Condensed Matter Theory

Abstract:

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.

Abstract:

Abstract Recent developments have led to a good understanding of universality; why phase transitions in systems as diverse as magnets, fluids, liquid crystals, and superconductors can be brought under the same theoretical umbrella and well described by simple models. This book describes the physics underlying universality and then lays out the theoretical approaches now available for studying phase transitions. Traditional techniques, mean-field theory, series expansions, and the transfer matrix, are described; the Monte Carlo method is covered, and two chapters are devoted to the renormalization group, which led to a break-through in the field. The book will be useful as a textbook for a course in `Phase Transitions', as an introduction for graduate students undertaking research in related fields, and as an overview for scientists in other disciplines who work with phase transitions but who are not aware of the current tools in the armoury of the theoretical physicist.