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Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic…
The formalism of Bayesian model selection provides a very elegant way of ranking different physical models in terms of how compatible they are with a given set of observed data. However, its practical application is often hampered by the…
PyVBMC is a Python implementation of the Variational Bayesian Monte Carlo (VBMC) algorithm for posterior and model inference for black-box computational models (Acerbi, 2018, 2020). VBMC is an approximate inference method designed for…
PyMilo is an open-source Python package that addresses the limitations of existing Machine Learning (ML) model storage formats by providing a transparent, reliable, and safe method for exporting and deploying trained models. Current…
We report the development of a python-based auxiliary-field quantum Monte Carlo (AFQMC) program, ipie, with preliminary timing benchmarks and new AFQMC results on the isomerization of [Cu$_2$O$_2$$]^{2+}$. We demonstrate how implementations…
This paper introduces ROmodel, an open source Python package extending the modeling capabilities of the algebraic modeling language Pyomo to robust optimization problems. ROmodel helps practitioners transition from deterministic to robust…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development. These…
With a view to provide a user-friendly interface for designing, training and developing deep learning frameworks, we have developed Expresso, a GUI tool written in Python. Expresso is built atop Caffe, the open-source, prize-winning…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Retrosynthesis planning remains a central challenge in molecular discovery due to the vast and complex chemical reaction space. While traditional template-based methods offer tractability, they suffer from poor scalability and limited…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
PyPartMC is a Pythonic interface to PartMC, a stochastic, particle-resolved aerosol model implemented in Fortran. Both PyPartMC and PartMC are free, libre, and open-source. PyPartMC reduces the number of steps and mitigates the effort…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the…
Radiomics enables the extraction of quantitative biomarkers from medical images for precision modeling, but reproducibility and scalability remain limited due to heterogeneous software implementations and incomplete adherence to standards.…
emcee is a Python library implementing a class of affine-invariant ensemble samplers for Markov chain Monte Carlo (MCMC). This package has been widely applied to probabilistic modeling problems in astrophysics where it was originally…
We have developed PGPG (Pipeline Generator for Programmable GRAPE), a software which generates the low-level design of the pipeline processor and communication software for FPGA-based computing engines (FBCEs). An FBCE typically consists of…
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…