An immersed boundary method for Brownian dynamics simulation of polymers in complex geometries: application to DNA flowing through a nanoslit with embedded nanopits

This work presents an immersed boundary method that allows fast Brownian dynamics simulation of solutions of polymer chains and other Brownian objects in complex geometries with fluctuating hydrodynamics. The approach is based on the general geometry Ewald-like method, which solves the Stokes equation with distributed regularized point forces in O(N) or O(NlogN) operations, where N is the number of point forces in the system. Time-integration is performed using a midpoint algorithm and Chebyshev polynomial approximation proposed by Fixman. This approach is applied to the dynamics of a genomic DNA molecule driven by flow through a nanofluidic slit with an array of nanopits on one wall of the slit. The dynamics of the DNA molecule was studied as a function of the Péclet number and chain length (the base case being λ-DNA). The transport characteristics of the hopping dynamics in this device differ at low and high Péclet number, and for long DNA, relative to the pit size, the dynamics is governed by the segments residing in the pit. By comparing with results that neglect them, hydrodynamic interactions are shown to play an important quantitative role in the hopping dynamics.     

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.     

Hydrodynamic interactions induce movement against an external load in a ratchet dimer Brownian motor

We use the Brownian dynamics with hydrodynamic interactions simulation in order to describe the movement of a elastically coupled dimer Brownian motor in a ratchet potential. The only external forces considered in our system were the load, the random thermal noise and an unbiased thermal fluctuation. For a given set of parameters we observe direct movement against the load force if hydrodynamic interactions were considered.     

Simulations of polyelectrolyte dynamics in an externally applied electric field in confined geometry

We consider the dynamics of charged polymers in free solution in a slit geometry under the influence of an electrical field, applied at an angle to the plane parallel walls of the confinement. The simulations are carried out using the Brownian dynamics method with explicit counterions and implicit hydrodynamics. The hydrodynamic interactions between all the particles and the plane parallel walls are taken into account using a diffusion matrix which depends on slit geometry and the actual polyelectrolyte-solute conformations. We observe a selective transport of the charged polymers, as a function of the degree of polymerization and slit height.     

Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations

The isotropic-nematic spinodals of solutions of rigid spherocylindrical colloids with various shape anisotropies L/D in a wide range from 10 to 60 are investigated by means of Brownian dynamics simulations. To make these simulations feasible, we developed a new event-driven algorithm that takes the excluded volume interactions between particles into account as instantaneous collisions, but neglects the hydrodynamic interactions. This algorithm is applied to dense systems of highly elongated rods and proves to be efficient. The calculated isotropic-nematic spinodals lie between the previously established binodals in the phase diagram and extrapolate for infinitely long rods to Onsager's [Ann. N. Y. Acad. Sci. 51, 627 (1949)] theoretical predictions. Moreover, we investigate the shear induced shifts of the spinodals, qualitatively confirming the theoretical prediction of the critical shear rate at which the two spinodals merge and the isotropic-nematic phase transition ceases to exist.     

Cross-streamline migration of a semiflexible polymer in a pressure driven flow

Experiments and simulations on single α-actin filaments in the Poiseuille flow through a microchannel show that the center-of-mass probability density across the channel assumes a bimodal shape as a result of pronounced cross-streamline migration. We reexamine the problem and perform Brownian dynamics simulations for a bead-spring chain with bending elasticity. Hydrodynamic interactions between the pointlike beads are taken into account by the two-wall Green tensor of the Stokes equations. Our simulations reproduce the bimodal distribution only when hydrodynamic interactions are taken into account. Numerical results on the orientational order of the end-to-end vector of the model polymer are also presented together with analytical hard-needle expressions at zero flow velocity. We derive a Smoluchowski equation for the center-of-mass distribution and carefully analyze the different contributions to the probability current that causes the bimodal distribution. As for flexible polymers, hydrodynamic repulsion explains the depletion at the wall. However, in contrast to flexible polymers, the deterministic drift current mainly determines migration away from the centerline and thereby depletion at the center. Diffusional currents due to a position-dependent diffusivity become less important with increasing polymer stiffness.     

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.     

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.     

Tracer diffusion in colloidal suspensions under dilute and crowded conditions with hydrodynamic interactions

We consider tracer diffusion in colloidal suspensions under solid loading conditions, where hydrodynamic interactions play an important role. To this end, we carry out computer simulations based on the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) technique. Many details of the simulation method are discussed in detail. In particular, our choices for the SRD-MD parameters and for the different scales are adapted to simulating colloidal suspensions under realistic conditions. Our simulation data are compared with published theoretical, experimental and numerical results and compared to Brownian dynamics simulation data. We demonstrate that our SRD-MD simulations reproduce many features of the hydrodynamics in colloidal fluids under finite loading. In particular, finite-size effects and the diffusive behavior of colloids for a range of volume fractions of the suspension show that hydrodynamic interactions are correctly included within the SRD-MD technique.     

电解质溶液自扩散系数的布朗动力学模拟

采用布朗动力学方法对电解质溶液进行了模拟,在传统布朗动力学的基础上综合考虑了流体力学的影响,并且引入SmartMonteCarlo方法的接受概率,避免了离子不现实的移动和位型重叠,这样不仅可以将模拟过程中的时间步长大幅度提高,而且还可使溶质在相空间的演化过程更接近实际.模拟过程以电解质溶液的原始模型为基础,将溶剂看作连续介质,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,长程静电力采用Ewald加和的处理方法.模拟得到KCl和NaCl溶液的径向分布函数g+-(r),g++(r)和g--(r),并与文献中HNC计算以及模拟的结果进行比较,使用推广的Green-Kubo公式模拟计算溶液中各种离子的自扩散性质,计算结果与实验数据吻合良好.     

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.     

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.     

Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics

It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.     

Reversible coagulation of colloidal suspension in shallow potential wells: Direct numerical simulation

Brownian dynamics computer simulations of aggregation in 2D 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. The chosen mathematical model enables to predict the correct values of diffusion coefficient of freely moving particle, the mean value of kinetic energy for each particle in ensemble of interacting colloidal particles and residence times of colloidal particles inside the potential wells of different depths. The simulations allow monitoring formation and breakage of clusters in a suspension as well as time dependence of the mean cluster size. The article is published in the original.     

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.     

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.     

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)].     

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.     

Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries

A numerical method to simulate the dynamics of polymer solutions in confined geometries has been implemented and tested. The method combines a fluctuating lattice-Boltzmann model of the solvent [Ladd, Phys. Rev. Lett. 70, 1339 (1993)] with a point-particle model of the polymer chains. A friction term couples the monomers to the fluid [Ahlrichs and Dunweg, J. Chem. Phys. 111, 8225 (1999)], providing both the hydrodynamic interactions between the monomers and the correlated random forces. The coupled equations for particles and fluid are solved on an inertial time scale, which proves to be surprisingly simple and efficient, avoiding the costly linear algebra associated with Brownian dynamics. Complex confined geometries can be represented by a straightforward mapping of the boundary surfaces onto a regular three-dimensional grid. The hydrodynamic interactions between monomers are shown to compare well with solutions of the Stokes equations down to distances of the order of the grid spacing. Numerical results are presented for the radius of gyration, end-to-end distance, and diffusion coefficient of an isolated polymer chain, ranging from 16 to 1024 monomers in length. The simulations are in excellent agreement with renormalization group calculations for an excluded volume chain. We show that hydrodynamic interactions in large polymers can be systematically coarse-grained to substantially reduce the computational cost of the simulation. Finally, we examine the effects of confinement and flow on the polymer distribution and diffusion constant in a narrow channel. Our results support the qualitative conclusions of recent Brownian dynamics simulations of confined polymers [Jendrejack et al., J. Chem. Phys. 119, 1165 (2003) and Jendrejack et al., J. Chem. Phys. 120, 2513 (2004)].