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Biomedical subjects

D J Wales

Publications and source records attributed to D J Wales.

8 recordsLinked to original sources
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.

Journal Article↗
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.

Journal Article↗
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.

Journal Article↗
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.

Algorithms↗
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.

Journal Article↗
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

Journal Article↗