The dynamics of single chains within a model polymer melt

Discontinuous molecular dynamics simulations are performed on a system containing 32 hard chains of length 192 at a volume fraction of phi = 0.45 to explore the idea that localized entanglements have a significant effect on the dynamics of the individual chains within an entangled polymer melt. Anomalous behavior can still be observed when studying the dynamics of the individual chains, although increased time averaging causes the anomalous relaxation-memory-release behavior that was observed previously in the system to smooth out. First, the individual chain mean squared displacements and apparent diffusion coefficients are calculated, and a wide distribution of diffusive behavior is found. Although the apparent diffusion coefficient curve averaged over all chains displays the predicted long-time diffusive behavior, the curves for the individual chains differ both qualitatively and quantitatively. They display superdiffusive, diffusive, and subdiffusive behavior, with the largest percentage of chains exhibiting superdiffusive behavior and the smallest percentage exhibiting the predicted diffusive behavior. Next, the individual chain end-to-end vector autocorrelation functions and relaxation times are determined, and a wide distribution of stress relaxation behavior is found. The times when the end-to-end vector autocorrelation functions relax completely span almost an order of magnitude in reduced time. For some chains, the end-to-end vector autocorrelation function relaxes smoothly toward zero similar to the system average; however, for other chains the relaxation is slowed greatly, indicating the presence of additional entanglements. Almost half of the chains exhibit the anomalous behavior in the end-to-end vector autocorrelation function. Finally, the dynamic properties are displayed for a single chain exhibiting anomalous relaxation-memory-release behavior, supporting the idea that the relaxation-memory-release behavior is a single-chain property.     

Polymer chains in a soft nanotube: a Monte Carlo study

We study the equilibrium properties of flexible polymer chains confined in a soft tube by means of extensive Monte Carlo simulations. The tube wall is that of a single sheet six-coordinated self-avoiding tethered membrane. Our study assumes that there is no adsorption of the chain on the wall. By varying the length N of the polymer and the tube diameter D we examine the variation of the polymer gyration radius Rg and diffusion coefficient Ddiff in soft and rigid tubes of identical diameter and compare them to scaling theory predictions. We find that the swollen region of the soft tube surrounding the chain exhibits a cigarlike cylindrical shape for sufficiently narrow tubes with D相似文献   

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping

Stochastic simulation of reaction-diffusion systems enables the investigation of stochastic events arising from the small numbers and heterogeneous distribution of molecular species in biological cells. Stochastic variations in intracellular microdomains and in diffusional gradients play a significant part in the spatiotemporal activity and behavior of cells. Although an exact stochastic simulation that simulates every individual reaction and diffusion event gives a most accurate trajectory of the system's state over time, it can be too slow for many practical applications. We present an accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems designed to improve the speed of simulation by reducing the number of time-steps required to complete a simulation run. This method is unique in that it employs two strategies that have not been incorporated in existing spatial stochastic simulation algorithms. First, diffusive transfers between neighboring subvolumes are based on concentration gradients. This treatment necessitates sampling of only the net or observed diffusion events from higher to lower concentration gradients rather than sampling all diffusion events regardless of local concentration gradients. Second, we extend the non-negative Poisson tau-leaping method that was originally developed for speeding up nonspatial or homogeneous stochastic simulation algorithms. This method calculates each leap time in a unified step for both reaction and diffusion processes while satisfying the leap condition that the propensities do not change appreciably during the leap and ensuring that leaping does not cause molecular populations to become negative. Numerical results are presented that illustrate the improvement in simulation speed achieved by incorporating these two new strategies.     

超临界水的分子动力学模拟

采用分子动力学(MD)模拟的方法对超临界条件下水的结构及扩散性质进行了研究.模拟结果表明超临界条件下水分子之间的氢键作用明显减弱,分子极性大大降低.扩散性质与常温下相比,其大小约上升了两个数量级.     

Concentration-gradient-dependent ion current rectification in charged conical nanopores

Ion current rectification (ICR) in negatively charged conical nanopores is shown to be controlled by the electrolyte concentration gradient depending on the direction of ion diffusion. The degree of ICR is enhanced with the increasing forward concentration difference. An unusual rectification inversion is observed when the concentration gradient is reversely applied. A numerical simulation based on the coupled Poisson and Nernst-Planck (PNP) equations is proposed to solve the ion distribution and ionic flux in the charged and structurally asymmetric nanofluidic channel with diffusive ion flow. Simulation results qualitatively describe the diffusion-induced ICR behavior in conical nanopores suggested by the experimental data. The concentration-gradient-dependent ICR enhancement and inversion is attributed to the cooperation and competition between geometry-induced asymmetric ion transport and the diffusive ion flow. The present study improves our understanding of the ICR in asymmetric nanofluidic channels associated with the ion concentration difference and provides insight into the rectifying biological ion channels.     

Development of a force field for zeolitic imidazolate framework-8 with structural flexibility

A force field is developed for zeolitic imidazolate framework-8 (ZIF-8) with structural flexibility by combining quantum chemical calculations and classical Amber force field. The predicted crystalline properties of ZIF-8 (lattice constants, bond lengths, angles, dihedrals, and x-ray diffraction patterns) agree well with experimental results. A structural transition from crystalline to amorphous as found in experiment is observed. The mechanical properties of ZIF-8 are also described fairly well by the force field, particularly the Young's modulus predicted matches perfectly with measured value. Furthermore, the heat capacity of ZIF-8 as a typical thermophysical property is predicted and close to experimental data available for other metal-organic frameworks. It is revealed the structural flexibility of ZIF-8 exerts a significant effect on gas diffusion. In rigid ZIF-8, no diffusive behavior is observed for CH(4) within the simulation time scale of current study. With the structural flexibility, however, the predicted diffusivities of CH(4) and CO(2) are close to reported data in the literature. The density distributions and free energy profiles of CH(4) and CO(2) in the pore of ZIF-8 are estimated to analyze the mechanism of gas diffusion.     

Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants

The bacterial porin OmpF found in the outer membrane of E. coli is a wide channel, characterized by its poor selectivity and almost no ion specificity. It has an asymmetric structure, with relatively large entrances and a narrow constriction. By applying continuum electrostatic methods we determine the ionization states of titratable amino acid residues in the protein and calculate self-consistently the electric potential 3-D distribution within the channel. The average electrostatic properties are then represented by an effective fixed charge distribution along the pore which is the input for a macroscopic electrodiffusion model. The theoretical predictions agree with measurements performed under different salt gradients and pH. The sensitivity of reversal potential and conductance to the direction of the salt gradient and the solution pH is captured by the model. The theory is also able to explain the influence of the lipid membrane charge. The same methodology is satisfactorily applied to some OmpF mutants involving slight structural changes but a large number of net charges. The correlation found between atomic structure and ionic selectivity shows that the transport characteristics of wide channels like OmpF and its mutants are mainly regulated by the collective action of a large number of residues, rather than by the specific interactions of residues at particular locations.     

Solvation shell dynamics studied by molecular dynamics simulation in relation to the translational and rotational dynamics of supercritical water and benzene

The solvation shell dynamics of supercritical water is analyzed by molecular dynamics simulation with emphasis on its relationship to the translational and rotational dynamics. The relaxation times of the solvation number (tau S), the velocity autocorrelation function (tau D), the angular momentum correlation function (tau J), and the second-order reorientational correlation function (tau 2R) are studied at a supercritical temperature of 400 degrees C over a wide density region of 0.01-1.5 g cm(-3). The relaxation times are decomposed into those conditioned by the solvation number n, and the effect of the short-ranged structure is examined in terms of its probability Pn of occurrence. In the low to medium-density range of 0.01-0.4 g cm(-3), the time scales of water dynamics are in the following sequence: tau D>tau S approximately or > tau J approximately or > tau 2R. This means that the rotation in supercritical water is of the "in-shell" type while the translational diffusion is not. The comparison to supercritical benzene is also performed and the effect of hydrogen bonding is examined. The water diffusion is not of the in-shell type up to the ambient density of 1.0 g cm(-3), which corresponds to the absence of the transition from the collision to the Brownian picture, whereas such transition is present in the case of benzene. The absence of the transition in water comes from the fast reorganization of the hydrogen bonds and the enhanced mobility of the solvation shell in supercritical conditions.     

The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water

The performance of density functional theory methods for the modeling of condensed aqueous systems is hard to predict and validation by ab initio molecular simulation of liquid water is absolutely necessary. In order to assess the reliability of these tests, the effect of temperature on the structure and dynamics of liquid water has been characterized with 16 simulations of 20 ps in the temperature range of 280-380 K. We find a pronounced influence of temperature on the pair correlation functions and on the diffusion constant including nonergodic behavior on the time scale of the simulation in the lower temperature range (which includes ambient temperature). These observations were taken into account in a consistent comparison of a series of density functionals (BLYP, PBE, TPSS, OLYP, HCTH120, HCTH407). All simulations were carried out using an ab initio molecular dynamics approach in which wave functions are represented using Gaussians and the density is expanded in an auxiliary basis of plane waves. Whereas the first three functionals show similar behavior, it is found that the latter three functionals yield more diffusive dynamics and less structure.     

Dynamics of relaxation of entangled polymers in shear flow

The application of shear flow to entangled polymer melts can strongly modify its rheological and physicochemical behaviors, giving rise to an acceleration of several chemical processes such as diffusion-controlled reactions. In the present work, we investigate the modification of conformational and diffusive properties of an entangled polymer in shear flow by numerical methods. The flow affects both the conformational and diffusive properties of the system, giving rise to a quasinematic ordering of the macromolecules which take prolate spheroid shape with the main axis aligned to the shear direction. The shear flow is found to accelerate the overall diffusion of the chains in all directions at times longer than the polymer relaxation time. The polymer chains display a quite peculiar displacement behavior in direction parallel to the flow. At the same conditions, the linear relation between the diffusion constant in direction perpendicular to the flow and the inverse of the relaxation time, usually adopted in equilibrium regimes, is shown to hold even in the presence of flow.     

Adsorption and diffusion of argon in disordered nanoporous carbons

Application-specific optimization of disordered nanoporous carbons remains a formidable challenge due to the difficulty in accurately characterizing their microstructures with current empirical methods. Using molecular simulation techniques, we investigated the adsorptive and diffusive behavior of argon in three models of disordered nanoporous carbons. We found that the structural and morphological differences between these models gave rise to distinct phenomenological properties. The adsorptive behavior of argon in both the low and high pressure regimes was enhanced dramatically in the models with more crystalline microstructures. As for dynamic properties, we found that the adsorbent’s structure and energetic topology significantly alters the rates of diffusion as well as the characteristics of the underlying diffusion mechanisms.     

Transient interfacial tension and dilatational rheology of diffuse polymer-polymer interfaces

We demonstrate the influence of molecular weight and molecular weight asymmetry across an interface on the transient behavior of the interfacial tension. The interfacial tension was measured as a function of time for a range of polymer combinations with a broad range of interfacial properties using a pendant/sessile drop apparatus. The results show that neglecting mutual solubility, assumed to be a reasonable approximation in many cases, very often does not sustain. Instead, a diffuse interface layer develops in time with a corresponding transient interfacial tension. Depending on the specific combination of polymers, the transient interfacial tension is found to increase or decrease with time. The results are interpreted in terms of a recently proposed model [Shi et al., Macromolecules 37, 1591 (2004)], giving relative characteristic diffusion time scales in terms of molecular weight, molecular weight distribution, and viscosities. However, the time scales obtained from this theoretical approach do not give a conclusive trend. Using oscillatory dilatational interfacial experiments the viscoelastic behavior of these diffusive interfaces is demonstrated. The time evolution of the interfacial tension and the dilatational elasticity show the same trend as predicted by the theory of diffuse interfaces, supporting the idea that the polymer combinations under consideration indeed form diffuse interfaces. The dilatational elasticity and the dilatational viscosity show a frequency dependency that is described qualitatively by a simple Fickian diffusion model and quantitatively by a Maxwell model. The characteristic diffusion times provided by the latter show that the systems with thick interfaces (tens of microseconds and more) can be considered as slower diffusive systems compared to the systems with thinner interfaces (a few micrometers in thickness and less) can be considered as fast diffusive systems.     

Dynamics near a liquid-liquid phase transition in a non-tetrahedral liquid: the case of gallium

We use molecular simulation to analyze liquid dynamics in the vicinity of the liquid-liquid phase transition (LLPT) recently discovered in the modified embedded-atom model for elemental gallium. For this purpose we analyze the diffusive behavior in terms of the mean-squared displacement and self-intermediate scattering functions for two systems obtained by cooling the stable liquid through the LLPT at different cooling rates. The results show a pronounced heterogeneity of the dynamics upon the onset of the LLPT. Furthermore, it is found that this heterogeneity is closely correlated to the structural properties of the 9-fold coordinated high-density and 8-fold coordinated low-density liquid forms involved in the transition, showing a mixture of domains with very different diffusion time scales. The dynamics of the low-density liquid is found to be much more sluggish than that of the high-density form. Analysis of the energetics suggests that the origin of this difference is rooted in the fact that the cohesion in the former is significantly stronger than that in the latter.     

A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study

We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes as well as the simulated GILs. The proposed diffusion model facilitates the qualitative a priori prediction of the impact of ion modifications on the diffusive characteristics of new ionic liquids.     

Fluorescence correlation spectroscopy simulations of photophysical phenomena and molecular interactions: a molecular dynamics/monte carlo approach

Fluorescence correlation spectroscopy (FCS) is being applied increasingly to study diffusion and interactions of fluorescently labeled macromolecules in complex biological systems. Fluctuations in detected fluorescence, deltaF(t), are expressed as time-correlation functions, G(tau), and photon-count histograms, P(k;DeltaT). Here, we developed a generalized simulation approach to compute G(tau) and P(k;DeltaT) for complex systems with arbitrary geometry, photophysics, diffusion, and macromolecular interactions. G(tau) and P(k;DeltaT) were computed from deltaF(t) generated by a Brownian dynamics simulation of single-molecule trajectories followed by a Monte Carlo simulation of fluorophore excitation and detection statistics. Simulations were validated by comparing analytical and simulated G(tau) and P(k;DeltaT) for diffusion of noninteracting fluorophores in a three-dimensional Gaussian excitation and detection volume. Inclusion of photobleaching and triplet-state relaxation produced significant changes in G(tau) and P(k;DeltaT). Simulations of macromolecular interactions and complex diffusion were done, including transient fluorophore binding to an immobile matrix, cross-correlation analysis of interacting fluorophores, and anomalous sub- and superdiffusion. The computational method developed here is generally applicable for simulating FCS measurements on systems complicated by fluorophore interactions or molecular crowding, and experimental protocols for which G(tau) and P(k;DeltaT) cannot be computed analytically.     

Molecular dynamics simulation of gas diffusion in polyethylene-clay nanocomposites with different silicate layers configurations

Barrier properties of pristine polyethylene (PE) and polyethylene/montmorillonite-clay (PE/MMT) nanocomposite films with different MMT layers configurations were studied using molecular dynamics simulation within NVT ensemble. The force field parameters were optimized for bond lengths, bond angles and torsion angles of the MMT structure. A special simulation box was designed to simulate the diffusion of oxygen, nitrogen and methane, through pristine PE and PE/MMT nanocomposite films. The diffusion coefficients of these gases and the tortuosity values were calculated and analyzed. Results showed that the configuration of clay nanoparticles has strong effect on the barrier properties of the nanocomposite films. The parallel configuration for layered silicates was predicted to have a low diffusion coefficient and a high tortuosity parameter for gas diffusive molecules. The simulation could also indicate that the diffusion coefficient of oxygen is higher than those of nitrogen and methane gases in the examined systems which can be attributed to the smaller kinetic diameter of oxygen.     

Intermolecular polarizability dynamics of aqueous formamide liquid mixtures studied by molecular dynamics simulations

A molecular dynamics simulation study is presented for the relaxation of the polarizability anisotropy in liquid mixtures of formamide and water, using a dipolar induction scheme that involves the intrinsic polarizability and first hyperpolarizability tensors of the molecules, and the dipole-quadrupole polarizability of water species. The long time diffusive decay of the collective polarizability anisotropy correlations exhibits a substantial slowing down as the formamide mole fraction increases in the mixture. The diffusive times for the polarizability relaxation obtained from the authors' simulations are in good agreement with optical Kerr effect experimental data, and they are found to correlate nearly linearly with the estimated mean lifetimes of the hydrogen bonds within the mixture, suggesting that the relaxation of the hydrogen bond network is responsible to some extent for the collective relaxation of the polarizability anisotropy of the mixture. The short time behavior of the polarizability anisotropy relaxation was investigated by computing the nuclear response function, R(t), which is very rapidly dominated by the formamide contribution as it is added to water, due to the much larger polarizability anisotropy of formamide molecules compared to that of water. Several contributions to the Raman spectrum were also analyzed as a function of composition, and the dynamical origin of the different bands was determined.     

Evaluation of asymmetrical structure dialysis membrane by tortuous capillary pore diffusion model

The tortuous capillary pore diffusion model (TCPDM) has been used for estimating diffusive and pure water permeability from simple structure parameters such as pore diameter, surface porosity, wall thickness and tortuosity. The validity of this model for evaluation of homogeneous membrane has been already confirmed. Recently, there is a trend toward the use of asymmetrical dialysis membranes made of synthetic polymer such as poly(acrylonitrile) (PAN), polysulfone (PS) and a polyethersulfone polyarylate (PEPA) blend polymer. The purpose of the present study is to apply the TCPDM to evaluation of commercially available hollow-fiber dialysis membranes with asymmetrical structures by simplifying them to a double-layer membrane. The TCPDM is capable of estimating pore tortuosity of asymmetrical dialysis membranes having skin and supporting layers from data on membrane thickness, pore diameter, pure water permeability and water content. Values for diffusive permeability obtained by the TCPDM are in a good agreement with experimental data. This TCPDM model is useful for evaluation of not only homogeneous membrane but also asymmetrical membrane.     

Structure-based prediction of the conductance properties of ion channels

The HOLE procedure allows the prediction of the absolute conductance of an ion channel model from its structure. The original prediction method uses an empirically corrected Ohmic method. It is most successful, with predictions being reliable to within a factor of two. A new modification of the procedure is presented in which the self-diffusion coefficients of water molecules from molecular dynamics simulation are used to replace the empirical correction factor. A "prediction" of the conductance for the porin OmpF by the new method is made and shown to be very close to the experimental value. HOLE also allows the prediction of the effect that the addition of non-electrolyte polymers will have on channel conductance. The method has great potential to yield structural information from data provided by single channel recordings but needs further validation by making measurements on channels of known structure. Preliminary results are given of single channel records establishing the effects of non-electrolytes on the conductance of gramicidin D channels. As an example of the potential uses of the procedure application is made to examine the oligomerization of alpha-toxin (alpha-hemolysin) channels. A model for the alpha-toxin hexamer, based on the crystal structure for the heptamer, is generated using molecular mechanics methods. The compatibility of the structures with single channel conductance data is assessed using HOLE.     

Mechanism and kinetics of hydrated electron diffusion

Molecular dynamics simulations are used to study the mechanism and kinetics of hydrated electron diffusion. The electron center of mass is found to exhibit Brownian-type behavior with a diffusion coefficient considerably greater than that of the solvent. As previously postulated by both experimental and theoretical works, the instantaneous response of the electron to the librational motions of surrounding water molecules constitutes the principal mode of motion. The diffusive mechanism can be understood within the traditional framework of transfer diffusion processes, where the diffusive step is akin to the exchange of an extramolecular electron between neighboring water molecules. This is a second-order process with a computed rate constant of 5.0 ps(-1) at 298 K. In agreement with experiment the electron diffusion exhibits Arrhenius behavior over the temperature range of 298-400 K. We compute an activation energy of 8.9 kJ mol(-1). Through analysis of Arrhenius plots and the application of a simple random walk model it is demonstrated that the computed rate constant for exchange of an excess electron is indeed the phenomenological rate constant associated with the diffusive process.