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. This study investigates the flow behavior of healthy and artificially hardened RBCs in a bifurcating microfluidic T-junction. We determine the RBC distribution across the channel width at multiple positions before and after the bifurcation. Thus, we reveal distinct focusing profiles in the feeding mother channel for rigid and healthy RBCs that dramatically impact the cell organization in the successive daughter channels. Moreover, we experimentally show how the characteristic asymmetric CFLs in the daughter vessels develop along their flow direction. Complimentary numerical simulations indicate that the buildup of the CFL is faster for healthy than for rigid RBCs. Our results provide fundamental knowledge to understand the partitioning of rigid RBC as a model of cells with pathologically impaired deformability in complex in vitro networks.

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. The mechanics of the capsule membrane elasticity is computed with the finite-element method. We obtain two main states: continuous passage of the particles and their blockage that leads to clogging the constriction. The transition from one state to another is dictated by the ratio between the size of the capsules and the constriction width and by the capsule membrane deformability. The latter is found to enhance particle passage through narrower constrictions, where rigid particles with similar diameter are blocked and lead to clogging.

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. Here, we use our recently-introduced numerical method that couples a fluid described using the lattice Boltzmann approach to a finite element description of deformable objects to investigate the drying process of a film with suspended soft particles. Our measured menisci deformations and lateral capillary forces, which agree well with previous theoretical and experimental works in case of rigid particles, show that the deformations become smaller with increasing particle softness, resulting in weaker lateral interaction forces. At large interparticle distances, the force approaches that of rigid particles. Finally, we investigate the time dependent formation of particle clusters at the late stages of the 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. However, an efficient and versatile numerical method is needed to model dense suspensions of many soft particles. In this article we propose a method to simulate soft particles in a multicomponent fluid, both at and near fluid-fluid interfaces, based on the lattice Boltzmann method, and characterize the error stemming from the fluid-structure coupling for the particle equilibrium shape when adsorbed onto a fluid-fluid interface. Furthermore, we characterize the influence of the preferential contact angle of the particle surface and the particle softness on the vertical displacement of the center of mass relative to the fluid interface. Finally, we demonstrate the capability of our model by simulating a soft capsule adsorbing onto a fluid-fluid interface with a shear flow parallel to the interface, and the covering of a droplet suspended in another fluid by soft particles with different wettability.

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. A detailed experimental and theoretical analysis of clusters of two cells shows that the deformation increases nonlinearly with the interaction energy. Models indicate a forward bifurcation in which the contacting membrane undergoes a buckling instability from a flat to a deformed contact zone at a critical value of the interaction energy. These results are not only relevant for the understanding of the morphology and stability of RBC aggregates, but also for a whole class of interacting soft deformable objects such as vesicles, capsules or cells in tissues.

Clusters of red blood cells in microcapillary flow: hydrodynamic versus macromolecule induced interaction.

We present experiments on RBCs that flow through micro-capillaries under physiological conditions. The strong flow-shape coupling of these deformable objects leads to a rich variety of cluster formation. We show that the RBC clusters form as a subtle imbrication between hydrodynamic interactions and adhesion forces because of plasma proteins, mimicked by the polymer dextran. Clusters form along the capillaries and macromolecule-induced adhesion contributes to their stability. However, at high yet physiological flow velocities, shear stresses overcome part of the adhesion forces, and cluster stabilization due to hydrodynamics becomes stronger. For the case of pure hydrodynamic interaction, cell-to-cell distances have a pronounced bimodal distribution. Our 2D-numerical simulations on vesicles capture the transition between adhesive and non-adhesive clusters at different flow velocities.

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. Rich and complex dynamics for vesicles are revealed, ranging from steady-state shapes (in the form of parachute and slipper shapes) to chaotic dynamics of shape. Chaos occurs through a cascade of multiple periodic oscillations of the vesicle shape. We summarize our results in a phase diagram in the parameter plane (degree of confinement and flow strength). This finding highlights the level of complexity of a flowing vesicle in the small Reynolds number where the flow is laminar in the absence of vesicles and can be rendered turbulent due to elasticity of vesicles.

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). In particular, we provide an explicit analytical expression for the tank-treading to tumbling bifurcation point. This expression is valid for excess areas up to 2.5. The results are compared with full 3D numerical simulations. The proposed method can be used for analytical or numerical solution of vesicle dynamics under weak flow of general form.

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. In this present study, we aim to highlight a comparative genome, proteome and phylogeny analysis between twenty-one mycobacterial (Tuberculosis and non tuberculosis) strains using a set of computational and bioinformatics tools (Pan and Core genome plotting, BLAST matrix and phylogeny analysis). RESULTS: Considerably the result of pan and core genome Plotting demonstrated that less than 1250 Mycobacterium gene families are conserved across all species, and a total set of about 20,000 gene families within the Mycobacterium pan-genome of twenty one mycobacterial genomes.Viewing the BLAST matrix a high similarity was found among the species of the complex Mycobacterium tuberculosis and less conservation is found with other slow growing pathogenic mycobacteria.Phylogeny analysis based on both protein conservation, as well as rRNA clearly resolve known relationships between slow growing mycobacteria. CONCLUSION: Mycobacteria include important pathogenic species for human and animals and the Mycobacterium tuberculosis complex is the most cause of death of the humankind. The comparative genome analysis could provide a new insight for better controlling and preventing these diseases.