Related papers: ThermoLIB -- A Python Library for Constructing and…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method…
The thermo-electrical properties of a complex silicon cantilever structure used in thermal scanning probe lithography are modeled based on well established empirical laws for the thermal conductivity in silicon, the electrical conductivity…
Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
We present NAVIS (NAnochannel Velocity and thermal Interfacial Slip), a LAMMPS-Python scripted toolkit for computing the Navier (hydrodynamic) friction coefficient and Kapitza (thermal) resistance at arbitrary solid-fluid interfaces. NAVIS…
We present a computer framework to store and evaluate likelihoods coming from High Energy Physics experiments. Due to its flexibility it can be interfaced with existing fitting codes and allows to uniform the interpretation of the…
This work introduces ChemPlasKin, a freely accessible solver optimized for zero-dimensional (0D) simulations of chemical kinetics of neutral gas in non-equilibrium plasma environments. By integrating the electron Boltzmann equation solver,…
The Clair library is intended to simplify a number of generic tasks in Natural Language Processing (NLP), Information Retrieval (IR), and Network Analysis. Its architecture also allows for external software to be plugged in with very little…
Thermodynamics establishes that information acquired through measurement can be converted into work, as exemplified by Maxwell's demon and Szilard engines. Most experimental realizations of information engines, however, implicitly assume…
Foundational Machine Learning Potentials can resolve the accuracy and transferability limitations of classical force fields. They enable microscopic insights into material behavior through Molecular Dynamics simulations, which can crucially…
The open-source code FESTIM (Finite Element Simulation of Tritium In Materials) is a powerful user-friendly software for hydrogen transport simulations. Up to now, it was capable of addressing various hydrogen transport problems with…
CurvPy is an open-source Python library for automated curve fitting and regression analysis, aiming to make advanced statistical and machine learning techniques more accessible. This paper explores the mathematical foundations and…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
We present SClib, a simple hack that allows easy and straightforward evaluation of C functions within Python code, boosting flexibility for better trade-off between computation power and feature availability, such as visualization and…
Microgels made of poly(N-isopropylacrylamide) are the prototype of soft, thermoresponsive particles widely used to study fundamental problems in condensed matter physics. However, their internal structure is far from homogeneous, and…
We further elaborate on the generalized formulation for cubic equation of state proposed by Cismondi and Mollerup [Fluid Phase Equilib. 232 (2005)]. With this formulation all well-known cubic equations of state can be described with a…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
In this study, we propose a theoretical framework to investigate the interactions between flexible polymer chains, specifically polyelectrolytes (PEs). By calculating the system's free energy while considering position-dependent mutual…
We introduce an approach to exploit the existence of multiple levels of description of a physical system to radically accelerate the determination of thermodynamic quantities. We first give a proof of principle of the method using two…
We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…