mechanistic / dynamical model

The paper develops a mechanistic replicator model to link vaginal microbiota composition to Nugent scores and predict bacterial vaginosis with high accuracy.

The paper analyzes engineered MagLOV variants to understand how mutations affect their magnetic response by examining conformational changes and electron transfer dynamics.

The paper integrates carbon utilization and transport processes into a crop growth model to predict soybean carbon allocation behavior under varying conditions.

This study identifies Atg1-mediated phosphorylation of Atg2 as a mechanism to activate lipid transfer during autophagosome biogenesis.

This paper investigates why aryl sulfatases are inhibited by sulfamate warheads while carbohydrate sulfatases are not, using structural and computational analyses.

This paper develops a coarse-grained MD model to study DNAJB6b's role in suppressing polyglutamine aggregation in Huntington's disease, finding that DNAJB6b co-condensates with polyQ and inhibits amyloid formation.

This study improves mechanistic models of Ixodes scapularis tick activity by incorporating humidity and overwinter development, showing better alignment with observed phenology across regions.

This study uses molecular dynamics simulations to analyze how glycosylation affects the free energy landscape of HCA IX's catalytic domain in monomeric and dimeric forms, revealing increased landscape complexity with glycosylation.

This paper investigates the interaction between influenza HA's cytoplasmic tail domain and PIP2 using MD and FPALM, finding electrostatic and hydrophobic contributions to HA-PIP2 binding.

This study uses molecular dynamics simulations to show how phosphorylation of alpha or beta-tubulin alters microtubule structure and affects GTP hydrolysis and dynamic instability.

This study demonstrates lipid-coated quantum dots with tunable surface charge that enhance membrane interactions and labeling density in HEK293 cells, supported by molecular dynamics simulations.

The paper models SARS-CoV-2 replication dynamics in human cells, identifies key bottlenecks, and evaluates antiviral drug effects using mathematical modeling and experimental data.

This study investigates the mechanism of Na+-dependent HCO3- transport by NBCn2 using structure prediction and simulations, revealing sequential ion binding and conformational changes.

The paper presents a mechanistic framework explaining the facilitation-to-competition transition in plant interactions along rainfall gradients, showing it depends on resource availability and woody density.

This study investigates the evolutionary and mechanistic diversity of bacterial NDH-2s, revealing lineage-specific catalytic mechanisms and their implications for drug development.

This study uses molecular dynamics simulations to show that early α-synuclein association with Aβ42 oligomers depends on their initial configuration, with distinct interaction patterns observed based on Aβ42's oligomeric state.

The paper provides a resource of 1,079 post-translationally modified protein systems with molecular dynamics simulations and descriptors for research and method evaluation.

This study shows that inhibiting KDM5A/B enhances antitumor innate immune responses and induces KSHV lytic reactivation in KSHV-positive B-cell lymphomas.

This study uses cryo-EM and computational methods to model the structure of HPV16 L2 protein within the capsid, revealing its conformational flexibility and positioning for virus entry.

This study quantifies molecular entropy and its changes during ligand binding using MD simulations and machine learning, revealing key motions and their thermodynamic impacts.

The paper identifies ligands that bind beyond a known hydrophobic pocket at the HBV core protein interface using molecular dynamics and fragment mapping.

The paper investigates how condensate material properties affect exopher cargo selection in neurons, finding that gel-like condensates are more efficiently recruited than liquid-like ones.

This study uses agent-based models to analyze how normal and cancer cells respond to shear stress, finding that heterogeneity in stiffness and activity leads to non-affine movements.

This study shows HMCES-DPC formation increases DNA template flexibility, enabling slippage and mutagenic bypass of AP sites during replication.

This paper reframes substrate crossover in microbial fuel cells as a design variable to sustain microbial metabolism and improve long-term operation.

This study shows the 8S caveolin complex generates positive membrane curvature through a conical shape, with cholesterol affecting curvature via stress relief rather than direct binding.

This study uses molecular dynamics simulations to show how lipid headgroup properties and cholesterol concentration cooperatively regulate domain registration and anti-registration in model membranes.

This paper determines the cryo-EM structure of CbrA, revealing its SLC5-STAC domains and how CbrX interacts with the transporter, providing insights into histidine transport and signaling mechanisms.

This study identifies SPINK1 as a regulator of epigenomic states and stemness in PDAC through its interaction with COL18A1 and endostatin release.