2,817 research outputs found
Theoretical study of finite temperature spectroscopy in van der Waals clusters. II Time-dependent absorption spectra
Using approximate partition functions and a master equation approach, we
investigate the statistical relaxation toward equilibrium in selected CaAr
clusters. The Gaussian theory of absorption (previous article) is employed to
calculate the average photoabsorption intensity associated with the 4s^2->
4s^14p^1 transition of calcium as a function of time during relaxation. In
CaAr_6 and CaAr_10 simple relaxation is observed with a single time scale.
CaAr_13 exhibits much slower dynamics and the relaxation occurs over two
distinct time scales. CaAr_37 shows much slower relaxation with multiple
transients, reminiscent of glassy behavior due to competition between different
low-energy structures. We interpret these results in terms of the underlying
potential energy surfaces for these clusters.Comment: 10 pages, 9 figure
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.Comment: 16 pages, 2 figure
Communication: optimal parameters for basin-hopping global optimization based on Tsallis statistics.
A fundamental problem associated with global optimization is the large free energy barrier for the corresponding solid-solid phase transitions for systems with multi-funnel energy landscapes. To address this issue we consider the Tsallis weight instead of the Boltzmann weight to define the acceptance ratio for basin-hopping global optimization. Benchmarks for atomic clusters show that using the optimal Tsallis weight can improve the efficiency by roughly a factor of two. We present a theory that connects the optimal parameters for the Tsallis weighting, and demonstrate that the predictions are verified for each of the test cases.This work was supported by the ERC and the EPSRC.This is the accepted manuscript version of the article. Copyright 2014 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in J. Chem. Phys. 141, 071101 (2014) and may be found at http://dx.doi.org/10.1063/1.4893344
Protein Structure Prediction Using Basin-Hopping
Associative memory Hamiltonian structure prediction potentials are not overly
rugged, thereby suggesting their landscapes are like those of actual proteins.
In the present contribution we show how basin-hopping global optimization can
identify low-lying minima for the corresponding mildly frustrated energy
landscapes. For small systems the basin-hopping algorithm succeeds in locating
both lower minima and conformations closer to the experimental structure than
does molecular dynamics with simulated annealing. For large systems the
efficiency of basin-hopping decreases for our initial implementation, where the
steps consist of random perturbations to the Cartesian coordinates. We
implemented umbrella sampling using basin-hopping to further confirm when the
global minima are reached. We have also improved the energy surface by
employing bioinformatic techniques for reducing the roughness or variance of
the energy surface. Finally, the basin-hopping calculations have guided
improvements in the excluded volume of the Hamiltonian, producing better
structures. These results suggest a novel and transferable optimization scheme
for future energy function development
Taming the rugged landscape: production, reordering, and stabilization of selected cluster inherent structures in the X_(13-n)Y_n system
We present studies of the potential energy landscape of selected binary
Lennard-Jones thirteen atom clusters. The effect of adding selected impurity
atoms to a homogeneous cluster is explored. We analyze the energy landscapes of
the studied systems using disconnectivity graphs. The required inherent
structures and transition states for the construction of disconnectivity graphs
are found by combination of conjugate gradient and eigenvector-following
methods. We show that it is possible to controllably induce new structures as
well as reorder and stabilize existing structures that are characteristic of
higher-lying minima. Moreover, it is shown that the selected structures can
have experimentally relevant lifetimes.Comment: 12 pages, 14 figures, submitted to J. Chem. Phys. Reasons for
replacing a paper: figures 2, 3, 7 and 11 did not show up correctl
Saddle Points and Dynamics of Lennard-Jones Clusters, Solids and Supercooled Liquids
The properties of higher-index saddle points have been invoked in recent
theories of the dynamics of supercooled liquids. Here we examine in detail a
mapping of configurations to saddle points using minimization of , which has been used in previous work to support these theories. The
examples we consider are a two-dimensional model energy surface and binary
Lennard-Jones liquids and solids. A shortcoming of the mapping is its failure
to divide the potential energy surface into basins of attraction surrounding
saddle points, because there are many minima of that do not
correspond to stationary points of the potential energy. In fact, most liquid
configurations are mapped to such points for the system we consider. We
therefore develop an alternative route to investigate higher-index saddle
points and obtain near complete distributions of saddles for small
Lennard-Jones clusters. The distribution of the number of stationary points as
a function of the index is found to be Gaussian, and the average energy
increases linearly with saddle point index in agreement with previous results
for bulk systems.Comment: 14 pages, 7 figure
Energy Landscape and Global Optimization for a Frustrated Model Protein
The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure
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