Cell-free layer development and spatial organization of healthy and rigid red blood cells in a microfluidic bifurcation.

Bifurcations and branches in the microcirculation dramatically affect blood flow as they determine the spatiotemporal organization of red blood cells (RBCs). Such changes in vessel geometries can further influence the formation of a cell-free layer (CFL) close to the vessel walls. Biophysical cell properties, such as their deformability, which is impaired in various diseases, are often thought to impact blood flow and affect the distribution of flowing RBCs.

Squeezing multiple soft particles into a constriction: Transition to clogging.

We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional simulations based on the lattice Boltzmann method to compute the flow of the suspending fluid and on the immersed boundary method to achieve the two-way fluid-structure interaction.

Lattice Boltzmann simulations of drying suspensions of soft particles.

The ordering of particles in the drying process of a colloidal suspension is crucial in determining the properties of the resulting film. For example, microscopic inhomogeneities can lead to the formation of cracks and defects that can deteriorate the quality of the film considerably. This type of problem is inherently multiscale and here we study it numerically, using our recently developed method for the simulation of soft polymeric capsules in multicomponent fluids.

Capillary interactions between soft capsules protruding through thin fluid films.

When a suspension dries, the suspending fluid evaporates, leaving behind a dry film composed of the suspended particles. During the final stages of drying, the height of the fluid film on the substrate drops below the particle size, inducing local interface deformations that lead to strong capillary interactions among the particles. Although capillary interactions between rigid particles are well studied, much is still to be understood about the behaviour of soft particles and the role of their softness during the final stages of film drying.

Mesoscale simulation of soft particles with tunable contact angle in multicomponent fluids.

Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of the complex dynamics of suspensions of many soft particles, whereas experiments typically either only capture bulk properties or require invasive methods. Computational methods are therefore a great tool to complement experimental work.

Shear thinning and shear thickening of a confined suspension of vesicles.

Widely regarded as an interesting model system for studying flow properties of blood, vesicles are closed membranes of phospholipids that mimic the cytoplasmic membranes of red blood cells. In this study we analyze the rheology of a suspension of vesicles in a confined geometry: the suspension, bound by two planar rigid walls on each side, is subject to a shear flow. Flow properties are then analyzed as a function of shear rate γ[over ̇], the concentration of the suspension ϕ, and the viscosity contrast λ=η_{in}/η_{out}, where η_{in} and η_{out} are the fluid viscosities of the inner and outer fluids, respectively.

The buckling instability of aggregating red blood cells.

Plasma proteins such as fibrinogen induce the aggregation of red blood cells (RBC) into rouleaux, which are responsible for the pronounced shear thinning behavior of blood, control the erythrocyte sedimentation rate (ESR) - a common hematological test - and are involved in many situations of physiological relevance such as structuration of blood in the microcirculation or clot formation in pathological situations. Confocal microscopy is used to characterize the shape of RBCs within rouleaux at equilibrium as a function of macromolecular concentration, revealing the diversity of contact zone morphology. Three different configurations that have only been partly predicted before are identified, namely parachute, male-female and sigmoid shapes, and quantitatively recovered by numerical simulations.

Vesicle dynamics in a confined Poiseuille flow: from steady state to chaos.

Red blood cells (RBCs) are the major component of blood, and the flow of blood is dictated by that of RBCs. We employ vesicles, which consist of closed bilayer membranes enclosing a fluid, as a model system to study the behavior of RBCs under a confined Poiseuille flow. We extensively explore two main parameters: (i) the degree of confinement of vesicles within the channel and (ii) the flow strength.

The plasma protein fibrinogen stabilizes clusters of red blood cells in microcapillary flows.

The supply of oxygen and nutrients and the disposal of metabolic waste in the organs depend strongly on how blood, especially red blood cells, flow through the microvascular network. Macromolecular plasma proteins such as fibrinogen cause red blood cells to form large aggregates, called rouleaux, which are usually assumed to be disaggregated in the circulation due to the shear forces present in bulk flow. This leads to the assumption that rouleaux formation is only relevant in the venule network and in arterioles at low shear rates or stasis.

Vesicle dynamics under weak flows: application to large excess area.

Dynamics of a vesicle under simple shear flow is studied in the limit of small capillary number. A perturbative approach is used to derive the equation of vesicle dynamics. The expansions are shown to converge for significantly deflated vesicles (with excess area from the sphere as high as 2).

Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains).

Background: The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have killed human and other mammals since millennia. Additionally, with the many different mycobacterial sequences available, there is a crucial need for the visualization and the simplification of their data.