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$_n$ 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 $|\nabla E|^2$, 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 $|\nabla E|^2$ 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