Hydrodynamic Interactions in Colloidal Ferrofluids: A Lattice Boltzmann Study

The effect of hydrodynamic interactions (HI) on the long-time self-diffusion in quasi-two-dimensional fluids of paramagnetic colloidal particles is investigated using a combination of experiments and Brownian dynamics (BD) simulations. In the BD simulations, the direct interactions (DI) between the particles consist of a short-ranged repulsive part and a long-ranged part that is proportional to 1/r^{3}, with r the interparticle distance. By studying the equation of state, the simulations allow for the identification of the regime where the properties of the fluid are fully controlled by the long-ranged interactions, and the thermodynamic state solely depends on the dimensionless interaction strength Γ. In this regime, the radial distribution functions from the simulations are in quantitative agreement with those from the experiments for different fluid area fractions. This agreement confirms that the DI in the experiments and simulations are identical, which thus allows us to isolate the role of HI, as these are not taken into account in the BD simulations. Experiment and simulation fall onto a master curve with respect to the Γ dependence of D_{L}^{★}=D_{L}/(D_{0}Γ^{1/2}), with D_{0} the self-diffusion coefficient at infinite dilution and D_{L} the long-time self-diffusion coefficient. Our results thus show that, although HI affect the short-time self-diffusion, for a quasi-two-dimensional system with 1/r^{3} long-ranged DI, the reduced quantity D_{L}^{★} is effectively not affected by HI. Interestingly, this is in agreement with prior work on quasi-two-dimensional colloidal hard spheres.

Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

A model for real-time generation of deep-water waves is suggested. It is based on a lattice-Boltzmann (LB) technique. Computation of wave dynamics and (ray-traced) rendering for a lattice of size 10242 can be carried out simultaneously on a single graphics card at 25 frames per second. In addition to the computational speed, the LB technique is seen to offer a simple and physically accurate method for handling both dispersion and wave reflection from obstructing objects.

In a recent study, the resolution of a polymer chain model was shown to significantly affect rheological predictions from Brownian dynamics (BD) simulations [Kumar and Dalal, “Effects of chain resolution on the configurational and rheological predictions from Brownian dynamics simulations of an isolated polymer chain in flow,” J. Non-Newtonian Fluid Mech. 315, 105017 (2023)], even in the absence of hydrodynamic interactions (HI) and excluded volume. In this study, we investigate the effects of chain resolution in the presence of HI. Toward this, we perform BD simulations of a long polymer chain, with the discretization level varying from a single Kuhn step (bead–rod model) to several tens of Kuhn-steps (bead–spring model). The chain models were subjected to flow fields of uniaxial extension (purely stretching) and steady shear (equal rates of stretching and rotation). Broadly, our results indicate an amplification of the differences observed between the differently resolved bead–rod and bead–spring models, in the presence of HI. Interestingly, all rheological predictions qualitatively fall in two groups for extensional flow, with the predictions from the bead–spring model with HI being close to those of the bead–rod model without HI. This indicates significantly reduced sensitivity of coarser bead–spring models to HI, relative to the one resolved to a single Kuhn step. However, in shear flow, the bead–spring rheological predictions fall between those of the bead–rod model with and without HI, forming a third group. This is linked to the presence of stretched and coiled states in the ensemble for shear flow. HI effects are large for the coiled states and weak for the stretched states, thereby yielding predictions that are intermediate between those for no HI and dominant HI. Thus, quite surprisingly, the quality of predictions of the bead–spring models is strongly affected by the physics of the flow field, irrespective of the parameterization.

The long time self-diffusion of highly charged colloidal particles consisting of polybutylacrylate was studied employing pulsed field gradient NMR (PFGNMR) and Brownian dynamics (BD) simulations. The potential parameters for the Yukawa interaction potential used in the BD simulations were derived from the static structure factor measured by means of light scattering. The long time self-diffusion coefficients resulting from NMR and BD were compared for different ionic strengths, which cause a screening of the interaction potential due to stray ions. Increasing the ionic strength of the colloidal suspensions, we observed a phase transition from a crystalline to a liquidlike structure. Whereas at high salt concentrations both long time diffusion coefficients agree within a few percent, at intermediate ionic strengths the values measured via PFGNMR are by a factor of 2 higher than those predicted by the BD simulation. This deviation is explained by hydrodynamic interactions which are expected to enhance long time self-diffusion and which are not taken into account in our BD algorithm.

Video microscopy (VM) experiments and Brownian dynamics (BD) simulations were used to measure and model superparamagnetic colloidal particles in rotating magnetic fields for interaction energies on the order of the thermal energy, kT. Results from experiments and simulations were compared for isolated particle rotation, particle rotation within doublets, doublet rotation, and separation within doublets vs field rotation frequency. Agreement between VM and BD results was obtained at all frequencies and amplitudes only by including exact two-body hydrodynamic interactions and relevant relaxation times of magnetic dipoles. Frequency-dependent particle forces and torques cause doublets to rotate at low frequencies via dipolar interactions and at high frequencies via hydrodynamic translation-rotation coupling. By matching measurements and simulations for a range of conditions, our findings unambiguously demonstrate the quantitative forms of dipolar and hydrodynamic interactions necessary to capture nonequilibrium, steady-state dynamics of Brownian colloids in magnetic fields.

Inclusion of hydrodynamic interactions (HIs) is essential in simulations of biological macromolecules that treat the solvent implicitly if the macromolecules are to exhibit correct translational and rotational diffusion. The present work describes the development and testing of a simple approach aimed at allowing more rapid computation of HIs in coarse-grained Brownian dynamics simulations of systems that contain large numbers of flexible macromolecules. The method combines a complete treatment of intramolecular HIs with an approximate treatment of the intermolecular HIs which assumes that the molecules are effectively spherical; all of the HIs are calculated at the Rotne-Prager-Yamakawa level of theory. When combined with Fixman's Chebyshev polynomial method for calculating correlated random displacements, the proposed method provides an approach that is simple to program but sufficiently fast that it makes it computationally viable to include HIs in large-scale simulations. Test calculations performed on very coarse-grained models of the pyruvate dehydrogenase (PDH) E2 complex and on oligomers of ParM (ranging in size from 1 to 20 monomers) indicate that the method reproduces the translational diffusion behavior seen in more complete HI simulations surprisingly well; the method performs less well at capturing rotational diffusion but its discrepancies diminish with increasing size of the simulated assembly. Simulations of residue-level models of two tetrameric protein models demonstrate that the method also works well when more structurally detailed models are used in the simulations. Finally, test simulations of systems containing up to 1024 coarse-grained PDH molecules indicate that the proposed method rapidly becomes more efficient than the conventional BD approach in which correlated random displacements are obtained via a Cholesky decomposition of the complete diffusion tensor.

Purpose This paper aims to study the natural convection of a nanofluid inside a cavity which contains obstacles using lattice Boltzmann method (LBM). The results have focused mainly on various parameters such as number and aspect ratio of roughness elements and different nanoparticle volume fraction. The isotherms and streamlines are presented to describe the hydrodynamics and thermal behaviors of the nanofluid flow throughout the enclosure. Design/methodology/approach The methodology of this paper consists of mathematical model, statement of the problem, nanofluid thermophysical properties, lattice Boltzmann method, LBM for fluid flow, LBM for heat transfer, numerical strategy, boundary conditions, Nusselt (Nu) number calculation, code validation and grid independence. Findings Natural convection heat transfers of a nanofluid inside cavities with and without rough elements have been studied. Lattice Boltzmann technique has been used as numerical approach. The results showed that at higher Rayleigh number (Ra = 106), there are denser streamlines near the left (source) and right wall (sink) which results in better cooling and enhances convective heat rejection to the heat sink. After a distinctive aspect ratio of rough elements (A = 0.1), change in streamline pattern which arises from increasing of aspect ratio does not have an important effect on isotherms. Results indicate that for lower Rayleigh number (Ra = 103), no variation in average Nu is observed with increasing in number of roughness, while for higher one (Ra = 106) average Nu decreases from N = 0 (smooth cavity) up to N = 4 and then remains constant (N = 6). Originality/value Currently, no argumentative and comprehensive extraction can be concluded without fully understanding the role of different arrangement of roughness. Some geometrical parameters such as aspect ratio, number and position of rough elements have been considered. Also, the effect of nanoparticle concentration was studied at different Ra number. Briefly, using LBM, this paper aims to investigate the natural convection of a nanofluid flow on the thermal and hydrodynamics parameters in the presence of rough element with various arrangements.

Many-body hydrodynamic interactions between spherical drops in an emulsion

Collective diffusion of charged spheres in the presence of hydrodynamic interaction

This document contains a summary of the work performed under the LDRD project entitled 'Interface Physics in Microporous Media'. The presence of fluid-fluid interfaces, which can carry non-zero stresses, distinguishes multiphase flows from more readily understood single-phase flows. In this work the physics active at these interfaces has been examined via a combined experimental and computational approach. One of the major difficulties of examining true microporous systems of the type found in filters, membranes, geologic media, etc. is the geometric uncertainty. To help facilitate the examination of transport at the pore-scale without this complication, a significant effort has been made in the area of fabrication of both two-dimensional and three-dimensional micromodels. Using these micromodels, multiphase flow experiments have been performed for liquid-liquid and liquid-gas systems. Laser scanning confocal microscopy has been utilized to provide high resolution, three-dimensional reconstructions as well as time resolved, two-dimensional reconstructions. Computational work has focused on extending lattice Boltzmann (LB) and finite element methods for probing the interface physics at the pore scale. A new LB technique has been developed that provides over 100x speed up for steady flows in complex geometries. A new LB model has been developed that allows for arbitrary density ratios, which has been a significant obstacle in applying LB to air-water flows. A new reduced order model has been developed and implemented in finite element code for examining non-equilibrium wetting in microchannel systems. These advances will enhance Sandia's ability to quantitatively probe the rich interfacial physics present in microporous systems.

The effect of fluctuating internal viscosity and hydrodynamic interactions on a range of rheological properties of dilute polymer solutions is examined using a finitely extensible dumbbell model for a polymer. Brownian dynamics simulations are used to compute both transient and steady state viscometric functions in shear flow. The results enable a careful differentiation of the influence, on rheological properties, of solvent-mediated friction from that of a dissipative mechanism that is independent of solvent viscosity. In particular, hydrodynamic interactions have a significant influence on the magnitude of the stress jump at the inception of shear flow, and on the transient viscometric functions, but a negligible effect on the steady state viscometric functions at high shear rates. Zero-shear rate viscometric functions of free-draining dumbbells remain essentially independent of the internal viscosity parameter, as predicted by the Gaussian approximation, but the inclusion of hydrodynamic interactions induces a dependence on both the hydrodynamic interaction and the internal viscosity parameter. Large values of the internal viscosity parameter lead to linear viscoelastic predictions that mimic the behavior of rigid dumbbell solutions. On the other hand, steady-shear viscometric functions at high shear rates differ in general from those for rigid dumbbells, depending crucially on the finite extensibility of the dumbbell spring.

To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules in vivo from that at infinite dilution. In an Escherichia coli cytoplasm model comprised of 15 different macromolecule types at physiological concentrations, BD simulations of molecular-shaped and equivalent sphere representations were performed with a soft repulsive potential. At cellular concentrations, the calculated diffusion constant of GFP is much larger than experiment, with no significant shape dependence. Next, using the equivalent sphere system, hydrodynamic interactions (HI) were considered. Without adjustable parameters, the in vivo experimental GFP diffusion constant was reproduced. Finally, the effects of nonspecific attractive interactions were examined. The reduction in diffusivity is very sensitive to macromolecular radius with the motion of the largest macromolecules dramatically slowed down; this is not seen if HI dominate. In addition, long-lived clusters involving the largest macromolecules form if attractions dominate, whereas HI give rise to significant, size independent intermolecular dynamic correlations. These qualitative differences provide a testable means of differentiating the importance of HI vs. nonspecific attractive interactions on macromolecular motion in cells.

A comprehensive non-isothermal Lattice Boltzmann (LB) algorithm is proposed in this article to simulate the thermofluidic transport phenomena encountered in a direct-current (DC) magnetohydrodynamic (MHD) micropump. Inside the pump, an electrically conducting fluid is transported through the microchannel by the action of an electromagnetic Lorentz force evolved out as a consequence of the interaction between applied electric and magnetic fields. The fluid flow and thermal characteristics of the MHD micropump depend on several factors such as the channel geometry, electromagnetic field strength and electrical property of the conducting fluid. An involved analysis is carried out following the LB technique to understand the significant influences of the aforementioned controlling parameters on the overall transport phenomena. In the LB framework, the hydrodynamics is simulated by a distribution function, which obeys a single scalar kinetic equation associated with an externally imposed electromagnetic force field. The thermal history is monitored by a separate temperature distribution function through another scalar kinetic equation incorporating the Joule heating effect. Agreement with analytical, experimental and other available numerical results is found to be quantitative.

Hydrodynamic and electrokinetic effects on the dynamics of charged colloids andmacromolecules