Challenges facing the scaling of microelectronics to sub-50 nm dimensions and the demanding material and structural requirements of integrated photonic and microelectromechanical systems suggest that alternative fabrication technologies are needed to produce nano-scale devices. Inspired by complex, functional, self-assembled structures and systems found in Nature we suggest that self-assembly c...

This paper presents the concept and the implementation of a communication-computation overlap in massively parallel System on Chip (mpSoC). This paradigm allows to decrease the execution time of parallel programs using specific strategies in the programming level and partially decoupled system control in the hardware level. The related experiment in VHDL language for system design and in assemb...

In parallel finite element solvers, sparse matrix assembly is often a bottleneck. Implemented using message passing, latency from message matching starts to limit performance as the number of cores increases. We here address this issue by using our own stack based representation of the sparse matrix, and a hybrid parallel programming model combining traditional message passing with one-sided co...

Theoretically, parallel kinematics machine tools should be very accurate and rigid due to their closed loop structure and no error accumulation characteristics. Unfortunately, these theoretical presumptions have not been confirmed in practice, due to manufacturing and assembly errors, kinematic errors in the actuators and joints, elastic deformations due to the gravity, thermal deformations, li...

This paper describes a distribution of elements for irregular nite element meshes as well as the associated parallel assembly algorithm , in the context of parallel solving of the resulting sparse linear system using a direct block solver. These algorithms are integrated in the software processing chain EMILIO being developped at LaBRI for structural mechanics applications. Some illustrative nu...

Formalized study of self-assembly has led to the definition of the tile assembly model [Erik Winfree, Algorithmic self-assembly of DNA, Ph.D. Thesis, Caltech, Pasadena, CA, June 1998; Paul Rothemund, Erik Winfree, The program-size complexity of selfassembled squares, in: ACM Symposium on Theory of Computing, STOC02, Montreal, Quebec, Canada, 2001, pp. 459–468]. Research has identified two issue...

MOTIVATION De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assemb...

De Bruijn graph is a vastly used technique for developing genome assembly software nowadays. The scale of this kind of graph can reach billions of vertices and edges which poses great challenges to the genome assembly task. It is of great importance to study scalable genome assembly algorithms in order to cope with this situation. Despite some recent works which begin to address the scalability...

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components,...