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We present an application, EasyScan_HEP, for connecting programs to scan the parameter space of High Energy Physics (HEP) models using various sampling algorithms. We develop EasyScan_HEP according to the principle of flexibility and…
The matrixdist R package provides a comprehensive suite of tools for the statistical analysis of matrix distributions, including phase-type, inhomogeneous phase-type, discrete phase-type, and related multivariate distributions. This paper…
The FEAST algorithm is a subspace iteration method that uses a spectral projector as a rational filter in order to efficiently solve interior eigenvalue problems in parallel. Although the solutions from the FEAST algorithm converge rapidly…
Functional Principal Components Analysis (FPCA) is a widely used analytic tool for dimension reduction of functional data. Traditional implementations of FPCA estimate the principal components from the data, then treat these estimates as…
We present a formalism of the transition matrix Monte Carlo method. A stochastic matrix in the space of energy can be estimated from Monte Carlo simulation. This matrix is used to compute the density of states, as well as to construct…
Calculating portions of eigenvalues and eigenvectors of matrices or matrix pencils has many applications. An approach to this calculation for Hermitian problems based on a density matrix has been proposed in 2009 and a software package…
An open-source, Python-based Temporal Analysis of Products (TAP) reactor simulation and processing program is introduced. TAPsolver utilizes algorithmic differentiation for the calculation of highly accurate derivatives, which are used to…
We present a general transfer method for the heterogeneous integration of different photonic and electronic materials systems and devices onto a single substrate. Called BLAST, for Bond, Lift, Align, and Slide Transfer, the process works at…
Monte Carlo (MC) simulations are powerful computational tools for investigating thermodynamic behavior and validating analytical approaches in complex physical systems. Here we present ETHER (Efficient Tool for THermodynamics Exploration…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
Non-differentiable and constrained optimization play a key role in machine learning, signal and image processing, communications, and beyond. For high-dimensional minimization problems involving large datasets or many unknowns, the…
We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction…
Traditional heterogeneous parallel algorithms, designed for heterogeneous clusters of workstations, are based on the assumption that the absolute speed of the processors does not depend on the size of the computational task. This assumption…
We describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…
In any valid Monte Carlo sampling that realizes microcanonical property we can collect statistics for a transition matrix in energy. This matrix is used to determine the density of states, from which most of the thermodynamical averages can…
We present recent developments in the parallelization scheme of ECHO-3DHPC, an efficient astrophysical code used in the modelling of relativistic plasmas. With the help of the Intel Software Development Tools, like Fortran compiler and…
The computer-assisted modeling of re-entrant production lines, and, in particular, simulation scalability, is attracting a lot of attention due to the importance of such lines in semiconductor manufacturing. Re-entrant flows lead to…
Two important enhanced sampling algorithms, simulated (ST) and parallel (PT) tempering, are commonly used when ergodic simulations may be hard to achieve, e.g, due to a phase space separated by large free-energy barriers. This is so for…
Modern analysis of high energy physics (HEP) data needs advanced statistical tools to separate signal from background. A C++ package has been implemented to provide such tools for the HEP community. The package includes linear and quadratic…
Reliable parameter extraction from experimental data is central to quantitative analysis in spectroscopy, diffraction, photoluminescence, chromatography, microscopy, and time-resolved measurements. We present FitED, a Python-based desktop…