Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

NUcache: an efficient multicore cache organization based on next-use distance

The effectiveness of the last-level shared cache is crucial to the performance of a multi-core system. In this paper, we observe and make use of the DelinquentPC - Next-Use characteristic to improve shared cache performance. We propose a new PC-centric cache organization, NUcache, for the shared last level cache of multi-cores. NUcache logically partitions the associative ways of a cache set into MainWays and DeliWays. While all lines have access to the MainWays, only lines brought in by a subset of delinquent PCs, selected by a PC selection mechanism, are allowed to enter the DeliWays. The PC selection mechanism is an intelligent cost-benefit analysis based algorithm that utilizes Next-Use information to select the set of PCs that can maximize the hits experienced in DeliWays. Performance evaluation reveals that NUcache improves the performance over a baseline design by 9.6%, 30% and 33% respectively for dual, quad and eight core workloads comprised of SPEC benchmarks. We also show that NUcache is more effective than other well-known cache-partitioning algorithms.

Organization of Mn-Clusters in pcu and bcu Networks: Synthesis, Structure, and Properties

Two new anionic inorganic-organic hybrid compounds H3O]Mn-3(mu(3)-OH)(C14H8O6S)(3)(H2O)](DMF)(5), I, and H3O](2)Mn-7(mu(3)-OH)(4)(C14H8O6S)(6)(H2O)(4)](H2O)(2)(DMF)(8), II have been prepared by employing mild solvothennal methods. Both the compounds have three-dimensionally extended structures formed by Mn-6 and Mn-7 clusters, respectively. The connectivity between Mn-6 and Mn-7 clusters and 4,4'-sulfonyldibenzoic acid anions (SDBA(2-)) results in a six connected pcu network in I and an eight connected bcu network in II. The presence of hydronium ion (H-3(O+)) along with the solvent molecules in the channels of both the compounds suggested proton conduction in the solids. Proton conductivity studies gave values of similar to 3 x 10(-4) Omega(-1) cm(-1) 98% relative humidity in both the compounds. The high activation energies indicate a vehicle mechanism in the compounds I and II. Magnetic studies indicate antiferromagnetic behavior in both the compounds.

Biomimetic molecular organization of naphthalene diimide in the solid state: tunable (chiro-) optical, viscoelastic and nanoscale properties

The interfacing of aromatic molecules with biomolecules to design functional molecular materials is a promising area of research. Intermolecular interactions determine the performance of these materials and therefore, precise control over the molecular organization is necessary to improve functional properties. Herein we describe the tunable biomimetic molecular engineering of a promising n-type organic semiconductor, naphthalene diimide (NDI), in the solid state by introducing minute structural mutations in the form of amino acids with variable Ca-functionality. For the first time we could achieve all four possible crystal packing modes, namely cofacial, brickwork, herringbone and slipped stacks of the NDI system. Furthermore, amino acid conjugated NDIs exhibit ultrasonication induced organogels with tunable visco-elastic and temperature responsive emission properties. The amino acid-NDI conjugates self-assemble into 0D nanospheres and 1D nanofibers in their gel state while the ethylamine-NDI conjugate forms 2D sheets from its solution. Photophysical studies indicated the remarkable influence of molecular ordering on the absorption and fluorescence properties of NDIs. Interestingly, the circular dichroism (CD) and X-ray diffraction (XRD) studies revealed the existence of helical ordering of NDIs in both solution and solid state. The chiral amino acids and their conformations with respect to the central NDI core are found to influence the nature of the helical organization of NDIs. Consequently, the origin of the preferential handedness in the helical organization is attributed to transcription of chiral information from the amino acid to the NDI core. On account of these unique properties, the materials derived from NDI-conjugates might find a wide range of future interdisciplinary applications from materials to biomedicine.

Towards complex system design and management in the engineering domain – the smart grid challenge

This is an Author's Accepted Manuscript of an article published in “Emergence: Complexity and Organization”, 15 (2), pp. 14-22 (2013), copyright Taylor & Francis.

Design of tailored strategies for preservation and re-use of information about heritage

[EN] This paper is an outcome of the following dissertation:

Design de jornal impresso: a relação entre formato e usabilidade

A presente pesquisa Design de jornal impresso: a relação entre formato e usabilidade tem como principal objetivo reforçar a importância do envolvimento do usuário no design de produtos, através da compreensão da influência que o formato definido pelo tamanho das páginas e organização dos cadernos exerce sobre a usabilidade do jornal impresso. São apresentados os aspectos tecnológicos e econômicos relacionados a esse produto e verificado a influência exercida por eles sobre o formato. É feito um mapeamento sobre os principais aspectos do design de jornais e sobre os diferentes formatos de jornais, suas origens e sua relevância para o design de jornais. Busca-se mapear o formato dos jornais em diferentes mercados e os possíveis impactos das mudanças de formato na circulação, no conteúdo e na publicidade dos jornais impressos. Faz-se uma revisão do panorama atual dos jornais eletrônicos e suas possíveis interferências nos hábitos de leitura. Revisa-se a bibliografia referente à usabilidade, concentrando-se na metodologia de design de documentos e sua aplicabilidade para testes de usabilidade em jornais impressos. Por fim, descreve-se a pesquisa de campo através de entrevistas com especialistas em design de jornais, de observações sistemáticas em gráficas de jornal e sobre o mercado de jornais impressos da cidade do Rio de Janeiro e de testes de usabilidade aplicados a jornais. Conclui-se que, considerando o público participante dos testes profissionais que trabalham com impressão de jornais , apenas o aspecto do formato relacionado à organização dos cadernos parece exercer influência sobre a usabilidade dos jornais.

Design de modelos colaborativos em sites de notícias

A colaboração de usuários em sites jornalísticos é um fenômeno crescente. Cada vez mais, a evolução tecnológica abre espaço para uma maior participação dos usuários no processo de construção da narrativa noticiosa. Nesse contexto, um olhar do design sobre os modelos colaborativos dos sites jornalísticos fornece subsídios para o entendimento deste fenômeno e para o aprofundamento em cada uma das etapas que compõe o processo colaborativo. Dessa forma, essa dissertação apresenta a análise teórica e prática dessas diferentes etapas, bem como das soluções de design aplicáveis aos modelos colaborativos, de maneira a estabelecer conceitos e diretrizes para a construção de modelos que otimizem o aproveitamento do conteúdo enviado por usuários e sua relação com o conteúdo editorial dos sites noticiosos.

Design e Marketing: uma relação de sinergia para a Sustentabilidade

Esta dissertação aborda os princípios do Design, os fundamentos do Marketing e as condições que ambas as atividades podem, em parceria, gerar ambientes criativos para a Sustentabilidade. Acredita-se que tanto Design quanto Marketing são campos de saber parceiros, complementares e transversais, tendo deste modo um natural potencial de sinergia para a construção de projetos consistentes e duráveis. A insistência nesta ideia se deve, em parte, à vivência profissional nesses setores de gestão de projeto, e também ao desenvolvimento de exames, através da pesquisa bibliográfica, sobre os sentidos de termos, conceitos e objetivos para a organização de dados, a análise e alinhamento conceitual e a verificação de tangências entre esses campos. Este trabalho objetiva contribuir para a interação e a integração de saberes, em cursos de nível superior, também com a sugestão de ferramenta criativo-analítica e criativo-gerativa para o desenvolvimento de soluções mais sustentáveis. A crescente necessidade de atuações adequadas e eficazes dos campos estudados nos setores produtivos, a necessidade de profissionais capazes de se adequarem estas demandas, e a oferta deficitária de pesquisas com esta abordagem reforçam a crença na utilidade desta investigação. Os saberes em foco têm em comum relações multidisciplinares, sistêmicas e interdependentes.

Com atitude e catiguria: visibilidades e Invisibilidades femininas: DASPU como possibilidades em Design

Trata-se de uma tese de doutoramento, cujo tema de estudo é DASPU. Fundada em 2005, reconhecida no Brasil e internacionalmente, é vinculada à ONG DAVIDA que se ocupa de questões relacionadas com Prostituição, Direitos Civis, Direitos Humanos e Prevenção de DST/AIDS. A proposta é a de abordar os quase cinco anos de existência da marca, considerando-os como quatro movimentos. Os pressupostos teóricos e metodológicos partem de Bruno Latour, dentre outros autores. A ênfase está na interdisciplinaridade entre Design, Moda e Psicologia Social. A prática da observação participante, adotada ao longo da trajetória, propicia intervenções com objetivos relacionados com a identificação das múltiplas possibilidades de rearranjos sociais e coletivos.

Self-organization, embodiment, and biologically inspired robotics.

Robotics researchers increasingly agree that ideas from biology and self-organization can strongly benefit the design of autonomous robots. Biological organisms have evolved to perform and survive in a world characterized by rapid changes, high uncertainty, indefinite richness, and limited availability of information. Industrial robots, in contrast, operate in highly controlled environments with no or very little uncertainty. Although many challenges remain, concepts from biologically inspired (bio-inspired) robotics will eventually enable researchers to engineer machines for the real world that possess at least some of the desirable properties of biological organisms, such as adaptivity, robustness, versatility, and agility.

A systematic approach to materials information management for aerospace design

The materials information requirements of the aerospace sector are considered, specifically 'consolidation' (management of raw test data), 'analysis' (investigation of material trade-offs) and 'dissemination (secure distribution of data throughout an organization). An information architecture that satisfies the complex requirements of the aerospace materials industry is discussed and a case-study is presented. © 2003 by Granta Design Limited. Published by the American Institute of Aeronautics and Astronautics, Inc.

Design for an IO block array in a tile-based FPGA

A design for an IO block array in a tile-based FPGA is presented.Corresponding with the characteristics of the FPGA, each IO cell is composed of a signal path, local routing pool and configurable input/output buffers.Shared programmable registers in the signal path can be configured for the function of JTAG, without specific boundary scan registers/latches, saving layout area.The local routing pool increases the flexibility of routing and the routability of the whole FPGA.An auxiliary power supply is adopted to increase the performance of the IO buffers at different configured IO standards.The organization of the IO block array is described in an architecture description file, from which the array layout can be accomplished through use of an automated layout assembly tool.This design strategy facilitates the design of FPGAs with different capacities or architectures in an FPGA family series.The bond-out schemes of the same FPGA chip in different packages are also considered.The layout is based on SMIC 0.13μm logic 1P8M salicide 1.2/2.5 V CMOS technology.Our performance is comparable with commercial SRAM-based FPGAs which use a similar process.

Ultrathin platinum-group metal coated hierarchical flowerlike gold microstructure: Electrochemical design and characterization

The deliberate tailoring of hierarchical flowerlike gold microstructure (HFGMs) at the ultrathin level is an ongoing challenge and could introduce opportunities for new fabrication and application in many fields. In this paper. a templateless, surfactantless, electrochemical strategy for fabrication of ultrathin platinum-group metal coated HFGMs is proposed. HFGMs were prepared by simple electrodeposition on an indium tin oxide (ITO) substrate.

Doxorubicin-paclitaxel: a safe regimen in terms of cardiac toxicity in metastatic breast carcinoma patients. Results from a European Organization for Research and Treatment of Cancer multicenter trial.

BACKGROUND: The potential cardiotoxicity of the doxorubicin-paclitaxel regimen, when paclitaxel is given shortly after the end of the anthracycline infusion, is an issue of concern, as suggested by small single institution Phase II studies. METHODS: In a large multicenter Phase III trial, 275 anthracycline naive metastatic breast carcinoma patients were randomized to receive either doxorubicin (60 mg/m(2)) followed 30 minutes later by paclitaxel (175 mg/m(2) 3-hour infusion; AT) or a standard doxorubicin-cyclophosphamide regimen (AC; 60/600 mg/m(2)). Both treatments were given once every 3 weeks for a maximum of six cycles. Close cardiac monitoring was implemented in the study design. RESULTS: Congestive heart failure (CHF) occurred in three patients in the AT arm and in one patient in the AC arm (P = 0.62). Decreases in left ventricular ejection fraction to below the limit of normal were documented in 33% AT and 19% AC patients and were not predictive of CHF development. CONCLUSIONS: AT is devoid of excessive cardiac risk among metastatic breast carcinoma patients, when the maximum planned cumulative dose of doxorubicin does not exceed 360 mg/m(2).