simulation

Computer-aided drug screening of anti-Neobenedenia melleni drugs based on annexin B1 in farmed pearl grouper

The paper screens anti-Neobenedenia melleni drugs using annexin B1 and identifies abamectin as effective with low toxicity.

Enhanced-Sampling Molecular Dynamics Recovers Rare Functional RNA Conformations Across Diverse Structural Contexts

This study compares enhanced sampling methods for RNA conformational sampling, finding T-REMD provides the most accurate ensembles and improves virtual screening.

A Premotor Excitation-Inhibition Motif Shapes Protopodium Dynamics During Drosophila Larval Forward Crawling

In Drosophila larvae, ventral oblique (VO) muscles drive protopodium folding, and a tri-segmental A27h–A18b3–A06c premotor excitation-inhibition motif restricts their activation to a late, forward-specific window.

antigen-prime: Simulating coupled genetic and antigenic evolution of influenza virus

The paper introduces a simulator called antigen-prime to model influenza virus evolution and benchmarks methods for variant assignment and growth rate estimation.

Membrane Phase, Charge, and Curvature Regulate α-Synuclein Binding Dynamics

This study investigates how membrane phase, charge, and curvature jointly regulate α-synuclein binding dynamics using experimental and simulation methods.

Metabolites form a globally connected chemical network across protein families

The paper analyzes protein-ligand interactions to show that ancient metabolites form a globally connected network across protein families, while non-ancient metabolites expand this network without disrupting its connectivity.

Eco-evolutionary dynamics in competitive systems: Rescue and murder

The paper simulates eco-evolutionary dynamics in one- and two-species systems, showing evolution can enable rescue in single-species systems but lead to evolutionary murder in multi-species systems.

Ancestors of Arylmalonate Decarboxylase show increased Activity, Stability and Stereoselectivity

Ancestral sequence reconstruction of a bacterial decarboxylase gave enzymes with up to 294-fold longer half-life at 45 °C, higher activity, and 99.7% ee on a vinyl malonate substrate.

SketchDNA: A GUI-Enabled Toolkit for Multiscale Modeling of Topological DNA Structures

SketchDNA provides a GUI tool for creating multiscale DNA models, enabling simulations of topological DNA structures and their dynamics.

Benchmarking Docking Protocols for GPCR Allosteric Modulators

This study benchmarks docking protocols for GPCR allosteric modulators using experimental structures and GaMD simulations, finding that ensemble re-ranking strategies improve early enrichment of known actives.

Anisotropic conductivity modeling for tDCS in Parkinsons disease using multidimensional diffusion MRI

tDCS fields from a multidimensional diffusion MRI conductivity model stayed within a few percent of DTI and isotropic predictions in 29 participants; whole-brain field instead tracked CSF fraction.

The cost-benefit trade-off of peritrichous flagellation in bacteria

This study quantifies the cost-benefit trade-off of peritrichous flagellation in Salmonella enterica, showing that increased flagellation reduces growth rate but enhances motility and competitive fitness in structured environments.

Redox heterogeneity as an engine of biodiversity: A quantitative murburn formalism for micro-oxic ecosystems

The paper develops a murburn formalism to explain how redox heterogeneity in micro-oxic environments drives biodiversity through dynamic fitness landscapes and coexistence.

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

Representation in genetic studies affects inference about genetic architecture

Across UK Biobank, All of Us and FinnGen, the inferred mean direction (sign bias) of rare minor-allele effects varies and is largely explained by each cohort's trait skewness.

DNA gyrase in live bacteria forms liquid condensates through weak multivalent bonding of excess GyrB

Live E. coli gyrase clusters hold excess GyrB (B:A 2.5:1), show hexanediol-sensitive liquid-like turnover, and docking suggests GyrB bridges heterotetramers.

Experimental and simulated FRAP for the quantitative determination of protein diffusion in helical cells

The paper develops a framework for quantitatively determining protein diffusion in helical cells using FRAP simulations and experiments, finding similar diffusion rates in helical and rod-shaped bacteria.

Interactions Underlying Stress Granule Structure and Therapeutic Dissolution

This study develops a minimal stress-granule model and uses simulations to identify small molecules that dissolve stress granules, aligning with experimental results.

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.

Reconstructing Prehistoric Waterscapes and Human Mobility during MIS 5 in North Africa

This study reconstructs human mobility patterns in North Africa during MIS 5 by analyzing climate-driven hydrological changes and their impact on landscape connectivity.

Collective Posterior Inference from Highly Variable Empirical Replicates

The paper introduces a method for fast and robust collective posterior inference from multiple noisy replicates, achieving state-of-the-art accuracy and efficiency.

stCNASim: Allele-aware spatial RNA-seq simulator enables systematic benchmarking of copy number inference

stCNASim is a spatial RNA-seq simulator that benchmarks copy number inference methods in spatial transcriptomics.

Phylogenetic inference from an incomplete fossil record

This study investigates how stratigraphic gaps affect phylogenetic inference using a simulation framework and finds that total-evidence analysis is robust to gap distribution but dominated by morphological character data.

Independent Mesh Realizations Introduce Percent-Level Variability in Temporal Interference Simulations

The paper quantifies variability in temporal interference simulations caused by non-deterministic mesh generation and shows that multi-run averaging reduces this noise.

Engineering Binding Efficiency and Interaction Stability of a Thermostable Cohesin-Dockerin Pair on the Bacterial Cell Surface

The paper improves the binding efficiency and interaction stability of thermophilic cohesin-dockerin pairs on bacterial cell surfaces using computational and experimental methods.

Stratigraphic Paleobiology of Carbonate Systems

Simulated tropical carbonate platforms and temperate ramps under identical sea-level forcing yield different fossil records: platform tops push apparent extinctions into transgressive tracts, while ramp unconformity bias fades gradually offshore.

Simulation-informed low-current anodal tDCS accelerates early motor recovery after photochemically induced cortical stroke in rats

This study shows that low-current anodal tDCS, calibrated to simulate human-equivalent weak electric fields, accelerates early motor recovery after photochemically induced cortical stroke in rats.

Dispersal mediates metapopulation response to local and regional stressors

This study uses a metapopulation simulation to show how dispersal interacts with landscape changes to affect species survival, highlighting the need for large-scale connectivity in conservation.

Continuous attractor circuits for decision making with Laplace-domain neural representations

This paper proposes a continuous attractor neural network model that implements decision making through complementary ramping and sequential neural responses, reproducing diffusion decision model behavior.

Flywheel Genomics: Simultaneous trait discovery and genetic gain in plant breeding

This paper introduces Flywheel Genomics, a framework that integrates trait discovery with rapid cycling breeding to improve plant breeding efficiency and genetic gain.