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- Jonathan P. K. Doye, Robert H. Leary, Marco Locatelli, Fabio Schoen
- INFORMS Journal on Computing
- 2004

- Jonathan P. K. Doye
- Physical review letters
- 2002

Here we analyze the topology of the network formed by the minima and transition states on the potential energy landscape of small clusters. We find that this network has both a small-world and… (More)

We have attempted to Ðnd the global minima of clusters containing between 20 and 80 atoms bound by the Morse potential, as a function of the range of the interatomic force. The e†ect of decreasing… (More)

- Claire P Massen, Jonathan P. K. Doye
- Physical review. E, Statistical, nonlinear, and…
- 2005

Potential energy landscapes can be represented as a network of minima linked by transition states. The community structure of such networks has been obtained for a series of small Lennard-Jones (LJ)… (More)

- Jonathan P. K. Doye, Claire P Massen
- The Journal of chemical physics
- 2005

By dividing potential energy landscapes into basins of attractions surrounding minima and linking those basins that are connected by transition state valleys, a network description of energy… (More)

- Thomas E. Ouldridge, Ard A. Louis, Jonathan P. K. Doye
- The Journal of chemical physics
- 2011

We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A.… (More)

- Sebastian E. Ahnert, Iain G. Johnston, T. M. A. Fink, Jonathan P. K. Doye, Ard A. Louis
- Physical review. E, Statistical, nonlinear, and…
- 2010

We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any… (More)

- Jonathan P. K. Doye, Claire P Massen
- Physical review. E, Statistical, nonlinear, and…
- 2005

The network of contacts in space-filling disk packings, such as the Apollonian packing, is examined. These networks provide an interesting example of spatial scale-free networks, where the topology… (More)

- Iain G. Johnston, Sebastian E. Ahnert, Jonathan P. K. Doye, Ard A. Louis
- Physical review. E, Statistical, nonlinear, and…
- 2011

We investigate the evolutionary dynamics of an idealized model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between… (More)

- Niranjan Srinivas, Thomas E. Ouldridge, +5 authors Erik Winfree
- Nucleic acids research
- 2013

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been… (More)