A frequency-domain pseudo-force method for dynamic structural analysis nonlinear systems and nonproportional damping

A frequency-domain method for nonlinear analysis of structural systems with viscous, hysteretic, nonproportional and frequency-dependent damping is presented. The nonlinear effects and nonproportional damping are considered through pseudo-force terms. The modal coordinates uncoupled equations are iteratively solved. The treatment of initial conditions in the frequency domain which is necessary for the treatment of the uncoupled equations is initially adressed.

Inverse convection problem of simultaneous estimation of two boundary heat fluxes in parallel plate channels

This paper deals with the use of the conjugate gradient method of function estimation for the simultaneous identification of two unknown boundary heat fluxes in parallel plate channels. The fluid flow is assumed to be laminar and hydrodynamically developed. Temperature measurements taken inside the channel are used in the inverse analysis. The accuracy of the present solution approach is examined by using simulated measurements containing random errors, for strict cases involving functional forms with discontinuities and sharp-corners for the unknown functions. Three different types of inverse problems are addressed in the paper, involving the estimation of: (i) Spatially dependent heat fluxes; (ii) Time-dependent heat fluxes; and (iii) Time and spatially dependent heat fluxes.

An Hp-Adaptive Hierarchical Formulation for the Boundary Element Method Applied to Elasticity in Two Dimensions

This paper presents an HP-Adaptive Procedure with Hierarchical formulation for the Boundary Element Method in 2-D Elasticity problems. Firstly, H, P and HP formulations are defined. Then, the hierarchical concept, which allows a substantial reduction in the dimension of equation system, is introduced. The error estimator used is based on the residual computation over each node inside an element. Finally, the HP strategy is defined and applied to two examples.

Wind tunnel simulation of atmospheric boundary layer flows

The present work shows how thick boundary layers can be produced in a short wind tunnel with a view to simulate atmospheric flows. Several types of thickening devices are analysed. The experimental assessment of the devices was conducted by considering integral properties of the flow and the spectra: skin-friction, mean velocity profiles in inner and outer co-ordinates and longitudinal turbulence. Designs based on screens, elliptic wedge generators, and cylindrical rod generators are analysed. The paper describes in detail the experimental arrangement, including the features of the wind tunnel and of the instrumentation. The results are compared with experimental data published by other authors and with naturally developed flows.

Effects of condensation in microchannels with a porous boundary: analytical investigation on heat transfer and meniscus shape

In two-phase miniature and microchannel flows, the meniscus shape must be considered due to effects that are affected by condensation and/or evaporation and coupled with the transport phenomena in the thin film on the microchannel wall, when capillary forces drive the working fluid. This investigation presents an analytical model for microchannel condensers with a porous boundary, where capillary forces pump the fluid. Methanol was selected as the working fluid. Very low liquid Reynolds numbers were obtained (Re~6), but very high Nusselt numbers (Nu~150) could be found due to the channel size (1.5 mm) and the presence of the porous boundary. The meniscus calculation provided consistent results for the vapor interface temperature and pressure, as well as the meniscus curvature. The obtained results show that microchannel condensers with a porous boundary can be used for heat dissipation with reduced heat transfer area and very high heat dissipation capabilities.

Target audience analysis in cyber domain

This thesis aims to find an effective way of conducting a target audience analysis (TAA) in cyber domain. There are two main focal points that are addressed; the nature of the cyber domain and the method of the TAA. Of the cyber domain the object is to find the opportunities, restrictions and caveats that result from its digital and temporal nature. This is the environment in which the TAA method is examined in this study. As the TAA is an important step of any psychological operation and critical to its success, the method used must cover all the main aspects affecting the choice of a proper target audience. The first part of the research was done by sending an open-ended questionnaire to operators in the field of information warfare both in Finland and abroad. As the results were inconclusive, the research was completed by assessing the applicability of United States Army Joint Publication FM 3-05.301 in the cyber domain via a theory-based content analysis. FM 3- 05.301 was chosen because it presents a complete method of the TAA process. The findings were tested against the results of the questionnaire and new scientific research in the field of psychology. The cyber domain was found to be “fast and vast”, volatile and uncontrollable. Although governed by laws to some extent, the cyber domain is unpredictable by nature and not controllable to reasonable amount. The anonymity and lack of verification often present in the digital channels mean that anyone can have an opinion, and any message sent may change or even be counterproductive to the original purpose. The TAA method of the FM 3-05.301 is applicable in the cyber domain, although some parts of the method are outdated and thus suggested to be updated if used in that environment. The target audience categories of step two of the process were replaced by new groups that exist in the digital environment. The accessibility assessment (step eight) was also redefined, as in the digital media the mere existence of a written text is typically not enough to convey the intended message to the target audience. The scientific studies made in computer sciences and both in psychology and sociology about the behavior of people in social media (and overall in cyber domain) call for a more extensive remake of the TAA process. This falls, however, out of the scope of this work. It is thus suggested that further research should be carried out in search of computer-assisted methods and a more thorough TAA process, utilizing the latest discoveries of human behavior. ---------------------------------------------------------------------------------------------------------------------------------- Tämän opinnäytetyön tavoitteena on löytää tehokas tapa kohdeyleisöanalyysin tekemiseksi kybertoimintaympäristössä. Työssä keskitytään kahteen ilmiöön: kybertoimintaympäristön luonteeseen ja kohdeyleisöanalyysin metodiin. Kybertoimintaympäristön osalta tavoitteena on löytää sen digitaalisesta ja ajallisesta luonteesta juontuvat mahdollisuudet, rajoitteet ja sudenkuopat. Tämä on se ympäristö jossa kohdeyleisöanalyysiä tarkastellaan tässä työssä. Koska kohdeyleisöanalyysi kuuluu olennaisena osana jokaiseen psykologiseen operaatioon ja on onnistumisen kannalta kriittinen tekijä, käytettävän metodin tulee pitää sisällään kaikki oikean kohdeyleisön valinnan kannalta merkittävät osa-alueet. Tutkimuksen ensimmäisessä vaiheessa lähetettiin avoin kysely informaatiosodankäynnin ammattilaisille Suomessa ja ulkomailla. Koska kyselyn tulokset eivät olleet riittäviä johtopäätösten tekemiseksi, tutkimusta jatkettiin tarkastelemalla Yhdysvaltojen armeijan kenttäohjesäännön FM 3-05.301 soveltuvuutta kybertoimintaympäristössä käytettäväksi teorialähtöisen sisällönanalyysin avulla. FM 3-05.301 valittiin koska se sisältää kokonaisvaltaisen kohdeyleisöanalyysiprosessin. Havaintoja verrattiin kyselytutkimuksen tuloksiin ja psykologian uusiin tutkimuksiin. Kybertoimintaympäristö on tulosten perusteella nopea ja valtava, jatkuvasti muuttuva ja kontrolloimaton. Vaikkakin lait hallitsevat kybertoimintaympäristöä jossakin määrin, on se silti luonteeltaan ennakoimaton eikä sitä voida luotettavasti hallita. Digitaalisilla kanavilla usein läsnäoleva nimettömyys ja tiedon tarkastamisen mahdottomuus tarkoittavat että kenellä tahansa voi olla mielipide asioista, ja mikä tahansa viesti voi muuttua, jopa alkuperäiseen tarkoitukseen nähden vastakkaiseksi. FM 3-05.301:n metodi toimii kybertoimintaympäristössä, vaikkakin jotkin osa-alueet ovat vanhentuneita ja siksi ne esitetään päivitettäväksi mikäli metodia käytetään kyseisessä ympäristössä. Kohdan kaksi kohdeyleisökategoriat korvattiin uusilla, digitaalisessa ympäristössä esiintyvillä ryhmillä. Lähestyttävyyden arviointi (kohta 8) muotoiltiin myös uudestaan, koska digitaalisessa mediassa pelkkä tekstin läsnäolo ei sellaisenaan tyypillisesti vielä riitä halutun viestin välittämiseen kohdeyleisölle. Tietotekniikan edistyminen ja psykologian sekä sosiologian aloilla tehty tieteellinen tutkimus ihmisten käyttäytymisestä sosiaalisessa mediassa (ja yleensä kybertoimintaympäristössä) mahdollistavat koko kohdeyleisöanalyysiprosessin uudelleenrakentamisen. Tässä työssä sitä kuitenkaan ei voida tehdä. Siksi esitetäänkin että lisätutkimusta tulisi tehdä sekä tietokoneavusteisten prosessien että vielä syvällisempien kohdeyleisöanalyysien osalta, käyttäen hyväksi viimeisimpiä ihmisen käyttäytymiseen liittyviä tutkimustuloksia.

Diversity and structure of the tree community of a fragment of tropical secondary forest of the brazilian Atlantic Forest domain 15 and 40 years after logging

Two adjacent tracts of tropical secondary forest, situated in Itambé do Mato Dentro, south-eastern Brazil, which had been regenerating for 15 and 40 years after clearing, were compared with the purpose of detecting differences in species diversity and composition, species guild composition (regeneration, stratification and dispersion), and stand structure. Four and three 1,125 m² plots laid on the 15- and 40-year-old stands, respectively, sampled 2,430 trees with diameter at the base of the stem > 5 cm. The number of species (S = 199) was high for this forest type and significantly higher for the older stand. Tree density was significantly higher in the younger stand, particularly for smaller trees, whereas the two stands did not differ in both basal area and volume per hectare. Trees of shade-tolerant and understory species were significantly more abundant in the older stand. Though sharing a large proportion of species (49%), the two stands differed significantly in the abundance of many species. Live stumps probably contributed to the relatively quick restoration of some forest characteristics, particularly species diversity, basal area and volume.

Large-scale production and purification of recombinant protein from an insect cell/baculovirus system in Erlenmeyer flasks: application to the chicken poly(ADP-ribose) polymerase catalytic domain

A simple and inexpensive shaker/Erlenmeyer flask system for large-scale cultivation of insect cells is described and compared to a commercial spinner system. On the basis of maximum cell density, average population doubling time and overproduction of recombinant protein, a better result was obtained with a simpler and less expensive bioreactor consisting of Erlenmeyer flasks and an ordinary shaker waterbath. Routinely, about 90 mg of pure poly(ADP-ribose) polymerase catalytic domain was obtained for a total of 3 x 109 infected cells in three liters of culture

Centromere domain organization and histone modifications

Centromere function requires the proper coordination of several subfunctions, such as kinetochore assembly, sister chromatid cohesion, binding of kinetochore microtubules, orientation of sister kinetochores to opposite spindle poles, and their movement towards the spindle poles. Centromere structure appears to be organized in different, separable domains in order to accomplish these functions. Despite the conserved nature of centromere functions, the molecular genetic definition of the DNA sequences that form a centromere in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, in the fruit fly Drosophila melanogaster, and in humans has revealed little conservation at the level of centromere DNA sequences. Also at the protein level few centromere proteins are conserved in all of these four organisms and many are unique to the different organisms. The recent analysis of the centromere structure in the yeast S. pombe by electron microscopy and detailed immunofluorescence microscopy of Drosophila centromeres have brought to light striking similarities at the overall structural level between these centromeres and the human centromere. The structural organization of the centromere is generally multilayered with a heterochromatin domain and a central core/inner plate region, which harbors the outer plate structures of the kinetochore. It is becoming increasingly clear that the key factors for assembly and function of the centromere structure are the specialized histones and modified histones which are present in the centromeric heterochromatin and in the chromatin of the central core. Thus, despite the differences in the DNA sequences and the proteins that define a centromere, there is an overall structural similarity between centromeres in evolutionarily diverse eukaryotes.

Large-eddy simulation of wind flows over complex terrains for wind energy applications

Wind energy has obtained outstanding expectations due to risks of global warming and nuclear energy production plant accidents. Nowadays, wind farms are often constructed in areas of complex terrain. A potential wind farm location must have the site thoroughly surveyed and the wind climatology analyzed before installing any hardware. Therefore, modeling of Atmospheric Boundary Layer (ABL) flows over complex terrains containing, e.g. hills, forest, and lakes is of great interest in wind energy applications, as it can help in locating and optimizing the wind farms. Numerical modeling of wind flows using Computational Fluid Dynamics (CFD) has become a popular technique during the last few decades. Due to the inherent flow variability and large-scale unsteadiness typical in ABL flows in general and especially over complex terrains, the flow can be difficult to be predicted accurately enough by using the Reynolds-Averaged Navier-Stokes equations (RANS). Large- Eddy Simulation (LES) resolves the largest and thus most important turbulent eddies and models only the small-scale motions which are more universal than the large eddies and thus easier to model. Therefore, LES is expected to be more suitable for this kind of simulations although it is computationally more expensive than the RANS approach. With the fast development of computers and open-source CFD software during the recent years, the application of LES toward atmospheric flow is becoming increasingly common nowadays. The aim of the work is to simulate atmospheric flows over realistic and complex terrains by means of LES. Evaluation of potential in-land wind park locations will be the main application for these simulations. Development of the LES methodology to simulate the atmospheric flows over realistic terrains is reported in the thesis. The work also aims at validating the LES methodology at a real scale. In the thesis, LES are carried out for flow problems ranging from basic channel flows to real atmospheric flows over one of the most recent real-life complex terrain problems, the Bolund hill. All the simulations reported in the thesis are carried out using a new OpenFOAM® -based LES solver. The solver uses the 4th order time-accurate Runge-Kutta scheme and a fractional step method. Moreover, development of the LES methodology includes special attention to two boundary conditions: the upstream (inflow) and wall boundary conditions. The upstream boundary condition is generated by using the so-called recycling technique, in which the instantaneous flow properties are sampled on aplane downstream of the inlet and mapped back to the inlet at each time step. This technique develops the upstream boundary-layer flow together with the inflow turbulence without using any precursor simulation and thus within a single computational domain. The roughness of the terrain surface is modeled by implementing a new wall function into OpenFOAM® during the thesis work. Both, the recycling method and the newly implemented wall function, are validated for the channel flows at relatively high Reynolds number before applying them to the atmospheric flow applications. After validating the LES model over simple flows, the simulations are carried out for atmospheric boundary-layer flows over two types of hills: first, two-dimensional wind-tunnel hill profiles and second, the Bolund hill located in Roskilde Fjord, Denmark. For the twodimensional wind-tunnel hills, the study focuses on the overall flow behavior as a function of the hill slope. Moreover, the simulations are repeated using another wall function suitable for smooth surfaces, which already existed in OpenFOAM® , in order to study the sensitivity of the flow to the surface roughness in ABL flows. The simulated results obtained using the two wall functions are compared against the wind-tunnel measurements. It is shown that LES using the implemented wall function produces overall satisfactory results on the turbulent flow over the two-dimensional hills. The prediction of the flow separation and reattachment-length for the steeper hill is closer to the measurements than the other numerical studies reported in the past for the same hill geometry. The field measurement campaign performed over the Bolund hill provides the most recent field-experiment dataset for the mean flow and the turbulence properties. A number of research groups have simulated the wind flows over the Bolund hill. Due to the challenging features of the hill such as the almost vertical hill slope, it is considered as an ideal experimental test case for validating micro-scale CFD models for wind energy applications. In this work, the simulated results obtained for two wind directions are compared against the field measurements. It is shown that the present LES can reproduce the complex turbulent wind flow structures over a complicated terrain such as the Bolund hill. Especially, the present LES results show the best prediction of the turbulent kinetic energy with an average error of 24.1%, which is a 43% smaller than any other model results reported in the past for the Bolund case. Finally, the validated LES methodology is demonstrated to simulate the wind flow over the existing Muukko wind farm located in South-Eastern Finland. The simulation is carried out only for one wind direction and the results on the instantaneous and time-averaged wind speeds are briefly reported. The demonstration case is followed by discussions on the practical aspects of LES for the wind resource assessment over a realistic inland wind farm.

In silico analysis identifies a C3HC4-RING finger domain of a putative E3 ubiquitin-protein ligase located at the C-terminus of a polyglutamine-containing protein

Almost identical polyglutamine-containing proteins with unknown structures have been found in human, mouse and rat genomes (GenBank AJ277365, AF525300, AY879229). We infer that an identical new gene (RING) finger domain of real interest is located in each C-terminal segment. A three-dimensional (3-D) model was generated by remote homology modeling and the functional implications are discussed. The model consists of 65 residues from terminal position 707 to 772 of the human protein with a total length of 796 residues. The 3-D model predicts a ubiquitin-protein ligase (E3) as a binding site for ubiquitin-conjugating enzyme (E2). Both enzymes are part of the ubiquitin pathway to label unwanted proteins for subsequent enzymatic degradation. The molecular contact specificities are suggested for both the substrate recognition and the residues at the possible E2-binding surface. The predicted structure, of a ubiquitin-protein ligase (E3, enzyme class number 6.3.2.19, CATH code 3.30.40.10.4) may contribute to explain the process of ubiquitination. The 3-D model supports the idea of a C3HC4-RING finger with a partially new pattern. The putative E2-binding site is formed by a shallow hydrophobic groove on the surface adjacent to the helix and one zinc finger (L722, C739, P740, P741, R744). Solvent-exposed hydrophobic amino acids lie around both zinc fingers (I717, L722, F738, or P765, L766, V767, V733, P734). The 3-D structure was deposited in the protein databank theoretical model repository (2B9G, RCSB Protein Data Bank, NJ).

Effect of ATP and 2-oxoglutarate on the in vitro interaction between the NifA GAF domain and the GlnB protein of Azospirillum brasilense

Azospirillum brasilense is a diazotroph that associates with important agricultural crops and thus has potential to be a nitrogen biofertilizer. The A. brasilense transcription regulator NifA, which seems to be constitutively expressed, activates the transcription of nitrogen fixation genes. It has been suggested that the nitrogen status-signaling protein GlnB regulates NifA activity by direct interaction with the NifA N-terminal GAF domain, preventing the inhibitory effect of this domain under conditions of nitrogen fixation. In the present study, we show that an N-terminal truncated form of NifA no longer required GlnB for activity and lost regulation by ammonium. On the other hand, in trans co-expression of the N-terminal GAF domain inhibited the N-truncated protein in response to fixed nitrogen levels. We also used pull-down assays to show in vitro interaction between the purified N-terminal GAF domain of NifA and the GlnB protein. The results showed that A. brasilense GlnB interacts directly with the NifA N-terminal domain and this interaction is dependent on the presence of ATP and 2-oxoglutarate.

The N-terminal 33 amino acid domain of Siva-1 is sufficient for nuclear localization

Siva-1 induces apoptosis in multiple pathological processes and plays an important role in the suppression of tumor metastasis, protein degradation, and other functions. Although many studies have demonstrated that Siva-1 functions in the cytoplasm, a few have found that Siva-1 can relocate to the nucleus. In this study, we found that the first 33 amino acid residues of Siva-1 are required for its nuclear localization. Further study demonstrated that the green fluorescent protein can be imported into the nucleus after fusion with these 33 amino acid residues. Other Siva-1 regions and domains showed less effect on Siva-1 nuclear localization. By site-mutagenesis of all of these 33 amino acid residues, we found that mutants of the first 1-18 amino acids affected Siva-1 nuclear compartmentalization but could not complete this localization independently. In summary, we demonstrated that the N-terminal 33 amino acid residues were sufficient for Siva-1 nuclear localization, but the mechanism of this translocation needs additional investigation.

Intelligence acquisition methods in cyber domain : examining the circumstantial applicability of cyber intelligence acquisition methods using a hierarchical model

Phenomena in cyber domain, especially threats to security and privacy, have proven an increasingly heated topic addressed by different writers and scholars at an increasing pace – both nationally and internationally. However little public research has been done on the subject of cyber intelligence. The main research question of the thesis was: To what extent is the applicability of cyber intelligence acquisition methods circumstantial? The study was conducted in sequential a manner, starting with defining the concept of intelligence in cyber domain and identifying its key attributes, followed by identifying the range of intelligence methods in cyber domain, criteria influencing their applicability, and types of operatives utilizing cyber intelligence. The methods and criteria were refined into a hierarchical model. The existing conceptions of cyber intelligence were mapped through an extensive literature study on a wide variety of sources. The established understanding was further developed through 15 semi-structured interviews with experts of different backgrounds, whose wide range of points of view proved to substantially enhance the perspective on the subject. Four of the interviewed experts participated in a relatively extensive survey based on the constructed hierarchical model on cyber intelligence that was formulated in to an AHP hierarchy and executed in the Expert Choice Comparion online application. It was concluded that Intelligence in cyber domain is an endorsing, cross-cutting intelligence discipline that adds value to all aspects of conventional intelligence and furthermore that it bears a substantial amount of characteristic traits – both advantageous and disadvantageous – and furthermore that the applicability of cyber intelligence methods is partly circumstantially limited.