Subdiffusion as a model of transport through the nuclear pore complex

Cargo transport through the nuclear pore complex continues to be a subject of considerable interest to experimentalists and theorists alike. Several recent studies have revealed details of the process that have still to be fully understood, among them the apparent nonlinearity between cargo size and the pore crossing time, the skewed, asymmetric nature of the distribution of such crossing times, and the non-exponentiality in the decay profile of the dynamic autocorrelation function of cargo positions. In this paper, we show that a model of pore transport based on subdiffusive particle motion is in qualitative agreement with many of these observations. The model corresponds to a process of stochastic binding and release of the particle as it moves through the channel. It suggests that the phenylalanine-glycine repeat units that form an entangled polymer mesh across the channel may be involved in translocation, since these units have the potential to intermittently bind to hydrophobic receptor sites on the transporter protein.     

Superficial segregation in nanoparticles: from facets to infinite surfaces

We compare the superficial segregations of the Cu-Ag system for a nanoparticle and for surfaces that are structurally equivalent to each of its facet. Based on a lattice-gas model and within a mean-field formalism, we derive segregation isotherms at various temperatures in the canonical ensemble, i.e., for a given overall solute concentration, and in the semigrand canonical ensemble, i.e., for a given bulk solute concentration. If both processes are very similar for high temperatures, they differ substantially at lower temperatures. Due to the finite-size effect and the indirect coupling between facets and edges, the relative position of the phase transitions of the facets and the corresponding surfaces is inversed when displayed as a function of the solute bulk concentration. Moreover, we show that working in the semigrand canonical ensemble is a much more efficient way to study this phenomenon, although nanoparticles are "canonical" objects in essence.     

Phase behavior and local structure of a binary mixture in pores: mean-field lattice model calculations for analyzing neutron scattering data

We investigate the phase behavior of an asymmetric binary liquid A-W mixture confined between two planar homogenous substrates (slit pore). Molecules of species W interact preferentially with the solid walls via a long-range potential. Assuming nearest-neighbor attractions between the liquid molecules, we employ a lattice-gas model and a mean-field approximation for the grand potential. Minimization of this potential yields the density profiles of thermodynamically stable phases for fixed temperature, chemical potentials of both species, pore width and strengths of attraction. This model is used to analyze experimental small-angle neutron-scattering (SANS) data on the microscopic structure of the binary system isobutyric acid (iBA)+heavy water (D2O) inside a mesoscopic porous matrix (controlled-pore glass of about 10 nm mean pore width). Confinement-independent model parameters are adjusted so that the theoretical liquid-liquid coexistence curve in the bulk matches its experimental counterpart. By choosing appropriate values of the pore width and the attraction strength between substrates and water we analyze the effect of confinement on the phase diagram. In addition to a depression of the liquid-liquid critical point we observe surface induced phase transitions as well as water-film adsorption near the walls. The temperature dependence of the structure of water-rich and iBA-rich phases of constant composition are discussed in detail. The theoretical predictions are consistent with results of the SANS study and assist their interpretation.     

Structures and adsorption of binary hard-core Yukawa mixtures in a slitlike pore: grand canonical Monte Carlo simulation and density-functional study

The grand canonical ensemble Monte Carlo simulation and density-functional theory are applied to calculate the structures, local mole fractions, and adsorption isotherms of binary hard-core Yukawa mixtures in a slitlike pore as well as the radial distribution functions of bulk mixtures. The excess Helmholtz energy functional is a combination of the modified fundamental measure theory of Yu and Wu [J. Chem. Phys. 117, 10156 (2002)] for the hard-core contribution and a corrected mean-field theory for the attractive contribution. A comparison of the theoretical results with the results from the Monte Carlo simulations shows that the corrected theory improves the density profiles of binary hard-core Yukawa mixtures in the vicinity of contact over the original mean-field theory. Both the present corrected theory and the simulations suggest that depletion and desorption occur at low temperature, and the local segregation can be observed in most cases. For binary mixtures in the hard slitlike pore, the present corrected theory predicts more accurate surface excesses than the original one does, while in the case of the attractive pore, no improvement is found in the prediction of a surface excess of the smaller molecule.     

Slow dynamics of the high density Gaussian core model

We numerically study crystal nucleation and glassy slow dynamics of the one-component Gaussian core model (GCM) at high densities. The nucleation rate at a fixed supercooling is found to decrease as the density increases. At very high densities, the nucleation is not observed at all in the time window accessed by long molecular dynamics (MD) simulation. Concomitantly, the system exhibits typical slow dynamics of the supercooled fluids near the glass transition point. We compare the simulation results of the supercooled GCM with the predictions of mode-coupling theory (MCT) and find that the agreement between them is better than any other model glassformers studied numerically in the past. Furthermore, we find that a violation of the Stokes-Einstein relation is weaker and the non-Gaussian parameter is smaller than canonical glassformers. Analysis of the probability distribution of the particle displacement clearly reveals that the hopping effect is strongly suppressed in the high density GCM. We conclude from these observations that the GCM is more amenable to the mean-field picture of the glass transition than other models. This is attributed to the long-ranged nature of the interaction potential of the GCM in the high density regime. Finally, the intermediate scattering function at small wavevectors is found to decay much faster than its self part, indicating that dynamics of the large-scale density fluctuations decouples with the shorter-ranged caging motion.     

Supercritical phase equilibria involving solids

The solubility of solids in supercritical solvents is reviewed in a phenomenological discussion of binary and ternary systems containing one highly volatile component. Solubility and selectivity are greatly determined by the course of the binary critical curves, the ternary critical end-point curves, and the locations of the triple points of the solids. The mean-field lattice-gas model is used to review some important molecular parameters.     

Anisotropic dynamics of dipolar liquids in narrow slit pores

We report molecular dynamics simulation results for Stockmayer fluids confined to narrow slitlike pores with structureless, nonconducting walls. The translational and rotational dynamics of the dipolar particles have been investigated by calculating autocorrelation functions, diffusion coefficients, and relaxation times for various pore widths (five or less particle diameters) and directions parallel and perpendicular to the walls. The dynamic properties of the confined systems are compared to bulk properties, where corresponding bulk and pore states at the same temperature and chemical potential are determined in parallel grand canonical Monte Carlo simulations. We find that the dynamic behavior inside the pore depends on the distance from the walls and can be strongly anisotropic even in globally isotropic systems. This concerns especially the particles in the surface layers close to the walls, where the single particle and collective dipolar relaxation resemble that of true two-dimensional dipolar fluids with different in-plane and out-of-plane relaxations. On the other hand, bulklike relaxation is observed in the pore center of sufficiently wide pores.     

Density functional theory model of adsorption on amorphous and microporous silica materials

We present a novel quenched solid density functional theory (QSDFT) model of adsorption on heterogeneous surfaces and porous solids, which accounts for the effects of surface roughness and microporosity. Within QSDFT, solid atoms are considered as quenched component(s) of the solid-fluid system with given density distribution(s). Solid-fluid intermolecular interactions are split into hard-sphere repulsive and mean-field attractive parts. The former are treated with the multicomponent fundamental measure density functional. Capabilities of QSDFT are demonstrated by drawing on the example of adsorption on amorphous silica materials. We show that, using established intermolecular potentials and a realistic model for silica surfaces, QSDFT quantitatively describes adsorption/desorption isotherms of Ar and Kr on reference MCM-41, SBA-15, and LiChrosphere materials in a wide range of relative pressures. QSDFT offers a systematic approach to the practical problems of characterization of microporous, mesoporous, and amorphous silica materials, including an assessment of microporosity, surface roughness, and adsorption deformation. Predictions for the pore diameter and the extent of pore surface roughness in MCM-41 and SBA-15 materials are in very good agreement with recent X-ray diffraction studies.     

Assessment of two methods for application in the prediction of the infrared spectra of polymers

Two simple simulation methods, which will be useful for the prediction of the infrared (IR) spectral features of polymers, are reported. This paper focusses on simple aromatic models of the main aromatic backbones of structural polymeric resins. These methods were normal coordinate analysis (NCA) using the PM3 Hamiltonian implemented under MOPAC6 and a dipole autocorrelation function (DACF) calculated using coordinates and velocities from a series of molecular dynamics runs performed using the universal force-field (UFF) as implemented in the Cerius² modelling package. The semi-empirical NCA approach yielded useful information about the fundamental modes of vibration of the molecules but, as expected, could not be used to predict combination modes for anything but the simplest of molecules. The DACF approach showed potential for the prediction of combination bands but thorough evaluation of the method was found to be extremely difficult, owing to problems with band assignment for all but the simplest of molecules. An estimate of the accuracy of prediction for the different types of vibrational mode is included for each method.     

Diffusion in tight confinement: a lattice-gas cellular automaton approach. II. Transport properties

In this second paper the authors study the transport properties of the lattice-gas cellular automaton presented in Paper I [J. Chem. Phys. 126, 194709 (2007)] to model adsorption and dynamics of particles in a lattice of confining cells. Their work shows how a surprisingly simple parallel rule applied to a static network of cells joined by links set in space and time can generate a wide range of dynamical behaviors. In their model the cells are the elementary constituent objects of the network. They are a portion of space structured in sites which are energetically different. Each cell can accommodate a given maximum number of particles, and each pair of neighboring cells can exchange at most one particle at a time. The predictions of the model are in qualitative agreement with both experimental observations and molecular dynamics simulation results.     

Structure and adsorption of a hard-core multi-Yukawa fluid confined in a slitlike pore: grand canonical Monte Carlo simulation and density functional study

Because of the increasing interest in studying the phenomenon exhibited by charge-stabilized colloidal suspensions in confining geometry, we present a density functional theory (DFT) for a hard-core multi-Yukawa fluid. The excess Helmholtz free-energy functional is constructed by using the modified fundamental measure theory and Rosenfeld's perturbative method, in which the bulk direct correlation function is obtained from the first-order mean spherical approximation. To validate the established theory, grand canonical ensemble Monte Carlo (GCMC) simulations are carried out to determine the density profiles and surface excesses of multi-Yukawa fluid in a slitlike pore. Comparisons of the theoretical results with the GCMC data suggest that the present DFT gives very accurate density profiles and surface excesses of multi-Yukawa fluid in the slitlike pore as well as the radial distribution functions of the bulk fluid. Both the DFT and the GCMC simulations predict the depletion of the multi-Yukawa fluid near a nonattractive wall, while the mean-field theory fails to describe this depletion in some cases. Because the simple form of the direct correlation function is used, the present DFT is computationally as efficient as the mean-field theory, but reproduces the simulation data much better than the mean-field theory.     

Condensation phenomena in nanopores: a Monte Carlo study

The nonequilibrium dynamics of condensation phenomena in nanopores is studied via Monte Carlo simulations of a lattice-gas model. Hysteretic behavior of the particle density as a function of the density of a reservoir is obtained for various pore geometries in two and three dimensions. The shape of the hysteresis loops depend on the characteristics of the pore geometry. The evaporation of particles from a pore can be fitted to a stretched exponential decay of the particle density. Phase-separation dynamics inside the pore is effectively described by a random walk of the non-wetting phases. Domain evolution is significantly slowed down in the presence of a random wall-particle potential and gives rise to a temperature-dependent growth exponent. A geometric roughness of the pore wall only delays the onset of a pure domain growth.     

Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. II. Simulation results

The results of a series of constant pressure and temperature molecular-dynamics (MD) simulation studies based on the rigorous shell particle formulation of the isothermal-isobaric (NpT) ensemble are presented. These MD simulations validate the newly proposed constant pressure equations of motion in which a "shell" particle is used to define uniquely the volume of the system [M. J. Uline and D. S. Corti, J. Chem. Phys. (to be published), preceding paper]. Ensemble averages obtained with the new MD NpT algorithm match the ensemble averages obtained using the previously derived shell particle Monte Carlo NpT method [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. In addition, we also verify that the Hoover NpT MD algorithm [W. G. Hoover, Phys. Rev. A 31, 1695 (1985); 34, 2499 (1986)] generates the correct ensemble averages, though only when periodic boundary conditions are employed. The extension of the shell particle MD algorithm to multicomponent systems is also discussed, in which we show for equilibrium properties that the identity of the shell particle is completely arbitrary when periodic boundary conditions are applied. Self-diffusion coefficients determined with the shell particle equations of motion are also identical to those obtained in other ensembles. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the effects of the shell particle on the dynamics of the system. Overall, the shell particle MD algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium MD methods.     

On the separation of nonadditive symmetric mixtures in nanoscopic slitlike pores: A simple model for racemic fluids

A grand canonical ensemble Monte Carlo simulation method is used to study the adsorption of nonadditive symmetric mixtures of Lennard-Jones spherical particles in nanoscopic slitlike pores. The walls of the pore are assumed to be formed by the parallel (100) planes of the model face centered cubic crystal of adjustable corrugation potential. It is demonstrated that depending on the nonadditivity effects in the mixture and the pore width the condensed phases formed inside the pore may have different structures. In particular, it is shown that the mixture may separate into layers containing only one component each and the stacking may depend on the pore width and properties of the mixture.     

Mesoscale simulation of polymer reaction equilibrium: combining dissipative particle dynamics with reaction ensemble Monte Carlo. I. Polydispersed polymer systems

We present a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics (RxDPD) method, for studying reaction equilibrium of polymer systems. The RxDPD method combines elements of dissipative particle dynamics (DPD) and reaction ensemble Monte Carlo (RxMC), allowing for the determination of both static and dynamical properties of a polymer system. The RxDPD method is demonstrated by considering several simple polydispersed homopolymer systems. RxDPD can be used to predict the polydispersity due to various effects, including solvents, additives, temperature, pressure, shear, and confinement. Extensions of the method to other polymer systems are straightforward, including grafted, cross-linked polymers, and block copolymers. To simulate polydispersity, the system contains full polymer chains and a single fractional polymer chain, i.e., a polymer chain with a single fractional DPD particle. The fractional particle is coupled to the system via a coupling parameter that varies between zero (no interaction between the fractional particle and the other particles in the system) and one (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the DPD equations of motion, accompanied by changes in the coupling parameter. The coupling-parameter changes are either accepted with a probability derived from the grand canonical partition function or governed by an equation of motion derived from the extended Lagrangian. The coupling-parameter changes mimic forward and reverse reaction steps, as in RxMC simulations.     

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

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

Thermodynamic properties of the Cu-Au system using a face-centered-cubic lattice model with a renormalized potential

A Monte Carlo simulation is carried out to study thermodynamic properties of Cu-Au alloys using a face-centered-cubic (fcc) lattice-gas model. To obtain quantitatively accurate results, a Finnis-Sinclair-type potential, which has been widely used for molecular dynamics (MD) simulations, is employed. To overcome some shortcomings of lattice-gas models such as neglecting vibrational entropy, the potential is mapped onto the fcc lattice using the renormalization technique. The renormalized potential gives an improved Cu-Au phase diagram compared to the original MD potential applied directly on the lattice.     

Theory of free volume in polymers

A number of theoretical approaches to the problem of free volume in polymers are discussed. Because some questions in the Bueche approach remain unresolved, the lattice-gas model was studied. Inconsistencies in the independent-vacancy approximation led to consideration of a mean-field model and then a precise Padé-approximant solution, neither of which gave satisfactory agreement with experiment. Introduction of an internal pressure parameter to model the effects of the chainlike structure of polymers restores agreement with experiment.