simulation

CloVarS: a simulation of single-cell clonal variability

CloVarS generates synthetic single-cell lineage data to model time-lapse microscopy experiments and test biological hypotheses.

Unsupervised learning reveals rapid gait adaption after leg loss and regrowth in spiders

Gait-space clustering shows juvenile tarantulas losing two same-tetrapod legs immediately adopt variable tripod-like gaits, regaining pre-autotomy speed within a day without evidence of learning.

Structural and Thermodynamic Impact of Oncogenic Mutations on the Nucleosome Core Particle

This study examines how two oncogenic histone mutations affect nucleosome stability through molecular dynamics simulations and biophysical assays, showing reduced interface stability and altered thermal properties.

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

The paper presents chromosome-level genomes for two orchids, revealing insights into their evolutionary relationships and genome size variation.

Cardiomyopathic mutations of lamin A perturb mutual interactions of lamin, nuclear membrane, and chromatin leading to LLPS

This study shows that cardiomyopathic lamin A mutations disrupt nuclear structure and chromatin organisation, leading to liquid-like aggregates and genome spatial disorganisation.

Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions

This study evaluates TE polymorphic detection tools using simulated data based on real genomes, finding that few tools perform well and all are sensitive to genomic and TE characteristics.

Root Contours Guided Design of a Multicellular PID Controller

The paper designs a multicellular PID controller using root contours for tuning control gains and validates it through in silico simulations.

Functional and compositional diversity peak at intermediate fire frequencies when modeling the plant-fire feedback

The paper models plant communities under varying fire frequencies to show that compositional and functional diversity peak at intermediate fire frequencies, with functional similarity needed for maximum species richness.

Effects of Extruder Dynamics and Noise on Simulated Chromatin Contact Probability Curves

This study compares dynamic and static loop extrusion models in chromatin folding, showing they produce distinct results and highlighting the importance of extruder behavior and noise in simulations.

Simulations provide a mechanistic interpretation of Bateman gradients

The paper uses simulations to show that Bateman gradients are influenced by covariances between mating success and other factors, not just direct causation.

Structural Acrobatics of IAA7: Exercising Fuzzy Regions to Aid Auxin-Mediated Catalysis

This study investigates how intrinsic disorder in IAA7 facilitates its ubiquitylation by SCFTIR1 through structural expansion and dynamic interactions.

Constitutive activation and allosteric mechanisms underlying Gi/Gq signaling bias in SUCNR1 revealed by AlphaFold-based modeling and enhanced sampling simulations

This study uses AlphaFold and simulations to show human SUCNR1 spontaneously adopts active conformations and exhibits constitutive signaling, while murine SUCNR1 requires agonist for activation.

The Art of Not Knowing: Accommodating Structured Missingness in Biomedical Research

This paper addresses structured missingness in biomedical data by introducing a hierarchical imputation framework and advocating for alternative evaluation metrics.

diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection

The paper introduces diplo-locus, a Python toolkit for simulating and inferring parameters from time-series genetic data under diploid selection models.

Simulated larvae dispersion of the invasive sun-coral (Tubastrea spp.) along Rio de Janeiro's coast: the role of submesoscale filaments on offshore transport and connectivity

This study uses numerical simulations to show that submesoscale ocean features like filaments enhance offshore transport of sun coral larvae along Rio de Janeiro's coast.

Environmental fluctuations trigger faster evolution and turnover

This study uses simulations to show that environmental instability increases extinction rates and phenotypic evolution, affecting species with limited adaptability.

Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference

This paper introduces cryoSBI, a method using simulation-based inference to infer biomolecular conformations from cryo-EM images, achieving fast and accurate results.

Morphogen gradients are regulated by porous media characteristics of the developing tissue

The paper simulates Fgf8a gradient formation in zebrafish epiboly using reconstructed 3D geometries to show that pore connectivity affects gradient shape and stability.

The kinetics of bedaquiline diffusion in tuberculous cavities opens a window for emergence of resistance.

Rabbit lesion microdissection and pharmacokinetic modeling show bedaquiline takes months to reach deep caseum and years to clear, while TBAJ-587 and TBAJ-876 shorten these windows.

One night of sleep deprivation reduces spatially patterned human brain clearance: implications for simulated tau propagation

This study shows that sleep deprivation reduces brain clearance rates but preserves their spatial pattern, affecting tau propagation differently in a computational model.

HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting

Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden

The paper simulates TB antibiotic regimens in a computational model to show rankings are influenced by spatial scale, detection limit, and initial bacterial burden.

Modeling Nitric Oxide Diffusion and Plasticity Modulation in Cerebellar Learning

This study models nitric oxide diffusion and its role in cerebellar learning using simulations, showing it modulates synaptic plasticity and learning rates.

Higher-order EEG microstate syntax and surrogate testing

The paper evaluates surrogate data generation methods for EEG microstate syntax analysis, finding that Markov chain surrogates are valid while shuffling is not.

Ammonia-mediated Conformational Dynamics in SCAP for SREBP Activation

This study uses molecular dynamics simulations to show ammonia induces conformational changes in SCAP that activate the SREBP pathway by promoting dissociation from Insig.

Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning

Shape-based fragment merging (FrankenROCS) with Thompson sampling over 22 billion molecules found neutral SARS-CoV-2 macrodomain inhibitors; analogs reached single-digit micromolar IC50, backed by 137 crystal structures.

General mechanisms for a top-down origin of the predator-prey power law

The paper investigates the top-down mechanisms underlying the predator-prey power law by combining differential equations and agent-based simulations.

Signal peptides as potential structural modulators of human splice isoforms

The paper investigates how signal peptides (SPs) can modulate the structure and function of human splice isoforms by stabilizing truncated domains through complementation.

REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators

This study uses molecular dynamics simulations to analyze REV-ERBβ ligand-binding domain dynamics and antagonist effects on NCoR peptide binding, informing rational drug design.

Towards Simulation Optimization: An Examination of the Impact of Scaling on Coalescent and Forward Simulations

This paper examines how scaling affects coalescent and forward simulations in human and Drosophila populations, finding that scaling impacts diversity estimates, runtime, and selection effects differently in each species.