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Identifying "communities" within energy landscapes
Claire P. Massen, Jonathan P. K. Doye
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…
Characterizing the network topology of the energy landscapes of atomic clusters
Jonathan P. K. Doye, Claire P. Massen
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…
Self-similar disk packings as model spatial scale-free networks
Jonathan P. K. Doye, Claire P. Massen
The network of contacts in space-filling disk packings, such as the Apollonian packing, are examined. These networks provide an interesting example of spatial scale-free networks,…
Lead clusters: different potentials, different structures
Jonathan P. K. Doye
The lowest-energy structures of lead clusters interacting via a Gupta potential are obtained for N<151. Structures based on Marks decahedra dominate at the larger sizes. These resu…
Inhibition of protein crystallization by evolutionary negative design
Jonathan P. K. Doye, Ard A. Louis, Michele Vendruscolo
In this perspective we address the question: why are proteins seemingly so hard to crystallize? We suggest that this is because of evolutionary negative design, i.e. proteins have…