Computer simulation of rheological phenomena in dense colloidal suspensions with dissipative particle dynamics

The rheological properties of colloidal suspensions of spheres and rods have been studied using dissipative particle dynamics (DPD). We have measured the viscosity as a function of shear rate and volume fraction of the suspended particles. The viscosity of a 30 vol% suspension of spheres displays characteristic shear-thinning behaviour as a function of shear rate. The values for the low- and high-shear viscosity are in good agreement with experimental data. For higher paniculate densities, good results are obtained for the high-shear viscosity, although the viscosity at low shear rates shows a dependence on the size of the suspended spheres. Dilute suspensions of rods show an intrinsic viscosity which is in excellent agreement with theoretical results. For concentrated rod suspensions, the viscosity increases with the third power of the volume fraction. We find the same scaling behaviour as Doi and Edwards for the semidilute regime, although the explanation is unclear. The DPD simulation technique therefore emerges as a useful tool for studying the rheology of paniculate suspensions

The TeraGyroid project -- collaborative steering and visualization in an HPC grid for modelling complex fluids

The TeraGyroid experiment[1] addressed a large scale problem of genuine scientific interest and showed how intercontinental Grids enable new paradigms for collaborative computational science that can dramatically reduce the time to insight. TeraGyroid used computational steering over a Grid to study the self-assembly and dynamics of gyroid mesophases (found in novel materials and living cells) using the largest set of lattice Boltzmann simulations ever performed

Foundations of Dissipative Particle Dynamics

We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the rules governing our new form of dissipative particle dynamics reflect the underlying molecular dynamics; in particular all the underlying conservation laws carry over from the microscopic to the mesoscopic descriptions. Whereas previously the dissipative particles were spheres of fixed size and mass, now they are defined as cells on a Voronoi lattice with variable masses and sizes. This Voronoi lattice arises naturally from the coarse-graining procedure which may be applied iteratively and thus represents a form of renormalisation-group mapping. It enables us to select any desired local scale for the mesoscopic description of a given problem. Indeed, the method may be used to deal with situations in which several different length scales are simultaneously present. Simulations carried out with the present scheme show good agreement with theoretical predictions for the equilibrium behavior.Comment: 18 pages, 7 figure

Ab initio molecular dynamics study of the interlayer and micropore structure of aqueous montmorillonite clays

Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (110) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (110) clay edge, we find the adjacent exposed apical oxygen behaves as a Br?nsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (110) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (010) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (?Si-O-H??SiO-+H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (010) surface can act as a Br?nsted acid, even at neutral pH.Qatar National Research Fund (QNRF) of Qatar Foundation, National Priorities Research Program (grant number 09-26-01-048). Our work made use of the facilities of HECToR, the UK's national high-performance computing service, which is provided by UoE HPCx Ltd at the University of Edinburgh, Cray Inc and NAG Ltd, and funded by the Office of Science and Technology through EPSRC's High End Computing Programme. Access to HECToR was through grants EP/F00521/1, EP/E045111/1, EP/I017763/1 and the UK Consortium on Mesoscopic Engineering Sciences (EP/L00030X/1). We also made use of High Performance Computing facilities at University College London.Scopu

PolNet Analysis: a software tool for the quantification of network-level endothelial cell polarity and blood flow during vascular remodelling

In this paper, we present PolNet, an open source software tool for the study of blood flow and cell-level biological activity during vessel morphogenesis. We provide an image acquisition, segmentation, and analysis protocol to quantify endothelial cell polarity in entire in vivo vascular networks. In combination, we use computational fluid dynamics to characterise the haemodynamics of the vascular networks under study. The tool enables, for the first time, network-level analysis of polarity and flow for individual endothelial cells. To date, PolNet has proven invaluable for the study of endothelial cell polarisation and migration during vascular patterning, as demonstrated by our recent papers (Franco 2015, Franco 2016a). Additionally, the tool can be easily extended to correlate blood flow with other experimental observations at the cellular/molecular level. We release the source code of our tool under the LGPL licence