T-Cell Receptors Binding Orientation over Peptide/MHC Class I Is Driven by Long-Range Interactions.

Crystallographic data about T-Cell Receptor - peptide - major histocompatibility complex class I (TCRpMHC) interaction have revealed extremely diverse TCR binding modes triggering antigen recognition. Understanding the molecular basis that governs TCR orientation over pMHC is still a considerable challenge. We present a simplified rigid approach applied on all non-redundant TCRpMHC crystal structures available. The CHARMM force field in combination with the FACTS implicit solvation model is used to study the role of long-distance interactions between the TCR and pMHC. We demonstrate that the sum of the coulomb interactions and the electrostatic solvation energies is sufficient to identify two orientations corresponding to energetic minima at 0° and 180° from the native orientation. Interestingly, these results are shown to be robust upon small structural variations of the TCR such as changes induced by Molecular Dynamics simulations, suggesting that shape complementarity is not required to obtain a reliable signal. Accurate energy minima are also identified by confronting unbound TCR crystal structures to pMHC. Furthermore, we decompose the electrostatic energy into residue contributions to estimate their role in the overall orientation. Results show that most of the driving force leading to the formation of the complex is defined by CDR1,2/MHC interactions. This long-distance contribution appears to be independent from the binding process itself, since it is reliably identified without considering neither short-range energy terms nor CDR induced fit upon binding. Ultimately, we present an attempt to predict the TCR/pMHC binding mode for a TCR structure obtained by homology modeling. The simplicity of the approach and the absence of any fitted parameters make it also easily applicable to other types of macromolecular protein complexes.

MIGCLIM: Predicting plant distribution and dispersal in a changing climate

Many studies have forecasted the possible impact of climate change on plant distribution using models based on ecological niche theory. In their basic implementation, niche-based models do not constrain predictions by dispersal limitations. Hence, most niche-based modelling studies published so far have assumed dispersal to be either unlimited or null. However, depending on the rate of climatic change, the landscape fragmentation and the dispersal capabilities of individual species, these assumptions are likely to prove inaccurate, leading to under- or overestimation of future species distributions and yielding large uncertainty between these two extremes. As a result, the concepts of "potentially suitable" and "potentially colonisable" habitat are expected to differ significantly. To quantify to what extent these two concepts can differ, we developed MIGCLIM, a model simulating plant dispersal under climate change and landscape fragmentation scenarios. MIGCLIM implements various parameters, such as dispersal distance, increase in reproductive potential over time, barriers to dispersal or long distance dispersal. Several simulations were run for two virtual species in a study area of the western Swiss Alps, by varying dispersal distance and other parameters. Each simulation covered the hundred-year period 2001-2100 and three different IPCC-based temperature warming scenarios were considered. Our results indicate that: (i) using realistic parameter values, the future potential distributions generated using MIGCLIM can differ significantly (up to more than 95% decrease in colonized surface) from those that ignore dispersal; (ii) this divergence increases both with increasing climate warming and over longer time periods; (iii) the uncertainty associated with the warming scenario can be nearly as large as the one related to dispersal parameters; (iv) accounting for dispersal, even roughly, can importantly reduce uncertainty in projections.

Metsäpolttoaineiden vesitiekuljetus proomukalustolla

Metsäpolttoaineiden käyttö kasvaa lämpö- ja voimalaitoksissa ja mahdollisissa biojalostamoissa. Metsäpolttoaineilla voidaan saavuttaa päästövähennyksiä korvaamalla päästöintensiivisempiä polttoaineita. Metsäpolttoaineen kysynnän kasvu suurkäyttöpaikoilla luo uusia vaatimuksia metsäbiomassan hankintaan. Metsäpolttoaineiden vesitiekuljetuksen sisältämiä logistiikkajärjestelmiä kehittämällä toimitusvarmuutta pystytään parantamaan ja hankintaa laajentamaan kustannustehokkaasti ja ympäristöystävällisesti. Kuljetuskokeilut antoivat uutta tietoa vesitiekuljetuksen sisältämästä hankinnasta. Lastikapasiteetti nykyisen kaltaisessa Eurooppa IIa -suurproomussa vaihtelee 1200 tonnista jopa 1800 tonniin (kosteus 40 %) riippuen tiivistymisestä ja proomun modifiointiasteesta. Metsähakkeen energiatiheys oli suurproomukuljetuksissa keskimäärin 1 MWh/i-m3, joka oli 25 % parempi kuin vertailun hakerekkakuljetuksissa. Vesitiekuljetuksen kustannukset olivat kuljetuskokeiluissa lastauksineen ja purkuineen 0,02 €/MWh/km, ollen noin 20 % ketjun kokonaiskustannuksista. Simuloinnin edullisimpien vesitiekuljetusvaihtoehtojen vaihteluvälin kustannukset olivat vastaavasti 0,013 - 0,026 €/MWh/km. Lastauksen ja purun kustannus oli 0,4 - 0,6 €/MWh ja vesitiekuljetus 0,9 - 2,0 €/MWh (100 km). Ketjun kokonaiskustannukset hakkuutähdehakkeelle vaihtelivat simuloinnin edullisimpien vaihtoehtojen perusteella välillä 10,8 - 12,1 €/MWh (30 km rekka, 100 km proomu). Kuljetusketjujen simuloinnin kustannukset osoittivat proomukuljetusketjun olevan kilpailukykyinen vaihtoehto hakerekkakuljetusketjulle kalustosta ja vuosittaisista käyttötunneista riippuen kuljetusetäisyyden ylittäessä 100 km. Kustannustehokkain ratkaisu vesitiekuljetuksessa saavutettiin pienen aluksen ja suuren kokoluokan proomuyksikön kytkyeellä. Haketus kannattaa toteuttaa ennen proomukuljetuksen osuutta metsähakkeen paremman tiiviyden ja käsiteltävyyden perusteella. Logistiikkajärjestelmiä pitää kehittää tapauskohtaisesti käyttöpaikan tarpeet ja olosuhteet huomioon ottaen. Metsäpolttoaineiden vesitiekuljetuksen sisältämän logistiikan liiketoimintamallien vertailussa arvioitiin vaihtoehtoiset ulkoistetut toimintamallit paremmaksi kuin nykyinen urakointimalli. Tämä mahdollistaa paremman metsähakkeen saatavuuden ja logistiikan tehokkuuden lastausterminaaleissa. Terminaalitoiminnot ja proomukuljetukset lisäävät uusia liiketoimintamahdollisuuksia ja mahdollistavat metsäpolttoaineiden

On Dynamic Monitoring Methods for Networks-on-Chip

Rapid ongoing evolution of multiprocessors will lead to systems with hundreds of processing cores integrated in a single chip. An emerging challenge is the implementation of reliable and efficient interconnection between these cores as well as other components in the systems. Network-on-Chip is an interconnection approach which is intended to solve the performance bottleneck caused by traditional, poorly scalable communication structures such as buses. However, a large on-chip network involves issues related to congestion problems and system control, for instance. Additionally, faults can cause problems in multiprocessor systems. These faults can be transient faults, permanent manufacturing faults, or they can appear due to aging. To solve the emerging traffic management, controllability issues and to maintain system operation regardless of faults a monitoring system is needed. The monitoring system should be dynamically applicable to various purposes and it should fully cover the system under observation. In a large multiprocessor the distances between components can be relatively long. Therefore, the system should be designed so that the amount of energy-inefficient long-distance communication is minimized. This thesis presents a dynamically clustered distributed monitoring structure. The monitoring is distributed so that no centralized control is required for basic tasks such as traffic management and task mapping. To enable extensive analysis of different Network-on-Chip architectures, an in-house SystemC based simulation environment was implemented. It allows transaction level analysis without time consuming circuit level implementations during early design phases of novel architectures and features. The presented analysis shows that the dynamically clustered monitoring structure can be efficiently utilized for traffic management in faulty and congested Network-on-Chip-based multiprocessor systems. The monitoring structure can be also successfully applied for task mapping purposes. Furthermore, the analysis shows that the presented in-house simulation environment is flexible and practical tool for extensive Network-on-Chip architecture analysis.

Eri laskentamenetelmien vertailu hitsatun rakenteen väsymislaskennassa

Tässä työssä tutkittiin eri mitoitusmenetelmien soveltuvuutta hitsattujen rakenteiden vä-symislaskennassa. Käytetyt menetelmät olivat rakenteellinen jännityksen menetelmä, te-hollisen lovijännityksen menetelmä ja murtumismekaniikka. Lisäksi rakenteellisen jänni-tyksen määrittämiseksi käytettiin kolmea eri menetelmää. Menetelmät olivat pintaa pitkin ekstrapolointi, paksuuden yli linearisointi ja Dongin menetelmä. Väsymiskestävyys määritettiin kahdelle hitsiliitoksen yksityiskohdalle. Laskenta tehtiin käyttäen elementtimenetelmää rakenteen 3D-mallille. Tutkittavasta aggregaattirungosta oli olemassa FE-malli mutta alimallinnustekniikkaa hyödyntämällä pystyttiin yksityiskohtai-semmin tutkimaan vain pientä osaa koko rungon mallista. Rakenteellisen jännityksen menetelmä perustuu nimellisiin jännityksiin. Kyseinen mene-telmä ei vaadi geometrian muokkausta. Yleensä rakenteellisen jännityksen menetelmää käytetään hitsin rajaviivan väsymislaskennassa, mutta joissain tapauksissa sitä on käytetty juuren puolen laskennassa. Tässä työssä rakenteellisen jännityksen menetelmää käytettiin myös juuren puolen tutkimisessa. Tehollista lovijännitystä tutkitaan mallintamalla 1 mm fiktiiviset pyöristykset sekä rajaviivalle että juuren puolelle. Murtumismekaniikan so-veltuvuutta tutkittiin käyttämällä Franc2D särön kasvun simulointiohjelmaa. Väsymislaskennan tulokset eivät merkittävästi poikkea eri laskentamenetelmien välillä. Ainoastaan rakenteellisen jännityksen Dongin menetelmällä saadaan poikkeavia tuloksia. Tämä johtuu pääasiassa siitä, että menetelmän laskentaetäisyydestä ei ole tietoa. Raken-teellisen jännityksen menetelmällä, tehollisen lovijännityksen menetelmällä ja murtumis-mekaniikalla saadaan samansuuntaiset tulokset. Suurin ero menetelmien välillä on mal-linnuksen ja laskennan vaatima työmäärä.

Développement d’une méthode de simulation multi-échelle pour l’étude des grandes transformations dans les protéines

Les films de simulations qui accompagnent le document ont été réalisés avec Pymol.

Epidemiological risk assessment using linked network and grid based modelling: Phytophthora ramorum and Phytophthora kernoviae in the UK

We developed a stochastic simulation model incorporating most processes likely to be important in the spread of Phytophthora ramorum and similar diseases across the British landscape (covering Rhododendron ponticum in woodland and nurseries, and Vaccinium myrtillus in heathland). The simulation allows for movements of diseased plants within a realistically modelled trade network and long-distance natural dispersal. A series of simulation experiments were run with the model, representing an experiment varying the epidemic pressure and linkage between natural vegetation and horticultural trade, with or without disease spread in commercial trade, and with or without inspections-with-eradication, to give a 2 x 2 x 2 x 2 factorial started at 10 arbitrary locations spread across England. Fifty replicate simulations were made at each set of parameter values. Individual epidemics varied dramatically in size due to stochastic effects throughout the model. Across a range of epidemic pressures, the size of the epidemic was 5-13 times larger when commercial movement of plants was included. A key unknown factor in the system is the area of susceptible habitat outside the nursery system. Inspections, with a probability of detection and efficiency of infected-plant removal of 80% and made at 90-day intervals, reduced the size of epidemics by about 60% across the three sectors with a density of 1% susceptible plants in broadleaf woodland and heathland. Reducing this density to 0.1% largely isolated the trade network, so that inspections reduced the final epidemic size by over 90%, and most epidemics ended without escape into nature. Even in this case, however, major wild epidemics developed in a few percent of cases. Provided the number of new introductions remains low, the current inspection policy will control most epidemics. However, as the rate of introduction increases, it can overwhelm any reasonable inspection regime, largely due to spread prior to detection. (C) 2009 Elsevier B.V. All rights reserved.

Gene flow, risk assessment and the environmental release of transgenic plants

The release of genetically modified plants is governed by regulations that aim to provide an assessment of potential impact on the environment. One of the most important components of this risk assessment is an evaluation of the probability of gene flow. In this review, we provide an overview of the current literature on gene flow from transgenic plants, providing a framework of issues for those considering the release of a transgenic plant into the environment. For some plants gene flow from transgenic crops is well documented, and this information is discussed in detail in this review. Mechanisms of gene flow vary from plant species to plant species and range from the possibility of asexual propagation, short- or long-distance pollen dispersal mediated by insects or wind and seed dispersal. Volunteer populations of transgenic plants may occur where seed is inadvertently spread during harvest or commercial distribution. If there are wild populations related to the transgenic crop then hybridization and eventually introgression in the wild may occur, as it has for herbicide resistant transgenic oilseed rape (Brassica napus). Tools to measure the amount of gene flow, experimental data measuring the distance of pollen dispersal, and experiments measuring hybridization and seed survivability are discussed in this review. The various methods that have been proposed to prevent gene flow from genetically modified plants are also described. The current "transgenic traits'! in the major crops confer resistance to herbicides and certain insects. Such traits could confer a selective advantage (an increase in fitness) in wild plant populations in some circumstances, were gene flow to occur. However, there is ample evidence that gene flow from crops to related wild species occurred before the development of transgenic crops and this should be taken into account in the risk assessment process.

The population genetic structure of clonal organisms generated by exponentially bounded and fat-tailed dispersal

Long distance dispersal (LDD) plays an important role in many population processes like colonization, range expansion, and epidemics. LDD of small particles like fungal spores is often a result of turbulent wind dispersal and is best described by functions with power-law behavior in the tails ("fat tailed"). The influence of fat-tailed LDD on population genetic structure is reported in this article. In computer simulations, the population structure generated by power-law dispersal with exponents in the range of -2 to -1, in distinct contrast to that generated by exponential dispersal, has a fractal structure. As the power-law exponent becomes smaller, the distribution of individual genotypes becomes more self-similar at different scales. Common statistics like G(ST) are not well suited to summarizing differences between the population genetic structures. Instead, fractal and self-similarity statistics demonstrated differences in structure arising from fat-tailed and exponential dispersal. When dispersal is fat tailed, a log-log plot of the Simpson index against distance between subpopulations has an approximately constant gradient over a large range of spatial scales. The fractal dimension D-2 is linearly inversely related to the power-law exponent, with a slope of similar to -2. In a large simulation arena, fat-tailed LDD allows colonization of the entire space by all genotypes whereas exponentially bounded dispersal eventually confines all descendants of a single clonal lineage to a relatively small area.

Distance teacher education – some experiences from Dalarna University, SwedenPaper presented at the 33rd Annual ATEE Conference Brussels, Belgium, 23rd – 27th August 2008

Distance teaching is now-a-days used in different shapes. However, it is something different from traditional campus organised education as it systematically uses Information Communication Technology (ICT) as a key element. When the distance teacher education started in Sweden many teacher educators doubted the wisdom of this. They expressed that the educational process to become a teacher would be deteriorated. For instance, they feared for high drop out rates and difficulties to examine in a proper way. The Swedish National Agency for Higher Education has recently edited a report that showed that this form of teacher education was well adapted to the labour market, but the possibilities for the teacher students to shape their education were relatively limited. However, we still know quite little about the effects of this way to educate teacher students. This paper explores the possibility of using distance teacher education.In a case study 20 students, who were the first to finish a complete a distance teacher education at Högskolan Dalarna, were asked in a questionnaire how they had apprehended their education. We also interviewed four of these students, as well as five teacher educators.One of our findings were that the distance teacher education reached new target groups, who not had been able to participate in university studies if it not had been offered in this form. Especially, this was valid for the middle-aged women, living a long distance away from a university, with social responsibilities for children or old parents. Other findings were that these students in general were target oriented and ambitious, wrote more than the campus students and developed that kind of skill better. Marratech, an ICT system for small groups, e-mail and chat were used for the communication. Marratech was considered to permit free and spontaneous communication, both of the teacher educators and the students. Initially the teacher educators were sceptical to distance teacher education, but afterwards they were surprised of how well it had worked. They declared that they had better and nearer contact with their students and more control over the students´ performance, but some parts of the teacher education were better suitable for campus education, for example, power of creating characters. Distance teacher education was considered time consuming and demanded much activity from the teacher educators as the students wanted rapid responses. This study indicates that distance teacher education works well for mature individuals with high motivation. However, it demands more time from the teacher educators, but it gives in general good results. Still, there are pedagogical challenges to overcome. Maybe we should reflect on a mix of distance teacher education and campus based teacher education, instead of separated ways of accomplishing teacher education?

Training courses for teachers through the distance learning: practice reports used virtual environment TELEDUC

This paper describes the experiences of long-distance courses, it focused on the continuing education of basic education teachers in all Brazilian territory. Such courses were offered by CECEMCA (Center for Continuing Education in Mathematics Education, Science and Environment), linked to the Universidade Estadual Paulista Julio de Mesquita Filho - Campus de Rio Claro during 15/01/2009 to 30/11/2009. The subjects report to the theme of Education, Geography and Environment, it was organized in four courses: "Introduction to Cartography," Environment and climate change - thinking a new paradigm of sustainable green planet "," Remote Sensing in environmental studies Environment "and" Methodological Alternatives for Inclusive Classroom: Experimenting with visual and hearing impairments". So, we show here, the feasibility and importance of distance learning tools for education, specifically teacher training, based on the results obtained in these courses.

Laboratório remoto de qualidade da energia elétrica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

SIMPLARCOM: simulador para planejamento de redes de comunicação sem fio utilizando realidade virtual e modelos de propagação

Este simulador é formado pela junção de técnicas de Realidade Virtual com modelos de propagação, desenvolvidos através dos estudos de rádio enlace, que descrevem a perda que o sinal transmitido sofre ao longo do percurso no ambiente. O simulador possui dois módulos. O primeiro permite a criação do ambiente virtual com o posicionamento, sobre um terreno, de prédios, árvores, carros, antenas e outras primitivas que permitem a construção de um ambiente tridimensional customizável. O segundo módulo permite a configuração dos parâmetros relacionados a propagação de sinal de antenas como a potência, a frequência, o ganho, etc., e também selecionar o modelo de propagação para a execução da simulação. Dentro deste segundo módulo, existe um submódulo responsável pelo estudo do planejamento da área de cobertura composta pelas antenas, em outras palavras, este submódulo simula a distância que cada antena no cenário consegue atingir e gera a respectiva área de cobertura. Para demonstrar a eficiência do simulador foram criados dois ambientes virtuais para testes. Um cenário representando um ambiente urbano onde empregou-se um modelo de propagação clássico, Okumura-Hata para cidades pequenas e médias, e um ambiente tridimensional arborizado utilizando um modelo especifico para simulação de propagação para regiões densamente arborizadas, desenvolvido na Universidade Federal do Pará chamado de Lyra-Castro-UFPA.

Short distance QCD contribution to the electroweak mass difference of pions

It is known that the short distance QCD contribution to the mass difference of pions is quadratic on the quark masses, and irrelevant with respect to the long distance part. It is also considered in the literature that its calculation contains infinities, which should be absorbed by the quark mass renormalization. Following a prescription by Craigie, Narison, and Riazuddin of a renormalization-group-improved perturbation theory to deal with the electromagnetic mass shift problem in QCD, we show that the short distance QCD contribution to the electroweak pion mass difference (with mu=md≠0) is finite and, of course, its value is negligible compared to other contributions.

Co-simulazione e co-progetto non lineare/elettromagnetico di sistemi wireless non convenzionali

L’attività di ricerca contenuta in questa tesi si è concentrata nello sviluppo e nell’implementazione di tecniche per la co-simulazione e il co-progetto non lineare/elettromagnetico di sistemi wireless non convenzionali. Questo lavoro presenta un metodo rigoroso per considerare le interazioni tra due sistemi posti sia in condizioni di campo vicino che in condizioni di campo lontano. In sostanza, gli effetti del sistema trasmittente sono rappresentati da un generatore equivalente di Norton posto in parallelo all’antenna del sistema ricevente, calcolato per mezzo del teorema di reciprocità e del teorema di equivalenza. La correttezza del metodo è stata verificata per mezzo di simulazioni e misure, concordi tra loro. La stessa teoria, ampliata con l’introduzione degli effetti di scattering, è stata usata per valutare una condizione analoga, dove l’elemento trasmittente coincide con quello ricevente (DIE) contenuto all’interno di una struttura metallica (package). I risultati sono stati confrontati con i medesimi ottenibili tramite tecniche FEM e FDTD/FIT, che richiedono tempi di simulazione maggiori di un ordine di grandezza. Grazie ai metodi di co-simulazione non lineari/EM sopra esposti, è stato progettato e verificato un sistema di localizzazione e identificazione di oggetti taggati posti in ambiente indoor. Questo è stato ottenuto dotando il sistema di lettura, denominato RID (Remotely Identify and Detect), di funzioni di scansione angolare e della tecnica di RADAR mono-pulse. Il sistema sperimentale, creato con dispositivi low cost, opera a 2.5 GHz ed ha le dimensioni paragonabili ad un normale PDA. E’ stato sperimentata la capacità del RID di localizzare, in scenari indoor, oggetti statici e in movimento.