Analysis of 2D THz-Raman spectroscopy using a non-Markovian Brownian oscillator model with nonlinear system-bath interactions

We explore and describe the roles of inter-molecular vibrations employing a Brownian oscillator (BO) model with linear-linear (LL) and square-linear (SL) system-bath interactions, which we use to analyze two-dimensional (2D) THz-Raman spectra obtained by means of molecular dynamics (MD) simulations. In addition to linear absorption (1D IR), we calculated 2D Raman-THz-THz, THz-Raman-THz, and THz-THz-Raman signals for liquid formamide, water, and methanol using an equilibrium non-equilibrium hybrid MD simulation. The calculated 1D IR and 2D THz-Raman signals are compared with results obtained from the LL+SL BO model applied through use of hierarchal Fokker-Planck equations with non-perturbative and non-Markovian noise. We find that all of the qualitative features of the 2D profiles of the signals obtained from the MD simulations are reproduced with the LL+SL BO model, indicating that this model captures the essential features of the inter-molecular motion. We analyze the fitted 2D profiles in terms of anharmonicity, nonlinear polarizability, and dephasing time. The origins of the echo peaks of the librational motion and the elongated peaks parallel to the probe direction are elucidated using optical Liouville paths.Comment: 37 pages with 14 figures and 3 table

Reduced hierarchy equations of motion approach with Drude plus Brownian spectral distribution: Probing electron transfer processes by means of two- dimensionalcorrelation spectroscopy

We theoretically investigate an electron transfer (ET) process in a dissipative environment by means of two-dimensional (2D) correlation spectroscopy. We extend the reduced hierarchy equations of motion approach to include both overdamped Drude and underdamped Brownian modes. While the overdamped mode describes the inhomogeneity of a system in the slow modulation limit, the underdamped mode expresses the primary vibrational mode coupled with the electronic states. We outline a procedure for calculating 2D correlation spectrum that incorporates the ET processes. The present approach has the capability of dealing with system-bath coherence under an external perturbation, which is important to calculate nonlinear response functions for non-Markovian noise. The calculated 2D spectrum exhibits the effects of the ET processes through the presence of ET transition peaks along the $\Omega_1$ axis, as well as the decay of echo signals.Comment: 28 pages, 8 figures; J. Chem. Phys. 137 (2012

Correlated fluctuations in the exciton dynamics and spectroscopy of DNA

The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between bases and the structure of the DNA environment. We model the effect of dynamical fluctuations in the environment and study correlation, which is present when multiple base pairs interact with the same mode in the environment. We find that the correlations strongly affect the exciton dynamics, and show how they are observed in the decay of the anisotropy as a function of a coherence and a population time in a non-linear optical experiment

Video semantic content analysis framework based on ontology combined MPEG-7

The rapid increase in the available amount of video data is creating a growing demand for efficient methods for understanding and managing it at the semantic level. New multimedia standard, MPEG-7, provides the rich functionalities to enable the generation of audiovisual descriptions and is expressed solely in XML Schema which provides little support for expressing semantic knowledge. In this paper, a video semantic content analysis framework based on ontology combined MPEG-7 is presented. Domain ontology is used to define high level semantic concepts and their relations in the context of the examined domain. MPEG-7 metadata terms of audiovisual descriptions and video content analysis algorithms are expressed in this ontology to enrich video semantic analysis. OWL is used for the ontology description. Rules in Description Logic are defined to describe how low-level features and algorithms for video analysis should be applied according to different perception content. Temporal Description Logic is used to describe the semantic events, and a reasoning algorithm is proposed for events detection. The proposed framework is demonstrated in sports video domain and shows promising results

Preliminary report on the effect of pituitary autotransplantation on the pars intermedia of the seawater goby, Gillichthys mirabilis

Estudou-se com a microscopia eletrônica os efeitos do autotransplante da parte intermédia da pituitária do cadoz de água salgada, Gullichthys mirabilis. No peixe sem transplante, a parte intermédia possui dois tipos de células secretoras: hematoxilina de Pb-positiva (PbH+) e hametoxilina de chumbo negativa (PbH-), diretamente inervadas pelo axônios neurossecretores (tipo A e B) originários do hipotálamo

QTL detection and allelic effects for growth and fat traits in outbred pig populations

Quantitative trait loci (QTL) for growth and fatness traits have previously been identified on chromosomes 4 and 7 in several experimental pig populations. The segregation of these QTL in commercial pigs was studied in a sample of 2713 animals from five different populations. Variance component analysis (VCA) using a marker-based identity by descent (IBD) matrix was applied. The IBD coefficient was estimated with simple deterministic (SMD) and Markov chain Monte Carlo (MCMC) methods. Data for two growth traits, average daily gain on test and whole life daily gain, and back fat thickness were analysed. With both methods, seven out of 26 combinations of population, chromosome and trait, were significant. Additionally, QTL genotypic and allelic effects were estimated when the QTL effect was significant. The range of QTL genotypic effects in a population varied from 4.8% to 10.9% of the phenotypic mean for growth traits and 7.9% to 19.5% for back fat trait. Heritabilities of the QTL genotypic values ranged from 8.6% to 18.2% for growth traits, and 14.5% to 19.2% for back fat. Very similar results were obtained with both SMD and MCMC. However, the MCMC method required a large number of iterations, and hence computation time, especially when the QTL test position was close to the marker

Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations

<p>Abstract</p> <p>Background</p> <p>Simultaneous detection of multiple QTLs (quantitative trait loci) may allow more accurate estimation of genetic effects. We have analyzed outbred commercial pig populations with different single and multiple models to clarify their genetic properties and in addition, we have investigated pleiotropy among growth and obesity traits based on allelic correlation within a gamete.</p> <p>Methods</p> <p>Three closed populations, (A) 427 individuals from a Yorkshire and Large White synthetic breed, (B) 547 Large White individuals and (C) 531 Large White individuals, were analyzed using a variance component method with one-QTL and two-QTL models. Six markers on chromosome 4 and five to seven markers on chromosome 7 were used.</p> <p>Results</p> <p>Population A displayed a high test statistic for the fat trait when applying the two-QTL model with two positions on two chromosomes. The estimated heritabilities for polygenic effects and for the first and second QTL were 19%, 17% and 21%, respectively. The high correlation of the estimated allelic effect on the same gamete and QTL test statistics suggested that the two separate QTL which were detected on different chromosomes both have pleiotropic effects on the two fat traits. Analysis of population B using the one-QTL model for three fat traits found a similar peak position on chromosome 7. Allelic effects of three fat traits from the same gamete were highly correlated suggesting the presence of a pleiotropic QTL. In population C, three growth traits also displayed similar peak positions on chromosome 7 and allelic effects from the same gamete were correlated.</p> <p>Conclusion</p> <p>Detection of the second QTL in a model reduced the polygenic heritability and should improve accuracy of estimated heritabilities for both QTLs.</p

Application of cross correlations between CMB and large scale structure to constraints on the primordial non-Gaussianity

The primordial non-Gaussianity of local type affects the clustering of dark matter halos, and the planned deep and wide photometric surveys are suitable for examining this class of non-Gaussianity. In our previous paper, we investigated the constraint from the cross correlation between CMB lensing potential and galaxy angular distribution on the primordial non-Gaussianity, without taking into account redshift slicing. To improve our previous analysis, in this paper, we add the galaxy lensing shear into our analysis and take into account redshift slicing to follow the redshift evolution of the clustering. By calculating 81 power spectra and using the Fisher matrix method, we find that the constraint on the primordial non-Gaussianity can be improved from {\Delta}fNL \sim 5.4 to 5.1 by including the galaxy-galaxy lensing shear cross correlations expected from the Hyper Suprime-Cam survey (HSC), in comparison with the constraint without any cross correlations. Moreover, the constraint can go down to {\Delta}fNL \sim 4.8 by including the galaxy-CMB lensing cross correlations from the ACTPol and Planck experiments.Comment: 17 pages, 9 figuers, 7 tables, published in Phys. Rev. D 201