Ard A. Louis

TL;DR: The structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers are explored, resulting in an "average base" description of DNA.

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: These calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity autocorrelation function in the colloidal regime, strongly underestimating it at short times and strongly overestimated it at long times.

TL;DR: This work maps dilute or semidilute solutions of nonintersecting polymer chains onto a fluid of "soft" particles interacting via a concentration dependent effective pair potential, by inverting the pair distribution function of the centers of mass of the initial polymer chains.

TL;DR: In this paper, the transferability and representability problems of effective pair potentials are discussed, and several pedagogical examples are illustrated by several examples, such as the mapping of charged (Debye-Huckel) and uncharged (Asakura-Oosawa) two component systems onto effective one component ones.