mechanistic / dynamical model

Anisotropic regulation of lateral surface tension directs invagination in C. elegans gastrulation

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

Mapping the reactive cysteine landscape of the NOD-like receptor pyrin domain-containing 3 protein

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

Opposing Roles of Cholesterol and Cholesterol Sulfate in Proton Transfer and Diffusion at Membrane Interfaces

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.

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

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.

TRPP Ion Channels Function in the π-Conformation Rather Than the α-Conformation

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.

Intrinsic timekeeping in Escherichia coli

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

PERTURBATION OF THE AMINO ACID STRESS RESPONSE PATHWAY EXPOSES A METABOLIC VULNERABILITY IN MULTIPLE AGGRESSIVE CANCER SUBTYPES

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

Emergence and robustness of 3D complex tissue architectures from simple physical forces

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.

GNG2-MRAS interaction regulates SHOC2-dependent RAF activation and MAPK signaling

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

Decoding stress-induced adaptation of cancer cells in spatial confinement by integrating live-cell imaging and mathematical modeling

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.

A Computational Model of Mechanical Stretching of Cultured Cells on a Flexible Membrane

This paper develops a computational model to simulate mechanical stretching of cultured cells on a flexible membrane and connects it to chromatin deformation.

USP18-STAT2 axis enhances hepatic resilience under proteotoxic stress

This study identifies the USP18-STAT2 axis as a critical factor enhancing hepatic resilience under proteotoxic stress by modulating interferon signaling and ISG solubility.

Modeling a Continuum of Drug-induced Persistence during Targeted Cancer Therapy

The paper develops a framework to model drug-induced persistence in cancer therapy, identifying optimal drug concentrations and schedules to reduce persistence-based resistance.

Modulating Transthyretin Fibril Stability with D-Retro-Inverso Peptides

The paper uses molecular dynamics simulations to study how D-Retro-Inverso peptides modulate TTR fibril stability and identifies DRI-K6V as a potential disruptor of TTR fibrils.

Insights on the effect of extracellular acidification on an HCNchannel: a molecular dynamics study

This study uses molecular dynamics simulations to investigate how extracellular acidification affects the structure and function of HCN2 channels by disrupting hydrogen bond networks involving residue E212.

Predicted structure of the 89-kDa invasion-tip protein of Holospora obtusa, an endonuclear symbiont of Paramecium caudatum, suggests a pH-dependent conformational change

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.