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Positive semidefinite programs are an important subclass of semidefinite programs in which all matrices involved in the specification of the problem are positive semidefinite and all scalars involved are non-negative. We present a parallel…

Based on the previously developed Energy Conserving Semi Implicit Method (ECsim) code, we present its cylindrical implementation, called ECsim-CYL, to be used for axially symmetric problems. The main motivation for the development of the…

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…

The recent rise of cryo-EM and X-ray high-throughput techniques is providing a wealth of new structures trapped in different conformations. Understanding how proteins transition between different conformers, and how they relate to each…

The Visual Physics Analysis (VISPA) project defines a toolbox for accessing software via the web. It is based on latest web technologies and provides a powerful extension mechanism that enables to interface a wide range of applications.…

This paper presents LIBTwinSVM, a free, efficient, and open source library for Twin Support Vector Machines (TSVMs). Our library provides a set of useful functionalities such as fast TSVMs estimators, model selection, visualization, a…

Software test cases can be defined as a set of condition where a tester needs to test and determine that the System Under Test (SUT) satisfied with the expected result correctly. This paper discusses the optimization technique in generating…

In the quest to realize a comprehensive EEG signal processing framework, in this paper, we demonstrate a toolbox and graphic user interface, EEGsig, for the full process of EEG signals. Our goal is to provide a comprehensive suite, free and…

Event-related potentials (ERPs) extracted from electroencephalography (EEG) data in response to stimuli are widely used in psychological and neuroscience experiments. A major goal is to link ERP characteristic components to subject-level…

TrueEBSD is an open-source MATLAB program for image alignment and spatial distortion correction of images and electron backscatter diffraction (EBSD) maps. We have re-implemented TrueEBSD as an add-on to MTEX, an established toolbox for…

This paper introduces variational representational similarity analysis RSA (vRSA) for electromagnetic recordings of neural responses (e.g., EEG, MEG, ECoG or LFP). Variational RSA is a Bayesian approach for testing whether the similarity of…

Mapping the conformational dynamics of proteins is crucial for elucidating their functional mechanisms. While Molecular Dynamics (MD) simulation enables detailed time evolution of protein motion, its computational toll hinders its use in…

We report a new particle in cell (PIC) method based on the semi-implicit approach. The novelty of the new method is that unlike any of its semi-implicit predecessors at the same time retains the explicit computational cycle and conserves…

The Extreme ultraviolet SpectroPhotometer (ESP) is one of five channels of the Extreme ultraviolet Variability Experiment (EVE) onboard the NASA Solar Dynamics Observatory (SDO). The ESP channel design is based on a highly stable…

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to…

We present a major update to ElecSus, a computer program and underlying model to calculate the electric susceptibility of an alkali-metal atomic vapour. Knowledge of the electric susceptibility of a medium is essential to predict its…

Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…

Software visualization helps to comprehend the system by providing a vivid illustration. The developers, as well as the analysts, can have a glance over the total system to understand the basic changes over time from a high-level point of…

The Stochastic Approximation EM (SAEM) algorithm, a variant stochastic approximation of EM, is a versatile tool for inference in incomplete data models. In this paper, we review the fundamental EM algorithm and then focus especially on the…

Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…