simulation

A responsivity theory of call timing patterns in bat echolocation

Decomposing bat echolocation interpulse intervals into acoustic acquisition and proportional behavioural intervals explains hyperbolic call-rate trajectories, terminal buzz update budgets, buzz readiness, and multi-target sonar strobe groups.

mock-fastq-generator: A synthetic FASTQ generator

mock-fastq-generator creates synthetic FASTQ files for testing bioinformatics pipelines without using biological data.

Compensation of Hyperexcitability with Simulation-Based Inference

This study uses simulation-based inference to quantify compensatory mechanisms in a spiking neuronal network model under hyperexcitability conditions.

Degeneracy in neuronal bifurcation landscapes: equivalent bifurcation sequences across distinct parameter sets

The paper shows that different biophysical parameters can produce equivalent bifurcation sequences in neuronal models, revealing degeneracy in neuronal dynamics.

Connectome simulations identify a central pattern generator circuit for fly walking

The paper identifies a minimal central pattern generator circuit for fly walking using connectome simulations and experimental validation.

A NEST-based framework unlocks massively parallel simulation of networks of multicompartment neurons with customizable subcellular dynamics.

The paper introduces a framework for simulating multicompartment neurons with customizable subcellular dynamics using NEST and NESTML, enabling efficient and scalable network simulations.

SARS-CoV-2 Main Protease Inhibition Through Dimerization Promotion by Peptidomimetic Inhibitors and Disruption by Ebselen

This study examines how different inhibitors affect the dimerization of SARS-CoV-2 main protease, revealing distinct mechanisms of action between peptidomimetics and ebselen.

Channelrhodopsin Ion Selectivity Determines Mechanisms and Efficacy of Optogenetic Defibrillation in Human Atria and Ventricles

This study compares the defibrillation efficacy of different channelrhodopsins in human cardiac tissue using simulations, finding that ion selectivity affects arrhythmia termination mechanisms and success.

RNA synthesis and degradation regulate biomolecular condensates through non-equilibrium feedback

This study shows RNA synthesis and degradation dynamically regulate transcriptional condensates through non-equilibrium feedback, affecting their composition and stability.

replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion

replicateFest uses negative binomial models for replicated and Fisher's exact tests for unreplicated FEST TCR-seq to call antigen-expanded clonotypes, recovering all nine published HIV-1 responders.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Hindmarsh-Rose neuronal network with spike-timing-dependent plasticity demonstrates coordinated reset neuromodulation for Parkinson's disease

This paper uses a computational model to study how coordinated reset stimulation can reduce neuronal synchrony in Parkinson's disease by adjusting synaptic weights through spike-timing-dependent plasticity.

Loss of Cerebral Autoregulation After Stroke Drives Abnormal Perfusion Patterns

This study develops an in silico model to simulate cerebral blood flow in mice with and without leptomeningeal collaterals, showing that myogenic reactivity, not collateral extent, drives hyperperfusion after stroke.

Associative synaptic plasticity creates dynamic persistent activity

The paper shows that coupling neuronal and synaptic dynamics in recurrent networks enables persistent oscillations, a dynamic form of memory without explicit storage or retrieval.

Transmembrane coupling of protein condensates via membrane-mediated interactions: A simulation study

This paper uses simulations to study how protein condensates on opposite sides of a membrane interact via membrane-mediated forces, finding that curvature plays a major role in their coupling.

Experiment-anchored abundance-coverage frontiers define conditional RHSVV exposure requirements in TP53-missense tumors

Experiment-anchored sweep of p53 abundance thresholds in CPTAC TP53-missense tumors maps how much RHSVV exposure contrast is needed as target coverage falls.

Euchromatin forms condensed domains with short active regions on the surface

The paper develops a simulation framework to infer nucleosome-resolution chromatin structures from RCMC data, revealing euchromatin as condensed domains with accessible promoter/enhancer regions.

The quasi systematic nature of splitter cells

This study shows splitter cells are not necessary for task performance, as their removal allows network reorganization to maintain behavior.

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Analysis of the off-target interaction of amyloid PET tracers with human brain sulfotransferases

The paper investigates off-target interactions of amyloid PET tracers with brain sulfotransferases using multi-omic and computational methods, revealing enzyme-specific binding dynamics and implications for PET signal variability.

iCSD can produce spurious results in dense electrode arrays

The paper shows that current source density estimation can produce incorrect results in dense electrode arrays due to small inter-electrode spacing.

Probabilistic inference of Homonymous and Heteronymous Recurrent Inhibition in Human Muscles from Large-Scale Motor Neuron Recordings

The paper uses motor neuron recordings and simulation-based inference to estimate homonymous and heteronymous recurrent inhibition in human muscles during contractions.

Seasonal fluctuations in fitness result in severe reductions in effective population size

The paper simulates seasonally fluctuating selection in Drosophila populations and shows it reduces genome-wide effective population size by ~50%.

NUCGEN3D: A synthetic framework for large-scale 3D nuclear segmentation with open-source training data and models

The paper introduces NucGen3D, a synthetic framework for generating 3D nuclear segmentation datasets, and trains models that outperform existing methods on real-world data.

On the effect of applied lateral tension on the deformation energetics of biological membranes and the lipid dynamics within

MARTINI 2.2 simulations show lateral tension changes the free energies of membrane bending and thickness deformations through a projected-area term (γΔΔA), while leaving lipid mixing, residence and exchange essentially unchanged.

Climate-driven niche tracking and genomic resilience shape future distribution of a widespread agricultural weed

The paper examines how blackgrass adapts to climate change by tracking its ecological niche and showing polygenic adaptation, suggesting resilience in agricultural systems.

Multiscale Free-Energy Methods for Protonation-Coupled Light-Responsive Binding of Ionizable Photoswitchable eDHFR Inhibitors

This study develops and benchmarks a multiscale free-energy method to predict light-responsive binding of ionizable photoswitchable inhibitors to eDHFR, showing that explicit treatment of protonation states is critical for accurate predictions.

In silico framework for benchmarking optogenetic hearing restoration

This paper develops an in silico framework to model optogenetic hearing restoration and finds that improved spectral selectivity compensates for lower temporal fidelity in optogenetic stimulation.

Granule cells reorient cortical trajectories to separate contexts

In mice learning two tasks, cerebellar granule cells kept the low-rank geometry of premotor cortical output within each task but rotated their population trajectories apart between tasks, while cortex generalized.

Membrane Phase, Charge, and Curvature Regulate α-Synuclein Binding Dynamics

This study investigates how membrane phase, charge, and curvature jointly regulate α-synuclein binding dynamics using experimental and simulation methods.