Related papers: Poster on MPI application in Computational Fluid D…
An increasing number of applications in biology, chemistry, and material sciences require fluid manipulation beyond what is possible with current automated pipette handlers, such as gradient generation, interface reactions, reagent…
Magnetic Particle Imaging (MPI) is a promising tracer-based, functional medical imaging technique which measures the non-linear magnetization response of magnetic nanoparticles to a dynamic magnetic field. For image reconstruction, system…
Huge data advent in high-performance computing (HPC) applications such as fluid flow simulations usually hinders the interactive processing and exploration of simulation results. Such an interactive data exploration not only allows…
This review examined the current advancements in data-driven methods for analyzing flow and transport in porous media, which has various applications in energy, chemical engineering, environmental science, and beyond. Although there has…
A material-based, i.e., Lagrangian, methodology for exact integration of flux by volume-preserving flows through a surface has been developed recently in [Karrasch, SIAM J. Appl. Math., 76 (2016), pp. 1178-1190]. In the present paper, we…
Pretrained language models (LMs) showcase significant capabilities in processing molecular text, while concurrently, message passing neural networks (MPNNs) demonstrate resilience and versatility in the domain of molecular science. Despite…
Asynchronous programming models (APM) are gaining more and more traction, allowing applications to expose the available concurrency to a runtime system tasked with coordinating the execution. While MPI has long provided support for…
This is a survey article written for the Springer's Intelligencer, in the occasion of the 2018 International Congress of Mathematicians.
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
Distributed memory programming is the established paradigm used in high-performance computing (HPC) systems, requiring explicit communication between nodes and devices. When FPGAs are deployed in distributed settings, communication is…
These lecture notes are written as reference material for the Advanced Course "Hydrodynamical Methods in Last Passage Percolation Models", given at the 28th Coloquio Brasileiro de Matematica at IMPA, Rio de Janeiro, July 2011.
The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs in a cluster environment. The tested technology is the INTEL Hyper Threading on real processors, and the…
We present a simple and easy to apply methodology for using high-level self-submitting parallel job queues in an MPI environment. Using C++, we implemented a library of functions, MPQueue, both for testing our concepts and for use in real…
Networks of interconnected resistors, springs and beams, or pores are standard models of studying scalar and vector transport processes in heterogeneous materials and media, such as fluid flow in porous media, and conduction, deformations,…
With multi-core processors a ubiquitous building block of modern supercomputers, it is now past time to enable applications to embrace these developments in processor design. To achieve exascale performance, applications will need ways of…
Many parallel applications rely on iterative stencil operations, whose performance are dominated by communication costs at large scales. Several MPI optimizations, such as persistent and partitioned communication, reduce overheads and…
In the emerging field of molecular communication (MC), testbeds are needed to validate theoretical concepts, motivate applications, and guide further modeling efforts. To this end, this paper presents a flexible and extendable in-vessel…
We present HTMPC, a Heavily Templated C++ library for large-scale simulations implementing multi-particle collision dynamics (MPC), a particle-based mesoscale hydrodynamic simulation method. The implementation is plugin-based, and designed…
Computational modeling and simulation are presented on the motion of red blood cells behind a moving interface in a capillary. The methodology is based on an immersed boundary method and the skeleton structure of the red blood cell (RBC)…