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).

Signatures of quantum phase transitions in parallel quantum dots: Crossover from local moment to underscreened spin-1 Kondo physics

We study a strongly interacting "quantum dot 1" and a weakly interacting "dot 2" connected in parallel to metallic leads. Gate voltages can drive the system between Kondo-quenched and non-Kondo free-moment phases separated by Kosterlitz-Thouless quantum phase transitions. Away from the immediate vicinity of the quantum phase transitions, the physical properties retain signatures of first-order transitions found previously to arise when dot 2 is strictly noninteracting. As interactions in dot 2 become stronger relative to the dot-lead coupling, the free moment in the non-Kondo phase evolves smoothly from an isolated spin-one-half in dot 1 to a many-body doublet arising from the incomplete Kondo compensation by the leads of a combined dot spin-one. These limits, which feature very different spin correlations between dot and lead electrons, can be distinguished by weak-bias conductance measurements performed at finite temperatures.

Theoretical luminescence spectra in p-type superlattices based on InGaAsN

In this work, we present a theoretical photoluminescence (PL) for p-doped GaAs/InGaAsN nanostructures arrays. We apply a self-consistent method in the framework of the effective mass theory. Solving a full 8 x 8 Kane's Hamiltonian, generalized to treat different materials in conjunction with the Poisson equation, we calculate the optical properties of these systems. The trends in the calculated PL spectra, due to many-body effects within the quasi-two-dimensional hole gas, are analyzed as a function of the acceptor doping concentration and the well width. Effects of temperature in the PL spectra are also investigated. This is the first attempt to show theoretical luminescence spectra for GaAs/InGaAsN nanostructures and can be used as a guide for the design of nanostructured devices such as optoelectronic devices, solar cells, and others.

Structural properties and energetics of diffuse Rb-87 clusters in three-dimension

A correlated two-body basis function is used to describe the three-dimensional bosonic clusters interacting via two-body van der Waals potential. We calculate the ground state and the zero orbital angular momentum excited states for Rb-N clusters with up to N = 40. We solve the many-particle Schrodinger equation by potential harmonics expansion method, which keeps all possible two-body correlations in the calculation and determines the lowest effective many-body potential. We study energetics and structural properties for such diffuse clusters both at dimer and tuned scattering length. The motivation of the present study is to investigate the possibility of formation of N-body clusters interacting through the van der Waals interaction. We also compare the system with the well studied He, Ne, and Ar clusters. We also calculate correlation properties and observe the generalised Tjon line for large cluster. We test the validity of the shape-independent potential in the calculation of the ground state energy of such diffuse cluster. These are the first such calculations reported for Rb clusters. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4730972]

Energy-level statistics of interacting trapped bosons

It is a well-established fact that statistical properties of energy-level spectra are the most efficient tool to characterize nonintegrable quantum systems. The statistical behavior of different systems such as complex atoms, atomic nuclei, two-dimensional Hamiltonians, quantum billiards, and noninteracting many bosons has been studied. The study of statistical properties and spectral fluctuations in interacting many-boson systems has developed interest in this direction. We are especially interested in weakly interacting trapped bosons in the context of Bose-Einstein condensation (BEC) as the energy spectrum shows a transition from a collective nature to a single-particle nature with an increase in the number of levels. However this has received less attention as it is believed that the system may exhibit Poisson-like fluctuations due to the existence of an external harmonic trap. Here we compute numerically the energy levels of the zero-temperature many-boson systems which are weakly interacting through the van der Waals potential and are confined in the three-dimensional harmonic potential. We study the nearest-neighbor spacing distribution and the spectral rigidity by unfolding the spectrum. It is found that an increase in the number of energy levels for repulsive BEC induces a transition from a Wigner-like form displaying level repulsion to the Poisson distribution for P(s). It does not follow the Gaussian orthogonal ensemble prediction. For repulsive interaction, the lower levels are correlated and manifest level-repulsion. For intermediate levels P(s) shows mixed statistics, which clearly signifies the existence of two energy scales: external trap and interatomic interaction, whereas for very high levels the trapping potential dominates, generating a Poisson distribution. Comparison with mean-field results for lower levels are also presented. For attractive BEC near the critical point we observe the Shnirelman-like peak near s = 0, which signifies the presence of a large number of quasidegenerate states.

Records of migration in the exoplanet configurations

When compared to our Solar System, many exoplanet systems exhibit quite unusual planet configurations; some of these are hot Jupiters, which orbit their central stars with periods of a few days, others are resonant systems composed of two or more planets with commensurable orbital periods. It has been suggested that these configurations can be the result of a migration processes originated by tidal interactions of the planets with disks and central stars. The process known as planet migration occurs due to dissipative forces which affect the planetary semi-major axes and cause the planets to move towards to, or away from, the central star. In this talk, we present possible signatures of planet migration in the distribution of the hot Jupiters and resonant exoplanet pairs. For this task, we develop a semi-analytical model to describe the evolution of the migrating planetary pair, based on the fundamental concepts of conservative and dissipative dynamics of the three-body problem. Our approach is based on an analysis of the energy and the orbital angular momentum exchange between the two-planet system and an external medium; thus no specific kind of dissipative forces needs to be invoked. We show that, under assumption that dissipation is weak and slow, the evolutionary routes of the migrating planets are traced by the stationary solutions of the conservative problem (Birkhoff, Dynamical systems, 1966). The ultimate convergence and the evolution of the system along one of these modes of motion are determined uniquely by the condition that the dissipation rate is sufficiently smaller than the roper frequencies of the system. We show that it is possible to reassemble the starting configurations and migration history of the systems on the basis of their final states, and consequently to constrain the parameters of the physical processes involved.

Accurate ab initio potential energy surfaces for the (3)A '' and (3)A ' electronic states of the O(P-3) plus HBr system

In this work, we report the construction of potential energy surfaces for the (3)A '' and (3)A' states of the system O(P-3) + HBr. These surfaces are based on extensive ab initio calculations employing the MRCI+Q/CBS+SO level of theory. The complete basis set energies were estimated from extrapolation of MRCI+Q/aug-cc-VnZ(-PP) (n = Q, 5) results and corrections due to spin-orbit effects obtained at the CASSCF/aug-cc-pVTZ(-PP) level of theory. These energies, calculated over a region of the configuration space relevant to the study of the reaction O(P-3) + HBr -> OH + Br, were used to generate functions based on the many-body expansion. The three-body potentials were interpolated using the reproducing kernel Hilbert space method. The resulting surface for the (3)A '' electronic state contains van der Waals minima on the entrance and exit channels and a transition state 6.55 kcal/mol higher than the reactants. This barrier height was then scaled to reproduce the value of 5.01 kcal/mol, which was estimated from coupled cluster benchmark calculations performed to include high-order and core-valence correlation, as well as scalar relativistic effects. The (3)A' surface was also scaled, based on the fact that in the collinear saddle point geometry these two electronic states are degenerate. The vibrationally adiabatic barrier heights are 3.44 kcal/mol for the (3)A '' and 4.16 kcal/mol for the (3)A' state. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4705428]

Word sense disambiguation via high order of learning in complex networks

Complex networks have been employed to model many real systems and as a modeling tool in a myriad of applications. In this paper, we use the framework of complex networks to the problem of supervised classification in the word disambiguation task, which consists in deriving a function from the supervised (or labeled) training data of ambiguous words. Traditional supervised data classification takes into account only topological or physical features of the input data. On the other hand, the human (animal) brain performs both low- and high-level orders of learning and it has facility to identify patterns according to the semantic meaning of the input data. In this paper, we apply a hybrid technique which encompasses both types of learning in the field of word sense disambiguation and show that the high-level order of learning can really improve the accuracy rate of the model. This evidence serves to demonstrate that the internal structures formed by the words do present patterns that, generally, cannot be correctly unveiled by only traditional techniques. Finally, we exhibit the behavior of the model for different weights of the low- and high-level classifiers by plotting decision boundaries. This study helps one to better understand the effectiveness of the model. Copyright (C) EPLA, 2012

Supersymmetric Isospectral Formalism for the Calculation of Near-Zero Energy States: Application to the Very Weakly Bound He-4 Trimer Excited State

We propose a novel mathematical approach for the calculation of near-zero energy states by solving potentials which are isospectral with the original one. For any potential, families of strictly isospectral potentials (with very different shape) having desirable and adjustable features are generated by supersymmetric isospectral formalism. The near-zero energy Efimov state in the original potential is effectively trapped in the deep well of the isospectral family and facilitates more accurate calculation of the Efimov state. Application to the first excited state in He-4 trimer is presented.

Histologia e ultraestrutura do rim e rim cefálico do pacu

O pacu, Piaractus mesopotamicus, é um teleósteo da Família Characidae, intensivamente cultivado no Brasil devido sua rusticidade, crescimento rápido e fácil adaptação. O conhecimento morfológico dos sistemas corpóreos, incluído órgãos linfóide, se faz necessário, para uma melhor produção no cultivo de peixes, fornecendo subsídios na manutenção dos estoques. O objetivo deste estudo foi descrever morfologicamente o rim e rim cefálico de Piaractus mesopotamicus, analisando os perfis celulares de cada órgão com o uso de microscopia de luz e microscopia eletrônica de transmissão. O resultado da análise macroscópica mostrou que a localização do rim e rim cefálico são as mesmas encontradas na maioria dos teleósteos. O rim apresentou uma forma em "H", onde a região média se expandia sobre a bexiga natatória. O rim cefálico se apresentou como uma dilatação na região cranial do rim, mostrando-se bem visível. Na microscopia eletrônica de transmissão também foram observadas similaridades ultraestruturais com outros teleósteos. Observando nossos resultados concluímos que histologicamente e ultraestruturalmente, os órgãos linfóides rim e rim cefálico de Piaractus mesopotamicus são similares aos de outros teleósteos.

Prion potency in stem cells biology

Prion protein (PrP) can be considered a pivotal molecule because it interacts with several partners to perform a diverse range of critical biological functions that might differ in embryonic and adult cells. In recent years, there have been major advances in elucidating the putative role of PrP in the basic biology of stem cells in many different systems. Here, we review the evidence indicating that PrP is a key molecule involved in driving different aspects of the potency of embryonic and tissue-specific stem cells in self-perpetuation and differentiation in many cell types. It has been shown that PrP is involved in stem cell self-renewal, controlling pluripotency gene expression, proliferation and neural and cardiomyocyte differentiation. PrP also has essential roles in distinct processes that regulate tissue-specific stem cell biology in nervous and hematopoietic systems and during muscle regeneration. Results from our own investigations have shown that PrP is able to modulate self-renewal and proliferation in neural stem cells, processes that are enhanced by PrP interactions with stress inducible protein 1 (STI1). Thus, the available data reveal the influence of PrP in acting upon the maintenance of pluripotent status or the differentiation of stem cells from the early embryogenesis through adulthood.

Polymeric micelles and molecular modeling applied to the development of radiopharmaceuticals

Micelles composed of amphiphilic copolymers linked to a radioactive element are used in nuclear medicine predominantly as a diagnostic application. A relevant advantage of polymeric micelles in aqueous solution is their resulting particle size, which can vary from 10 to 100 nm in diameter. In this review, polymeric micelles labeled with radioisotopes including technetium (99mTc) and indium (111In), and their clinical applications for several diagnostic techniques, such as single photon emission computed tomography (SPECT), gamma-scintigraphy, and nuclear magnetic resonance (NMR), were discussed. Also, micelle use primarily for the diagnosis of lymphatic ducts and sentinel lymph nodes received special attention. Notably, the employment of these diagnostic techniques can be considered a significant tool for functionally exploring body systems as well as investigating molecular pathways involved in the disease process. The use of molecular modeling methodologies and computer-aided drug design strategies can also yield valuable information for the rational design and development of novel radiopharmaceuticals.