Related papers: PHAST: Protein-like heteropolymer analysis by stat…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
The MAterials Simulation Toolkit (MAST) is a workflow manager and post-processing tool for ab initio defect and diffusion workflows. MAST codifies research knowledge and best practices for such workflows, and allows for the generation and…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We employ a mesoscopic model for studying aggregation processes of protein-like hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
Performance has always been a hot topic in computing. However, the viable ways to achieve it have taken many forms in the different moments of computing history. Today, technological limits have pushed the adoption of increasingly parallel…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
Multidimensional separations data have the capacity to reveal detailed information about complex biological samples. However, data analysis has been an ongoing challenge in the area since the peaks that represent chemical factors may drift…
In this contribution we present the FAST, which is a comprehensive software suite that aims to streamline and automatically manage the forecast of atmospheric and astroclimatic parameters (provided respectively by Meso-Nh and Astro-Meso-Nh…
In this paper we announce the public release of a massively-parallel, GPU-accelerated software, which is the first to combine both coarse-grained molecular dynamics and field-theoretical simulations in one simulation package. MATILDA.FT…
Probabilistic programming is perfectly suited to reliable and transparent data science, as it allows the user to specify their models in a high-level language without worrying about the complexities of how to fit the models. Static analysis…
AI compliance is becoming increasingly critical as AI systems grow more powerful and pervasive. Yet the rapid expansion of AI policies creates substantial burdens for resource-constrained practitioners lacking policy expertise. Existing…
ASTRA is a Python package that provides a modular, instrument-independent interface for working with high-resolution stellar spectra. Designed to support data from multiple spectrographs, including ESPRESSO (Pepe et al., 2021), HARPS (Mayor…
A special aspect of parameter identification in finite-strain elasto-plasticity is considered. Namely, we analyze the impact of the measurement errors on the resulting set of material parameters. In order to define the sensitivity of…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
A new parallelized simulation code is presented, which uses a Monte Carlo method to determine particle spectra in the KATRIN source. Reaction chains are generated from the decay of tritium within the source. The code includes all relevant…
The purpose of this article is to provide a starter kit for multicanonical simulations in statistical physics. Fortran code for the $q$-state Potts model in $d=2, 3,...$ dimensions can be downloaded from the Web and this paper describes…
We present ParaDRAM, a high-performance Parallel Delayed-Rejection Adaptive Metropolis Markov Chain Monte Carlo software for optimization, sampling, and integration of mathematical objective functions encountered in scientific inference.…
Numerical simulations based on particle methods have been widely used in various fields including astrophysics. To date, simulation softwares have been developed by individual researchers or research groups in each field, with a huge amount…
We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase…