Related papers: ThermoLIB -- A Python Library for Constructing and…
We introduce TorchSim, an open-source atomistic simulation engine tailored for the Machine Learned Interatomic Potential (MLIP) era. By rewriting core atomistic simulation primitives in PyTorch, TorchSim can achieve orders of magnitude…
Enhanced sampling techniques such as umbrella sampling and metadynamics are now routinely used to provide information on how the thermodynamic potential, or free energy, depends on a small number of collective variables. The free energy…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
HepLib is a C++ Library for computations in High Energy Physics, it works on top of GiNaC, a well-established C++ library used to perform symbolic computations. HepLib combines serval well-known packages to get high efficiency, including…
Nowadays the analysis of dynamics of and on networks represents a hot topic in the Social Network Analysis playground. To support students, teachers, developers and researchers in this work we introduce a novel framework, namely NDlib, an…
ergodicity is an open-source Python library for computational work on stochastic dynamics, with particular emphasis on non-ergodicity, time-average behavior, heavy-tailed processes, and decision making under uncertainty. The package brings…
Machine learning interatomic potentials (MLIPs) enable atomistic simulations with near ab initio accuracy at significantly reduced computational cost, but their broader adoption is often limited by fragmented tooling, limited scalability,…
The Vortex-induced vibration (VIV) prediction of long flexible cylindrical structures relies on the accuracy of the hydrodynamic database constructed via rigid cylinder forced vibration experiments. However, to create a comprehensive…
The NTMpy code package allows for simulating the one-dimensional thermal response of multilayer samples after optical excitation, as in a typical pump-probe experiment. Several Python routines are combined and optimized to solve coupled…
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…
The package CosmoLib is a combination of a cosmological Boltzmann code and a simulation toolkit to forecast the constraints on cosmological parameters from future observations. In this paper we describe the released linear-order part of the…
As the use of text-to-image generative models increases, so does the adoption of automatic benchmarking methods used in their evaluation. However, while metrics and datasets abound, there are few unified benchmarking libraries that provide…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
Estimating the free energy, as well as other thermodynamic observables, is a key task in lattice field theories. Recently, it has been pointed out that deep generative models can be used in this context [1]. Crucially, these models allow…
Thorough characterization of the thermo-mechanical properties of materials requires difficult and time-consuming experiments. This severely limits the availability of data and it is one of the main obstacles for the development of effective…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…
In this paper we present SurvLIMEpy, an open-source Python package that implements the SurvLIME algorithm. This method allows to compute local feature importance for machine learning algorithms designed for modelling Survival Analysis data.…
We present fast-vollib, an open-source Python library that provides high-performance European option pricing, implied volatility (IV) computation, and Greeks under the Black-76, Black-Scholes, and Black-Scholes-Merton models. The library is…
The lattice Boltzmann method (LBM) has emerged as a prominent technique for solving fluid dynamics problems due to its algorithmic potential for computational scalability. We introduce XLB library, a Python-based differentiable LBM library…