Related papers: PHAST: Protein-like heteropolymer analysis by stat…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
HIPSTER (Heavily Ionising Particle Standard Toolkit for Event Recognition) is an open source Python package designed to facilitate the use of TensorFlow in a high energy physics analysis context. The core functionality of the software is…
Meta-analysis methods are used to combine evidence from multiple studies. Meta-regression as well as model-based meta-analysis are extensions of standard pairwise meta-analysis in which information about study-level covariates and…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
The paper presents a combination of the time-parallel "parallel full approximation scheme in space and time" (PFASST) with a parallel multigrid method (PMG) in space, resulting in a mesh-based solver for the three-dimensional heat equation…
Data mining, particularly the analysis of multivariate time series data, plays a crucial role in extracting insights from complex systems and supporting informed decision-making across diverse domains. However, assessing the similarity of…
Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…
Spatial-Temporal Graph (STG) forecasting on large-scale networks has garnered significant attention. However, existing models predominantly focus on short-horizon predictions and suffer from notorious computational costs and memory…
We demonstrate neural-network runtime prediction for complex, many-parameter, massively parallel, heterogeneous-physics simulations running on cloud-based MPI clusters. Because individual simulations are so expensive, it is crucial to train…
Monte Carlo techniques, including MCMC and other methods, are widely used in Bayesian inference to generate sets of samples from a parameter space of interest. The Python GetDist package provides tools for analysing these samples and…
Program SMART (Spectra and Model Atmospheres by Radiative Transfer) has been composed for modelling atmospheres and spectra of hot stars (O, B and A spectral classes) and studying different physical processes in them (Sapar & Poolam\"ae…
Reactor grade plasmas are likely to be fuelled by pellet injection. This technique transiently perturbs the profiles, driving the density profile hollow and flattening the edge temperature profile. After the pellet perturbation, the density…
The simulated tempering (ST) is an important method to deal with systems whose phase spaces are hard to sample ergodically. However, it uses accepting probabilities weights which often demand involving and time consuming calculations. Here…
This paper presents a new statistical method for clustering step data, a popular form of health record data easily obtained from wearable devices. Since step data are high-dimensional and zero-inflated, classical methods such as K-means and…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
One of the major challenges providing large databases like the WFCAM Science Archive (WSA) is to minimize ingest times for pixel/image metadata and catalogue data. In this article we describe how the pipeline processed data are ingested…
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) obtained from any ab-initio density-functional theory (DFT) code. The current version of…