simulation

On the Curvature and Relaxation of Microtubule Plus-endTips

This study uses multiscale modeling to show that microtubule plus-end tips bend outward into curved structures regardless of GTP hydrolysis state, challenging existing models linking curvature to nucleotide state.

Simulations reveal how touchdown kinematic variables affect top sprinting speed: implications for coaching

This study uses simulations to show that horizontal touchdown distance (HTD) affects sprinting speed, while inter-knee touchdown distance (IKTD) does not, providing guidance for coaching techniques.

Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome

The paper uses simulations to study how synaptic plasticity interacts with network structure and dendritic organization to shape cortical microcircuit function and learning.

Personalized cancer treatment strategies incorporating irreversible and reversible drug resistance mechanisms

This study enhances a personalized cancer treatment strategy by incorporating both irreversible and reversible drug resistance mechanisms, showing improved patient outcomes compared to current approaches.

Reciprocal host-Wolbachia interactions shape infection persistence upon loss of cytoplasmic incompatibility in haplodiploids

This study uses simulations to show that FM-CI extends infection persistence in haplodiploids and that hypomorphic Sd expression can maintain infection stability when CI is lost.

Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell

Apollo simulates within-host viral evolution and infection dynamics, validating limitations of transmission inference tools using HIV cohort data.

White matter geometry confounds Diffusion Tensor Imaging Along Perivascular Space (DTI-ALPS) measures

Radial diffusivity asymmetry driving DTI-ALPS indices pervades white matter, persists at high b-values, and tracks crossing fibers, axonal undulation and dispersion rather than perivascular diffusion.

Estimating the contribution of musculoskeletal impairments to altered gait kinematics in children with cerebral palsy using predictive simulations

This study uses predictive simulations to assess how musculoskeletal impairments affect gait in children with cerebral palsy, finding that these impairments explain up to 39% of kinematic deviations.

In silico evolution of globular protein folds from random sequences

This study uses a computational simulator to show how globular protein folds can evolve from random sequences, finding that stable folds emerge with 3-8 amino acid replacements per site.

Pharmacokinetic-Pharmacodynamic Trade-offs in SARS-CoV-2 Main Protease Inhibitors Unveiled through Machine Learning and Molecular Dynamics Simulations

SVM and logistic regression classifiers of Mpro inhibitor potency reach test ROC AUC 0.86 and 0.83; potency favours hydrophilic compounds, trading off against drug-likeness.

Unlocking Antiviral Potentials of Traditional Plants: A Multi-Method Computational Study against Human Metapneumovirus (HMPV)

This study identifies antiviral compounds from traditional plants against HMPV using computational methods, finding Glycyrrhizin and Withaferin A as promising candidates with strong binding and pharmacokinetic properties.

Molecular signatures of longevity identify compounds that extendmouse lifespan and healthspan

The paper identifies compounds that extend mouse lifespan and healthspan using a biomarker-driven platform integrating gene expression, chemical screening, and lifespan studies.

Extreme long-range migration distorts flower colour clines in an Antirrhinum hybrid zone

The paper examines flower colour clines in a hybrid zone of Antirrhinum majus, finding that long-distance dispersal, not linkage disequilibrium, shapes the stepped cline patterns.

Functional Specialization of Ca2+ - Binding Motifs in Human MICU1

This paper identifies a novel Ca2+-binding motif in MICU1 that functions as an early sensor, triggering structural changes that refine its regulatory role in mitochondrial Ca2+ uptake.

Protein Dynamics at Different Timescales Unlock Access to Hidden Post-Translational Modification Sites

The paper investigates how protein conformational dynamics reveal hidden post-translational modification sites and their functional relevance across timescales.

Strengthening intraguild predation increases the temporal variability of biomass across all trophic levels in model food webs

This study shows that increasing intraguild predation (IGP) in food webs leads to greater temporal variability in biomass across all trophic levels, potentially destabilizing ecosystems.

Simulation and experimental study on the strategy of soil auxiliary heating in a solar greenhouse in northeast China

The paper simulates and validates soil heating strategies for solar greenhouses in northeast China under extreme weather conditions to maintain optimal soil temperatures.

Communication pathway analysis within protein-nucleic acid complexes

The paper introduces ComPASS, a computational method to analyze communication networks in protein-nucleic acid complexes, revealing distinct signal transmission mechanisms across various systems.

Gradual sensory maturation promotes abstract representation learning

This paper shows that gradual sensory maturation in humans supports the development of abstract, bias-resistant visual representations, enabling generalization and compositional reconstruction.

Substrate binding and channeling allosterically modulate the interactions within the AlkB-AlkG electron transfer complex

This study investigates the dynamics and interactions of the AlkB-AlkG electron transfer complex using computational methods, revealing how substrate binding and channeling modulate allosteric effects and electron transfer efficiency.

Genome-wide rules of transcription factor cooperativity revealed through in silico binding site ablation

The paper introduces DeepCompARE, an in silico ablation framework to analyze TF cooperativity, finding most TF motifs are independent with defined synergy and redundancy effects.

Rhagovelia uses interfacial run-and-tumble locomotionto improve food capture in flowing environments

This paper studies the locomotion of Rhagovelia oriander in flowing environments, finding that its run-and-tumble movement improves food capture efficiency.

Modular architecture confers robustness to damage and facilitates recovery in spiking neural networks modeling in vitro neurons

This paper models how modular structure and spike-timing-dependent plasticity influence recovery in damaged neuronal networks.

Average miniature post-synaptic potential size is inversely proportional to membrane capacitance across neocortical pyramidal neurons of different sizes

The paper introduces a method to estimate quantal sizes in neurons by comparing somatic recordings with simulated minis, finding that mPSP amplitude inversely correlates with membrane capacitance.

Data Representation Bias and Conditional Distribution Shift Drive Predictive Performance Disparities in Multi-Population Machine Learning

This study evaluates how data representation bias and distribution shifts affect multi-population machine learning performance using synthetic genotype-phenotype datasets across five continental populations.

Optimizing the use of cryopreserved genetic resources for the selection and conservation of animal populations

This study shows that using cryopreserved genetic resources can help manage genetic diversity in animal populations, either by slowing its loss or guiding selection, but requires careful management to avoid issues with old genetic material.

Membrane-bound cargo carried by teams of motors with heterogeneous velocities go faster and further than rigid cargo

The paper uses simulations to show that motor velocity heterogeneity increases lipid cargo transport speed and distance compared to rigid cargo.

Evaluating the effectiveness of various small RNA alignment techniques in transcriptomic analysis by examining different sources of variability through a multi-alignment approach

This paper evaluates small RNA alignment techniques using a multi-alignment framework, finding STAR and Bowtie2 to be more effective than BBMap, with STAR-Salmon being the most reliable approach.

In silico discovery of pathogenic PD-L1 nsSNVs with altered glycosylation and immunotherapy binding

The paper identifies pathogenic PD-L1 nsSNVs that alter glycosylation and ICI binding through bioinformatics and experimental methods.

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.