simulation

tMHG-Finder: Tree-guided Maximal Homologous Group Finder for Bacterial Genomes

tMHG-Finder uses Mash guide trees and consensus representative sequences to find maximal homologous groups in bacterial genomes with linear scaling, reaching F-score 0.932 on simulated data.

Efficient incorporation of dendrites into a large-scale cortical model reveals their surprising role in sharpening optogenetic responses

The paper uses simulations to show dendrites sharpen optogenetic responses in cortex, improving spatial fidelity of stimulation.

Cortex Folding by Combined Progenitor Expansion and Adhesion-Controlled Neuronal Migration

The paper shows that combining progenitor expansion with adhesion-controlled neuronal migration enhances cortex folding in mice, leading to sulci and gyri formation.

Interplay of immigration and coevolution constrains the structure of specialist-generalist communities

This study examines how coevolution and immigration shape specialist-generalist community structures, finding that evolutionary rates and dispersal influence diversity and community composition.

Self-Assembling Synthetic Peptides Remodel Mitochondrial Properties via Nanopore Formation

This paper demonstrates that synthetic peptides can target mitochondria, form nanopores, and alter mitochondrial function through self-assembly.

Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria

This paper models recombination's impact on multi-drug resistance evolution in malaria, showing that most recombinant genotypes arise from multi-clonal infections and that ACT strategies reduce treatment failures and delay resistance.

In vitro Pharmacological Evaluation, In silico pharmacokinetics and TOPKAT validation of Eichhornia crassipes: Formulation of a Collagen-Based Matrix for Wound Healing Applications

This study evaluates the pharmacological properties of Eichhornia crassipes extract, validates its drug-like potential using in silico methods, and formulates a collagen-based matrix for wound healing.

The Role of Purine Interactions in Biogenic Crystal Shape Determination

This paper investigates how purine interactions regulate crystal shape in zebrafish iridosomes, finding that crystal growth along the b-axis is controlled by purine molecular interactions.

An AlphaFold guided model for the evolution of the CaMKII interactome

The paper analyzes the evolution of the CaMKII interactome across species using 3D structures and transcriptome data, finding conservation of activation machinery and reduced co-expression in simpler organisms.

The promise and peril of comparing fluorescence lifetime in biology revealed by simulations

This paper introduces FLiSimBA, a simulation framework to analyze fluorescence lifetime data, revealing limitations and proposing advancements in FLIM for biological applications.

Early-stage sparse testing strategies to increase genetic gain in plant breeding programmes

This paper shows that early-stage sparse testing strategies increase genetic gain in plant breeding by improving selection accuracy and intensity through broader TPE sampling and reduced replication.

Quantifying Effects of Dataset Size, Data Variability, and Data Curvature on Modelling of Simulated Age-Related Motor Development Data

This study simulates motor performance data to assess how dataset size, variability, and curvature affect model accuracy and repeatability in children and youth.

Thinging Through Modelling. Active Inference Meets Material Engagement

This paper uses Active Inference to simulate and explore the concept of thinging in Material Engagement Theory, showing how creative processes minimize internal model complexity through material engagement.

The impact of insertion bias into piRNA clusters on the invasion of transposable elements

This study uses simulations to show that transposable element insertion bias into piRNA clusters can alter invasion dynamics but is generally not beneficial for TE spread, with limited scenarios where it might be advantageous.

Deciphering binding site conformational variability of substrate promiscuous and specialist enzymes

The paper investigates the role of active site conformational flexibility in substrate promiscuity by comparing promiscuous and specialist enzymes using molecular dynamics simulations and tICA.

Causal single-cell RNA-seq simulation, in silico perturbation, and GRN inference benchmarking using GRouNdGAN-Toolkit

The paper introduces GRouNdGAN-Toolkit, a toolkit for simulating scRNA-seq data and benchmarking GRN inference methods using causal generative models.

Anticipating others' future behaviours alters collective movement and enhances survival

The paper simulates the impact of anticipatory abilities on collective animal movement and shows that anticipation can provide a survival advantage.

Helix-to-Beta-Sheet Transition Drives Self-Assembly of Glutamate Transporter EAA1 Splice Peptides

The paper characterizes truncated isoforms of the glutamate transporter EAA1, showing they self-assemble into β-sheet oligomers and may contribute to neurodegeneration.

A hierarchical multiscale model of forward and backward alpha-band traveling waves in the visual system

This paper presents a multi-scale network model of alpha-band traveling waves in the visual system, showing how forward and backward waves arise from distinct sub-networks and are influenced by pulvinar engagement.

When Firing Rate Falls Short: Spike Synchrony Reliably Disentangles Stimulus Saliency and Familiarity

The paper shows spike synchrony reliably detects stimulus familiarity while firing rate detects stimulus class, demonstrating complementary coding mechanisms in neural computation.

Geometry effects on protein mobility in a synapse

This study uses in silico FRAP experiments to analyze how synaptic geometry and protein-vesicle binding affect protein mobility, identifying two key mechanisms influencing recovery times.

Function aligns with geometry in locally connected neuronal networks

The paper shows functional connectivity gradients in zebrafish brains align with geometric eigenmodes when connectivity is local, but this alignment breaks down with more long-range connections.

Multiple, not single, recipient muscle tendon transfers produce well-directed thumb-tip forces in lateral pinch grasp: a simulation study with application to restoration of improved grasp after tetraplegia

The paper uses simulation to show that multi-site tendon transfers can produce better-directed thumb-tip forces than single-site transfers for lateral pinch grasp in tetraplegia.

Cooperativity in septin polymerization is tunable by ionic strength and membrane adsorption

This study investigates how ionic strength and membrane adsorption influence septin polymerization, showing salt-dependent cooperativity and context-dependent assembly modes.

Multi-scale Simulations of MUT-16 Scaffold Protein Phase Separation and Client Recognition

This study uses multiscale simulations to investigate MUT-16 phase separation and its role in recruiting MUT-8, confirming key interactions through in vitro experiments.

Enhanced beta power emerges from simulated parkinsonian primary motorcortex

The paper simulates Parkinson's disease effects on primary motor cortex neurons, showing increased beta band power in simulated networks.

mzrtsim: Raw Data Simulation for Reproducible Gas/Liquid Chromatography Mass Spectrometry Based Non-targeted Metabolomics Data Analysis

The paper introduces mzrtsim, an R package that simulates raw metabolomics data for comparing software tools against a ground truth.

Targeting the CAPON-NOS Axis: A Computational Strategy for Small Molecule Modulator Discovery

This paper identifies two small-molecule hits targeting the nNOS/CAPON interface using virtual screening and introduces computational tools for structure-based drug discovery.

Shape and rate of landscape change trajectories influence species persistence

This study shows that species persistence in changing landscapes depends on historical habitat trajectories and the rate of landscape change, not just current conditions.

The integration of network biology and pharmacophore modeling suggests repurposing Clindamycin as an inhibitor of pyroptosis via Caspase-1 blockage in tumor-associated macrophages

The paper identifies Clindamycin as a potential inhibitor of pyroptosis in tumor-associated macrophages by integrating network biology and pharmacophore modeling.