57 research outputs found
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
We describe a global optimization technique using `basin-hopping' in which
the potential energy surface is transformed into a collection of
interpenetrating staircases. This method has been designed to exploit the
features which recent work suggests must be present in an energy landscape for
efficient relaxation to the global minimum. The transformation associates any
point in configuration space with the local minimum obtained by a geometry
optimization started from that point, effectively removing transition state
regions from the problem. However, unlike other methods based upon hypersurface
deformation, this transformation does not change the global minimum. The lowest
known structures are located for all Lennard-Jones clusters up to 110 atoms,
including a number that have never been found before in unbiased searches.Comment: 8 pages, 3 figures, revte
Unbiased Global Optimization of Lennard-Jones Clusters for N <= 201 by Conformational Space Annealing Method
We apply the conformational space annealing (CSA) method to the Lennard-Jones
clusters and find all known lowest energy configurations up to 201 atoms,
without using extra information of the problem such as the structures of the
known global energy minima. In addition, the robustness of the algorithm with
respect to the randomness of initial conditions of the problem is demonstrated
by ten successful independent runs up to 183 atoms. Our results indicate that
the CSA method is a general and yet efficient global optimization algorithm
applicable to many systems.Comment: revtex, 4 pages, 2 figures. Physical Review Letters, in pres
New Tetrahedral Global Minimum for the 98-atom Lennard-Jones Cluster
A new atomic cluster structure corresponding to the global minimum of the
98-atom Lennard-Jones cluster has been found using a variant of the
basin-hopping global optimization algorithm. The new structure has an unusual
tetrahedral symmetry with an energy of -543.665361, which is 0.022404 lower
than the previous putative global minimum. The new LJ_98 structure is of
particular interest because its tetrahedral symmetry establishes it as one of
only three types of exceptions to the general pattern of icosahedral structural
motifs for optimal LJ microclusters. Similar to the other exceptions the global
minimum is difficult to find because it is at the bottom of a narrow funnel
which only becomes thermodynamically most stable at low temperature.Comment: 3 pages, 2 figures, revte
Trends in template/fragment-free protein structure prediction
Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward
Towards crystal structure prediction of complex organic compounds - a report on the fifth blind test
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1: 1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome
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