simulation

Interpreting the Effects of DNA Polymerase Variants at the Structural Level Using MAVISp and Molecular Dynamics Simulations

The paper uses MAVISp and molecular dynamics simulations to analyze DNA polymerase variants, classifying VUS and predicting functional consequences of POLE and POLD1 variants.

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

The paper develops a dynamic barrier model to explain genome folding features using biophysically measured CTCF and cohesin dynamics, showing that barrier bound times influence ChIP-seq, Hi-C, and chromosome morphology.

Sample size considerations for species co-occurrence models.

This study evaluates co-occurrence model performance under varying sample sizes and interaction strengths, showing that reliable inference requires larger datasets than commonly used.

Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response

The paper investigates how peripheral heterochromatin tethering influences nuclear mechanical response through simulations and experiments.

RadiSeq: a single- and bulk-cell whole-genome DNA sequencing simulator for radiation-damaged cell models

RadiSeq simulates single- and bulk-cell whole-genome sequencing of radiation-damaged cell models, validated against experimental data to aid radiation genomics research.

The interplay between biomechanics and cell kinetics explains the spatial pattern in liver fibrosis

This paper develops a digital twin model to simulate liver fibrosis patterns, showing that ECM distribution results from cell death zones and biomechanical compression.

Revealing reassortment in influenza A viruses with TreeSort

TreeSort detects influenza A reassortment in thousands of genomes via clock-based tests; avian H7 reassorts most, and HA, NA, MP rarely reassort in human and H5N1.

Uneven Walking is Challenging: step-ups or extended steps that is the question

The paper investigates whether extending step length or stepping over perturbations is more energy-efficient during uneven walking, finding a velocity-dependent threshold for each strategy.

Agent-Based Simulation of Cortical Microtubule Band Movement in the Arabidopsis Zygote

The paper uses an agent-based simulation to study cortical microtubule band movement in Arabidopsis zygotes, identifying self-organization processes and the role of directional cues.

Validation of Structure Tensor Analysis for Orientation Estimation in Brain Tissue Microscopy

This study evaluates structure tensor analysis for estimating fiber orientations in brain imaging, showing parameter sensitivity in crossing fibers and anisotropic data.

Is the cortical dynamics ergodic? A numerical study in partially symmetric networks of spiking neurons

This study shows that slow cortical dynamics emerge in partially symmetric spiking neuron networks, leading to non-ergodic behavior with long-lived activity states.

How chromatin-binding proteins direct distinct folding pathways of tetra-nucleosomes: Insights from coarse-grained simulations

This study uses simulations to show how HP1 and tPHC3 influence tetra-nucleosome folding pathways and stability through different interaction mechanisms.

Deciphering Cannabidiol Neuroregulatory Role in Addiction Pathways , A Systems Level Comparison with THC via Intrinsic Network Pharmacology

This paper uses computational modeling to compare CBD and THC effects on addiction pathways, showing CBD stabilizes neuroregulatory circuits while THC amplifies reward circuits.

Detecting epidemic-driven selection: a simulation-based tool to optimize sampling design and analysis strategies

This paper introduces a simulation framework to detect epidemic-driven selection by optimizing sampling design and analysis strategies.

Effects of central dogma processes on the compaction and segregation of bacterial nucleoids

This study uses simulations to show that transcription and translation processes expand bacterial nucleoids and aid in chromosome segregation.

Probabilities of finding trace profile donors and their paternal relatives in Y-STR reference databases

The paper estimates the probability of finding Y-STR profile matches and related individuals in forensic databases using simulation studies.

Insights into the spool-like architecture and infectionstrategy of the archaeal virus SEV1

This study uses cryo-electron tomography to reveal the spool-like architecture and infection strategies of the archaeal virus SEV1, showing its flexibility and unique assembly process.

Generating brain-wide connectome using synthetic axonal morphologies

The paper generates whole-brain connectivity by predicting detailed axonal morphologies from sparse data, enabling in silico experimentation of large brain regions.

Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy

This study investigates how cooling temperature, immersion medium, and EM grid material affect devitrification in cryo-SMLM, showing that metallic supports in cold nitrogen tolerate higher laser intensities.

Benchmarking Phenotypic Clustering Algorithms via Empirically Calibrated Simulations: A Diagnostic Framework to Improve Biodiversity Assessment in Neglected Crops

This paper benchmarks clustering algorithms on simulated phenotypic data from West African fonio to improve biodiversity assessment in neglected crops.

Simulated Language Acquisition in a Biologically Realistic Model of the Brain

This paper presents a simulated neuromorphic system that learns language acquisition through exposure to grounded sentences, demonstrating the ability to understand semantics, syntax, and generate novel sentences.

Deciphering the Mechanistic Continuum of Broadly Neutralizing Class 4 Antibodies Targeting Conserved Cryptic Epitopes of the SARS-CoV-2 Spike Protein : Operating at the Intersection of Binding, Allostery and Immune Escape

This study uses computational methods to analyze how class 4 antibodies neutralize SARS-CoV-2 by targeting cryptic epitopes, revealing mechanisms involving allostery, binding energetics, and immune escape.

Scalable emulation of protein equilibrium ensembles with generative deep learning

BioEmu, a diffusion model trained on structures, molecular dynamics trajectories, and stability assays, samples protein equilibrium ensembles and folding free energies within ~1 kcal/mol in GPU-hours.

Maternal smoking in early pregnancy disrupts placental function through syncytiotrophoblast and macrophage dysregulation.

This study shows maternal smoking disrupts placental function by altering syncytiotrophoblast and macrophage biology, leading to fetal growth restriction.

Computational simulation of ecological drift for generating functional minimal microbiomes identifies key experimental and biotic factors influencing success

The paper uses computational simulations to study ecological drift in generating minimal microbiomes, identifying factors affecting their success.

Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells

The temporal analysis of gene regulatory networks in human neural stem cells reveals multiple early critical phases associated with cortical disorders and neuropsychiatric traits.

Frequency-dependent communication of information innetworks of non-oscillatory neurons in response to oscillatory inputs

This paper investigates how neuronal networks process oscillatory inputs using mathematical models and simulations, revealing frequency-dependent communication mechanisms and new phenomena like K-resonance and ΔΦ-phasonance.

Dissecting Molecular Origins of the Mechano-Adaptive Behaviors of Actomyosin Bundles

This study investigates how actomyosin bundles adapt to mechanical stress through experiments and simulations, revealing rate-dependent behaviors and key factors influencing their response.

In Silico Evaluation and Therapeutic Targeting of LVDD9B Protein for WSSV Inhibition: Molecular and Ecological Insights for Aquaculture Solutions

The paper evaluates the structural dynamics and interactions of LVDD9B protein with WSSV VP26 and identifies potential therapeutic compounds for antiviral therapy in aquaculture.

From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses

The paper uses imaging and simulations to estimate hindered diffusion rates in platelet masses, finding rates range from 2% to 40% of unhindered rates.