mechanistic / dynamical model

The paper develops a computational model to explain how mechanical stimuli drive the formation of perinuclear actin structures through mechanosensitive actin polymerization.

This study shows lateral membrane heterogeneity influences antimicrobial association and leads to a common loss of membrane mechanical stability across different compounds.

This study identifies molecular mechanisms of Quizartinib resistance in FLT3 mutants using molecular dynamics simulations and experimental validation, showing distinct electrostatic and hydrophobic effects of D835Y and F691L mutations.

The paper shows that anisotropic lateral surface tension, mediated by HMR-1/E-cadherin, directs invagination in C. elegans gastrulation, complementing apical constriction.

This study identifies reactive cysteine residues in NLRP3 and shows how their oxidation by ROS affects NLRP3 conformation and inflammasome activation.

This study shows cholesterol and cholesterol sulfate have opposing effects on proton transfer and diffusion at membrane interfaces, with cholesterol promoting local transfer and inhibiting long-range diffusion, while cholesterol sulfate does the opposite.

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

This study uses molecular dynamics simulations to show that the π-conformation of PKD2 supports ion conduction, challenging the previous model that the α-conformation is the conductive state.

This study shows Escherichia coli has an intrinsic timekeeping system that anticipates daily temperature cycles through rhythmic curli plaque formation.

This study shows that disrupting the amino acid stress response pathway reduces tumor growth in multiple aggressive cancers by targeting chronic metabolic stress adaptation.

This study builds a 3D mathematical model of adipose tissue showing complex architectures emerge from simple mechanical rules, suggesting mechanical forces drive tissue structure more than genetic programs.

This study identifies GNG2 as an inhibitor of the SMP complex by binding MRAS, disrupting its assembly and inhibiting MAPK signaling.

This study combines live-cell imaging and mathematical modeling to show how cancer cells adapt to stress in spatially confined environments, revealing cooperative and competitive strategies influenced by spatial organization and microenvironment dynamics.

The paper predicts the structure of a 89-kDa invasion-tip protein from Holospora obtusa and suggests a pH-dependent conformational change may aid in escaping the host digestive vacuole.

This study investigates how substituting the azadithiolate ligand in ToHydA affects O2-stability by preventing the formation of specific states and altering structural dynamics.

This study shows that maleic acid enhances BCG vaccination to induce CD4+CD8+ T cells that sterilize Mtb infection in mice.

This study compares the structural features of human and C. elegans alpha2delta subunits to assess gabapentinoid binding site conservation using docking and molecular dynamics simulations.

The paper shows that ether linkages in phospholipids modulate membrane mechanics and topology through distinct physical mechanisms, explaining their evolutionary conservation and biological roles.

This study investigates how geothermal stress reorganizes microbial metabolism in hot spring communities using integrated genomic and metabolic modeling approaches.

This paper introduces a mechanical model to simulate subcellular and tissue remodelling in epithelial monolayers, showing how deformation history affects tissue recovery.

This study uses molecular dynamics simulations to show how curcumin tautomers and solvent environment affect gold nanoparticle stability, drug loading, and membrane interactions.

The paper uses molecular dynamics simulations to study conformational switching in a SAM-III riboswitch, showing Mg2+ stabilizes the ON-state and multiple pathways contribute to the transition between ON and OFF states.

The paper investigates salt- and temperature-dependent gel-like behavior of a fungal exopolysaccharide using rheology and molecular simulations, revealing distinct mechanisms for NaCl and LiCl.

This study develops an eco-evolutionary model showing how microbial dormancy and exoenzyme production affect soil carbon dynamics and feedbacks to climate.

This study shows that phosphoinositide protonation microstates determine AKT1 membrane binding specificity and how mutations alter this interaction.

This study identifies SAA1-TLR4 signaling as a tumor-derived pathway driving muscle wasting in pancreatic cancer, showing that targeting this pathway can preserve muscle mass and improve survival without affecting tumor growth.

The paper screens 64 tetrapeptides for binding to IL-17A using molecular dynamics simulations and identifies LYS-THR-CYS-ASP as the top binder with detailed interaction analysis.

The study uses molecular dynamics simulations to show that wild-type hERG fails to conduct K+ and evolves toward an inactivated-like conformation, contrasting with the N629D mutant which maintains conductivity.

CoralBlox is a computationally efficient coral ecology model that supports rapid scenario exploration and decision making for reef management.

This study shows that protein-protein interactions can follow static or dynamic binding paradigms, with distinct temperature dependencies and mechanisms affecting affinity prediction.