simulation

Identification of Prospective PETases Across Prokaryotes Using an in silico Approach

The paper identifies eight prospective PETases from prokaryotes using in silico methods, with three showing structural and functional similarity to PETase from Ideonella sakaiensis.

Structural and Computational Analysis of Pseudomonas Aeruginosa DNA Gyrase Reveals Molecular Characteristics That May Contribute to Ciprofloxacin Resistance

The paper analyzes the molecular mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa by solving the gyrase structure and performing MD simulations of wild-type and mutant systems.

Longitudinal Live Imaging Derived 4D Hemodynamics and Dynamic Tissue Mechanics Across Outflow Tract Morphogenesis

The paper uses 4D CFD simulations to study hemodynamics and tissue mechanics in the cardiac outflow tract during development, revealing correlations between wall shear stress and tissue extension.

Integration of In Vitro and In Silico Approaches Enables Prediction of Drug-Induced Liver Injury

Dividing Cmax by lowest in vitro toxicity potency separates drugs by liver-injury (DILI) risk, AUC up to 96%; PBK-predicted Cmax without clinical data reaches 91%.

On the Accuracy of Internal Circadian Time Prediction Methods from a Single Sample

The paper evaluates ICT prediction methods using single samples and finds ZT outperforms models, but TimeSignature can surpass ZT with additional predictors.

A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics

This paper compares statistical methods for differential gene expression in spatial transcriptomics, finding that the GEE framework better controls false positives than the Wilcoxon test.

Tension shapes memory: Computational insights into neural plasticity

This paper presents a spiking neural network model showing how mechanical tension affects memory recall speed, inter-regional synchrony, and memory association in neural networks.

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

This study uses neutron crystallography and simulations to analyze proton sharing in low-barrier hydrogen bonds in DJ-1 and YajL, showing how mutations affect proton delocalization and mobility.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

Compression Efficiency and Structural Learning as a Computational Model of DLN Cognitive Stages

The paper evaluates a computational model of cognitive stages using a bandit-like simulation, showing Network policies outperform Linear policies in utility with shared latent structures.

Quantifying transmembrane water exchange by diffusion NMR methods: From yeast cells to optic nerve ex vivo

This paper compares two diffusion NMR methods for measuring water exchange in yeast cells and optic nerves, finding differences in results that suggest more complex compartmental models are needed for accurate analysis.

Rapid gene exchange explains differences in bacterial pangenome structure

The paper develops a model to analyze pangenome dynamics and finds that differences in bacterial pangenomes are mainly due to variation in the number of rapidly exchanged genes.

SIMULATING TUMOR MITOCHONDRIAL ENERGETICS THROUGH ENGINEERING-STYLE ENERGY METRICS

The paper develops a simulation framework using engineering energy metrics to quantify mitochondrial bioenergetics changes in tumors and immune cells after mitochondrial transfer.

The rate of identical-by-descent segment sharing between close and distant relatives

The paper simulates IBD segment sharing between relatives and finds that sharing rates drop significantly with genetic distance, with most distant relatives sharing no IBD segments.

Unraveling the Mechanistic Links Between Blood Pressure Regulation and Calcium-Magnesium Homeostasis: Insights into Hypertension, Hyperparathyroidism, and Mineral Disorders

This study develops a computational model of blood pressure regulation and calcium-magnesium homeostasis in rats, showing how disruptions in these systems affect each other and contribute to hypertension and hyperparathyroidism.

Habitat fragmentation controls bacterial community composition outcomes

This study shows that habitat fragmentation increases bacterial community evenness and species coexistence by creating isolated microhabitats with varying taxa compositions.

A Multiscale Model of Collective Decision-Making in Hybrid Aspen Tree Tissues Describes Bud-Dormancy Break

The paper develops a multiscale model of bud-dormancy break in hybrid aspen trees, showing how tissue-level decisions are influenced by both cellular interactions and organismal constraints.

The genetic architecture of local adaptation is historically contingent

This study uses simulations to show how ecological and genetic factors shape the genetic architecture of local adaptation, highlighting the role of demographic history and allele age in genotype-environmental associations.

Out with the Old: Contrasting Histone Marks are Associated with Dosage Compensation on the Ancient and New Z of a Moth with Complex Sex Chromosomes

This study investigates dosage compensation mechanisms on sex chromosomes in a moth, revealing distinct patterns on ancestral and neo-sex chromosomes and suggesting new mechanisms evolved in neo-sex chromosomes.

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm

The paper discovers a novel chromatin folding structure, compartment S, in the silkworm Bombyx mori using Hi-C, showing unique loop extrusion and contact patterns.

Xeno amino acid alphabets form peptides with familiar secondary structure

The paper shows that peptides made from non-standard amino acids can form protein-like secondary structures, expanding the known sequence-structure space beyond Earth's 20 amino acids.

Integrative modelling reveals the structure of the human Mic60-Mic19 subcomplex and its role as a diffusion barrier in mitochondria

The paper uses integrative structural biology to model the human Mic60-Mic19 subcomplex and validate its role as a diffusion barrier in mitochondrial crista junctions.

Benchmarking remote sensing methods to capture plant functional diversity from space

This study benchmarks remote sensing methods to estimate plant functional diversity using synthetic data from BOSSE, identifying optimal metrics, variables, and validation strategies.

Epithelial-mesenchymal transition couples with cell cycle arrest at various stages

The paper shows that EMT paths are influenced by cell cycle phase coupling and highlights the limitations of low-dimensional representations in capturing transition dynamics.

Wetting-mediated extracellular phase separation drives long-range cell adhesion

The paper identifies a physical mechanism, liquid-like adhesion by phase separation (LAPS), that enables long-range cell adhesion through dynamic wetting layers, independent of classical receptor-ligand binding.

Virtual prototyping of non-invasive spinal cord electrical stimulation targeting upper limb motor function

The paper develops a computational model to simulate tSCS effects on motor function, finding that somatosensory afferents have lower thresholds than motor efferents, and that anode placement and waveform type influence recruitment patterns.

Biomechanical simplification of the motor control of whisking

The paper investigates how the biomechanics of the rat whisker array simplify motor control during whisking by simulating uniform motor commands and analyzing resulting movements.

3D Microscale Mechanical Simulations of Hydrogel Coated Electrospun Meshes

This paper uses 3D microscale mechanical simulations to predict bulk mechanical properties of hydrogel-coated electrospun meshes, revealing non-affine deformations and stress-strain differences.

2D spatial tissue analysis often misrepresents true biological patterns of 3D tissues

This study shows that 2D spatial analysis of tissues often leads to spurious associations and misrepresentation of 3D biological patterns.

A Realistic Simulation Framework for EvaluatingMicrobiome Normalization in Sample Stratification and Differential Abundance

The paper introduces a simulation framework to evaluate microbiome normalization methods' impact on sample stratification and differential abundance across taxonomic levels.