Boëder PDF Brownian simulations for macromolecular rod-like particles near uneven solid surfaces

A molecular dynamics simulation is presented to calculate the Probability Distribution Functions (PDF) for the spatial positions and angular orientations of macromolecular rod-like particles in dilute solutions, under hydrodynamic flow, in the vicinity of uneven solid boundaries. The Brownian and hydrodynamic restitution model for ideally flat surfaces is generalized to simulate the diffusive collisions between the macromolecular particles and an uneven solid surface. Two types of uneven surfaces are particularly considered: the periodic grating and the random rough, with characteristic profiles of heights and lateral variations. Different from ideally flat surfaces, the simulation results demonstrate that uneven surfaces have characteristic depletion layers, and characteristic and variable PDF. This is the case under varying conditions of hydrodynamic flow, Brownian movement and diffusive collisions. These characteristics uniquely identify Boeder PDF signatures for the uneven surface topography.     

Dielectrophoresis of nanoparticles

A numerical scheme based on the distributed Lagrange multiplier method (DLM) is used to study the motion of nano-sized particles of dielectric suspensions subjected to uniform and nonuniform electric fields. Particles are subjected to both electrostatic and hydrodynamic forces, as well as Brownian motion. The results of the simulations presented in this paper show that uniform electric fields the evolution of the particle structures depends on the ratio of electrostatic particle-particle interactions and Brownian forces. When this ratio is of the order of 100 or greater, particles form stable chains and columns, whereas when it is of the order of 10 or smaller the particle distribution is random. For the nonuniform electric field cases considered in this paper, the relative magnitude of Brownian forces is in the range such that it does not influence the eventual collection of particles by dielectrophoresis and the particular locations where the particles are collected. However, Brownian motion is observed to influence the transient particle trajectories. The deviation of the particle trajectories compared to those determined by the electrostatic and hydrodynamic forces alone is characterized by the ratio of Brownian and dielectrophoretic forces.     

The Effects of Extensional Flow and Hydrodynamic Interaction on the Nonequilibrium Brownian Dynamics of Dendrimers. A Bead‐Spring Model for Dendrimeric Molecules

We present the effects of incorporating hydrodynamic interactions into the nonequilibrium Brownian dynamics model describing the rheological properties of dendrimers under simple shear flow. The model response to uniaxial extensional flow is considered and compared with the extensional flow behavior of conventional linear molecules. The dendrimers are characterized by low viscosities and display little visco‐elasticity which makes them attractive materials from the stand‐point of energy‐intensive polymer forming processes.     

Density-induced coupling effects on the dispersivity of a flexible chain particle

A model is introduced to investigate the transport properties of an inhomogeneously dense flexible chain particle. The specific model used is a sedimenting non-neutrally buoyant inhomogenously weighted flexible Brownian dumbbell, and it is shown that density inhomogeneity gives rise to a novel coupling effect between the "shape-fluctuation" and "size-fluctuation" dispersion mechanisms. The previously reported shape-fluctuation dispersion term stems from the dumbbell's nonspherical shape and the ensuing anisotropic mobility tensor, while the already investigated size fluctuation term is the result of the dependence of the overall dumbbell translational mobility on the separation distance between the constitutive spheres. Because the density of the constitutive spheres is unequal, the external force simultaneously reorients and deforms the flexible dumbbell, and it is this mutual dependence between dumbbell orientation and size that induces the coupling. Numerical results are presented for the case of a tethered dumbbell composed of two spheres, identical in size but differing in density. The "weak-field" limit is addressed, where the externally applied torque and particle deformation forces are dominated by the thermal fluctuations associated with rotational and deformation Brownian motion. This numerical solution, obtained by including a large number of higher order hydrodynamic interactions (120 terms), describes the Brownian particle's long-time transport without resorting to ad hoc approximations, such as preaveraging the hydrodynamic force or incorporating only first-order hydrodynamic interaction effects (such as employing the Burgers-Oseen tensor). Separate analytical solutions, based on these respective approximations, are also presented and it is concluded that in the limit of "long tethers," where the ratio of tether length to sphere size is greater than seven, no more than 15% error is introduced by neglecting higher-order hydrodynamic interactions. Similarly, the preaveraging approximation introduces no more than a few percent error in the limit of "almost-rigid" dumbbells, where the ratio of tether length to sphere size is less than three. For tethers of "intermediate" length, the full numerical solution must be employed.     

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)].     

Transport coefficients of aqueous dodecyltrimethylammonium bromide solutions: comparison between experiments, analytical calculations and numerical simulations

We study dynamical properties of ionic species in aqueous solutions of dodecyltrimethylammonium bromide, for several concentrations below and above the critical micellar concentration (cmc). New experimental determinations of the electrical conductivity are given which are compared to results obtained from an analytical transport theory; transport coefficients of ions in these solutions above the cmc are also computed from Brownian dynamics simulations. Analytical calculations as well as the simulation treat the solution within the framework of the continuous solvent model. Above the cmc, three ionic species are considered: the monomer surfactant, the micelle and the counterion. The analytical transport theory describes the structural properties of the electrolyte solution within the mean spherical approximation and assumes that the dominant forces which determine the deviations of transport processes from the ideal behavior (i.e., without any interactions between ions) are hydrodynamic interactions and electrostatic relaxation forces. In the simulations, both direct interactions and hydrodynamic interactions between solutes are taken into account. The interaction potential is modeled by pairwise repulsive 1/r(12) interactions and Coulomb interactions. The input parameters of the simulation (radii and self-diffusion coefficients of ions at infinite dilution) are partially obtained from the analytical transport theory which fits the experimental determinations of the electrical conductivity. Both the electrical conductivity of the solution and the self-diffusion coefficients of each species computed from Brownian dynamics are compared to available experimental data. In every case, the influence of hydrodynamic interactions (HIs) on the transport coefficients is investigated. It is shown that HIs are crucial to obtain agreement with experiments. In particular, the self-diffusion coefficient of the micelle, which is the largest and most charged species in the present system, is enhanced when HIs are included whereas the diffusion coefficients of the monomer and the counterion are roughly not influenced by HIs.     

Communication: Generalizing Rosenfeld's excess-entropy scaling to predict long-time diffusivity in dense fluids of Brownian particles: from hard to ultrasoft interactions

Computer simulations are used to test whether a recently introduced generalization of Rosenfeld's excess-entropy scaling method for estimating transport coefficients in systems obeying molecular dynamics can be extended to predict long-time diffusivities in fluids of particles undergoing Brownian dynamics in the absence of interparticle hydrodynamic forces. Model fluids with inverse-power-law, Gaussian-core, and Hertzian pair interactions are considered. Within the generalized Rosenfeld scaling method, long-time diffusivities of ultrasoft Gaussian-core and Hertzian particle fluids, which display anomalous trends with increasing density, are predicted (to within 20%) based on knowledge of interparticle interactions, excess entropy, and scaling behavior of simpler inverse-power-law fluids.     

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. However, the calculation of correlated Brownian noise vectors in these simulations is computationally very demanding and alternative methods are desirable. This paper studies methods based on Krylov subspaces for computing Brownian noise vectors. These methods are related to Chebyshev polynomial approximations, but do not require eigenvalue estimates. We show that only low accuracy is required in the Brownian noise vectors to accurately compute values of dynamic and static properties of polymer and monodisperse suspension models. With this level of accuracy, the computational time of Krylov subspace methods scales very nearly as O(N(2)) for the number of particles N up to 10 000, which was the limit tested. The performance of the Krylov subspace methods, especially the "block" version, is slightly better than that of the Chebyshev method, even without taking into account the additional cost of eigenvalue estimates required by the latter. Furthermore, at N = 10 000, the Krylov subspace method is 13 times faster than the exact Cholesky method. Thus, Krylov subspace methods are recommended for performing large-scale Brownian dynamics simulations with hydrodynamic interactions.     

Long-time self-diffusion of charged colloidal particles: electrokinetic and hydrodynamic interaction effects

The authors analyze the long-time self-diffusion of charge-stabilized colloidal macroions in nondilute suspensions using a mode-coupling scheme developed for multicomponent suspensions of interacting Brownian spheres. In this scheme, all ionic species, including counterions and electrolyte ions, are treated on an equal footing as charged hard spheres undergoing overdamped Brownian motion. Hydrodynamic interactions between all ions are accounted for on the far-field level. We show that the influence on the colloidal long-time self-diffusion coefficient arising from the relaxation of the microionic atmosphere surrounding the colloids, the so-called electrolyte friction effect, is usually insignificant in comparison with the friction contributions arising from direct and hydrodynamic interactions between the colloidal particles. This finding is true even for small colloid concentrations unless the mobility difference between colloidal particles and microions is not large. Furthermore, we observe an interesting nonmonotonic density dependence of the colloidal long-time self-diffusion coefficient in suspensions with low amount of added salt. We show that this unusual density dependence is due to colloid-colloid hydrodynamic interactions.     

Screening of hydrodynamic interactions in Brownian rod suspensions

We present the details and results of a simulation study addressing the dynamics and rheology of rod suspensions over a wide regime of concentrations ranging from dilute to concentrated systems. Our study compares the results of two complementary simulation methods. The first method adapts a recently proposed explicit solvent simulation strategy and incorporates both hydrodynamical effects and steric interactions between the rod units. We compare the results of such a method with those obtained from a Brownian dynamics simulation approach which retains the steric interactions but neglects the effects of hydrodynamic interactions. Overall, our results in the context of the translational and rotational diffusivities are in agreement with the hydrodynamical predictions in the dilute regime and the corresponding results of the tube model and its extensions thereof in the semidilute regimes. The latter results suggest that effects of hydrodynamic interactions on the translational and rotational diffusivities are secondary relative to the steric interactions and at best lead only to a small correction to the results of the classical tube model. Our results in the context of linear viscoelasticity also broadly confirms the predictions of the tube model for the storage and loss moduli and allows us to extract for the first time the independent hydrodynamic and Brownian contributions to the zero shear viscosity. While the relative magnitudes of these contributions are consistent with the theoretical predictions, the quantitative magnitudes are quite different from the theoretical predictions. Overall, these results confirm the validity of the hydrodynamic "screening" hypothesis and ratify the neglect of hydrodynamical stresses in quantifying the linear rheology of Brownian rod suspensions.     

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Theta temperature: a Brownian dynamics study

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Theta conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.     

A Brownian dynamics study on the self-diffusion of charged tracers in dilute polyelectrolyte solutions

Brownian dynamics simulations with hydrodynamic interactions are conducted to investigate the self-diffusion of charged tracer particles in a dilute solution of charged polymers, which are modeled by bead-spring chains. The Debye-Hückel approximation is used for the electrostatic interactions. The hydrodynamic interactions are implemented by the Ewald summation of the Rotne-Prager tensor. Our simulations find that the difference in short- and long-time diffusivities is very slight in uncharged short-chain solutions. For charged systems, to the contrary, the difference becomes considerable. The short-time diffusivity is found to increase with increasing chain length, while an opposite behavior is obtained for the long-time diffusivity. The former is attributed to the hydrodynamic screening among beads in a same chain due to the bead connectivity. The latter is explained by the memory effect arising from the electrostatic repulsion and chain length. The incorporation of hydrodynamic interactions improves the agreement between the simulation prediction and the experimental result.     

流体动力学作用对粒子聚集影响的布朗动力学模拟

采用布朗动力学模拟方法, 研究了流体动力学作用对稀溶液中悬浮粒子聚集过程的影响. 模拟中忽略了一个粒子同时与多个粒子碰撞聚集的可能, 引入了前人有关两粒子间流体动力学作用影响的研究成果. 模拟结果证实了流体动力学的作用在比较大的幅度上减缓了粒子的聚集过程, 是导致粒子聚集速率的实验值低于Smoluchowski理论值的重要原因之一. 另外, 在分别加入和排除重力作用, 以及考虑和忽略粒子间流体动力学作用在内的各种条件下模拟了粒子的聚集过程, 得到了两种因素相互耦合作用时各因素对粒子聚集过程影响的结果, 并从动力学的角度对这些因素的影响机制进行了相应的讨论.     

电解质水溶液传递性质的布朗动力学模拟研究

在传统布朗动力学的基础上, 考虑流体力学的影响, 并且引入Smart Monte Carlo方法的接受概率, 对电解质溶液进行布朗动力学模拟, 得到不同浓度和温度下KCl溶液中离子间的径向分布函数, 并且与超网链积分方程理论计算结果进行了比较, 同时, 模拟了KCl和NaCl溶液的摩尔电导率. 模拟过程基于电解质溶液的原始模型, 溶剂被看作连续介质, 溶质分子之间的相互作用采用软核加静电的势能函数模型, 长程静电力的处理采用Ewald加和方法. 结果显示, 流体力学的作用对于电解质溶液的结构性质没有明显的影响, 但是对于传递性质的影响显著; 考虑流体力学作用的布朗动力学模拟结果与实验数据吻合良好.     

Substrate concentration dependence of the diffusion-controlled steady-state rate constant

The Smoluchowski approach to diffusion-controlled reactions is generalized to interacting substrate particles by including the osmotic pressure and hydrodynamic interactions of the nonideal particles in the Smoluchoswki equation within a local-density approximation. By solving the strictly linearized equation for the time-independent case with absorbing boundary conditions, we present an analytic expression for the diffusion-limited steady-state rate constant for small substrate concentrations in terms of an effective second virial coefficient B2*. Comparisons to Brownian dynamics simulations excluding hydrodynamic interactions show excellent agreement up to bulk number densities of B2*rho0 < approximately = 0.4 for hard sphere and repulsive Yukawa-like interactions between the substrates. Our study provides an alternative way to determine the second virial coefficient of interacting macromolecules experimentally by measuring their steady-state rate constant in diffusion-controlled reactions at low densities.     

Computer simulation on the collision-sticking dynamics of two colloidal particles in an optical trap

Collisions of a particle pair induced by optical tweezers have been employed to study colloidal stability. In order to deepen insights regarding the collision-sticking dynamics of a particle pair in the optical trap that were observed in experimental approaches at the particle level, the authors carry out a Brownian dynamics simulation. In the simulation, various contributing factors, including the Derjaguin-Landau-Verwey-Overbeek interaction of particles, hydrodynamic interactions, optical trapping forces on the two particles, and the Brownian motion, were all taken into account. The simulation reproduces the tendencies of the accumulated sticking probability during the trapping duration for the trapped particle pair described in our previous study and provides an explanation for why the two entangled particles in the trap experience two different statuses.     

Effects of pre-oxidation temperature on coal secondary spontaneous combustion

The hydrodynamic force (drag) on spherical and irregularly shaped particles significantly increases when the particles move close to solid and permeable boundaries. The overall effect of the increased hydrodynamic drag is to hinder the particle movement in the vicinity of boundaries and this includes the Brownian movement and electrophoresis. The Monte Carlo simulation method is used to model the Brownian movement, the resulting diffusion, and the electrophoresis of spherical particles in narrow, cylindrical pores, filled with Newtonian fluids. It is observed that the effect of the pore walls is a significant reduction of the space-averaged electrophoretic velocity of the particles, which implies reduced particle flux through the pores. The hindered electrophoresis is primarily a geometric phenomenon, caused by the increased drag and depends on the size of the particles and the pore-to-particle diameter ratio. The temperature of the fluid slightly affects the hindered electrophoresis through its effect on the viscosity, which is a determinant of the Brownian force, the diffusivity and the electrophoretic velocity. The hindered electrophoresis is almost independent of the other fluid and particle properties, such as density. Based on the simulation results a non-linear correlation for the flux of particles is derived, valid in the ranges 5?<?R/α?<?120, 5 nm?<?α?<?100 nm and 273 K?<?T?<?355 K.

     

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 simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.