DNA Systems Under Internal and External Forcing

Beschreibung

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 is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.
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 is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.
Nominated as an outstanding Ph.D. thesis by the Rudolf Peierls Centre for Theoretical Physics, University of Oxford, UK Presents a new method for calculating polymer entropic forces in coarse-grained models that can overcome pitfalls associated with commonly-used techniques Provides an informative introduction to the use of non-equilibrium analyses with coarse-grained biophysical models along with practical guidelines for applying them Maps the unfolding process of DNA origami nanostructures through detailed colour illustrations and analysis, shedding light on design principles

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Megan Clare Engel

Themen in »DNA Systems Under Internal and External Forcing«

Biological Self-Assembly DNA Nanotechnology DNA Coarse-Grained Modelling Non-Equilibrium Statistical Mechanics Jarzynski Equality DNA Origami Simulated Single Molecule Force Spectroscopy Folding Energy Landscapes OxDNA MODEL Entropic Polymer Forces Computing DNA self-assembly

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