Related papers: PHAST: Protein-like heteropolymer analysis by stat…
We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…
Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static,…
We review the literature on scaled particle theory (SPT) and its extensions and discuss results applied to describe the thermodynamics of hard particle mixtures. After explaining the basic concepts of scaled particle theory to compute the…
This work introduces ParAMS -- a versatile Python package that aims to make parameterization workflows in computational chemistry and physics more accessible, transparent and reproducible. We demonstrate how ParAMS facilitates the parameter…
In collider physics, experiments are often based on counting the numbers of events in bins of a histogram. We present a new way to build and analyze statistical models that describe these experiments, based on the probabilistic programming…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
The usage of the high-level scripting language Python has enabled new mechanisms for data interrogation, discovery and visualization of scientific data. We present yt, an open source, community-developed astrophysical analysis and…
ESPSim is an open source JAVA program that enables the comparisons of protein electrostatic potential maps via the computation of an electrostatic similarity measure. This program has been utilized to demonstrate a high degree of…
We investigate the behaviour of randomly cross-linked (co)polymer blends using a combination of replica theory and large-scale molecular dynamics simulations. In particular, we derive the analogue of the random phase approximation for…
We introduce the public version of the BAyesian STellar Algorithm (BASTA), an open-source code written in {\tt Python} to determine stellar properties based on a set of astrophysical observables. BASTA has been specifically designed to…
The thermodynamics of solid (hcp) He-4 is studied theoretically by means of unbiased Monte Carlo simulations at finite temperature, in a wide range of density. This study complements and extends previous theoretical work, mainly by…
Simulation of atomic resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated…
Phase-Field Crystal (PFC) models are able to resolve atomic length scale features of materials during temporal evolution over diffusive time scales. Traditional PFC models contain solid and liquid phases, however many important materials…
We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include…
Consumer grade cyber-physical systems (CPS) are becoming an integral part of our life, automatizing and simplifying everyday tasks. Indeed, due to complex interactions between hardware, networking and software, developing and testing such…
The training of large multimodal models fundamentally relies on massive image-text datasets, which inevitably incur prohibitive computational overhead. Dataset selection offers a promising paradigm by identifying a highly informative…
This paper reports the development of a Python Non-Uniform Fast Fourier Transform (PyNUFFT) package, which accelerates non-Cartesian image reconstruction on heterogeneous platforms. Scientific computing with Python encompasses a mature and…
The efficient extraction of force constants (FCs) is crucial for the analysis of many thermodynamic materials properties. Approaches based on the systematic enumeration of finite differences scale poorly with system size and can rarely…