Surface-enhanced Raman scattering (SERS) applied to cancer diagnosis and detection of pesticides, explosives, and drugs

The inelastic scattering of light, Raman scattering, presents a very low cross section. However, the signal can be amplified by several orders of magnitude, leading to the so-called surface-enhanced Raman scattering (SERS) phenomenon. Basically, the SERS effect is achieved when the target molecule (analyte) is adsorbed onto metallic nanoparticles, usually noble metals. This article presents an overview of the applications of SERS to cancer diagnosis and the detection of pesticides, explosives, and drugs (illicit and pharmacological). SERS is routinely applied nowadays to detect and identify analytes at very low concentrations, including for single-molecule detection. However, the application of SERS as an analytical tool requires reliable and reproducible SERS substrates, in terms of enhancement factors, which depends on the size, shape, and aggregation of the metallic nanoparticles. Therefore, the production of reliable and reproducible SERS substrates is a challenge in the field. Besides, the metallic nanoparticles can also induce changes in the system by possible interactions with the analyte under investigation, which must be taken into account. This review will present work in which, under certain specific experimental conditions, SERS has been analytically applied.

Small-angle X-ray scattering and structural modeling of full-length: Cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations. © 2013 Springer Science+Business Media Dordrecht.

Sodium dodecyl sulfate (SDS) effect on the thermal stability of oxy-HbGp: Dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) studies

Glossoscolex paulistus (HbGp) hemoglobin is an oligomeric protein, presenting a quaternary structure constituted by 144 globin and 36 non-globin chains (named linkers) with a total molecular mass of 3.6MDa. SDS effects on the oxy-HbGp thermal stability were studied, by DLS and SAXS, at pH 5.0, 7.0 and 9.0. DLS and SAXS data show that the SDS-oxy-HbGp interactions induce a significant decrease of the protein thermal stability, with the formation of larger aggregates, at pH 5.0. At pH 7.0, oxy-HbGp undergoes complete oligomeric dissociation, with increase of temperature, in the presence of SDS. Besides, oxy-HbGp 3.0mg/mL, pH 7.0, in the presence of SDS, has the oligomeric dissociation process reduced as compared to 0.5mg/mL of protein. At pH 9.0, oxy-HbGp starts to dissociate at 20°C, and the protein is totally dissociated at 50°C. The thermal dissociation kinetic data show that oxy-HbGp oligomeric dissociation at pH 7.0, in the presence of SDS, is strongly dependent on the protein concentration. At 0.5mg/mL of protein, the oligomeric dissociation is complete and fast at 40 and 42°C, with kinetic constants of (2.1±0.2)×10-4 and (5.5±0.4)×10-4s-1, respectively, at 0.6mmol/L SDS. However, at 3.0mg/mL, the oligomeric dissociation process starts at 46°C, and only partial dissociation, accompanied by aggregates formation is observed. Moreover, our data show, for the first time, that, for 3.0mg/mL of protein, the oligomeric dissociation, denaturation and aggregation phenomena occur simultaneously, in the presence of SDS. Our present results on the surfactant-HbGp interactions and the protein thermal unfolding process correspond to a step forward in the understanding of SDS effects. © 2013 Elsevier B.V.

Some mathematical aspects and scattering amplitudes in the pure spinor formalism

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Amplitudes e padrões de polarização de pulsos em meios anisotrópicos

Extrair informações litológicas da subsuperfície através de dados sísmicos constitui-se num grande desafio à prospecção sísmica, pois a hipótese de estratificações formadas por camadas isotrópicas se mostra insuficiente para representar o comportamento do campo elástico em levantamentos com grandes afastamentos entre fonte e receptor, geofones multicomponentes, medidas de VSP tridimensional, entre outros. Sob este panorama, a prospecção sísmica passa a considerar modelos anisotrópicos de subsuperfície para, por exemplo, caracterizar reservatórios. O objetivo deste texto é apresentar um formalismo para modelar o espalhamento de pulsos a partir de ondas planas incidentes em interfaces planas horizontais que separam meios anisotrópicos. Este espalhamento é obtido primeiramente, através da formulação explícita dos campos de deformação e tração como função das matrizes propagadoras, de polarização e de impedância do meio. Em seguidaeste formalismo é usado para a obtenção das matrizes dos coeficientes de reflexão e transmissão através de uma interface plana horizontal para posteriormente, ser generalizado para o espalhamento através de múltiplas camadas. Finalmente, inserem-se ao campo da onda incidente as amplitudes de um pulso analítico para calcular o espalhamento do pulso através de estratificações.

Modelagem e imageamento 2.5D no domínio do tempo através de diferenças finitas

A modelagem 2.5D consiste em simular a propagação do campo de ondas em 3D em meios com simetria de translação em uma direção. Nesta tese esta abordagem é formulada para meios elásticos e anisotrópicos com classe de simetria arbitrária e a geometria de aquisição não precisa coincidir com um plano de simetria do meio. A migração por reversão no tempo do campo de ondas é formulada e implementada através de diferenças finitas 2.5D. Para reduzir os efeitos de retro-espalhamento e melhorar a recuperação da amplitude dos eventos migrados, propomos uma nova condição de imagem para migração reversa no tempo baseada na análise assintótica da condição de imagem clássica por correlação cruzada. Experimentos numéricos indicam que a migração reversa no tempo 2.5D com a nova condição de imagem proposta, melhora a resolução da imagem em relação à migração reversa no tempo 2D e reduz acentuadamente os ruídos causados por retro-espalhamento.

Study of double parton scattering using W+2-jet events in proton-proton collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Biomaterials from blends of fluoropolymers and corn starch-implant and structural aspects

The development of polymeric blends to be used as matrices for bone regeneration is a hot topic nowadays. In this article we report on the blends composed by corn starch and poly(vinylidene fluoride), PVDF, or poly(vinylidene fluoride-trifluoroethylene), P(VDF-TrFE), to obtain biocompatible materials. Blends were produced by compressing/annealing and chemically/structurally characterized by micro-Raman scattering and Fourier transform infrared (FTIR) absorption spectroscopies, dynamic mechanical analysis (DMA) and scanning electron microscopy (SEM), besides in vivo study to evaluate the tissue response. Vibrational spectroscopy reveals no chemical interaction between the polymers and starch, absence of material degradation due to compressing/annealing process or organism implantation, and maintenance of a and ferroelectric crystalline phases of PVDF and P(VDF-TrFE), respectively. As a consequence of absence of interaction between polymers and starch, it was possible to identify by SEM each material, with starch acting as filler. Elastic modulus (E') obtained from DMA measurement, independent of the material proportion used in blends, reaches values close to those of cancellous bone. Finally, the in vivo study in animals shows that the blends, regardless of the composition, were tolerated by cancellous bone. (C) 2013 Elsevier B.V. All rights reserved.

Inferring a weighted elastic network from partial unfolding with coarse-grained simulations

A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental C coordinates, and they only take the pairs of C atoms within a given cutoff distance r(c) into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two C atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures. Proteins 2014; 82:119-129. (c) 2013 Wiley Periodicals, Inc.

Interpolating scattering amplitudes between the instant form and the front form of relativistic dynamics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

N-point tree-level scattering amplitude in the new Berkovits' string

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Massless scattering at special kinematics as Jacobi polynomials

We study the scattering equations recently proposed by Cachazo, He and Yuan in the special kinematics where their solutions can be identified with the zeros of the Jacobi polynomials. This allows for a non-trivial two-parameter family of kinematics. We present explicit and compact formulas for the n-gluon and n-graviton partial scattering amplitudes for our special kinematics in terms of Jacobi polynomials. We also provide alternative expressions in terms of gamma functions. We give an interpretation of the common reduced determinant appearing in the amplitudes as the product of the squares of the eigenfrequencies of small oscillations of a system whose equilibrium is the solutions of the scattering equations.

Scattering Amplitudes Interpolating Between Instant Form and Front Form of Relativistic Dynamics

Among the three forms of relativistic Hamiltonian dynamics proposed by Dirac in 1949, the front form has the largest number of kinematic generators. This distinction provides useful consequences in the analysis of physical observables in hadron physics. Using the method of interpolation between the instant form and the front form, we introduce the interpolating scattering amplitude that links the corresponding time-ordered amplitudes between the two forms of dynamics and provide the physical meaning of the kinematic transformations as they allow the invariance of each individual time-ordered amplitude for an arbitrary interpolation angle. We discuss the rationale for using front form dynamics, nowadays known as light-front dynamics (LFD), and present a few explicit examples of hadron phenomenology that LFD uniquely can offer from first-principles quantum chromodynamics. In particular, model-independent constraints are provided for the analyses of deuteron form factors and the N Delta transition form factors at large momentum transfer squared Q(2). The swap of helicity amplitudes between the collinear and non-collinear kinematics is also discussed in deeply virtual Compton scattering.

Cetyltrimethylammonium chloride (CTAC) effect on the thermal stability of oxy-HbGp: Dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) studies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)