498 citations · 3.5k across the 66 of their papers we have counts for
7 papers · 1 filter
Modelling DNA Origami Self-Assembly at the Domain Level
Frits Dannenberg, Katherine E. Dunn, Jonathan Bath +3
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does no…
Coarse-grained modelling of strong DNA bending II: Cyclization
Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge +2
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuati…
Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge +2
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than i…
Fundamental Limits to Cellular Sensing
Pieter Rein ten Wolde, Nils B. Becker, Thomas E. Ouldridge +1
In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what s…
Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
Benedict E. K. Snodin, Ferdinando Randisi, Majid Mosayebi +8
We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded…
The thermodynamics of computational copying in biochemical systems
Thomas E. Ouldridge, Christopher C. Govern, Pieter Rein ten Wolde
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can c…