mechanistic / dynamical model

This study uses a continuum mechanics framework to show that epithelial tissues regulate energy expenditure to maintain efficient migration, and demonstrates this through electrotaxis experiments.

The paper uses molecular simulations to identify state-dependent cholesterol interactions at an allosteric site in glycine receptors, linking lipid binding to receptor function and pharmaceutical relevance.

This study uses network pharmacology to identify the molecular mechanism of Huanglian Jiedu Decoction in treating Alzheimer's disease, revealing its anti-inflammatory effects through multiple targets and pathways.

This study shows serotonin enhances vesicle association and fusion with lipid bilayers by altering their mechanical properties through water content changes.

This study uses molecular dynamics simulations to investigate how hydrophobic mismatch affects the lateral sorting of transmembrane peptides by analyzing free energy profiles and peptide orientation.

The paper shows that time-dependent interaction modifications in plant-soil feedback depend on germination phenology and microbiome overlap, affecting plant coexistence.

This study investigates how vortioxetine interacts with human and rodent 5-HT3 receptors, revealing structural differences and mechanisms of action.

This study shows that lipid II in bacterial membranes stabilizes pores formed by nisin, enhancing its antimicrobial effect by altering membrane properties.

This study uses molecular dynamics to show how fluoxetine and escitalopram inhibit TREK-2 channels through different mechanisms involving the selectivity filter and lipid interactions.

This paper develops a kinetic model to predict triglyceride digestion in the intestine, showing it aligns with experimental data and outperforms simpler models.

The paper enhances a hybrid multiscale cancer invasion model to better reflect biological dynamics and introduces a multi-organ metastasis framework.

This study identifies the Na2 site as the potassium binding site in SERT using molecular dynamics simulations and site-directed mutagenesis.

This paper evaluates the toxicity of Aflatoxin B1 using network toxicology and molecular docking, identifying key targets and pathways involved in liver injury.

This paper identifies five IL37 mutations that disrupt dimer formation while preserving monomer structure, aiding in the design of anti-inflammatory therapeutics.

This study shows Nrf2 modulates CD4+ T-cell activation and expansion by altering glucose and glutamine metabolism, offering insights for improving immunotherapies.

This study uses molecular dynamics simulations to show that cholesterol modulates conformational changes in mGluR1 dimers, with 10% cholesterol causing the most significant effects.

This study uses molecular dynamics simulations to elucidate the conformational mechanism and proton-substrate coupling in mammalian POTs, revealing key structural differences and functional insights.

This study evaluates movement rules for simulating species dispersal in a mosaic landscape model, showing that simpler rules produce less accurate dispersal kernels compared to more complex ones.

This study uses AlphaFold2 and molecular dynamics to predict conformational ensembles and binding mechanisms of SARS-CoV-2 Omicron variants, showing agreement with experimental data.

The paper identifies a mechanism by which eIF2γ binding to PPP1R15A enhances catalytic efficiency of the holophosphatase that terminates the integrated stress response.

This study uses MD simulations to investigate the structural mechanisms of S1P transport by Spns2, identifying key residues and a rocker-switch model for potential inhibitor development.

This study shows that targeting EZH2 and HDACs together induces ferroptosis in hematological malignancies by upregulating cholesterol biosynthesis and causing metabolic stress.

The paper evaluates six 1-deazapurine derivatives for their alpha-glucosidase inhibition and identifies L4 and L11 as promising lead molecules for type 2 diabetes treatment.

The paper investigates how spatial arrangements in groups of flow-coupled swimmers affect energetic costs, finding equal energy distribution in side-by-side formations and energetic savings for trailing swimmers in inline formations up to a limit.

The paper develops a spatially explicit predator-prey model to study how climate change affects multispecies interactions and species distribution.

This study shows PRMT5 deficiency disrupts Nur77 methylation, impairing endometrial stromal cell differentiation and contributing to recurrent implantation failure.

The paper reveals power law residence scaling in both passive and active liquids, showing sensitivity to liquid environment and suggesting active phase separation as a scaling proofreading mechanism in gene regulation.

This study uses molecular dynamics simulations to reveal the bending-unbending mechanism of integrin, showing it functions like a molecular arm with the β leg acting as a bicep.

The paper uses molecular dynamics simulations to study how MutSbeta interacts with mismatched DNA, showing its stabilization and scanning initiation after ~75ns, and validates these findings for a biosensing application.