simulation

Spider: a flexible and unified framework for simulating spatial transcriptomics data

Spider generates synthetic spatial transcriptomics data by simulating cell type proportions and transitions, enabling benchmarking of analysis tools.

What is happening in Dorsal Root Ganglia? A computational analysis of cross-excitation phenomenon

The paper tests diffusion and gap-junction hypotheses for cross-excitation in DRG neurons and finds neither adequately explains the phenomenon.

Individual trajectories for recovery of neocortical activity in disorders of consciousness

The paper uses biophysical simulations to study recovery of neocortical activity in disorders of consciousness, finding that excitatory corticothalamic synaptic strength loss correlates with cerebral glucose uptake and potential for recovery.

Ionizable networks mediate pH-dependent allostery in SH2 signaling proteins

This paper investigates how pH dynamics regulate SH2 signaling proteins like SHP2 and Src through allosteric mechanisms involving ionizable networks.

Landscape context drives within-species variation in dispersal kernels and limits transferability

The paper simulates dispersal patterns across different landscapes to show that dispersal kernels vary with habitat configuration and are not transferable across environments.

Division of labor in cargo and membrane recognition by SNX1-SNX5: Insights from multiscale modelling

This paper uses multiscale modeling to investigate how SNX1-SNX5 heterodimers recognize cargo and membranes in a retromer-independent manner.

SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments

SPARK generates simulated nascent RNA sequencing data to benchmark computational tools for analyzing transcriptional dynamics.

From Atoms to Neuronal Spikes: A Multi-Scale Simulation Framework

This paper presents a multi-scale simulation framework that links molecular events in ion channels to neuronal excitability by coupling molecular dynamics with neuronal simulations.

Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed

The paper introduces Cleo, a simulation testbed for systems neuroscience experiments, integrating optogenetics, electrophysiology, and closed-loop control to improve experimental design and model validation.

Non-uniform filament turnover and mechanically-driven contractility and bundle formation in disordered actomyosin networks

This study uses simulations to show how different filament turnover models and mechanical factors affect contractility and bundle formation in actomyosin networks.

A rapidly closing window for coral persistence under global warming

Eco-evolutionary simulations of 3,806 Great Barrier Reef reefs project coral cover falling to ∼14% by 2040 under every emission scenario; recovery afterwards needs warming below 2°C.

Representational drift shows same-class acceleration in visual cortex and artificial neural networks

The paper shows that representational drift in visual cortex and neural networks is driven by sensory input rather than elapsed time, with same-class acceleration observed during stimulus presentation.

Phylogenetic signal dynamics during niche filling in food webs

The paper simulates food web evolution to study how phylogenetic signal in trophic structure changes over time and examines its relationship with species network positions and diversification dynamics.

How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight

This paper shows that indirect steering muscles in Drosophila help stabilize flight by adjusting wing pitch during large perturbations, using a nonlinear control strategy.

Cholinergic heterogeneity facilitates synchronization and information flow in a whole-brain model

This study uses a whole-brain model to show that cholinergic heterogeneity enhances synchronization and information flow in brain dynamics.

Influence of STDP rule choice and network connectivity on polychronous groups and cell ensembles in spiking neural networks

The paper compares polychronous groups and cell ensembles in spiking neural networks under different STDP rules and network connectivity, showing discrepancies between anatomical and spike-pattern memory representations.

Neural oscillation as a selective modulatory mechanism on decision confidence, speed and accuracy

This study shows how neural oscillations modulate decision confidence, speed, and accuracy by altering synaptic time scales and oscillatory phase, challenging the speed-accuracy trade-off.

TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations

TyCHE improves time-resolved lineage tracing by accounting for heterogeneous mutation rates, applied to memory B cells, germinal centers, gliomas, and bacterial infections.

Dynamic shape remodeling of vesicles by internal active filaments

This study uses simulations to show how active filaments inside vesicles drive dynamic shape changes under osmotic stress, forming unstable structures like branched tubes and compartmentalized vesicles.

Targeting Ubiquitin-Specific Protease 7 (USP7): A Pharmacophore-Guided Drug Repurposing and Physics-Based Molecular Simulations Study

This study identifies potential USP7 inhibitors through virtual screening and molecular simulations, finding 12 compounds with favorable binding and anticancer activity.

Structural specialization of mossy fiber boutons is necessary for their unique computational functions

The paper develops a computational model of mossy fiber boutons to show that structural features like loose VDCC coupling and large inter-AZ distances are essential for short-term plasticity and pattern separation.

Evolutionary branching points in multi-dimensional trait spaces

This paper extends evolutionary branching theory to multi-dimensional trait spaces by introducing branching possibility and inevitability criteria, showing they can induce branching under both asexual and sexual reproduction.

Robotics-assisted acoustic surveys could deliver reliable, landscape-level biodiversity insights

This study evaluates UAV-based acoustic monitoring for biodiversity assessment, finding that sampling intensity affects results but not strategy, and highlights its utility for broad trends over exhaustive inventories.

The ultrastructural properties of the endoplasmic reticulum govern microdomain signaling in perisynaptic astrocytic processes

The paper investigates how the ultrastructural properties of the endoplasmic reticulum (ER) in perisynaptic astrocytic processes (PAPs) influence calcium signaling and microdomain activity.

Thermal shifts can override the effects of Transcription-targeting Antibiotics

The paper shows that thermal shifts override antibiotic effects in E. coli by altering transcriptomes and physiological responses across multiple levels.

Longevity in plants impacts phylogenetic and population dynamics

This study uses simulations to show that plant longevity and overlapping generations explain phylogenetic patterns, with somatic mutations potentially exacerbating these effects.

Computational biophysical characterization of a superradiant virus-like particle in its ground state

This study uses molecular dynamics simulations to investigate how dye conjugation affects the biophysical properties of virus-like particles, revealing structural and electrostatic changes that influence superradiance.

sCCIgen: A high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.

sCCIgen generates synthetic spatial transcriptomics data with known cell-cell interaction features to evaluate analytical tools.

Electrostatics facilitate mid-air host attachment in parasitic jumping nematodes

This study shows electrostatic forces help parasitic nematodes attach to insect hosts in the air, improving their survival.

Numerical study of the size-based, shear-induced separation of circulating tumour cells from white blood cells in liquid biopsies

This study uses simulations to show that circulating tumour cells enhance white blood cell migration in microfluidic systems, affecting separation efficiency.