Soliton dynamics at an interface between a uniform medium and a nonlinear optical lattice

We study trapping and propagation of a matter-wave soliton through the interface between uniform medium and a nonlinear optical lattice. Different regimes for transmission of a broad and a narrow solitons are investigated. Reflections and transmissions of solitons are predicted as a function of the lattice phase. The existence of a threshold in the amplitude of the nonlinear optical lattice, separating the transmission and reflection regimes, is verified. The localized nonlinear surface state, corresponding to the soliton trapped by the interface, is found. Variational approach predictions are confirmed by numerical simulations for the original Gross-Pitaevskii equation with nonlinear periodic potentials.

Connectivity and dynamics of neuronal networks as defined by the shape of individual neurons

Biological neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of neuron shape on the overall connectivity and dynamics of the emerging networks. The current work addresses this issue by considering simplified neuronal shapes consisting of circular regions (soma/axons) with spokes (dendrites). Networks are grown by placing these patterns randomly in the two-dimensional (2D) plane and establishing connections whenever a piece of dendrite falls inside an axon. Several topological and dynamical properties of the resulting graph are measured, including the degree distribution, clustering coefficients, symmetry of connections, size of the largest connected component, as well as three hierarchical measurements of the local topology. By varying the number of processes of the individual basic patterns, we can quantify relationships between the individual neuronal shape and the topological and dynamical features of the networks. Integrate-and-fire dynamics on these networks is also investigated with respect to transient activation from a source node, indicating that long-range connections play an important role in the propagation of avalanches.

Thermodynamic modeling of pyroelectric and piezoelectric properties of cellular polymers

A thermodynamic approach is presented to model devices manufactured with cellular polymers. They are heterogeneous nonpolar space-charge electrets that exhibit much higher piezoelectricity than the well-known ferroelectric polymers. Their pyroelectric and piezoelectric properties are characterized by adequate coefficients which quantify the performance of devices manufactured with those materials. The method presented in this contribution to calculate those coefficients is exact and consistent avoiding ad hoc simplifications introduced in other approaches. The results obtained by this method allow drawing conclusions regarding device optimization.

Weak measurement: Effect of the detector dynamics

The contribution of the detector dynamics to the weak measurement is analyzed. According to the usual theory [Y. Aharonov, D. Z. Albert, and L. Vaidman, Phys. Rev. Lett. 60, 1351 (1988)] the outcome of a weak measurement with preselection and postselection can be expressed as the real part of a complex number: the weak value. By accounting for the Hamiltonian evolution of the detector, here we find that there is a contribution proportional to the imaginary part of the weak value to the outcome of the weak measurement. This is due to the coherence of the probe being essential for the concept of complex weak value to be meaningful. As a particular example, we consider the measurement of a spin component and find that the contribution of the imaginary part of the weak value is sizable.

Evolutionary dynamics on rugged fitness landscapes: Exact dynamics and information theoretical aspects

The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the random energy model (REM) and by a ferromagnetic version of the REM. The solution method uses the mapping of the evolutionary dynamics into a quantum Ising chain in a transverse field and the Suzuki-Trotter formalism to calculate the transition probabilities between configurations at different times. We find that in the case of the REM landscape the dynamics can exhibit three distinct regimes: pure diffusion or stasis for short times, depending on the fitness of the initial configuration, and a spin-glass regime for large times. The dynamic transition between these dynamical regimes is marked by discontinuities in the mean-fitness as well as in the overlap with the initial reference sequence. The relaxation to equilibrium is described by an inverse time decay. In the ferromagnetic REM, we find in addition to these three regimes, a ferromagnetic regime where the overlap and the mean-fitness are frozen. In this case, the system relaxes to equilibrium in a finite time. The relevance of our results to information processing aspects of evolution is discussed.

Non-Markovian dynamics of quantum discord

We evaluate the quantum discord dynamics of two qubits in independent and common non-Markovian environments. We compare the dynamics of entanglement with that of quantum discord. For independent reservoirs the quantum discord vanishes only at discrete instants whereas the entanglement can disappear during a finite time interval. For a common reservoir, quantum discord and entanglement can behave very differently with sudden birth of the former but not of the latter. Furthermore, in this case the quantum discord dynamics presents sudden changes in the derivative of its time evolution which is evidenced by the presence of kinks in its behavior at discrete instants of time.

Density functional theory and ab initio molecular dynamics study of NO adsorption on Pd(111) and Pt(111) surfaces

The origin of the unique geometry for nitric oxide (NO) adsorption on Pd(111) and Pt(111) surfaces as well as the effect of temperature were studied by density functional theory calculations and ab initio molecular dynamics at finite temperature. We found that at low coverage, the adsorption geometry is determined by electronic interactions, depending sensitively on the adsorption sites and coverages, and the effect of temperature on geometries is significant. At coverage of 0.25 monolayer (ML), adsorbed NO at hollow sites prefer an upright configuration, while NO adsorbed at top sites prefer a tilting configuration. With increase in the coverage up to 0.50 ML, the enhanced steric repulsion lead to the tilting of hollow NO. We found that the tilting was enhanced by the thermal effects. At coverage of 0.75 ML with p(2 x 2)-3NO(fcc+hcp+top) structure, we found that there was no preferential orientation for tilted top NO. The interplay of the orbital hybridization, thermal effects, steric repulsion, and their effects on the adsorption geometries were highlighted at the end.

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624408]

Polarization effects in molecular dynamics simulations of glass-formers Ca(NO(3))(2)center dot nH(2)O, n=4, 6, and 8

Thermodynamics, equilibrium structure, and dynamics of glass-forming liquids Ca(NO(3))(2)center dot nH(2)O, n=4, 6, and 8, have been investigated by molecular dynamics (MD) simulations. A polarizable model was considered for H(2)O and NO(3)- on the basis of previous fluctuating charge models for pure water and the molten salt 2Ca(NO(3))(2)center dot 3KNO(3). Similar thermodynamic properties have been obtained with nonpolarizable and polarizable models. The glass transition temperature, T(g), estimated from MD simulations was dependent on polarization, in particular the dependence of T(g) with electrolyte concentration. Significant polarization effects on equilibrium structure were observed in cation-cation, cation-anion, and water-water structures. Polarization increases the diffusion coefficient of H(2)O, but does not change significantly the diffusion coefficients of ions. Viscosity decreases upon inclusion of polarization, but the conductivity calculated with the polarizable model is smaller than the nonpolarizable model because polarization enhances anion-cation interactions.

Fragility and glassy dynamics of 2Ca(NO(3))(2)center dot 3KNO(3) under pressure: Molecular dynamics simulations

Molecular dynamics simulations of the glass-forming liquid 2Ca(NO(3))(2)center dot 3KNO(3) (CKN) were performed from high temperature liquid states down to low temperature glassy states at six different pressures from 10(-4) to 5.0 GPa. The temperature dependence of the structural relaxation time indicates that the fragility of liquid CKN changes with pressure. In line with recent proposal [Scopigno , Science 302, 849 (2003)], the change on liquid fragility is followed by a proportional change of the nonergodicity factor of the corresponding glass at low temperature. (c) 2008 American Institute of Physics.

Nitrogen dynamics during ecosystem development in tropical forest restoration

We considered whether ecological restoration using high diversity of native tree species serves to restore nitrogen dynamics in the Brazilian Atlantic Forest. We measured delta(15)N and N content in green foliage and soil; vegetation N:P ratio; and soil N mineralization in a preserved natural forest and restored forests of ages 21 and 52 years. Green foliage delta(15)N values, N content, N:P ratio, inorganic N and net mineralization and nitrification rates were all higher, the older the forest. Our findings indicate that the recuperation of N cycling has not been achieved yet in the restored forests even after 52 years, but show that they are following a trajectory of development that is characterized by their N cycling intensity becoming similar to a natural mature forest of the same original forest formation. This study demonstrated that some young restored forests are more limited by N compared to mature natural forests. We document that the recuperation of N cycling in tropical forests can be achieved through ecological restoration actions. (C) 2011 Elsevier B.V. All rights reserved.

Conversion to soy on the Amazonian agricultural frontier increases streamflow without affecting stormflow dynamics

Large-scale soy agriculture in the southern Brazilian Amazon now rivals deforestation for pasture as the region`s predominant form of land use change. Such landscape-level change can have substantial consequences for local and regional hydrology, but these effects remain relatively unstudied in this ecologically and economically important region. We examined how the conversion to soy agriculture influences water balances and stormflows using stream discharge (water yields) and the timing of discharge (stream hydrographs) in small (2.5-13.5 km2) forested and soy headwater watersheds in the Upper Xingu Watershed in the state of Mato Grosso, Brazil. We monitored water yield for 1 year in three forested and four soy watersheds. Mean daily water yields were approximately four times higher in soy than forested watersheds, and soy watersheds showed greater seasonal variability in discharge. The contribution of stormflows to annual streamflow in all streams was low (< 13% of annual streamflow), and the contribution of stormflow to streamflow did not differ between land uses. If the increases in water yield observed in this study are typical, landscape-scale conversion to soy substantially alters water-balance, potentially altering the regional hydrology over large areas of the southern Amazon.

Historical carbon emissions and uptake from the agricultural frontier of the Brazilian Amazon

Tropical ecosystems play a large and complex role in the global carbon cycle. Clearing of natural ecosystems for agriculture leads to large pulses of CO(2) to the atmosphere from terrestrial biomass. Concurrently, the remaining intact ecosystems, especially tropical forests, may be sequestering a large amount of carbon from the atmosphere in response to global environmental changes including climate changes and an increase in atmospheric CO(2). Here we use an approach that integrates census-based historical land use reconstructions, remote-sensing-based contemporary land use change analyses, and simulation modeling of terrestrial biogeochemistry to estimate the net carbon balance over the period 1901-2006 for the state of Mato Grosso, Brazil, which is one of the most rapidly changing agricultural frontiers in the world. By the end of this period, we estimate that of the state`s 925 225 km(2), 221 092 km(2) have been converted to pastures and 89 533 km(2) have been converted to croplands, with forest-to-pasture conversions being the dominant land use trajectory but with recent transitions to croplands increasing rapidly in the last decade. These conversions have led to a cumulative release of 4.8 Pg C to the atmosphere, with similar to 80% from forest clearing and 20% from the clearing of cerrado. Over the same period, we estimate that the residual undisturbed ecosystems accumulated 0.3 Pg C in response to CO2 fertilization. Therefore, the net emissions of carbon from Mato Grosso over this period were 4.5 Pg C. Net carbon emissions from Mato Grosso since 2000 averaged 146 Tg C/yr, on the order of Brazil`s fossil fuel emissions during this period. These emissions were associated with the expansion of croplands to grow soybeans. While alternative management regimes in croplands, including tillage, fertilization, and cropping patterns promote carbon storage in ecosystems, they remain a small portion of the net carbon balance for the region. This detailed accounting of a region`s carbon balance is the type of foundation analysis needed by the new United Nations Collaborative Programmme for Reducing Emissions from Deforestation and Forest Degradation (REDD).

Greenhouse gas emissions from alternative futures of deforestation and agricultural management in the southern Amazon

The Brazilian Amazon is one of the most rapidly developing agricultural areas in the world and represents a potentially large future source of greenhouse gases from land clearing and subsequent agricultural management. In an integrated approach, we estimate the greenhouse gas dynamics of natural ecosystems and agricultural ecosystems after clearing in the context of a future climate. We examine scenarios of deforestation and postclearing land use to estimate the future (2006-2050) impacts on carbon dioxide (CO(2)), methane (CH(4)), and nitrous oxide (N(2)O) emissions from the agricultural frontier state of Mato Grosso, using a process-based biogeochemistry model, the Terrestrial Ecosystems Model (TEM). We estimate a net emission of greenhouse gases from Mato Grosso, ranging from 2.8 to 15.9 Pg CO(2)-equivalents (CO(2)-e) from 2006 to 2050. Deforestation is the largest source of greenhouse gas emissions over this period, but land uses following clearing account for a substantial portion (24-49%) of the net greenhouse gas budget. Due to land-cover and land-use change, there is a small foregone carbon sequestration of 0.2-0.4 Pg CO(2)-e by natural forests and cerrado between 2006 and 2050. Both deforestation and future land-use management play important roles in the net greenhouse gas emissions of this frontier, suggesting that both should be considered in emissions policies. We find that avoided deforestation remains the best strategy for minimizing future greenhouse gas emissions from Mato Grosso.

Stable isotopes of bulk organic matter to trace carbon and nitrogen dynamics in an estuarine ecosystem in Babitonga Bay (Santa Catarina, Brazil)

The biogeochemical processes affecting the transport and cycling of terrestrial organic carbon in coastal and transition areas are still not fully understood One means of distinguishing between the sources of organic materials contributing to particulate organic matter (POM) in Babitonga Bay waters and sediments is by the direct measurement of delta(13)C of dissolved inorganic carbon (DIC) and delta(13)C and delta(15)N in the organic constituents. An isotopic survey was taken from samples collected in the Bay in late spring of 2004. The results indicate that the delta(13)C and delta(15)N compositions of OM varied from -21.7 parts per thousand to -26 2 parts per thousand. and from + 9 2 parts per thousand. to -0 1 parts per thousand, respectively. delta(13)C from DIC ranges from +0.04 parts per thousand to -12.7 parts per thousand The difference in the isotope compositions enables the determination of three distinct end-members terrestrial, marine and urban Moreover, the evaluation of source contribution to the particulate organic matter (POM) in the Bay, enables assessment of the anthropogenic impact. Comparing the depleted values of delta(13)C(DIC) and delta(13)C(POC) it is possible to further understand the carbon dynamic within Babitonga Bay (C) 2010 Elsevier BV All rights reserved