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The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally…
The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms…
Computational materials science produces large quantities of data, both in terms of high-throughput calculations and individual studies. Extracting knowledge from this large and heterogeneous pool of data is challenging due to the wide…
Partitioning large machine learning models across distributed accelerator systems is a complex process, requiring a series of interdependent decisions that are further complicated by internal sharding ambiguities. Consequently, existing…
This paper documents package for the particle level fast simulation. The package is designed to complete the AcerMC generator framework with the easy-to-use simulation and reconstruction algorithms. The package provides, starting from list…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
UltraNest is a general-purpose Bayesian inference package for parameter estimation and model comparison. It allows fitting arbitrary models specified as likelihood functions written in Python, C, C++, Fortran, Julia or R. With a focus on…
We discuss a sampling algorithm which generates flat histogram in energy. In combination with transition matrix Monte Carlo, the density of states and derived quantities such as entropy and free energy as a function of temperature can be…
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…
Large language models have achieved remarkable success but remain largely black boxes with poorly understood internal mechanisms. To address this limitation, many researchers have proposed various interpretability methods including…
Thermodynamic profiles, based on bioinformatic hydropathicity scales and membrane-fitted sliding windows, exhibit accurately level sets of hydrophobic peaks or valleys in the constant fragment Fc of monoclonal antibodies. These sets provide…
Finite-state transducers (FSTs) are frequently used in speech recognition. Transducer composition is an essential operation for combining different sources of information at different granularities. However, composition is also one of the…
Modern `smart' materials have complex microscale structure, often with unknown macroscale closure. The Equation-Free Patch Scheme empowers us to non-intrusively, efficiently, and accurately simulate over large scales through computations on…
Static code analysis tools are designed to aid software developers to build better quality software in less time, by detecting defects early in the software development life cycle. Even the most experienced developer regularly introduces…
A MATLAB program has been developed for simulation of polymer blend self-assembly with nano-scaled features. The Cahn-Hilliard equation is implemented to calculate the free energy profile of the polymer blends. The Flory-Huggins type of…
Theoretical predictions in high energy physics are routinely provided in the form of Monte Carlo generators. Comparisons of predictions from different programs and/or different initialization set-ups are often necessary. MC-TESTER can be…
Inclusive Monte-Carlo samples are indispensable for signal selection and background suppression in many high energy physics experiments. A clear knowledge of the physics processes involved in the samples, including the types of processes…
We provide three Fortran programs which evaluate the QCD analytic (holomorphic) couplings $\mathcal{A}_{\nu}(Q^2)$ for complex or real squared momenta $Q^2$. These couplings are holomorphic analogs of the powers $a(Q^2)^{\nu}$ of the…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
Phase retrieval deals with the estimation of complex-valued signals solely from the magnitudes of linear measurements. While there has been a recent explosion in the development of phase retrieval algorithms, the lack of a common interface…