3,714 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
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
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
A Poset Connected to Artin Monoids of Simply Laced Type
Let W be a Weyl group whose type is a simply laced Dynkin diagram. On several
W-orbits of sets of mutually commuting reflections, a poset is described which
plays a role in linear representatons of the corresponding Artin group A. The
poset generalizes many properties of the usual order on positive roots of W
given by height. In this paper, a linear representation of the positive monoid
of A is defined by use of the poset
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
BMW algebras of simply laced type
It is known that the recently discovered representations of the Artin groups
of type A_n, the braid groups, can be constructed via BMW algebras. We
introduce similar algebras of type D_n and E_n which also lead to the newly
found faithful representations of the Artin groups of the corresponding types.
We establish finite dimensionality of these algebras. Moreover, they have
ideals I_1 and I_2 with I_2 contained in I_1 such that the quotient with
respect to I_1 is the Hecke algebra and I_1/I_2 is a module for the
corresponding Artin group generalizing the Lawrence-Krammer representation.
Finally we give conjectures on the structure, the dimension and parabolic
subalgebras of the BMW algebra, as well as on a generalization of deformations
to Brauer algebras for simply laced spherical type other than A_n.Comment: 39 page
Understanding fragility in supercooled Lennard-Jones mixtures. II. Potential energy surface
We numerically investigated the connection between isobaric fragility and the
properties of high-order stationary points of the potential energy surface in
different supercooled Lennard-Jones mixtures. The increase of effective
activation energies upon supercooling appears to be driven by the increase of
average potential energy barriers measured by the energy dependence of the
fraction of unstable modes. Such an increase is sharper, the more fragile is
the mixture. Correlations between fragility and other properties of high-order
stationary points, including the vibrational density of states and the
localization features of unstable modes, are also discussed.Comment: 13 pages, 13 figures, minor revisions, one figure adde
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