Hydrodynamic screening near planar boundaries: effects on semiflexible polymer dynamics

The influence of hydrodynamic screening near a surface on the dynamics of a single semiflexible polymer is studied by means of Brownian dynamics simulations and hydrodynamic mean field theory. The polymer motion is characterized in terms of the mean squared displacements of the end-monomers, the end-to-end vector, and the scalar end-to-end distance. In order to control hydrodynamic screening effects, the polymer is confined to a plane at a fixed separation from the wall. When gradually decreasing this separation, a crossover from Zimm-type towards Rouse (free-draining) polymer dynamics is induced. However, this crossover is rather slow and the free-draining limit is not completely reached--substantial deviations from Rouse-like dynamics are registered in both simulations and theory--even at distances of the polymer from the wall on the order of the monomer size. Remarkably, the effect of surface-induced screening of hydrodynamic interactions sensitively depends on the type of dynamic observable considered. For vectorial quantities such as the end-to-end vector, hydrodynamic interactions are important and therefore surface screening effects are sizeable. For a scalar quantity such as the end-to-end distance, on the other hand, hydrodynamic interactions are less important, but a pronounced dependence of dynamic scaling exponents on the persistence length to contour length ratio becomes noticeable. Our findings are discussed against the background of single-molecule experiments on f-actin [L. Le Goff et al., Phys. Rev. Lett. 89, 258101 (2002)].     

Hydrodynamic interaction in polymer solutions simulated with dissipative particle dynamics

The authors analyzed extensively the dynamics of polymer chains in solutions simulated with dissipative particle dynamics (DPD), with a special focus on the potential influence of a low Schmidt number of a typical DPD fluid on the simulated polymer dynamics. It has been argued that a low Schmidt number in a DPD fluid can lead to underdevelopment of the hydrodynamic interaction in polymer solutions. The authors' analyses reveal that equilibrium polymer dynamics in dilute solution, under typical DPD simulation conditions, obey the Zimm [J. Chem. Phys. 24, 269 (1956)] model very well. With a further reduction in the Schmidt number, a deviation from the Zimm model to the Rouse model is observed. This implies that the hydrodynamic interaction between monomers is reasonably developed under typical conditions of a DPD simulation. Only when the Schmidt number is further reduced, the hydrodynamic interaction within the chains becomes underdeveloped. The screening of the hydrodynamic interaction and the excluded volume interaction as the polymer volume fraction is increased are well reproduced by the DPD simulations. The use of soft interaction between polymer beads and a low Schmidt number do not produce noticeable problems for the simulated dynamics at high concentrations, except for the entanglement effect which is not captured in the simulations.     

Lock-exchange experiments with an autocatalytic reaction front

A viscous lock-exchange gravity current corresponds to the reciprocal exchange of two fluids of different densities in a horizontal channel. The resulting front between the two fluids spreads as the square root of time, with a diffusion coefficient reflecting the buoyancy, viscosity, and geometrical configuration of the current. On the other hand, an autocatalytic reaction front between a reactant and a product may propagate as a solitary wave, namely, at a constant velocity and with a stationary concentration profile, resulting from the balance between molecular diffusion and chemical reaction. In most systems, the fluid left behind the front has a different density leading to a lock-exchange configuration. We revisit, with a chemical reaction, the classical situation of lock-exchange. We present an experimental analysis of buoyancy effects on the shape and the velocity of the iodate arsenous acid autocatalytic reaction fronts, propagating in horizontal rectangular channels and for a wide range of aspect ratios (1/3 to 20) and cylindrical tubes. We do observe stationary-shaped fronts, spanning the height of the cell and propagating along the cell axis. Our data support the contention that the front velocity and its extension are linked to each other and that their variations scale with a single variable involving the diffusion coefficient of the lock-exchange in the absence of chemical reaction. This analysis is supported by results obtained with lattice Bathnagar-Gross-Krook (BGK) simulations Jarrige et al. [Phys. Rev. E 81, 06631 (2010)], in other geometries (like in 2D simulations by Rongy et al. [J. Chem. Phys. 127, 114710 (2007)] and experiments in cylindrical tubes by Pojman et al. [J. Phys. Chem. 95, 1299 (1991)]), and for another chemical reaction Schuszter et al. [Phys. Rev. E 79, 016216 (2009)].     

良溶剂中环形高分子单链的结构与动力学性质的模拟研究

本文采用多粒子碰撞动力学与分子动力学耦合的模拟方法研究了环形高分子单链在良溶剂中的静态与动态性质,并与线形分子进行了对比.研究发现,环形高分子链内粒子之间的平均距离小于线形链,即粒子排列得更加紧密;相应的均方回转半径也小于线形链,线形链与环形链的均方回转半径的比值为1.77;同时,环形链扩散的速度也比线形链快,两者比值为1.10.模拟结果揭示了扩散行为是排斥体积作用和流体力学相互作用耦合的结果,在扩散过程中,流体力学相互作用消减了排斥体积作用对扩散行为的贡献.此外,通过对有和没有流体力学相互作用的多粒子碰撞动力学得到的结果作对比,研究了流体力学相互作用对高分子静态和动态行为的影响,结果表明,流体力学相互作用使高分子链在极稀溶液中的扩散速度变快.     

Comparison of Brownian dynamics algorithms with hydrodynamic interaction

The hydrodynamic interaction is an essential effect to consider in Brownian dynamics simulations of polymer and nanoparticle dilute solutions. Several mathematical approaches can be used to build Brownian dynamics algorithms with hydrodynamic interaction, the most common of them being the exact but time demanding Cholesky decomposition and the Chebyshev polynomial expansion. Recently, Geyer and Winter [J. Chem. Phys. 130, 1149051 (2009)] have proposed a new approximation to treat the hydrodynamic interaction that seems quite efficient and is increasingly used. So far, a systematic comparison among those approaches has not been clearly made. In this paper, several features and the efficiency of typical implementations of those approaches are evaluated by using bead-and-spring chain models. The different sensitivity to the bead overlap detected for the different implementations may be of interest to select the suitable algorithm for a given simulation.     

Local ordering of polymer-tethered nanospheres and nanorods and the stabilization of the double gyroid phase

We present results of Brownian dynamics simulations of tethered nanospheres and tethered nanorods. Immiscibility between tether and nanoparticle facilitates microphase separation into the bicontinuous, double gyroid structure (first reported by Iacovella et al. [Phys. Rev. E 75, 040801(R) (2007)] and Horsch et al. [J. Chem. Phys. 125, 184903 (2006)], respectively). We demonstrate the ability of these nanoparticles to adopt distinct, minimal energy local packings, in which nanospheres form icosahedral-like clusters and nanorods form splayed hexagonal bundles. These local structures reduce packing frustration within the nodes of the double gyroid. We argue that the ability to locally order into stable structures is key to the formation of the double gyroid phase in these systems.     

Describing the component dynamics in miscible polymer blends: towards a fully predictive model

We have recently proposed [D. Cangialosi et al., J. Chem. Phys. 123, 144908 (2005)] an extension of the Adam-Gibbs [J. Chem. Phys. 43, 139 (1965)] theory, combined with the concept of self-concentration, to describe the temperature dependence of the relaxation time for the component segmental dynamics in miscible polymer blends. Thus, we were able to obtain the dynamics of each component in the blend starting from the knowledge of the dynamic and thermodynamic data of the pure polymers, with a single fitting parameter (alpha) which had to be obtained from the fitting of the experimental data. In the present work we demonstrate that this model is also suitable to describe the polymer segmental dynamics in concentrated polymer solutions. From this result we have developed a new route for determining the value of the alpha parameter associated with any given polymer. Once this value is known for the two components of a possible polymer blend, our model for polymer blends dynamics becomes fully predictive.     

Effect of excluded volume interactions on the interfacial properties of colloid-polymer mixtures

We report a numerical study of equilibrium phase diagrams and interfacial properties of bulk and confined colloid-polymer mixtures using grand canonical Monte Carlo simulations. Colloidal particles are treated as hard spheres, while the polymer chains are described as soft repulsive spheres. The polymer-polymer, colloid-polymer, and wall-polymer interactions are described by density-dependent potentials derived by Bolhuis and Louis [Macromolecules 35, 1860 (2002)]. We compared our results with those of the Asakura-Oosawa-Vrij model [J. Chem. Phys. 22, 1255 (1954); J. Polym Sci 33, 183 (1958); Pure Appl. Chem. 48, 471 (1976)] that treats the polymers as ideal particles. We find that the number of polymers needed to drive the demixing transition is larger for the interacting polymers, and that the gas-liquid interfacial tension is smaller. When the system is confined between two parallel hard plates, we find capillary condensation. Compared with the Asakura-Oosawa-Vrij model, we find that the excluded volume interactions between the polymers suppress the capillary condensation. In order to induce capillary condensation, smaller undersaturations and smaller plate separations are needed in comparison with ideal polymers.     

Simulating critical dynamics in liquid mixtures: short-range and long-range contributions

Recently, Das et al. [J. Chem. Phys. 125, 024506 (2006)] established that computer simulations of critical dynamics in a binary Lennard-Jones mixture are consistent with the predicted Stokes-Einstein behavior of the asymptotic decay rate of the order-parameter fluctuations near criticality. Here, we show that the noncritical or "background" contributions to the computed diffusion coefficient are also in agreement with both theory and experiment, thus further validating the feasibility of molecular dynamics simulations for studying dynamic critical behavior.     

Polarizable and flexible model for ethanol

A polarizable, flexible model for ethanol is obtained based on an extensive series of B3LYP/6-311++G(d,p) calculations and molecular dynamics simulations. The ethanol model includes electric-field dependence in both the atomic charges and the intramolecular degrees of freedom. Field-dependent intramolecular potentials have been attempted only once previously, for OH and HH stretches in water [P. Cicu et al., J. Chem. Phys. 112, 8267 (2000)]. The torsional potential involving the hydrogen-bonding hydrogen in ethanol is found to be particularly field sensitive. The methodology for developing field-dependent potentials can be readily generalized to other molecules and is discussed in detail. Molecular dynamics simulations of bulk ethanol are performed and the results are assessed based on comparisons with the self-diffusion coefficient [N. Karger et al., J. Chem. Phys. 93, 3437 (1990)], dielectric constant [J. T. Kindt and C. A. Schmuttenmaer, J. Phys. Chem. 100, 10373 (1996)], enthalpy of vaporization [R. C. Wilhoit and B. J. Zwolinski, J. Phys. Chem. Ref. Data, Suppl. 2, 2 (1973)], and experimental interatomic distributions [C. J. Benmore and Y. L. Loh, J. Chem. Phys. 112, 5877 (2000)]. The simultaneous variation of the atomic charges and the intramolecular potentials requires modified equations of motion and a multiple time step algorithm has been implemented to solve these equations. The article concludes with a discussion of the bulk structure and properties with an emphasis on the hydrogen bonding network.     

Modeling real dynamics in the coarse-grained representation of condensed phase systems

This work presents a systematic multiscale methodology to provide a more faithful representation of real dynamics in coarse-grained molecular simulation models. The theoretical formalism is based on the recently developed multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B. 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] and relies on the generalized Langevin equation approach and its simpler Langevin equation limit. The friction coefficients are determined in multiscale fashion from the underlying all-atom molecular dynamics simulations using force-velocity and velocity-velocity correlation functions for the coarse-grained sites. The diffusion properties in the resulting CG Brownian dynamics simulations are shown to be quite accurate. The time dependence of the velocity autocorrelation function is also well-reproduced relative to the all-atom model if sufficient resolution of the CG sites is implemented.     

Brownian dynamics algorithm for bead-rod semiflexible chain with anisotropic friction

A model of semiflexible bead-rod chain with anisotropic friction can mimic closely the hydrodynamics of a slender filament. We present an efficient algorithm for Brownian dynamics simulations of this model with configuration dependent anisotropic bead friction coefficients. The algorithm is an extension of that given previously for the case of configuration independent isotropic friction coefficients by Grassia and Hinch [J. Fluid Mech. 308, 255 (1996)]. We confirm that the algorithm yields predicted values for various equilibrium properties. We also present a stochastic algorithm for evaluation of the stress tensor, and we show that in the limit of stiff chains the algorithm recovers the results of Kirkwood and Plock [J. Chem. Phys. 24, 665 (1956)] for rigid rods with hydrodynamic interactions.     

Colloidal dynamics: influence of diffusion, inertia and colloidal forces on cluster formation

Computer simulations of colloidal suspensions are discussed. The simulations are based on the Langevin equations, pairwise interaction between colloidal particles and take into account Brownian, hydrodynamic and colloidal forces. Comparison of two models, one taking into account inertial term in Langevin equation and another based on diffusional approximation proposed in [D.L. Ermak, J.A. McCammon, J. Chem. Phys. 69 (1978) 1352], has shown that both models enable the prediction of the correct values of the diffusion coefficient and residence time of particle in a doublet and are therefore suitable to study the dynamics of formation and breakage of clusters in colloidal suspensions. It is shown that the appropriate selection of the time step and taking into account inertia of particles provides also the correct value of the average kinetic energy of each particle during the simulations, what allows to use the model based on full Langevin equations as a reference model to verify the validity of the numerical scheme for simulation using diffusion approximation.     

Chemical reaction equilibrium in nanoporous materials: NO dimerization reaction in carbon slit nanopores

We present a molecular-level simulation study of the effects of confinement on chemical reaction equilibrium in nanoporous materials. We use the reaction ensemble Monte Carlo (RxMC) method to investigate the effects of temperature, nanopore size, bulk pressure, and capillary condensation on the nitric oxide dimerization reaction in a model carbon slit nanopore in equilibrium with a bulk reservoir. In addition to the RxMC simulations, we also utilize the molecular-dynamics method to determine self-diffusion coefficients for confined nonreactive mixtures of nitric oxide monomers and dimers at compositions obtained from the RxMC simulations. We analyze the effects of the temperature, nanopore width, bulk pressure, and capillary condensation on the reaction equilibrium with respect to the reaction conversion, fluid structure, and self-diffusion coefficients. We show that the influence of the temperature, nanopore size, and capillary condensation on the confined reaction equilibrium is quite dramatic while the effect of the bulk pressure on the reaction equilibrium in the carbon slit nanopore is only moderate. This work is an extension of previous work by Turner et al. [J. Chem. Phys. 114, 1851 (2001)] on the confined reactive nitric oxide system.     

Effect of nanoconfinement on liquid-crystal polymer chains

We apply a Monte Carlo polymerization model for Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] monomers that we have recently introduced [J. Chem. Phys. 121, 9123 (2004)] to investigate with computer simulations the effects of nanoconfinement and anchoring type on the structure of the main-chain liquid-crystal polymers formed in thin films, in the presence of several types of surface alignment: parallel to the interface (random and uniform) or perpendicular to it (homeotropic). We perform first a study of the confined monomers and then we examine the features of the polymer chains obtained from an isotropic or nematic sample. We find a significant effect of the anchoring conditions on the characteristics of the chains and particularly striking differences between planar and homeotropic boundaries. Furthermore, our results indicate that the choice of different anchorings could be used to tune the linearity and degree of polymerization of the chains.     

Molecular dynamics simulations of surface-initiated melting of nitromethane

The melting of nitromethane initiated at solid-vacuum interfaces has been investigated using molecular dynamics nvt simulations with a realistic force field [D. C. Sorescu et al., J. Phys. Chem. B 104, 8406 (2000)]. The calculated melting point (251+/-5 K) is in good agreement with experiment (244.73 K) and values obtained previously (approximately 255.5 and 266.5+/-8 K) using other simulation methods [P. M. Agrawal et al., J. Chem. Phys. 119, 9617 (2003)]. Analyses of the molecular orientations and diffusion during the simulations as functions of the distance from the exposed surfaces show that the melting is a direct crystal-to-liquid transition, in which the molecules first gain rotational freedom, then mobility. There is a slight dependence of the melting temperature on the exposed crystallographic face.     

Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)] relates the work done on a system during a nonequilibrium transformation to the free energy difference between the final and the initial state of the transformation. Recently, the authors have derived the Crooks equation for systems in the canonical ensemble thermostatted by the Nose-Hoover or Nose-Hoover chain method [P. Procacci et al., J. Chem. Phys. 125, 164101 (2006)]. That proof is essentially based on the fluctuation theorem by Evans and Searles [Adv. Phys. 51, 1529 (2002)] and on the equations of motion. Following an analogous approach, the authors derive here the Crooks equation in the context of molecular dynamics simulations of systems in the isothermal-isobaric (NPT) ensemble, whose dynamics is regulated by the Martyna-Tobias-Klein algorithm [J. Chem. Phys. 101, 4177 (1994)]. Their present derivation of the Crooks equation correlates to the demonstration of the Jarzynski identity for NPT systems recently proposed by Cuendet [J. Chem. Phys. 125, 144109 (2006)].     

Polymer chain generation for coarse-grained models using radical-like polymerization

A versatile method is proposed to generate configurations of coarse-grained models for polymer melts. This method, largely inspired by chemical "radical polymerization," is divided in three stages: (i) nucleation of radicals (reacting molecules caching monomers), (ii) growth of chains within a solvent of monomers and (iii) termination: annihilation of radicals and removal of residual monomers. The main interest of this method is that relaxation is performed while chains are generated. Pure mono and polydisperse polymer melts are generated and compared to the configurations generated by the push off method from Auhl et al. [J. Chem. Phys. 119, 12718 (2003)]. A detailed study of the static properties (radius of gyration, mean square internal distance, entanglement length) confirms that the radical-like polymerization technique is suitable to generate equilibrated melts. Moreover, the method is flexible and can be adapted to generate nanostructured polymers, namely, diblock and triblock copolymers.