Magnetic birefringence of cobalt ferrite ferrofluids

Properties of chemically synthesized ferrofluids based on nanoparticles of CoFe₂O₄ are investigated. Their rigid dipole behaviour is established through magnetic birefringence experiments. The dynamical response of such particles to crossed magnetic fields is analysed. In large applied fields, it leads to characteristic relaxation times independent of the mean particle size of the sample, allowing viscosity determination in anisotropic systems.     

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.     

Fractional Brownian dynamics in proteins

Correlation functions describing relaxation processes in proteins and other complex molecular systems are known to exhibit a nonexponential decay. The simulation study presented here shows that fractional Brownian dynamics is a good model for the internal dynamics of a lysozyme molecule in solution. We show that both the dynamic structure factor and the associated memory function fit well the corresponding analytical functions calculated from the model. The numerical analysis is based on autoregressive modeling of time series.     

Non-Markovian dynamics and entanglement in quantum Brownian motion

Dynamical aspects of quantum Brownian motion in a low temperature environment are investigated. We give a systematic calculation of quantum entanglement among two Brownian oscillators without invoking Born–Markov approximation widely used for the study of open systems. Our approach is suitable to probe short time dynamics at cold temperatures where many experiments on quantum information processing are performed.     

Brownian dynamics studies of dilute dispersions

The method of brownian dynamics of used to study the non-equilibrium properties of very dilute colloids electrostatically stabilised in dilute aqueous electrolyte. It is assumed that the colloid is a monodisperse system of structureless spherical particles embedded in a hydrodynamic continuum. Although the particles are interacting electrostatically through a screened Coulomb potential, the dilution is such that effects arising from coupling of hydrodynamic flow can be ignore. Studies of the self-diffusion coefficient and van Howe functions show that after an initial period, during which the particles move essentially independently, the flow properties of the colloids are significantly different from those expected on the basis of free brownian motion.     

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.     

Memory effects in collective dynamics of Brownian suspensions

We obtain macroscopic equations for average suspension velocity and particle current in a Brownian suspension valid on long time scales for which the memory effects are important. The coefficients in these equations depend solely on local properties of the medium. This formalism allows one to obtain well-defined theoretical expressions for transport coefficients, free of the integrals diverging with the size of the system. As an example, the expression for long-time collective diffusion coefficient is derived and the memory contribution to this coefficient is estimated.     

Brownian dynamics simulations of associating diblock copolymers

A novel coarse-grained computational model for associating polymers is proposed that is based on a Gaussian "blob" representation of the polymer chains. The model allows a large number of model polymers to be simulated at moderate computational cost over a wide packing fraction range using the Brownian dynamics, BD, technique. The attraction of the hydrophobic part of the polymer to those on other molecules can lead to strong aggregation of the polymer molecules in real systems, and this is included in the model by an attractive potential felt by the Gaussian blobs to a common "nodal" point that represents the center of the micelle. Attention here is confined to model AB diblock copolymers in which the hydrophilic block, A, has a much higher mass than the hydrophobic moiety, B, which leads to relatively small aggregation numbers, Nagg, of approximately 8. The aggregation number at low packing fractions is found to increase with packing fraction, as observed in experiments, with a functional form that closely follows a simple theory derived here that is based on entropy-derived mean-field terms for the free-energy change associated with the incorporation of the polymer molecule into the micelle. The computational model exhibits an extremely low critical micelle concentration (cmc), and micelles with Nagg approximately 5 are observed at the lowest packing fractions, phi, simulated ( approximately 10-4), which is consistent with experiment. The long-time self-diffusion coefficient of the polymers (and hence micelles) decreases logarithmically with packing fraction, and the viscosity increased with concentration according to the Huggins equation. The spherical blob coarse graining results in the simulable time scales being longer than the Rouse time of the chain, and hence for the nonassociating polymers the intrinsic viscosity is an input parameter in the model. The introduction of association leads to the partial inclusion of the intrinsic viscosity in the simulation and has an effect on the computed Huggins coefficient, kH, which is found to be approximately 6 in those cases.     

Atomistic Brownian dynamics simulation of peptide phosphorylation

We report the implementation of an all-atom Brownian dynamics simulation model of peptides using the constraint algorithm LINCS. The algorithm has been added as a part of UHBD. It uses adaptive time steps to achieve a balance between computational speed and stability. The algorithm was applied to study the effect of phosphorylation on the conformational preference of the peptide Gly-Ser-Ser-Ser. We find that the middle serine residue experiences considerable conformational change from the C(7eq) to the alpha(R) structure upon phosphorylation. NMR (3)J coupling constants were also computed from the Brownian trajectories using the Karplus equation. The calculated (3)J results agree reasonably well with experimental data for phosphorylated peptide but less so for doubly charged phosphorylated one.     

Brownian dynamics simulation of grafted polymer brushes

We present results of computer simulations by the method of Brownian dynamics of polymeric brushes attached to impenetrable planes. For testing both model and method we have used one polymer brush attached to a repulsive plane and compare some results with Monte Carlo results of Lai and Binder on the bond fluctuation model. We have also studied two polymeric brushes attached to two parallel planes at different distances between planes, and investigate the interplay between the interpenetration of the brushes and the configurational properties of the grafted chains.     

Brownian dynamics simulations of polyelectrolyte adsorption in shear flow

Brownian dynamics simulations are used to study the adsorption of an isolated polyelectrolyte molecule onto an oppositely charged flat surface in the absence and the presence of an imposed shear flow. The polyelectrolyte is modeled as a freely jointed bead-rod chain where excluded volume interactions are incorporated by using a hard-sphere potential. The total charge along the backbone is distributed uniformly among all the beads, and the beads are allowed to interact with one another and the charged surface through screened Coulombic interactions. The simulations are performed by placing the molecule a fixed distance above the surface, and the adsorption behavior is then studied as a function of screening length. In the absence of an imposed flow, the chain is found to lie flat and extended on the adsorbing surface in the limit of weak screening, whereas in the limit of strong screening it desorbs from the surface and attains free-solution behavior. For intermediate screening, only a small portion of the chain adsorbs and it becomes highly extended in the direction normal to the surface. An imposed shear flow tends to orient the chain in the direction of flow and also leads to increased contact of the chain with the surface.     

Brownian dynamics of polymeric chain in strong external field

The cooperativity of conformational transitions in strained linear polymer chain was investigated by the method of Brownian dynamics. Deformation of a chain consisting of N=32 and 64 bonds was created by strong external field of dipole type. Correlations are discussed in terms of hazard-plot analysis.     

Critical dynamics of ballistic and Brownian particles in a heterogeneous environment

The dynamic properties of a classical tracer particle in a random, disordered medium are investigated close to the localization transition. For Lorentz models obeying Newtonian and diffusive motion at the microscale, we have performed large-scale computer simulations, demonstrating that universality holds at long times in the immediate vicinity of the transition. The scaling function describing the crossover from anomalous transport to diffusive motion is found to vary extremely slowly and spans at least five decades in time. To extract the scaling function, one has to allow for the leading universal corrections to scaling. Our findings suggest that apparent power laws with varying exponents generically occur and dominate experimentally accessible time windows as soon as the heterogeneities cover a decade in length scale. We extract the divergent length scales, quantify the spatial heterogeneities in terms of the non-Gaussian parameter, and corroborate our results by a thorough finite-size analysis.     

Low-frequency and high-frequency relaxations in dynamic electric birefringence of poly(γ-benzyl-L-glutamate) in m-cresol

The dc component Δn of the electric birefringence of poly(γ-benzyl-L -glutamate) in m-cresol is measured under an ac electric field at frequencies from 0.5 Hz to 200 kHz for solutions covering the dilute and semidilute regions. The dispersion curve indicates that at low frequencies Δn decreases with increasing frequency (low-frequency relaxation). For high-molecular-weight polymers at high concentration, Δn becomes negative at high frequency and its absolute value decreases with further increase in frequency (high-frequency relaxation). A unified theory for the two relaxations is developed on the basis of a model in which, in the semidilute regime, the rodlike polymer is confined in a cage formed by neighboring polymers and the lifetime of the cage lies between relaxation times of the two relaxations. The low-frequency relaxation is ascribed to end-over-end rotation of the polymer and the high-frequency relaxation to the rotation within a limited angle in the cage. The dependences of relaxation parameters on polymer concentration and molecular weight are reasonably explained by the theory.     

Treadmilling of actin filaments via Brownian dynamics simulations

Actin polymerization is coupled to the hydrolysis of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and inorganic phosphate (P(i)). Therefore, each protomer within an actin filament can attain three different nucleotide states corresponding to bound ATP, ADP/P(i), and ADP. These protomer states form spatial patterns on the growing (or shrinking) filaments. Using Brownian dynamics simulations, the growth behavior of long filaments is studied, together with the associated protomer patterns, as a function of ATP-actin monomer concentration, C(T), within the surrounding solution. For concentrations close to the critical concentration C(T)=C(T,cr), the filaments undergo treadmilling, i.e., they grow at the barbed and shrink at the pointed end, which leads to directed translational motion of the whole filament. The corresponding nonequilibrium states are characterized by several global fluxes and by spatial density and flux profiles along the filaments. We focus on a certain set of transition rates as deduced from in vitro experiments and find that the associated treadmilling (or turnover) rate is about 0.08 monomers per second.     

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.