Chromatin organization regulates viral egress dynamics

Various types of DNA viruses are known to elicit the formation of a large nuclear viral replication compartment and marginalization of the cell chromatin. We used three-dimensional soft x-ray tomography, confocal and electron microscopy, combined with numerical modelling of capsid diffusion to analyse the molecular organization of chromatin in herpes simplex virus 1 infection and its effect on the transport of progeny viral capsids to the nuclear envelope. Our data showed that the formation of the viral replication compartment at late infection resulted in the enrichment of heterochromatin in the nuclear periphery accompanied by the compaction of chromatin. Random walk modelling of herpes simplex virus 1-sized particles in a three-dimensional soft x-ray tomography reconstruction of an infected cell nucleus demonstrated that the peripheral, compacted chromatin restricts viral capsid diffusion, but due to interchromatin channels capsids are able to reach the nuclear envelope, the site of their nuclear egress.Peer reviewe

Lattice Boltzmann simulation of multiscale systems: Dimensional analysis and time-scale hierarchy

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Designing a graphics processing unit accelerated petaflop capable lattice Boltzmann solver: Read aligned data layouts and asynchronous communication

The lattice Boltzmann method is a well-established numerical approach for complex fluid flow simulations. Recently, general-purpose graphics processing units (GPUs) have become available as high-performance computing resources at large scale. We report on designing and implementing a lattice Boltzmann solver for multi-GPU systems that achieves 1.79 PFLOPS performance on 16,384 GPUs. To achieve this performance, we introduce a GPU compatible version of the so-called bundle data layout and eliminate the halo sites in order to improve data access alignment. Furthermore, we make use of the possibility to overlap data transfer between the host central processing unit and the device GPU with computing on the GPU. As a benchmark case, we simulate flow in porous media and measure both strong and weak scaling performance with the emphasis being on large-scale simulations using realistic input data.peerReviewe

Investigation of an entropic stabilizer for the lattice-Boltzmann method

The lattice-Boltzmann (LB) method is commonly used for the simulation of fluid flows at the hydrodynamic level of description. Due to its kinetic theory origins, the standard LB schemes carry more degrees of freedom than strictly needed, e.g., for the approximation of solutions to the Navier-stokes equation. In particular, there is freedom in the details of the so-called collision operator. This aspect was recently utilized when an entropic stabilizer, based on the principle of maximizing local entropy, was proposed for the LB method [I. V. Karlin, F. Bosch, and S. S. Chikatamarla, ¨ Phys. Rev. E 90, 031302(R) (2014)]. The proposed stabilizer can be considered as an add-on or extension to basic LB schemes. Here the entropic stabilizer is investigated numerically using the perturbed double periodic shear layer flow as a benchmark case. The investigation is carried out by comparing numerical results obtained with six distinct LB schemes. The main observation is that the unbounded, and not explicitly controllable, relaxation time for the higher-order moments will directly influence the leading-order error terms. As a consequence, the order of accuracy and, in general, the numerical behavior of LB schemes are substantially altered. Hence, in addition to systematic numerical validation, more detailed theoretical analysis of the entropic stabilizer is still required in order to properly understand its properties.peerReviewe

Exploring with simulations the transport properties of multi-scale porous material

EGU2015-12761201

Fluid flow simulations meet high-speed video : Computer vision comparison of droplet dynamics

Hypothesis While multiphase flows, particularly droplet dynamics, are ordinary in nature as well as in industrial processes, their mathematical and computational modelling continue to pose challenging research tasks - patent approaches for tackling them are yet to be found. The lack of analytical flow field solutions for non-trivial droplet dynamics hinders validation of computer simulations and, hence, their application in research problems. High-speed videos and computer vision algorithms can provide a viable approach to validate simulations directly against experiments. Experiments Droplets of water (or glycerol-water mixtures) impacting on both hydrophobic and superhydrophobic surfaces were imaged with a high-speed camera. The corresponding configurations were simulated using a lattice-Boltzmann multiphase scheme. Video frames from experiments and simulations were compared, by means of computer vision, over entire droplet impact events. Findings The proposed experimental validation procedure provides a detailed, dynamic one-on-one comparison of a droplet impact. The procedure relies on high-speed video recording of the experiments, computer vision, and on a software package for the analyzation routines. The procedure is able to quantitatively validate computer simulations against experiments and it is widely applicable to multiphase flow systems in general.peerReviewe

High-Accuracy Approximation of High-Rank Derivatives: Isotropic Finite Differences Based on Lattice-Boltzmann Stencils

We propose isotropic finite differences for high-accuracy approximation of high-rank derivatives. These finite differences are based on direct application of lattice-Boltzmann stencils. The presented finite-difference expressions are valid in any dimension, particularly in two and three dimensions, and any lattice-Boltzmann stencil isotropic enough can be utilized. A theoretical basis for the proposed utilization of lattice-Boltzmann stencils in the approximation of high-rank derivatives is established. In particular, the isotropy and accuracy properties of the proposed approximations are derived directly from this basis. Furthermore, in this formal development, we extend the theory of Hermite polynomial tensors in the case of discrete spaces and present expressions for the discrete inner products between monomials and Hermite polynomial tensors. In addition, we prove an equivalency between two approaches for constructing lattice-Boltzmann stencils. For the numerical verification of the presented finite differences, we introduce 5th-, 6th-, and 8th-order two-dimensional lattice-Boltzmann stencils