A simulation study of methane-hydrogen gas mixture permeation through nanoporous palladium membrane using molecular dynamics

Modulating ion transport through nanoporous membranes is critical to many important chemical and biological separation processes. The corresponding transport timescales, however, are often too long to capture accurately using conventional molecular dynamics (MD). Recently, path sampling techniques, such as forward-flux sampling (FFS), have emerged as attractive alternatives for efficiently and accurately estimating arbitrarily long ionic passage times. Here, we use non-equilibrium MD and FFS to explore how the kinetics and mechanisms of pressure-driven chloride transport through a nanoporous graphitic membrane are affected by its lateral dimensions. We not only find ionic passage times and free energy barriers to decrease dramatically upon increasing the membrane surface area but also observe an abrupt and discontinuous change in the locus of the transition state. These strong finite size effects arise due to the cumulative effect of the periodic images of the leading ion entering the pore on the distribution of the induced excess charge at the membrane surface in the feed. By assuming that the feed is an ideal conductor, we analytically derive a finite size correction term that can be computed from the information obtained from a single simulation and successfully use it to obtain corrected free energy profiles with no dependence on the system size. We then estimate ionic passage times in the thermodynamic limit by assuming an Eyring-type dependence of rates on barriers with a size-independent prefactor. This approach constitutes a universal framework for removing finite size artifacts in molecular simulations of ion transport through nanoporous membranes and biological channel proteins.

Molecular dynamics simulation-directed rational design of nanoporous graphitic carbon nitride membranes for water desalination

The molecular dynamics (MD) calculation was performed for BaUO3 in the temperature range from 300 K to 2000 K to evaluate the physicochemical properties viz., the lattice parameter, thermal expansion coefficient (α), compressibility (β), heat capacity, and thermal conductivity. The parameters of the interatomic potential were determined by fitting to the experimental values of the lattice parameter for BaUO3. The heat capacity at constant volume (CV) was evaluated from the variation of the internal energy of the system by fixed volume MD calculation. The lattice dilational contribution to the heat capacity (Cd) was calculated from α and β. The MD calculation results of (Cv + Cd) almost agreed with the experimental data. The thermal conductivity (γ) was calculated by using a Green-Kubo relation. The temperature dependence of calculated γ followed a 1/T law, which indicates that the lattice contribution to the thermal conductivity (γlat) could be evaluated by the MD calculation. These results showed that MD techniques can be usefully applied to evaluate the physicochemical properties of BaUO3.

Efficient separation of He/CH4 mixture by functionalized graphenylene membranes: A theoretical study

Prediction of the morphology of the as-implanted damage in silicon using a novel combination of BCA and MD simulations

Molecular dynamics (MD) calculations have been performed on carboxypeptidase A and on its adducts with inhibitors, such as d-phenylalanine (dPhe) and acetate. The catalytically essential zinc ion present in the protein was explicitly included in all the simulations. The simulation was carried out over a sphere of 15 A centered on the zinc ion. The crystallographic water molecules were explicitly taken into account; then the protein was solvated with a 18 A sphere of water molecules. MD calculations were carried out for 45-60 ps. There is no large deviation from the available X-ray structures of native and the dPhe adduct for the MD structures. Average MD structures were calculated starting from the X-ray structure of the dPhe adduct, and, from a structure obtained by docking the inhibitor in the native structure. Comparison between these two structures and with that of the native protein shows that some of the key variations produced by inhibitor binding are reproduced by MD calculations. Addition of acetate induces structural changes relevant for the understanding of the interaction network in the active cavity. The structural variations induced by different inhibitors are examined. The effects of these interactions on the catalytic mechanism and on the binding of substrate are discussed.

Molecular modeling techniques were used to investigate the permeability and selectivity of various natural gas components through nano-porous polyimide membranes for the environmentally-friendly “Green” separation of natural gas. The polyimide membranes showed the ability of creating nano-scale channels within the polymeric matrix during the molecular mobility of the polymeric chains through which specific gas molecules can penetrate the membrane surface. The four natural gas components investigated in this study were methane, ethane, propane and butane, all hydrocarbon materials of similar basic chemical structures. The self-diffusion coefficients of the gas molecules were thus used to express the permeability of the various gases through the membranes since the solubility of the gas molecules in the polymeric substances were assumed to be constant. Methane showed a noticeably high self-diffusion coefficient calculated from the application of Einstein relation to the generated molecular dynamics trajectories. All other gases had similar values for the self-diffusion coefficients, which indicate the ability of the methane molecules to penetrate the polymeric membrane in a much larger speed due to a possible matching between the methane molecular size and the size of the interconnected nano-channels within the membranes. The results also showed that the polymer molecules had lower self-diffusion coefficients than the gas ones due to the large size of the polymeric segments. Other structural parameters such as the radial distribution function in direct relationship to the local packing of the polymeric segments and penetrant molecules are also illustrated. [DOI: 10.1380/ejssnt.2012.63]

Molecular dynamics study on electric field-facilitated separation of H2O/O2 through nanoporous graphene oxide membrane

WHERE WE ARE IN MODELING MECHANICAL, TRAFFIC, AND SOCIO-ECONOMICAL DISCRETE SYSTEMS Discrete systems have been firstly introduced in physics (Fisher and Wiodm, 1969; Noor and Nemeth, 1980; Adhikari et al., 1996; Kornyak, 2009) to simulate materials at the microand nano-scales where a continuum description of matter breaks down. The constituents can be atoms or molecules and their interactions are usually modeled by force fields resulting from chemical potentials or weak van der Waals interactions, depending on the type of bonding. These models have been further exploited in mechanics with the aim of predicting macroscopic properties such as strength and toughness from the non-linear interactions taking place between the constituents at the different scales. Pioneering attempts in mechanics to model discrete mechanical systems are those using lattice models (van Mier et al., 1995; Schlangen and Garboczi, 1997) characterized by a network of nodes connected by links modeled by beams. Although proven to suffer from meshdependency, they have been broadly used for studying the non-linear fracture behavior of concrete at the meso-scale. Another line of research regards the generalizedBorn approach (Pellegrini and Field, 2002; Marenich et al., 2013), firstly used in chemistry to model a solute represented as a set of three-dimensional spheres into a continuum medium solvent, then applied in molecular mechanics (called MM/GBSA) to investigate contact and fracture of bodies at the micro-scale. The high-computational power and the development of powerful open source software allow nowadays the design of wide discrete scalable models composed of up to millions of particles or molecules whose equations of motions and mutual interactions are described by highly nonlinear interatomic potential laws. This is the field of molecular dynamics (MD), which led to the development of specific explicit time integration schemes (like the velocity-verlet integration scheme) to solve large systems of equations with a reduced computational cost. Car and Parrinello (1985) proposed a minimization of the total energy of the system by applying a dynamical simulated annealing based on MD. MD computations can also be coupled with continuum simulations by multi-scale methods. Among the many strategies available in the literature, (Shenoy et al., 1999; Knap and Ortiz, 2001) developed an approach based on the Tadmor’s quasi-continuum method (Tadmor et al., 1996) operating on a representative atomistic zone with a reduced number of degrees of freedom. Local minima of the whole system potential energy are determined via the total energy from a cluster of atoms, avoiding the complete calculation of the full atomistic force field. The MD enriched continuum method by Belytschko and Xiao (2003) and Xiao and Belytschko (2003) was also another pioneering approach to couple a potential energy Hamiltonian calculation conducted on a fine scale MD domain with a Lagrangian calculation on a coarse scale continuum domain with an overlapped bridging domain among the two representations. Recently, an implementation of interatomic potential laws within a displacement-based finite element (FE) formulation has also been proposed in Nasdala et al. (2010), with a rigorous implicit solution scheme, aiming at generating models where non-linear discrete and continuous systems can be suitably combined. Discrete systems made of nodes and links are also used in other disciplines than mechanics to model transport or socio-economical networks (Caldarelli and Vespignani, 2007; Whrittle, 2012). Based on a continuum version of traffic conservation along a link, Lighthill and Whitham (1955) and Whitham (1974) and independently Richards (1956) proposed the LWR model where the governing equation describing the dependency of the traffic flux on time and on location along a link is a nonlinear hyperbolic partial differential equation (PDE) analogous to that describing the propagation of the front of a wave inside a medium. For a homogenous link where the velocity of traffic is the same at any location and no shocks on the traffic flow are present, the integration of the LWR PDE leads to a non-linear relation between the traffic flow and the density of vehicles, which fully represents the traffic state. Also, in economics, it is of great interest to quantify the effect of breaking a link over the whole network response by simulating the dynamics of flow redistribution. Again a flow model can be used as suggested in Zhou et al. (2010) to decode a huge human crowd without distinction between

Graphene-derived membranes has gained much interest recently due to its promising potential in filtration and separation applications. Molecular Sieving phenomena of gas molecules in the interlayer of graphene oxide nanopore have been investigated using molecular dynamic (MD) simulation. We explore I-129 gas radionuclides sequestration from natural air in nanoporous graphene oxide membranes in which different sizes and geometries of pores were modeled on the graphene oxide sheet. In the present work, mean-squared displacement (MSD), diffusion, flow of gas and the number of crossed gas molecules through graphene oxide nanopore membrane have been calculated and the results showed, selective proper nanopores in graphene oxide membrane could dramatically improve separation. The aim of this paper is to show that for the well-defined pore size called P-12, it is possible to separate I-129 from a gas mixture containing I-129, O 2 and N 2 . The results would be benefited by the oil industry and others.

Time-Trimming Tricks for Dynamic Simulations: Splitting Force Updates to Reduce Computational Work

Molecular dynamics calculations are reported on the sorption and diffusion of small gas molecules (He, H2, and O2) in amorphous polyisobutylene. An all-atom force field (with explicit hydrogen atoms) was used. In addition to the standard method of obtaining the diffusion coefficient from an equilibrium calculation via the mean-square displacement we used a nonequilibrium technique that applies a fictitious external field selectively to the gas molecules. To our knowledge, nonequilibrium MD is, for the first time, applied to the problem of gas diffusion in polymers. Results of both techniques are compared. Energy profiles of the jump events underlying gas diffusion through polymers are studied. We also discuss the possible presence of anomalous (non-Einstein) behavior of gas molecules diffusing through an amorphous polymer. Gas solubilities in polyisobutylene are calculated by particle-insertion techniques.

The Multi-Stage model for diatomic molecules scattering from solid surfaces is presented, which is based on the large body of data obtained from molecular dynamics calculations and molecular beam experiments. The molecular dynamics method is used for the numerical analysis on the scattering of an oxygen gas molecule from a clean graphite surface. The angular and velocity distribution agrees well with experimental results, which was shown in our previous report. The scattering direction, translational energy and rotational energy of the gas molecule after each collision is saved for the data base. The basic idea of the model is to separate the collision into different stages. At each stage, the energy loss, the scattering direction and the trapping probability of the gas molecule will be determined. The angular and velocity distribution of the model agrees with those of molecular beam experiments.

Among proteins utilized as sweeteners, neoculin and miraculin are taste-modifying proteins that exhibit pH-dependent sweetness. Several experiments on neoculin have shown that His11 of neoculin is responsible for pH dependence. We investigated the molecular mechanism of the pH dependence of neoculin by molecular dynamics (MD) calculations. The MD calculations for the dimeric structures of neoculin and His11 mutants showed no significant structural changes for each monomer at neutral and acidic pH levels. The dimeric structure of neoculin dissociated to form isolated monomers under acidic conditions but was maintained at neutral pH. The dimeric structure of the His11Ala mutant, which is sweet at both neutral and acidic pH, showed dissociation at both pH 3 and 7. The His11 residue is located at the interface of the dimer in close proximity to the Asp91 residue of the other monomer. The MD calculations for His11Phe and His11Tyr mutants demonstrated the stability of the dimeric structures at neutral pH and the dissociation of the dimers to isolated monomers. The dissociation of the dimer caused a flexible backbone at the surface that was different from the dimeric interface at the point where the other monomer interacts to form an oligomeric structure. Further MD calculations on the tetrameric structure of neoculin suggested that the flexible backbone contributed to further dissociation of other monomers under acidic conditions. These results suggest that His11 plays a role in the formation of oligomeric structures at pH 7 and that the isolated monomer of neoculin at acidic pH is responsible for sweetness.

Super square (SS) carbon nanotube (CNT) networks, acting as a new kind of nanoporous membrane, manifest excellent water desalination performance. Nanopores in SS CNT network can efficiently filter NaCl from water. The water desalination ability of such nanoporous membranes critically depends on the pore diameter, permitting water molecule permeatration while salt ion obstruction. On the basis of the systematical analysis on the interaction among water permeability, salt concentration limit and pressure on the membranes, an empirical formula is developed to describe the relationship between pressure and concentration limit. In the meantime, the nonlinear relationship between pressure and water permeability is examined. Hence, by controlling pressure, optimal plan can be easily made to efficiently filter the saltwater. Moreover, steered molecular dynamics (MD) method uncovers bending and local buckling of SS CNT network that leads to salt ions passing through membranes. These important mechanical behaviours are neglected in most MD simulations, which may overestimate the filtration ability. Overall, water permeability of such material is several orders of magnitude higher than the conventional reverse osmosis membranes and several times higher than nanoporous graphene membranes. SS CNT networks may act as a new kind of membrane developed for water desalination with excellent filtration ability.