DNA Systems Under Internal and External Forcing

An Exploration Using Coarse-Grained Modelling

  • Megan Clare¬†Engel

Part of the Springer Theses book series (Springer Theses)

Table of contents

  1. Front Matter
    Pages i-xv
  2. Megan Clare Engel
    Pages 1-17
  3. Megan Clare Engel
    Pages 19-24
  4. Megan Clare Engel
    Pages 69-93
  5. Megan Clare Engel
    Pages 95-125
  6. Megan Clare Engel
    Pages 127-130
  7. Back Matter
    Pages 131-144

About this book


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.


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

Authors and affiliations

  • Megan Clare¬†Engel
    • 1
  1. 1.John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeUSA

Bibliographic information