Stochastic simulation of time-series models combined with geostatistics to predict water-table scenarios in a Guarani Aquifer System outcrop area, Brazil

Stochastic methods based on time-series modeling combined with geostatistics can be useful tools to describe the variability of water-table levels in time and space and to account for uncertainty. Monitoring water-level networks can give information about the dynamic of the aquifer domain in both dimensions. Time-series modeling is an elegant way to treat monitoring data without the complexity of physical mechanistic models. Time-series model predictions can be interpolated spatially, with the spatial differences in water-table dynamics determined by the spatial variation in the system properties and the temporal variation driven by the dynamics of the inputs into the system. An integration of stochastic methods is presented, based on time-series modeling and geostatistics as a framework to predict water levels for decision making in groundwater management and land-use planning. The methodology is applied in a case study in a Guarani Aquifer System (GAS) outcrop area located in the southeastern part of Brazil. Communication of results in a clear and understandable form, via simulated scenarios, is discussed as an alternative, when translating scientific knowledge into applications of stochastic hydrogeology in large aquifers with limited monitoring network coverage like the GAS.

Generalized Metropolis dynamics with a generalized master equation: An approach for time-independent and time-dependent Monte Carlo simulations of generalized spin systems

The extension of Boltzmann-Gibbs thermostatistics, proposed by Tsallis, introduces an additional parameter q to the inverse temperature beta. Here, we show that a previously introduced generalized Metropolis dynamics to evolve spin models is not local and does not obey the detailed energy balance. In this dynamics, locality is only retrieved for q = 1, which corresponds to the standard Metropolis algorithm. Nonlocality implies very time-consuming computer calculations, since the energy of the whole system must be reevaluated when a single spin is flipped. To circumvent this costly calculation, we propose a generalized master equation, which gives rise to a local generalized Metropolis dynamics that obeys the detailed energy balance. To compare the different critical values obtained with other generalized dynamics, we perform Monte Carlo simulations in equilibrium for the Ising model. By using short-time nonequilibrium numerical simulations, we also calculate for this model the critical temperature and the static and dynamical critical exponents as functions of q. Even for q not equal 1, we show that suitable time-evolving power laws can be found for each initial condition. Our numerical experiments corroborate the literature results when we use nonlocal dynamics, showing that short-time parameter determination works also in this case. However, the dynamics governed by the new master equation leads to different results for critical temperatures and also the critical exponents affecting universality classes. We further propose a simple algorithm to optimize modeling the time evolution with a power law, considering in a log-log plot two successive refinements.

Multi-planet extrasolar systems - detection and dynamics

20 years after the discovery of the first planets outside our solar system, the current exoplanetary population includes more than 700 confirmed planets around main sequence stars. Approximately 50% belong to multiple-planet systems in very diverse dynamical configurations, from two-planet hierarchical systems to multiple resonances that could only have been attained as the consequence of a smooth large-scale orbital migration. The first part of this paper reviews the main detection techniques employed for the detection and orbital characterization of multiple-planet systems, from the (now) classical radial velocity (RV) method to the use of transit time variations (TTV) for the identification of additional planetary bodies orbiting the same star. In the second part we discuss the dynamical evolution of multi-planet systems due to their mutual gravitational interactions. We analyze possible modes of motion for hierarchical, secular or resonant configurations, and what stability criteria can be defined in each case. In some cases, the dynamics can be well approximated by simple analytical expressions for the Hamiltonian function, while other configurations can only be studied with semi-analytical or numerical tools. In particular, we show how mean-motion resonances can generate complex structures in the phase space where different libration islands and circulation domains are separated by chaotic layers. In all cases we use real exoplanetary systems as working examples.

Modeling and Identification of an Open-frame Underwater Vehicle: The Yaw Motion Dynamics

A semi-autonomous unmanned underwater vehicle (UUV), named LAURS, is being developed at the Laboratory of Sensors and Actuators at the University of Sao Paulo. The vehicle has been designed to provide inspection and intervention capabilities in specific missions of deep water oil fields. In this work, a method of modeling and identification of yaw motion dynamic system model of an open-frame underwater vehicle is presented. Using an on-board low cost magnetic compass sensor the method is based on the utilization of an uncoupled 1-DOF (degree of freedom) dynamic system equation and the application of the integral method which is the classical least squares algorithm applied to the integral form of the dynamic system equations. Experimental trials with the actual vehicle have been performed in a test tank and diving pool. During these experiments, thrusters responsible for yaw motion are driven by sinusoidal voltage signal profiles. An assessment of the feasibility of the method reveals that estimated dynamic system models are more reliable when considering slow and small sinusoidal voltage signal profiles, i.e. with larger periods and with relatively small amplitude and offset.

Dynamics of adventitious rooting in mini-cuttings of Eucalyptus benthamii x Eucalyptus dunnii

It is possible to determine the optimum time for permanence of vegetative propagules (mini-cuttings) inside a greenhouse for rooting, and this value can be used to optimize the structure of the nursery. The aim of this study was to determine the dynamics of adventitious rooting in mini-cuttings of three clones of Eucalyptus benthamii x Eucalyptus dunnii. Sprouts of H12, H19 and H20 clones were collected from mini-stumps that were planted in gutters containing sand and grown in a semi-hydroponic system. The basal region of the mini-cuttings was immersed in 2,000 mg L-1 indole-3-butyric acid (IBA) solution for 10 seconds. The rooting percentage of the mini-cuttings, the total length of the root system and the rooting rate per mini-cutting were also evaluated at 0 (time of planting), 7, 14, 21, 28, 35, 42, 49 and 56 days. We used logistic and exponential regression to mathematically model the speed of rhizogenesis. The rooting percentage was best represented as a logistic model, and the total length of the root system was best represented as an exponential model. The clones had different speeds of adventitious rooting. The optimum time for permanence of the mini-cuttings inside the greenhouse for rooting was between 35 and 42 days, and varied depending on the genetic material.

An in-depth analysis of the HIV-1/AIDS dynamics by comprehensive mathematical modeling

This work presents major results from a novel dynamic model intended to deterministically represent the complex relation between HIV-1 and the human immune system. The novel structure of the model extends previous work by representing different host anatomic compartments under a more in-depth cellular and molecular immunological phenomenology. Recently identified mechanisms related to HIV-1 infection as well as other well known relevant mechanisms typically ignored in mathematical models of HIV-1 pathogenesis and immunology, such as cell-cell transmission, are also addressed. (C) 2011 Elsevier Ltd. All rights reserved.

Self-similarities of periodic structures for a discrete model of a two-gene system

We report self-similar properties of periodic structures remarkably organized in the two-parameter space for a two-gene system, described by two-dimensional symmetric map. The map consists of difference equations derived from the chemical reactions for gene expression and regulation. We characterize the system by using Lyapunov exponents and isoperiodic diagrams identifying periodic windows, denominated Arnold tongues and shrimp-shaped structures. Period-adding sequences are observed for both periodic windows. We also identify Fibonacci-type series and Golden ratio for Arnold tongues, and period multiple-of-three windows for shrimps. (C) 2012 Elsevier B.V. All rights reserved.

Bifurcation analysis of an aeroelastic system with concentrated nonlinearities

Analytical and numerical analyses of the nonlinear response of a three-degree-of-freedom nonlinear aeroelastic system are performed. Particularly, the effects of concentrated structural nonlinearities on the different motions are determined. The concentrated nonlinearities are introduced in the pitch, plunge, and flap springs by adding cubic stiffness in each of them. Quasi-steady approximation and the Duhamel formulation are used to model the aerodynamic loads. Using the quasi-steady approach, we derive the normal form of the Hopf bifurcation associated with the system's instability. Using the nonlinear form, three configurations including supercritical and subcritical aeroelastic systems are defined and analyzed numerically. The characteristics of these different configurations in terms of stability and motions are evaluated. The usefulness of the two aerodynamic formulations in the prediction of the different motions beyond the bifurcation is discussed.

Analysis of nonlinear dynamics of vocal folds using high-speed video observation and biomechanical modeling

Primary voice production occurs in the larynx through vibrational movements carried out by vocal folds. However, many problems can affect this complex system resulting in voice disorders. In this context, time-frequency-shape analysis based on embedding phase space plots and nonlinear dynamics methods have been used to evaluate the vocal fold dynamics during phonation. For this purpose, the present work used high-speed video to record the vocal fold movements of three subjects and extract the glottal area time series using an image segmentation algorithm. This signal is used for an optimization method which combines genetic algorithms and a quasi-Newton method to optimize the parameters of a biomechanical model of vocal folds based on lumped elements (masses, springs and dampers). After optimization, this model is capable of simulating the dynamics of recorded vocal folds and their glottal pulse. Bifurcation diagrams and phase space analysis were used to evaluate the behavior of this deterministic system in different circumstances. The results showed that this methodology can be used to extract some physiological parameters of vocal folds and reproduce some complex behaviors of these structures contributing to the scientific and clinical evaluation of voice production. (C) 2010 Elsevier Inc. All rights reserved.

Dynamics of the 3:1 resonant planetary systems

Many of the discovered exoplanetary systems are involved inside mean-motion resonances. In this work we focus on the dynamics of the 3:1 mean-motion resonant planetary systems. Our main purpose is to understand the dynamics in the vicinity of the apsidal corotation resonance (ACR) which are stationary solutions of the resonant problem. We apply the semi-analytical method (Michtchenko et al., 2006) to construct the averaged three-body Hamiltonian of a planetary system near a 3:1 resonance. Then we obtain the families of ACR, composed of symmetric and asymmetric solutions. Using the symmetric stable solutions we observe the law of structures (Ferraz-Mello,1988), for different mass ratio of the planets. We also study the evolution of the frequencies of σ1, resonant angle, and Δω, the secular angle. The resonant domains outside the immediate vicinity of ACR are studied using dynamical maps techniques. We compared the results obtained to planetary systems near a 3:1 MMR, namely 55 Cnc b-c, HD 60532 b-c and Kepler 20 b-c.

Stability and dynamics of terrestrial planets in binary star systems: application on Alpha Centauri

Binary stars are frequent in the universe, with about 50% of the known main sequence stars being located at a multiple star system (Abt, 1979). Even though, they are universally thought as second rate sites for the location of exo-planets and the habitable zone, due to the difficulties of detection and high perturbation that could prevent planet formation and long term stability. In this work we show that planets in binary star systems can have regular orbits and remain on the habitable zone. We introduce a stability criterium based on the solution of the restricted three body problem and apply it to describe the short period planar and three-dimentional stability zones of S-type orbits around each star of the Alpha Centauri system. We develop as well a semi-analytical secular model to study the long term dynamics of fictional planets in the habitable zone of those stars and we verify that planets on the habitable zone would be in regular orbits with any eccentricity and with inclination to the binary orbital plane up until 35 degrees. We show as well that the short period oscillations on the semi-major axis is 100 times greater than the Earth's, but at all the time the planet would still be found inside the Habitable zone.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).

Currents controlling sedimentation, deposits recording palaeo-hydrodynamics – lessons from the continental shelf-slope system off SE South America

The continental margin off SE South America hosts one of the world’s most energetic hydrodynamic regimes but also the second largest drainage system of the continent. Both, the ocean current system as well as the fluvial runoff are strongly controlled by the atmospheric circulation modes over the region. The distribution pattern of particular types of sediments on shelf and slope and the long-term built-up of depositional elements within the overall margin architecture are, thus, the product of both, seasonal to millennial variability as well as long-term environmental trends. This talk presents how the combination of different methodological approaches can be used to obtain a comprehensive picture of the variability of a shelf and upper-slope hydrodynamic system during Holocene times. The particular methods applied are: (a) Margin-wide stratigraphic information to elucidate the role of sea level for the oceanographic and sedimentary systems since the last glacial maximum; (b) Palaeoceanographic sediment proxies combined with palaeo-temperature indicating isotopes of bivalve shells to trace lateral shifts in the coastal oceanography (particularly of the shelf front) during the Holocene; (c) Neodymium isotopes to identify the shelf sediment transport routes resulting from the current regime; (d) Sedimentological/geochemical data to show the efficient mechanism of sand export from the shelf to the open ocean; (e) Diatom assemblages and sediment element distributions indicating palaeo-salinity and the changing marine influence to illustrate the Plata runoff history. Sea level has not only controlled the overall configuration of the shelf but also the position of the main sediment routes from the continent towards the ocean. The shelf front has shifted frequently since the last glacial times probably resulting from both, changes in the Westerly Winds intensity and in the shelf width itself. Remarkable is a southward shift of this front during the past two centuries possibly related to anthropogenic influences on the atmosphere. The oceanographic regime with its prominent hydrographic boundaries led to a clear separation of sedimentary provinces since shelf drowning. It is especially the shelf front which enhances shelf sediment export through a continuous high sand supply to the uppermost slope. Finally, the Plata River does not continuously provide sediment to the shelf but shows significant climate-related changes in discharge during the past centuries. Starting from these findings, three major fields of research should, in general, be further developed in future: (i) The immediate interaction of the hydrodynamic and sedimentary systems to close the gaps between deposit information and modern oceanographic dynamics; (ii) Material budget calculations for the marginal ocean system in terms of material fluxes, storage/retention capacities, and critical thresholds; (iii) The role of human activity on the atmospheric, oceanographic and solid material systems to unravel natural vs. anthropogenic effects and feedback mechanisms

Effect of resonant tunneling on exciton dynamics in coupled dot-well nanostructures

Excitonic dynamics in a hybrid dot-well system composed of InAs quantum dots (QDs) and an InGaAs quantum well (QW) is studied by means of femtosecond pump-probe reflection and continuous wave (cw) photoluminescence (PL) spectroscopy. The system is engineered to bring the QW ground exciton state into resonance with the third QD excited state. The resonant tunneling rate is varied by changing the effective barrier thickness between the QD and QW layers. This strongly affects the exciton dynamics in these hybrid structures as compared to isolated QW or QD systems. Optically measured decay times of the coupled system demonstrate dramatically different response to temperature change depending on the strength of the resonant tunneling or coupling strength. This reflects a competition between purely quantum mechanical and thermodynamical processes.