Constitutive modeling of shape memory alloy wire with non-local rate kinetics

A constitutive modeling approach for shape memory alloy (SMA) wire by taking into account the microstructural phase inhomogeneity and the associated solid-solid phase transformation kinetics is reported in this paper. The approach is applicable to general thermomechanical loading. Characterization of various scales in the non-local rate sensitive kinetics is the main focus of this paper. Design of SMA materials and actuators not only involve an optimal exploitation of the hysteresis loops during loading-unloading, but also accounts for fatigue and training cycle identifications. For a successful design of SMA integrated actuator systems, it is essential to include the microstructural inhomogeneity effects and the loading rate dependence of the martensitic evolution, since these factors play predominant role in fatigue. In the proposed formulation, the evolution of new phase is assumed according to Weibull distribution. Fourier transformation and finite difference methods are applied to arrive at the analytical form of two important scaling parameters. The ratio of these scaling parameters is of the order of 10(6) for stress-free temperature-induced transformation and 10(4) for stress-induced transformation. These scaling parameters are used in order to study the effect of microstructural variation on the thermo-mechanical force and interface driving force. It is observed that the interface driving force is significant during the evolution. Increase in the slopes of the transformation start and end regions in the stress-strain hysteresis loop is observed for mechanical loading with higher rates.

Reflexive Incidence Matrx (RIM) Representation of Petr Nets

Although incidence matrix representation has been used to analyze the Petri net based models of a system, it has the limitation that it does not preserve reflexive properties (i.e., the presence of selfloops) of Petri nets. But in many practical applications self-loops play very important roles. This paper proposes a new representation scheme for general Petri nets. This scheme defines a matrix called "reflexive incidence matrix (RIM) c which is a combination of two matrices, a "base matrix Cb,,, and a "power matrix CP." This scheme preserves the reflexive and other properties of the Petri nets. Through a detailed analysis it is shown that the proposed scheme requires less memory space and less processing time for answering commonly encountered net queries compared to other schemes. Algorithms to generate the RIM from the given net description and to decompose RIM into input and output function matrices are also given. The proposed Petri net representation scheme is very useful to model and analyze the systems having shared resources, chemical processes, network protocols, etc., and to evaluate the performance of asynchronous concurrent systems.

"Like a monkey with a miniature cymbal": Cultural practices of repetition in visual social media

Looping media are recurring components of online content, from gifs to Vine videos, in addition to the conceptual repetition of memes and related practices. This paper analyses practices around looping visual media as examples of vernacular creativity, social media literacies, and internet culture, especially for irreverent and playful purposes. Focusing on the LGBTQ digital cultural context as a pilot study, this research examines multi-platform uses of looping media, including personal narratives through Vine videos and animated gifs on Tumblr. In addition to textual analysis of LGBTQ looping visual social media content, the study will further explore the platform context as part of the experience of looped media. The research will address how these factors may also contribute to practices of irreverence and play, both within the specific case of LGBTQ culture and internet culture more generally.

Reversals of polypeptide chain in globular proteins.

A simple algorithm has been developed to detect β-bends and 'loops'-chain reversals containing five amino acid residues, using only coordinates of Cα-atoms from crystal structure data of globular proteins using the above algorithm. Analysis of bends have showed that the total number of bends in each protein (TB) is linearly related to total number of non-hydrophobic residues in that protein which in turn is related linearly to total number of amino acid residues. Secondly, we found that a large number of consecutive bends occur in each protein which give rise to on an average only three independent residues per turn. Positional preference of amino acid residues in chain reversals is stressed. Consideration of pairs of amino acid residues in positions (i + 1) and (i + 2) of bends seems to provide a more reliable basis for predicting chain reversals in proteins.

Oikein, nurin - miten Suomessa kudin : Tutkimus neulonnan työotteista.

The aim of this work was to study what kind of working grips people use to knit in Finland and decide if one grip is superior to others. I investigated how knitters have adopted their grips and how they experience their knitting. I also explored whether it is possible to change one's grip. To provide a theoretical basis for the research I observed knitting in terms of culture, skill and ergonomics. The first part of the study material comprised video recordings of the grips of 95 knitters together with background information collected via a questionnaire during the education of craft teachers at the University of Helsinki in spring 2004, 2005 and 2006. Using the data obtained I focused on three knitters, whose grip of the knitting needles clearly differed from the ergonomically good grip. In addition to them I interviewed one student, who had changed over to more ergonomic way of knitting after participating in the first part of this study. In this respect my study is a several events' case study. In order to analyse my data I used both qualitative and quantitative content analysis methods to complement each other. Most of my research participants had learned to knit in first years of elementary school or comprehensive school. Almost everyone had adopted the basics of knitting by imitating, and many of them had corrected "incorrect" positions from verbal instructions. Through practice the imitated position had gradually become the style unique to each knitter. The findings showed that students' background in knitting is quite varied due to the diverse level of craft teaching. This is reflected in their knitting grips and their interest in knitting. Students do not think that there is one right working grip. The most important thing is that working seems as fluent and relaxed as possible, at which point knitting is easy and flows freely. They often consider their own style so pleasing and well-functioning that they do not think there could be any room for improvement. This study pointed out that, while it is possible to change a knitter's working grip, there is a bigger challenge in acknowledging weaknesses in one's know how. According to the results of my research, the most common working grip among Finnish knitters' corresponds with the grip that has been described as ergonomically good. Over one third of all participants knitted this way. Hands keep the knitting firmly but without tension. The forefinger that guides the yarn from the ball rests gently against the knitting needle, and the yarn goes in front of the first joint of the forefinger. The position of the hands and loops is the same as in the ergonomically good grip, i.e. the fingertips of both hands and the loops are near the tips of the knitting needles, so that the fingers only have to move small distances. When knitters purl and plain, they commonly pick up the yarn from the back of the knitting needle in the same way as when knitting. While researching the common features of working grips I have learned what abnormal grips are like. Although I recognized many different ways to knit, all the peculiar grips were modifications of the continental way of knitting. The results of this study give a clear picture of those points knitters should focus their attention on in order to gain a good hold of the needles.

Dynamic Bayesian network inferencing for non-homogeneous complex systems

Dynamic Bayesian Networks (DBNs) provide a versatile platform for predicting and analysing the behaviour of complex systems. As such, they are well suited to the prediction of complex ecosystem population trajectories under anthropogenic disturbances such as the dredging of marine seagrass ecosystems. However, DBNs assume a homogeneous Markov chain whereas a key characteristics of complex ecosystems is the presence of feedback loops, path dependencies and regime changes whereby the behaviour of the system can vary based on past states. This paper develops a method based on the small world structure of complex systems networks to modularise a non-homogeneous DBN and enable the computation of posterior marginal probabilities given evidence in forwards inference. It also provides an approach for an approximate solution for backwards inference as convergence is not guaranteed for a path dependent system. When applied to the seagrass dredging problem, the incorporation of path dependency can implement conditional absorption and allows release from the zero state in line with environmental and ecological observations. As dredging has a marked global impact on seagrass and other marine ecosystems of high environmental and economic value, using such a complex systems model to develop practical ways to meet the needs of conservation and industry through enhancing resistance and/or recovery is of paramount importance.

Microbial life and deposits in paper machine circuits

Väitöskirjani käsittele mikrobien ja erilaisten kemikaalien rooleja saostumien ja biofilmien muodostumisessa paperi- ja kartonkikoneilla. "Saostuma" tässä työssä tarkoittaa kiinteän aineen kertymää konepinnoille tai rajapinnoille konekierroissa, jotka on tarkoitettu massasulppujen, lietteiden, vesien tai ilman kuljetukseen. Saostumasta tulee "biofilmi" silloin kun sen oleellinen rakennekomponentti on mikrobisolut tai niiden tuotteet. Väitöstyöni työhypoteesina oli, että i. tietämys saostumien koostumuksesta, sekä ii. niiden rakenteesta, biologisista, fysikaalis-kemiallisista ja teknisistä ominaisuuksista ohjaavat tutkijaa löytämään ympäristöä säästäviä keinoja estää epätoivottujen saostumien muodostus tai purkaa jo muodostuneita saostumia. Selvittääkseni saostumien koostumista ja rakennetta käytin monia erilaisia analytiikan työkaluja, kuten elektronimikroskopiaa, konfokaali-laser mikroskopiaa (CLSM), energiadispersiivistä röntgenanalyysiä (EDX), pyrolyysi kaasukromatografiaa yhdistettynä massaspektrometriaan (Py-GCMS), joninvaihtokromatografiaa, kaasukromatografiaa ja mikrobiologisia analyysejä. Osallistuin aktiivisesti innovatiivisen, valon takaisinsirontaan perustuvan sensorin kehittämistyöhön, käytettäväksi biofilmin kasvun mittaukseen suoraan koneen vesikierroista ja säiliöistä. Työni osoitti, että monet paperinvalmistuksessa käytetyistä kemikaaleista reagoivat keskenään tuottaen orgaanisia tahmakerroksia konekiertojen teräspinnoille. Löysin myös kerrostumia, jotka valomikroskooppisessa tarkastelussa oli tulkittu mikrobeiksi, mutta jotka elektronimikroskopia paljasti alunasta syntyneiksi, alumiinihydroksidiksi joka saostui pH:ssa 6,8 kiertokuitua käyttävän koneen viiravesistä. Monet paperintekijät käyttävät vieläkin alunaa kiinnitysaineena vaikka prosessiolot ovat muuttuneet happamista neutraaleiksi. Sitä pidetään paperitekijän "aspiriinina", mutta väitöstutkimukseni osoitti sen riskit. Löysin myös orgaanisia saostumia, joiden alkuperä oli aineiden, kuten pihkan, saippuoituminen (kalsium saippuat) niin että muodostui tahmankasvua ylläpitävä alusta monilla paperi- ja kartonkikoneilla. Näin solumuodoiltaan Deinococcus geothermalista muistuttavia bakteereita kasvamassa lujasti teräskoepalojen pintaan kiinnittyneinä pesäkkeinä, kun koepaloja upotettiin paperikoneiden vesikiertoihin. Nämä deinokokkimaiset pesäkkeet voivat toimia jalustana, tarttumisalustana muiden mikrobien massoille, joka selittäisi miksi saostumat yleisesti sisältävät deinokokkeja pienenä, muttei koskaan pääasiallisena rakenneosana. Kun paperikoneiden käyttämien vesien (raakavedet, lämminvesi, biologisesti puhdistettu jätevesi) laatua tutkitaan, mittausmenetelmällä on suuri merkitys. Koepalan upotusmenetelmällä todettu biofilmikasvu ja viljelmenetelmällä mitattu bakteerisaastuneisuus korreloivat toisiinsa huonosti etenkin silloin kun likaantumisessa oli mukana rihmamaiseti kasvavia bakteereja. Huoli ympäristöstä on pakottanut paperi- ja kartonkikoneiden vesikiertojen sulkemiseen. Vesien kierrätys ja prosessivesien uudelleenkäyttö nostavat prosessilämpötilaa ja lisäävät koneella kiertävien kolloidisten ja liuenneiden aineiden määriä. Tutkin kiertovesien pitoisuuksia kolmessa eriasteisesti suljetussa tehtaassa, joiden päästöt olivat 0 m3, 0,5 m3 ja 4 m3 jätevettä tuotetonnia kohden, perustuen puhdistetun jäteveden uudelleen käyttöön. Nollapäästöisellä tehtaalla kiertovesiin kertyi paljon orgaanisesti sidottua hiiltä (> 10 g L-1), etenkin haihtuvina happoina (maito-, etikka-, propioni- ja voi-). Myös sulfaatteja, klorideja, natriumia ja kalsiumia kertyi paljon, > 1 g L-1 kutakin. Pääosa (>40%) kaikista bakteereista oli 16S rRNA geenisekvenssianalyysien tulosten perusteella sukua, joskin etäistä (< 96%) ainoastaan Enterococcus cecorum bakteerille. 4 m3 päästävältä tehtaalta löytyi lisäksi Bacillus thermoamylovorans ja Bacillus coagulans. Tehtaiden saostumat sisälsivät arkkeja suurina pitoisuuksina, ≥ 108 g-1, mutta tunnistukseen riittävää sekvenssisamanlaisuutta löytyi vain yhteen arkkisukuun, Methanothrix. Tutkimustulokset osoittivat että tehtaan vesikiertojen sulkeminen vähensi rajusti mikrobiston monimuotoisuutta, muttei estänyt liuenneen aineen ja kiintoaineen mineralisoitumista.

Single network adaptive critic design for power system stabilisers

The recently developed single network adaptive critic (SNAC) design has been used in this study to design a power system stabiliser (PSS) for enhancing the small-signal stability of power systems over a wide range of operating conditions. PSS design is formulated as a discrete non-linear quadratic regulator problem. SNAC is then used to solve the resulting discrete-time optimal control problem. SNAC uses only a single critic neural network instead of the action-critic dual network architecture of typical adaptive critic designs. SNAC eliminates the iterative training loops between the action and critic networks and greatly simplifies the training procedure. The performance of the proposed PSS has been tested on a single machine infinite bus test system for various system and loading conditions. The proposed stabiliser, which is relatively easier to synthesise, consistently outperformed stabilisers based on conventional lead-lag and linear quadratic regulator designs.

Regularized numerical integration of multibody dynamics with the generalized alpha method*

This paper discusses the consistent regularization property of the generalized α method when applied as an integrator to an initial value high index and singular differential-algebraic equation model of a multibody system. The regularization comes from within the discretization itself and the discretization remains consistent over the range of values the regularization parameter may take. The regularization involves increase of the smallest singular values of the ill-conditioned Jacobian of the discretization and is different from Baumgarte and similar techniques which tend to be inconsistent for poor choice of regularization parameter. This regularization also helps where pre-conditioning the Jacobian by scaling is of limited effect, for example, when the scleronomic constraints contain multiple closed loops or singular configuration or when high index path constraints are present. The feed-forward control in Kane's equation models is additionally considered in the numerical examples to illustrate the effect of regularization. The discretization presented in this work is adopted to the first order DAE system (unlike the original method which is intended for second order systems) for its A-stability and same order of accuracy for positions and velocities.

Senataxin controls meiotic silencing through ATR activation and chromatin remodeling

Senataxin, defective in ataxia oculomotor apraxia type 2, protects the genome by facilitating the resolution of RNA–DNA hybrids (R-loops) and other aspects of RNA processing. Disruption of this gene in mice causes failure of meiotic recombination and defective meiotic sex chromosome inactivation, leading to male infertility. Here we provide evidence that the disruption of Setx leads to reduced SUMOylation and disruption of protein localization across the XY body during meiosis. We demonstrate that senataxin and other DNA damage repair proteins, including ataxia telangiectasia and Rad3-related protein-interacting partner, are SUMOylated, and a marked downregulation of both ataxia telangiectasia and Rad3-related protein-interacting partner and TopBP1 leading to defective activation and signaling through ataxia telangiectasia and Rad3-related protein occurs in the absence of senataxin. Furthermore, chromodomain helicase DNA-binding protein 4, a component of the nucleosome remodeling and deacetylase chromatin remodeler that interacts with both ataxia telangiectasia and Rad3-related protein and senataxin was not recruited efficiently to the XY body, triggering altered histone acetylation and chromatin conformation in Setx−/− pachytene-staged spermatocytes. These results demonstrate that senataxin has a critical role in ataxia telangiectasia and Rad3-related protein- and chromodomain helicase DNA-binding protein 4-mediated transcriptional silencing and chromatin remodeling during meiosis providing greater insight into its critical role in gene regulation to protect against neurodegeneration.

Ferroelectricity in lithium potassium sulphate

. Measurement of the relation between polarisation P and electric field E for lithium potassium sulphate (LiKSO4) was made in the low temperature range below room temperature. The P-E hysteresis loops along the c axis of LiKSO4 were observed in the low-temperature phase below the lower transition point Ttl of about -70 degrees C, and in the intermediate phase below the upper transition point Ttu of about -25 degrees C. These phases were found to be ferroelectric. The temperature dependence of the spontaneous polarisation Ps and the electric coercive field Ec were obtained.

Partial Integrated Guidance and Control of Surface-to-Air Interceptors for High Speed Targets

An important limitation of the existing IGC algorithms, is that they do not explicitly exploit the inherent time scale separation that exist in aerospace vehicles between rotational and translational motions and hence can be ineffective. To address this issue, a two-loop partial integrated guidance and control (PIGC) scheme has been proposed in this paper. In this design, the outer loop uses a recently developed, computationally efficient, optimal control formulation named as model predictive static programming. It gives the commanded pitch and yaw rates whereas necessary roll-rate command is generated from a roll-stabilization loop. The inner loop tracks the outer loop commands using the Dynamic inversion philosophy. Uncommonly, Six-Degree of freedom (Six-DOF) model is used directly in both the loops. This intelligent manipulation preserves the inherent time scale separation property between the translational and rotational dynamics, and hence overcomes the deficiency of current IGC designs, while preserving its benefits. Comparative studies of PIGC with one loop IGC and conventional three loop design were carried out for engaging incoming high speed target. Simulation studies demonstrate the usefulness of this method.

Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

CXCL-8 (Interleukin 8) is a CXC chemokine with a central role in the human immune response. We have undertaken extensive in silico analyses to elucidate the interactions of CXCL-8 with its various binding partners, which are crucial for its biological function. Sequence and structure analyses showed that residues in the thirdq β-sheet and basic residues in the heparin binding site are highly variable, while residues in the second β-sheet are highly conserved. Molecular dynamics simulations in aqueous solution of dimeric CXCL-8 have been performed with starting geometries from both X-ray and NMR structures showed shearing movements between the two antiparallel C-terminal helices. Dynamic conservation analyses of these simulations agreed with experimental data indicating that structural differences between the two structures at quaternary level arise from changes in the secondary structure of the N-terminal loop, the 310-helix, the 30s, 40s, and 50s loops and the third β-sheet, resulting in a different interhelical separation. Nevertheless, the observation of these different states indicates that CXCL-8 has the potential to undergo conformational changes, and it seems likely that this feature is relevant to the mode of binding of glycosaminoglycan (GAG) mimetics such as cyclitols. Simulations of the receptor peptide fragment−CXCL-8 complex identified several specific interactions of the receptor peptide with CXCL-8 that could be exploited in the structure-based design of competitive peptides and nonpeptidic molecules targeting CXCL-8 for combating inflammatory diseases. Simulations of the CXCL-8 dimer complexed with a 24-mer heparin fragment and of the CXCL-8−receptor peptide complex revealed that Arg60, Lys64, and Arg68 in the dimer bind to cyclitols in a horseshoe pattern, defining a region which is spatially distinct from the receptor binding site. There appears to be an optimum number of sulfates and an optimum length of alkyl spacers required for the interaction of cyclitol inhibitors with the dimeric form of CXCL-8. Calculation of the binding affinities of cyclitol inhibitors reflected satisfactorily the ranking of experimentally determined inhibitory potencies. The findings of these molecular modeling studies will help in the search for inhibitors which can modulate various CXCL-8 biological activities and serve as an excellent model system to study CXC-inhibitor interactions.

Substrate Selectivity and Molecular Adaptation in the Outer Membrane Proteases of Yersinia pestis and Salmonella enterica

Proteolysis is important in bacterial pathogenesis and colonization of animal and plant hosts. In this work I have investigated the functions of the bacterial outer membrane proteases, omptins, of Yersinia pestis and Salmonella enterica. Y. pestis is a zoonotic pathogen that causes plague and has evolved from gastroenteritis-causing Yersinia pseudotuberculosis about 13 000 years ago. S. enterica causes gastroenteritis and typhoid fever in humans. Omptins are transmembrane β-barrels with ten antiparallel β-strands and five surface-exposed loops. The loops are important in substrate recognition, and variation in the loop sequences leads to different substrate selectivities between omptins, which makes omptins an ideal platform to investigate functional adaptation and to alter their polypeptide substrate preferences. The omptins Pla of Y. pestis and PgtE of S. enterica are 75% identical in their amino acid sequences. Pla is a multifunctional protein with proteolytic and non-proteolytic functions, and it increases bacterial penetration and proliferation in the host. Functions of PgtE increase migration of S. enterica in vivo and bacterial survival in mouse macrophages, thus enhancing bacterial spread within the host. Mammalian plasminogen/fibrinolytic system maintains the balance between coagulation and fibrinolysis and participates in several cellular processes, e.g., cell migration and degradation of extracellular matrix proteins. This system consists of activation cascades, which are strictly controlled by several regulators, such as plasminogen activator inhibitor 1 (PAI-1), α2-antiplasmin (α2AP), and thrombin-activatable fibrinolysis inhibitor (TAFI). This work reveals novel interactions of the omptins of Y. pestis and S. enterica with the regulators of the plasminogen/fibrinolytic system: Pla and PgtE inactivate PAI-1 by cleavage at the reactive site peptide bond, and degrade TAFI, preventing its activation to TAFIa. Structure-function relationship studies with Pla showed that threonine 259 of Pla is crucial in plasminogen activation, as it prevents degradation of the plasmin catalytic domain by the omptin and thus maintains plasmin stability. In this work I constructed chimeric proteins between Pla and Epo of Erwinia pyrifoliae that share 78% sequence identity to find out which amino acids and regions in Pla are important for its functions. Epo is neither a plasminogen activator nor an invasin, but it degrades α2AP and PAI-1. Cumulative substitutions towards Pla sequence turned Epo into a Pla-like protein. In addition to threonine 259, loops 3 and 5 are critical in plasminogen activation by Pla. Turning Epo into an invasin required substitution of 31 residues located at the extracellular side of the Epo protein above the lipid bilayer, and also of the β1-strand in the N-terminal transmembrane region of the protein. These studies give an example of how omptins adapt to novel functions that advantage their host bacteria in different ecological niches.

Outer Membrane Protease/Adhesin PgtE of Salmonella enterica: Role in Salmonella-Host Interaction

Salmonella enterica serovar Typhimurium is a common cause of gastroenteritis in humans and, occasionally, also causes systemic infection. During systemic infection an important characteristic of Salmonella is its ability to survive and replicate within macrophages. The outer membrane protease PgtE of S. enterica is a member of the omptin family of outer membrane aspartate proteases, which are beta-barrel proteins with five surface-exposed loops. The main goals of this study were to characterize biological substrates and pathogenesis-associated functions of PgtE and to determine the conditions where PgtE is fully active. In this study we found that PgtE requires rough lipopolysaccharide (LPS) to be functional but is sterically inhibited by the long O-antigen side chain in smooth LPS. Salmonella isolates normally are smooth with a long oligosaccharide O-antigen, and PgtE remains functionally cryptic in wild-type Salmonella cultivated in vitro. Interestingly, our results showed that due to increased expression of PgtE and to reduced length of the LPS O-antigen chains, the wild-type Salmonella expresses highly functional PgtE when isolated from mouse macrophage-like J774A.1 cells. Salmonella is thought to be continuously released from macrophages to infect new ones, and our results suggest that PgtE is functional during these transient extracellular growth phases. Six novel host protein substrates were identified for PgtE in this work. PgtE was previously known to activate human plasminogen (Plg) to plasmin, a broad-spectrum serine protease, and in this study PgtE was shown to interfere with the Plg system by inactivating the main inhibitor of plasmin, alpha2-antiplasmin. PgtE also interferes with another important proteolytic system of mammals by activating pro-matrix metalloproteinase-9 to an active gelatinase. PgtE also directly degrades gelatin, a component of extracellular matrices. PgtE also increases bacterial resistance against complement-mediated killing in human serum and enhances survival of Salmonella within murine macrophages as well as in the liver and spleen of intraperitoneally infected mice. Taken together, the results in this study suggest that PgtE is a virulence factor of Salmonella that has adapted to interfere with host proteolytic systems and to modify extracellular matrix; these features likely assist the migration of Salmonella during systemic salmonellosis.