A simple two-module problem to exemplify building-block assembly under crossover

Theoretically and empirically it is clear that a genetic algorithm with crossover will outperform a genetic algorithm without crossover in some fitness landscapes, and vice versa in other landscapes. Despite an extensive literature on the subject, and recent proofs of a principled distinction in the abilities of crossover and non-crossover algorithms for a particular theoretical landscape, building general intuitions about when and why crossover performs well when it does is a different matter. In particular, the proposal that crossover might enable the assembly of good building-blocks has been difficult to verify despite many attempts at idealized building-block landscapes. Here we show the first example of a two-module problem that shows a principled advantage for cross-over. This allows us to understand building-block assembly under crossover quite straightforwardly and build intuition about more general landscape classes favoring crossover or disfavoring it

Apparent phase transitions in finite one-dimensional sine-Gordon lattices

We study the one-dimensional sine-Gordon model as a prototype of roughening phenomena. In spite of the fact that it has been recently proven that this model can not have any phase transition [J. A. Cuesta and A. Sanchez, J. Phys. A 35, 2373 (2002)], Langevin as well as Monte Carlo simulations strongly suggest the existence of a finite temperature separating a flat from a rough phase. We explain this result by means of the transfer operator formalism and show as a consequence that sine-Gordon lattices of any practically achievable size will exhibit this apparent phase transition at unexpectedly large temperatures.Comment: 7 pages, 4 figure

Crossover effects in a discrete deposition model with Kardar-Parisi-Zhang scaling

We simulated a growth model in 1+1 dimensions in which particles are aggregated according to the rules of ballistic deposition with probability p or according to the rules of random deposition with surface relaxation (Family model) with probability 1-p. For any p>0, this system is in the Kardar-Parisi-Zhang (KPZ) universality class, but it presents a slow crossover from the Edwards-Wilkinson class (EW) for small p. From the scaling of the growth velocity, the parameter p is connected to the coefficient of the nonlinear term of the KPZ equation, lambda, giving lambda ~ p^gamma, with gamma = 2.1 +- 0.2. Our numerical results confirm the interface width scaling in the growth regime as W ~ lambda^beta t^beta, and the scaling of the saturation time as tau ~ lambda^(-1) L^z, with the expected exponents beta =1/3 and z=3/2 and strong corrections to scaling for small lambda. This picture is consistent with a crossover time from EW to KPZ growth in the form t_c ~ lambda^(-4) ~ p^(-8), in agreement with scaling theories and renormalization group analysis. Some consequences of the slow crossover in this problem are discussed and may help investigations of more complex models.Comment: 16 pages, 7 figures; to appear in Phys. Rev.

High-Energy Aspects of Solar Flares: Overview of the Volume

In this introductory chapter, we provide a brief summary of the successes and remaining challenges in understanding the solar flare phenomenon and its attendant implications for particle acceleration mechanisms in astrophysical plasmas. We also provide a brief overview of the contents of the other chapters in this volume, with particular reference to the well-observed flare of 2002 July 23Comment: This is the introductory article for a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

Optical nanofibers and spectroscopy

We review our recent progress in the production and characterization of tapered optical fibers with a sub-wavelength diameter waist. Such fibers exhibit a pronounced evanescent field and are therefore a useful tool for highly sensitive evanescent wave spectroscopy of adsorbates on the fiber waist or of the medium surrounding. We use a carefully designed flame pulling process that allows us to realize preset fiber diameter profiles. In order to determine the waist diameter and to verify the fiber profile, we employ scanning electron microscope measurements and a novel accurate in situ optical method based on harmonic generation. We use our fibers for linear and non-linear absorption and fluorescence spectroscopy of surface-adsorbed organic molecules and investigate their agglomeration dynamics. Furthermore, we apply our spectroscopic method to quantum dots on the surface of the fiber waist and to caesium vapor surrounding the fiber. Finally, towards dispersive measurements, we present our first results on building and testing a single-fiber bi-modal interferometer.Comment: 13 pages, 18 figures. Accepted for publication in Applied Physics B. Changes according to referee suggestions: changed title, clarification of some points in the text, added references, replacement of Figure 13

Fast-neutron induced pre-equilibrium reactions on 55Mn and 63,65Cu at energies up to 40 MeV

Excitation functions were measured for the $^{55}$Mn(n,2n)$^{54}$Mn, $^{55}$Mn(n,$\alpha$)$^{52}$V, $^{63}$Cu(n,$\alpha$)$^{60}$Co, $^{65}$Cu(n,2n)$^{64}$Cu, and $^{65}$Cu(n,p)$^{65}$Ni reactions from 13.47 to 14.83 MeV. The experimental cross sections are compared with the results of calculations including all activation channels for the stable isotopes of Mn and Cu, for neutron incident energies up to 50 MeV. Within the energy range up to 20 MeV the model calculations are most sensitive to the parameters related to nuclei in the early stages of the reaction, while the model assumptions are better established by analysis of the data in the energy range 20-40 MeV. While the present analysis has taken advantage of both a new set of accurate measured cross sections around 14 MeV and the larger data basis fortunately available between 20 and 40 MeV for the Mn and Cu isotopes, the need of additional measurements below as well as above 40 MeV is pointed out. Keywords: 55Mn, 63,65Cu, E$\leq$40 MeV, Neutron activation cross section measurements, Nuclear reactions, Model calculations, Manganese, CopperComment: 39 pages, 12 figure

Simultaneous alignment and folding of protein sequences

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically,partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments,partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu

Recent Advances in Understanding Particle Acceleration Processes in Solar Flares

We review basic theoretical concepts in particle acceleration, with particular emphasis on processes likely to occur in regions of magnetic reconnection. Several new developments are discussed, including detailed studies of reconnection in three-dimensional magnetic field configurations (e.g., current sheets, collapsing traps, separatrix regions) and stochastic acceleration in a turbulent environment. Fluid, test-particle, and particle-in-cell approaches are used and results compared. While these studies show considerable promise in accounting for the various observational manifestations of solar flares, they are limited by a number of factors, mostly relating to available computational power. Not the least of these issues is the need to explicitly incorporate the electrodynamic feedback of the accelerated particles themselves on the environment in which they are accelerated. A brief prognosis for future advancement is offered.Comment: This is a chapter in a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

Effect of Local Environment and Stellar Mass on Galaxy Quenching and Morphology at 0.5 < z < 2.0

Large scale structure and cosmolog

Employing Travel Time to Compare the Value of Competing Cultural Organizations

A number of studies have applied non-market valuation techniques to measure the value of cultural goods. Virtually all of these studies are single case applications and rely mostly on stated preferences, such as contingent valuation techniques. We compare the relative value of multiple, competing goods and show how revealed preferences, in particular travel time, may be used for this. In addition, we account for heterogeneity. Using a unique transaction database with the visiting behavior of 80,821 Museum Cardholders to 108 Dutch museums, we propose a latent class application of a logit model to account for the different distances of museums to the population and for differences in willingness-to-travel.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44648/1/10824_2005_Article_5796.pd