Algerian Terrorism

These are the words of M. Jacques Soustelle, Governor General of French Algeria in 1955. He had just returned from viewing the bodies of dozens of massacred European settlers, who had looked lo him for the protection of their lives and property. This description of fatalism and despair dramatically portrays, aU that those who would apply terror hope to achieve

Supersymmetric Langevin equation to explore free energy landscapes

The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose large time-scale separation hampers the usefulness of standard molecular dynamics techniques. The first realistic application is here presented. The system chosen is a minimalist model for a short alanine peptide exhibiting a helix-coil transition.Comment: 9 pages, 9 figures, RevTeX 4 v2: conclusive section enlarged, references adde

Prediction of long and short time rheological behavior in soft glassy materials

We present an effective time approach to predict long and short time rheological behavior of soft glassy materials from experiments carried out over practical time scales. Effective time approach takes advantage of relaxation time dependence on aging time that allows time-aging time superposition even when aging occurs over the experimental timescales. Interestingly experiments on variety of soft materials demonstrate that the effective time approach successfully predicts superposition for diverse aging regimes ranging from sub-aging to hyper-aging behaviors. This approach can also be used to predict behavior of any response function in molecular as well as spin glasses.Comment: 13 pages, 4 figure

Quantum annealing of the Traveling Salesman Problem

We propose a path-integral Monte Carlo quantum annealing scheme for the symmetric Traveling Salesman Problem, based on a highly constrained Ising-like representation, and we compare its performance against standard thermal Simulated Annealing. The Monte Carlo moves implemented are standard, and consist in restructuring a tour by exchanging two links (2-opt moves). The quantum annealing scheme, even with a drastically simple form of kinetic energy, appears definitely superior to the classical one, when tested on a 1002 city instance of the standard TSPLIB.Comment: 5 pages, 2 figure

The Gentlest Ascent Dynamics

Dynamical systems that describe the escape from the basins of attraction of stable invariant sets are presented and analyzed. It is shown that the stable fixed points of such dynamical systems are the index-1 saddle points. Generalizations to high index saddle points are discussed. Both gradient and non-gradient systems are considered. Preliminary results on the nature of the dynamical behavior are presented

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

Topological methods for searching barriers and reaction paths

We present a family of algorithms for the fast determination of reaction paths and barriers in phase space and the computation of the corresponding rates. The method requires the reaction times be large compared to the microscopic time, irrespective of the origin - energetic, entropic, cooperative - of the timescale separation. It lends itself to temperature cycling as in simulated annealing and to activation-relaxation routines. The dynamics is ultimately based on supersymmetry methods used years ago to derive Morse theory. Thus, the formalism automatically incorporates all relevant topological information.Comment: 4 pages, 4 figures, RevTex

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

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