simulation

A framework for constructing insect steering circuits

The paper presents a framework for constructing insect steering circuits based on six general rules derived from Drosophila melanogaster data, showing functional equivalence across different wiring configurations.

Parsing Contributions of Physical Phenomena to smFRET Statistical Inhomogeneity via Multiparameter Stochastic Simulations

The paper develops a simulation framework to analyze how different physical processes affect smFRET data by isolating and varying their contributions.

Thermodynamic rigidity of harmonic brain states relates to general mental ability in juvenile myoclonic epilepsy

The paper uses EEG and machine learning to show that thermodynamic rigidity in brain states correlates with general mental ability in juvenile myoclonic epilepsy.

Flow molecular dynamics simulations reveal mechanosensitive regulation of von Willebrand factor through glycan-modulated autoinhibitory modules

The paper uses flow molecular dynamics simulations to study how mechanical forces regulate von Willebrand factor's conformational changes through glycan-modulated autoinhibitory modules.

Organism-Environment Topological Interfaces Drive the Origination of Organismal Form

This paper proposes a topological framework explaining the origin of organismal forms through interfaces with the environment, validated by cross-kingdom empirical data.

Integrative AlphaFold Modeling, Fragment Mapping, and Microsecond Molecular Dynamics Reveal Ligand-Specific Structural Plasticity at the Human Urotensin II Receptor

This study uses computational methods to analyze how different peptide ligands interact with the human urotensin II receptor, revealing structural differences in receptor activation.

Forecasting bryozoan assemblage dynamics under simulated climate change

This study uses a simulation model to examine how climate change affects bryozoan assemblage dynamics by altering disturbance regimes and biotic interactions.

Task-dependence of network-to-network variability in learning, performance, and dynamics of heterogeneous recurrent networks

The paper investigates how task-dependent variability arises in artificial recurrent networks with intrinsic heterogeneities, showing functional degeneracy and non-monotonic relationships between heterogeneity, task demands, and performance.

Structure-Guided Design and Dynamic Evaluation of VP4-Targeting siRNAs Against Rotavirus A

The paper designs and evaluates VP4-targeting siRNAs using computational methods to identify an optimized siRNA with improved structural compatibility and stability.

Molecular mechanisms of immune evasion by host protein glycosylation of a bacterial immunogen used in nucleic acid vaccines

This study identifies how host glycosylation of bacterial antigens in nucleic acid vaccines reduces immune recognition by shielding epitopes and altering antibody binding.

Shapes of condensate droplets containing filaments

This study investigates how filaments deform biomolecular condensate droplets and identifies physical mechanisms governing their shapes.

The LAST mile: Evaluating genetic biocontrol as a supplemental tool for eradicating invasive rodents on islands

This study evaluates genetic biocontrol methods as supplements to toxicant-based eradication of invasive rodents on islands, finding Gravid Lethal to be effective under certain strategies.

Non-random brain connectome wiring enables robust and efficient neural network function under high sparsity

The paper shows that non-random brain connectome wiring improves robustness and efficiency in sparse neural networks compared to random wiring.

Haplotype-resolved genome assemblies for Norwegian Red cattle

The paper develops haplotype-resolved genome assemblies for Norwegian Red cattle to improve variant detection and genomic predictions.

Genomic mosaicism reveals developmental organization of trunk neural crest-derived ganglia

The paper uses genomic mosaicism to study clonal dynamics of trunk neural crest-derived ganglia, finding conserved developmental patterns across species.

Decoding the Structural and Functional Impact of the Leukaemia-Associated A338V Mutation in GPR183

This study examines how the A338V mutation in GPR183 affects receptor function, showing preserved G protein activation but impaired GRK2 and β-arrestin2 recruitment.

Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds

This study shows that optimizing the number of filaments per aster in cytoskeletal networks enhances mechanical strength and rigidity, as revealed by computational simulations and percolation theory.

Collective learning and manifold behaviors in predator groups

This study shows that stable behavioral diversity can emerge in predator groups through shared learning, with group performance depending on specific strategy combinations.

Dual Nanoparticle-Driven Therapeutics for Leishmaniasis: A Mathematical Model of Targeted Macrophage and Parasite Elimination

This paper develops a mathematical model to evaluate nano-drug efficacy against leishmaniasis by simulating macrophage-parasite interactions and comparing iron oxide and citric acid-coated iron oxide nanoparticles.

Functional distinction between ionic and electric ephaptic effects on neuronal firing dynamics

This study presents a computational framework to explore the functional distinction between ionic and electric ephaptic effects on neuronal firing dynamics, showing they regulate population rates and spike timing differently.

Topology-aware multiscale modeling of viral genomes reveals stability determinants in circoviruses

This study uses computational models to analyze the topology of PCV2 viral genomes, revealing that different internal arrangements can produce similar external structures but vary in stability and function.

The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization

This paper integrates single-cell Hi-C, RNA-seq, and microscopy to uncover how hypertranscription shapes lampbrush chromosome structure through transcription-dependent chromatin organization.

Bimodal Coupling Optimization in Biological Rhythms: Balancing Energy Efficiency and Functional Demand

The paper introduces a bimodal coupling optimization strategy for biological rhythms, showing how systems switch between energy-efficient and function-priority modes to balance oxygen uptake and efficiency.

Serotonin, dopamine, and norepinephrine transporter assembly is selectively disrupted by a NET truncation isoform as revealed through near-million-atom simulations

The paper uses simulations to show a truncated NET isoform disrupts MAT bio-assembly by forming non-native heterodimers and causing structural instability.

Interplay of the ribosome A and CAR sites

The paper uses molecular dynamics simulations to study the interaction between the ribosome's A site and CAR site, revealing sequence-dependent modulation of hydrogen bonding and π-stacking interactions.

Optimizing scheduling in dual-pulse nucleoside labeling experiments for cell cycle analysis

This study optimizes the waiting time between dual-pulse nucleoside labeling pulses to improve signal-to-noise ratio in cell cycle analysis, particularly for experiments with small cell numbers.

Collective microfibril sliding underlies plant cell wall creep

The paper models plant cell wall creep as microfibril sliding, showing how localized defects and stress influence deformation mechanisms and structural integrity.

Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework

This paper benchmarks circRNA detection tools using a simulation framework and finds they vary in performance, with limited overlap in detected circRNAs and significant computational efficiency differences.

The Duplicate Monophyly Criterion: An Empirical Approach to Bootstrapping Distance-Based Structural Phylogenies

The paper introduces the Duplicate Monophyly Criterion to calibrate distance-matrix perturbations for phylogenetic support estimation using synthetic duplicates.

Beneficial microbes may have favoured the evolution of adaptive immunity

This study uses simulations to show that beneficial microbes, rather than parasites, drive the evolution and maintenance of adaptive immunity by reducing selection pressure on innate immunity.