simulation

A novel phylogenetic comparative model reveals strong signals for early high disparity in ichthyosaurs

Combining Early Burst and Ornstein-Uhlenbeck processes, an Early High Disparity model best fits ichthyosaur skull length across 108 phylogenies, placing median peak disparity at 231.1 Ma.

NeuWalk: A Python Library for Data-Driven Synthesis of Neuron Morphologies Using Random Walks

NeuWalk synthesizes neuron morphologies using random walks, validated against real neurons with statistical similarity in key metrics.

From seven combination hypotheses to one testable interaction: a gated agentic AI QSP workflow applied to healthy ageing interventions

The paper develops a gated agentic AI QSP workflow to evaluate healthy ageing interventions, resulting in a single testable interaction and a trial design with an audit trail of discarded hypotheses.

Growth-Aware Optogenetic Control for Cross-Scale Disturbance Rejection in Bacterial Batch Cultures

The paper develops growth-aware optogenetic control strategies to maintain gene expression in bacterial batch cultures under population-level disturbances.

Evaluating Clustering and Imputation Approaches for Multivariate Longitudinal Clinical Data Using a Real-World eCDF-Copula Resampling Framework

The paper evaluates clustering methods for multivariate longitudinal data using a real-world eCDF-Copula resampling framework to address missing data and improve benchmarking.

Emergence of mutants in bacterial populations: a simulation-based approach for parameter inference in extended Luria & Delbru&x0308;ck scenarios

This paper introduces a simulation-based method to infer mutation rates and fitness effects in bacterial populations, accounting for ecological complexities not handled by traditional models.

Loss of Cerebral Autoregulation After Stroke Drives Abnormal Perfusion Patterns

This study develops an in silico model to simulate cerebral blood flow in mice with and without leptomeningeal collaterals, showing that myogenic reactivity, not collateral extent, drives hyperperfusion after stroke.

Mice adapt their learning rate to stochasticity and volatility through a simple heuristic

The paper shows mice adjust their learning rate based on environmental volatility and stochasticity in a probabilistic reversal task, using a meta-learning rule that captures these dependencies.

Integrative proteomic analysis and molecular dynamics simulations of ANKLE2 reveal mechanisms of microcephaly

The paper uses proteomic analysis and molecular dynamics simulations to uncover how ANKLE2 mutations disrupt protein interactions and phosphorylation, leading to microcephaly.

Rapid spatial cognition in mice, with and without neocortex and hippocampus

Naive mice learn a 9-turn route in a reconfigurable 3D maze within about 20 rewards; mutants lacking neocortex and hippocampus also learn, remember and generalize, though early exploration is inefficient.

Associative synaptic plasticity creates dynamic persistent activity

The paper shows that coupling neuronal and synaptic dynamics in recurrent networks enables persistent oscillations, a dynamic form of memory without explicit storage or retrieval.

Transmembrane coupling of protein condensates via membrane-mediated interactions: A simulation study

This paper uses simulations to study how protein condensates on opposite sides of a membrane interact via membrane-mediated forces, finding that curvature plays a major role in their coupling.

Experiment-anchored abundance-coverage frontiers define conditional RHSVV exposure requirements in TP53-missense tumors

Experiment-anchored sweep of p53 abundance thresholds in CPTAC TP53-missense tumors maps how much RHSVV exposure contrast is needed as target coverage falls.

Prion Protein Deficiency Results in Synaptic, Neural Network and Behavioral Alterations

Lifelong prion protein (PrP) loss in mice lowers excitatory synaptic proteins, makes network bursts in mature cortical cultures rarer and neuronal activity more correlated, and increases adult dimming-disk escapes.

SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences

SCAR introduces controlled mutations, fragmentation, and damage to sequencing data for benchmarking analyses affected by these factors.

Senescence-associated KRAS upregulation in peripheral T cells links to premature coronary artery disease

The paper identifies KRAS upregulation in senescent CD8+ T cells as linked to premature coronary artery disease through single-cell and bulk transcriptomic analyses.

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

The paper identifies widespread mosaic structural variants in normal human tissues and tumors, with repeat-mediated variants impacting functional elements and enabling noninvasive tumor monitoring through cell-free DNA.

The Apolipoprotein E N-Terminal Bundle Rendered Membrane-Compatible by Reverse-QTY Conversion Without Loss of Fold

This paper converts the N-terminal bundle of Apolipoprotein E to be membrane-compatible using reverse-QTY substitutions without altering its fold, demonstrating preserved helix content and increased hydrophobicity.

AnnoAudit: a marker-based protocol for auditing single-cell atlas annotations reveals systematic, state-dependent annotation failure in a widely used traumatic brain injury resource

A marker audit finds 97.9% of CEREBRI's 45,051 official 'glutamatergic neuron' cells are not glutamatergic (four-check composite 82.6%), creating false ion-channel and OXPHOS signals; true neurons show acute KCNC3 up-regulation.

Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling

The paper develops a multiscale model to study how conformational dynamics regulate the PP1-GADD34-eIF2 complex, showing folding-dependent assembly enhances biochemical function.

Combining CHARMM36m with OPC water improves accuracy

This paper assesses the accuracy of different force field combinations for simulating intrinsically disordered proteins and finds that combining C36m with OPC water improves accuracy for IDPs without compromising globular protein simulations.

The building blocks of social structure: simulating constraints of social network analysis for inference about group-level properties

This paper builds a model to simulate social network data and shows how changes in underlying behavioural processes affect global network metrics in animal social systems.

Selection mode changes the fate of nearly neutral deleterious mutations

This study shows that competitive soft selection can purge recessive deleterious mutations that are nearly neutral under hard selection, reducing genetic load and inbreeding depression.

Performance of Rilpivirine-Based Hydrophobic Tags and PROTACs Directed Against HIV-1 Reverse Transcriptase

The paper evaluates rilpivirine-based hydrophobic tags and PROTACs for HIV-1 RT degradation, finding that PEG4-Ad shows low nanomolar potency but limited efficacy against resistance mutations.

Euchromatin forms condensed domains with short active regions on the surface

The paper develops a simulation framework to infer nucleosome-resolution chromatin structures from RCMC data, revealing euchromatin as condensed domains with accessible promoter/enhancer regions.

Computational Framework for Identifying Ion Channel Mutation-Compensating Interventions

The paper presents a computational framework to identify interventions that compensate for ion channel mutations by modulating other conductances, demonstrating feasibility through simulations and a differentiable Hodgkin-Huxley model.

A water-pinning hotspot drives templated tau aggregation

In a minimal tau fibril model, residue 300/301 binds incoming peptide first and carries the most release-prone hydration water. Spin-labelling site 300 impairs locking and suppresses seeded growth.

Shedding light on Gaussia Luciferase conformational space using multi-conformation enhanced sampling simulation

This study uses enhanced sampling simulations to explore the conformational space of Gaussia luciferase, revealing structural dynamics and substrate-binding features not captured by existing methods.

Inversion characterization in Timema stick insects: from local PCA to pangenome approaches

The paper evaluates methods for detecting and characterizing inversions in Timema stick insects, showing differences in their ability to identify and describe inversion structures.

Rewiring Oncogenic Transcriptional Complexes with Domain-ALTerAtion Chimeras (DALTACs) in Prostate Cancer

A bifunctional AR–p300/CBP molecule, DALTAC-1, forces a non-native contact between AR and p300 domains, silences AR enhancers and regresses AR-driven prostate tumors in mice while sparing AR-negative lines.