Steady state particle distribution of a dilute sedimenting suspension

Sedimentation of a non-Brownian suspension of hard particles is studied. It is shown that in the low concentration limit a two-particle distribution function ensuring finite particle correlation length can be found and explicitly calculated. The sedimentation coefficient is computed. Results are compared with experiment.Comment: 4 pages, 2 figure

Pex19 and cytosolic Hsp70 are involved in the import of mitochondrial tail- anchored proteins

The Majority of mitochondrial proteins are synthetized in the cytosol and afterwards targeted to the organelle. The transport process is accompanied by cytosolic factors, which ensure targeting specificity and prevent the proteins from aggregation in the aqueous environment of the cytosol. This especially applies to tail-anchored (TA) proteins that are directed to membranes in a post-translational manner. Tail-anchored proteins are embedded into their corresponding membrane via a single transmembrane segment at their C-terminus whereas the majority of the protein is facing the cytosol. The targeting pathways of these proteins to the ER or to peroxisomes have been characterized. However, so far, cellular factors that mediate the integration of such proteins into the mitochondrial outer membrane have not been found. Equally elusive remains the existence of mitochondrial membrane insertases or receptors for TA import. Thus, it is currently postulated that import of mitochondrial TA proteins is mediated solely by unassisted insertion without the requirement of any protein factors. Using budding yeast as a model system, we identified the cytosolic Hsp70 chaperone Ssa1, its co-chaperone Sti1, and the peroxisome import factor Pex19 as mediators of import of mitochondrial TA proteins. Accordingly, deletion of PEX19 results in: (i) growth defect under respiration conditions; (ii) alteration in mitochondrial morphology; (iii) reduced steady-state levels of the mitochondrial single span proteins Fis1, Gem1, and Atg32; and (iv) hampered in organello import of the TA proteins Fis1 and Gem1. Furthermore, we demonstrate that recombinant Pex19 can bind directly the TA proteins Fis1 and Gem1 and that all three proteins share a mitochondrial and peroxisomal dual localization. Alteration in Atg32 levels are dependent on the mitochondrial receptors Mim1 and Tom20 suggesting that both can mediate Pex19 binding to mitochondria. Collectively, this work identified the first factors that are involved in the biogenesis of mitochondrial TA proteins and uncovered an unexpected function of Pex19

First-order virial expansion of short-time diffusion and sedimentation coefficients of permeable particles suspensions

For suspensions of permeable particles, the short-time translational and rotational self-diffusion coefficients, and collective diffusion and sedimentation coefficients are evaluated theoretically. An individual particle is modeled as a uniformly permeable sphere of a given permeability, with the internal solvent flow described by the Debye-Bueche-Brinkman equation. The particles are assumed to interact non-hydrodynamically by their excluded volumes. The virial expansion of the transport properties in powers of the volume fraction is performed up to the two-particle level. The first-order virial coefficients corresponding to two-body hydrodynamic interactions are evaluated with very high accuracy by the series expansion in inverse powers of the inter-particle distance. Results are obtained and discussed for a wide range of the ratio, x, of the particle radius to the hydrodynamic screening length inside a permeable sphere. It is shown that for x >= 10, the virial coefficients of the transport properties are well-approximated by the hydrodynamic radius (annulus) model developed by us earlier for the effective viscosity of porous-particle suspensions

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Generalized Rotne–Prager–Yamakawa approximation for Brownian dynamics in shear flow in bounded, unbounded, and periodic domains

Inclusion of hydrodynamic interactions is essential for a quantitatively accurate Brownian dynamics simulation of colloidal suspensions or polymer solutions. We use the generalized Rotne–Prager–Yamakawa (GRPY) approximation, which takes into account all long-ranged terms in the hydrodynamic interactions, to derive the complete set of hydrodynamic matrices in different geometries: unbounded space, periodic boundary conditions of Lees–Edwards type, and vicinity of a free surface. The construction is carried out both for non-overlapping as well as for overlapping particles. We include the dipolar degrees of freedom, which allows one to use this formalism to simulate the dynamics of suspensions in a shear flow and to study the evolution of their rheological properties. Finally, we provide an open-source numerical package, which implements the GRPY algorithm in Lees–Edwards periodic boundary conditions

Rotational and translational self-diffusion in concentrated suspensions of permeable particles

In our recent work on concentrated suspensions of uniformly porous colloidal spheres with excluded volume interactions, a variety of short-time dynamic properties were calculated, except for the rotational self-diffusion coefficient. This missing quantity is included in the present paper. Using a precise hydrodynamic force multipole simulation method, the rotational self-diffusion coefficient is evaluated for concentrated suspensions of permeable particles. Results are presented for particle volume fractions up to 45%, and for a wide range of permeability values. From the simulation results and earlier results for the first-order virial coefficient, we find that the rotational self-diffusion coefficient of permeable spheres can be scaled to the corresponding coefficient of impermeable particles of the same size. We also show that a similar scaling applies to the translational self-diffusion coefficient considered earlier. From the scaling relations, accurate analytic approximations for the rotational and translational self-diffusion coefficients in concentrated systems are obtained, useful to the experimental analysis of permeable-particle diffusion. The simulation results for rotational diffusion of permeable particles are used to show that a generalized Stokes-Einstein-Debye relation between rotational self-diffusion coefficient and high-frequency viscosity is not satisfied.Comment: 4 figure

On accuracy of PDF divergence estimators and their applicability to representative data sampling

Generalisation error estimation is an important issue in machine learning. Cross-validation traditionally used for this purpose requires building multiple models and repeating the whole procedure many times in order to produce reliable error estimates. It is however possible to accurately estimate the error using only a single model, if the training and test data are chosen appropriately. This paper investigates the possibility of using various probability density function divergence measures for the purpose of representative data sampling. As it turned out, the first difficulty one needs to deal with is estimation of the divergence itself. In contrast to other publications on this subject, the experimental results provided in this study show that in many cases it is not possible unless samples consisting of thousands of instances are used. Exhaustive experiments on the divergence guided representative data sampling have been performed using 26 publicly available benchmark datasets and 70 PDF divergence estimators, and their results have been analysed and discussed