Two-photon absorption spectra of carotenoids compounds

Carotenoids are biosynthetic organic pigments that constitute an important class of one-dimensional pi-conjugated organic molecules with enormous potential for application in biophotonic devices. In this context, we studied the degenerate two-photon absorption (2PA) cross-section spectra of two carotenoid compounds (beta-carotene and beta-apo-8'-carotenal) employing the conventional and white-light-continuum Z-scan techniques and quantum chemistry calculations. Because carotenoids coexist at room temperature as a mixture of isomers, the 2PA spectra reported here are due to samples containing a distribution of isomers, presenting distinct conjugation length and conformation. We show that these compounds present a defined structure on the 2PA spectra, that peaks at 650 nm with an absorption cross-section of approximately 5000 GM, for both compounds. In addition, we observed a 2PA band at 990 nm for beta-apo-8'-carotenal, which was attributed to a overlapping of I(I)B(u) +-like and 2(I)Ag(-)-like states, which are strongly one- and two-photon allowed, respectively. Spectroscopic parameters of the electronic transitions to singlet-excited states, which are directly related to photophysical properties of these compounds, were obtained by fitting the 2PA spectra using the sum-over-states approach. The analysis and interpretations of the 2PA spectra of the investigated carotenoids were supported by theoretical predictions of one- and two-photon transitions carried out using the response functions formalism within the density functional theory framework, using the long-range corrected CAM-B3LYP functional. (C) 2011 American Institute of Physics. [doi:10.1063/1.3590157]

Experimental and theoretical study of two-photon absorption in nitrofuran derivatives: Promising compounds for photochemotherapy

We report experimental and theoretical studies of the two-photon absorption spectrum of two nitrofuran derivatives: nitrofurantoine, (1-(5-nitro-2-furfurilideneamine)-hidantoine) and quinifuryl, 2-(5`-nitro-2`-furanyl) ethenyl-4-{N-[4`-(N,N-diethylamino)-1`-methylbutyl]carbamoyl} quinoline. Both molecules are representative of a family of 5-nitrofuran-ethenyl-quinoline drugs that have been demonstrated to display high toxicity to various species of transformed cells in the dark. We determine the two-photon absorption cross-section for both compounds, from 560 to 880 nm, which present peak values of 64 GM for quinifuryl and 20 GM for nitrofurantoine (1 GM = 1 x 10(-50) cm(4).s.photon(-1)). Besides, theoretical calculations employing the linear and quadratic response functions were carried out at the density functional theory level to aid the interpretations of the experimental results. The theoretical results yielded oscillator strengths, two-photon transition probabilities, and transition energies, which are in good agreement with the experimental data. A higher number of allowed electronic transitions was identified for quinifuryl in comparison to nitrofurantoine by the theoretical calculations. Due to the planar structure of both compounds, the differences in the two-photon absorption cross-section values are a consequence of their distinct conjugation lengths. (c) 2011 American Institute of Physics. [doi:10.1063/1.3514911]

Theoretical study of one- and two-photon absorption spectra of azoaromatic compounds

In this study, the one- and two-photon absorption spectra of seven azoaromatic compounds (five pseudostilbenes-type and two aminoazobenzenes) were theoretically investigated using the density functional theory combined with the response functions formalism. The equilibrium molecular structure of each compound was obtained at three different levels of theory: Hartree-Fock, density functional theory (DFT), and Moller-Plesset 2. The effect of solvent on the equilibrium structure and the electronic transitions of the compounds were investigated using the polarizable continuum model. For the one-photon absorption, the allowed pi ->pi(*) transition energy showed to be dependent on the molecular structures and the effect of solvent, while the n ->pi(*) and pi ->pi(*)(n) transition energies exhibited only a slight dependence. An inversion between the bands corresponding to the pi ->pi(*) and n ->pi(*) states due to the effect of solvent was observed for the pseudostilbene-type compounds. To characterize the allowed two-photon absorption transitions for azoaromatic compounds, the response functions formalism combined with DFT using the hybrid B3LYP and PBE0 functionals and the long-range corrected CAM-B3LYP functional was employed. The theoretical results support the previous findings based on the three-state model. The model takes into account the ground and two electronic excited states and has already been used to describe and interpret the two-photon absorption spectrum of azoaromatic compounds. The highest energy two-photon allowed transition for the pseudostilbene-type compounds shows to be more effectively affected (similar to 20%) by the torsion of the molecular structure than the lowest allowed transition (similar to 10%). In order to elucidate the effect of the solvent on the two-photon absorption spectra, the lowest allowed two-photon transition (dipolar transition) for each compound was analyzed using a two-state approximation and the polarizable continuum model. The results obtained reveal that the effect of solvent increases drastically the two-photon cross-section of the dipolar transition of the pseudostilbene-type compounds. In general, the features of both one- and two-photon absorption spectra of the azoaromatic compounds are well reproduced by the theoretical calculations.

Three-dimensional fabrication of optically active microstructures containing an electroluminescent polymer

Microfabrication via two-photon absorption polymerization is a technique to design complex microstructures in a simple and fast way. The applications of such structures range from mechanics to photonics to biology, depending on the dopant material and its specific properties. In this paper, we use two-photon absorption polymerization to fabricate optically active microstructures containing the conductive and luminescent polymer poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV). We verify that MEH-PPV retains its optical activity and is distributed throughout the microstructure after fabrication. The microstructures retain the emission characteristics of MEH-PPV and allow waveguiding of locally excited fluorescence when fabricated on top of low refractive index substrates. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3232207]

Extending Bell's beables to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories

In this paper, employing the Ito stochastic Schrodinger equation, we extend Bell's beable interpretation of quantum mechanics to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories. For a particular choice of the source of stochasticity, the one leading to a dissipative Lindblad-type correction to the Hamiltonian dynamics, we find that the diffusive terms in Nelsons stochastic trajectories are naturally incorporated into Bohm's causal dynamics, yielding a unified Bohm-Nelson theory. In particular, by analyzing the interference between quantum trajectories, we clearly identify the decoherence time, as estimated from the quantum formalism. We also observe the quantum-to-classical transition in the convergence of the infinite ensemble of quantum trajectories to their classical counterparts. Finally, we show that our extended beables circumvent the problems in Bohm's causal dynamics regarding stationary states in quantum mechanics.

NMR analog of Bell's inequalities violation test

In this paper, we present an analog of Bell's inequalities violation test for N qubits to be performed in a nuclear magnetic resonance (NMR) quantum computer. This can be used to simulate or predict the results for different Bell's inequality tests, with distinct configurations and a larger number of qubits. To demonstrate our scheme, we implemented a simulation of the violation of the Clauser, Horne, Shimony and Holt (CHSH) inequality using a two-qubit NMR system and compared the results to those of a photon experiment. The experimental results are well described by the quantum mechanics theory and a local realistic hidden variables model (LRHVM) that was specifically developed for NMR. That is why we refer to this experiment as a simulation of Bell's inequality violation. Our result shows explicitly how the two theories can be compatible with each other due to the detection loophole. In the last part of this work, we discuss the possibility of testing some fundamental features of quantum mechanics using NMR with highly polarized spins, where a strong discrepancy between quantum mechanics and hidden variables models can be expected.

Social interaction as a heuristic for combinatorial optimization problems

We investigate the performance of a variant of Axelrod's model for dissemination of culture-the Adaptive Culture Heuristic (ACH)-on solving an NP-Complete optimization problem, namely, the classification of binary input patterns of size F by a Boolean Binary Perceptron. In this heuristic, N agents, characterized by binary strings of length F which represent possible solutions to the optimization problem, are fixed at the sites of a square lattice and interact with their nearest neighbors only. The interactions are such that the agents' strings (or cultures) become more similar to the low-cost strings of their neighbors resulting in the dissemination of these strings across the lattice. Eventually the dynamics freezes into a homogeneous absorbing configuration in which all agents exhibit identical solutions to the optimization problem. We find through extensive simulations that the probability of finding the optimal solution is a function of the reduced variable F/N(1/4) so that the number of agents must increase with the fourth power of the problem size, N proportional to F(4), to guarantee a fixed probability of success. In this case, we find that the relaxation time to reach an absorbing configuration scales with F(6) which can be interpreted as the overall computational cost of the ACH to find an optimal set of weights for a Boolean binary perceptron, given a fixed probability of success.

Ultra-high-energy cosmic rays from centaurus A: jet interaction with gaseous shells

Ultra-high-energy cosmic rays (UHECRs), with energies above similar to 6 x 10(19) eV, seem to show a weak correlation with the distribution of matter relatively near to us in the universe. It has earlier been proposed that UHECRs could be accelerated in either the nucleus or the outer lobes of the nearby radio galaxy Cen A. We show that UHECR production at a spatially intermediate location about 15 kpc northeast from the nucleus, where the jet emerging from the nucleus is observed to strike a large star-forming shell of gas, is a plausible alternative. A relativistic jet is capable of accelerating lower energy heavy seed cosmic rays (CRs) to UHECRs on timescales comparable to the time it takes the jet to pierce the large gaseous cloud. In this model, many CRs arising from a starburst, with a composition enhanced in heavy elements near the knee region around PeV, are boosted to ultra-high energies by the relativistic shock of a newly oriented jet. This model matches the overall spectrum shown by the Auger data and also makes a prediction for the chemical composition as a function of particle energy. We thus predict an observable anisotropy in the composition at high energy in the sense that lighter nuclei should preferentially be seen toward the general direction of Cen A. Taking into consideration the magnetic field models for the Galactic disk and a Galactic magnetic wind, this scenario may resolve the discrepancy between HiRes and Auger results concerning the chemical composition of UHECRs.

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.

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.

ON ISOMORPHIC CLASSIFICATIONS OF SPACES OF COMPACT OPERATORS

We prove an extension of the classical isomorphic classification of Banach spaces of continuous functions on ordinals. As a consequence, we give complete isomorphic classifications of some Banach spaces K(X,Y(n)), eta >= omega, of compact operators from X to Y(eta), the space of all continuous Y-valued functions defined in the interval of ordinals [1, eta] and equipped with the supremum norm. In particular, under the Continuum Hypothesis, we extend a recent result of C. Samuel by classifying, up to isomorphism, the spaces K(X(xi), c(0)(Gamma)(eta)), where omega <= xi < omega(1,) eta >= omega, Gamma is a countable set, X contains no complemented copy of l(1), X* has the Mazur property and the density character of X** is less than or equal to N(1).

Can we make a Bohmian electron reach the speed of light, at least for one instant?

In Bohmian mechanics, a version of quantum mechanics that ascribes world lines to electrons, we can meaningfully ask about an electron's instantaneous speed relative to a given inertial frame. Interestingly, according to the relativistic version of Bohmian mechanics using the Dirac equation, a massive particle's speed is less than or equal to the speed of light, but not necessarily less. That is, there are situations in which the particle actually reaches the speed of light-a very nonclassical behavior. That leads us to the question of whether such situations can be arranged experimentally. We prove a theorem, Theorem 5, implying that for generic initial wave functions the probability that the particle ever reaches the speed of light, even if at only one point in time, is zero. We conclude that the answer to the question is no. Since a trajectory reaches the speed of light whenever the quantum probability current (psi) over bar gamma(mu)psi is a lightlike 4-vector, our analysis concerns the current vector field of a generic wave function and may thus be of interest also independently of Bohmian mechanics. The fact that the current is never spacelike has been used to argue against the possibility of faster-than-light tunneling through a barrier, a somewhat similar question. Theorem 5, as well as a more general version provided by Theorem 6, are also interesting in their own right. They concern a certain property of a function psi : R(4) -> C(4) that is crucial to the question of reaching the speed of light, namely being transverse to a certain submanifold of C(4) along a given compact subset of space-time. While it follows from the known transversality theorem of differential topology that this property is generic among smooth functions psi : R(4) -> C(4), Theorem 5 asserts that it is also generic among smooth solutions of the Dirac equation. (C) 2010 American Institute of Physics. [doi:10.1063/1.3520529]

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]

Frozen Chicken for Wild Fish: Nutritional Transition in the Brazilian Amazon Region Determined by Carbon and Nitrogen Stable Isotope Ratios in Fingernails

Objectives: Amazonian populations are experiencing dietary changes characteristic of the nutrition transition. However, the degree of change appears to vary between urban and rural settings. To investigate this process, we determined carbon and nitrogen stable isotope ratios in fingernails and dietary intake of Amazonian populations living along a rural to urban continuum along the Solimoes River in Brazil. Methods: Carbon and nitrogen stable isotope ratios were analyzed from the fingernails of 431 volunteer subjects living in different settings ranging from rural villages, small towns to urban centers along the Solimoes River. Data from 200 dietary intake surveys were also collected using food frequency questionnaires and 24-h recall interviews in an effort to determine qualitative aspects of diet composition. Results: Fingernail delta(13)C values (mean standard deviation) were -23.2 +/- 1.3, 20.2 +/- 1.5, and 17.4 +/- 1.3 parts per thousand and delta(15)N values were 11.8 +/- 0.6, 10.4 +/- 0.8, and 10.8 +/- 0.7 parts per thousand for those living in rural villages, small towns, and major cities, respectively. We found a gradual increase in the number of food items derived from C(4) plant types (meat and sugar) and the replacement of food items derived from C(3) plant types (fish and manioc flour) with increasing size of urban centers. Conclusion: Increasing urbanization in the Brazilian Amazon is associated with a significant change in food habits with processed and industrialized products playing an increasingly important role in the diet and contributing to the nutrition transition in the region. Am. J. Hum. Biol. 23:642-650, 2011. (C) 2011 Wiley-Liss, Inc.

An opinion dynamics model for the diffusion of innovations

We study the dynamics of the adoption of new products by agents with continuous opinions and discrete actions (CODA). The model is such that the refusal in adopting a new idea or product is increasingly weighted by neighbor agents as evidence against the product. Under these rules, we study the distribution of adoption times and the final proportion of adopters in the population. We compare the cases where initial adopters are clustered to the case where they are randomly scattered around the social network and investigate small world effects on the final proportion of adopters. The model predicts a fat tailed distribution for late adopters which is verified by empirical data. (C) 2009 Elsevier B.V. All rights reserved.