134 research outputs found
Basin Hopping with Occasional Jumping
Basin-Hopping (BH) or Monte-Carlo Minimization (MCM) is so far the most
reliable algorithms in chemical physics to search for the lowest-energy
structure of atomic clusters and macromolecular systems. BH transforms the
complex energy landscape into a collection of basins, and explores them by
hopping, which is achieved by random Monte Carlo moves and acceptance/rejection
using the Metropolis criterion. In this report, we introduce the jumping
process in addition to the hopping process in BH. Jumping are invoked when the
hopping stagnates by reaching the local optima, and are achieved using the
Monte Carlo move at the temperature without rejection. Our
Basin-Hopping with Occasional Jumping (BHOJ) algorithm is applied to the
Lennard-Jones clusters of several notoriously difficult sizes. It was found
that the probability of locating the true global optima using BHOJ is
significantly higher than the original BH
Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders
Purpose: To identify the genomic location of previously uncharacterized canine retina-expressed expressed sequence tags (ESTs), and thus identify potential candidate genes for heritable retinal disorders. Methods: A set of over 500 retinal canine ESTs were mapped onto the canine genome using the RHDF ₅₀₀₀₋₂ radiation hybrid (RH) panel, and the resulting map positions were compared to their respective localization in the CanFam2 assembly of the canine genome sequence. Results: Unique map positions could be assigned for 99% of the mapped clones, of which only 29% showed significant homology to known RefSeq sequences. A comparison between RH map and sequence assembly indicated some areas of discrepancy. Retinal expressed genes were not concentrated in particular areas of the canine genome, and also were located on the canine Y chromosome (CFAY). Several of the EST clones were located within areas of conserved synteny to human retinal disease loci. Conclusions: RH mapping of canine retinal ESTs provides insight into the location of potential candidate genes for hereditary retinal disorders, and, by comparison with the assembled canine genome sequence, highlights inconsistencies with the current assembly. Regions of conserved synteny between the canine and the human genomes allow this information to be extrapolated to identify potential positional candidate genes for mapped human retinal disorders. Furthermore, these ESTs can help identify novel or uncharacterized genes of significance for better understanding of retinal morphology, physiology, and pathology.10 page(s
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
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
Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique
The potential energy surface (PES) of Lennard-Jones clusters is investigated
using the activation-relaxation technique (ART). This method defines events in
the configurational energy landscape as a two-step process: (a) a configuration
is first activated from a local minimum to a nearby saddle-point and (b) is
then relaxed to a new minimum. Although ART has been applied with success to a
wide range of materials such as a-Si, a-SiO2 and binary Lennard-Jones glasses,
questions remain regarding the biases of the technique. We address some of
these questions in a detailed study of ART-generated events in Lennard-Jones
(LJ) clusters, a system for which much is already known. In particular, we
study the distribution of saddle-points, the pathways between configurations,
and the reversibility of paths. We find that ART can identify all trajectories
with a first-order saddle point leaving a given minimum, is fully reversible,
and samples events following the Boltzmann weight at the saddle point.Comment: 8 pages, 7 figures in postscrip
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
Entropic effects on the structure of Lennard-Jones clusters
We examine in detail the causes of the structural transitions that occur for
those small Lennard-Jones clusters that have a non-icosahedral global minima.
Based on the principles learned from these examples we develop a method to
construct structural phase diagrams that show in a coarse-grained manner how
the equilibrium structure of large clusters depends on both size and
temperature. The method can be augmented to account for anharmonicity and
quantum effects. Our results illustrate that the vibrational entropy can play a
crucial role in determining the equilibrium structure of a cluster.Comment: 13 pages, 9 figure
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2–3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3–6 Å RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at
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