simulation

Conformational changes, excess area, and elasticity of the Piezo protein-membrane nanodome from coarse-grained and atomistic simulations

This study uses simulations to analyze the conformational changes and elasticity of Piezo proteins in membrane nanodomains under tension, finding a half-maximal reduction of excess area at 3-4 mN/m tension.

Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communication

The paper identifies rare, long-lived chromatin encounters driven by cohesin-mediated loop extrusion as key to enhancer-promoter communication and shows they explain transcriptional dynamics.

Progressive chromosome shape changes quantified during cell divisions

The paper quantifies progressive changes in chromosome shape during cell divisions and finds that an alternative loop capture model explains the observed arm length to width relationship better than the loop extrusion model.

PyRID: A Brownian dynamics simulator for reacting and interacting particles written in Python

PyRID is a Python-based reaction-diffusion simulator for molecular biological systems, capable of simulating reactions and interactions between proteins and substrates.

Exploring endothelial cell environments across organs in spatially resolved omics data

The paper analyzes endothelial cell environments across organs using spatially resolved omics data and provides an interactive tool for visualizing cell distances and neighborhoods.

Can Random Walking on a Hi-C Contact Matrix Lead to Data Quality Improvement? An Assessment

This study evaluates random walk methods for improving Hi-C data quality, finding no significant benefit for TAD identification despite parameter tuning challenges.

CRISPR-Cas12a REC2 - NUC interactions drive target-strand cleavage and constrain trans cleavage.

This study investigates differences in cis and trans cleavage efficiency among Cas12a orthologues and identifies REC2-NUC interactions as key determinants of their function.

Computational Binding Affinities of Disheveled PDZ Protein-Ligand Complexes

The paper evaluates the computational tool BFEE2 for predicting binding affinities of DVL PDZ domain-peptide complexes in Wnt/{beta}-catenin signaling.

Computational Modeling and Visualization of Ischemic Effects on an Advanced Purkinje Network

This study presents a computational model of the Purkinje network that simulates ischemic effects on conduction and refractoriness, providing insights into arrhythmogenic risk.

Surface-Tethering Enhances Precision in Measuring Diffusion Within 3D Protein Condensates

This study shows surface tethering improves accuracy in measuring diffusion within 3D protein condensates by reducing motion artifacts while preserving their native properties.

Droplet-assisted folding of long regulatory RNAs

The paper proposes a mechanism called droplet-assisted RNA folding, where RNA-binding protein condensates guide the folding of long regulatory RNAs by preventing premature interactions and enabling long-range contacts.

Interictal activity fluctuations follow rather than precede seizures on multiple time scales in a mouse model of focal cortical dysplasia

Ancient atmospheric changes could favour C3-to-CAM transition: A simulation-based evidence

The paper simulates ancient atmospheric conditions to show how reduced CO2 and increased aridity could drive the evolution of CAM from C3 plants, with drought consistently favoring CAM regardless of CO2 levels.

Signatures of selective sweeps in continuous-space populations

This study simulates selective sweeps in spatially structured populations and finds that low dispersal leads to distinct genetic signatures, including reduced diversity and intermediate-frequency variants.

Simulated metabolic profiles reveal biases in pathway analysis methods

This study simulates metabolic profiles to evaluate pathway analysis methods, revealing biases when applied to metabolomics data.

Eco-genomic analysis uncovers precision-conservation targets for the western Pacific's southernmost salmonid

The paper uses genomic and ecological data to show that a critically endangered salmonid population has hidden resilience and supports targeted conservation strategies.

Experimenting with Two Recent Feature Selection Methods for High-Dimensional Biological Data

This study compares two feature selection methods, Stabl and Nullstrap, showing Nullstrap is more accurate and efficient for high-dimensional biological data.

Computational screening and automatic filtering for the discovery of novel inhibitors of TMPRSS2, a type II transmembrane serine protease

The paper uses structure-based virtual screening to identify novel TMPRSS2 inhibitors from a large compound library, selecting 10 hit candidates through a reproducible filtering workflow.

Widefield Acoustics Heuristic: Advancing Microphone Array Design for Accurate Spatial Tracking of Echolocating Bats

This paper introduces Array WAH, a simulation framework for designing microphone arrays to accurately track echolocating bats, showing that tetrahedral and octahedral geometries provide better localisation than planar arrays.

Insights into the linker domain in ABCB1/P-glycoprotein

This study investigates the role of the linker domain in ABCB1/P-glycoprotein using simulations, cryo-EM, and computational methods, revealing its impact on protein structure and function.

Atomistic Simulation of Voltage Activation of a Truncated BK Channel

The paper uses atomistic simulations to study voltage activation of BK channels, revealing unique VSD movement and coupling mechanisms distinct from canonical Kv channels.

Beyond Locomotion: How Specialized Motor Rhythms Enable Vertebrate Escape from Capture

This study shows how Xenopus laevis tadpoles use specialized motor rhythms and body mechanics to escape capture by generating reactive forces through direct mechanical interactions.

The ParB-CTP Cycle Activates Phase Separation in Bacterial DNA Segregation

The paper shows the ParB-CTP cycle enables phase separation in bacterial DNA segregation by enhancing ParB-ParB interactions, supported by simulations and experiments.

Insilico Investigation of Terpenoid efficacy on Cannabinoid Receptors using QSAR models and fragment-based Pharmacophore modelling

This paper uses in silico methods to identify terpenoids from Cannabis sativa that may interact with cannabinoid receptors to relieve pain.

Shaker it OFF: Biophysical Characterization of an Inactivating Potassium Conductance Mediating Object Segmentation in a Collision-Detecting Neuron

The paper characterizes a Shaker potassium channel in a grasshopper neuron involved in visual object segmentation through electrophysiology and computational modeling.

Computational study of heme b595 to heme d electron transfer in E. coli cytochrome bd-I oxidase

This study uses computational methods to analyze electron transfer in E. coli cytochrome bd-I oxidase, identifying contributions from hemes, protein, and environment.

Integrative reverse vaccinology approach for identification of a vaccine antigen candidate with immunoprotective and anti-fibrotic potential against Schistosoma japonicum-associated liver fibrosis

The paper identifies a vaccine antigen candidate, DRE2_SCHJA, with potential to prevent and treat Schistosoma japonicum-associated liver fibrosis using an integrative computational approach.

The role of contact guidance and ECM remodelling in cancer invasion: a computational study

This paper develops a computational model to study how cancer cells interact with and remodel the extracellular matrix, revealing how structural and chemical cues influence invasion.

Biophysical mechanisms of morphogenesis in lizard lungs

The paper investigates morphogenesis in lizard lungs, finding that stress ball morphogenesis is conserved but luminal inflation varies, with apical constriction contributing to transitional chambers in veiled chameleons.

Influence of duty-cycle recording on measuring bat activity in passive acoustic monitoring

The paper simulates how duty-cycle subsampling affects bat activity measurements using three metrics and provides guidance on selecting sampling parameters and metrics for passive acoustic monitoring.