Joseph M. Schaeffer

TL;DR: This work study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects to provide a biophysical explanation of strand displacement kinetics.

TL;DR: This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures.

TL;DR: Data structures and algorithms are developed that allow the model to take advantage of local properties of secondary structure, improving the efficiency of the simulator so that the model can handle larger systems.

TL;DR: A computational method for verifying sequence-level systems by identifying discrepancies between the domain-level and sequence- level behaviour, implemented as the Python package KinDA, will allow researchers to predict the kinetic and thermodynamic behaviour of domain- level systems after sequence assignment, as well as to detect violations of the intended behaviour.

TL;DR: An Arrhenius model of interacting nucleic acid kinetics that relates the activation energy of a state transition with the immediate local environment of the affected base pair is introduced.