Stick-slip chaos in a non-ideal self-excited system

In engineering practical systems the excitation source is generally dependent on the system dynamic structure. In this paper we analyze a self-excited oscillating system due to dry friction which interacts with an energy source of limited power supply (non ideal problem). The mechanical system consists of an oscillating system sliding on a moving belt driven by a limited power supply. In the oscillating system considered here, dry friction acts as an excitation mechanism for stick-slip oscillations. The stick-slip chaotic oscillations are investigated because the knowledge of their dynamic characteristics is an important step in system design and control. Many engineering systems present stick-slip chaotic oscillations such as machine tools, oil well drillstrings, car brakes and others.

Análise e modelagem hidrometeorológica na Bacia do Rio Tocantins em Marabá-PA

Esta pesquisa objetivou desenvolver um modelo estatístico de previsão de vazão para Marabá - PA, bem como avaliar a estrutura dinâmica atmosférica associada aos extremos do regime hidrológico da bacia do rio Tocantins. O modelo hidrológico de regressão linear múltipla utilizou as séries de observações fluviométricas e pluviométricas obtidas no banco de dados da ANA. Os testes de validação do modelo estatístico com coeficiente de Nash acima de 0,9 e erro padrão de 1,5 % e 5% nos períodos de cheia e estiagem, respectivamente, permitem que as previsões de vazão em Marabá possam ser geradas com antecedência de 2 a 4 (3 a 5) dias para o período da cheia (estiagem). Através da técnica de composições considerando todos os anos com registro de vazão acima/muito acima e abaixo/muito abaixo do normal, obtidos pela metodologia dos percentis, investigaram-se as características regionais da precipitação e a estrutura dinâmica atmosférica em cada mês (Novembro a Abril). As composições dos anos com vazão acima/muito acima mostraram que a precipitação sobre a bacia foi acima do normal em todos os meses, sendo que os padrões de grande escala indicaram a configuração associada ao fenômeno La Niña no Pacífico e condições de resfriamento no Atlântico Sul; intensificação tanto do ramo ascendente zonal da célula de Walker como do ramo ascendente meridional da célula de Hadley; intensificação da Alta da Bolívia posicionada mais a leste e anomalias negativas de ROL associadas à atuação conjunta da ZCAS e ZCIT. Inversamente, as composições dos anos com vazão abaixo/muito abaixo evidenciaram a predominância de precipitação abaixo do normal em toda bacia hidrográfica, a qual se associou com as condições de aquecimento (El Niño) sobre o Pacífico, Atlântico sul aquecido, célula de Walker e Hadley com enfraquecimento dos movimentos ascendentes, posicionamento da Alta da Bolívia mais a oeste com anomalias positivas de ROL indicando inibição da atividade convectiva tropical. Adicionalmente, uma análise quantitativa dos impactos sócio-econômicos sobre os principais núcleos da cidade de Marabá revelou que aproximadamente 10 mil pessoas (5% da população) são atingidas pela cheia do rio Tocantins com custos nas operações de enchente acima de R$ 500.000,00, considerando o caso de 2005.

Eventos extremos da zona de convergência intertropical sobre o Atlântico durante o período chuvoso da Amazônia oriental

Este trabalho reporta uma investigação observacional sobre as características climatológicas (período de 1985 a 2007) associadas aos eventos extremos da ZCIT observados sobre o Oceano Atlântico equatorial, procurando estabelecer as influências na variabilidade pluviométrica da Amazônia oriental, durante os meses de fevereiro, março e abril. Tais eventos foram selecionados objetivamente através da análise de Funções Ortogonais Empíricas e os padrões oceano-atmosfera associados aos eventos da ZCIT, bem como seus impactos na precipitação da Amazônia oriental, foram investigados com base em composições mensais. Os resultados evidenciaram algumas diferenças mensais, principalmente no padrão da circulação atmosférica em 200 hPa e na configuração vertical da circulação troposférica meridional associada à célula de Hadley equatorial. Quanto à estrutura dinâmica dos padrões oceano-atmosfera observada nos meses de fevereiro, março e abril, basicamente evidenciou-se que a ZCIT forma-se sobre o Oceano Atlântico equatorial numa região de confluência dos ventos alísios de sudeste e nordeste, coincidente com áreas contendo TSM anomalamente quente, movimento vertical ascendente associado à célula de Hadley, com divergência do vento em altos níveis. Os impactos de tais eventos na variabilidade espacial da precipitação sobre a Amazônia oriental mostrou que os principais estados afetados pela ZCIT são: Amapá, Pará e Maranhão. Adicionalmente, relatam-se alguns impactos sócio-ambientais (enchentes, alagamentos, queda de árvores, proliferação de doenças, entre outros) que ocorreram na Região Metropolitana de Belém, associados a ocorrência dos eventos extremos da ZCIT selecionados neste trabalho.

Estudo observacional sobre os eventos de seca meteorológica e hidrológica na região de Marabá-PA no sudeste da Amazônia Oriental

O objetivo do presente trabalho foi investigar os aspectos observacionais dos eventos de seca meteorológica e hidrológica na região de Marabá localizada no sudeste do Pará na Amazônia oriental. Utilizou-se uma base de dados mensais de precipitação e cota no período de 1971 a 2010. Os eventos de seca meteorológica foram selecionados através de índices de precipitação negativa (segundo a metodologia do índice de anomalia de chuva- IAC) e os eventos de seca hidrológica do rio Tocantins foram baseados em índices extremos de cota fluviométrica abaixo do normal (através da metodologia da anomalia padronizada). Para as condições de seca meteorológica, os eventos concentram-se em sua grande maioria nas categorias de seca Fraca (FRA) e Moderada (MOD), com maior frequência de seca FRA nos meses de Fevereiro (38%), Junho (37%) e Dezembro (34%), enquanto que a seca MOD é mais frequente em Agosto (39%), Setembro (42%) e Outubro (32%). Quanto aos eventos de seca hidrológica (cota fluviométrica abaixo do normal) do rio Tocantins, os resultados mostram que a ocorrência mensal dos eventos é aleatória e pode ser observado ao longo de todo ano, independente do mês ser de enchente ou vazante. A duração dos eventos não apresenta regularidade ao longo do período estudado. Quanto à estrutura dinâmica dos padrões oceânicos e atmosféricos de grande escala associados aos eventos de seca meteorológica e hidrológica observaram-se que os eventos estão relacionados com um padrão de aquecimento (El Niño) no Pacífico equatorial e condições de aquecimento no Atlântico tropical norte, cujas condições oceano-atmosféricas de grande escala propiciam a intensificação tanto do ramo descendente zonal da célula de Walker como do ramo descendente meridional da célula de Hadley, que induzem a inibição significativa da atividade convectiva, explicando consequentemente a ocorrência dos eventos de seca na região. Analisou-se também a relação entre os eventos de seca e o registro de focos de calor (queimadas) na região de Marabá, durante os anos de 2000 a 2009, sendo que a correlação em torno de 43% confirma a sinergia entre seca e queimada, ou seja, a floresta torna-se mais inflamável sob condições de déficit hídrico.

Modelo dinâmico bayesiano multivariado para análise espaço-temporal de dados de área

Pós-graduação em Matematica Aplicada e Computacional - FCT

Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae)

Buteonine hawks represent one of the most diverse groups in the Accipitridae, with 58 species distributed in a variety of habitats on almost all continents. Variations in migratory behavior, remarkable dispersal capability, and unusual diversity in Central and South America make buteonine hawks an excellent model for studies in avian evolution. To evaluate the history of their global radiation, we used an integrative approach that coupled estimation of the phylogeny using a large sequence database (based on 6411 bp of mitochondrial markers and one nuclear intron from 54 species), divergence time estimates, and ancestral state reconstructions. Our findings suggest that Neotropical buteonines resulted from a long evolutionary process that began in the Miocene and extended to the Pleistocene. Colonization of the Nearctic, and eventually the Old World, occurred from South America, promoted by the evolution of seasonal movements and development of land bridges. Migratory behavior evolved several times and may have contributed not only to colonization of the Holarctic, but also derivation of insular species. In the Neotropics, diversification of the buteonines included four disjunction events across the Andes. Adaptation of monophyletic taxa to wet environments occurred more than once, and some relationships indicate an evolutionary connection among mangroves, coastal and varzea environments. On the other hand, groups occupying the same biome, forest, or open vegetation habitats are not monophyletic. Refuges or sea-level changes or a combination of both was responsible for recent speciation in Amazonian taxa. In view of the lack of concordance between phylogeny and classification, we propose numerous taxonomic changes. (C) 2009 Elsevier Inc. All rights reserved.

Charge dynamics in half-filled Hubbard chains with finite on-site interaction

We study the charge dynamic structure factor of the one-dimensional Hubbard model with finite on-site repulsion U at half-filling. Numerical results from the time-dependent density matrix renormalization group are analyzed by comparison with the exact spectrum of the model. The evolution of the line shape as a function of U is explained in terms of a relative transfer of spectral weight between the two-holon continuum that dominates in the limit U -> infinity and a subset of the two-holon-two-spinon continuum that reconstructs the electron-hole continuum in the limit U -> 0. Power-law singularities along boundary lines of the spectrum are described by effective impurity models that are explicitly invariant under spin and eta-spin SU(2) rotations. The Mott-Hubbard metal-insulator transition is reflected in a discontinuous change of the exponents of edge singularities at U = 0. The sharp feature observed in the spectrum for momenta near the zone boundary is attributed to a van Hove singularity that persists as a consequence of integrability.

Molekulardynamik-Simulationen supramolekularer Komplexe unter Einfluss einer externen Kraft

Supramolekulare Komplexe werden durch nichtkovalente Bindungen stabilisiert. Legt man eine externe Kraft an einen solchen Komplex an, ist es möglich, diese Bindungen zu öffnen. Anhand der dafür benötigten Kraft läßt sich die Stabilität des Komplexes bestimmen. Im Rahmen dieser Arbeit wurden zwei supramolekulare Komplexe, die unterschiedliche Arten von nichtkovalenten Bindungen enthalten, mit Hilfe von Molekulardynamik (MD) Simulationen untersucht. In beiden Fällen wurden die relevanten Bindungsstrukturen und deren Stabilität ermittelt.rnZum einen wurden zwei synthetische Calix[4]aren-Catenan-Dimersysteme betrachtet, in denen die beiden Monomere über Wasserstoffbrückenbindungen aneinander gebunden sind. Die Besonderheit dieser Komplexe ist, dass die Monomere aufgrund von verschlauften Alkylketten (Catenan-Struktur) nicht vollständig voneinander getrennt werden können. In Abhängigkeit der Länge derrnAlkylketten findet man für die beiden Komplexe eine unterschiedliche Zahl von relevanten Bindungsstrukturen (Zustände). Für ein System mit relativ kurzen Alkylketten findet man zwei Zustände, eine kompakte Struktur, die auch im Gleichgewicht beobachtet wird und eine gestreckte Struktur, die nur unter dem Einfluss der externen Kraft stabil ist. Verlängert man die Alkylketten,rnbeobachtet man einen weiteren Zustand, in dem das Dimer vollständig gestreckt ist und die Monomere eine größere Separation aufweisen.rnBei dem zweiten System, das untersucht wurde, handelte es sich um einen Carbohydrat-Kation-Carbohydrat Komplex, der für die Selbstadhäsion von Meeresschwämmen eine wichtige Rolle spielt. Experimentell ist bekannt, dass sich dieser Komplex zwar mit Calciumionen, nicht aber mit Magnesiumionen bildet. Im Rahmen dieser Arbeit wurde gezeigt, dass die wesentlichen Unterschiede der beiden Kationarten in Bezug auf die Komplexbildung auf den kleineren Ionenradius des Magnesiumions zurückzuführen sind. Aufgrund des kleineren Radius bindet ein solvatisiertes Magnesiumion die Hydrathülle stärker und die Komplexbindung wird kinetisch gehemmt. Zum anderen bindet im Magnesiumkomplex nur eines der beiden Carbohydrate direkt an das Kation.rnDas andere Carbohydrat bindet nur indirekt über ein Wassermolekül an das Kation. Da diese indirekte Bindung gegenüber einer direkten Bindung schwächer ist, weist der Magensiumkomplex eine geringere Stabilität auf als ein vergleichbarer Calciumkomplex.rnDes Weiteren wurde untersucht, inwieweit die Ergebnisse von MD Simulationen vom verwendeten Modell (Kraftfeld) abhängen. Allgemein ist bekannt, dass die Ergebnisse von Gleichgewichtssimulationen kraftfeldabhängig sind. Im Rahmen diese Arbeit konnte gezeigt werden, dass sich für Zugsimulationen, in denen eine externe Kraft an das System angelegt wird, eine ähnliche Kraftfeldabhängigkeit ergibt. Da sich die Unterschiede der Ergebnisse auf Unterschiede in den Gleichgewichtssimulationen zurückführen lassen, kann man annehmen, dass die externe Kraft keine zusätzliche Einschränkung in Bezug auf die Zuverlässigkeit der Kraftfelder darstellt.rnAbgesehen von den MD Simulationen wurde eine in der Literatur beschriebene Methode zur Analyse von Zweizustandssystemen unter dem Einfluss einer konstanten externen Kraft erweitert. Ein Komplex läßt sich als Zweizustandssystem beschreiben, wenn dieser zwei relevante Bindungsstrukturen aufweist. Wird an solch einen Komplex eine konstante Kraft angelegt, lassen sich Übergänge zwischen den beiden Zuständen beobachten. Ist das System weit entfernt vom Gleichgewicht, kann es problematisch sein, einen der beiden Übergänge vollständig aufzulösen. In diesen Fällen wird nun vorgeschlagen, die beiden Übergänge zu einem sogenannten Kreisübergang zusammen zu fassen und diese zu zählen. Bestimmt man die Zahl der Übergänge pro Zeit in Abhängigkeit der angelegten Kraft, können die Übergangsraten bestimmt werden. Um die Methode zu validieren wurden kinetische Monte-Carlo Simulationen durchgeführt. Es zeigt sich, dass schon mit relativ kleinen Datensätzen gute Ergebnisse erzielt werden können.

Regulation of Set1-mediated methylation of Dam1

Eukaryotic genomes exist within a dynamic structure named chromatin in which DNA is wrapped around an octamer of histones forming the nucleosome. Histones are modified by a range of posttranslational modifications including methylation, phosphorylation, and ubiquitination, which are integral to a range of DNA-templated processes including transcriptional regulation. A hallmark for transcriptional activity is methylation of histone H3 on lysine (K) 4 within active gene promoters. In S. cerevisiae, H3K4 methylation is mediated by Set1 within the COMPASS complex. Methylation requires prior ubiquitination of histone H2BK123 by the E2-E3 ligases Rad6 and Bre1, as well as the Paf1 transcriptional elongation complex. This regulatory pathway exemplifies cross-talk in trans between posttranslational modifications on distinct histone molecules. Set1 has an additional substrate in the kinetochore protein Dam1, which is methylated on K233. This methylation antagonizes phosphorylation of adjacent serines by the Ipl1 Aurora kinase. The discovery of a second Set1 substrate raised the question of how Set1 function is regulated at the kinetochore. I hypothesized that transcriptional regulatory factors essential for H3K4 methylation at gene promoters might also regulate Set1-mediated methylation of Dam1K233. Here I show that the regulatory factors essential for COMPASS activity at gene promoters is also indispensable for the methylation of Dam1K233. Deletion of members of the COMPASS complex leads to loss of Dam1K233 methylation. In addition, deletion of Rad6, Bre1, or members of the Paf1 complex abolishes Dam1 methylation. The role of Rad6 and Bre1 in Dam1 methylation is dependent on H2BK123 ubiquitination, as mutation of K123 within H2B results in complete loss of Dam1 methylation. Importantly, methylation of Dam1K233 is independent of transcription and occurs at the kinetochore. My results demonstrate that Set1-mediated methylation is regulated by a general pathway regardless of substrate that is composed of transcriptional regulatory factors functioning independently of transcription at the kinetochore. My data provide the first example of cross-talk in trans between modifications on a histone and a non-histone protein. Additionally, my results indicate that several factors previously thought to be required for Set1 function at gene promoters are more generally required for the catalytic activity of the COMPASS complex regardless of substrate or cellular process.

The role of the secondary cell wall in plant resistance to pathogens

Plant resistance to pathogens relies on a complex network of constitutive and inducible defensive barriers. The plant cell wall is one of the barriers that pathogens need to overcome to successfully colonize plant tissues. The traditional view of the plant cell wall as a passive barrier has evolved to a concept that considers the wall as a dynamic structure that regulates both constitutive and inducible defense mechanisms, and as a source of signaling molecules that trigger immune responses. The secondary cell walls of plants also represent a carbon-neutral feedstock (lignocellulosic biomass) for the production of biofuels and biomaterials. Therefore, engineering plants with improved secondary cell wall characteristics is an interesting strategy to ease the processing of lignocellulosic biomass in the biorefinery. However, modification of the integrity of the cell wall by impairment of proteins required for its biosynthesis or remodeling may impact the plants resistance to pathogens. This review summarizes our understanding of the role of the plant cell wall in pathogen resistance with a focus on the contribution of lignin to this biological process.

Signwalling: signals derived from arabiopsis cell wall activate specific resistance to pathogens

The cell wall is a dynamic structure that regulates both constitutive and inducible plant defence responses. Different molecules o DAMPs (damage-associated molecular patterns) can be released from plant cell walls upon pathogen infection or wounding and can trigger immune responses. To further characterize the function of cell wall on the regulation of these immune responses, we have performed a biased resistance screening of putative/well-characterized primary/secondary Arabidopsis thaliana cell wall mutants (cwm). In this screening we have identified more than 20 cwm mutants with altered susceptibility/resistance to at least one of the following pathogens: the necrotrophic fungi Plectosphaerella cucumerina, the vascular bacterium Ralstonia solanacearum, the biotrophic oomycete Hyaloperonospora arabidopsidis and the powdery mildew fungus Erisyphe cruciferarum. We found that cell wall extracts from some of these cwm plants contain novel DAMPs that activate immune responses and conferred enhanced resistance to particular pathogens when they were applied to wild-type plants. Using glycomic profiling we have performed an initial characterization of the active carbohydrate structures present in these cwm wall fractions, and we have determined the signalling pathways regulated by thesse fractions. . The data generated with this collection of wall mutants support the existence of specific correlations between cell wall structure/composition, resistance to particular type of pathogens and plant fitness. Remarkably, we have identified specific cwm mutations that uncoupled resistance to pathogens from plant trade-offs, further indicating the plasticity of wall structures in the regulation of plant immune responses.

Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA

Skipping of internal exons during removal of introns from pre-mRNA must be avoided for proper expression of most eukaryotic genes. Despite significant understanding of the mechanics of intron removal, mechanisms that ensure inclusion of internal exons in multi-intron pre-mRNAs remain mysterious. Using a natural two-intron yeast gene, we have identified distinct RNA–RNA complementarities within each intron that prevent exon skipping and ensure inclusion of internal exons. We show that these complementarities are positioned to act as intron identity elements, bringing together only the appropriate 5′ splice sites and branchpoints. Destroying either intron self-complementarity allows exon skipping to occur, and restoring the complementarity using compensatory mutations rescues exon inclusion, indicating that the elements act through formation of RNA secondary structure. Introducing new pairing potential between regions near the 5′ splice site of intron 1 and the branchpoint of intron 2 dramatically enhances exon skipping. Similar elements identified in single intron yeast genes contribute to splicing efficiency. Our results illustrate how intron secondary structure serves to coordinate splice site pairing and enforce exon inclusion. We suggest that similar elements in vertebrate genes could assist in the splicing of very large introns and in the evolution of alternative splicing.

SRPDB (Signal Recognition Particle Database)

Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-supported base pairs in SRP RNA and conserved residues in the proteins. Data are provided in various formats including a column arrangement for improved access and simplified computational usability. Included are motifs for identification of new sequences, SRP RNA secondary structure diagrams, 3-D models and links to high-resolution structures. This release includes 11 new SRP RNA sequences (total of 129), two protein SRP9 sequences (total of seven), two protein SRP14 sequences (total of 10), two protein SRP19 sequences (total of 16), 10 new SRP54 (ffh) sequences (total of 66), two protein SRP68 sequences (total of seven) and two protein SRP72 sequences (total of nine). Seven sequences of the SRP receptor α-subunit and its FtsY homolog (total of 51) are new. Also considered are β-subunit of SRP receptor, Flhf, Hbsu, CaM kinase II and cpSRP43. Access to SRPDB is at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and the European mirror http://www.medkem.gu.se/dbs/SRPDB/SRPDB.html

Cardiac expression of the cystic fibrosis transmembrane conductance regulator involves novel Exon 1 usage to produce a unique amino-terminal protein

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a chloride channel present in many cells. In cardiomyocytes, we report that multiple exon 1 usage and alternative splicing produces four CFTR transcripts, with different 5'-untranslated regions, CFTRTRAD-139, CFTR-1C/-1A, CFTR-1C, and CFTR-1B. CFTR transcripts containing the novel upstream exons (exons -1C, -1B, and -1A) represent more than 90% of cardiac expressed CFTR mRNA. Regulation of cardiac CFTR expression, in response to developmental and pathological stimuli, is exclusively due to the modulation of CFTR-1C and CFTR-1C/-1A expression. Upstream open reading frames have been identified in the 5'-untranslated regions of all CFTR transcripts that, in conjunction with adjacent stem-loop structures, modulate the efficiency of translation initiation at the AUG codon of the main CFTR coding region in CFTRTRAD-139 and CFTR-1C/-1A transcripts. Exon(-1A), only present in CFTR-1C/-1A transcripts, encodes an AUG codon that is in-frame with the main CFTR open reading frame, the efficient translation of which produces a novel CFTR protein isoform with a curtailed amino terminus. As the expression of this CFTR transcript parallels the spatial and temporal distribution of the cAMP-activated whole-cell current density in normal and diseased hearts, we suggest that CFTR-1C/-1A provides the molecular basis for the cardiac cAMP-activated chloride channel. Our findings provide further insight into the complex nature of in vivo CFTR expression, to which multiple mRNA transcripts, protein isoforms, and post-transcriptional regulatory mechanisms are now added.

Lessons from tomographic studies of the mammalian Golgi

Basic structure studies of the biosynthetic machinery of the cell by electron microscopy (EM) have underpinned much of our fundamental knowledge in the areas of molecular cell biology and membrane traffic. Driven by our collective desire to understand how changes in the complex and dynamic structure of this enigmatic organelle relate to its pivotal roles in the cell, the comparatively high-resolution glimpses of the Golgi and other compartments of the secretory pathway offered to us through EM have helped to inspire the development and application of some of our most informative, complimentary (molecular, biochemical and genetic) approaches. Even so, no one has yet even come close to relating the basic molecular mechanisms of transport, through and from the Golgi, to its ultrastructure, to everybody's satisfaction. Over the past decade, EM tomography has afforded new insights into structure -function relationships of the Golgi and provoked a re-evaluation of older paradigms. By providing a set of tools for structurally dissecting cells at high-resolution in three-dimensions (3D), EM tomography has emerged as a method for studying molecular cell biology in situ. As we move rapidly toward the establishment of molecular atlases of organelles through advances in proteomics and genomics, tomographic studies of the Golgi offer the tantalizing possibility that one day, we will be able to map the spatio-temporal coordinates of Golgi-related proteins and lipids accurately in the context of 4D cellular space. (c) 2005 Elsevier B.V. All rights reserved.