Descriptor-based analysis is a powerful tool for understanding the trends across various catalysts. In general, the rate of a reaction over a given catalyst is a function of many parameters-reaction energies, activation barriers, thermodynamic conditions, etc. The high dimensionality of this problem makes it very difficult and expensive to solve completely, and even a full solution would not give much insight into the rational design of new catalysts. The descriptor-based approach seeks to determine a few ''descriptors'' upon which the other parameters are dependent. By doing this it is possible to reduce the dimensionality of the problem-preferably to 1 or 2 descriptors-thus greatly reducing computational efforts and simultaneously increasing the understanding of trends in catalysis. The ''CatMAP'' Python module seeks to standardize and automate many of the mathematical routines necessary to move from ''descriptor space'' to reaction rates for heterogeneous (electro) catalysts. The module is designed to be both flexible and powerful, and is available for free online. A ''reaction model'' can be fully defined by a configuration file, thus no new programming is necessary to change the complexity or assumptions of a model. Furthermore, various steps in the process of moving from descriptors to reaction rates have been abstracted into separate Python classes, making it easy to change the methods used or add new functionality. This work discusses the structure of the code and presents the underlying algorithms and mathematical expressions both generally and via an example for the CO oxidation reaction. Graphical Abstract

The volume fraction of red blood cells (RBCs) in a capillary affects the degree to which platelets are promoted to marginate to near a vessel wall and form blood clots. In this work we investigate the relationship between RBC hematocrit and platelet adhesion activity. We perform experiments flowing blood samples through a microfluidic channel coated with type 1 collagen and observe the rate at which platelets adhere to the wall. We compare these results with three-dimensional boundary integral simulations of a suspension of RBCs and platelets in a periodic channel where platelets can adhere to the wall. In both cases, we find that the rate of platelet adhesion varies greatly with the RBC hematocrit. We observe that the relative decrease in platelet activity as hematocrit falls shows a similar profile for simulation and experiment.

The linear stability of a homogeneous dilute suspension of chemotactic bacteria in a constant chemoattractant gradient is analyzed. The bacteria execute a run-and-tumble motion, typified by the species E. coli, wherein periods of smooth swimming (runs) are interrupted by abrupt uncorrelated changes in swimming direction (tumbles). Bacteria tumble less frequently when swimming toward regions of higher chemoattractant concentration, leading to a mean bacterial orientation and velocity in the base state. The stability of an unbounded suspension, both with and without a chemoattractant, is controlled by coupled long wavelength perturbations of the fluid velocity and bacterial orientation fields. In the former case, the most unstable perturbations have their wave vector oriented along the chemoattractant gradient. Chemotaxis reduces the critical bacteria concentration, for the onset of collective swimming, compared with that predicted by Subramanian and Koch [“Critical bacterial concentration for the onset of collective swimming,” J. Fluid Mech. 632, 359 (2009)] in the absence of a chemoattractant. A part of this decrease may be attributed to the increase in the mean tumbling time in the presence of a chemoattractant gradient. A second destabilizing influence comes from the ability of the shearing motion, associated with a velocity perturbation in which the velocity and chemical gradients are aligned, to sweep prealigned bacteria into the local extensional quadrant thereby creating a stronger destabilizing active stress than in an initially isotropic suspension. The chemoattractant gradient also fundamentally alters the unstable spectrum for any finite wavenumber. In suspensions of bacteria that do not tumble, Saintillan and Shelley [“Instabilities and pattern formation in active particle suspensions: Kinetic theory and continuum simulations,” Phys. Rev. Lett. 100, 178103 (2008); “Instabilities, pattern formation and mixing in active suspensions,” Phys. Fluids 20, 123304 (2008)] showed that the growth rate has two real solutions (stationary modes) below a critical wavenumber at which the two solutions merge and then bifurcate to form a pair of complex conjugate solutions (propagating modes) for larger wavenumbers. The discrete spectrum terminates at a second critical wavenumber, and beyond this wavenumber, the only remaining solutions are neutrally stable waves comprising the continuous spectrum. In the presence of a chemoattractant gradient, however, the aforementioned perfect bifurcation is broken and a pair of traveling wave solutions is found for all wavenumbers. Furthermore, instead of terminating at a critical wavenumber, the solutions for the growth rate asymptote to the negative of the tumbling frequency at large wavenumbers.

It has long been known that platelets undergo margination when flowing in blood vessels, such that there is an excess concentration near the vessel wall. We conduct experiments and three-dimensional boundary integral simulations of platelet-sized spherical particles in a microchannel 30 μm in height to measure the particle-concentration distribution profile and observe its margination at 10%, 20%, and 30% red blood cell hematocrit. The experiments involved adding 2.15-μm-diameter spheres into a solution of red blood cells, plasma, and water and flowing this mixture down a microfluidic channel at a wall shear rate of 1000 s(-1). Fluorescence imaging was used to determine the height and velocity of particles in the channel. Experimental results indicate that margination has largely occurred before particles travel 1 cm downstream and that hematocrit plays a role in the degree of margination. With simulations, we can track the trajectories of the particles with higher resolution. These simulations also confirm that margination from an initially uniform distribution of spheres and red blood cells occurs over the length scale of O(1 cm), with higher hematocrit showing faster margination. The results presented here, from both experiments and 3D simulations, may help explain the relationship between bleeding time in vessel trauma and red blood cell hematocrit as platelets move to a vessel wall.

While critically important, the platelet function at the high shear rates typical of the microcirculation is relatively poorly understood. Using a large scale Stokes flow simulation, Zhao et al. recently showed that RBC-induced velocity fluctuations cause platelets to marginate into the RBC free near-wall region [Zhao et al., Physics of Fluids, 2012, 24, 011902]. We extend their work by investigating the dynamics of platelets in shear after margination. An overall platelet adhesion model is proposed in terms of a continuous time Markov process and the transition rates are established with numerical simulations involving platelet-wall adhesion. Hydrodynamic drag and Brownian forces are calculated with the boundary element method, while the RBC collisions are incorporated through an autoregressive process. Hookean springs with first order bond kinetics are used to model receptor-ligand bonds formed between the platelet and the wall. The simulations are compared with in vitro microfluidic experiments involving platelet adhesion to Von Willebrand Factor (VWF) coated surfaces.