simulation

Neural dynamics for working memory and evidence integration during olfactory navigation in Drosophila

This study identifies a specific group of neurons in Drosophila that exhibit working memory and evidence integration during olfactory navigation, showing their role in maintaining goal-directed behavior after odor loss.

Parameterization of the PA endonuclease bimetallic center reveals the dynamics of clinically relevant mutations

This study benchmarks metal-parameterization strategies for simulating the PAN endonuclease domain to understand resistance mutations in influenza virus.

Magic traits, search costs, and the persistence of species in secondary contact

The paper simulates secondary contact between populations to show how search costs and pleiotropy affect mating trait differentiation and species persistence.

Recombination on 'non-recombining' sex chromosomes: empirical insights from the blackspotted stickleback

The paper identifies a recombination event within a non-recombining sex chromosome in blackspotted sticklebacks, challenging the notion that recombination suppression is irreversible.

Statistical tests for bivariate spatial association across multi-omics data with disjoint coordinates

Autocorrelation-aware bivariate Moran's I, bivariate Gaussian process tests and generalized additive models (R package sbivar) test cross-modality colocalisation on disjoint coordinates; many existing permutation tests inflate false positives.

Conformational dynamics of exopolysaccharides underlie biofilm matrix mechanics in Vibrio cholerae

This study characterizes the physical properties and conformational dynamics of Vibrio cholerae exopolysaccharides to understand their role in biofilm matrix mechanics.

Inferring and simulating a gene regulatory network for the sympathoadrenal differentiation from single-cell transcriptomics in human.

The paper infers and simulates a gene regulatory network for sympathoadrenal differentiation using single-cell RNA-seq data from human cells, identifying a 97-gene network that drives the transition from Schwann cell precursors to chromaffin cells and sympathoblasts.

Convergent Cysteine Enrichment in Diverse Gut Phage Capsids Suggests Gut-Associated Structural Adaptation

The paper identifies convergent cysteine enrichment in gut phage MCPs, suggesting structural adaptations for capsid stability in the gut environment.

Bacterial RNA polymerase exemplifies a general physical mechanism for accelerating protein-DNA association

The paper shows that bacterial RNA polymerase's C-terminal domains accelerate DNA binding through a physical mechanism involving flexible tethers.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations

This study uses weighted ensemble simulations to assess how molecular glues stabilize protein-protein interactions, showing distinct behaviors that correlate with reported EC50 values.

The contribution of non-additive genetic effects to the genetic variance of polyploid species.

This study investigates how genome doubling affects genetic variance in polyploid species, finding that genetic variance generally decreases, though non-additive effects can increase diversity in some cases.

Thousandfold Expansion Microscopy

A four-network sodium acrylate/dimethylacrylamide hydrogel, cast ionic-within-ionic without neutral re-embedding, reaches about 1000-fold linear expansion and resolves individual peptide residues on standard confocal microscopes.

A Composite Endomembrane Suspension Governs Cytoplasm Rheology

The paper investigates how composite endomembrane suspensions in eukaryotic cells contribute to cytoplasm rheology, finding that ER structures enable viscoelastic properties through yolk flocculation.

UniFlow: Unifying protein conformational ensemble generation and machine-learned force fields with a scalable normalizing Flow

A normalizing flow over backbone internal-coordinate angles generates protein ensembles comparable to BioEmu in one step and doubles as a differentiable coarse-grained potential for Langevin dynamics.

Computational simulations reproduce in vivo population receptive field mapping fMRI results

The paper shows that large-scale simulations can replicate in vivo pRF mapping variability patterns, offering insights into retinotopic mapping paradigms.

The ecology of remembering and forgetting: quantity-quality trade-offs in the spatiotemporal memory of a forager

This study uses simulations to show that memory trade-offs between quantity and quality affect foraging efficiency, with larger memory not always being beneficial in certain environments.

Synth4bench: Synthetic Data Generation for Benchmarking Tumor-Only Somatic Variant Calling Algorithms

The paper develops synth4bench, a synthetic data pipeline to benchmark tumor-only somatic variant callers, revealing inconsistencies in tool performance and highlighting the need for sequencing optimization and caller selection.

Do we understand orientation selectivity? A simulation study

This study shows that current mechanisms for orientation selectivity in the visual cortex fail in realistic models, suggesting homeostatic plasticity may be necessary.

Computational design of a multi-epitope vaccine against M. tuberculosis

The paper designs a multi-epitope vaccine against M. tuberculosis using computational methods, showing strong structural quality and simulated immune responses.

Representational capacity shapes both the "whether" and "how" of social learning

This paper uses simulations to show that social learning benefits are strongest for populations with moderate information-processing capacity, and that learning strategies shift from success bias to conformism as capacity increases.

Modeling breeding programs considering social behavior in large groups of farmed fish

This study evaluates how social interactions affect fish breeding programs through stochastic simulations, showing increased phenotypic variability and altered genetic gains under different selection strategies.

Multimolecular proofreading overcomes the activity-fidelity trade-off

The paper designs a multimolecular proofreading circuit that overcomes the activity-fidelity trade-off in synthetic biological systems.

Biomarker Variability Limits Individualized Amyloid Time Estimation in Alzheimer Disease

This study evaluates how biomarker variability affects individualized amyloid time estimation in Alzheimer's disease, finding that inter-individual variability is the main source of error.

Impact of mitochondrial fission and fusion onneuronal health and incidence of dementia

This study uses simulation models to show that high rates of mitochondrial DNA mixing increase neuron loss and dementia risk, but selective mitophagy can prevent this, contradicting observations of normal aging.

Simulations show increased lipid interdigitation in transmembrane coupling of protein condensates

The paper uses simulations to show that increased lipid interdigitation mediates transbilayer coupling of protein condensates by reducing lipid entropy and altering membrane curvature.

Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohns disease

A realistic in-silico brain phantom for quantifying susceptibility anisotropy-induced error in susceptibility separation

The paper creates an in-silico brain phantom to evaluate how susceptibility anisotropy affects susceptibility separation algorithms, finding increased error in negative susceptibility estimates with anisotropy.

VLab4Mic: prediction of structural resolvability in super-resolution microscopy

VLab4Mic predicts structural resolvability in super-resolution microscopy by simulating imaging configurations and comparing results to experimental data.

The mammalian muscle spindle as a tunable feedback controller in locomotion

This paper develops a biophysical model of the muscle spindle to simulate how gamma motor neuron drive modulates spindle firing during locomotion, revealing its role as a tunable feedback controller.