The interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to probe the principles of biological self-assembly, and the operation of cellular nanomachines. This work presents a survey of three distinct ways coarse-grained simulations can help characterize these interactions. A non-equilibrium energy landscape reconstruction technique is validated for use with the oxDNA model and a practical framework to guide future applications is established. A novel method for calculating entropic forces in DNA molecules...
The interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to pr...