simulation

Metabolic-Epigenetic Coupling in Cellular Senescence: In Silico Cristae Remodeling Depletes Alpha-Ketoglutarate to Drive KDM4/6 Inhibition and SASP Amplification

The paper develops a computational systems biology framework to model metabolic-epigenetic coupling in cellular senescence, showing how mitochondrial remodeling and alpha-ketoglutarate depletion inhibit KDM4/KDM6 and amplify SASP.

Somatic genetic variation shapes clonal selection of memory NK cells

Whole-exome sequencing of memory NK cells from 81 CMV-seropositive donors reveals dominant somatic clones, early-life origin, and positive selection, with Kmt2d loss shifting mouse NK fitness.

Sex differences in exploration-exploitation strategies during home-cage decision making

In 136 mice on FED3 tasks, males showed slightly higher win-stay in all three choice tasks, with higher accuracy in a deterministic bandit but not a probabilistic one.

Cophylogeny simulators are not interchangeable: similarities, differences and structural biases in synthetic host-symbiont

The paper analyzes cophylogeny simulators to compare their assumptions and structural biases in generating synthetic host-symbiont data.

Cell-specific heteroclinic orbits govern interaction dynamics in inertial microfluidics for circulating tumour cell separation

This study shows that cell-specific heteroclinic orbits and migration rates affect WBC carryover in inertial microfluidics for CTC separation.

The same plasticity rule rescues networks built from one conductance set and destabilises networks built from another

The paper shows that a single plasticity rule can stabilize one network of neurons and destabilize another, depending on the conductance set used, with no single conductance or firing rate explaining the difference.

Standing genetic variation drives polygenic adaptation to different environmental shifts

This study uses simulations to show how environmental shifts affect genetic adaptation, highlighting the role of standing genetic variation and using a CNN to predict environmental changes and mutation effects.

Neuronal loss reshapes survivor dynamics and limits mechanism inference in excitatory inhibitory neural fields

The paper shows neuronal loss can reshape network dynamics and limit mechanism inference in excitatory-inhibitory neural fields by separating loss effects from activity changes.

Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities

This study shows that longer equilibration times in umbrella sampling can alter free energy landscapes and reduce agreement with experimental data for RNA hairpin folding.

stably: error-controlled stability selection for biomarker panel discovery

stably (Python) applies error-controlled stability selection to DIA-NN output; its 17-protein pancreatic cancer panel reached held-out AUC 0.93 versus 0.82 for a published two-protein panel rescored on the same data.

Discovery of Bavachin as a Dual Trk-A/Trk-B Agonist via Integrated Computational Screening and Experimental Validation

This study identifies Bavachin as a dual Trk-A/Trk-B agonist using computational screening and experimental validation for neurodegenerative disease therapeutics.

Computational investigation of circuit mechanisms underlying short-latency responses to cortical stimulation

The paper uses computational models of cortical circuits to investigate the mechanisms behind D- and I-wave responses to cortical stimulation, finding consistent patterns across different cortical regions.

QuantiTrack: A unified software to study protein dynamics in living cells

QuantiTrack, a MATLAB GUI, unifies single-molecule detection, tracking, quality control and mobility analyses; for glucocorticoid receptor, hormone washout cut bound fraction, dwell times and low-mobility occupancy.

iCSD can produce spurious results in dense electrode arrays

The paper shows that current source density estimation can produce incorrect results in dense electrode arrays due to small inter-electrode spacing.

Transient morphogenetic constraints organize self-assembling axon neighborhoods for robust yet flexible wiring

The paper shows how transient morphogenetic structures and stochastic innervation models shape reproducible yet flexible wiring in C. elegans nervous systems through a trade-off between physical constraints and molecular specificity.

Evidence of Chemical Wave-Electric Field Interaction in Bacterial Cells

The paper shows electric fields in bacterial cells influence chemical waves, affecting pattern formation and robustness through wave-field interactions.

Spurious model comparisons are widespread in biomedical artificial intelligence

97% of 184 high-impact biomedical AI studies compare cross-validated models with tests assuming fold independence; in 69% of re-analyzable studies a significant comparison does not survive correction.

Embodied Emergence of Temporal Complexity in Finger Tapping: Synaptic and Dopaminergic Control in Cortico-Basal Ganglia Loops

This paper presents a computational model of finger tapping that shows how temporal complexity arises from neural and physical interactions, and how dopamine depletion disrupts this complexity, mimicking Parkinson's disease features.

Animals or plants? Evolutionary branching of sessile versus mobile cognitive agents in noisy environments

This study shows that sessile and mobile cognitive strategies evolve as alternative solutions to foraging in uncertain environments, depending on resource return structures and ecological feedbacks.

RNAPII and XPC remodel the 3D genome for UV repair

This study shows that RNAPII and XPC remodel chromatin loops and domains during UV repair, enhancing lesion recognition and repair efficiency.

What an atlas-fitted connectome can and cannot do: evolutionary search over interneuron stimulation in a whole-body C. elegans model

The paper uses a whole-body C. elegans simulation to test which neural stimulation strategies can produce chemotaxis, finding that specific interneurons are sufficient while sensory neurons are not.

A multiscale modeling framework for transport of PEGylated lipid nanoparticle through the extracellular matrix

This paper develops a multiscale computational framework to model PEGylated lipid nanoparticle transport through the extracellular matrix, showing that even low PEG density significantly enhances diffusivity.

Fast-ripples are emergent properties of neuronal networks

Most fast-ripples (250-500 Hz) in rat and human recordings are consistent with chance clustering of action potentials; in awake patients, distinct events make up an estimated 37.5% of detections.

Joint loading in the presence of torsional deformities is overestimated unless gait adaptations are considered: a predictive simulation approach

This study uses predictive simulations to show that joint loading in lower limbs with torsional deformities is overestimated without considering gait adaptations.

Revisiting bacterial division control with likelihood inference: limited identifiability of simple models

Likelihood comparison on six E. coli mother-machine datasets finds sizer, adder, and log-foldchange division rules only weakly separable, while a neural conditional cycle-duration model fits best.

Probabilistic inference of Homonymous and Heteronymous Recurrent Inhibition in Human Muscles from Large-Scale Motor Neuron Recordings

The paper uses motor neuron recordings and simulation-based inference to estimate homonymous and heteronymous recurrent inhibition in human muscles during contractions.

Mesoscale Heterogeneity Shapes Molecular Selectivity and Transport in Biomolecular Condensates

This study uses simulations to show that mesoscale heterogeneity in biomolecular condensates affects client selectivity and transport dynamics.

Integrated in silico identification of fungal-derived dual-target inhibitors for anti-schistosomal drug discovery

This paper identifies two fungal-derived compounds with dual inhibitory action against Schistosoma mansoni DHODH and cathepsin B1 using computational methods.

OCTOPUS: A versatile open-source tool creating realistic numericalbrain cells

OCTOPUS generates realistic digital brain cells with complex geometries to improve dMRI signal modeling and validate biophysical models.

The Cerebellar Engine: Multiscale Digital Brain Co-simulations Reveal How Cerebellar Spiking Architecture Shapes Cortical Coherence

In a mouse whole-brain co-simulation with a spiking olivocerebellar network, cutting mossy-fiber input to cerebellar nuclei lowers M1-S1 gamma coherence, while removing Purkinje inhibition raises it.