CONTRA: Improving the performance of dynamic investigations in natural abundance organic solids by mirror-symmetric constant-time CODEX

We present a minor but essential modification to the CODEX 1D-MAS exchange experiment. The new CONTRA method, which requires minor changes of the original sequence only, has advantages over the previously introduced S-CODEX, since it is less sensitive to artefacts caused by finite pulse lengths. The performance of this variant, including the finite pulse effect, was confirmed by SIMPSON calculations and demonstrated on a number of dynamic systems. (C) 2007 Elsevier Inc. All rights reserved.

Effects of species turnover on reserve site selection in a fragmented landscape

Changes in species composition is an important process in many ecosystems but rarely considered in systematic reserve site selection. To test the influence of temporal variability in species composition on the establishment of a reserve network, we compared network configurations based on species data of small mammals and frogs sampled during two consecutive years in a fragmented Atlantic Forest landscape (SE Brazil). Site selection with simulated annealing was carried out with the datasets of each single year and after merging the datasets of both years. Site selection resulted in remarkably divergent network configurations. Differences are reflected in both the identity of the selected fragments and in the amount of flexibility and irreplaceability in network configuration. Networks selected when data for both years were merged did not include all sites that were irreplaceable in one of the 2 years. Results of species number estimation revealed that significant changes in the composition of the species community occurred. Hence, temporal variability of community composition should be routinely tested and considered in systematic reserve site selection in dynamic systems.

Exact Search Directions for Optimization of Linear and Nonlinear Models Based on Generalized Orthonormal Functions

A novel technique for selecting the poles of orthonormal basis functions (OBF) in Volterra models of any order is presented. It is well-known that the usual large number of parameters required to describe the Volterra kernels can be significantly reduced by representing each kernel using an appropriate basis of orthonormal functions. Such a representation results in the so-called OBF Volterra model, which has a Wiener structure consisting of a linear dynamic generated by the orthonormal basis followed by a nonlinear static mapping given by the Volterra polynomial series. Aiming at optimizing the poles that fully parameterize the orthonormal bases, the exact gradients of the outputs of the orthonormal filters with respect to their poles are computed analytically by using a back-propagation-through-time technique. The expressions relative to the Kautz basis and to generalized orthonormal bases of functions (GOBF) are addressed; the ones related to the Laguerre basis follow straightforwardly as a particular case. The main innovation here is that the dynamic nature of the OBF filters is fully considered in the gradient computations. These gradients provide exact search directions for optimizing the poles of a given orthonormal basis. Such search directions can, in turn, be used as part of an optimization procedure to locate the minimum of a cost-function that takes into account the error of estimation of the system output. The Levenberg-Marquardt algorithm is adopted here as the optimization procedure. Unlike previous related work, the proposed approach relies solely on input-output data measured from the system to be modeled, i.e., no information about the Volterra kernels is required. Examples are presented to illustrate the application of this approach to the modeling of dynamic systems, including a real magnetic levitation system with nonlinear oscillatory behavior.

Critical behavior of a contact process with aperiodic transition rates

We performed Monte Carlo simulations to investigate the steady-state critical behavior of a one-dimensional contact process with an aperiodic distribution of rates of transition. As in the presence of randomness, spatial fluctuations can lead to changes of critical behavior. For sufficiently weak fluctuations, we give numerical evidence to show that there is no departure from the universal critical behavior of the underlying uniform model. For strong spatial fluctuations, the analysis of the data indicates a change of critical universality class.

Shared information in stationary states at criticality

We consider bipartitions of one-dimensional extended systems whose probability distribution functions describe stationary states of stochastic models. We define estimators of the information shared between the two subsystems. If the correlation length is finite, the estimators stay finite for large system sizes. If the correlation length diverges, so do the estimators. The definition of the estimators is inspired by information theory. We look at several models and compare the behaviors of the estimators in the finite-size scaling limit. Analytical and numerical methods as well as Monte Carlo simulations are used. We show how the finite-size scaling functions change for various phase transitions, including the case where one has conformal invariance.

Cellular automaton model for molecular traffic jams

We consider the time evolution of an exactly solvable cellular automaton with random initial conditions both in the large-scale hydrodynamic limit and on the microscopic level. This model is a version of the totally asymmetric simple exclusion process with sublattice parallel update and thus may serve as a model for studying traffic jams in systems of self-driven particles. We study the emergence of shocks from the microscopic dynamics of the model. In particular, we introduce shock measures whose time evolution we can compute explicitly, both in the thermodynamic limit and for open boundaries where a boundary-induced phase transition driven by the motion of a shock occurs. The motion of the shock, which results from the collective dynamics of the exclusion particles, is a random walk with an internal degree of freedom that determines the jump direction. This type of hopping dynamics is reminiscent of some transport phenomena in biological systems.

Paper surfaces and dynamical limits

It is very common in mathematics to construct surfaces by identifying the sides of a polygon together in pairs: For example, identifying opposite sides of a square yields a torus. In this article the construction is considered in the case where infinitely many pairs of segments around the boundary of the polygon are identified. The topological, metric, and complex structures of the resulting surfaces are discussed: In particular, a condition is given under which the surface has a global complex structure (i.e., is a Riemann surface). In this case, a modulus of continuity for a uniformizing map is given. The motivation for considering this construction comes from dynamical systems theory: If the modulus of continuity is uniform across a family of such constructions, each with an iteration defined on it, then it is possible to take limits in the family and hence to complete it. Such an application is briefly discussed.

Dynamic portrait of the planetary 2/1 mean-motion resonance - I. Systems with a more massive outer planet

We analyse the global structure of the phase space of the planar planetary 2/1 mean-motion resonance in cases where the outer planet is more massive than its inner companion. Inside the resonant domain, we show the existence of two families of periodic orbits, one associated to the librational motion of resonant angle (sigma-family) and the other related to the circulatory motion of the difference in longitudes of pericentre (Delta pi-family). The well-known apsidal corotation resonances (ACR) appear as intersections between both families. A complex web of secondary resonances is also detected for low eccentricities, whose strengths and positions are dependent on the individual masses and spatial scale of the system. The construction of dynamical maps for various values of the total angular momentum shows the evolution of the families of stable motion with the eccentricities, identifying possible configurations suitable for exoplanetary systems. For low-moderate eccentricities, several different stable modes exist outside the ACR. For larger eccentricities, however, all stable solutions are associated to oscillations around the stationary solutions. Finally, we present a possible link between these stable families and the process of resonance capture, identifying the most probable routes from the secular region to the resonant domain, and discussing how the final resonant configuration may be affected by the extension of the chaotic layer around the resonance region.

Dynamic portrait of the planetary 2/1 mean-motion resonance - II. Systems with a more massive inner planet

This paper presents the second part in our study of the global structure of the planar phase space of the planetary three-body problem, when both planets lie in the vicinity of a 2/1 mean-motion resonance. While Paper I was devoted to cases where the outer planet is the more massive body, the present work is devoted to the cases where the more massive body is the inner planet. As before, outside the well-known Apsidal Corotation Resonances (ACR), the phase space shows a complex picture marked by the presence of several distinct regimes of resonant and non-resonant motion, crossed by families of periodic orbits and separated by chaotic zones. When the chosen values of the integrals of motion lead to symmetric ACR, the global dynamics are generally similar to the structure presented in Paper I. However, for asymmetric ACR the resonant phase space is strikingly different and shows a galore of distinct dynamical states. This structure is shown with the help of dynamical maps constructed on two different representative planes, one centred on the unstable symmetric ACR and the other on the stable asymmetric equilibrium solution. Although the study described in the work may be applied to any mass ratio, we present a detailed analysis for mass values similar to the Jupiter-Saturn case. Results give a global view of the different dynamical states available to resonant planets with these characteristics. Some of these dynamical paths could have marked the evolution of the giant planets of our Solar system, assuming they suffered a temporary capture in the 2/1 resonance during the latest stages of the formation of our Solar system.

An incremental space to visualize dynamic data sets

In Information Visualization, adding and removing data elements can strongly impact the underlying visual space. We have developed an inherently incremental technique (incBoard) that maintains a coherent disposition of elements from a dynamic multidimensional data set on a 2D grid as the set changes. Here, we introduce a novel layout that uses pairwise similarity from grid neighbors, as defined in incBoard, to reposition elements on the visual space, free from constraints imposed by the grid. The board continues to be updated and can be displayed alongside the new space. As similar items are placed together, while dissimilar neighbors are moved apart, it supports users in the identification of clusters and subsets of related elements. Densely populated areas identified in the incSpace can be efficiently explored with the corresponding incBoard visualization, which is not susceptible to occlusion. The solution remains inherently incremental and maintains a coherent disposition of elements, even for fully renewed sets. The algorithm considers relative positions for the initial placement of elements, and raw dissimilarity to fine tune the visualization. It has low computational cost, with complexity depending only on the size of the currently viewed subset, V. Thus, a data set of size N can be sequentially displayed in O(N) time, reaching O(N (2)) only if the complete set is simultaneously displayed.