Parallel Distributed Breadth First Search on the Kepler Architecture

We present the results obtained by using an evolution of our CUDA-based solution for the exploration, via a breadth first search, of large graphs. This latest version exploits at its best the features of the Kepler architecture and relies on a combination of techniques to reduce both the number of communications among the GPUs and the amount of exchanged data. The final result is a code that can visit more than 800 billion edges in a second by using a cluster equipped with 4,096 Tesla K20X GPUs.

On the properties of a bundle of flexible actin filaments in an optical trap

We establish the statistical mechanics framework for a bundle of N-f living and uncrosslinked actin filaments in a supercritical solution of free monomers pressing against a mobile wall. The filaments are anchored normally to a fixed planar surface at one of their ends and, because of their limited flexibility, they grow almost parallel to each other. Their growing ends hit a moving obstacle, depicted as a second planar wall, parallel to the previous one and subjected to a harmonic compressive force.

Comparing first-order microscopic and macroscopic crowd models for an increasing number of massive agents

A comparison between first-order microscopic and macroscopic differential models of crowd dynamics is established for an increasing number N of pedestrians. The novelty is the fact of considering massive agents, namely, particles whose individual mass does not become infinitesimal when N grows. This implies that the total mass of the system is not constant but grows with N. The main result is that the two types of models approach one another in the limit N -> ?, provided the strength and/or the domain of pedestrian interactions are properly modulated by N at either scale.

Speeding up a Rollout algorithm for complex parallel machine scheduling

Rollout methodology is a constructive metaheuristic algorithm and its main characteristics are its modularity, the adaptability to different objectives and constraints and the easiness of implementation. Multi-heuristic Rollout extends the Rollout by incorporating several constructive heuristics in the Rollout framework and it is able to easily incorporate human experience inside its research patterns to fulfil complex requirements dictated by the application at hand. However, a drawback for both Rollout and multi-heuristic Rollout is often represented by the required computation time.

Mathematical model for transport of DNA plasmids from the external medium up to the nucleus by electroporation

We propose a mathematical model for the transport of DNA plasmids from the extracellular matrix up to the cell nucleus. The model couples two phenomena: the electroporation process, describing the cell membrane permeabilization to plasmids and the intracellular transport enhanced by the presence of microtubules. Numerical simulations of cells with arbitrary geometry, in 2D and 3D, and a network of microtubules show numerically the importance of the microtubules and the electroporation on the effectiveness of the DNA transfection, as observed by previous biological data.

On a class of parameters estimators in linear models dominating the least squares one

The estimation of parameters in a linear model is considered under the hypothesis that the noise, with finite second order statistics, can be represented by random coefficients in a given deterministic basis. An extended underdetermined design matrix is then formed, and the estimator of the extended parameters with minimum l(1) norm is computed.

Particle-based modeling of living actin filaments in an optical trap

We report a coarse-grained molecular dynamics simulation study of a bundle of parallel actin filaments under supercritical conditions pressing against a loaded mobile wall using a particle-based approach where each particle represents an actin unit. The filaments are grafted to a fixed wall at one end and are reactive at the other end, where they can perform single monomer (de) polymerization steps and push on a mobile obstacle.