Adsorption of charged dendrimers: a Brownian dynamics study

The adsorption of isolated charged dendrimers onto oppositely charged flat surfaces is studied in this work using Brownian dynamics simulations. The dendrimer is modeled as a freely jointed bead-rod chain in which excluded-volume interactions are modeled by a repulsive Lennard-Jones potential and bead-bead and bead-surface electrostatic interactions are described by screened Coulombic potentials. Adsorption behavior is studied as a function of inverse screening length, dendrimer generation, and dendrimer charge distribution. Adsorbed dendrimers adopt a disclike conformation in which they flatten in the direction normal to the surface and expand in the direction parallel to the surface. As the inverse screening length increases, the dendrimer expands in the normal direction and contracts in the parallel direction, adopting a conformation that is more stretched in the normal direction. When the inverse screening length becomes sufficiently large, the dendrimer desorbs and adopts a spherelike conformation. Bead density profiles show that adsorbed dendrimers form a two-layer structure, with one layer corresponding to adsorbed beads and a second, less dense layer corresponding to beads one rod length away from the surface. They also reveal how the distribution of monomers within the dendrimer and near the surface can be tailored by changing various problem parameters. The results presented here are expected to be helpful in providing qualitative guidance for dendrimer design in various applications.     

Aging in a Laponite colloidal suspension: a Brownian dynamics simulation study

The authors report Brownian dynamics simulation of the out-of-equilibrium dynamics (aging) in a colloidal suspension composed of rigid charged disks, one possible model for Laponite, a synthetic clay deeply investigated in the last few years by means of various experimental techniques. At variance with previous numerical investigations, mainly focusing on static structure and equilibrium dynamics, the authors explore the out-of-equilibrium aging dynamics. They analyze the wave vector and waiting time dependence of the dynamics, focusing on the single-particle and collective density fluctuations (intermediate scattering functions), the mean-squared displacement, and the rotational dynamics. Their findings confirm the complexity of the out-of-equilibrium dynamical behavior of this class of colloidal suspensions and suggest that an arrested disordered state driven by a repulsive Yukawa potential, i.e., a Wigner glass, can be observed in this model.     

Electrophoresis of a bead-rod chain through a narrow slit: a Brownian dynamics study

We use two-dimensional Brownian dynamics simulations to study the electrophoresis of a bead-rod chain through a narrow slit. A constant electric field is assumed to act inside and outside of the slit, and each bead on the chain is assigned a constant uniform charge. We calculate the dependence of the polymer transit velocity on chain length, slit dimensions (width-to-length ratio), and electric-field strength. For sufficiently narrow slits, the transit velocity increases nonlinearly with the applied field for low-field strengths, whereas it increases linearly for high-field strengths. In the low-field strength region and for sufficiently narrow slits, the transit velocity decreases rapidly for small chain lengths and then decreases slowly beyond a critical chain length. As the slit width increases, the transit velocity decreases with chain length in more continuous manner, and for sufficiently large slits the transit velocity becomes independent of chain length as expected. Distributions of the chain end-to-end distances and the translocation times depend strongly on the relative size of the chain to the slit. These results show the sensitivity of the transit velocity vs chain length relationship to the slit dimensions and applied electric-field strength, and suggest that there may be an optimal slit width for a given field strength and vice versa. The results may be useful for microfluidic separations and for understanding the motion of biological polymers through narrow constrictions.     

Structural properties of charge-stabilized ferrofluids under a magnetic field: a Brownian dynamics study

We present Brownian dynamics simulations of real charge-stabilized ferrofluids, which are stable colloidal dispersions of magnetic nanoparticles, with and without the presence of an external magnetic field. The colloidal suspensions are treated as collections of monodisperse spherical particles, bearing point dipoles at their centers and undergoing translational and rotational Brownian motions. The overall repulsive isotropic interactions between particles, governed by electrostatic repulsions, are taken into account by a one-component effective pair interaction potential. The potential parameters are fitted in order that computed structure factors are close to the experimental ones. Two samples of ferrofluid differing by the particle diameter and consequently by the intensity of the magnetic interaction are considered here. The magnetization and birefringence curves are computed: a deviation from the ideal Langevin behaviors is observed if the dipolar moment of particles is sufficiently large. Structure factors are also computed from simulations with and without an applied magnetic field H: the microstructure of the repulsive ferrofluid becomes anisotropic under H. Even our simple modeling of the suspension allows us to account for the main experimental features: an increase of the peak intensity is observed in the direction perpendicular to the field whereas the peak intensity decreases in the direction parallel to the field.     

Limitations of differential electrophoresis for measuring colloidal forces: a Brownian dynamics study

Differential electrophoresis experiments are often used to measure subpiconewton forces between two spheres of a heterodoublet. The experiments have been interpreted by solving the electrokinetic equations to obtain a simple Stokes law-type equation. However, for nanocolloids, the effects of Brownian motion alter the interpretation: (1) Brownian translation changes the rate of axial separation. (2) Brownian rotation reduces the alignment of the doublet with the applied electric field. (3) Particles can reaggregate by Brownian motion after they break, forming either heterodoublets or homodoublets, and because homodoublets cannot be broken by differential electrophoresis, this effectively terminates the experiment. We tackle points 1 and 2 using Brownian dynamics simulations (BDS) with electrophoresis as an external force, accounting for convective translation and rotation as well as Brownian translation and rotation. Our simulations identify the lower particle size limit of differential electrophoresis to be about 1 microm for desired statistical accuracy. Furthermore, our simulations predict that particles around 10 nm in size and at ambient conditions will break primarily by Brownian motion, with a negligible effect due to the electric field.     

Statistics of polymer capture by a nanopore: A Brownian dynamics simulation study

We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0(N)~N-0.8.     

Adsorption and order formation of colloidal nanoparticles on a substrate: a Brownian dynamics study

Adsorption process and order formation of electrostatically stabilized colloidal particles with a radius of 50 nm onto a planar surface with countercharge are examined. We perform Brownian dynamics simulations with a new three-dimensional cell model, in which the particle-particle and particle-substrate interactions are modeled based on the DLVO theory. The simulations yield the following results: (1) a larger bulk concentration would be required for larger kappaa to reach order formation to compensate for the decrease in the bulk potential; (2) the phase transition from a disordered to an ordered structure of the adsorbed particles on the substrate is considered to be of the Kirkwood-Alder type of transition through the examination of the two-dimensional pressure of the adsorbed particles; (3) the adsorbed particles are found to form a hexagonally ordered array, only if what we call "one-directional average force" acting on an adsorbed particle exceeds a critical value, which is independent of the ionic strength, or the interaction potentials. The critical value of the one-directional average force is interpreted as the force needed to keep an ordered structure by localizing adsorbed particles at fixed positions. In addition, the critical force is used to develop a new model to estimate the surface coverage at the order-disorder transition and it is demonstrated that the new model gives better estimation than other models previously reported.     

Brownian dynamics simulations of electrophoretic DNA separations in a sparse ordered post array

We use Brownian dynamics simulations to analyze the electrophoretic separation of λ-DNA (48.5 kbp) and T4-DNA (169 kbp) in a hexagonal array of 1 μm diameter posts with a 3 μm center-to-center distance. The simulation method takes advantage of an efficient interpolation algorithm for the non-uniform electric field to reach an ensemble size (100 molecules) and simulation length scale (1 mm) that produces meaningful results for the average electrophoretic mobility and effective diffusion (dispersion) coefficient of these macromolecules as they move through the array. While the simulated electrophoretic mobility for λ-DNA is close to the experimental data, the simulation underestimates the magnitude of the corresponding dispersion coefficient. The simulations predict baseline resolution in a 15 mm device after 7 min using an electric field around 30 V/cm, with the resolution increasing exponentially as the electric field further decreases. The mobility and dispersivity data point out two essential phenomena that have been overlooked in previous models of DNA electrophoresis in post arrays: the relaxation time between collisions and simultaneous collisions with multiple posts.     

Melting in two-dimensional Yukawa systems: a Brownian dynamics simulation

We studied the melting behavior of two-dimensional colloidal crystals with a Yukawa pair potential by Brownian dynamics simulations. The melting follows the Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) scenario with two continuous phase transitions and a middle hexatic phase. The two phase-transition points were accurately identified from the divergence of the translational and orientational susceptibilities. Configurational temperatures were employed to monitor the equilibrium of the overdamped system and the strongest temperature fluctuation was observed in the hexatic phase. The inherent structure obtained by rapid quenching exhibits three different behaviors in the solid, hexatic, and liquid phases. The measured core energy of the free dislocations, E(c) = 7.81 ± 0.91 k(B)T, is larger than the critical value of 2.84 k(B)T, which consistently supports the KTHNY melting scenario.     

Protein dynamics from a NMR perspective: networks of coupled rotators and fractional Brownian dynamics

Nuclear magnetic resonance (NMR) has proven to be the most valuable tool for investigating internal dynamics of proteins. In this perspective, the interpretation of NMR relaxation data eventually relies on a model of the motions. In this article, we propose to compare two radically different approaches that aim at describing internal dynamics in proteins. It is shown that the correlation functions predicted by a network of coupled rotators can be interpreted in terms of a heuristic approach based on fractional Brownian dynamics for each of the vectors in the network. Our results are interpreted in terms of the probability distributions of relaxation modes in both processes, the median of which turns out to be the relevant quantity for the comparison of both models.     

The mechanism of the self-assembly of associating DNA molecules under shear flow: Brownian dynamics simulation

A shear flow induces the assembly of DNAs with the sticky spots. In order to strictly interpret the mechanism of shear-induced DNA assembly, Brownian dynamics simulations with the bead-spring model were carried out for these molecules at various ranges of the Weissenberg numbers (We). We calculate a formation time and analyze the radial distribution function of end beads and the probability distribution of fractional extension at the formation time to understand the mechanism of shear-induced assembly. At low Weissenberg number the formation time, which is defined as an elapsed time until a multimer forms for the first time, decreases rapidly, reaching a plateau at We = 1000. A shear flow changes the radial distribution of end beads, which is almost the same regardless of the Weissenberg number. A shear flow deforms and stretches the molecules and generates different distributions between end beads with a stickly spot. The fractional extension progresses rapidly in shear flow from a Gaussian-like distribution to a uniform distribution. The progress of the distribution of fractional extension increases the possibility of meeting of end beads. In shear flow, the inducement of the assembly mainly results from the progress of the probability distribution of fractional extension. We also calculate properties such as the radius of gyration, stretch, and so on. As the Weissenberg number increases, the radius of gyration at the formation time also increases rapidly, reaching a plateau at We = 1000.     

Brownian dynamics simulation and experimental study of colloidal particle deposition in a microchannel flow

This paper reports an analysis of the irreversible deposition of colloidal particles from the pressure-driven flow in a microchannel within the framework of DLVO theory. A theoretical model is presented on the basis of the stochastic Langevin equation, incorporating the random Brownian motion of colloidal particles. Brownian dynamics simulation is used to compute the particle deposition in terms of the surface coverage. To validate the theoretical model, experiments are carried out using the parallel-plate flow cell technique, enabling direct videomicroscopic observation of the deposition kinetics of polystyrene latex particles in NaCl electrolytes. The theoretical predictions are compared with the experimental results, and good agreement is found.     

Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow

The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. A stochastic model is derived on the basis of the balance equation for forces acting on the chain. The Euler method is applied to the solution of the model. The extensions of DNA molecules for different Weissenberg numbers are analyzed. Comparison with the experimental results available in the literature is carried out to estimate the contribution of the effect of internal viscosity.     

Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix

As a first step toward developing simulation models for studying the indirect mechanism of radiation damage to DNAs, we have carried out Brownian dynamics simulations to study the reactions of hydrated electrons with a 12-base-pair B-DNA, (dA)₁₂(dT)₁₂, and with bases, monodeoxynucleotides, and polydeoxynucleotides. We first studied in detail the sensitivity of diffusion reaction rate constants to different model and simulation parameters. Based on the sensitivity studies, a set of model and simulation parameters was obtained for the final production runs. The use of this set of parameters reduced the computational costs but delivered reasonably reliable results. The calculated reaction rate constants were in qualitative agreement with experiments. For the DNA double-helix, (dA)₁₂(dT)₁₂, the simulations demonstrated that hydrated electrons preferred to attack the two ends of the double-helix. Electrostatic interactions between the DNA and the hydrated electrons make the T strand more susceptible to attack than the A strand. The increased reactivity of the T strand due to electrostatic interactions results from the increased reactivity of the C6 sites of the thymine bases, at the expense of the reactivity of the C8 sites of the adenine bases. The reactivity of the relatively buried reactive sites of the adenine and thymine bases are less affected by electrostatic interactions. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 888–901, 1997     

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.     

Communication: Universal Markovian reduction of Brownian particle dynamics

Non-Markovian processes can often be turned Markovian by enlarging the set of variables. Here we show, by an explicit construction, how this can be done for the dynamics of a Brownian particle obeying the generalized Langevin equation. Given an arbitrary bath spectral density J(0), we introduce an orthogonal transformation of the bath variables into effective modes, leading stepwise to a semi-infinite chain with nearest-neighbor interactions. The transformation is uniquely determined by J(0) and defines a sequence {J(n)}(n∈N) of residual spectral densities describing the interaction of the terminal chain mode, at each step, with the remaining bath. We derive a simple one-term recurrence relation for this sequence and show that its limit is the quasi-Ohmic expression provided by the Rubin model of dissipation. Numerical calculations show that, irrespective of the details of J(0), convergence is fast enough to be useful in practice for an effective Ohmic reduction of the dissipative dynamics.     

Brownian dynamics of mixed surfactant micelles

We investigate micelle formation in a system containing two or more different amphiphiles with different geometries using a stochastic molecular-dynamics (MD) simulation method. For a binary system containing two amphiphiles, we calculate the critical micelle concentration (CMC) and cluster distribution for the mixture at several mole fractions and compare the simulation results with those predicted by analytic theories in the dilute limit and with experiments. We find that the CMC obtained from molecular mean-field theory agrees well with our simulation results. Motivated by the industrial use of mixed surfactant systems, we then extend our studies to a system containing six different chain lengths drawn from a Poisson distribution. We find that unlike a binary mixture of amphiphiles, the different species cancel the effects of each other so that the cluster distribution for the mixture has a shape of a system consisted entirely of amphiphiles of length equal to the mean chain length of the Poisson distribution.     

Brownian dynamics simulation of protein association

Summary The Brownian Dynamics (BD) method is applied to study the diffusive dynamics and interaction of two proteins, cytochrome c (CYTC) and cytochrome c peroxidase (CYP). We examine the role of protein electrostatic charge distribution in the facilitation of protein-protein docking prior to the electron transfer step, assessing the influence of individual charged amino acid residues. Accurate interaction potentials are computed by iterating the linearized Poisson-Boltzmann (PB) equation around the larger protein CYP. The low dielectric constant inside proteins, electrolyte screening effects and irregular protein surface topography are taken into account. We observe a large ensemble of electrostatically stable encounter complexes seemingly with acceptable geometric requirements for electron transfer rather than a single dominant complex. Stabilities of the large variety of docking complexes are rationalized in terms of generalized charged residue complementarities. However, it is found that the electrostatic interactions giving rise to complex stabilities are somewhat nonspecific in nature. A large series of additional simulations are performed in which individual charged residues on CYTC have been chemically modified. Resulting perturbations of the association rate are significant and qualitatively similar to results observed in comparable kinetics experiments. We therefore demonstrate the potential of the Brownian dynamics method to estimate the effects of site-directed mutagenesis on protein-protein and protein-ligand diffusional association rates.