Related papers: Virtual Micromagnetics: A Framework for Accessible…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
In our days, the necessity of laboratory apparatus accustoming by building up specific software objects for studying the virtual evolution of physical phenomena is a major request. In this respect, the aim of the present paper is to present…
Build-time configuration and environment assumptions are hampering progress and usability in scientific software. That which would be utterly unacceptable in non-scientific software somehow passes for the norm in scientific packages. The…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…
Increasing complexity in the power system and the transformation towards a smart grid lead to the necessity of new tools and methods for the development and testing of new technologies. One testing method is co-simulation, which allows…
Quantum simulation of chemistry and materials is predicted to be an important application for both near-term and fault-tolerant quantum devices. However, at present, developing and studying algorithms for these problems can be difficult due…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
Purpose: Conventional MRI is relying on the assumption of the magnetic field being homogeneous in direction and amplitude. However, with the growing interest in portable, affordable point-of-care MRI systems, these assumptions do not…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
We present a Mathematica program package MagneticTB, which can generate the tight-binding model for arbitrary magnetic space group. The only input parameters in MagneticTB are the (magnetic) space group number and the orbital information in…
This paper presents a new technique for the virtual reality (VR) visu-alization of complex volume images obtained from computer tomography (CT) and Magnetic Resonance Imaging (MRI) by combining three-dimensional (3D) mesh processing and…
The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…
Co-simulation consists of the theory and techniques to enable global simulation of a coupled system via the composition of simulators. Despite the large number of applications and growing interest in the challenges, the field remains…
We have developed a finite-element micromagnetic simulation code based on the FEniCS package called magnum.fe. Here we describe the numerical methods that are applied as well as their implementation with FEniCS. We apply a transformation…
Cardiovascular disease affects millions of people worldwide and its social and economic cost clearly motivates scientific research. Computer simulation can lead to a better understanding of cardiac physiology, and for pathology presents…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance…
We present Vinamax, a simulation tool for nanoparticles that aims at simulating magnetization dynamics on very large timescales. To this end, each in dividual nanoparticle is approximated by a macrospin. Vinamax numerically solves the…
Quantum simulation is a leading candidate for demonstrating practical quantum advantage over classical computation, as it is believed to provide exponentially more compute power than any classical system. It offers new means of studying the…