10 papers · ranked by Valyu relevance
Jiri Dokulil, Siegfried Benkner
Task-based runtime systems are an important branch of parallel programming research, since tasks decouple computation from the compute units, giving the runtime systems greater flexibility than a thread-based solution. This makes it easier to deal with the ever-increasing complexity of parallel architectures by…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Paul Leger, Felipe Ruiz, Hiroaki Fukuda, Nicolás Cardozo + 1 more
'Muhammad Aleem'] JavaScript Web applications are a common product in industry. As with most applications, Web applications can acquire software flaws (known as bugs), whose symptoms are seen during the development stage and, even worse, in production. The use of debuggers is beneficial for detecting bugs.…
A. Lucas Martins, Alexandre Laborde, Michael Orger
We present Sardine, a software framework built with.NET to control experimental setups through the reliable execution of dynamic networks of independent modules, where each module can interface with a hardware device (e.g., camera, motor) or represent an operation over data (e.g., image filter, data stream). The…
Marco Savioli, Paolo Calligari, Ugo Locatelli, Gianfranco Bocchinfuso
We introduce GROMODEX, a novel tool designed to optimise GROMACS molecular dynamics (MD) simulations using a structured Design of Experiments (DoE) approach. GROMACS, though efficient, requires extensive tuning of parameters to perform optimally on different hardware and molecular systems. Manual tuning is tedious and…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Yeongung Park, Seokwoo Choi, Un Yeong Choi, Haimin Jin + 2 more
'Nurul Harzira Mohamad Nor' 'Yongsu Park'] As IoT devices are being widely used, malicious code is increasingly appearing in Linux environments. Sophisticated Linux malware employs various evasive techniques to deter analysis. The embedded trace microcell (ETM) supported by modern Arm CPUs is a suitable hardware tracer…
Cristian Vidal-Silva, Vannessa Duarte, Jesennia Cárdenas-Cobo, Iván Veas
Parallel computing is a current algorithmic approach to looking for efficient solutions; that is, to define a set of processes in charge of performing at the same time the same task. Advances in hardware permit the massification of accessibility to and applications of parallel computing. Nonetheless, some algorithms…