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This paper introduces a novel frequency-shift chirp spread spectrum (FSCSS) system with index modulation (IM). By using combinations of orthogonal chirp signals for message representation, the proposed FSCSS-IM system is very flexible to…
In this paper we present Simgrid, a toolkit for the versatile simulation of large scale distributed systems, whose development effort has been sustained for the last fifteen years. Over this time period SimGrid has evolved from a…
In the era of post-Moore computing, network offload emerges as a solution to two challenges: the imperative for low-latency communication and the push towards hardware specialisation. Various methods have been employed to offload protocol-…
This paper discusses recent research that aims to enable computation close to data, an approach we broadly call processing-in-memory (PIM). PIM places computation mechanisms in or near where the data is stored (i.e., inside memory chips or…
The advent of modern data processing has led to an increasing tendency towards interdisciplinarity, which frequently involves the importation of different technical approaches. Consequently, there is an urgent need for a unified data…
MGSim is an open source discrete event simulator for on-chip hardware components, developed at the University of Amsterdam. It is intended to be a research and teaching vehicle to study the fine-grained hardware/software interactions on…
The Python package fluidsim is introduced in this article as an extensible framework for Computational Fluid Mechanics (CFD) solvers. It is developed as a part of FluidDyn project (Augier et al., 2018), an effort to promote open-source and…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
pyssam is a Python library for creating statistical shape and appearance models (SSAMs) for biological (and other) shapes such as bones, lungs or other organs. A point cloud best describing the anatomical 'landmarks' of the organ are…
Flow-based microfluidic biochips have attracted much atten- tion in the EDA community due to their miniaturized size and execution efficiency. Previous research, however, still follows the traditional computing model with a dedicated…
The new polarization program SPASCHARM is being prepared in Protvino. The program has two stages. The first stage is dedicated to single-spin asymmetries in the production of miscellaneous light resonances with the use of 34 GeV…
A fungal skin is a thin flexible sheet of a living homogeneous mycelium made by a filamentous fungus. The skin could be used in future living architectures of adaptive buildings and as a sensing living skin for soft self-growing/adaptive…
Manycore System-on-Chip include an increasing amount of processing elements and have become an important research topic for improvements of both hardware and software. While research can be conducted using system simulators, prototyping…
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
CMOS-based sensor array chips provide new and attractive features as compared to today's standard tools for medical, diagnostic, and biotechnical applications. Examples for molecule- and cell-based approaches and related circuit design…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
The term ``neuromorphic'' refers to systems that are closely resembling the architecture and/or the dynamics of biological neural networks. Typical examples are novel computer chips designed to mimic the architecture of a biological brain,…