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We present a data-parallel software package for fitting Gaussian Approximation Potentials (GAPs) on multiple nodes using the ScaLAPACK library with MPI and OpenMP. Until now the maximum training set size for GAP models has been limited by…
This paper addresses the validation of electric vehicle supply equipment by means of a real-time capable co-simulation approach. This setup implies both pure software and real-time simulation tasks with different sampling rates dependent on…
Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase where they can be accurately…
The totally asymmetric simple exclusion process (TASEP), which describes the stochastic dynamics of interacting particles on a lattice, has been actively studied over the past several decades and applied to model important biological…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
We present an open-source MATLAB package, entitled OpenPIV-Matlab, for analyzing particle image velocimetry (PIV) data. We extend the PIV analysis with additional tools for post-processing the PIV results including the estimation of…
This paper presents a method of constructing Parseval frames from any collection of complex envelopes. The resulting Enveloped Sinusoid Parseval (ESP) frames can represent a wide variety of signal types as specified by their physical…
This paper presents PointSSIM, a novel low-dimensional image-to-image comparison metric that is resolution invariant. Drawing inspiration from the structural similarity index measure and mathematical morphology, PointSSIM enables robust…
We define and discuss the first sparse coding algorithm based on closed-form EM updates and continuous latent variables. The underlying generative model consists of a standard `spike-and-slab' prior and a Gaussian noise model. Closed-form…
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
An Equivalent Circuit Programming (ECP) approach that expresses the optimality conditions of an optimization problem in terms of an equivalent circuit model and uses circuit simulation techniques to solve for an optimal solution, is applied…
SPES (Study for the Production of Exotic Species) is a LNL project that will produce by the end of this year the conceptual design of a specialized facility for Radioactive Ion Beam (RIB) originated by fission fragments produced by…
Electrochemical impedance spectroscopy (EIS) is an effective method for studying the electrochemical systems. The interpretation of EIS is the biggest challenge in this technology, which requires reasonable modeling. However, the modeling…
We describe a computer application designed to analyze hyperspectral data collected by the Compact Infrared Spectrometer for Mars (CRISM). The application links the spectral, imaging and mapping perspectives on the eventual CRISM dataset by…
This thesis introduces PEMS2, an improvement to PEMS (Parallel External Memory System). PEMS executes Bulk-Synchronous Parallel (BSP) algorithms in an External Memory (EM) context, enabling computation with very large data sets which exceed…
Data movement between memory and processors is a major bottleneck in modern computing systems. The processing-in-memory (PIM) paradigm aims to alleviate this bottleneck by performing computation inside memory chips. Real PIM hardware (e.g.,…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying the electron emission characteristics and the atomic structure evolution of micro- and nano-protrusions made of pure…
Estimating the effort of software systems is an essential topic in software engineering, carrying out an estimation process reliably and accurately for a software forms a vital part of the software development phases. Many researchers have…