Autosolitons in trapped Bose-Einstein condensates with two- and three-body inelastic processes

The conditions for the existence of autosolitons were considered in trapped Bose-Einstein condensates with attractive atomic interactions. The expression for the parameters of the autosoliton was derived using the time-dependent variational approach for the nonconservative 3-dimensional Gross-pitaevskii equation and their stability was checked. The results were in agreement with the exact numerical calculations. It was shown that the transition from unstable to stable point solely depends on the magnitude of the parameters.

Double optical monitoring of time-dependent film formation

A brief overview of optical monitoring for vacuum and wet bench film deposition processes is presented. Interferometric and polarimetric measurements are combined with regard to simultaneous real-time monitoring of refractive index and physical thickness. Monitor stability and accuracy are verified with transparent oil standards. This double optical technique is applied to dip coating with a multi-component Zirconyl Chloride aqueous solution, whose time varying refractive index and physical thickness curves indicate significant sensitivity to changes of film flow properties during the process.

Search for exotic resonances decaying into WZ/ZZ in pp collisions at √s=7 TeV

A search for new exotic particles decaying to the VZ final state is performed, where V is either a W or a Z boson decaying into two overlapping jets and the Z decays into a pair of electrons, muons or neutrinos. The analysis uses a data sample of pp collisions corresponding to an integrated luminosity of 5 fb-1 collected by the CMS experiment at the LHC at √s=7 TeV in 2011. No significant excess is observed in the mass distribution of the VZ candidates compared with the background expectation from standard model processes. Model-dependent upper limits at the 95% confidence level are set on the product of the cross section times the branching fraction of hypothetical particles decaying to the VZ final state as a function of mass. Sequential standard model W′ bosons with masses between 700 and 940 GeV are excluded. In the Randall-Sundrum model for graviton resonances with a coupling parameter of 0.05, masses between 750 and 880 GeV are also excluded. © 2013 CERN for the benefit of the CMS collaboration.

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Connectivity processes and riparian vegetation of the upper Paraná River, Brazil

In fluvial systems, the relationship between a dominant variable (e.g. flood pulse) and its dependent ones (e.g. riparian vegetation) is called connectivity. This paper analyzes the connectivity elements and processes controlling riparian vegetation for a reach of the upper Paraná River (Brazil) and estimates the future changes in channel-vegetation relationship as a consequence of the managing of a large dam. The studied reach is situated 30km downstream from the Porto Primavera Dam (construction finished in 1999). Through aerial photography (1:25,000, 1996), RGB-CBERS satellite imagery and a previous field botany survey it was possible to elaborate a map with the five major morpho-vegetation units: 1) Tree-dominated natural levee, 2) Shrubby upper floodplain, 3) Shrub-herbaceous mid floodplain, 4) Grass-herbaceous lower floodplain and 5) Shrub-herbaceous flood runoff channel units. By use of a detailed topographic survey and statistical tools each morpho-vegetation type was analyzed according to its connectivity parameters (frequency, recurrence, permanence, seasonality, potamophase, limnophase and FCQ index) in the pre- and post-dam closure periods of the historical series. Data showed that most of the morpho-vegetation units were predicted to present changes in connectivity parameters values after dam closing and the new regime could affect, in different intensity, the river ecology and particularly the riparian vegetation. The methods used in this study can be useful for dam impact studies in other South American tropical rivers. © 2012 Elsevier Ltd.

Vidros a base de óxido de telúrio para dispositivos fotônicos

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

Estudo de composições vítreas no sistema ternário Ga-Ge-Te para o armazenamento de dados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ability of Salmonella spp. to Produce Biofilm Is Dependent on Temperature and Surface Material

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

Biotransformed soybean extract induces cell death of estrogen-dependent breast cancer cells by modulation of apoptotic proteins

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

Homology in a context dependent predatory behavior in spiders (Araneae)

Stereotyped behaviors have been routinely used as characters for phylogeny inference, but the same cannot be said of the plastic aspects of performance, which routinely are taken as a result of ecological processes. In this paper we examine the evolution of one of these plastic behavioral phenotypes, thus fostering a bridge between ecological and evolutionary processes. Foraging behavior in spiders is context dependent in many aspects, since it varies with prey type and size, spider nutritional and developmental state, previous experience and, in webweavers, is dependent on the structure of the web. Reeling is a predatory tactic typical of cobweb weavers (Theridiidae), in which the spider moves the prey toward her by pulling the capture thread (gumfoot) to which it is adhered. Predatory reeling is dependent on the gumfoot for its expression, and has not been previously reported in orbweavers. In order to investigate the evolution of this web dependent behavior, we built artificial, pseudogumfoot lines in orbwebs and registered parameters of the predatory tactics in this modified web. Aspects of the predatory tactics of 240 individuals (12 species in 4 families) were measured, and the resulting data were optimized on the phylogeny of Orbiculariae. All species perform predatory reeling with the pseudogumfoot lines. Thus, predatory reeling is homologous for the whole Orbiculariae group. In nature, holes made by insects in ecribellate orbs produce pseudogumfoot lines (similar to out experimentally modified webs), and thus reeling occurred naturally in ecribellates. Nevertheless, outside lab conditions, predatory reeling does not occur among cribellate orbweavers, so that this behavior could not have been selected for in the cribellate ancester of orbweavers. Cribellate spiders are flexible enough as to present novel and adaptive predatory responses (reeling) even when exposed for the first time to conditions outside their usual environment. Thus, the evolution of reeling suggests and alternative mechanism for the production of evolutionary novelties; that is, the exploration of unusual ecological conditions and of the regular effects these abnormal conditions have on phenotype expression.

mu(1)- and 5-HT1-dependent mechanisms in the anterior pretectal nucleus mediate the antinociceptive effects of retrosplenial cortex stimulation in rats

Aim: This study examines if injection of cobalt chloride (CoCl2) or antagonists of muscarinic cholinergic (atropine), mu(1)-opioid (naloxonazine) or 5-HT1 serotonergic (methiothepin) receptors into the dorsal or ventral portions of the anterior pretectal nucleus (APtN) alters the antinociceptive effects of stimulating the retrosplenial cortex (RSC) in rats. Main method: Changes in the nociceptive threshold were evaluated using the tail flick or incision pain tests in rats that were electrically stimulated at the RSC after the injection of saline, CoCl2 (1 mM, 0.10 mu L) or antagonists into the dorsal or ventral APtN. Key findings: The injection of CoCl2, naloxonazine (5 mu g/0.10 mu L) or methiothepin (3 mu g/0.10 mu L) into the dorsal APtN reduced the stimulation-produced antinociception from the RSC in the rat tail flick test. Reduction of incision pain was observed following stimulation of the RSC after the injection of the same substances into the ventral APtN. The injection of atropine (10 ng/0.10 mu L) or ketanserine (5 mu g/0.10 mu L) into the dorsal or ventral APtN was ineffective against the antinociception resulting from RSC stimulation. Significance: mu(1)-opioid- and 5-HT1-expressing neurons and cell processes in dorsal and ventral APtN are both implicated in the mediation of stimulation-produced antinociception from the RSC in the rat tail flick and incision pain tests, respectively. (c) 2012 Elsevier Inc. All rights reserved.

Computational chemistry studies of UV induced processes in human skin

This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme. The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified. Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the cis isomer where competition between intra- and inter-molecular interactions increases flexibility. A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture between isomers significantly enhances the agreement between theory and experiment , and resolves several peculiarities in the spectrum. A model for the photochemistry in the aqueous phase of urocanic acid is then developed, in which two excited states governs the efficiency of photoisomerization. The point of entrance into a conical intersection seam is shown to explain the wavelength dependence of photoisomerization quantum yield. Finally some mechanistic aspects of the DNA repair enzyme 8-oxoguanine glycosylase is investigated with density functional theory. It is found that the critical amino acid of the active site can provide catalytic power in several different manners, and that a recent proposal involving a SN1 type of mechanism seems the most efficient one.

NMR, Metabonomics and Molecular Profiles: Applications to the Quality Assessment of Foodstuffs

Nuclear Magnetic Resonance (NMR) is a branch of spectroscopy that is based on the fact that many atomic nuclei may be oriented by a strong magnetic field and will absorb radiofrequency radiation at characteristic frequencies. The parameters that can be measured on the resulting spectral lines (line positions, intensities, line widths, multiplicities and transients in time-dependent experi-ments) can be interpreted in terms of molecular structure, conformation, molecular motion and other rate processes. In this way, high resolution (HR) NMR allows performing qualitative and quantitative analysis of samples in solution, in order to determine the structure of molecules in solution and not only. In the past, high-field NMR spectroscopy has mainly concerned with the elucidation of chemical structure in solution, but today is emerging as a powerful exploratory tool for probing biochemical and physical processes. It represents a versatile tool for the analysis of foods. In literature many NMR studies have been reported on different type of food such as wine, olive oil, coffee, fruit juices, milk, meat, egg, starch granules, flour, etc using different NMR techniques. Traditionally, univariate analytical methods have been used to ex-plore spectroscopic data. This method is useful to measure or to se-lect a single descriptive variable from the whole spectrum and , at the end, only this variable is analyzed. This univariate methods ap-proach, applied to HR-NMR data, lead to different problems due especially to the complexity of an NMR spectrum. In fact, the lat-ter is composed of different signals belonging to different mole-cules, but it is also true that the same molecules can be represented by different signals, generally strongly correlated. The univariate methods, in this case, takes in account only one or a few variables, causing a loss of information. Thus, when dealing with complex samples like foodstuff, univariate analysis of spectra data results not enough powerful. Spectra need to be considered in their wholeness and, for analysing them, it must be taken in consideration the whole data matrix: chemometric methods are designed to treat such multivariate data. Multivariate data analysis is used for a number of distinct, differ-ent purposes and the aims can be divided into three main groups: • data description (explorative data structure modelling of any ge-neric n-dimensional data matrix, PCA for example); • regression and prediction (PLS); • classification and prediction of class belongings for new samples (LDA and PLS-DA and ECVA). The aim of this PhD thesis was to verify the possibility of identify-ing and classifying plants or foodstuffs, in different classes, based on the concerted variation in metabolite levels, detected by NMR spectra and using the multivariate data analysis as a tool to inter-pret NMR information. It is important to underline that the results obtained are useful to point out the metabolic consequences of a specific modification on foodstuffs, avoiding the use of a targeted analysis for the different metabolites. The data analysis is performed by applying chemomet-ric multivariate techniques to the NMR dataset of spectra acquired. The research work presented in this thesis is the result of a three years PhD study. This thesis reports the main results obtained from these two main activities: A1) Evaluation of a data pre-processing system in order to mini-mize unwanted sources of variations, due to different instrumental set up, manual spectra processing and to sample preparations arte-facts; A2) Application of multivariate chemiometric models in data analy-sis.

Crustal heterogeneities and complexities of fault processes

In this work we study the relation between crustal heterogeneities and complexities in fault processes. The first kind of heterogeneity considered involves the concept of asperity. The presence of an asperity in the hypocentral region of the M = 6.5 earthquake of June 17-th, 2000 in the South Iceland Seismic Zone was invoked to explain the change of seismicity pattern before and after the mainshock: in particular, the spatial distribution of foreshock epicentres trends NW while the strike of the main fault is N 7◦ E and aftershocks trend accordingly; the foreshock depths were typically deeper than average aftershock depths. A model is devised which simulates the presence of an asperity in terms of a spherical inclusion, within a softer elastic medium in a transform domain with a deviatoric stress field imposed at remote distances (compressive NE − SW, tensile NW − SE). An isotropic compressive stress component is induced outside the asperity, in the direction of the compressive stress axis, and a tensile component in the direction of the tensile axis; as a consequence, fluid flow is inhibited in the compressive quadrants while it is favoured in tensile quadrants. Within the asperity the isotropic stress vanishes but the deviatoric stress increases substantially, without any significant change in the principal stress directions. Hydrofracture processes in the tensile quadrants and viscoelastic relaxation at depth may contribute to lower the effective rigidity of the medium surrounding the asperity. According to the present model, foreshocks may be interpreted as induced, close to the brittle-ductile transition, by high pressure fluids migrating upwards within the tensile quadrants; this process increases the deviatoric stress within the asperity which eventually fails, becoming the hypocenter of the mainshock, on the optimally oriented fault plane. In the second part of our work we study the complexities induced in fault processes by the layered structure of the crust. In the first model proposed we study the case in which fault bending takes place in a shallow layer. The problem can be addressed in terms of a deep vertical planar crack, interacting with a shallower inclined planar crack. An asymptotic study of the singular behaviour of the dislocation density at the interface reveals that the density distribution has an algebraic singularity at the interface of degree ω between -1 and 0, depending on the dip angle of the upper crack section and on the rigidity contrast between the two media. From the welded boundary condition at the interface between medium 1 and 2, a stress drop discontinuity condition is obtained which can be fulfilled if the stress drop in the upper medium is lower than required for a planar trough-going surface: as a corollary, a vertically dipping strike-slip fault at depth may cross the interface with a sedimentary layer, provided that the shallower section is suitably inclined (fault "refraction"); this results has important implications for our understanding of the complexity of the fault system in the SISZ; in particular, we may understand the observed offset of secondary surface fractures with respect to the strike direction of the seismic fault. The results of this model also suggest that further fractures can develop in the opposite quadrant and so a second model describing fault branching in the upper layer is proposed. As the previous model, this model can be applied only when the stress drop in the shallow layer is lower than the value prescribed for a vertical planar crack surface. Alternative solutions must be considered if the stress drop in the upper layer is higher than in the other layer, which may be the case when anelastic processes relax deviatoric stress in layer 2. In such a case one through-going crack cannot fulfil the welded boundary conditions and unwelding of the interface may take place. We have solved this problem within the theory of fracture mechanics, employing the boundary element method. The fault terminates against the interface in a T-shaped configuration, whose segments interact among each other: the lateral extent of the unwelded surface can be computed in terms of the main fault parameters and the stress field resulting in the shallower layer can be modelled. A wide stripe of high and nearly uniform shear stress develops above the unwelded surface, whose width is controlled by the lateral extension of unwelding. Secondary shear fractures may then open within this stripe, according to the Coulomb failure criterion, and the depth of open fractures opening in mixed mode may be computed and compared with the well studied fault complexities observed in the field. In absence of the T-shaped decollement structure, stress concentration above the seismic fault would be difficult to reconcile with observations, being much higher and narrower.

Mathematical models of cognitive processes

The research activity carried out during the PhD course was focused on the development of mathematical models of some cognitive processes and their validation by means of data present in literature, with a double aim: i) to achieve a better interpretation and explanation of the great amount of data obtained on these processes from different methodologies (electrophysiological recordings on animals, neuropsychological, psychophysical and neuroimaging studies in humans), ii) to exploit model predictions and results to guide future research and experiments. In particular, the research activity has been focused on two different projects: 1) the first one concerns the development of neural oscillators networks, in order to investigate the mechanisms of synchronization of the neural oscillatory activity during cognitive processes, such as object recognition, memory, language, attention; 2) the second one concerns the mathematical modelling of multisensory integration processes (e.g. visual-acoustic), which occur in several cortical and subcortical regions (in particular in a subcortical structure named Superior Colliculus (SC)), and which are fundamental for orienting motor and attentive responses to external world stimuli. This activity has been realized in collaboration with the Center for Studies and Researches in Cognitive Neuroscience of the University of Bologna (in Cesena) and the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA). PART 1. Objects representation in a number of cognitive functions, like perception and recognition, foresees distribute processes in different cortical areas. One of the main neurophysiological question concerns how the correlation between these disparate areas is realized, in order to succeed in grouping together the characteristics of the same object (binding problem) and in maintaining segregated the properties belonging to different objects simultaneously present (segmentation problem). Different theories have been proposed to address these questions (Barlow, 1972). One of the most influential theory is the so called “assembly coding”, postulated by Singer (2003), according to which 1) an object is well described by a few fundamental properties, processing in different and distributed cortical areas; 2) the recognition of the object would be realized by means of the simultaneously activation of the cortical areas representing its different features; 3) groups of properties belonging to different objects would be kept separated in the time domain. In Chapter 1.1 and in Chapter 1.2 we present two neural network models for object recognition, based on the “assembly coding” hypothesis. These models are networks of Wilson-Cowan oscillators which exploit: i) two high-level “Gestalt Rules” (the similarity and previous knowledge rules), to realize the functional link between elements of different cortical areas representing properties of the same object (binding problem); 2) the synchronization of the neural oscillatory activity in the γ-band (30-100Hz), to segregate in time the representations of different objects simultaneously present (segmentation problem). These models are able to recognize and reconstruct multiple simultaneous external objects, even in difficult case (some wrong or lacking features, shared features, superimposed noise). In Chapter 1.3 the previous models are extended to realize a semantic memory, in which sensory-motor representations of objects are linked with words. To this aim, the network, previously developed, devoted to the representation of objects as a collection of sensory-motor features, is reciprocally linked with a second network devoted to the representation of words (lexical network) Synapses linking the two networks are trained via a time-dependent Hebbian rule, during a training period in which individual objects are presented together with the corresponding words. Simulation results demonstrate that, during the retrieval phase, the network can deal with the simultaneous presence of objects (from sensory-motor inputs) and words (from linguistic inputs), can correctly associate objects with words and segment objects even in the presence of incomplete information. Moreover, the network can realize some semantic links among words representing objects with some shared features. These results support the idea that semantic memory can be described as an integrated process, whose content is retrieved by the co-activation of different multimodal regions. In perspective, extended versions of this model may be used to test conceptual theories, and to provide a quantitative assessment of existing data (for instance concerning patients with neural deficits). PART 2. The ability of the brain to integrate information from different sensory channels is fundamental to perception of the external world (Stein et al, 1993). It is well documented that a number of extraprimary areas have neurons capable of such a task; one of the best known of these is the superior colliculus (SC). This midbrain structure receives auditory, visual and somatosensory inputs from different subcortical and cortical areas, and is involved in the control of orientation to external events (Wallace et al, 1993). SC neurons respond to each of these sensory inputs separately, but is also capable of integrating them (Stein et al, 1993) so that the response to the combined multisensory stimuli is greater than that to the individual component stimuli (enhancement). This enhancement is proportionately greater if the modality-specific paired stimuli are weaker (the principle of inverse effectiveness). Several studies have shown that the capability of SC neurons to engage in multisensory integration requires inputs from cortex; primarily the anterior ectosylvian sulcus (AES), but also the rostral lateral suprasylvian sulcus (rLS). If these cortical inputs are deactivated the response of SC neurons to cross-modal stimulation is no different from that evoked by the most effective of its individual component stimuli (Jiang et al 2001). This phenomenon can be better understood through mathematical models. The use of mathematical models and neural networks can place the mass of data that has been accumulated about this phenomenon and its underlying circuitry into a coherent theoretical structure. In Chapter 2.1 a simple neural network model of this structure is presented; this model is able to reproduce a large number of SC behaviours like multisensory enhancement, multisensory and unisensory depression, inverse effectiveness. In Chapter 2.2 this model was improved by incorporating more neurophysiological knowledge about the neural circuitry underlying SC multisensory integration, in order to suggest possible physiological mechanisms through which it is effected. This endeavour was realized in collaboration with Professor B.E. Stein and Doctor B. Rowland during the 6 months-period spent at the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA), within the Marco Polo Project. The model includes four distinct unisensory areas that are devoted to a topological representation of external stimuli. Two of them represent subregions of the AES (i.e., FAES, an auditory area, and AEV, a visual area) and send descending inputs to the ipsilateral SC; the other two represent subcortical areas (one auditory and one visual) projecting ascending inputs to the same SC. Different competitive mechanisms, realized by means of population of interneurons, are used in the model to reproduce the different behaviour of SC neurons in conditions of cortical activation and deactivation. The model, with a single set of parameters, is able to mimic the behaviour of SC multisensory neurons in response to very different stimulus conditions (multisensory enhancement, inverse effectiveness, within- and cross-modal suppression of spatially disparate stimuli), with cortex functional and cortex deactivated, and with a particular type of membrane receptors (NMDA receptors) active or inhibited. All these results agree with the data reported in Jiang et al. (2001) and in Binns and Salt (1996). The model suggests that non-linearities in neural responses and synaptic (excitatory and inhibitory) connections can explain the fundamental aspects of multisensory integration, and provides a biologically plausible hypothesis about the underlying circuitry.