simulation

Early nascent polypeptide dynamics are coupled to the flexibility of the ribosomal tunnel constriction

The paper quantifies the conformational dynamics of the ribosomal tunnel constriction in E. coli, showing its flexibility and response to nascent polypeptides.

Accessible Gibbs energy at metabolic activation limits long-term cell growth

The paper shows that accessible Gibbs energy at metabolic activation limits long-term cell growth by constraining metabolic reorganization and ATP production.

Burst suppression: a default brain state associated with loss of network complexity

The paper identifies burst suppression as a default brain state linked to loss of network complexity, distinguishing between two forms with different clinical implications.

Sampling design and inference of the caecal-skin Campylobacter relationship in broilers

This study evaluates how sampling strategies affect the recovery of the Campylobacter relationship between broiler caeca and carcass skin using simulation.

Single-Molecule Kinetic Exploration of Functional Substates in an Evolving Phosphotriesterase

This study investigates how functional and conformational substates change during enzyme evolution using single-molecule kinetic assays and simulations, showing coordinated shifts in substate equilibria that optimize catalytic efficiency.

Effects of muscle mass on muscle force predictions in human movement

Adding distributed muscle mass to 1D Hill-type models alters predicted human leg-muscle forces by under 1% at natural size; differences grow with scale and cadence.

Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments

This study develops and validates coarse-grained models of mycobacterial outer membranes to investigate lipid organization and PDIM behavior under different lipid environments.

Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant effect predictors

The paper develops MDmis, a method using molecular dynamics simulations of intrinsically disordered regions to predict variant pathogenicity, finding Long IDRs show stronger pathogenic effects than Short IDRs.

Neuromuscular impairments alter energetic cost landscape curvature and stride speed variability in post-stroke locomotion

Foot perfusion. Insights from an anatomically detailed arterial network model

This paper models foot perfusion during a cuff-induced ischaemia test to assess how arterial occlusions and collateral impairment affect tissue perfusion in different foot regions.

vcfsim: flexible simulation of all-sites VCFs with missing data

vcfsim simulates all-sites VCFs with missing data, enabling accurate population genetic studies and benchmarking.

Clustering of SARS-CoV-2 membrane proteins in lipid bilayer membranes

This study shows that M protein interactions alone can drive clustering in ERGIC-like lipid bilayers, with direct interactions being stronger than membrane-mediated ones.

Ancestra: A lineage-explicit simulator for benchmarking B-cell receptor repertoire and lineage inference methods

Ancestra simulates B-cell receptor repertoires with known lineage histories to benchmark clonal grouping and lineage reconstruction methods.

Short and long-term consequences of Habitat Transformation for Biodiversity

This paper uses simulations to study how habitat transformation affects biodiversity, finding that adaptation can reduce species diversity while habitat change has mixed short- and long-term effects.

U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism

This study reveals a loaded-spring mechanism by which U2 snRNP recognizes the branch site through spontaneous strand invasion driven by conformational energy release.

Parametric Physics-Based Synthesis of 3D Fluorescence Organoid Images with Exact Ground Truth for Deep Learning Pipeline Development

Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers

The paper systematically perturbs enhancer sequences to study their functional properties and robustness, revealing insights into regulatory sequence space and enhancer activity.

Integrating targeted genome mining and structure-guided modeling reveals unexplored 7-deazapurine-containing pathways

The paper integrates genome mining and structure-guided modeling to discover new 7-deazapurine-containing biosynthetic gene clusters and their chemical functions.

Mechanical response of the RecA nucleoprotein filament to increasing D-loop length

The paper uses molecular dynamics simulations to study how the mechanical properties of RecA nucleoprotein filaments change with increasing D-loop length during homologous recombination.

Proteome-wide identification and modeling of interactions between transactivation domains and arginine-glycine-rich regions

The paper identifies and models interactions between transactivation domains and arginine-glycine-rich regions using proteome-scale data and simulations, revealing electrostatic mechanisms driving TF-RBP coupling.

A deterministic computational kernel encoded in the human genome

The paper demonstrates that the human genome encodes a deterministic computational kernel with four properties, validated through analysis of proteome and chromosome data.

Simulation-guided design of exotendons to reduce the energetic cost of running

This paper uses simulations to predict optimal exotendon designs for reducing running energy costs at higher speeds and validates these predictions experimentally.

Uncovering putative neural mechanisms of neurotherapeutic impacts on EEG using the Human Neocortical Neurosolver

This paper demonstrates how physics-based neural simulations can interpret EEG biomarkers of neurotherapeutics by connecting localized EEG signals to multi-scale neural generators.

Using Virtual Patients to Predict Perceptual Outcomes for Optogenetic Sight Recovery Technologies

This paper introduces a virtual patient framework to predict perceptual outcomes of optogenetic therapies by linking opsin sensitivity and kinetics to temporal contrast sensitivity functions.

Investigating the sensitivity of the diffusion MRI signal to magnetization transfer and permeability via Monte-Carlo simulations

This study uses Monte-Carlo simulations to show that permeability and magnetization transfer significantly affect diffusion MRI signal and parameter estimation in cylindrical substrates.

Trapped in the web: network architectures spread coevolution and shape adaptation

The paper investigates how network architectures influence coevolutionary dynamics and adaptation in ecological communities through simulations across empirical and artificial networks.

Identification of neuronatin as a SERCA2b regulin-like protein and assessment of its aggregation propensity via coarse grained simulations.

This study models NNAT isoforms and assesses their interaction with SERCA2b using computational methods, suggesting NNAT acts as a regulin-like protein with aggregation potential.

SAMPLE-BASED TRAINING DATA FOR EFFECTIVE 3D CELL SEGMENTATION

The paper proposes a method to generate synthetic 3D cell segmentation data to reduce reliance on scarce hand-annotated samples, showing that a standard UNet trained on synthetic data can accurately segment single motile cells with branching filopodia.

Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells

This study shows that linker histone H1 acts as a liquid-like glue in chromatin domains, enabling dynamic interactions that support DNA transactions in human cells.

A framework for constructing insect steering circuits

The paper presents a framework for constructing insect steering circuits based on six general rules derived from Drosophila melanogaster data, showing functional equivalence across different wiring configurations.