D. P. Nickerson

The paper presents a framework to convert SBML models into bond graphs to ensure physical plausibility and thermodynamic consistency in biochemical models.

The paper proposes an automated method to compose biosimulation models using semantic annotations and bond graphs, demonstrating it by integrating Ras-MAPK and EGFR models.

The paper develops a modular mathematical model of epithelial transport in the proximal convoluted tubule, providing an open-source Python implementation for simulation and analysis.

This paper introduces a method to compose biosimulation models using bond graphs and semantic annotations, demonstrating it on a human arterial circulation model to improve modularity and physical consistency.

The paper identifies a gatekeeper helix in Sly1 that binds membranes to relieve autoinhibition and mediate close-range vesicle tethering in the early secretory pathway.

The paper investigates how Sec17 and SM-tethering complexes influence SNARE zippering, showing divergent effects on fusion depending on zippering states and demonstrating HOPS's role in controlling Sec17's impact.