The double Caldeira-Leggett model: Derivation and solutions of the master equations, reservoir-induced interactions and decoherence

In this paper we analyze the double Caldeira-Leggett model: the path integral approach to two interacting dissipative harmonic oscillators. Assuming a general form of the interaction between the oscillators, we consider two different situations: (i) when each oscillator is coupled to its own reservoir, and (ii) when both oscillators are coupled to a common reservoir. After deriving and solving the master equation for each case, we analyze the decoherence process of particular entanglements in the positional space of both oscillators. To analyze the decoherence mechanism we have derived a general decay function, for the off-diagonal peaks of the density matrix, which applies both to common and separate reservoirs. We have also identified the expected interaction between the two dissipative oscillators induced by their common reservoir. Such a reservoir-induced interaction, which gives rise to interesting collective damping effects, such as the emergence of relaxation- and decoherence-free subspaces, is shown to be blurred by the high-temperature regime considered in this study. However, we find that different interactions between the dissipative oscillators, described by rotating or counter-rotating terms, result in different decay rates for the interference terms of the density matrix. (C) 2010 Elsevier B.V. All rights reserved.

Effect of zinc insertion and hydrophobicity on the membrane interactions and PDT activity of porphyrin photosensitizers

A series of photosensitizers (PS), which are meso-substituted tetra-cationic porphyrins, was synthesized in order to study the role of amphiphilicity and zinc insertion in photodynamic therapy (PDT) efficacy. Several properties of the PS were evaluated and compared within the series including photophysical properties (absorption spectra, fluorescence quantum yield Phi(f), and singlet oxygen quantum yield Phi(Delta)), uptake by vesicles, mitochondria and HeLa cells, dark and phototoxicity in HeLa cells. The photophysical properties of all compounds are quite similar (Phi(f) <= 0.02; Phi(Delta) similar to 0.8). An increase in lipophilicity and the presence of zinc in the porphyrin ring result in higher vesicle and cell uptake. Binding in mitochondria is dependent on the PS lipophilicity and on the electrochemical membrane potential, i.e., in uncoupled mitochondria PS binding decreases by up to 53%. The porphyrin substituted with octyl groups (TC8PyP) is the compound that is most enriched in mitochondria, and its zinc derivative (ZnTC8PyP) has the highest global uptake. The stronger membrane interaction of the zinc-substituted porphyrins is attributed to a complexing effect with phosphate groups of the phospholipids. Zinc insertion was also shown to decrease the interaction with isolated mitochondria and with the mitochondria of HeLa cells, an effect that has been explained by the particular characteristics of the mitochondrial internal membrane. Phototoxicity was shown to increase proportionally with membrane binding efficiency, which is attributed to favorable membrane interactions which allow more efficient membrane photooxidation. For this series of compounds, photodynamic efficiency is directly proportional to the membrane binding and cell uptake, but it is not totally related to mitochondrial targeting.

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.

Isotropic and anisotropic spin-spin interactions and a quantum phase transition in a dinuclear Cu(II) compound

We report electron-paramagnetic resonance (EPR) studies at similar to 9.5 GHz (X band) and similar to 34 GHz (Q band) of powder and single-crystal samples of the compound Cu(2)[TzTs](4) [N-thiazol-2-yl-toluenesulfonamidatecopper(II)], C(40)H(36)Cu(2)N(8)O(8)S(8), having copper(II) ions in dinuclear units. Our data allow determining an antiferromagnetic interaction J(0)=(-113 +/- 1) cm(-1) (H(ex)=-J(0)S(1)center dot S(2)) between Cu(II) ions in the dinuclear unit and the anisotropic contributions to the spin-spin coupling matrix D (H(ani)=S(1)center dot D center dot S(2)), a traceless symmetric matrix with principal values D/4=(0.198 +/- 0.003) cm(-1) and E/4=(0.001 +/- 0.003) cm(-1) arising from magnetic dipole-dipole and anisotropic exchange couplings within the units. In addition, the single-crystal EPR measurements allow detecting and estimating very weak exchange couplings between neighbor dinuclear units, with an estimated magnitude parallel to J(')parallel to=(0.060 +/- 0.015) cm(-1). The interactions between a dinuclear unit and the ""environment"" of similar units in the structure of the compound produce a spin dynamics that averages out the intradinuclear dipolar interactions. This coupling with the environment leads to decoherence, a quantum phase transition that collapses the dipolar interaction when the isotropic exchange coupling with neighbor dinuclear units equals the magnitude of the intradinuclear dipolar coupling. Our EPR experiments provide a new procedure to follow the classical exchange-narrowing process as a shift and collapse of the line structure (not only as a change of the resonance width), which is described with general (but otherwise simple) theories of magnetic resonance. Using complementary procedures, our EPR measurements in powder and single-crystal samples allow measuring simultaneously three types of interactions differing by more than three orders of magnitude (between 113 cm(-1) and 0.060 cm(-1)).

Amplification and diffusion of manual preference from lateralized practice in children

The effect of lateralized practice on manual preference was investigated in right-handed children. Probing tasks required reaching and grasping a pencil at distinct eccentricities in the right and left hemifields (simple), and its transportation and insertion into a small hole (complex). During practice, the children experienced manipulative tasks different from that used for probing, using the left hand only. Results showed that before practice the children used almost exclusively the right hand in the right hemifield and at the midline position. Following lateralized practice frequency of use of the left hand increased in most lateral positions. A more evident effect of lateralized practice on shift of manual preference was detected in the complex task. Implications for lateralization of behavior in a developmental timescale are discussed on the basis of the proposition of amplification and diffusion of manual preference from lateralized practice. (C) 2010 Wiley Periodicals, Inc. Dev Psychobiol 52: 723-730, 2010.

Clustering and diffusion in a symplectic map lattice with non-local coupling

We study a symplectic chain with a non-local form of coupling by means of a standard map lattice where the interaction strength decreases with the lattice distance as a power-law, in Such a way that one can pass continuously from a local (nearest-neighbor) to a global (mean-field) type of coupling. We investigate the formation of map clusters, or spatially coherent structures generated by the system dynamics. Such clusters are found to be related to stickiness of chaotic phase-space trajectories near periodic island remnants, and also to the behavior of the diffusion coefficient. An approximate two-dimensional map is derived to explain some of the features of this connection. (C) 2008 Elsevier Ltd. All rights reserved.

Final state hadronic interactions and non-resonant B(+/-)-> K(+/-)pi(+)pi(-) decays

We evaluate the non-resonant decay amplitude of the process B(+/-) -> K(+/-)pi(+)pi(-) using an approach based on final state hadronic interactions described in terms of meson exchanges. We conclude that this mechanism generates inhomogeneities in the Dalitz plot of the B decay. (C) 2008 Published by Elsevier B.V.

Design and assembly of an experimental laboratory for the study of atmosphere-plant interactions in the system of fumigation chambers

An experimental laboratory was designed and assembled at the Botanical Institute of So Paulo, Brazil, in order to research atmosphere-plant interactions through the use of a system of fumigation chambers. A system of three ""closed"" fumigation chambers was designed to be used inside or outside the laboratory. The system was built to be used with a single pollutant or a mix of them. The innovation in this system is to allow chemical reactions inside the chambers that simulate atmospheric chemistry, especially photochemical processes involving high levels of ozone. Assessment of the performance and applicability of the system was based on the response of Nicotiana tabacum Bel W3 exposed to ozone produced alternatively by a generator and inside the chamber by reactions of its precursors. The results showed that the system can be well applied to the study of atmospheric chemistry interactions and the effects on plants.

Effect of SO(2) on the Transport Properties of an Imidazolium Ionic Liquid and Its Lithium Solution

Transport coefficients have been measured as a function of the concentration of sulfur dioxide, SO(2), dissolved in 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)-imide, [BMMI][Tf(2)N], as well as in its lithium salt solution, Li[Tf(2)N]. The SO(2) reduces viscosity and density and increases conductivity and diffusion coefficients in both the neat [BMMI] [Tf(2)N] and the [BMMI][Tf(2)N]-Li[Tf(2)N] solution. The conductivity enhancement is not assigned to a simple viscosity effect; the weakening of ionic interactions upon SO(2) addition also plays a role. Microscopic details of the SO(2) effect were unraveled using Raman spectroscopy and molecular dynamics (MD) simulations. The Raman spectra suggest that the Li(+)-[Tf(2)N] interaction is barely affected by SO(2), and the SO(2)-[Tf(2)N] interaction is weaker than previously observed in an investigation of an ionic liquid containing the bromide anion. Transport coefficients calculated by MD simulations show the same trend as the experimental data with respect to SO(2) content. The MD simulations provide structural information on SO(2) molecules around [Tf(2)N], in particular the interaction of the sulfur atom of SO(2) with oxygen and fluorine atoms of the anion. The SO(2)-[BMMI] interaction is also important because the [BMMI] cations with above-average mobility have a larger number of nearest-neighbor SO(2) molecules.

Alcohol dehydrogenase activities and ethanol tolerance in Anastrepha (Diptera, Tephritidae) fruit-fly species and their hybrids

The ADH (alcohol dehydrogenase) system is one of the earliest known models of molecular evolution, and is still the most studied in Drosophila. Herein, we studied this model in the genus Anastrepha (Diptera, Tephritidae). Due to the remarkable advantages it presents, it is possible to cross species with different Adh genotypes and with different phenotype traits related to ethanol tolerance. The two species studied here each have a different number of Adh gene copies, whereby crosses generate polymorphisms in gene number and in composition of the genetic background. We measured certain traits related to ethanol metabolism and tolerance. ADH specific enzyme activity presented gene by environment interactions, and the larval protein content showed an additive pattern of inheritance, whilst ADH enzyme activity per larva presented a complex behavior that may be explained by epistatic effects. Regression models suggest that there are heritable factors acting on ethanol tolerance, which may be related to enzymatic activity of the ADHs and to larval mass, although a pronounced environmental effect on ethanol tolerance was also observed. By using these data, we speculated on the mechanisms of ethanol tolerance and its inheritance as well as of associated traits.

Modified silicas covalently bounded to 5,10,15,20-tetrakis(2-hydroxy-5-nitrophenyl)porphyrinato iron(III): synthesis, spectroscopic and EPR characterization. Catalytic studies

In this work we have studied cyclooctene epoxidation with PhIO, using a new iron porphyrin, 5,10,15,20-tetrakis(2-hydroxy-5-nitrophenyl)porphyrinato iron(III), supported on silica matrices via eletrostatic interaction and / or covalent bonds as catalyst. These catalysts were obtained and immobilized on the solid supports propyltrimethylammonium silica (SiN+); propyltrimethylammonium and propylimidazole silica [SiN+(IPG)] and chloropropylsilica (CPS) via elestrostatic interactions and covalent binding. Characterization of the supported catalysts by UV-Vis spectroscopy and EPR (Electron paramagnetic resonance) indicated the presence of a mixture of FeII and FeIII species in all of the three obtained catalysts. In the case of (Z)-cyclooctene epoxidation by PhIO the yields observed for cis-epoxycyclooctane were satisfactory for the reactions catalyzed by the three materials (ranging from 68% to 85%). Such results indicate that immobilization of metalloporphyrins onto solid supports via groups localized on the ortho positions of their mesophenyl rings can lead to efficient catalysts for epoxidation reactions. The catalyst 1-CPS is less active than 1-SiN and 1-SiN(IPG), this argues in favour of the immobilization of this metalloporphyrin onto solids via electrostatic interactions, which is easier to achieve and results in more active oxidation catalysts. Interestingly, the activity of the supported catalysts remained the same even after three successive recyclings; therefore, they are stable under the oxidizing conditions.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

RNA interference-mediated knockdown of CD49e (alpha 5 integrin chain) in human thymic epithelial cells modulates the expression of multiple genes and decreases thymocyte adhesion

Background: The thymus is a central lymphoid organ, in which bone marrow-derived T cell precursors undergo a complex process of maturation. Developing thymocytes interact with thymic microenvironment in a defined spatial order. A component of thymic microenvironment, the thymic epithelial cells, is crucial for the maturation of T-lymphocytes through cell-cell contact, cell matrix interactions and secretory of cytokines/chemokines. There is evidence that extracellular matrix molecules play a fundamental role in guiding differentiating thymocytes in both cortical and medullary regions of the thymic lobules. The interaction between the integrin alpha 5 beta 1 (CD49e/CD29; VLA-5) and fibronectin is relevant for thymocyte adhesion and migration within the thymic tissue. Our previous results have shown that adhesion of thymocytes to cultured TEC line is enhanced in the presence of fibronectin, and can be blocked with anti-VLA-5 antibody. Results: Herein, we studied the role of CD49e expressed by the human thymic epithelium. For this purpose we knocked down the CD49e by means of RNA interference. This procedure resulted in the modulation of more than 100 genes, some of them coding for other proteins also involved in adhesion of thymocytes; others related to signaling pathways triggered after integrin activation, or even involved in the control of F-actin stress fiber formation. Functionally, we demonstrated that disruption of VLA-5 in human TEC by CD49e-siRNA-induced gene knockdown decreased the ability of TEC to promote thymocyte adhesion. Such a decrease comprised all CD4/CD8-defined thymocyte subsets. Conclusion: Conceptually, our findings unravel the complexity of gene regulation, as regards key genes involved in the heterocellular cell adhesion between developing thymocytes and the major component of the thymic microenvironment, an interaction that is a mandatory event for proper intrathymic T cell differentiation.

Experimental studies of di-jet survival and surface emission bias in Au plus Au collisions via angular correlations with respect to back-to-back leading hadrons

We report first results from an analysis based on a new multi-hadron correlation technique, exploring jet-medium interactions and di-jet surface emission bias at the BNL Relativistic Heavy Ion Collider (RHIC). Pairs of back-to-back high-transverse-momentum hadrons are used for triggers to study associated hadron distributions. In contrast with two-and three-particle correlations with a single trigger with similar kinematic selections, the associated hadron distribution of both trigger sides reveals no modification in either relative pseudorapidity Delta eta or relative azimuthal angle Delta phi from d + Au to central Au + Au collisions. We determine associated hadron yields and spectra as well as production rates for such correlated back-to-back triggers to gain additional insights on medium properties.

Photochemistry of anthocyanins and their biological role in plant tissues

Anthocyanins, the major red, purple, and blue pigments of plants, absorb visible as well as UV radiation and are effective antioxidants and scavengers of active oxygen species. In plant leaves, one of the functional roles proposed for anthocyanins is protection of the photosynthetic apparatus from the effects of excess incident visible or UV-B radiation and photooxidative stress. In essence, a photoprotective role requires that the excited singlet states of both complexed and uncomplexed anthocyanins deactivate back to the ground state so quickly that intersystem crossing, photoreaction, and diffusion-controlled quenching processes cannot compete. Studies of the photochemical properties of synthetic analogs of anthocyanins and of several naturally occurring anthocyanins show that this is indeed the case, uncomplexed anthocyanins decaying back to the ground state via fast (subnanosecond) excited-state proton transfer (ESPT) and anthocyanin-copigment complexes by fast (sub-picosecond) charge-transfer-mediated internal conversion.