Population-based local search for protein folding simulation in the MJ energy model and cubic lattices

We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the population. In terms of the total number of energy function evaluations both methods perform equally well, however. PLS has the potential of being parallelised with an expected speed-up in the region of the population size. Furthermore, both methods require a significant smaller number of function evaluations when compared to Monte Carlo simulations with kink-jump moves. (C) 2009 Elsevier Ltd. All rights reserved.

Nonlinear theory of solitary waves associated with longitudinal particle motion in lattices - Application to longitudinal grain oscillations in a dust crystal

The nonlinear aspects of longitudinal motion of interacting point masses in a lattice are revisited, with emphasis on the paradigm of charged dust grains in a dusty plasma (DP) crystal. Different types of localized excitations, predicted by nonlinear wave theories, are reviewed and conditions for their occurrence (and characteristics) in DP crystals are discussed. Making use of a general formulation, allowing for an arbitrary (e.g. the Debye electrostatic or else) analytic potential form phi(r) and arbitrarily long site-to-site range of interactions, it is shown that dust-crystals support nonlinear kink-shaped localized excitations propagating at velocities above the characteristic DP lattice sound speed v(0). Both compressive and rarefactive kink-type excitations are predicted, depending on the physical parameter values, which represent pulse- (shock-)like coherent structures for the dust grain relative displacement. Furthermore, the existence of breather-type localized oscillations, envelope-modulated wavepackets and shocks is established. The relation to previous results on atomic chains as well as to experimental results on strongly-coupled dust layers in gas discharge plasmas is discussed.

Localized excitations of charged dust grains in dusty plasma lattices

The nonlinear aspects of charged dust grain motion in a one-dimensional dusty plasma (DP) monolayer are discussed. Both horizontal (longitudinal, acoustic mode) and vertical (transverse, optic mode) displacements are considered, and various types of localized excitations are reviewed, in a continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic longitudinal solitary excitations, as well as modulated envelope (either longitudinal or transverse) localized modes. The possibility for Discrete Breather (DB-) type excitations (Intrinsic Localized Modes, ILMs) to occur is investigated, from first principles. These highly localized excitations owe their existence to lattice discreteness, in combination with the interaction and/or
substrate (sheath) potential nonlinearity. This possibility may open new directions in DP- related research. The relation to previous results on atomic chains as well as to experimental results on strongly-coupled dust layers in gas discharge plasmas is discussed.

Discrete solitons and vortices in hexagonal and honeycomb lattices: Existence, stability, and dynamics

We consider a prototypical dynamical lattice model, namely, the discrete nonlinear Schrodinger equation on nonsquare lattice geometries. We present a systematic classification of the solutions that arise in principal six-lattice-site and three-lattice-site contours in the form of both discrete multipole solitons and discrete vortices. Additionally to identifying the possible states, we analytically track their linear stability both qualitatively and quantitatively. We find that among the six-site configurations, the

Discrete breathers in hexagonal dusty plasma lattices

The occurrence of single-site or multisite localized vibrational modes, also called discrete breathers, in two-dimensional hexagonal dusty plasma lattices is investigated. The system is described by a Klein-Gordon hexagonal lattice characterized by a negative coupling parameter epsilon in account of its inverse dispersive behavior. A theoretical analysis is performed in order to establish the possibility of existence of single as well as three-site discrete breathers in such systems. The study is complemented by a numerical investigation based on experimentally provided potential forms. This investigation shows that a dusty plasma lattice can support single-site discrete breathers, while three-site in phase breathers could exist if specific conditions, about the intergrain interaction strength, would hold. On the other hand, out of phase and vortex three-site breathers cannot be supported since they are highly unstable.

Existence and stability of multisite breathers in honeycomb and hexagonal lattices

We study the existence and stability of multisite discrete breathers in two prototypical non-square Klein-Gordon lattices, namely a honeycomb and a hexagonal one. In the honeycomb case we consider six-site configurations and find that for soft potential and positive coupling the out-of-phase breather configuration and the charge-two vortex breather are linearly stable, while the in-phase and charge-one vortex states are unstable. In the hexagonal lattice, we first consider three-site configurations. In the case of soft potential and positive coupling, the in-phase configuration is unstable and the charge-one vortex is linearly stable. The out-of-phase configuration here is found to always be linearly unstable. We then turn to six-site configurations in the hexagonal lattice. The stability results in this case are the same as in the six-site configurations in the honeycomb lattice. For all configurations in both lattices, the stability results are reversed in the setting of either hard potential or negative coupling. The study is complemented by numerical simulations which are in very good agreement with the theoretical predictions. Since neither the form of the on-site potential nor the sign of the coupling parameter involved have been prescribed, this description can accommodate inverse-dispersive systems (e. g. supporting backward waves) such as transverse dust-lattice oscillations in dusty plasma (Debye) crystals or analogous modes in molecular chains.

Nonlinear excitations in strongly-coupled plasma lattices: envelope solitons, kinks and intrinsic localized modes

Ensembles of charged particles (plasmas) are a highly complex form of matter, most often modeled as a many-body system characterized by weak inter-particle interactions (electrostatic coupling). However, strongly-coupled plasma configurations have recently been produced in laboratory, either by creating ultra-cold plasmas confined in a trap or by manipulating dusty plasmas in discharge experiments. In this paper, the nonlinear aspects involved in the motion of charged dust grains in a one-dimensional plasma monolayer (crystal) are discussed. Different types of collective excitations are reviewed, and characteristics and conditions for their occurrence in dusty plasma crystals are discussed, in a quasi-continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic solitary longitudinal excitations, as well as modulated envelope localized modes associated with longitudinal and transverse vibrations. Furthermore, the possibility for intrinsic localized modes (ILMs) — Discrete Breathers (DBs) — to occur is investigated, from first principles. The effect of mode-coupling is also briefly considered. The relation to previous results on atomic chains, and also to experimental results on strongly-coupled dust layers in gas discharge plasmas, is briefly discussed.

Separable Banach lattices on which every bounded linear operator is regular

We give a complete description of those separable Banach lattices E with the property that every bounded linear from E into itself is the difference of two positive operators.