arXiv subjects

Jonathan P. K. Doye

Publications and source records attributed to Jonathan P. K. Doye.

At least 91 records · Page 5Linked to original sources

arXiv2005

Structural transitions in the 309-atom magic number Lennard-Jones cluster

The thermal behaviour of the 309-atom Lennard-Jones cluster, whose structure is a complete Mackay icosahedron, has been studied by parallel tempering Monte Carlo simulations. Surprisingly for a magic number cluster, the heat capacity shows a very pronounced peak before melting, which is attributed to several coincident structural transformation processes. The main transformation is somewhat akin to surface roughening, and involves a cooperative condensation of vacancies and adatoms that leads to the formation of pits and islands one or two layers thick on the Mackay icosahedron. The second transition in order of importance involves a whole scale transformation of the cluster structure, and leads to a diverse set of twinned structures that are assemblies of face-centred-cubic tetrahedra with 6 atoms along their edges, i.e., one atom more than the edges of the 20 tetrahedra that make up the 309-atom Mackay icosahedron. A surface reconstruction of the icosahedron from a Mackay to an anti-Mackay overlayer is also observed, but with a lower probability.

cond-mat.other↗

arXiv2005

Protein crystallization in vivo

Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the crystals thatare exploited. Where known, we emphasize how the nature of the protein-protein interactions leads to control of the crystallization behaviour.

q-bio.BM↗

arXiv2005

Melting of aluminium clusters

The melting of Al clusters in the size range 49 <= N <= 62 has been studied using two model interatomic potentials. The results for the two models are significantly different. The glue potential exhibits a smooth relatively featureless heat capacity curve for all sizes except for N = 54 and N = 55, sizes at which icosahedral structures are favoured over the polytetrahedral. Gupta heat capacity curves, instead, show a well-defined peak that is indicative of a first-order-like transition. The differences between the two models reflect the different ground-state structures, and neither potential is able to reproduce or explain the size dependence of the melting transition recently observed in experiments.

cond-mat.other↗

arXiv2005

Geometric magic numbers of sodium clusters: Interpretation of the melting behaviour

Putative global minima of sodium clusters with up to 380 atoms have been located for two model interatomic potentials. Structures based upon the Mackay icosahedra predominate for both potentials, and the magic numbers for the Murrell-Mottram model show excellent agreement with the sizes at which maxima in the latent heat and entropy change at melting have been found in experiment.

cond-mat.other↗

arXiv2005

Mapping the magic numbers in binary Lennard-Jones clusters

Using a global optimization approach that directly searches for the composition of greatest stability, we have been able to find the particularly stable structures for binary Lennard-Jones clusters with up to 100 atoms for a range of Lennard-Jones parameters. In particular, we have shown that just having atoms of different size leads to a remarkable stabilization of polytetrahedral structures, including both polyicosahedral clusters and at larger sizes structures with disclination lines.

cond-mat.mtrl-sci↗

arXiv2004

Identifying "communities" within energy landscapes

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 clusters. This community structure is compared to the concept of funnels in the potential energy landscape. Two existing algorithms have been used to find community structure, one involving removing edges with high betweenness, the other involving optimization of the modularity. The definition of the modularity has been refined, making it more appropriate for networks such as these where multiple edges and self-connections are not included. The optimization algorithm has also been improved, using Monte Carlo methods with simulated annealing and basin hopping, both often used successfully in other optimization problems. In addition to the small clusters, two examples with known heterogeneous landscapes, LJ_13 with one labelled atom and LJ_38, were studied with this approach. The network methods found communities that are comparable to those expected from landscape analyses. This is particularly interesting since the network model does not take any barrier heights or energies of minima into account. For comparison, the network associated with a two-dimensional hexagonal lattice is also studied and is found to have high modularity, thus raising some questions about the interpretation of the community structure associated with such partitions.

cond-mat.stat-mech↗

arXiv2004

Self-similar disk packings as model spatial scale-free networks

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, where the topology reflects the broad distribution of disk areas. A wide variety of topological and spatial properties of these systems are characterized. Their potential as models for networks of connected minima on energy landscapes is discussed.

cond-mat.stat-mech↗

arXiv2004

Characterizing the network topology of the energy landscapes of atomic clusters

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 landscapes naturally arises. These networks are characterized in detail for a series of small Lennard-Jones clusters and show behaviour characteristic of small-world and scale-free networks. However, unlike many such networks, this topology cannot reflect the rules governing the dynamics of network growth, because they are static spatial networks. Instead, the heterogeneity in the networks stems from differences in the potential energy of the minima, and hence the hyperareas of their associated basins of attraction. The low-energy minima with large basins of attraction act as hubs in the network.Comparisons to randomized networks with the same degree distribution reveals structuring in the networks that reflects their spatial embedding.

cond-mat.stat-mech↗

arXiv2004

Lead clusters: different potentials, different structures

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 results are very different from those obtained previously using a lead glue potential, and the origins of the differences are related back to differences in the potential.

cond-mat.other↗

arXiv2004

Inhibition of protein crystallization by evolutionary negative design

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 evolved not to crystallize, because crystallization, as with any type of protein aggregation, compromises the viability of the cell. There is much evidence in the literature that supports this hypothesis, including the effect of mutations on the crystallizability of a protein, the correlations found in the properties of crystal contacts in bioinformatics databases, and the positive use of protein crystallization by bacteria and viruses.

q-bio.BM↗

arXiv2003

Comment on ``Strontium clusters: Many-body potential, energetics, and structural transitions'' [J. Chem. Phys. 115, 3640 (2001)]

Parallel tempering simulations for Sr_34 and Sr_61 indicate that, contrary to Wang et al.'s predictions [J. Chem. Phys. 115, 3640 (2001)], there are no solid-solid transitions for these clusters, in which symmetrical polytetrahedral structures become most stable. These results have implications for the structural interpretation of the magic numbers observed experimentally for strontium clusters.

cond-mat↗

arXiv2003

Some Further Results for the Stationary Points and Dynamics of Supercooled Liquids

We present some new theoretical and computational results for the stationary points of bulk systems. First we demonstrate how the potential energy surface can be partitioned into catchment basins associated with every stationary point using a combination of Newton-Raphson and eigenvector-following techniques. Numerical results are presented for a 256-atom supercell representation of a binary Lennard-Jones system. We then derive analytical formulae for the number of stationary points as a function of both system size and the Hessian index, using a framework based upon weakly interacting subsystems. This analysis reveals a simple relation between the total number of stationary points, the number of local minima, and the number of transition states connected on average to each minimum. Finally we calculate two measures of localisation for the displacements corresponding to Hessian eigenvectors in samples of stationary points obtained from the Newton-Raphson-based geometry optimisation scheme. Systematic differences are found between the properties of eigenvectors corresponding to positive and negative Hessian eigenvalues, and localised character is most pronounced for stationary points with low values of the Hessian index.

cond-mat↗

arXiv2003

Identifying structural patterns in `disordered' metal clusters

Zinc and cadmium clusters interacting with a Gupta potential have previously been identified as prototypical metallic systems that exhibiting disordered cluster structures. Here, putative global minima of the potential energy have been located for these clusters for all sizes up to N<125. Although none of the usual structural forms are lowest in energy and many of the clusters have no overall order, strong structural preferences have been identified.Many of the clusters are based on distorted oblate Marks decahedra, where the distortion involves the bringing together of atoms on either side of a re-entrant groove of the Marks decahedron.

cond-mat↗

arXiv2003

A model metal potential exhibiting polytetrahedral clusters

Putative global minima have been located for clusters interacting with an aluminium glue potential for N<190. Virtually all the clusters have polytetrahedral structures, which for larger sizes involve an ordered array of disclinations that are similar to those in the Z, H and sigma Frank-Kasper phases. Comparisons of sequences of larger clusters suggest that the majority of the global minima will adopt the bulk face-centred-cubic structure beyond N=500.

cond-mat↗

arXiv2003

Comment on ``Quasisaddles as relevant points of the potential energy surface in the dynamics of supercooled liquids'' [J. Chem. Phys. 116, 10297 (2002); cond-mat/0203301]

Recently, the properties of supercooled liquids have been studied by mapping instaneous configurations onto minima of the gradient squared. It was originally suggested that this mapping would probe higher-order saddle points of the potential energy surface. However, it was subsequently shown that the majority of the minima of this function are only local minima and so do not correspond to saddles. In this comment, we provide a critique of the suggestion made by Angelani et al. [J. Chem. Phys. 116, 10297 (2002); cond-mat/0203301] that although these minima are not true saddles, they are almost saddles (hence the term quasisaddles). This issue has important implications for the interpretation of the results obtained by this approach.

cond-mat↗

arXiv2002

Surface-reconstructed Icosahedral Structures for Lead Clusters

We describe a new family of icosahedral structures for lead clusters. In general, structures in this family contain a Mackay icosahedral core with a reconstructed two-shell outer-layer. This family includes the anti-Mackay icosahedra, which have have a Mackay icosahedral core but with most of the surface atoms in hexagonal close-packed positions. Using a many-body glue potential for lead, we identify two icosahedral structures in this family which have the lowest energies of any known structure in the size range from 900 to 15000 lead atoms. We show that these structures are stabilized by a feature of the many-body glue part of the interatomic potential.

cond-mat↗

arXiv2002

The favoured cluster structures of model glass formers

We examine the favoured cluster structures for two new potentials, which both behave as monatomic model glass-formers in bulk. We find that the oscillations in the interatomic potential lead to global minima that are non-compact arrangements of linked 13-atom icosahedra. We find that the structural properties of the clusters correlate with the glass-forming propensities of the potentials, and with the fragilities of the corresponding supercooled liquids.

cond-mat↗

arXiv2002

The structure of small lead clusters

We have located the global minimum for all lead clusters with up to 160 atoms using a glue potential to model the interatomic interactions. The lowest-energy structures are not face-centred cubic as suggested previously. Rather, for N<40 the majority of structures are decahedral or hexagonal close-packed, and beyond this size the structures do not correspond to any of the structural forms commonly found in clusters. However, these latter clusters are not simply disordered. High symmetry, magic number clusters are still present, the most prominent of which is the 148-atom D3d hexagonal barrel. We relate these structural preferences back to the form of the interactions.

cond-mat↗