Micro-Capsules in Shear Flow

This paper deals with flow-induced shape transitions of elastic capsules. The state of the art concerning both theory and experiments is briefly reviewed starting with dynamically induced small deformation of initially spherical capsules and the formation of wrinkles on polymerized membranes. Initially non-spherical capsules show tumbling and tank-treading motion in shear flow. Theoretical descriptions of the transition between these two types of motion assuming a fixed shape are at variance with the full capsule dynamics obtained numerically. To resolve the discrepancy, we expand the exact equations of motion for small deformations and find that shape changes play a dominant role. We classify the dynamical phase transitions and obtain numerical and analytical results for the phase boundaries as a function of viscosity contrast, shear and elongational flow rate. We conclude with perspectives on timedependent flow, on shear-induced unbinding from surfaces, on the role of thermal fluctuations, and on applying the concepts of stochastic thermodynamics to these systems.Comment: 34 pages, 15 figure

A quantitative theory of current-induced step bunching on Si(111)

We use a one-dimensional step model to study quantitatively the growth of step bunches on Si(111) surfaces induced by a direct heating current. Parameters in the model are fixed from experimental measurements near 900 deg C under the assumption that there is local mass transport through surface diffusion and that step motion is limited by the attachment rate of adatoms to step edges. The direct heating current is treated as an external driving force acting on each adatom. Numerical calculations show both qualitative and quantitative agreement with experiment. A force in the step down direction will destabilize the uniform step train towards step bunching. The average size of the step bunches grows with electromigration time as t^beta, with beta = 0.5, in agreement with experiment and with an analytical treatment of the steady states. The model is extended to include the effect of direct hopping of adatoms between different terraces. Monte-Carlo simulations of a solid-on-solid model, using physically motivated assumptions about the dynamics of surface diffusion and attachment at step edges, are carried out to study two dimensional features that are left out of the present step model and to test its validity. These simulations give much better agreement with experiment than previous work. We find a new step bending instability when the driving force is along the step edge direction. This instability causes the formation of step bunches and antisteps that is similar to that observed in experiment.Comment: 11 pages, 7 figure

Persistence and survival in equilibrium step fluctuations

Results of analytic and numerical investigations of first-passage properties of equilibrium fluctuations of monatomic steps on a vicinal surface are reviewed. Both temporal and spatial persistence and survival probabilities, as well as the probability of persistent large deviations are considered. Results of experiments in which dynamical scanning tunneling microscopy is used to evaluate these first-passage properties for steps with different microscopic mechanisms of mass transport are also presented and interpreted in terms of theoretical predictions for appropriate models. Effects of discrete sampling, finite system size and finite observation time, which are important in understanding the results of experiments and simulations, are discussed.Comment: 30 pages, 12 figures, review paper for a special issue of JSTA

Non-isothermal model for the direct isotropic/smectic-A liquid crystalline transition

An extension to a high-order model for the direct isotropic/smectic-A liquid crystalline phase transition was derived to take into account thermal effects including anisotropic thermal diffusion and latent heat of phase-ordering. Multi-scale multi-transport simulations of the non-isothermal model were compared to isothermal simulation, showing that the presented model extension corrects the standard Landau-de Gennes prediction from constant growth to diffusion-limited growth, under shallow quench/undercooling conditions. Non-isothermal simulations, where meta-stable nematic pre-ordering precedes smectic-A growth, were also conducted and novel non-monotonic phase-transformation kinetics observed.Comment: First revision: 20 pages, 7 figure

Pattern formation in directional solidification under shear flow. I: Linear stability analysis and basic patterns

An asymptotic interface equation for directional solidification near the absolute stabiliy limit is extended by a nonlocal term describing a shear flow parallel to the interface. In the long-wave limit considered, the flow acts destabilizing on a planar interface. Moreover, linear stability analysis suggests that the morphology diagram is modified by the flow near the onset of the Mullins-Sekerka instability. Via numerical analysis, the bifurcation structure of the system is shown to change. Besides the known hexagonal cells, structures consisting of stripes arise. Due to its symmetry-breaking properties, the flow term induces a lateral drift of the whole pattern, once the instability has become active. The drift velocity is measured numerically and described analytically in the framework of a linear analysis. At large flow strength, the linear description breaks down, which is accompanied by a transition to flow-dominated morphologies, described in a companion paper. Small and intermediate flows lead to increased order in the lattice structure of the pattern, facilitating the elimination of defects. Locally oscillating structures appear closer to the instability threshold with flow than without.Comment: 20 pages, Latex, accepted for Physical Review

Ammonia mobility in chabazite: insight into the diffusion component of the NH ₃-SCR process

To assess the effect of counterion presence on NH3 mobility in commercial automotive emission control zeolite catalysts, NH3 mobility in NH3-SCR catalyst Cu-CHA was compared with H-CHA using quasielastic neutron scattering and molecular dynamics simulations.</p

Multi-Particle Collision Dynamics -- a Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids

In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD). The method consists of alternating streaming and collision steps in an ensemble of point particles. The multi-particle collisions are performed by grouping particles in collision cells, and mass, momentum, and energy are locally conserved. This simulation technique captures both full hydrodynamic interactions and thermal fluctuations. The first part of the review begins with a description of several widely used MPC algorithms and then discusses important features of the original SRD algorithm and frequently used variations. Two complementary approaches for deriving the hydrodynamic equations and evaluating the transport coefficients are reviewed. It is then shown how MPC algorithms can be generalized to model non-ideal fluids, and binary mixtures with a consolute point. The importance of angular-momentum conservation for systems like phase-separated liquids with different viscosities is discussed. The second part of the review describes a number of recent applications of MPC algorithms to study colloid and polymer dynamics, the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of viscoelastic fluids

Dynamics of Fluid Vesicles in Oscillatory Shear Flow

The dynamics of fluid vesicles in oscillatory shear flow was studied using differential equations of two variables: the Taylor deformation parameter and inclination angle $\theta$. In a steady shear flow with a low viscosity $\eta_{\rm {in}}$ of internal fluid, the vesicles exhibit steady tank-treading motion with a constant inclination angle $\theta_0$. In the oscillatory flow with a low shear frequency, $\theta$ oscillates between $\pm \theta_0$ or around $\theta_0$ for zero or finite mean shear rate $\dot\gamma_{\rm m}$, respectively. As shear frequency $f_{\gamma}$ increases, the vesicle oscillation becomes delayed with respect to the shear oscillation, and the oscillation amplitude decreases. At high $f_{\gamma}$ with $\dot\gamma_{\rm m}=0$, another limit-cycle oscillation between $\theta_0-\pi$ and $-\theta_0$ is found to appear. In the steady flow, $\theta$ periodically rotates (tumbling) at high $\eta_{\rm {in}}$, and $\theta$ and the vesicle shape oscillate (swinging) at middle $\eta_{\rm {in}}$ and high shear rate. In the oscillatory flow, the coexistence of two or more limit-cycle oscillations can occur for low $f_{\gamma}$ in these phases. For the vesicle with a fixed shape, the angle $\theta$ rotates back to the original position after an oscillation period. However, it is found that a preferred angle can be induced by small thermal fluctuations.Comment: 11 pages, 13 figure

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner