A characteristic based numerical method with tracking for nonlinear wave equations

Many physical problems can be modeled by scalar, first-order, nonlinear, hyperbolic, partial differential equations (PDEs). The solutions to these PDEs often contain shock and rarefaction waves, where the solution becomes discontinuous or has a discontinuous derivative. One can encounter difficulties using traditional finite difference methods to solve these equations. In this paper, we introduce a numerical method for solving first-order scalar wave equations. The method involves solving ordinary differential equations (ODEs) to advance the solution along the characteristics and to propagate the characteristics in time. Shocks are created when characteristics cross, and the shocks are then propagated by applying analytical jump conditions. New characteristics are inserted in spreading rarefaction fans. New characteristics are also inserted when values on adjacent characteristics lie on opposite sides of an inflection point of a nonconvex flux function, Solutions along characteristics are propagated using a standard fourth-order Runge-Kutta ODE solver. Shocks waves are kept perfectly sharp. In addition, shock locations and velocities are determined without analyzing smeared profiles or taking numerical derivatives. In order to test the numerical method, we study analytically a particular class of nonlinear hyperbolic PDEs, deriving closed form solutions for certain special initial data. We also find bounded, smooth, self-similar solutions using group theoretic methods. The numerical method is validated against these analytical results. In addition, we compare the errors in our method with those using the Lax-Wendroff method for both convex and nonconvex flux functions. Finally, we apply the method to solve a PDE with a convex flux function describing the development of a thin liquid film on a horizontally rotating disk and a PDE with a nonconvex flux function, arising in a problem concerning flow in an underground reservoir.

Time-resolved resonance Raman spectroscopic studies on the triplet excited state of fluoranil

Perfluoro substituted organic compounds have attracted attention owing to their unique structure and reactivity induced by the perfluoro effect. Fluoranil, a perfluoro derivative of p-benzoquinone, is the subject of this paper. Although the perfluoro effect in the ground state seems to have been well understood there is no information available about such effects on the excited state. Here, the time-resolved resonance Raman spectra of the triplet excited state of fluoranil are reported along with the Raman excitation profiles (REPs) of the various vibrational modes. The vibrational spectral analyses have been carried out by analogy with the fluoranil ground state, triplet benzoquinone, and triplet chloranil vibrational spectral assignments. Also, the assignments are further supported by the calculated frequencies using ab initio theoretical methods. It is observed that for fluoranil in the triplet excited state, due to the perfluoro effect, the structure is considerably less distorted than benzoquinone and also the electron delocalization in the pi* antibonding orbital is less than that of triplet excited state of benzoquinone.

Symmetry-dependent phonon renormalization in monolayer MoS2 transistor

A strong electron-phonon interaction which limits the electronic mobility of semiconductors can also have significant effects on phonon frequencies. The latter is the key to the use of Raman spectroscopy for nondestructive characterization of doping in graphene-based devices. Using in situ Raman scattering from a single-layer MoS2 electrochemically top-gated field-effect transistor (FET), we show softening and broadening of the A(1g) phonon with electron doping, whereas the other Raman-active E-2g(1) mode remains essentially inert. Confirming these results with first-principles density functional theory based calculations, we use group theoretical arguments to explain why the A(1g) mode specifically exhibits a strong sensitivity to electron doping. Our work opens up the use of Raman spectroscopy in probing the level of doping in single-layer MoS2-based FETs, which have a high on-off ratio and are of technological significance.

Higher spin quasinormal modes and one-loop determinants in the BTZ black hole

We solve the wave equations of arbitrary integer spin fields in the BTZ black hole background and obtain exact expressions for their quasinormal modes. We show that these quasinormal modes precisely agree with the location of the poles of the corresponding two point function in the dual conformal field theory as predicted by the AdS/CFT correspondence. We then use these quasinormal modes to construct the one-loop determinant of the higher spin field in the thermal BTZ background. This is shown to agree with that obtained from the corresponding heat kernel constructed recently by group theoretic methods.

Higher spin fermions in the BTZ black hole

Recently it has been shown that the wave equations of bosonic higher spin fields in the BTZ background can be solved exactly. In this work we extend this analysis to fermionic higher spin fields. We solve the wave equations for arbitrary half-integer spin fields in the BTZ black hole background and obtain exact expressions for their quasinormal modes. These quasinormal modes are shown to agree precisely with the poles of the corresponding two point function in the dual conformal field theory as predicted by the AdS/CFT correspondence. We also obtain an expression for the 1-loop determinant for the Euclidean non-rotating BTZ black hole in terms of the quasinormal modes which agrees with that obtained by integrating the heat kernel found by group theoretic methods.

DNA Elasticity from Short DNA to Nucleosomal DNA

Active biological processes like transcription, replication, recombination, DNA repair, and DNA packaging encounter bent DNA. Machineries associated with these processes interact with the DNA at short length (<100 base pair) scale. Thus, the study of elasticity of DNA at such length scale is very important. We use fully atomistic molecular dynamics (MD) simulations along with various theoretical methods to determine elastic properties of dsDNA of different lengths and base sequences. We also study DNA elasticity in nucleosome core particle (NCP) both in the presence and the absence of salt. We determine stretch modulus and persistence length of short dsDNA and nucleosomal DNA from contour length distribution and bend angle distribution, respectively. For short dsDNA, we find that stretch modulus increases with ionic strength while persistence length decreases. Calculated values of stretch modulus and persistence length for DNA are in quantitative agreement with available experimental data. The trend is opposite for NCP DNA. We find that the presence of histone core makes the DNA stiffer and thus making the persistence length 3-4 times higher than the bare DNA. Similarly, we also find an increase in the stretch modulus for the NCP DNA. Our study for the first time reports the elastic properties of DNA when it is wrapped around the histone core in NCP. We further show that the WLC model is inadequate to describe DNA elasticity at short length scale. Our results provide a deeper understanding of DNA mechanics and the methods are applicable to most protein-DNA complexes.

Equivalent Model Of Expansion Of Cement Mortar Under Sulphate Erosion

The expansion property of cement mortar under the attack of sulfate ions is studied by experimental and theoretical methods. First, cement mortars are fabricated with the ratio of water to cement of 0.4, 0.6, and 0.8. Secondly, the expansion of specimen immerged in sulphate solution is measured at different times. Thirdly, a theoretical model of expansion of cement mortar under sulphate erosion is suggested by virtue of represent volume element method. In this model, the damage evolution due to the interaction between delayed ettringite and cement mortar is taken into account. Finally, the numerical calculation is performed. The numerical and experimental results indicate that the model perfectly describes the expansion of the cement mortar.

EQUIVALENT MODEL OF EXPANSION OF CEMENT MORTAR UNDER SULPHATE EROSION

The expansion property of cement mortar under the attack of sulfate ions is studied by experimental and theoretical methods. First, cement mortars are fabricated with the ratio of water to cement of 0.4, 0.6, and 0.8. Secondly, the expansion of specimen immerged in sulphate solution is measured at different times. Thirdly, a theoretical model of expansion of cement mortar under sulphate erosion is suggested by virtue of represent volume element method. In this model, the damage evolution due to the interaction between delayed ettringite and cement mortar is taken into account. Finally, the numerical calculation is performed. The numerical and experimental results indicate that the model perfectly describes the expansion of the cement mortar.

A comparative study of Young's modulus of single-walled carbon nanotube by CPMD, MD, and first principle simulations

Carbon nanotubes (CNTs), due to their exceptional magnetic, electrical and mechanical properties, are promising candidates for several technical applications ranging from nanoelectronic devices to composites. Young's modulus holds the special status in material properties and micro/nano-electromechanical systems (MEMS/NEMS) design. The excellently regular structures of CNTs facilitate accurate simulation of CNTs' behavior by applying a variety of theoretical methods. Here, three representative numerical methods, i.e., Car-Parrinello molecular dynamics (CPMD), density functional theory (DFT) and molecular dynamics (MD), were applied to calculate Young's modulus of single-walled carbon nanotube (SWCNT) with chirality (3,3). The comparative studies showed that the most accurate result is offered by time consuming DFT simulation. MID simulation produced a less accurate result due to neglecting electronic motions. Compared to the two preceding methods the best performance, with a balance between efficiency and precision, was deduced by CPMD.

Biotechnologies for cancer diagnostics : cell sorting, protein analysis and imaging of cellular metabolism

This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called “Nucleic Acid Cell Sorting (NACS)”, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.

Secondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called “Radiopharmaceutical Imaging Chip” (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.

The last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.

Studies of phonon anharmonicity in solids

Today our understanding of the vibrational thermodynamics of materials at low temperatures is emerging nicely, based on the harmonic model in which phonons are independent. At high temperatures, however, this understanding must accommodate how phonons interact with other phonons or with other excitations. We shall see that the phonon-phonon interactions give rise to interesting coupling problems, and essentially modify the equilibrium and non-equilibrium properties of materials, e.g., thermodynamic stability, heat capacity, optical properties and thermal transport of materials. Despite its great importance, to date the anharmonic lattice dynamics is poorly understood and most studies on lattice dynamics still rely on the harmonic or quasiharmonic models. There have been very few studies on the pure phonon anharmonicity and phonon-phonon interactions. The work presented in this thesis is devoted to the development of experimental and computational methods on this subject.

Modern inelastic scattering techniques with neutrons or photons are ideal for sorting out the anharmonic contribution. Analysis of the experimental data can generate vibrational spectra of the materials, i.e., their phonon densities of states or phonon dispersion relations. We obtained high quality data from laser Raman spectrometer, Fourier transform infrared spectrometer and inelastic neutron spectrometer. With accurate phonon spectra data, we obtained the energy shifts and lifetime broadenings of the interacting phonons, and the vibrational entropies of different materials. The understanding of them then relies on the development of the fundamental theories and the computational methods.

We developed an efficient post-processor for analyzing the anharmonic vibrations from the molecular dynamics (MD) calculations. Currently, most first principles methods are not capable of dealing with strong anharmonicity, because the interactions of phonons are ignored at finite temperatures. Our method adopts the Fourier transformed velocity autocorrelation method to handle the big data of time-dependent atomic velocities from MD calculations, and efficiently reconstructs the phonon DOS and phonon dispersion relations. Our calculations can reproduce the phonon frequency shifts and lifetime broadenings very well at various temperatures.

To understand non-harmonic interactions in a microscopic way, we have developed a numerical fitting method to analyze the decay channels of phonon-phonon interactions. Based on the quantum perturbation theory of many-body interactions, this method is used to calculate the three-phonon and four-phonon kinematics subject to the conservation of energy and momentum, taking into account the weight of phonon couplings. We can assess the strengths of phonon-phonon interactions of different channels and anharmonic orders with the calculated two-phonon DOS. This method, with high computational efficiency, is a promising direction to advance our understandings of non-harmonic lattice dynamics and thermal transport properties.

These experimental techniques and theoretical methods have been successfully performed in the study of anharmonic behaviors of metal oxides, including rutile and cuprite stuctures, and will be discussed in detail in Chapters 4 to 6. For example, for rutile titanium dioxide (TiO₂), we found that the anomalous anharmonic behavior of the B_1g mode can be explained by the volume effects on quasiharmonic force constants, and by the explicit cubic and quartic anharmonicity. For rutile tin dioxide (SnO₂), the broadening of the B_2g mode with temperature showed an unusual concave downwards curvature. This curvature was caused by a change with temperature in the number of down-conversion decay channels, originating with the wide band gap in the phonon dispersions. For silver oxide (Ag₂O), strong anharmonic effects were found for both phonons and for the negative thermal expansion.

Perspectiva estética/sociopoética ao cuidar de clientes com alterações de autoimagem devido a afecções dermatológicas

Tratar sobre dimensões vivenciais que envolvem o adoecimento cutâneo é indispensável em uma sociedade onde as pessoas vivem sujeitas às pressões quanto à: modelos socioculturais, preocupações com crenças e valores e imposições estéticas, podendo assim sofrer distorções em sua autoimagem corporal e autoestima. Refletindo sobre a teoria de adaptação de Roy quanto à singularidade do ser humano para reagir, aprender e se adaptar na sua convivência no mundo, consigo e com os outros, indaga-se: quais são as repercussões do acometimento cutâneo na vida das pessoas? Assim, formulou-se o objeto de estudo - Repercussões do acometimento de afecções cutâneas na vida das pessoas. Teve-se como objetivos propor uma perspectiva de cuidar em enfermagem compatível com as necessidades humanas de pessoas com alteração de autoimagem e autoestima devido a afecções dermatológicas; identificar as características sociodemográficas e clínicas das pessoas com afecções dermatológicas; analisar a dimensão imaginativa de pessoas referente à sua convivência com afecções dermatológicas, destacando seus sentimentos quanto à autoimagem e à autoestima. Este trabalho se insere no Grupo de Pesquisa Concepções teóricas para o cuidar em saúde e enfermagem - CNPq, na Linha de pesquisa Fundamentos filosóficos, teóricos e tecnológicos do cuidar em saúde e enfermagem e no projeto denominado A perspectiva estética/sociopoética do cuidar em enfermagem: identificando necessidades de autocuidado para promoção da saúde da Bolsa de Produtividade em Pesquisa CNPq, período 2011-2014, e da Bolsa de Professor Visitante da Universidade do Estado do Rio de Janeiro. Escolheu-se como referencial teórico metodológico a sociopoética e as técnicas de pesquisa dinâmica do corpo como território mínimo e a narrativa da lenda da beleza. O Grupo-Pesquisador, (GP) dispositivo analítico da sociopoética foi composto por 18 clientes da Enfermaria de Dermatologia do Hospital Universitário Pedro Ernesto, que desenvolveram as fases do método sociopoético no período de maio a agosto de 2013. Os dados produzidos foram analisados conforme os estudos sociopoéticos transversal, classificatório e filosófico. No transversal se destacam as categorias - Investindo no cuidado para o autocuidado e o desejo por uma pele íntegra x Imagem corporal elevada. No classificatório, a categoria Percebendo e conhecendo a afecção dermatológica x Descuidado consciente com o corpo. No estudo filosófico, destacam-se as categorias: comprometimento da autoimagem frente às repercussões da afecção dermatológica e a beleza existente no ser humano amado. Os resultados permitiram responder a questão inicialmente formulada e alcançar os objetivos propostos. Conclui-se que, a sociopoética como uma construção coletiva revelou-se, nesta pesquisa, como uma importante ferramenta tanto no cuidar/educar/pesquisar em enfermagem como na abordagem humanista aos clientes com afecções dermatológicas. Sendo assim, ao analisar a dimensão imaginativa referente à convivência das pessoas com a enfermidade citada, esta dissertação contribuiu para uma ampliação da perspectiva da imagem e estima das mesmas, na tentativa de possibilitar o desenvolvimento do cuidado de enfermagem cada vez mais próximo ao cliente por meio da interação e do diálogo.

Avaliação de modelos preditivos de sorção em membranas de pervaporação para a remoção de sulfurados da nafta

A remoção de compostos sulfurados da gasolina é um assunto de grande interesse na indústria de refino de petróleo em função das restrições ambientais cada vez mais rígidas em relação ao teor máximo de enxofre de produtos acabados. A solução mais comum para remoção de contaminantes são as unidades de hidrotratamento que operam a alta pressão e possuem alto custo de instalação e de operação além de levarem à perda de octanagem do produto acabado. O uso de membranas é uma alternativa promissora para a redução do teor de enxofre de correntes de gasolina e possui diversas vantagens em relação ao hidrotratamento convencional. O conhecimento aprofundado dos parâmetros que influenciam as etapas de sorção e difusão é crítico para o desenvolvimento da aplicação. Este trabalho avalioua seletividade e sorção do sistema formado por n-heptano e tiofeno em polímeros através de modelos termodinâmicos rigorosos, baseados em contribuição de grupos. O modelo UNIFAC-FV, variante do tradicional modelo UNIFAC para sistemas poliméricos, foi o modelo escolhido para cálculo de atividade dos sistemas estudados. Avaliou-se ainda a disponibilidade de parâmetros para desenvolvimento da modelagem e desenvolveu-se uma abordagem com alternativas para casos de indisponibilidade de parâmetros UNIFAC. Nos casos com ausência de parâmetros, o cálculo do termo residual da atividade das espécies é feito na forma proposta por Flory-Hugginsutilizando-se parâmetros de solubilidade obtidos também por contribuição de grupos. Entre os métodos de contribuição de grupos existentes para cálculo de parâmetros de solubilidade, o método de Hoy mostrou menores desvios para os sistemas estudados. A abordagem utilizada neste trabalho permite, ao final, uma análise de alterações da configuração da cadeia principal de polímeros de forma a influenciar sua seletividade e sorção para dessulfurização de naftas

MCMC-based tracking and identification of leaders in groups

We present a novel framework for identifying and tracking dominant agents in groups. Our proposed approach relies on a causality detection scheme that is capable of ranking agents with respect to their contribution in shaping the system's collective behaviour based exclusively on the agents' observed trajectories. Further, the reasoning paradigm is made robust to multiple emissions and clutter by employing a class of recently introduced Markov chain Monte Carlo-based group tracking methods. Examples are provided that demonstrate the strong potential of the proposed scheme in identifying actual leaders in swarms of interacting agents and moving crowds. © 2011 IEEE.

A theory of slow feature analysis for transformation-based input signals with an application to complex cells

We develop a group-theoretical analysis of slow feature analysis for the case where the input data are generated by applying a set of continuous transformations to static templates. As an application of the theory, we analytically derive nonlinear visual receptive fields and show that their optimal stimuli, as well as the orientation and frequency tuning, are in good agreement with previous simulations of complex cells in primary visual cortex (Berkes and Wiskott, 2005). The theory suggests that side and end stopping can be interpreted as a weak breaking of translation invariance. Direction selectivity is also discussed. © 2011 Massachusetts Institute of Technology.