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Path Integral Molecular Dynamics (PIMD) is a well established simulation technique to compute exact equilibrium properties for a quantum system using classical trajectories in an extended phase space. Standard PIMD simulations are…
Domain-Driven Solver (DDS) is a MATLAB-based software package for convex optimization problems in Domain-Driven form [Karimi and Tun\c{c}el, arXiv:1804.06925]. The current version of DDS accepts every combination of the following…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
The `equation-free toolbox' empowers the computer-assisted analysis of complex, multiscale systems. Its aim is to enable you to immediately use microscopic simulators to perform macro-scale system level tasks and analysis, because…
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…
Many real-world decision-theoretic planning problems can be naturally modeled with discrete and continuous state Markov decision processes (DC-MDPs). While previous work has addressed automated decision-theoretic planning for DCMDPs,…
In this paper, we introduce a technique to enhance the computational efficiency of solution algorithms for high-dimensional discrete simulation-based optimization problems. The technique is based on innovative adaptive partitioning…
Partial differential equation (PDE) solvers are extensively utilized across numerous scientific and engineering fields. However, achieving high performance and scalability often necessitates intricate and low-level programming, particularly…
Heterogeneous systems are becoming more common on High Performance Computing (HPC) systems. Even using tools like CUDA and OpenCL it is a non-trivial task to obtain optimal performance on the GPU. Approaches to simplifying this task include…
We introduce QDsim, a python package tailored for the rapid generation of charge stability diagrams in large-scale quantum dot devices, extending beyond traditional double or triple dots. QDsim is founded on the constant interaction model…
GPTIPS is a free, open source MATLAB based software platform for symbolic data mining (SDM). It uses a multigene variant of the biologically inspired machine learning method of genetic programming (MGGP) as the engine that drives the…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Hierarchical $\mathcal{H}^2$-matrices are asymptotically optimal representations for the discretizations of non-local operators such as those arising in integral equations or from kernel functions. Their $O(N)$ complexity in both memory and…
Quantum computers promise to solve several categories of problems faster than classical computers ever could. Current research mostly focuses on qubits, i.e., systems where the unit of information can assume only two levels. However, the…
We demonstrate a high-performance vendor-agnostic method for massively parallel solving of ensembles of ordinary differential equations (ODEs) and stochastic differential equations (SDEs) on GPUs. The method is integrated with a widely used…
The availability of multi-omics data has revolutionized the life sciences by creating avenues for integrated system-level approaches. Data integration links the information across datasets to better understand the underlying biological…
\textbf{FlexBox} is a flexible MATLAB toolbox for finite dimensional convex variational problems in image processing and beyond. Such problems often consist of non-differentiable parts and involve linear operators. The toolbox uses a…
Fluid flow simulation is a highly active area with applications in a wide range of engineering problems and interactive systems. Meshless methods like the Moving Particle Semi-implicit (MPS) are a great alternative to deal efficiently with…
Machine learning (ML) applications become increasingly common in many domains. ML systems to execute these workloads include numerical computing frameworks and libraries, ML algorithm libraries, and specialized systems for deep neural…