498 citations · 3.5k across the 66 of their papers we have counts for
5 papers · 1 filter
Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling
Jonathan P. K. Doye, Ard A. Louis, John S. Schreck +5
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the…
Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions
Jordan Juritz, Jenny M Poulton, Thomas E Ouldridge
The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthe…
A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
Aditya Sengar, Thomas E. Ouldridge, Oliver Henrich +2
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we pre…
What would it take to build a thermodynamically reversible Universal Turing machine? Computational and thermodynamic constraints in a molecular design
Rory A. Brittain, Nick S. Jones, Thomas E. Ouldridge
We outline the construction of a molecular system that could, in principle, implement a thermodynamically reversible Universal Turing Machine (UTM). By proposing a concrete-albeit…
Integral feedback in synthetic biology: Negative-equilibrium catastrophe
Tomislav Plesa, Alex Dack, Thomas E. Ouldridge
A central goal of synthetic biology is the design of molecular controllers that can manipulate the dynamics of intracellular networks in a stable and accurate manner. To address th…