Brownian dynamics with constraints

Systems possessing degrees of freedom operating on widely separated timescales, where the effects of those operating on the smaller timescales are relatively unimportant, may be modelled by the use of the Langevin equation. In order to study such systems containing complex polyatomic particles, holonomic constraints may be used. Though there is no lack of published algorithms for the numerical solution of the Langevin equation, few of them have been developed with sufficient rigour to ensure their precision, nor to demonstrate their compatibility with constraints. This study recapitulates an approach based upon Runge-Kutta equations which has the advantage of being perfectible to any desired order in the time-step, and shows how it may be combined with the SHAKE method in order to perform constrained Brownian dynamics simulations. Results are presented for some simple systems with a third order algorithm, and it is found that the correct dynamic and statistical behaviour is recovered.     

Brownian dynamics of a microswimmer

We report on dynamic properties of a simple model microswimmer composed of three spheres and propelling itself in a viscous fluid by spinning motion of the spheres under zero net torque constraint. At a fixed temperature and increasing the spinning frequency, the swimmer demonstrates a transition from dissipation-dominated to a pumping-dominated motion regime characterized by negative effective friction coefficient. In the limit of high frequencies, the diffusion of the swimmer can be described by a model of an active particle with constant velocity.     

More efficient Brownian dynamics algorithms

We examine the relative efficiencies of three- algorithms for performing Brownian Dynamics simulations without many-body hydrodynamics. We compare the conventional Brownian Dynamics algorithm of Ermak (CBD), Smart Monte Carlo (SMC) which incorporates Boltzmann sampling into essentially a CBD procedure, and the Stochastic Runge Kutta (SRK) method. We show, using the repulsive potential φ(r) = ε(σ/r) ⁿ , where n = 36 and 72, that the SRK algorithm gives the most accurate short-time dynamics for the mean-square displacements. The SRK algorithm static and dynamical properties converge better with a reducing time step to the exact values, than those generated by the CBD algorithm; giving efficiency gains typically of a factor of 3–4. Both CBD and SMC have the incorrect sign for the first correction term to the mean square displacement in a time step, whereas the SRK algorithm gives essentially the exact solution to order Δt ², where Δt is the simulation time step. In fact, these correction terms are almost equal and opposite in sign. Expressions for these terms were derived in terms of the average interaction energy per particle. The force, shear and bulk stress autocorrelation functions were calculated. The average energy per particle and time correlation functions at short time have values in excess of the exact values, while the corresponding quantities for SRK are below this. This difference in behaviour can be traced back to the extent of compliance of the particle trajectories with the exact expansion of the Smoluchowski equation. The accuracy, at a given value of the time step, of the stochastic algorithms can significantly depend on the form of the interaction potential between particles. It is also demonstrated that the long time limits of various correlation functions are fairly insensitive to a particular scheme (SRK or CBD) used in the simulations. All the correlation functions have a stretched exponential region at intermediate to long times, and the values of the exponents on density and force law steepness have been determined.     

Brownian dynamics simulation of electrostatically interacting proteins

Brownian dynamics simulation software has been developed to study the dynamics of proteins as a whole in solution. The proteins were modelled as spheres with point dipoles embedded in the centre of sphere. A set of Brownian dynamics simulations at different values of the dipole moments, protein concentration and translational diffusion coefficient was performed to investigate the influence of interprotein electrostatic interactions on dynamic protein behaviour in solution. It was shown that these interactions led to the slowing down of protein rotation and a complex non-exponential shape of the rotational correlation function. Analysis of the correlation functions was performed within the frame of the model of electrostatic interprotein interactions advanced earlier on the basis of NMR and dielectric spectroscopy data. This model assumes that, due to electrostatic interactions, protein Brownian rotation becomes anisotropic. The lifetime of this anisotropy is controlled mainly by translational diffusion of proteins. Thus, the correlation function can be decomposed into two components corresponding to anisotropic Brownian rotation and an isotropic motion of an external electric field vector produced by the surrounding proteins.     

Rotational Brownian dynamics of semiflexible broken rods

Using the Brownian dynamics simulation technique, we study the rotational dynamics of a semiflexible broken rod. We employ a suitable bead model with stiff springs between beads and strong forces opposing to bending, except at the joint where flexibility is variable. We consider mostly broken rods with equal arms. From the simulated Brownian trajectories we obtain the correlation function for the second order Legendre polynomial of the reorientational angle of the end-to-end vector and of the arm vector. These correlation functions are closely related to fluorescence anisotropy decay and electric birefringence decay, respectively. In the first case, the relaxation time for a completely flexible rod agrees with the Harvey-Wegener theory, and in the second, the longest relaxation time agrees well with that obtained from the rigid-body treatment over the whole range of flexibility. Furthermore, we discuss the relative importance of flexibility in both types of decay. Finally, we present results for a case with unequal arms, confirming the validity of the Harvey-Wegener theory and the rigid-body treatment.     

Collective dynamics of two-dimensional coupled Brownian motors

The transport properties of coupled Brownian particles in a two-dimensional rocking ratchet are investigated via Langevin simulation. The results show that the average center-of-mass velocity is multi-peaks function of the frequency of the driving force. Furthermore, in the 2D coupled Brownian motor system there are the collective effect and ratchet behavior, which can switch depending on the frequency of driving force. It turns out that the cooperative effect between the interaction of coupled particles and external rocking driving force facilitates collective directional motion and energy conversion.     

Brownian dynamics simulation of linear chain growth

Growth of linear chains is simulated by the technique of Brownian dynamics. The influence of the initial volume fraction of particles on the rate of the process and the structure of the chains is studied. Results show that aggregation is swift at the beginning of the process and very slow at the end. This is due to the decrease of the number of flocs in solution and the decrease in the efficiency of collisions when the degree of aggregation increases. The polydispersity of the system increases during aggregation and reaches a maximum value when the reaction is 96% complete. This increase is greater at higher concentrations. Results indicate that for lower concentrations aggregate growth is principally by reactive collision between aggregates of similar molecular weight, while for higher concentrations there is a relatively high fraction of reactive collisions between aggregates with very different molecular weights. The concentration effect on the structure of the chains is studied, evaluating the fractal dimensions of the chains. When the concentration increases there is a transition from very open structures (fractal dimension 1.76) to very tangled structures, where chains are collapsed (fractal dimension 3).     

Brownian dynamics simulation of polydisperse hard spheres

Standard algorithms used for the numerical integration of the Langevin equation require that interactions should slowly vary during the integration time-step. This in not the case for hard-body systems, where there is no clear-cut between the correlation time of the noise and the time-scale of the interactions. Starting with a short time approximation of the Smoluchowski equation, we introduce an algorithm for the simulation of the over-damped Brownian dynamics of polydisperse hard-spheres in absence of hydrodynamic interactions and briefly discuss the extension to the case of external drifts.     

A gas of Brownian particles in statistical dynamics

We consider a large number of particles on a one-dimensional latticel Z in interaction with a heat particle; the latter is located on the bond linking the position of the particle to the point to which it jumps. The energy of a single particle is given by a potentialV(x), x∈Z. In the continuum limit, the classical version leads to Brownian motion with drift. A quantum version leads to a local drift velocity which is independent of the applied force. Both these models obey Einstein's relation between drift, diffusion, and applied force. The system obeys the first and second laws of thermodynamics, with the time evolution given by a pair of coupled non linear heat equations, one for the density of the Brownian particles and one for the heat occupation number; the equation for a tagged Brownian particle can be written as a stochastic differential equation.     

Brownian dynamics simulation of two confined colloidal particles

The dynamics of two confined colloidal particles is studied by means of Brownian dynamics simulation. The autocorrelation function and cross-correlation function of the two colloidal spheres are computed by utilizing the formulae of hydrodynamic diffusion matrix expanded to different orders, as well as the accurate tensor through numerical algorithm. Furthermore, the numerical results are compared with the experimental results and the theoretical approximation. It is found that the relatively simple theoretical approximation gives good predictions when two spheres are far away from each other, but fails when the two spheres are very close.     

Tracer dynamics in Dyson's model of interacting Brownian particles

We prove that the mean square displacement of a tracer particle grows as logt for larget. We point out a connection to the low-temperature floating phase of the ANNNI model.     

Memory function approach to the dynamics of interacting Brownian particles

We investigate some of the dynamic properties of diffusing particles described by a many-body Smoluchowski equation. The dynamic structure factor is expressed in terms of a memory function which is evaluated in the cases of i) weak interaction and ii) low particle density, but arbitrary interaction. A one-dimensional system with a hard-core pair potential is treated explicitly. Furthermore, by including a periodic single-particle potential, a model is obtained which has relevance to superionic conductors. For this case we discuss how the frequency-dependent conductivity is affected by the correlated motion of particles.     

DNA与组蛋白相互作用的布朗动力学研究

在真核生物中,DNA按左手手征性的方式,缠绕在组蛋白八聚体的周围,形成稳定的核小体结构.文章作者运用布朗动力学,数值模拟了DNA与组蛋白相互作用最终形成核小体的动力学过程,揭示了DNA与组蛋白相互作用的详细图景,并提出了组蛋白八聚体旋转模型,以解释这一过程.文章作者还计算了组成核小体的DNA在受到拉伸力时,组蛋白被从核小体中剥离下来的动力学过程,得到了组装和剥离过程的详细图像,给出了与前人单分子实验一致的拉伸力与拉伸长度的关系曲线和拉伸台阶.此外,还通过建立的组蛋白手征性模型,模拟了核小体手征性的形成过程,发现DNA的缠绕方向强烈依赖于组蛋白的手征性,显示出环境温度对核小体手征性有重要影响.     

Hydrodynamic interactions in Brownian dynamics: I. Periodic boundary conditions for computer simulations

Because of the long range nature of hydrodynamic interactions, the problem of boundary conditions on a finite simulation cell of a hydrodynamically dense suspension of particles in Brownian motion is quite as complicated as the analogous problem in simulation of the statistical mechanics of charged and dipolar systems. One resolution of this problem is to use periodic boundary conditions and to view them as a way of describing a physical system composed of a large spherical array of periodic replicas of the simulation cell. The hydrodynamic interactions are calculated using the quasi-static linearized Navier-Stokes equation. This requires that the suspending fluid velocity remains small throughout the array. That the sum of the particle velocities in the simulation cell be zero is insufficient to force boundedness of the fluid velocity as the array becomes large. Boundedness in the array of the suspending fluid velocity is achieved if a rigid wall boundary condition is applied at the outer edge of the array as the array becomes large. With this condition the net particle velocity equals zero condition is not needed. The condition allows lattice sum representations for the suspending fluid velocity to be derived. These lattice sums are absolutely and rapidly convergent and periodic. Representations of the velocity in the array with boundary condition allow calculation of mobility tensors which are also periodic and can be evaluated numerically in tolerable amounts of computer time. A major effect of these calculations is to identify the physical model system corresponding to a truly periodic fluid velocity and mobility tensor as a large array with rigid wall boundary condition.     

Coupling effect of Brownian motion and laminar shear flow on colloid coagulation:a Brownian dynamics simulation study

Simultaneous orthokinetic and perikinetic coagulations(SOPCs) are studied for small and large Peclet numbers(P e) using Brownian dynamics simulation.The results demonstrate that the contributions of the Brownian motion and the shear flow to the overall coagulation rate are basically not additive.At the early stages of coagulation with small Peclet numbers,the ratio of overall coagulation rate to the rate of pure perikinetic coagulation is proportional to P 1/2 e,while with high Peclet numbers,the ratio of overall coagulation rate to the rate of pure orthokinetic coagulation is proportional to P 1/2 e.Moreover,our results show that the aggregation rate generally changes with time for the SOPC,which is different from that for pure perikinetic and pure orthokinetic coagulations.By comparing the SOPC with pure perikinetic and pure orthokinetic coagulations,we show that the redistribution of particles due to Brownian motion can play a very important role in the SOPC.In addition,the effects of redistribution in the directions perpendicular and parallel to the shear flow direction are different.This perspective explains the behavior of coagulation due to the joint effects of the Brownian motion(perikinetic) and the fluid motion(orthokinetic).     

Brownian dynamics simulations with spin Brownian motion on the negative magneto-rheological effect of a rod-like hematite particle suspension

We have investigated the behaviour of a suspension of magnetic rod-like hematite particles in a simple shear flow with the addition of an applied magnetic field. A significant feature of the present hematite particle suspension is the fact that the magnetic moment of the hematite particle lies normal to the particle-axis direction. From simulations, we have attempted to clarify the dependence of the negative magneto-rheological effect on the particle aggregation and orientational distribution of particles. The present Brownian dynamics method has a significant advantage in that it takes into account the spin rotational Brownian motion about the particle axis in addition to the ordinary translational and rotational Brownian motion. The net viscosity is decomposed into three components and discussed at a deeper level and in detail: these three viscosity components arise from (1) the torque due to the magnetic particle–field interaction, (2) the torque and (3) the force due to the interaction between particles. It is found that a slight change in the orientational distribution has a significant influence on the negative magneto-rheological effect. In a relatively dense suspension, the viscosity components arising from an applied magnetic field and the interaction between particles come to change rapidly for a certain strength of the magnetic particle–particle interaction, which is due to the onset of the formation of raft-like clusters.     

Field-induced dynamics in the quantum Brownian oscillator: An exact treatment

We consider a quantum linear oscillator coupled to a bath in equilibrium at an arbitrary temperature and then exposed to an external field arbitrary in form and strength. We then derive the reduced density operator in closed form of the coupled oscillator in a non-equilibrium state at an arbitrary time.