Bernhard Bardach Collection Album Album

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Movement-associated proteins of Potato virus A: attachment to virus particles and phosphorylation

The particles of Potato virus A (PVA; genus Potyvirus) are helically constructed filaments that contain multiple copies of a single type of coat-protein (CP) subunit and a single copy of genome-linked protein (VPg), attached to one end of the virion. Examination of negatively-stained virions by electron microscopy revealed flexuous, rod-shaped particles with no obvious terminal structures. It is known that particles of several filamentous plant viruses incorporate additional minor protein components, forming stable complexes that mediate particle disassembly, movement or transmission by insect vectors. The first objective of this work was to study the interaction of PVA movement-associated proteins with virus particles and how these interactions contribute to the morphology and function of the virus particles. Purified particles of PVA were examined by atomic force microscopy (AFM) and immuno-gold electron microscopy. A protrusion was found at one end of some of the potyvirus particles, associated with the 5' end of the viral RNA. The tip contained two virus-encoded proteins, the genome-linked protein (VPg) and the helper-component proteinase (HC-Pro). Both are required for cell-to-cell movement of the virus. Biochemical and electron microscopy studies of purified PVA samples also revealed the presence of another protein required for cell-to-cell movement the cylindrical inclusion protein (CI), which is also an RNA helicase/ATPase. Centrifugation through a 5-40% sucrose gradient separated virus particles with no detectable CI to a fraction that remained in the gradient, from the CI-associated particles that went to the pellet. Both types of particles were infectious. AFM and translation experiments demonstrated that when the viral CI was not present in the sample, PVA virions had a beads-on-a-string phenotype, and RNA within the virus particles was more accessible to translation. The second objective of this work was to study phosphorylation of PVA movement-associated and structural proteins (CP and VPg) in vitro and, if possible, in vivo. PVA virion structural protein CP is necessary for virus cell-to-cell movement. The tobacco protein kinase CK2 was identified as a kinase phosphorylating PVA CP. A major site of CK2 phosphorylation in PVA CP was identified as a single threonine within a CK2 consensus sequence. Amino acid substitutions affecting the CK2 consensus sequence in CP resulted in viruses that were defective in cell-to-cell and long-distance movement. The CK2 regulation of virion assembly and cell-to-cell movement by phosphorylation of CP was possibly due to the inhibition of CP binding to viral RNA. Four putative phosphorylation sites were identified from an in vitro phosphorylated recombinant VPg. All four were mutated and the spread of mutant viruses in two different host plants was studied. Two putative phosphorylation site mutants (Thr45 and Thr49) had phenotypes identical to that of a wild type (WT) virus infection in both Nicotiana benthamiana and N. tabacum plants. The other two mutant viruses (Thr132/Ser133 and Thr168) showed different phenotypes with increased or decreased accumulation rates, respectively, in inoculated and the first two systemically infected leaves of N. benthamiana. The same mutants were occasionally restricted to single cells in N. tabacum plants, suggesting the importance of these amino acids in the PVA infection cycle in N. tabacum.

Noncommutative Gravitation as a Gauge Theory of Twisted Poincaré Symmetry

Gravitaation kvanttiteorian muotoilu on ollut teoreettisten fyysikkojen tavoitteena kvanttimekaniikan synnystä lähtien. Kvanttimekaniikan soveltaminen korkean energian ilmiöihin yleisen suhteellisuusteorian viitekehyksessä johtaa aika-avaruuden koordinaattien operatiiviseen ei-kommutoivuuteen. Ei-kommutoivia aika-avaruuden geometrioita tavataan myös avointen säikeiden säieteorioiden tietyillä matalan energian rajoilla. Ei-kommutoivan aika-avaruuden gravitaatioteoria voisi olla yhteensopiva kvanttimekaniikan kanssa ja se voisi mahdollistaa erittäin lyhyiden etäisyyksien ja korkeiden energioiden prosessien ei-lokaaliksi uskotun fysiikan kuvauksen, sekä tuottaa yleisen suhteellisuusteorian kanssa yhtenevän teorian pitkillä etäisyyksillä. Tässä työssä tarkastelen gravitaatiota Poincarén symmetrian mittakenttäteoriana ja pyrin yleistämään tämän näkemyksen ei-kommutoiviin aika-avaruuksiin. Ensin esittelen Poincarén symmetrian keskeisen roolin relativistisessa fysiikassa ja sen kuinka klassinen gravitaatioteoria johdetaan Poincarén symmetrian mittakenttäteoriana kommutoivassa aika-avaruudessa. Jatkan esittelemällä ei-kommutoivan aika-avaruuden ja kvanttikenttäteorian muotoilun ei-kommutoivassa aika-avaruudessa. Mittasymmetrioiden lokaalin luonteen vuoksi tarkastelen huolellisesti mittakenttäteorioiden muotoilua ei-kommutoivassa aika-avaruudessa. Erityistä huomiota kiinnitetään näiden teorioiden vääristyneeseen Poincarén symmetriaan, joka on ei-kommutoivan aika-avaruuden omaama uudentyyppinen kvanttisymmetria. Seuraavaksi tarkastelen ei-kommutoivan gravitaatioteorian muotoilun ongelmia ja niihin kirjallisuudessa esitettyjä ratkaisuehdotuksia. Selitän kuinka kaikissa tähänastisissa lähestymistavoissa epäonnistutaan muotoilla kovarianssi yleisten koordinaattimunnosten suhteen, joka on yleisen suhteellisuusteorian kulmakivi. Lopuksi tutkin mahdollisuutta yleistää vääristynyt Poincarén symmetria lokaaliksi mittasymmetriaksi --- gravitaation ei-kommutoivan mittakenttäteorian saavuttamisen toivossa. Osoitan, että tällaista yleistystä ei voida saavuttaa vääristämällä Poincarén symmetriaa kovariantilla twist-elementillä. Näin ollen ei-kommutoivan gravitaation ja vääristyneen Poincarén symmetrian tutkimuksessa tulee jatkossa keskittyä muihin lähestymistapoihin.

Noncommutativity and Some of Its Present-Day Developments

This masters thesis explores some of the most recent developments in noncommutative quantum field theory. This old theme, first suggested by Heisenberg in the late 1940s, has had a renaissance during the last decade due to the firmly held belief that space-time becomes noncommutative at small distances and also due to the discovery that string theory in a background field gives rise to noncommutative field theory as an effective low energy limit. This has led to interesting attempts to create a noncommutative standard model, a noncommutative minimal supersymmetric standard model, noncommutative gravity theories etc. This thesis reviews themes and problems like those of UV/IR mixing, charge quantization, how to deal with the non-commutative symmetries, how to solve the Seiberg-Witten map, its connection to fluid mechanics and the problem of constructing general coordinate transformations to obtain a theory of noncommutative gravity. An emphasis has been put on presenting both the group theoretical results and the string theoretical ones, so that a comparison of the two can be made.

The Spin-Statistics Relation and Noncommutative Quantum Field Theory

The efforts of combining quantum theory with general relativity have been great and marked by several successes. One field where progress has lately been made is the study of noncommutative quantum field theories that arise as a low energy limit in certain string theories. The idea of noncommutativity comes naturally when combining these two extremes and has profound implications on results widely accepted in traditional, commutative, theories. In this work I review the status of one of the most important connections in physics, the spin-statistics relation. The relation is deeply ingrained in our reality in that it gives us the structure for the periodic table and is of crucial importance for the stability of all matter. The dramatic effects of noncommutativity of space-time coordinates, mainly the loss of Lorentz invariance, call the spin-statistics relation into question. The spin-statistics theorem is first presented in its traditional setting, giving a clarifying proof starting from minimal requirements. Next the notion of noncommutativity is introduced and its implications studied. The discussion is essentially based on twisted Poincaré symmetry, the space-time symmetry of noncommutative quantum field theory. The controversial issue of microcausality in noncommutative quantum field theory is settled by showing for the first time that the light wedge microcausality condition is compatible with the twisted Poincaré symmetry. The spin-statistics relation is considered both from the point of view of braided statistics, and in the traditional Lagrangian formulation of Pauli, with the conclusion that Pauli's age-old theorem stands even this test so dramatic for the whole structure of space-time.

On the Geometry of Infinite-Dimensional Grassmannian Manifolds and Gauge Theory

This PhD Thesis is about certain infinite-dimensional Grassmannian manifolds that arise naturally in geometry, representation theory and mathematical physics. From the physics point of view one encounters these infinite-dimensional manifolds when trying to understand the second quantization of fermions. The many particle Hilbert space of the second quantized fermions is called the fermionic Fock space. A typical element of the fermionic Fock space can be thought to be a linear combination of the configurations m particles and n anti-particles . Geometrically the fermionic Fock space can be constructed as holomorphic sections of a certain (dual)determinant line bundle lying over the so called restricted Grassmannian manifold, which is a typical example of an infinite-dimensional Grassmannian manifold one encounters in QFT. The construction should be compared with its well-known finite-dimensional analogue, where one realizes an exterior power of a finite-dimensional vector space as the space of holomorphic sections of a determinant line bundle lying over a finite-dimensional Grassmannian manifold. The connection with infinite-dimensional representation theory stems from the fact that the restricted Grassmannian manifold is an infinite-dimensional homogeneous (Kähler) manifold, i.e. it is of the form G/H where G is a certain infinite-dimensional Lie group and H its subgroup. A central extension of G acts on the total space of the dual determinant line bundle and also on the space its holomorphic sections; thus G admits a (projective) representation on the fermionic Fock space. This construction also induces the so called basic representation for loop groups (of compact groups), which in turn are vitally important in string theory / conformal field theory. The Thesis consists of three chapters: the first chapter is an introduction to the backround material and the other two chapters are individually written research articles. The first article deals in a new way with the well-known question in Yang-Mills theory, when can one lift the action of the gauge transformation group on the space of connection one forms to the total space of the Fock bundle in a compatible way with the second quantized Dirac operator. In general there is an obstruction to this (called the Mickelsson-Faddeev anomaly) and various geometric interpretations for this anomaly, using such things as group extensions and bundle gerbes, have been given earlier. In this work we give a new geometric interpretation for the Faddeev-Mickelsson anomaly in terms of differentiable gerbes (certain sheaves of categories) and central extensions of Lie groupoids. The second research article deals with the question how to define a Dirac-like operator on the restricted Grassmannian manifold, which is an infinite-dimensional space and hence not in the landscape of standard Dirac operator theory. The construction relies heavily on infinite-dimensional representation theory and one of the most technically demanding challenges is to be able to introduce proper normal orderings for certain infinite sums of operators in such a way that all divergences will disappear and the infinite sum will make sense as a well-defined operator acting on a suitable Hilbert space of spinors. This research article was motivated by a more extensive ongoing project to construct twisted K-theory classes in Yang-Mills theory via a Dirac-like operator on the restricted Grassmannian manifold.

Some Unique Features of Egg Laying and Reproduction in Ichthyophis Malabarensis (Taylor) (Apoda:Amphibia)

The paper describes egg laying and reproduction in ICHTHYOPHIS MALABARENSIS. 100 eggs, the largest ever in Apoda, are laid in a single string and manipulated by the female into a massive clutch. The reproductive strategies in the species are discussed.

Using Mathematical Morphology for Geometric Music Retrieval

The usual task in music information retrieval (MIR) is to find occurrences of a monophonic query pattern within a music database, which can contain both monophonic and polyphonic content. The so-called query-by-humming systems are a famous instance of content-based MIR. In such a system, the user's hummed query is converted into symbolic form to perform search operations in a similarly encoded database. The symbolic representation (e.g., textual, MIDI or vector data) is typically a quantized and simplified version of the sampled audio data, yielding to faster search algorithms and space requirements that can be met in real-life situations. In this thesis, we investigate geometric approaches to MIR. We first study some musicological properties often needed in MIR algorithms, and then give a literature review on traditional (e.g., string-matching-based) MIR algorithms and novel techniques based on geometry. We also introduce some concepts from digital image processing, namely the mathematical morphology, which we will use to develop and implement four algorithms for geometric music retrieval. The symbolic representation in the case of our algorithms is a binary 2-D image. We use various morphological pre- and post-processing operations on the query and the database images to perform template matching / pattern recognition for the images. The algorithms are basically extensions to classic image correlation and hit-or-miss transformation techniques used widely in template matching applications. They aim to be a future extension to the retrieval engine of C-BRAHMS, which is a research project of the Department of Computer Science at University of Helsinki.

Application of optimization methods to vibration control of stretched strings

In this paper, non-linear programming techniques are applied to the problem of controlling the vibration pattern of a stretched string. First, the problem of finding the magnitudes of two control forces applied at two points l1 and l2 on the string to reduce the energy of vibration over the interval (l1, l2) relative to the energy outside the interval (l1, l2) is considered. For this problem the relative merits of various methods of non-linear programming are compared. The more complicated problem of finding the positions and magnitudes of two control forces to obtain the desired energy pattern is then solved by using the slack unconstrained minimization technique with the Fletcher-Powell search. In the discussion of the results it is shown that the position of the control force is very important in controlling the energy pattern of the string.

Automated feature engineering for HTTP tunnel detection

Generating discriminative input features is a key requirement for achieving highly accurate classifiers. The process of generating features from raw data is known as feature engineering and it can take significant manual effort. In this paper we propose automated feature engineering to derive a suite of additional features from a given set of basic features with the aim of both improving classifier accuracy through discriminative features, and to assist data scientists through automation. Our implementation is specific to HTTP computer network traffic. To measure the effectiveness of our proposal, we compare the performance of a supervised machine learning classifier built with automated feature engineering versus one using human-guided features. The classifier addresses a problem in computer network security, namely the detection of HTTP tunnels. We use Bro to process network traffic into base features and then apply automated feature engineering to calculate a larger set of derived features. The derived features are calculated without favour to any base feature and include entropy, length and N-grams for all string features, and counts and averages over time for all numeric features. Feature selection is then used to find the most relevant subset of these features. Testing showed that both classifiers achieved a detection rate above 99.93% at a false positive rate below 0.01%. For our datasets, we conclude that automated feature engineering can provide the advantages of increasing classifier development speed and reducing development technical difficulties through the removal of manual feature engineering. These are achieved while also maintaining classification accuracy.

Giant magnons in the D1-D5 system

We study giant magnons in the the D1-D5 system from both the boundary CFT and as classical solutions of the string sigma model in AdS(3) x S-3 x T-4. Re-examining earlier studies of the symmetric product conformal field theory we argue that giant magnons in the symmetric product are BPS states in a centrally extended SU(1 vertical bar 1) x SU(1 vertical bar 1) superalgebra with two more additional central charges. The magnons carry these additional central charges locally but globally they vanish. Using a spin chain description of these magnons and the extended superalgebra we show that these magnons obey a dispersion relation which is periodic in momentum. We then identify these states on the string theory side and show that here too they are BPS in the same centrally extended algebra and obey the same dispersion relation which is periodic in momentum. This dispersion relation arises as the BPS condition for the extended algebra and is similar to that of magnons in N = 4 Yang-Mills Yang-Mills.

Performance studies on mechanical + adsorption hybrid compression refrigeration cycles with HFC 134a

This paper presents the results of an investigation on the efficacy of hybrid compression process for refrigerant HFC 134a in cooling applications. The conventional mechanical compression is supplemented by thermal compression using a string of adsorption compressors. Activated carbon is the adsorbent for the thermal compression segment. The alternatives of bottoming either mechanical or thermal compression stages are investigated. It is shown that almost 40% energy saving is realizable by carrying out a part of the compression in a thermal compressor compared to the case when the entire compression is carried out in a single-stage mechanical compressor. The hybrid compression is feasible even when low grade heat is available. Some performance indictors are defined and evaluated for various configurations.

On gravitational fields of stars in f(R) gravity theories

Einstein's general relativity is a classical theory of gravitation: it is a postulate on the coupling between the four-dimensional, continuos spacetime and the matter fields in the universe, and it yields their dynamical evolution. It is believed that general relativity must be replaced by a quantum theory of gravity at least at extremely high energies of the early universe and at regions of strong curvature of spacetime, cf. black holes. Various attempts to quantize gravity, including conceptually new models such as string theory, have suggested that modification to general relativity might show up even at lower energy scales. On the other hand, also the late time acceleration of the expansion of the universe, known as the dark energy problem, might originate from new gravitational physics. Thus, although there has been no direct experimental evidence contradicting general relativity so far - on the contrary, it has passed a variety of observational tests - it is a question worth asking, why should the effective theory of gravity be of the exact form of general relativity? If general relativity is modified, how do the predictions of the theory change? Furthermore, how far can we go with the changes before we are face with contradictions with the experiments? Along with the changes, could there be new phenomena, which we could measure to find hints of the form of the quantum theory of gravity? This thesis is on a class of modified gravity theories called f(R) models, and in particular on the effects of changing the theory of gravity on stellar solutions. It is discussed how experimental constraints from the measurements in the Solar System restrict the form of f(R) theories. Moreover, it is shown that models, which do not differ from general relativity at the weak field scale of the Solar System, can produce very different predictions for dense stars like neutron stars. Due to the nature of f(R) models, the role of independent connection of the spacetime is emphasized throughout the thesis.

Applications of Gauge/Gravity Duality to QCD and Heavy Ion Collisions

The description of quarks and gluons, using the theory of quantum chromodynamics (QCD), has been known for a long time. Nevertheless, many fundamental questions in QCD remain unanswered. This is mainly due to problems in solving the theory at low energies, where the theory is strongly interacting. AdS/CFT is a duality between a specific string theory and a conformal field theory. Duality provides new tools to solve the conformal field theory in the strong coupling regime. There is also some evidence that using the duality, one can get at least qualitative understanding of how QCD behaves at strong coupling. In this thesis, we try to address some issues related to QCD and heavy ion collisions, applying the duality in various ways.

Quantum Space-Time and Noncommutative Gauge Field Theories

Arguments arising from quantum mechanics and gravitation theory as well as from string theory, indicate that the description of space-time as a continuous manifold is not adequate at very short distances. An important candidate for the description of space-time at such scales is provided by noncommutative space-time where the coordinates are promoted to noncommuting operators. Thus, the study of quantum field theory in noncommutative space-time provides an interesting interface where ordinary field theoretic tools can be used to study the properties of quantum spacetime. The three original publications in this thesis encompass various aspects in the still developing area of noncommutative quantum field theory, ranging from fundamental concepts to model building. One of the key features of noncommutative space-time is the apparent loss of Lorentz invariance that has been addressed in different ways in the literature. One recently developed approach is to eliminate the Lorentz violating effects by integrating over the parameter of noncommutativity. Fundamental properties of such theories are investigated in this thesis. Another issue addressed is model building, which is difficult in the noncommutative setting due to severe restrictions on the possible gauge symmetries imposed by the noncommutativity of the space-time. Possible ways to relieve these restrictions are investigated and applied and a noncommutative version of the Minimal Supersymmetric Standard Model is presented. While putting the results obtained in the three original publications into their proper context, the introductory part of this thesis aims to provide an overview of the present situation in the field.