simulation

Invasion analysis for structured populations: analytical principles and numerical workflows

The paper develops a framework for analyzing invasion in structured populations using analytical and numerical methods to determine invasion success across different ecological scenarios.

Electrostatic control of conformational dynamics drives proton translocation in respiratory Complex I

The paper investigates how electrostatic interactions control conformational changes and proton translocation in Complex I using a combination of experimental and computational methods.

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

Laminin-Derived Peptides Bind Neuropilin-1 at the VEGF-A165 Binding Pocket

The paper investigates whether laminin-derived peptides bind to the VEGF-A165 binding pocket of NRP-1 using computational and experimental methods, finding that peptide 1 has the highest binding occupancy.

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.

Ecological networks balance connectivity with flexibility to perturbations

Across 1,569 food-web, mutualistic and host–parasite networks, connectance falls as S^−0.65 while links per species rise; a diffusion-efficiency metric places networks near a local optimum.

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

Lipopolysaccharide chain length and coat assembly keep guanylate-binding proteins upright on bacterial membranes

This study uses molecular dynamics simulations to show that open-state GBP1 and GBP2 require specific membrane environments to remain stable on bacterial membranes.

Somatic variant detection using an individual-specific pangenome reference: a case study of a pediatric acute myeloid leukemia patient

This study evaluates the impact of an individual-specific pangenome on somatic variant calling in a pediatric AML patient, finding reduced false positives and altered phylogenetic branching.

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.

Thermodynamic Model and Experiments Indicate Kinetically Trapped States in Ionisable Lipid Nanoparticles

This study combines experiments and simulations to develop a continuum model explaining pH-dependent mesophase transitions in ionizable lipid nanoparticles and identifies metastable states.

Linking clinical border morphology to cell-scale growth mechanisms in melanoma: a segmentation-to-simulation alignment study

Across 1,581 ISIC 2018 lesions, melanoma borders differ from nevi mainly by coarse lobulation rather than fractal dimension; of six simulated mechanisms, only an imposed long-range growth-rate field reproduces this.

Coordinated Drift of Image Representations in Human EEG

The paper investigates drift in human EEG responses to images across sessions, finding coordinated drift along image identity dimensions and preserved global structure.

Predictive adequacy and measurement dependence of metabolic representations in controlled synthetic systems

The paper evaluates metabolic representations in synthetic systems, finding that adequacy, compactness, and responsiveness are distinct properties, and adequacy certification does not guarantee predictive accuracy.

Early bird dynamics reduce selection imposed by species interactions in boom-and-bust regimes

The paper shows that boom-and-bust growth regimes reduce selection from species interactions that affect growth rates but not from interactions that affect mortality.

Mixtures of stably coexisting species overyield

In generalized Lotka–Volterra communities, stable coexistence almost always requires overyielding; in four long-term biodiversity experiments, underyielding raised species-loss odds within two observations (pooled odds ratio 2.61).

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.

Human prion proteins and mutants through the lens of systems biology

The paper uses network analysis, MD simulations, and experiments to identify critical residues in human PrP that affect structural stability and misfolding.

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.

Examining the Atypical Structure Adopted by the 37-51 Segment of α-synuclein in the Early Stage of Aggregation

This study uses molecular dynamics simulations to identify a previously unreported braid conformation in the 37-51 segment of α-synuclein that may influence aggregation.

Direct engagement of mycobacterial RadA by c-di-AMP at a non-catalytic site suppresses its DNA-stimulated ATPase activity

This study shows c-di-AMP binds to Mycobacterium smegmatis RadA at a non-catalytic site, reducing its DNA-stimulated ATPase activity.

Computational Profiling and Pathogenicity Assessment of VHL Missense Mutations

This study assesses the pathogenicity of VHL missense mutations using AlphaMissense, protein stability simulations, and molecular dynamics to identify critical regions and mutation effects.

An Efficient Implicit Tau-Leaping Method for Estimating Second-Order Sensitivities of Stiff Stochastic Biochemical Systems

The paper introduces an efficient implicit tau-leaping method to estimate second-order sensitivities of stiff stochastic biochemical systems, achieving comparable accuracy with reduced computational cost.

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

From Coral Color to Tissue Heating: How Host Pigments Redirect Light Within the Tissue

The paper models how coral host pigments affect light propagation and tissue heating, showing distinct roles of chromoproteins and fluorescent proteins in energy distribution and heat generation.

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

Integrating Genetic Domestication and Model-Guided Kill-Switch Engineering in a Non-Model Bacterial Therapeutic

Host-measured parts and inducible systems for Brucella melitensis ΔvjbR guided a modeled Cas9 kill-switch, which cut mouse liver bacterial burden by about 91% at 30 mg/kg doxycycline.

Mechanistic Insights into Adaptive Binding of Vitamins and Hormones at Hotspot-Enriched Interfaces of the Synaptotagmin 1 C2AB Domain

This study investigates the adaptive binding of seven molecules to the Synaptotagmin 1 C2AB domain using molecular docking and simulations, revealing that desolvation and structural flexibility, not just binding energy, govern ligand interactions.

Synaptotagmin-mediated plasma membrane homeostasis is required to recruit the endocytic machinery during cold stress

This study shows that SYT1 and SYT3 are essential for maintaining endocytosis during cold stress in Arabidopsis by preserving membrane composition and TPC subunit association.

Hemodynamic-Structural Multi-Fidelity Assessment of Endovascular Flow Diversion Strategies for Cerebral Aneurysm Treatment: An Integrated Computational and Experimental Framework

The paper evaluates hemodynamic and structural outcomes of endovascular flow diversion strategies for cerebral aneurysms using computational models and experimental tests.