simulation

Modelling trypanosome motility

This study develops a trypanosome model and uses hydrodynamic simulations to analyze how mechanical features affect swimming behavior, showing the importance of body elasticity and flagellum dynamics.

Differential conformational expansion of Nup98-HOXA9 oncoprotein in micro- and macrophases

This study examines the conformational changes of Nup98-HOXA9's FG domain across different assembly states, revealing micelle-like structures and dynamic transitions during condensate formation.

Automated inference of disease mechanisms in patient-hiPSC-derived neuronal networks

This study uses simulation-based inference to automatically identify molecular mechanisms from patient-derived neuronal network activity measured by MEA.

Depth-Dependent Contributions of Various Vascular Zones to Cerebral Autoregulation and Functional; Hyperemia: An In-Silico Analysis

This paper develops an in-silico model of the mouse cerebrovasculature to analyze how different vascular zones contribute to cerebral autoregulation and functional hyperemia across cortical depths.

Activation of Wnt/β-catenin signalling by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary gland basal cell adenoma

Exome and transcriptome sequencing of salivary basal cell adenomas reveals a recurrent FBXW11 p.F517S mutation, exclusive with CTNNB1 p.I35T, together accounting for 94% of cases.

Pharmacophore modeling, 2D-QSAR, Molecular Docking and ADME studies for the discovery of inhibitors of PBP2a in MRSA

The paper identifies potential inhibitors of PBP2a in MRSA using pharmacophore modeling, 2D-QSAR, docking, and MD simulations, highlighting two compounds with favorable ADME properties and binding potential.

Binder and monomer valencies determine the extent of collapse and reswelling of chromatin

This study uses simulations to show that binder valency drives chromatin collapse while monomer valency determines reswelling, with two distinct mechanisms identified.

The Neuromusculoskeletal Modeling Pipeline: MATLAB-based Model Personalization and Treatment Optimization Functionality for OpenSim

MATLAB toolsets add joint, muscle, synergy, and foot-contact personalization and optimal-control treatment design to OpenSim; one post-stroke case predicted 60% faster walking at equal metabolic cost.

The cost of data aggregation: spatiotemporal compression obscures causal attribution in biodiversity monitoring

This study shows that aggregating spatiotemporal biodiversity data reduces causal inference accuracy, with full-resolution models outperforming compressed time series and distribution models.

Off-target interaction of the amyloid PET imaging tracer PiB with acetylcholinesterase

This study shows that the amyloid PET tracer PiB interacts with acetylcholinesterase, potentially affecting PET signal interpretation in Alzheimer's disease.

Integrating experiments and simulations to unravel coacervate-membrane interactions: Insights into de-mixing and morphology modulation

This study combines experiments and simulations to investigate how coacervate-membrane interactions affect membrane morphology and fluidity, showing that anionic lipid content modulates these effects.

Factors influencing the accuracy and precision in dating single gene trees

This study benchmarks molecular dating accuracy for single gene trees, identifying factors like alignment length, rate heterogeneity, and selection pressure that affect divergence time estimation.

A freely accessible, adaptable hollow-fiber setup to reproduce first-order absorption: illustration with linezolid cerebrospinal fluid pharmacokinetic data

Splitting each dose into equal-amount continuous infusions of varying duration, computed by a new algorithm, lets a standard hollow-fiber model reproduce linezolid CSF pharmacokinetics within 20% of target parameters.

Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1

The paper identifies small molecule modulators of TMC1 channels using structure-based screening and validates their effects on dye uptake in cochlear explants.

Caveolin assemblies displace one bilayer leaflet to organize and bend membranes

This paper investigates how the CAV1-8S caveolin complex interacts with lipid membranes through a novel leaflet replacement mechanism, revealing its role in membrane curvature and organization.

Looking for the optimal pathway to stimulate hippocampus in human participants using transcranial ultrasound stimulation (TUS): a simulation study

This study simulates low-intensity transcranial ultrasound stimulation (TUS) to identify optimal pathways for targeting the hippocampus in humans.

Identifying myocardial regions perfused by coronary arteriesthrough detailed human microvasculature data

The paper uses detailed human coronary microvasculature data to build a tool for personalized coronary-myocardium association and assesses its impact on myocardial perfusion simulations.

Breaking Balance: Encoding local error signals in perturbations of excitation-inhibition balance

The paper proposes that deviations from excitation-inhibition balance encode local error signals for synaptic plasticity, enabling efficient learning in neural networks.

Mechanical forces drive mitochondrial matrix extrusion and apoptotic pore growth

The paper investigates the role of mechanical forces in mitochondrial inner membrane extrusion and apoptotic pore growth using CLOSE microscopy.

Assessing analysis methods of brain synchrony in social interaction: Simulation-based comparison

This paper compares methods for analyzing brain synchrony in social interactions using simulations and proposes a new GLM-based approach that better captures dynamic relationships.

Generating 3D Models of Carbohydrates with GLYCAM-Web

GLYCAM-Web provides interactive and API-driven carbohydrate 3D structure builders that assemble, resolve steric overlaps, and energy-minimize oligosaccharides up to 100 residues in under a minute.

Prioritization of Deleterious Mutations Improves Genomic Prediction and Increases the Rate of Genetic Gain in Common Bean (Phaseolus vulgaris L.), a Simulation Study

This study shows that prioritizing deleterious mutations improves genomic prediction accuracy for yield in common bean and increases genetic gain through optimized breeding strategies.

Understanding the physical processes behind DNA-DNA proximity ligation assays

This study uses numerical experiments and theoretical modeling to investigate the physical processes in DNA-DNA proximity ligation assays and their impact on experimental outcomes.

Antibody-Based Targeting of the SPP1-CD44 Axis in Pediatric High-Grade Glioma through Single-Cell and Structural Bioinformatics

This study identifies the SPP1-CD44 axis as an immunosuppressive pathway in pediatric high-grade glioma and develops an antibody to disrupt it using single-cell and structural bioinformatics.

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

This study identifies the structural and sequence basis of epistatic interactions driving drug resistance in HIV by combining sequence models and molecular dynamics simulations.

Synaptic plasticity facilitates oscillations in a V1 cortical column model with multiple interneuron types

The paper shows that synaptic plasticity, not intrinsic circuit structure, enables oscillations in a mouse V1 cortical column model with multiple interneuron types.

Thermal Dynamics of Ectotherm Behavioral Strategies: Insights from Agent-Based Simulations

This paper uses agent-based simulations to analyze thermoregulatory strategies in ectotherms, finding minimal differences between strategies and highlighting environmental factors' role in thermal refugia occupancy.

Simulation of neurotrophin receptor transmembrane helix interactions reveals active states and distinct signaling mechanisms

This study uses molecular dynamics simulations to identify active and inactive states of neurotrophin receptor transmembrane domains and suggests distinct signaling mechanisms for different receptors.

Quantifying the net effect of biodiversity on stability

The paper quantifies how biodiversity affects ecosystem stability using simulations and experiments, finding stability often exceeds expectations due to diversity.

Stimulus representation in human frontal cortex supports flexible control in working memory

The paper investigates how stimulus representation in the frontal cortex supports flexible control in working memory using fMRI and simulations.