Group Leaders Optimization Algorithm

We present a new global optimization algorithm in which the influence of the leaders in social groups is used as an inspiration for the evolutionary technique which is designed into a group architecture. To demonstrate the efficiency of the method, a standard suite of single and multidimensional optimization functions along with the energies and the geometric structures of Lennard-Jones clusters are given as well as the application of the algorithm on quantum circuit design problems. We show that as an improvement over previous methods, the algorithm scales as N^2.5 for the Lennard-Jones clusters of N-particles. In addition, an efficient circuit design is shown for two qubit Grover search algorithm which is a quantum algorithm providing quadratic speed-up over the classical counterpart

Stress release mechanisms for Cu on Pd(111) in the submonolayer and monolayer regimes

We study the strain relaxation mechanisms of Cu on Pd(111) up to the monolayer regime using two different computational methodologies, basin-hopping global optimization and energy minimization with a repulsive bias potential. Our numerical results are consistent with experimentally observed layer-by-layer growth mode. However, we find that the structure of the Cu layer is not fully pseudomorphic even at low coverages. Instead, the Cu adsorbates forms fcc and hcp stacking domains, separated by partial misfit dislocations. We also estimate the minimum energy path and energy barriers for transitions from the ideal epitaxial state to the fcc-hcp domain pattern.Comment: 4 pages, 4 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

Deceptive signals of phase transitions in small magnetic clusters

We present an analysis of the thermodynamic properties of small transition metal clusters and show how the commonly used indicators of phase transitions like peaks in the specific heat or magnetic susceptibility can lead to deceptive interpretations of the underlying physics. The analysis of the distribution of zeros of the canonical partition function in the whole complex temperature plane reveals the nature of the transition. We show that signals in the magnetic susceptibility at positive temperatures have their origin at zeros lying at negative temperatures.Comment: 4 pages, 5 figures, revtex4, for further information see http://www.smallsystems.d

Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002

Structural Transitions and Global Minima of Sodium Chloride Clusters

In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we determine reaction pathways between the low energy isomers of one of these clusters, (NaCl)35Cl-. The key process in these structural transitions is a highly cooperative rearrangement in which two parts of the nanocrystal slip past one another on a {110} plane in a direction. In this way the nanocrystals can plastically deform, in contrast to the brittle behaviour of bulk sodium chloride crystals at the same temperatures; the nanocrystals have mechanical properties which are a unique feature of their finite size. We also report and compare the global potential energy minima for (NaCl)NCl- using two empirical potentials, and comment on the effect of polarization.Comment: extended version, 13 pages, 8 figures, revte

Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $\beta$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog

Symmetries of microcanonical entropy surfaces

Symmetry properties of the microcanonical entropy surface as a function of the energy and the order parameter are deduced from the invariance group of the Hamiltonian of the physical system. The consequences of these symmetries for the microcanonical order parameter in the high energy and in the low energy phases are investigated. In particular the breaking of the symmetry of the microcanonical entropy in the low energy regime is considered. The general statements are corroborated by investigations of various examples of classical spin systems.Comment: 15 pages, 5 figures include

Slow relaxation to equipartition in spring-chain systems

In this study, one-dimensional systems of masses connected by springs, i.e., spring-chain systems, are investigated numerically. The average kinetic energy of chain-end particles of these systems is larger than that of other particles, which is similar to the behavior observed for systems made of masses connected by rigid links. The energetic motion of the end particles is, however, transient, and the system relaxes to thermal equilibrium after a while, where the average kinetic energy of each particle is the same, that is, equipartition of energy is achieved. This is in contrast to the case of systems made of masses connected by rigid links, where the energetic motion of the end particles is observed in equilibrium. The timescale of relaxation estimated by simulation increases rapidly with increasing spring constant. The timescale is also estimated using the Boltzmann-Jeans theory and is found to be in quite good agreement with that obtained by the simulation