Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

Rowena F. Stern is with University of British Columbia, Ales Horak is with University of British Columbia, Rose L. Andrew is with University of British Columbia, Mary-Alice Coffroth is with State University of New York at Buffalo, Robert A. Andersen is with the Bigelow Laboratory for Ocean Sciences, Frithjof C. Küpper is with the Scottish Marine Institute, Ian Jameson is with CSIRO Marine and Atmospheric Research, Mona Hoppenrath is with the German Center for Marine Biodiversity Research, Benoît Véron is with University of Caen Lower Normandy and the National Institute for Environmental Studies, Fumai Kasai is with the National Institute for Environmental Studies, Jerry Brand is with UT Austin, Erick R. James is with University of British Columbia, Patrick J. Keeling is with University of British Columbia.Background -- Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings -- In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance -- COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.This project was funded by Genome Canada and the Canadian Barcode of Life Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

The role of particle-particle interactions in bubbling gas-fluidized beds of Geldart A particles: a discrete particle study

Discrete particle simulations are by now well established as an effective tool to study the mechanics of complex gas-solid flows in gas-fluidized beds. In this study, a state-of-the-art discrete particle model is used to explore the role of particle-particle interactions in bubbling gas-fluidized beds of Geldart A particles. We find that the particle-particle interactions, including inelastic particle-particle collision; inter-particle friction and slightly cohesive forces, only have a negligible effect on the hydrodynamics of bubbling gas-fluidized beds of Geldart A particles. This is due to the fact that only a very small fraction of the energy input is dissipated during the non-ideal particle-particle interaction. We finally show that the selected drag correlation model significantly affects the bed hydrodynamics

Simulation study of air-induced segregation of equal-sized bronze and glass particles

We have investigated the effect of air on the density segregation of fine, equal-sized bronze and glass particles under vertical sinusoidal vibrations by numerical simulation, using a hybrid granular dynamics-computational fluid dynamics model. We find both the bronze-on-top and the sandwich configurations as observed in previous experiments. The simulations allow us to give a detailed explanation of the phenomena. The key observation is the precise timing of the decompaction of the bed with the oscillating gas flow, which will cause the bronze to move to the top, due to the difference in acceleration from the air drag. For higher frequencies, the different inertia in collisions will cause the bronze clusters on top to sink through the bed, leading to a sandwich formation

Numerical study of segregation using a new drag force correlation for polydisperse systems derived from lattice-Boltzmann simulations

Discrete particle simulations of a segregating system are performed using various drag relations and boundary conditions, and compared to experiments. The boundary conditions on the walls are found to have a large influence on the segregation behaviour of the fluidised bed, where no-slip conditions result in unrealistic flow patterns. A polydispersity factor, which was recently derived on the basis of lattice-Boltzmann (LBM) simulations, is found to have a major effect on the segregation velocity and the final degree of segregation. The best agreement with experimental results is obtained with drag relations that were recently proposed based on LBM-simulations in combination with the aforementioned polydispersity factor

A numerical study of fluidization behavior of Geldart A particles using a discrete particle model

This paper reports on a numerical study of fluidization behavior of Geldart A particles by use of a 2D soft-sphere discrete particle model (DPM). Some typical features, including the homogeneous expansion, gross particle circulation in the absence of bubbles, and fast bubbles, can be clearly displayed if the interparticle van der Waals forces are relatively weak. An anisotropy of the velocity fluctuation of particles is found in both the homogeneous fluidization regime and the bubbling regime. The homogeneous fluidization is shown to represent a transition phase resulting from the competition of three kinds of basic interactions: the fluid¨Cparticle interaction, the particle¨Cparticle collisions (and particle¨Cwall collisions) and the interparticle van der Waals forces. In the bubbling regime, however, the effect of the interparticle van der Waals forces vanishes and the fluid¨Cparticle interaction becomes the dominant factor determining the fluidization behavior of Geldart A particles. This is also evidenced by the comparisons of the particulate pressure with other theoretical and experimental results

Why the two-fluid model fails to predict the bed expansion characteristics of Geldart A particles in gas-fluidized beds: A tentative answers

It is well known that two-fluid models (TFMs) can successfully predict the hydrodynamics of Geldart B and D particles. However, up to now, TFM have failed to accurately describe the hydrodynamics of Geldart A particles inside bubbling gas-fluidized beds: Researchers have reported that bed expansions are over-predicted by as much as 70%. In this work we show—for the first time—that TFM can predict the correct bed expansion, without any artificial modifications, provided that a sufficiently fine grid size and small time step is used. This suggests that the previously reported failure of TFM is mainly due to the lack of scale resolution, and that from a modeling point of view there is no fundamental difference between Geldart A particles and Geldart B and D particles