Teollisuuspuhaltimille tarkoitetun suunnittelujärjestelmän kehittäminen

Diplomityön tavoitteena oli kehittää Dust Control Systems Oy:n nykyistä suunnittelujärjestelmää yrityksen toiminnan laadun ja suunnittelun tehokkuuden parantamiseksi. Suunnittelun suurin pullonkaula on valmistusdokumenttien tuottaminen, joten keskeinen tehtävä oli dokumenttien laadun parantaminen ja tuottamisen nopeuttaminen. Lisäksi tärkeää oli selkeyttää nykyistä nimikkeiden hallintaa ja ylläpitoa. Kehitystyö keskittyi suurelta osin suunnittelujärjestelmän ohjelmistoympäristön päivittämiseen ja sen muokkaamiseen. Teoriaosuudessa käsiteltiin nykyaikaista suunnittelua ja sen kehittämismahdollisuuksia. Lisäksi tarkasteltiin suunnittelun automatisoinnin tuomia hyötyjä sekä erilaisia tuotannon tehostamismenetelmiä. Kehitysosiossa tutkittiin yrityksen nykyistä suunnittelujärjestelmää ja ohjelmistoympäristöä, tuotteiden asettamia vaatimuksia sekä järjestelmän puutteita. Näihin liittyi suuresti yhteistyö henkilöstön sekä ohjelmistotoimittajan kanssa. Tutkimuksen perusteella ryhdyttiin kehittämään uutta järjestelmäkokonaisuutta, johon liitettiin tarvittavia ohjelmistoja ja päivityksiä. Käyttöönottoa varten ohjelmistot konfiguroitiin yrityksen tarpeita vastaaviksi. Työn tuloksena saatiin kehittyneempi ja nykyaikaisempi suunnittelujärjestelmä ja ohjelmistoympäristö. Suunnittelijoiden työtaakkaa saadaan kevennettyä toistuvien työvaiheiden pidemmälle viedyllä automatisoinnilla. Uudistettu ohjelmistoympäristö luo osaltaan ehtoja ja sääntöjä, jotta virheitä syntyy yhä vähemmän. Lisäksi suunnittelun läpimenoaikaa saadaan lyhennettyä parannetulla dokumenttien tuottamisella.

A synchronous multimedia annotation system for secure collaboratories

In this paper, we describe the Vannotea system - an application designed to enable collaborating groups to discuss and annotate collections of high quality images, video, audio or 3D objects. The system has been designed specifically to capture and share scholarly discourse and annotations about multimedia research data by teams of trusted colleagues within a research or academic environment. As such, it provides: authenticated access to a web browser search interface for discovering and retrieving media objects; a media replay window that can incorporate a variety of embedded plug-ins to render different scientific media formats; an annotation authoring, editing, searching and browsing tool; and session logging and replay capabilities. Annotations are personal remarks, interpretations, questions or references that can be attached to whole files, segments or regions. Vannotea enables annotations to be attached either synchronously (using jabber message passing and audio/video conferencing) or asynchronously and stand-alone. The annotations are stored on an Annotea server, extended for multimedia content. Their access, retrieval and re-use is controlled via Shibboleth identity management and XACML access policies.

Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei

Blumeria graminis is an economically important obligate plant-pathogenic fungus, whose entire genome was recently sequenced and manually annotated using ab initio in silico predictions [7]. Employing large scale proteogenomic analysis we are now able to verify independently the existence of proteins predicted by 24% of open reading frame models. We compared the haustoria and sporulating hyphae proteomes and identified 71 proteins exclusively in haustoria, the feeding and effector-delivery organs of the pathogen. These proteins are ‘significantly smaller than the rest of the protein pool and predicted to be secreted. Most do not share any similarities with Swiss–Prot or Trembl entries nor possess any identifiable Pfam domains. We used a novel automated prediction pipeline to model the 3D structures of the proteins, identify putative ligand binding sites and predict regions of intrinsic disorder. This revealed that the protein set found exclusively in haustoria is significantly less disordered than the rest of the identified Blumeria proteins or random (and representative) protein sets generated from the yeast proteome. For most of the haustorial proteins with unknown functions no good templates could be found, from which to generate high quality models. Thus, these unknown proteins present potentially new protein folds that can be specific to the interaction of the pathogen with its host.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Structural and chemical basis for anticancer activity of a series of 'beta'-tubulin ligands: molecular modeling and 3D QSAR studies

An important approach to cancer therapy is the design of small molecule modulators that interfere with microtubule dynamics through their specific binding to the ²-subunit of tubulin. In the present work, comparative molecular field analysis (CoMFA) studies were conducted on a series of discodermolide analogs with antimitotic properties. Significant correlation coefficients were obtained (CoMFA(i), q² =0.68, r²=0.94; CoMFA(ii), q² = 0.63, r²= 0.91), indicating the good internal and external consistency of the models generated using two independent structural alignment strategies. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the 3D contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of discodermolide analogs, and should be useful for the design of new specific ²-tubulin modulators with potent anticancer activity.

Stress distribution in the cervical region of an upper central incisor in a 3D finite element model

The aim of this study was to evaluate the stress distribution in the cervical region of a sound upper central incisor in two clinical situations, standard and maximum masticatory forces, by means of a 3D model with the highest possible level of fidelity to the anatomic dimensions. Two models with 331,887 linear tetrahedral elements that represent a sound upper central incisor with periodontal ligament, cortical and trabecular bones were loaded at 45º in relation to the tooth's long axis. All structures were considered to be homogeneous and isotropic, with the exception of the enamel (anisotropic). A standard masticatory force (100 N) was simulated on one of the models, while on the other one a maximum masticatory force was simulated (235.9 N). The software used were: PATRAN for pre- and post-processing and Nastran for processing. In the cementoenamel junction area, tensile forces reached 14.7 MPa in the 100 N model, and 40.2 MPa in the 235.9 N model, exceeding the enamel's tensile strength (16.7 MPa). The fact that the stress concentration in the amelodentinal junction exceeded the enamel's tensile strength under simulated conditions of maximum masticatory force suggests the possibility of the occurrence of non-carious cervical lesions such as abfractions.

Dynamical Lorentz symmetry breaking in 3D and charge fractionalization

We analyze the breaking of Lorentz invariance in a 3D model of fermion fields self-coupled through four-fermion interactions. The low-energy limit of the theory contains various submodels which are similar to those used in the study of graphene or in the description of irrational charge fractionalization.

Density functional theory investigation of 3d, 4d, and 5d 13-atom metal clusters

The knowledge of the atomic structure of clusters composed by few atoms is a basic prerequisite to obtain insights into the mechanisms that determine their chemical and physical properties as a function of diameter, shape, surface termination, as well as to understand the mechanism of bulk formation. Due to the wide use of metal systems in our modern life, the accurate determination of the properties of 3d, 4d, and 5d metal clusters poses a huge problem for nanoscience. In this work, we report a density functional theory study of the atomic structure, binding energies, effective coordination numbers, average bond lengths, and magnetic properties of the 3d, 4d, and 5d metal (30 elements) clusters containing 13 atoms, M(13). First, a set of lowest-energy local minimum structures (as supported by vibrational analysis) were obtained by combining high-temperature first- principles molecular-dynamics simulation, structure crossover, and the selection of five well-known M(13) structures. Several new lower energy configurations were identified, e. g., Pd(13), W(13), Pt(13), etc., and previous known structures were confirmed by our calculations. Furthermore, the following trends were identified: (i) compact icosahedral-like forms at the beginning of each metal series, more opened structures such as hexagonal bilayerlike and double simple-cubic layers at the middle of each metal series, and structures with an increasing effective coordination number occur for large d states occupation. (ii) For Au(13), we found that spin-orbit coupling favors the three-dimensional (3D) structures, i.e., a 3D structure is about 0.10 eV lower in energy than the lowest energy known two-dimensional configuration. (iii) The magnetic exchange interactions play an important role for particular systems such as Fe, Cr, and Mn. (iv) The analysis of the binding energy and average bond lengths show a paraboliclike shape as a function of the occupation of the d states and hence, most of the properties can be explained by the chemistry picture of occupation of the bonding and antibonding states.

Improved finite element for 3D laminate frame analysis including warping for any cross-section

The most ordinary finite element formulations for 3D frame analysis do not consider the warping of cross-sections as part of their kinematics. So the stiffness, regarding torsion, should be directly introduced by the user into the computational software and the bar is treated as it is working under no warping hypothesis. This approach does not give good results for general structural elements applied in engineering. Both displacement and stress calculation reveal sensible deficiencies for both linear and non-linear applications. For linear analysis, displacements can be corrected by assuming a stiffness that results in acceptable global displacements of the analyzed structure. However, the stress calculation will be far from reality. For nonlinear analysis the deficiencies are even worse. In the past forty years, some special structural matrix analysis and finite element formulations have been proposed in literature to include warping and the bending-torsion effects for 3D general frame analysis considering both linear and non-linear situations. In this work, using a kinematics improvement technique, the degree of freedom ""warping intensity"" is introduced following a new approach for 3D frame elements. This degree of freedom is associated with the warping basic mode, a geometric characteristic of the cross-section, It does not have a direct relation with the rate of twist rotation along the longitudinal axis, as in existent formulations. Moreover, a linear strain variation mode is provided for the geometric non-linear approach, for which complete 3D constitutive relation (Saint-Venant Kirchhoff) is adopted. The proposed technique allows the consideration of inhomogeneous cross-sections with any geometry. Various examples are shown to demonstrate the accuracy and applicability of the proposed formulation. (C) 2009 Elsevier Inc. All rights reserved.

A solid-like FEM for geometrically non-linear 3D frames

This study presents a solid-like finite element formulation to solve geometric non-linear three-dimensional inhomogeneous frames. To achieve the desired representation, unconstrained vectors are used instead of the classic rigid director triad; as a consequence, the resulting formulation does not use finite rotation schemes. High order curved elements with any cross section are developed using a full three-dimensional constitutive elastic relation. Warping and variable thickness strain modes are introduced to avoid locking. The warping mode is solved numerically in FEM pre-processing computational code, which is coupled to the main program. The extra calculations are relatively small when the number of finite elements. with the same cross section, increases. The warping mode is based on a 2D free torsion (Saint-Venant) problem that considers inhomogeneous material. A scheme that automatically generates shape functions and its derivatives allow the use of any degree of approximation for the developed frame element. General examples are solved to check the objectivity, path independence, locking free behavior, generality and accuracy of the proposed formulation. (C) 2009 Elsevier B.V. All rights reserved.

A FEM procedure based on positions and unconstrained vectors applied to non-linear dynamic of 3D frames

This study presents an alternative three-dimensional geometric non-linear frame formulation based on generalized unconstrained vector and positions to solve structures and mechanisms subjected to dynamic loading. The formulation is classified as total Lagrangian with exact kinematics description. The resulting element presents warping and non-constant transverse strain modes, which guarantees locking-free behavior for the adopted three-dimensional constitutive relation, Saint-Venant-Kirchhoff, for instance. The application of generalized vectors is an alternative to the use of finite rotations and rigid triad`s formulae. Spherical and revolute joints are considered and selected dynamic and static examples are presented to demonstrate the accuracy and generality of the proposed technique. (C) 2010 Elsevier B.V. All rights reserved.

Experimental study of a Tollmien-Schlichting wave interacting with a shallow 3D roughness element

The paper is devoted to an experimental study of the effect of a shallow 3D roughness element on the evolution of a 2D Tollmien-Schlichting wave in a Blasius boundary layer. The experiments were carried out under controlled disturbance conditions on an airfoil section which could provide a long run with zero pressure gradient flow. A pneumatically driven slit source was used to introduce the Tollmien-Schilichting wave upstream of the lower branch of the neutral stability curve. A few wavelengths downstream, the T-S wave interacts with a cylindrical roughness element. The height of the roughness was slowly oscillating in time, which allows a continuous measurement of the T-S wave response downstream the roughness. The oscillation frequency was approximately 1500 times lower than the frequency of the studied Tollmien-Schlichting wave and therefore, behaved as a steady roughness with respect to the T-S wave. Hot wire anemometry was used to measure wall normal profiles and spanwise scans close to the maximum of the eigenfunction of the T-S wave. The oscillation of the roughness and the synchronization of all-equipments permitted the use of ensemble average techniques. Two different amplitudes of T-S waves with a non-dimensional frequency of F120E-06 were studied. They show a strong amplification of the disturbances in a small spanwise wave number range. The analysis of the wall normal T-S profiles suggests the growth of oblique modes.

3D CFD Simulation of Vortex-induced Vibration of Cylinder

The 3D flow around a circular cylinder free to oscillate transversely to the free stream was simulated using Computational Fluid Dynamics (CFD) and the Spalart-Allmaras Detached Eddy Simulation (DES) turbulence model for a Reynolds number Re = 10(4). Simulations were carried out for a small mass-damping parameter m*zeta = 0.00858, where m* = 3.3 and zeta = 0.0026. We found good agreement between the numerical results and experimental data. The simulations predicted the high observed amplitudes of the upper branch of vortex-induced vibrations for low mass-damping parameters.

3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r (2) ranging from 0.83 to 0.92 and q (2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.

Rational Design and 3D-Pharmacophore Mapping of 5 `-Thiourea-Substituted alpha-Thymidine Analogues as Mycobacterial TMPK Inhibitors

Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5`-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5`-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.