simulation

Unexpected excess heterozygosity in a threatened, mycoheterotrophic, self-pollinating orchid

The paper investigates excess heterozygosity in the self-pollinating orchid Corallorhiza bentleyi, finding overdominance likely explains the phenomenon despite selfing and small population size.

Mechanistic simulation identifies predictive dose-dependent biomarkers of propofol anesthesia

The paper uses a mechanistic model to simulate propofol's effects on brain circuits, identifying a dose-dependent biomarker confirmed in empirical data.

Rapid simulation of organ-scale oxygen transport for tissue ischemia prediction

The paper introduces a computational toolkit to simulate organ-scale oxygen transport and predict tissue ischemia by analyzing vessel networks and physiological conditions.

Molecular sterics guide tmRNA translocation on the ribosome

The paper uses a simulation model to show how ribosome structure and molecular sterics guide tmRNA translocation during trans-translation.

Impaired value estimation over space explains turn-induced freezing of gait in Parkinson's disease: A cortico-basal ganglia-inspired reinforcement learning model

fuzzyfold: a high-performance framework for stochastic RNA folding kinetics

The paper introduces fuzzyfold, a Rust-based software framework for stochastic RNA folding kinetics, enabling efficient simulation of long RNA molecules and flexible model integration.

Interchain base-stacking and spermine bridges govern ssDNA condensation and reentrant transitions

This study shows that spermine induces two phase transitions in ssDNA through stacking and electrostatic interactions, with sequence-dependent behavior.

Thalamocortical credit routing from the basal ganglia and cerebellum: anatomical constraints and circuit principles

The paper investigates how thalamocortical pathways from the basal ganglia and cerebellum route credit signals to cortical circuits, revealing anatomical segregation and plasticity mechanisms that enhance learning.

scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation

scStable evaluates scRNA-seq analysis stability by generating synthetic samples with between-sample variation, showing better performance than existing methods in gastric cancer data.

Chameleonicity Beyond Compactness: Conformational Persistence and Passive Permeability Across 20 PROTAC Ensembles

This study investigates the conformational properties of 20 PROTACs to determine factors influencing their passive permeability, finding that compactness alone is not sufficient and introducing a new metric, maximum ring size.

Multi-Domain Interplay Controls Full-Length TDP-43 Phase Separation and Condensate Dynamics

This study shows how different domains of TDP-43 interact to control phase separation and condensate dynamics through simulations and experiments.

Activation pathway of the human voltage-gated proton channel

This study determines the activation pathway of the human voltage-gated proton channel hHV1 using computational methods, revealing voltage-driven structural changes and lipid effects validated by experiments.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

Myristoylation licenses disordered viral VP4 protein to anchor to and perforate the membrane through phase separation

This study shows that myristoylation of VP4 enables membrane anchoring, phase separation, and pore formation in enteroviruses through multiple functional roles.

Measurement-Induced Decision Loss: A feasible-set theory of microbiome intervention under observation loss

Measurement-induced decision loss (MIDL), host benefit forgone versus perfect observation, grows linearly with microbiome information loss in a binary model, then plateaus once the optimal policy becomes signal-independent.

Learning source weights for target-position estimation: comparing fixed weights and an input-dependent rule

In simulation, under reduced accuracy or temporally correlated errors, recalibration or fixed-weight learning captured most gains; a disagreement-dependent rule beat fixed weights mainly under occasional large errors (4.05% lower MSE).

"Double-dipping" in testing for phenotypic differences with scRNA-Seq

The paper identifies a 'double-dipping' issue in scRNA-Seq where cell-type clustering and phenotype testing are performed on the same data, leading to inflated false discovery rates, and proposes solutions to mitigate this problem.

HIV-1 Ribonucleoprotein Complex Organization Facilitates Assembly of the Mature HIV-1 Capsid

This study uses molecular dynamics simulations to show that IN-RNA filaments guide HIV-1 capsid assembly and shape, with octameric filaments forming more conical capsids than tetrameric ones.

RNA synthesis and degradation regulate biomolecular condensates through non-equilibrium feedback

This study shows RNA synthesis and degradation dynamically regulate transcriptional condensates through non-equilibrium feedback, affecting their composition and stability.

HIV-1 Assembly is Assisted by IRSp53 Through an Interaction that Extends Gag Conformation

The paper shows that IRSp53 assists HIV-1 assembly by interacting with Gag and extending its conformation, which is validated through simulations and experiments.

β-Hairpin Fold Peptide Brush Polymers

This study examines peptide-brush polymers mimicking protein structure, finding that polymer backbones disrupt secondary structures and alter free-energy landscapes.

LGR5-high colorectal cancer defines a Wnt-active stem-like state with multimodal therapeutic vulnerabilities

The paper identifies LGR5-high colorectal cancer as a Wnt-active stem-like state with therapeutic vulnerabilities across multiple modalities.

Cortical organoid diffusion MRI reveals protocol-associated spatial reproducibility and increasing apparent diffusivity with diffusion time

This study uses cortical organoids to examine diffusion MRI reproducibility and apparent diffusivity changes with diffusion time, finding increased apparent mean diffusivity in most tissue voxels.

Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis

The paper investigates adaptive introgression in subdivided populations, finding no correlation between adaptive allele frequency and introgressed tract length, suggesting local adaptation rather than a traveling wave.

replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion

replicateFest uses negative binomial models for replicated and Fisher's exact tests for unreplicated FEST TCR-seq to call antigen-expanded clonotypes, recovering all nine published HIV-1 responders.

Simulating Bead-Tethered Biomolecules: Force-Probe Coupled Steered Molecular Dynamics (fp-SMD) in Optical Tweezers Force Spectroscopy

This paper introduces fp-SMD to simulate single-molecule force spectroscopy data by aligning simulation timescales with experiments, revealing force-induced pathway switching in a host-guest complex.

A Dimer-Seeded Pathway Governs the Nucleation of ProTα-H1 Biomolecular Condensates

This study reveals a dimer-seeded nucleation mechanism for ProTα-H1 biomolecular condensates using simulations and shows how electrostatic screening and protein supersaturation control nucleation and condensate properties.

Dataset structure outweighs method choice in single-cell cell-type annotation

In a 63-tool benchmark, dataset identity explained ≈84% of Cohen's κ variance on synthetic data versus ≈4% for tool identity, and k-nearest-neighbor (kNN) purity predicted accuracy near-linearly (R² = 0.85–0.99).

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Hindmarsh-Rose neuronal network with spike-timing-dependent plasticity demonstrates coordinated reset neuromodulation for Parkinson's disease

This paper uses a computational model to study how coordinated reset stimulation can reduce neuronal synchrony in Parkinson's disease by adjusting synaptic weights through spike-timing-dependent plasticity.