State protection under collective damping and diffusion

In this paper we provide a recipe for state protection in a network of oscillators under collective damping and diffusion. Our strategy is to manipulate the network topology, i.e., the way the oscillators are coupled together, the strength of their couplings, and their natural frequencies, in order to create a relaxation-diffusion-free channel. This protected channel defines a decoherence-free subspace (DFS) for nonzero-temperature reservoirs. Our development also furnishes an alternative approach to build up DFSs that offers two advantages over the conventional method: it enables the derivation of all the network-protected states at once, and also reveals, through the network normal modes, the mechanism behind the emergence of these protected domains.

Fluoride-modified electrical properties of lead borate glasses and electrochemically induced crystallization in the glassy state

Lead fluoroborate glasses were prepared by the melt-quenching technique and characterized in terms of (micro)structural and electrical properties. The study was conducted on as prepared as well as temperature- and/or electric field-treated glass samples. The results show that, in the as-prepared glassy-state materials, electrical conductivity improved with increasing the PbF(2) glass content. This result involves both an increase of the fluoride charge carrier density and, especially, a decrease of the activation energy from a glass structure expansion improving charge carrier mobility. Moreover, for the electric field-treated glass samples, surface crystallization was observed even below the glass transition temperature. As previously proposed in literature, and shown here, the occurrence of this phenomenon arose from an electrochemically induced redox reaction at the electrodes, followed by crystallite nucleation. Once nucleated, growth of beta-PbF(2) crystallites, with the indication of incorporating reduced lead ions (Pb(+)), was both (micro)structurally and electrically detectable and analyzed. The overall crystallization-associated features observed here adapt well with the floppy-rigid model that has been proposed to further complete the original continuous-random-network model by Zachariasen for closely addressing not only glasses' structure but also crystallization mechanism. Finally, the crystallization-modified kinetic picture of the glasses' electrical properties, through application of polarization/depolarization measurements originally combined with impedance spectroscopy, was extensively explored. (c) 2008 American Institute of Physics.

Intermediate motions as studied by solid-state separated local field NMR experiments

In this report, the application of a class of separated local field NMR experiments named dipolar chemical shift correlation (DIPSHIFT) for probing motions in the intermediate regime is discussed. Simple analytical procedures based on the Anderson-Weiss (AW) approximation are presented. In order to establish limits of validity of the AW based formulas, a comparison with spin dynamics simulations based on the solution of the stochastic Liouville-von-Neumann equation is presented. It is shown that at short evolution times (less than 30% of the rotor period), the AW based formulas are suitable for fitting the DIPSHIFT curves and extracting kinetic parameters even in the case of jumplike motions. However, full spin dynamics simulations provide a more reliable treatment and extend the frequency range of the molecular motions accessible by DIPSHIFT experiments. As an experimental test, molecular jumps of imidazol methyl sulfonate and trimethylsulfoxonium iodide, as well as the side-chain motions in the photoluminescent polymer poly[2-methoxy-5-(2(')-ethylhexyloxy)-1,4-phenylenevinylene], were characterized. Possible extensions are also discussed. (c) 2008 American Institute of Physics.

A comparative solid state (13)C NMR and thermal study of CO(2) capture by amidines PMDBD and DBN

The present work shows study of the CO(2) capture by amidines DBN and PMDBD using (13)C solid-state NMR and thermal techniques. The solid state (13)C NMR analyses demonstrate the formation of a single PMDBD-CO(2) product which was assigned to stable bicarbonate. In the case of DBN, it is shown that two DBN-CO(2) products are formed, which are suggested to be stable bicarbonate and unstable carbamate. The role of water in the DBN-CO(2) capture as well as the stability of the products to environmental moisture was also investigated. The results suggest that the carbamate formation is favored in dry DBN, but in the presence of water it decompose to form bicarbonate. Thermal analysis shows a good gravimetric CO(2) absorption of DBN. Release of CO(2) was found to be almost quantitative from the PMDBDH(+) bicarbonate about 110 degrees C.

Ground-state functional for quantum spin chains with bond defects

We have developed a nonlocal functional of the exchange interaction for the ground-state energy of quantum spin chains described by the Heisenberg Hamiltonian. An alternating chain is used to obtain the correlation energy and a local unit-cell approximation is defined in the context of the density-functional theory. The agreement with our exact numerical data, for small chains, is significantly better than a previous formulation, even for chains with several ferromagnetic or antiferromagnetic bond defects. The results can be particularly relevant in the study of finite spin-1/2 Heisenberg chains, with exchange couplings changing, magnitude, or even sign, from bond-to-bond.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Full-dimensional analytical ab initio potential energy surface of the ground state of HOI

Extensive ab initio calculations using a complete active space second-order perturbation theory wavefunction, including scalar and spin-orbit relativistic effects with a quadruple-zeta quality basis set were used to construct an analytical potential energy surface (PES) of the ground state of the [H, O, I] system. A total of 5344 points were fit to a three-dimensional function of the internuclear distances, with a global root-mean-square error of 1.26 kcal mol(-1). The resulting PES describes accurately the main features of this system: the HOI and HIO isomers, the transition state between them, and all dissociation asymptotes. After a small adjustment, using a scaling factor on the internal coordinates of HOI, the frequencies calculated in this work agree with the experimental data available within 10 cm(-1). (C) 2011 American Institute of Physics. [doi: 10.1063/1.3615545]

Autocatalysis in the open circuit interaction of alcohol molecules with oxidized Pt surfaces

We studied the open circuit interaction of methanol and ethanol with oxidized platinum electrodes using in situ infrared spectroscopy. For methanol, it was found that formic acid is the main species formed in the initial region of the transient and that the steep decrease of the open circuit potential coincides with an explosive increase in the CO(2) production, which is followed by an increase in the coverage of adsorbed CO. For ethanol, acetaldehyde was the main product detected and only traces of dissolved CO(2) and adsorbed CO were found after the steep potential decay. In both cases, the transients were interpreted in terms of (a) the emergence of sub-surface oxygen in the beginning of the transient, where the oxide content is high, and (b) the autocatalytic production of free platinum sites for lower oxide content during the steep decay of the open circuit potential.

Excitation energies from ground-state density-functionals by means of generator coordinates

The generator-coordinate method is a flexible and powerful reformulation of the variational principle. Here we show that by introducing a generator coordinate in the Kohn-Sham equation of density-functional theory, excitation energies can be obtained from ground-state density functionals. As a viability test, the method is applied to ground-state energies and various types of excited-state energies of atoms and ions from the He and the Li isoelectronic series. Results are compared to a variety of alternative DFT-based approaches to excited states, in particular time-dependent density-functional theory with exact and approximate potentials.

Implications of long-term land-use change for the hydrology and solute budgets of small catchments in Amazonia

The replacement of undisturbed tropical forest with cattle pasture has the potential to greatly modify the hydrology of small watersheds and the fluxes of solutes. We examined the fluxes of water, Cl(-), NO(3)(-)-N: SO(4)(2--)-S, NH(4)(+)-N, Na(+), K(+), Mg(2+) and Ca(2+) in different flow paths in similar to 1 ha catchments of undisturbed open tropical rainforest and a 20 year-old pasture established from forest in the southwestern Brazilian Amazon state of Rondonia. Storm flow discharge was 18% of incident rainfall in pasture, but only 1% in forest. Quickflow predominated over baseflow in both catchments and in both wet and dry seasons. In the pasture, groundwater and quickflow were important flow paths for the export of all solutes. In the forest, quickflow was important for NO(3)(-)-N export, but all other solutes were exported primarily by groundwater outflow. Both catchments were sinks for SO(4)(2-)-S and Ca(2+), and sources of Na(+). The pasture catchment also lost K(+) and Mg(2+) because of higher overland flow frequency and volume and to cattle excrement. These results show that forest clearing dramatically influences small watershed hydrology by increasing quickflow and water export to streams. They also indicate that tropical forest watersheds are highly conservative for most solutes but that pastures continue to lose important cations even decades after deforestation and pasture establishment. (c) 2008 Elsevier B.V. All rights reserved.

Sedimentary Organic Matter in Cores of the Cananeia-Iguape Lagoonal-Estuarine System, Sao Paulo State, Brazil

Sedimentary organic matter is a good tool for environmental evaluation where the sediments are deposited. We determined the elemental and C- and N-isotopic compositions of 211 sub-surface sediment samples from 13 cores (ranging from 18 to 46cm), collected in the Cananeia-Iguape estuarine-lagoonal system. The aim of this research is to evaluate the environmental variations of this tropical coastal micro-tidal system over the last decades, through SOM distribution. The studied parameters show differences between the cores located in the northern (sandy-silt sediments) and southern (sand and silty-sand) portions. The whole area presents a mixed organic matter origin signature (local mangrove plants: < -25.6 parts per thousand PDB/ phytoplancton delta(13)C values: -19.4 parts per thousand PDB). The northern cores, which submitted higher sedimentation deposition (1.46cm year(-1)), are more homogenous, presenting lower delta(13)C (< -25.2 parts per thousand PDB) and higher C/N values (in general >14), directly related to the terrestrial input from Ribeira de Iguape River (24,000 km(2) basin). The southern portion presents lower sedimentation rates (0.38cm year(-1)) and is associated to a small river basin (1,340 km(2)), presenting values Of delta(13)C: -25.0 to 23.0 parts per thousand PDB and of C/N ratio: 11 to 15. In general, the elemental contents in the 15 cores may be considered from low to medium (< 2.0% C - < 0.1% N), compared to similar environments. Although a greater marine influence is observed in the southern system portion, the majority of the cores present an elevated increase of continental deposition, most likely related to the strong silting process that the area has been subjected to since the 1850s, when an artificial channel was built linking, directly, the Ribeira River to the estuarine-lagoonal system.

Late Pleistocene and Holocene vegetation changes in northeastern Brazil determined from carbon isotopes and charcoal records in soils

Northeastern Brazil represents a strategic area in terms of Quaternary records of environmental changes in South America due to its distinct semi-arid climate in near equatorial latitudes. In this study, carbon isotope and charcoal distribution records in soils are used to characterize vegetation dynamics, forest fires and their relation to climate change since the Late Pleistocene in the States of Ceara, Piaui and Paraiba, Northeastern Brazil. At the Ceara site, the carbon isotope record showed an enrichment trend from -24%(o) to 19%(o) during the early-mid Holocene, indicating an opening of vegetation and expansion of savanna vegetation (C(4) plants) during this period. A trend toward more depleted delta(13)C values (similar to-32%.) in the late Holocene indicates an expansion of forest vegetation (C(3) plants). A similar trend is observed at the Piaui and Paraiba sites where values of similar to-24%0 are associated with open forest vegetation during the late Pleistocene. In the early-mid Holocene, delta(13)C values of up to -18.0%(o), suggest the expansion of C4 plants. Based on the carbon isotope data, it is postulated that from similar to 18,000 cal yr B.P. to similar to 11,800 cal yr B.P.-similar to 10,000 cal yr B.P. arboreal vegetation was dominant in northeastern Brazil and is associated with humid climates. The savanna expanded from similar to 10,000 cal yr B.P. to similar to 4500-3200 cal yr B.P. due to a less humid/drier climatic phase, also supported by the significant presence of fires (charcoal fragments in the soil). From approximately 3200-2000 cal yr B.P. to the present, carbon isotope records suggest forest expansion and a more humid phase. These results form part of a regional pattern since they are in agreement with paleovegetation records obtained in regions of Maranhao, northeastern Brazil and in the Amazon and Rondonia States, northern Brazil. (C) 2010 Elsevier B.V. All rights reserved.

PLANT ACCUMULATIONS ALONG THE ITANHAEM RIVER BASIN, SOUTHERN COAST OF SAO PAULO STATE, BRAZIL

Examination of the mechanisms involved in the construction of present-day vegetative deposits along coastal waterways has made it possible to establish depositional patterns that can be compared with those found in similar environments in geologic time. These patterns include not only the composition and transport of the debris but also an estimation of the time involved in its deposition. Six sites with active deposits of plant macrodebris in the coastal basin of the Itanhaem River, Sao Paulo State, Brazil, were used in the study. In the central portion of the basin, the interior coastal plain is covered with restinga forest (dense, wet tropical forest of low altitudes), while the lower portion consists of mangrove swamps. The coast reflects anthropogenic intervention, and only a few scattered remnants of precolonization dune vegetation remain. The results after three years of study suggest that the accumulation of plant macrodebris in the middle and lower portions of the basin is parautochthonous, since only the leaves of genera typical of the restinga forest and mangrove swamp, respectively, were found. Along the coast the accumulations involved a mixture of parautochthonous and allochthonous elements. On the levee of the Branco River and within the mangrove swamp, deposition was slow, and many of the elements decayed quickly; such accumulations show little potential for preservation and eventual fossilization. A different site, however, reveals the rapid deposition of thick layers of plant debris, presumably associated with storms, and these accumulations are preserved for long periods, constituting good candidates for possible fossilization.

Last glacial maximum (LGM) vegetation changes in the Atlantic Forest, southeastern Brazil

This study was carried out in a continental Atlantic Forest located in the southern region of Sao Paulo State, southeastern Brazil. The aim of the study was to evaluate the vegetation dynamics in similar to 70 km forest ecosystem transect that occurred during the late Pleistocene and Holocene in this region, using the stable carbon isotopes (delta C-13) analysis on soil organic matter (SOM) and the C-14 dating of buried charcoal fragments and the humin fraction of SOM. The isotope data (delta C-13) of SOM in the deeper horizons, indicating the presence of more open vegetation than the present, with a probable mixture of C-3 and C-4 plants, suggesting the presence of a drier climate in the period of similar to 20 ka to similar to 16-14 ka BP. From similar to 16 to 14 ka BP to the present, a significant predominance Of C3 plants was observed, indicating an expansion of the forest, probably associated with the presence of a more humid climate than the previous period. The results indicated the presence of open vegetation during the late glacial, probably associated with a drier period, also observed in other regions of Brazil. The Atlantic Forest ecosystem seems to have developed at least since the early Holocene in Southeastern Brazil. (c) 2007 Elsevier Ltd and INQUA. All rights reserved.