mechanistic / dynamical model

The paper develops a deformation gradient tensor model to describe the roll-spiral transformation in protein refractile bodies, linking macroscopic morphology with microscopic lattice deformation.

The paper demonstrates that bacterial flagellar torque has two components driving spin and precession, supported by bead assay experiments and a mechanical model.

This study identifies diverse tetrodotoxin analogs in Pacific newts and shows some are more effective against resistant garter snake sodium channels.

This study uses MD simulations to show that preorganized thumb-subdomain motions in SARS-CoV-2 polymerase drive functional transitions through structurally coupled regulatory regions.

The paper uses molecular dynamics simulations and electrophysiology to study conformational changes in TMEM16A upon inhibitor removal, revealing conductive and non-conductive states and mechanisms of Ca2+-dependent gating.

This paper develops a mechanochemical model to show that force loading rate and magnitude on adhesion molecules control lamellipodia stability and mechanosensing.

The paper shows that fasting disrupts the TGF-β-InsP6-HDAC3 axis, inducing ER stress and eliminating DNA-damaged cells to maintain tissue quality.

The paper assesses habitat loss impacts using geometric and mechanistic metrics, finding geometric metrics overestimate persistence while mechanistic indicators show accelerating extinction risks.

The paper quantifies differences in cation-π interaction strengths between Arg and Lys in biomolecular condensates, showing Arg is more effective than Lys due to higher dehydration penalty of Lys.

This study simulates antibody-spike protein binding for SARS-CoV-2 variants and finds a decline in binding strength with viral evolution, but some re-entrance of binding strength for most antibodies.

The paper determines the mechanism of teichoic acid transport by the flippase TacF in Streptococcus pneumoniae using cryo-EM and computational methods.

This study examines how charge patterning affects the conformational behavior and dynamics of intrinsically disordered proteins using experimental techniques and simulations.

This paper develops a unified ensemble-allosteric framework to explain how gain- and loss-of-function mutations in IP3R1 cause disease by altering conformational dynamics and allosteric communication.

This paper develops a 3D tumor microenvironment model to predict CAR-T therapy outcomes in solid tumors, finding that collagen density and metabolic competition are key determinants of efficacy.

This study identifies ferrous iron accumulation as a hallmark of therapy-induced senescence and shows that ferroptosis induction can eliminate residual tumor cells.

The paper shows that temporal changes in surface tension at the growing tip of Arabidopsis zygotes maintain cortical microtubule bands, which guide the formation of the preprophase band and ensure asymmetric cell division.

This study uses multiscale simulations to reveal how SDS disrupts MS2 bacteriophage capsid, showing pH-dependent effects and molecular mechanisms of surfactant-virus interaction.

This study shows that iPSC-derived epithelial cortinoids use reversible cytoskeletal instabilities to withstand large deformations during morphogenesis.

The paper models the active conformation of Mycobacterium tuberculosis FAS-I complex with ACP at KS, revealing cross-dome interactions and dynamic ACP conformations during FA synthesis.

This study designs a novel FLT3 inhibitor with improved binding stability and potency through molecular docking, modification, and simulation.

This paper investigates the dimerization and catalytic mechanism of MilM, a PLP-dependent enzyme involved in mildiomycin biosynthesis, revealing its role in substrate binding, catalysis, and product formation.

The paper shows that reduced Trp-to-heme energy transfer in Class II peroxidases facilitates efficient lignin degradation by promoting long-range electron transfer.

The paper explores how stochastic sampling of imperfect environmental cues generates phenotypic variation and shows stochastic sampling is often favored over bet-hedging strategies.

This study shows how mechanical forces and substrate properties enhance T-cell receptor proofreading by delaying decision-making and improving ligand discrimination.

This study identifies cryptotanshinone as a potential antitumor compound in bladder cancer, showing immunomodulatory effects through modulation of the cGAS-STING-IFN-I-JAK-STAT-IFIT signaling pathway.

This paper designs phage-antibiotic cocktails to suppress resistance by exploiting evolutionary tradeoffs, showing that LPS-targeting phages enhance sensitivity to lipophilic antibiotics.

The paper identifies a mechanochemical mechanism in Physarum polycephalum that links intracellular calcium oscillations to coordinated behaviors, showing how simple organisms can generate complex adaptive responses.

The paper shows that reticulate leaf venation in Pilea peperomioides forms an approximate Voronoi diagram around hydathodes and proposes a model based on auxin transport.

This study optimizes pembrolizumab therapy for de novo metastatic MSI-H/dMMR colorectal cancer using delay integro-differential equations, balancing efficacy, efficiency, and toxicity.

This study provides the structural model of the Bcl-xL/tBid complex at the mitochondrial membrane, revealing its dynamic architecture and mechanism of indirect apoptosis inhibition.