Nonequilibrium inertial dynamics of colloidal systems

We consider the properties of a one-dimensional fluid of Brownian inertial hard-core particles, whose microscopic dynamics is partially damped by a heat bath. Direct interactions among the particles are represented as binary, instantaneous elastic collisions. Collisions with the heat bath are accounted for by a Fokker-Planck collision operator, whereas direct collisions among the particles are treated by a well known method of kinetic theory, the revised Enskog theory. By means of a time multiple time-scale method we derive the evolution equation for the average density. Remarkably, for large values of the friction parameter and/or of the mass of the particles we obtain the same equation as the one derived within the dynamic density functional theory (DDF). In addition, at moderate values of the friction constant, the present method allows to study the inertial effects not accounted for by DDF method. Finally, a numerical test of these corrections is provided.     

Dynamics of interacting Brownian particles: a diagrammatic formulation

We present a diagrammatic formulation of a theory for the time dependence of density fluctuations in equilibrium systems of interacting Brownian particles. To facilitate derivation of the diagrammatic expansion, we introduce a basis that consists of orthogonalized many-particle density fluctuations. We obtain an exact hierarchy of equations of motion for time-dependent correlations of orthogonalized density fluctuations. To simplify this hierarchy we neglect contributions to the vertices from higher-order cluster expansion terms. An iterative solution of the resulting equations can be represented by diagrams with three- and four-leg vertices. We analyze the structure of the diagrammatic series for the time-dependent density correlation function and obtain a diagrammatic interpretation of reducible and irreducible memory functions. The one-loop self-consistent approximation for the latter function coincides with mode-coupling approximation for Brownian systems that was derived previously using a projection operator approach.     

The van Hove distribution function for brownian hard spheres: dynamical test particle theory and computer simulations for bulk dynamics

We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self?" component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.     

Use of Cartesian Rotation Vectors in Brownian Dynamics Algorithms: Theory and Simulation Results

Summary: We have shown that the components of Cartesian rotation vectors can be used successfully as generalized coordinates describing angular orientation in Brownian dynamics simulations of non‐spherical nanoparticles. For this particular choice of generalized coordinates, we rigorously derived the conformation‐space diffusion equations from kinetic theory for both free nanoparticles and nanoparticles interconnected by springs or holonomic constraints into polymer chains. The equivalent stochastic differential equations were used as a foundation for the Brownian dynamics algorithms. These new algorithms contain singularities only for points in the conformation‐space where both the probability density and its first coordinate derivative equal zero (weak singularities). In addition, the coordinate values after a single Brownian dynamics time step are throughout the conformation‐space equal to the old coordinate values plus the respective increments. For some parts of the conformation‐space these features represent a major improvement compared to the situation when Eulerian angles describe rotational dynamics. The presented simulation results of the equilibrium probability density for free nanoparticles are in perfect agreement with the results from kinetic theory.

Simulation of p^(eq)(Φ) for free nanoparticles.     

Mean first passage time for the contact between the ends of a chain polymer

We investigate the first passage times for the contact between the ends of a Rouse chain, whose initial separation is greater than a predefined contact distance, sigma, and equilibrium-distributed. An approximate analytic expression for the mean first passage time is obtained and compared with the results of previous theories and Brownian dynamics simulations. We find that the results of the present theory are in better agreement with Brownian dynamics simulation results than those of previously reported theories.     

A dynamic density functional theory for particles in a flowing solvent

We present a dynamic density functional theory (dDFT) which takes into account the advection of the particles by a flowing solvent. For potential flows, we can use the same closure as in the absence of solvent flow. The structure of the resulting advected dDFT suggests that it could be used for nonpotential flows as well. We apply this dDFT to Brownian particles (e.g., polymer coils) in a solvent flowing around a spherical obstacle (e.g., a colloid) and compare the results with direct simulations of the underlying Brownian dynamics. Although numerical limitations do not allow for an accurate quantitative check of the advected dDFT both show the same qualitative features. In contrast to previous works which neglected the deformation of the flow by the obstacle, we find that the bow wave in the density distribution of particles in front of the obstacle as well as the wake behind it are reduced dramatically. As a consequence, the friction force exerted by the (polymer) particles on the colloid can be reduced drastically.     

Dynamical density functional theory and its application to spinodal decomposition

We present an alternative derivation of the dynamical density functional theory for the one-body density profile of a classical fluid developed by Marconi and Tarazona [J. Chem. Phys. 110, 8032 (1999)]. Our derivation elucidates further some of the physical assumptions inherent in the theory and shows that it is not restricted to fluids composed of particles interacting solely via pair potentials; rather it applies to general, multibody interactions. The starting point for our derivation is the Smoluchowski equation and the theory is therefore one for Brownian particles and as such is applicable to colloidal fluids. In the second part of this paper we use the dynamical density functional theory to derive a theory for spinodal decomposition that is applicable at both early and intermediate times. For early stages of spinodal decomposition our nonlinear theory is equivalent to the (generalized) linear Cahn-Hilliard theory, but for later times it incorporates coupling between different Fourier components of the density fluctuations (modes) and therefore goes beyond Cahn-Hilliard theory. We describe the results of calculations for a model (Yukawa) fluid which show that the coupling leads to the growth of a second maximum in the density fluctuations, at a wave number larger than that of the main peak.     

Polymerization behaviour of 2,5-dimethylene- 2,5-dihydrofuran

Spontaneous homopolymerization of 2,5-dimethylene-2,5-dihydrofuran (DDF) was studied. The polymerization rates in two different initial monomer concentrations of DDF were analyzed with the first-order and second-order kinetics, and the homopolymerization of DDF was found to obey the first-order kinetics. The Arrhenius plot of the apparent rate constants at 30, 40, 50, and 60° gave an overall activation energy of 68.0 kJ/mol for the polymerization of DDF. From the comparison of the apparent rate constants at –78° and the time (the so-called half-life time) to decrease in half the monomer concentration for DDF with the corresponding values for p-xylylene (QM), DDF was found to be a less reactive monomer than QM. The copolymerizations of DDF with vinyl monomers such as acrylonitrile (AN), α-chloroacrylonitrile (CIAN), diethyl fumarate (DEF), and fumaronitrile (FN) were carried out in chloroform at 50° in the presence of AIBN to obtain the monomer reactivity ratios r₁(DDF) = 30.0 ± 3.0 and r₂ (AN) = 0 for the DDF-AN system, r₁ (DDF) = 1.55 ± 0.2 and r₂(CIAN) = 0 for the DDF-CIAN system, r₁(DDF) = 3.88 ± 0.2 and r₂(DEF) = 0 for the DDF-DEF system, and r₁(DDF) = 2.41 ± 0.1 and r₂ (FN) = 0 for the DDF-FN system, respectively. As the monomer reactivity ratios of r₂ for all systems were zero, Q and e values of DDF were calculated from the combination of two r₁ (DDF) values of any two copolymerization systems to be the 7.64 to 6.63 ×10²¹ range for Q and the –0.70 to –6.31 range for e, indicating that DDF is a highly conjugative and electron-donating monomer. © 1995 John Wiley & Sons, Inc.     

Reactions on cell membranes: comparison of continuum theory and Brownian dynamics simulations

Biochemical transduction of signals received by living cells typically involves molecular interactions and enzyme-mediated reactions at the cell membrane, a problem that is analogous to reacting species on a catalyst surface or interface. We have developed an efficient Brownian dynamics algorithm that is especially suited for such systems and have compared the simulation results with various continuum theories through prediction of effective enzymatic rate constant values. We specifically consider reaction versus diffusion limitation, the effect of increasing enzyme density, and the spontaneous membrane association/dissociation of enzyme molecules. In all cases, we find the theory and simulations to be in quantitative agreement. This algorithm may be readily adapted for the stochastic simulation of more complex cell signaling systems.     

Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static or temporally fluctuating far away from equilibrium. We study the dynamics of semiflexible polymer looping in the presence of such tensions by using Brownian dynamics simulation combined with an analytical theory. We show a minute tension dramatically changes the looping time, especially for long chains. Considering a dichotomically flipping noise as a simple example of the nonequilibrium tension, we find the phenomenon of resonant activation, where the looping time can be the minimum at an optimal flipping time. We discuss our results in connection with recent experiments.     

Influence of diffusion on the kinetics of excited-state association--dissociation reactions: comparison of theory and simulation

Several recent theories of the kinetics of diffusion influenced excited-state association--dissociation reactions are tested against accurate Brownian dynamics simulation results for a wide range of parameters. The theories include the relaxation time approximation (RTA), multiparticle kernel decoupling approximations and the so-called kinetic theory. In the irreversible limit, none of these theories reduce to the Smoluchowski result. For the pseudo-first-order target problem, we show how the RTA can be modified so that the resulting formalism does reduce correctly in the irreversible limit. We call this the unified Smoluchowski approximation, because it unites modern theories of reversible reactions with Smoluchowski's theory of irreversible reactions.     

Flat pancake distant dipolar fields for enhancement of intermolecular multiple-quantum coherence signals

Intermolecular multiple-quantum coherences (iMQCs) originated from distant dipolar field (DDF) possess some appealing unique properties for magnetic resonance imaging (MRI). DDF is usually induced with continuous wave (i.e., sine- or square-wave) magnetization modulation in the whole sample. In this article, a spatially localized and enhanced DDF was optimally tailored in a thin slice with an adiabatic inversion pulse. Evidence was provided to show that careful tailoring of the spatially localized DDF can generate highly efficient iMQC signals, with more than two-fold enhancement compared to the conventional sine-wave magnetization modulation method, and 1.5 times of that with the square-wave modulation under the similar condition. Theoretical predictions, simulation results, and experimental verifications agree well with each other. Practical implementation of this approach for efficient iMQC MRI was explored.     

Entropic noise-induced nonequilibrium transition

We consider a system of Brownian particles confined in a two-dimensional bilobal enclosure. Varying cross-section of the confinement results in an effective entropic potential in reduced dimension. We show that the system may undergo an entropic noise-induced transition when the shape of the stationary probability density changes qualitatively from bimodal to trimodal type under the influence of a multiplicative noise.     

Theory of nanoparticle diffusion in unentangled and entangled polymer melts

We propose a statistical dynamical theory for the violation of the hydrodynamic Stokes-Einstein (SE) diffusion law for a spherical nanoparticle in entangled and unentangled polymer melts based on a combination of mode coupling, Brownian motion, and polymer physics ideas. The non-hydrodynamic friction coefficient is related to microscopic equilibrium structure and the length-scale-dependent polymer melt collective density fluctuation relaxation time. When local packing correlations are neglected, analytic scaling laws (with numerical prefactors) in various regimes are derived for the non-hydrodynamic diffusivity as a function of particle size, polymer radius-of-gyration, tube diameter, degree of entanglement, melt density, and temperature. Entanglement effects are the origin of large SE violations (orders of magnitude mobility enhancement) which smoothly increase as the ratio of particle radius to tube diameter decreases. Various crossover conditions for the recovery of the SE law are derived, which are qualitatively distinct for unentangled and entangled melts. The dynamical influence of packing correlations due to both repulsive and interfacial attractive forces is investigated. A central finding is that melt packing fraction, temperature, and interfacial attraction strength all influence the SE violation in qualitatively different directions depending on whether the polymers are entangled or not. Entangled systems exhibit seemingly anomalous trends as a function of these variables as a consequence of the non-diffusive nature of collective density fluctuation relaxation and the different response of polymer-particle structural correlations to adsorption on the mesoscopic entanglement length scale. The theory is in surprisingly good agreement with recent melt experiments, and new parametric studies are suggested.     

Excluded volume effects on the intrachain reaction kinetics

On the basis of the recently developed optimized Rouse-Zimm theory of chain polymers with excluded volume interactions, we calculate the long-time first-order rate constant k(1) for end-to-end cyclization of linear chain polymers. We first find that the optimized Rouse-Zimm theory provides the longest chain relaxation times tau(1) of excluded volume chains that are in excellent agreement with the available Brownian dynamics simulation results. In the free-draining limit, the cyclization rate is diffusion-controlled and k(1) is inversely proportional to tau(1), and the k(1) values calculated using the Wilemski-Fixman rate theory are in good agreement with Brownian dynamics simulation results. However, when hydrodynamic interactions are included, noticeable deviations are found. The main sources of errors are fluctuating hydrodynamic interaction and correlation hole effects as well as the non-Markovian reaction dynamic effect. The physical natures of these factors are discussed, and estimates for the magnitudes of required corrections are given. When the corrections are included, the present theory allows the prediction of accurate k(1) values for the cyclization of finite-length chains in good solvents as well as the correct scaling exponent in the long-chain limit.     

Brownian dynamics of a compressed polymer brush model. Off-equilibrium response as a function of surface coverage and compression rate

We study the compressive behaviour of a polymer-covered surface (i.e., a "polymer brush") using Brownian dynamics simulations. The model consists of grafted chains with variable flexibility, variable intra- and inter-chain interactions, as well as different surface coverage. We discuss the polymer brush response to confinement by considering variable rates of compression under a hard plane. Our results show a small degree of inter-chain entanglement, regardless of whether the interaction is attractive or merely excluded volume. We observe that the molecular shape depends strongly on the surface coverage. Dense brushes exhibit a limited degree of lateral deformation under compression; instead, chains undergo a transition that produces a local patch with near-solid packing. This effect due to surface density can be undone partially by increasing the attractive nature of the chain interaction, by modulating the rate of compression, or by allowing "soft anchoring", i.e., the possible Brownian drift of the grafting bead on the surface. We have also studied the polymer brush relaxation while maintaining the compressing plane, as well as after its sudden removal. We find evidence that also the relaxation depends on surface density; dense brushes appear to be configurationally frustrated at high compression and are unable to undergo swelling, regardless of the pressure applied.     

Dwell time of a Brownian molecule in a microdomain with traps and a small hole on the boundary

We calculate the mean time a Brownian particle spends in a domain with traps and the number of bonds it makes before escaping through a small hole in the boundary. This mean time, called the Dwell time, depends on the backward binding rate (with the trap, e.g., scaffolding molecules), the mean time to reach the trap (forward binding rate), and the size of the hole. We estimate the mean and variance of the number of bonds made prior to exit. In a biochemical context, a quantitative signal occurs when the mean number of bonds exceeds a certain threshold, which may initiate a cascade of chemical reactions that have physiological consequences. We apply the present results to obtain estimates of the mean time a Brownian receptor spends inside a synaptic domain, when it moves freely by lateral diffusion on the membrane of a neuron and interacts at a synapse with scaffolding molecules.     

Significance of cross correlations in the stress relaxation of polymer melts

According to linear response theory, all relaxation functions in the linear regime can be obtained using time correlation functions calculated under equilibrium. In this paper, we demonstrate that the cross correlations make a significant contribution to the partial stress relaxation functions in polymer melts. We present two illustrations in the context of polymer rheology using (1) Brownian dynamics simulations of a single chain model for entangled polymers, the slip-spring model, and (2) molecular dynamics simulations of a multichain model. Using the single chain model, we analyze the contribution of the confining potential to the stress relaxation and the plateau modulus. Although the idea is illustrated with a particular model, it applies to any single chain model that uses a potential to confine the motion of the chains. This leads us to question some of the assumptions behind the tube theory, especially the meaning of the entanglement molecular weight obtained from the plateau modulus. To shed some light on this issue, we study the contribution of the nonbonded excluded-volume interactions to the stress relaxation using the multichain model. The proportionality of the bonded/nonbonded contributions to the total stress relaxation (after a density dependent "colloidal" relaxation time) provides some insight into the success of the tube theory in spite of using questionable assumptions. The proportionality indicates that the shape of the relaxation spectrum can indeed be reproduced using the tube theory and the problem is reduced to that of finding the correct prefactor.     

The Reaction of 2,5-Dimethoxy-2,5-Dihydrofuran with Dichloroketene

2,5-Dimethoxy-2,5-dihydrofuran (DDF) reacts with dichloroketene to give 7,9-dimethoxy-3,3,5,5-tetrachloro-8-oxabicyclo[4,3,0]-noan-2,4-dione (I), and methyl chloro-(2,5-dihydro-5-methoxy-2-furanylidene) acetate (II). The reactions of 2,5-dihydrofuran and 2,5-dimethoxy-tetrahydrofuran with dichloroketene were also-studied for comparison. Compound II was derived from the insertion of a molecule of dichloroketene into the C-O bond of DDF with subsequent dehydrochlorination. Compound I resulted from the cycloaddition of two molecules of dichloroketene to the C=C bond of DDF. A mechanism involving a 1,5-dipolar intermediate is proposed to account for this novel reaction.