simulation

Simulation of neurotrophin receptor transmembrane helix interactions reveals active states and distinct signaling mechanisms

This study uses molecular dynamics simulations to identify active and inactive states of neurotrophin receptor transmembrane domains and suggests distinct signaling mechanisms for different receptors.

Quantifying the net effect of biodiversity on stability

The paper quantifies how biodiversity affects ecosystem stability using simulations and experiments, finding stability often exceeds expectations due to diversity.

Stimulus representation in human frontal cortex supports flexible control in working memory

The paper investigates how stimulus representation in the frontal cortex supports flexible control in working memory using fMRI and simulations.

Network-Based Kidney Allocation Simulation: Evaluating Organ Matching Strategies in Variable Hospital Networks

This paper presents a network-based kidney allocation simulation to evaluate matching strategies in realistic hospital networks, showing how network structure and policies affect transplant outcomes.

Structural and functional role of residues undergoing hereditary spastic paraplegias-linked mutations: insights from a simulation of the spiral to ring transition in katanin

The paper investigates how hereditary spastic paraplegia mutations affect katanin's conformational transition using molecular simulations, revealing that some mutations impact an intermediate state.

Principles and Operation of Virtual Brain Twins

This paper introduces Virtual Brain Twins (VBTs) as personalized digital brain models that integrate structural and functional data to improve understanding of brain function and support personalized treatment.

Discovery of Novel Trypanothione Reductase Inhibitors through Pharmacophore Modeling, virtual Screening and Molecular Dynamics Simulations. New insights for Human African Trypanosomiasis

The paper identifies two novel inhibitors of Trypanothione Reductase through pharmacophore modeling, virtual screening, and molecular dynamics simulations, showing better efficacy than Melarsoprol.

Stable coexistence and transport of lytic phage infections with migrating bacterial hosts

The paper shows how spatial interactions enable stable coexistence and transport of virulent phages with migrating bacteria, using theory, simulation, and experiments across multiple systems.

Rare-variant aggregate association analysis using imputed data is a powerful approach.

The paper evaluates the power of rare variant aggregate association analysis using imputed data and finds that imputation can detect significant associations even for ultra-rare variants, though with reduced power compared to sequence data.

Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis

The paper develops a multi-scale computational model of wound healing that simulates senescent cell dynamics and SASP profiles to understand their role in tissue repair and disease states.

Predicting Savings in the Metabolic Cost of Running With an Exotendon

This paper uses simulations to predict energy savings from exotendons at 4 m/s, finding that longer, stiffer designs offer greater savings than shorter, more compliant ones.

The Role of Ribose Modifications on the Structural Stability of Nucleotide Analogs with α-thiotriphosphate at the Active Site of SARS-CoV-2 RdRp

This study uses molecular dynamics simulations to investigate how ribose modifications interact with thio modifications in nucleotide analogs at the SARS-CoV-2 RdRp active site, revealing structural stability effects.

Pleiotropy accelerates tooth phenotypic and genomic evolution - An in silico study under the lens of development

This paper uses in silico evolution to study how pleiotropy affects genetic and phenotypic evolution, finding that it accelerates genetic divergence and promotes fitness improvements.

Aevol-9: A simulation platform to decipher the evolution of genome architecture

Aevol-9 simulates genome architecture evolution through mutational operators to study how evolutionary conditions affect genome organization.

Rules of engagement for condensins and cohesins guide mitotic chromosome formation

In DT40 cells, condensins displace extrusive cohesin, bypass cohesive cohesin and stall against each other while extruding ~1-3 kb/sec, yielding irregular helical chromatids of consecutive loops.

Induction of Chimera States in Hindmarsh-Rose Neurons through Astrocytic Modulation: Implications for Learning Mechanisms

This study shows astrocytes can convert hyper-synchronized neural states into chimera states in Hindmarsh-Rose neurons, suggesting a mechanism for restoring normal brain function in neurological disorders.

ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events

This study uses molecular dynamics simulations to show that ERK activation requires ordered phosphorylation events, with threonine phosphorylation as the second step being essential for catalytic activity.

Effect of very long-chain lipids on the organization of biological membranes: A simulation perspective

The paper uses simulations to study how very long-chain lipids affect membrane organization, finding gel-like domains form and exclude ergosterol.

Coevolving Residues Distant from the Ligand Binding Site are Involved in GAF Domain Function

The paper identifies two coevolving residues distant from the ligand binding site in GAF domains that are critical for allostery, using computational and experimental methods.

Current estimates of population resilience are not robust to the longer-term impacts of directional environmental shifts

The paper shows current resilience estimates fail to account for long-term environmental shifts, highlighting the need to consider resource allocation between survival and reproduction.

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion

Methods for simulations with thousands of interacting objects to model mass transport in the brain

The paper describes methods for simulating mass transport around thousands of interacting objects in the brain at nanoscale resolution, demonstrating accuracy with model geometries.

Intensifying marine heatwaves and limited protection threaten global kelp forests

The paper assesses future threats to global kelp forests from intensifying marine heatwaves and limited protection, finding increased exposure and low current conservation coverage.

Genetic basis of reproductive isolation in Torrey pine (Pinus torreyana Parry): insights from hybridization and adaptation

The paper identifies candidate loci for reproductive isolation in Torrey pine populations using GWAS and ddRADseq, finding SNPs associated with growth and fitness that may contribute to reproductive barriers.

The Arousal-Regulated Filter: Modulating Feedforward and Recurrent Dynamics for Adaptive Neural Tracking

This paper introduces the arousal-regulated filter (ARF), a computational model that links arousal effects on neural dynamics with behavioral and neurophysiological findings.

Employing Steered MD Simulations for Effective Virtual Screening: Active Pharmacophore Search by Dynamic Corrections to target MKK3-MYC Interactions

The paper uses steered MD simulations to screen small molecules targeting MKK3-MYC interactions, identifying compounds with promising binding affinities.

Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.

Charm simulates Hi-C-like data with chromosomal rearrangements to benchmark SV detection tools and provides a dataset for future benchmarking.

Simulation study of factors affecting the accuracy of transcriptome models under complex environments

This study identifies key factors affecting field transcriptome model accuracy through simulation and validation with real data, showing gene expression patterns, sample size, and environmental coverage are most influential.

Alternatives to photorespiration: A systems-level analysis reveals mechanisms of enhanced plant productivity

Modelling 12 alternative photorespiratory pathways predicts the largest carbon-export gains for carbon-fixing designs (TaCo); complete decarboxylation bypasses help mainly by releasing CO2 in chloroplasts, raising carboxylation and recapturing lost CO2.

Comparative study of protein X-ray and NMR structures: molecular docking-based virtual screening

This study compares X-ray and NMR protein structures in virtual ligand screening, finding X-ray structures generally perform better in ligand enrichment and binding-site configuration.