and Quasi-Equilibrated Desorption

Adsorption of polar and nonpolar molecules in hydrophilic–hydrophobic STAM-1 metal–organic framework was studied by means of quasi-equilibrated temperature-programmed desorption and adsorption (QE-TPDA) experimental technique and molecular simulation. The QE-TPDA measurements revealed that thermal stability of the studied material in the presence of water may be lower than determined from thermogravimetric analysis. Molecular dynamics showed evident impact of diffusion on the adsorption mechanism in STAM-1. The QE-TPDA profiles recorded for adsorption of n-alkanes, water, and alcohols indicate the gate-opening effect occurring only upon adsorption of polar molecules, which was confirmed by in situ IR spectroscopy. Monte Carlo molecular simulations agree with experimental data revealing preferable adsorption sites for the molecules of alcohols in STAM-1. Simulations also showed that the molecular mechanism of the gate-opening is dependent on the size of polar guest molecules.

Guaiacol and its mixtures: New data and predictive models. Part 2: Gibbs energy of solvation

Guaiacol is a model molecule for lignocellulosic biomass processing, and thus understanding its interactions with solvents is an important step when developing units for processing lignocellulosic biomass. In this work, activity coefficient measurements of different solvents (acetonitrile, ethanol, tetrahydrofuran) in guaiacol have been performed at different concentrations and temperatures. These measurements have been used to estimate the infinite dilution activity coefficients and the Gibbs energy of solvation of guaiacol in the different solvents, and of each solvent in guaiacol. These estimated values were compared to those obtained with different predictive models: UNIFAC DMD, Monte Carlo Molecular Simulation, COSMO-SAC and GC-PPC-SAFT. The predictions are in very good agreement with the Gibbs energies of solvation derived from experimental data. Some conclusions are also drawn regarding the inter- and intramolecular hydrogen bonding in guaiacol and about its affinity with different solvents on the basis of the inter- and intramolecular interactions taking place.

Numerical evidence of heterogeneity and nanophases in a binary liquid confined at the nanoscale

Recent results suggest that a binary liquid that is usually homogeneous in the bulk phase can demix and form a core–shell organisation in a confined medium. In this work, we combine molecular dynamics and Monte Carlo simulations to verify this specific structure and to capture the driving force governing this possible segregation at the nanoscale.

Growth of silver on zinc oxide via lattice and off-lattice adaptive kinetic Monte Carlo

The growth of Ag on ZnO was modeled using a reactive force field potential and a combination of molecular dynamics and adaptive kinetic Monte Carlo (AKMC) simulations. An adaptive lattice-based AKMC model is described as a method of extending timescales and length scales that can be simulated. Reusing previously found transitions to reduce computational time is discussed for both the lattice and off-lattice AKMC approaches. With these methods, growth of over 1 monolayer’s worth of Ag is simulated corresponding to a real deposition time of up to 0.1 s. The results show that the deposited silver aggregates on the surface through mainly single atom moves with few concerted motions. Initially silver adatoms do not agglomerate and the energy barriers for silver dimers to form are larger than for them to break apart. The first layer of silver grows as a series of connected regions rather than forming well-defined centro-symmetric islands.

An Innovative Approach for Molecular Simulation of Nanostructured Adsorption Isotherms via the Ant Colony Method

The original grand canonical Monte Carlo (GCMC) molecular simulation method heavily relies on pure random steps for its various phases of displacement, removal and insertion. A new algorithm is presented in this Article which employs the global optimization ant colony technique in a state-of-the-art algorithm to predict the adsorption isotherm of any adsorbate inside nanostructured adsorbents. Several experimentally measured isotherms are used from the literature to successfully validate the proposed method. A detailed flowchart is presented to describe the entire algorithm. The Akaike information criterion is used as a part of the proposed method to determine the optimum number of required iterations. It was clearly demonstrated that our in-house ant colony molecular simulation (ACMS) method outperforms the conventional GCMC method for all case studies. The simulation results also indicate that the newly proposed algorithm performs several orders of magnitude faster than GCMC with the same or better accu...

Phase Diagram of Hydrogen and a Hydrogen-Helium Mixture at Planetary Conditions by Quantum MonteCarlo Simulations.

Understanding planetary interiors is directly linked to our ability of simulating exotic quantum mechanical systems such as hydrogen (H) and hydrogen-helium (H-He) mixtures at high pressures and temperatures. Equation of state (EOS) tables based on density functional theory are commonly used by planetary scientists, although this method allows only for a qualitative description of the phase diagram. Here we report quantum MonteCarlo (QMC) molecular dynamics simulations of pure H and H-He mixture. We calculate the first QMC EOS at 6000K for a H-He mixture of a protosolar composition, and show the crucial influence of He on the H metallization pressure. Our results can be used to calibrate other EOS calculations and are very timely given the accurate determination of Jupiter's gravitational field from the NASA Juno mission and the effort to determine its structure.

Hydrogen storage comparison of M doped vanadium oxide nanotubes (M = Mo, Zr and W): A molecular simulation study

Zr, Mo and W doped Vanadium oxide nanotube were considered as remarkable materials for hydrogen storage applications. Monte Carlo molecular simulation was performed to study the adsorption behavior of hydrogen molecules on Vanadium oxide nanotubes (VONTs). The effects of temperature, pressure and mole percent of hydrogen on adsorption capacity of VONTs were investigated to provide deep insight of adsorption behavior. The results represented that hydrogen adsorption is an increasing function of pressure and at about 50 MPa all three metal doped VONT has maximum hydrogen capacity. At 5 MPa and room temperature, the hydrogen capacities of Mo, W and Zr doped VONTs were 1.39, 0.88 and 1.43 w% respectively. With temperature increment up to room temperature, more reduction in initial hydrogen capacity were observed in Mo and Zr doped VONTs.Evaluating hydrogen adsorption of Zr doped VONT from pure and hydrogen /nitrogen mixtures at 300 K indicated that under 2 Mpa, modifications in adsorption capacities were insignificant after N2 addition to the environment. Therefore, Zr doped VONT in hydrogen /nitrogen mixture environment can act as a capable adsorbent for Hydrogen storage system in comparison with Mo and W doped VONTs.

The role of differing probe and target strand lengths in DNA microarrays investigated via Monte Carlo molecular simulation

DNA duplexes consisting of a 25mer together with shorter complementary sequences were studied over a range of temperature and surface binding motifs using a coarse-grained two-site nucleotide model. Results were analyzed in terms of hydrogen bonding interactions and structural characteristics and indicate that hybridization is most stable when furthest from the surface binding site. Strand elongation and straightening near the bound end are found to be correlated to duplex destabilization.

Update 0.2 to “pysimm: A python package for simulation of molecular systems”

An update to the pysimm Python molecular simulation API is presented. A major part of the update is the implementation of a new interface with CASSANDRA — a modern, versatile Monte Carlo molecular simulation program. Several significant improvements in the LAMMPS communication module that allow better and more versatile simulation setup are reported as well. An example of an application implementing iterative CASSANDRA–LAMMPS interaction is illustrated.

Carbon Dioxide Adsorption over Amine-Functionalized MOFs

This paper focused on the CO2 absorption process of UiO-66/PEI composites by using experimental and computational methods. UiO-66 was synthesized by hydrothermal method and further modified with Polyethylenimine (PEI) molecules. The synthetic samples were characterized through X-ray diffraction, infrared IR, and nitrogen adsorption-desorption. The effect of PEI loading and adsorption temperature on CO2 adsorption are investigated. The results indicate that the CO2 adsroptioncapacity of UiO-66/PEI at 25℃ were up to 3.13 mmol/g, which is 1.5 times greater than that of the parent UiO-66. On the basis of the validated experimental result, the Grand Canninical Monte Carlo (GCMC) molecular simulation method was used to calculate the probability density distribution of the CO2 adsorption in the skeleton, adsorption position, adsorption energy distribution as well as diffusion characteristics. The simulated results discover that the amine-group play a key role to increase adsorption capacity of compound MOFs, and these excellent properties make it a type of promising adsorbents in CO2 storage and separation.

Molecular Understanding of Laccase Adsorption on Charged Self-Assembled Monolayers.

Controlling the orientation of laccase on electrodes is crucial for the achievement of fast direct electron transfer. It is important to find a short pathway between the T1 copper site of laccase and a substrate during the laccase immobilization. In this work, we studied the adsorption orientation and conformation of Trametes versicolor laccase (TvL) on two kinds of charged self-assembled monolayers (SAMs), including NH2-SAM and COOH-SAM, by parallel tempering Monte Carlo and all-atom molecular dynamics simulations. TvL adsorbs on positively and negatively charged surface with "end-on" and "lying" orientation, respectively. On the positively charged surface, T1 copper site of TvL is closer to the surface. The orientation of TvL on positively charged surface is narrower than that on negatively charged surface. Thus, the positively charged surface is more conducive to the immobilization of TvL. The conformational changes of TvL on the charged surfaces are analyzed by RMSD, superimposed structures, dipole moment, gyration radius, and eccentricity. Results show that native structures of TvL are well preserved when it adsorbs on the charged surfaces. This work provides atomistic insight into the mechanism of TvL adsorption on charged surface and is helpful for the design and development of laccase-based electrodes.

An improved theoretical procedure for the pore-size analysis of activated carbon by gas adsorption

Abstract Amorphous carbon materials play a vital role in adsorbed natural gas (ANG) storage. One of the key issues in the more prevalent use of ANG is the limited adsorption capacity, which is primarily determined by the porosity and surface characteristics of porous materials. To identify suitable adsorbents, we need a reliable computational tool for pore characterization and, subsequently, quantitative prediction of the adsorption behavior. Within the framework of adsorption integral equation (AIE), the pore-size distribution (PSD) is sensitive to the adopted theoretical models and numerical algorithms through isotherm fitting. In recent years, the classical density functional theory (DFT) has emerged as a common choice to describe adsorption isotherms for AIE kernel construction. However, rarely considered is the accuracy of the mean-field approximation (MFA) commonly used in commercial software. In this work, we calibrate four versions of DFT methods with grand canonical Monte Carlo (GCMC) molecular simulation for the adsorption of CH 4 and CO 2 gas in slit pores at 298 K with the pore width varying from 0.65 to 5.00 nm and pressure from 0.2 to 2.0 MPa. It is found that a weighted-density approximation proposed by Yu (WDA-Yu) is more accurate than MFA and other non-local DFT methods. In combination with the trapezoid discretization of AIE, the WDA-Yu method provides a faithful representation of experimental data, with the accuracy and stability improved by 90.0% and 91.2%, respectively, in comparison with the corresponding results from MFA for fitting CO 2 isotherms. In particular, those distributions in the feature pore width range (FPWR) are proved more representative for the pore-size analysis. The new theoretical procedure for pore characterization has also been tested with the methane adsorption capacity in seven activated carbon samples.

Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations.

Four pseudorandom number generators were compared with a physical, quantum-based random number generator using the NIST suite of statistical tests, which only the quantum-based random number generator could successfully pass. We then measured the effect of the five random number generators on various calculated properties in different Markov-chain Monte Carlo simulations. Two types of systems were tested: conformational sampling of a small molecule in aqueous solution and liquid methanol under constant temperature and pressure. The results show that poor quality pseudorandom number generators produce results that deviate significantly from those obtained with the quantum-based random number generator, particularly in the case of the small molecule in aqueous solution setup. In contrast, the widely used Mersenne Twister pseudorandom generator and a 64-bit Linear Congruential Generator with a scrambler produce results that are statistically indistinguishable from those obtained with the quantum-based random number generator. © 2017 Wiley Periodicals, Inc.

Molecular simulation of homogeneous crystal nucleation of AB2 solid phase from a binary hard sphere mixture.

Co-crystal formation from fluid-mixtures is quite common in a large number of systems. The simplest systems that show co-crystal (also called substitutionally ordered solids) formation are binary hard sphere mixtures. In this work, we study the nucleation of AB2 type solid compounds using Monte Carlo molecular simulations in binary hard sphere mixtures with the size ratio of 0.55. The conditions chosen for the study lie in the region where nucleation of an AB2 type solid competes with that of a pure A solid with a face-centered-cubic structure. The fluid phase composition is kept equal to that of the AB2 type solid. The nucleation free-energy barriers are computed using the seeding technique of Sanz et al. [J. Am. Chem. Soc. 135, 15008 (2013)]. Our simulation results show that the nucleation of the AB2 type solid is favored even under conditions where the pure A solid is more stable. This is primarily due to the similarity in the composition of the fluid phase and the AB2 type solid which in turn leads to much lower interfacial tension between the crystal nucleus and the fluid phase. This system is an example of how the fluid phase composition affects the structure of the nucleating solid phase during crystallization and has relevance to crystal polymorphism during crystallization processes.

Phase Diagram of Methane and Carbon Dioxide Hydrates Computed by Monte Carlo Simulations.

Molecular Monte Carlo simulations are used to compute the three-phase (hydrate-liquid water-gas) equilibrium lines of methane and carbon dioxide hydrates, using the Transferable Potentials for Phase Equilibria model for carbon dioxide, the united atom optimized potential for liquid simulations model for methane, and the TIP4P/Ice and TIP4P/2005 models for water. The three-phase equilibrium temperatures have been computed for pressures between 50 and 4000 bar via free-energy calculations. The computed results are as expected for methane hydrates but deviate from the direct-coexistence molecular dynamics (MD) studies for carbon dioxide hydrates. At pressures higher than 1000 bar, both the methane and carbon dioxide hydrates dissociate at lower temperatures than expected from experiments and MD studies. The dissociation enthalpy is found to be largely independent on water models, and its values are measured to be 7.6 and 6.0 kJ/mol of water for methane hydrates and carbon dioxide hydrates, respectively. We evaluate the effect of systematic errors on the determination of chemical potentials and show that systematic errors of 0.1 kJ/mol in the chemical potential of water correspond to deviations of 5 K in the three-phase equilibrium temperatures.