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D J Wales

Publications and source records attributed to D J Wales.

12 recordsLinked to original sources
PubMed2006

Global potential energy minima of C60(H2O)n clusters.

Likely candidates for the global potential energy minima of C60(H2O)n clusters with n < or = 21 are found using basin-hopping global optimization. The potential energy surfaces are constructed using the TIP4P intermolecular potential for the water molecules, a Lennard-Jones water-fullerene potential, and a water-fullerene polarization potential, which depends on the first few nonvanishing C60 multipole polarizabilities. This combination produces a rather hydrophobic water-fullerene interaction. As a consequence, the water component of the lowest C60(H2O)n minima is quite closely related to low-lying minima of the corresponding TIP4P (H2O)n clusters. In most cases, the geometrical substructure of the water molecules in the C60(H2O)n global minimum coincides with that of the corresponding free water cluster. Exceptions occur when the interaction with C60 induces a change in geometry. This qualitative picture does not change significantly if we use the TIP3P model for the water-water interaction. Structures such as C60@(H2O)60, in which the water molecules surround the C60 fullerene, correspond to local minima with much higher potential energies. For such a structure to become the global minimum, the magnitude of the water-fullerene interaction must be increased to an unphysical value.

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PubMed2005

Finite-size effects in the dynamics and thermodynamics of two-dimensional Coulomb clusters.

The dynamics and thermodynamics of melting in two-dimensional Coulomb clusters is revisited using molecular dynamics and Monte Carlo simulations. Several parameters are considered, including the Lindemann index, the largest Lyapunov exponent, and the diffusion constant. In addition to the orientational and radial melting processes, isomerizations and complex size effects are seen to occur in a very similar way to atomic and molecular clusters. The results are discussed in terms of the energy landscape represented through disconnectivity graphs, with proper attention paid to the broken ergodicity problems in simulations. Clusters bound by 1/r3 and e(-kappar)/r forces, and heterogeneous clusters made of singly and doubly charged species, are also studied, as well as the evolution toward larger systems.

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PubMed2005

Stacked clusters of polycyclic aromatic hydrocarbon molecules.

Clusters of polycyclic aromatic hydrocarbon (PAH) molecules are modeled using explicit all-atom potentials using a rigid-body approximation. The considered range of PAHs goes from pyrene (C10H8) to circumcoronene (C54H18) and clusters containing between 2 and 32 molecules are investigated. In addition to the usual repulsion-dispersion interactions, electrostatic point-charge interactions are incorporated, as obtained from density functional theory calculations. The general electrostatic distribution in neutral or singly charged PAHs is reproduced well using a fluctuating-charges analysis, which provides an adequate description of the multipolar distribution. Global optimization is performed using a variety of methods, including basin-hopping and parallel tempering Monte Carlo. We find evidence that stacking the PAH molecules generally yields the most stable motif. A structural transition between one-dimensional stacks and three-dimensional shapes built from multiple stacks is observed at larger sizes, and the threshold for this transition increases with the size of the monomer. Larger aggregates seem to evolve toward the packing observed for benzene in bulk. Difficulties met in optimizing these clusters are analyzed in terms of the strong anisotropy of the molecules. We also discuss segregation in heterogeneous clusters and vibrational properties in the context of astrophysical observations.

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PubMed2004

Lowest-energy structures of (C60)nX (X=Li+,Na+,K+,Cl-) and (C60)nYCl (Y=Li,Na,K) clusters for n</=13.

Basin-hopping global optimization is used to find likely candidates for the lowest minima on the potential energy surface of (C(60))(n)X (X=Li(+),Na(+),K(+),Cl(-)) and (C(60))(n)YCl (Y=Li,Na,K) clusters with n</=13. The energy is evaluated using the Girifalco form for the C(60) intermolecular potential along with a polarization potential, which depends on the first few nonvanishing C(60) multipole polarizabilities. We find that the ions occupy interstitial sites of a (C(60))(n) cluster, the coordination shell being triangular for Li(+), tetrahedral for Na(+) and K(+), and octahedral for Cl(-). When the required coordination site does not exist in the corresponding (C(60))(n) global minimum, the lowest minimum of the doped system may be based on an alternative geometry. This situation is particularly common in the Cl(-) complexes, where the (C(60))(n) global minima with icosahedral packing change into decahedral or closed-packed forms for the ions. In all the ions we find a significant binding energy for the doped cluster. In the alkali chloride complexes the preferred coordination for the diatomic moiety is octahedral and is basically determined by the Cl(-) ion. However, the smaller polarization energies in this case mean that a change in structure from the (C(60))(n) global minimum does not necessarily occur if there is no octahedral site.

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PubMed2001

A microscopic basis for the global appearance of energy landscapes.

It is shown that the appearance of a multidimensional potential energy surface, or potential energy landscape, can be related to the form of the interatomic or intermolecular potential. Catastrophe theory enables us to describe how the geometry of the surface changes with parameters in the potential, and provides universal scaling relations that explain, for example, the asymmetric reaction profiles observed for systems bound by long-range forces. The principal result is an unexpected connection between barrier heights, path lengths, and vibrational frequencies, with applications to a wide variety of problems in chemical physics, ranging from Hammond's postulate in organic chemistry, to the relaxation dynamics of complex systems such as glasses and biomolecules.

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PubMed2001

Polytetrahedral clusters.

By studying the structures of clusters bound by a model potential that favors polytetrahedral order, we find a previously unknown series of "magic numbers" (i.e., sizes of special stability) whose polytetrahedral structures are characterized by disclination networks that are analogous to hydrocarbons.

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PubMed2001

Global optimization and the energy landscapes of Dzugutov clusters.

The global minima of clusters bound by a Dzugutov potential form non-compact polytetrahedral clusters mainly composed of interpenetrating and face-sharing 13-atom icosahedra. As the size increases, these icosahedral units first form linear arrays, then two-dimensional rings, then three-dimensional networks. Characterization of the energy landscapes of these clusters shows that they are particularly rough and generally exhibit a multiple-funnel topography. These results provide new insights into the structure and dynamics of bulk supercooled Dzugutov liquids and the form of the bulk phase diagram.

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PubMed1999

Global optimization of clusters, crystals, and biomolecules.

Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design of microprocessor circuitry. Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules. These methods have produced promising results and should enable larger and more complex systems to be treated in the future.

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PubMed1999

Structural relaxation in atomic clusters: master equation dynamics.

The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters, and the double funnel landscape of the 38-atom Lennard-Jones cluster. Interwell rate constants are calculated using Rice-Ramsperger-Kassel-Marcus theory within the harmonic approximation, but anharmonic model partition functions are also considered. Decreasing the range of the potential in the Morse clusters is shown to hinder relaxation toward the global minimum, and this effect is related to the concomitant changes in the energy landscape. The relaxation modes that emerge from the master equation are interpreted and analyzed to extract interfunnel rate constants for the Lennard-Jones cluster. Since this system is too large for a complete characterization of the energy landscape, the conditions under which the master equation can be applied to a limited database are explored. Connections are made to relaxation processes in proteins and structural glasses.

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PubMed1991

Stable configurations of confined cold ionic systems.

The simple structures formed by charged particles confined in a harmonic potential have been investigated and the configurations of minimum potential energy were identified. For fewer than 12 particles these form polyhedrons centered on the origin. For structures with 13-22 particles one sits in the middle, for 23-26 particles two are in the interior, etc., until a third shell starts forming at 60. When the isotropy of the trap is changed, distortions and discrete phase changes are seen. These structures should correspond to ones formed in ion traps at very low temperatures

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