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RSS FeedNMR structural studies of oligosaccharides and other natural products
http://orbit.dtu.dk/en/publications/nmr-structural-studies-of-oligosaccharides-and-other-natural-products(7420df81-3623-497b-825c-09fa6e29c7db).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/nmr-structural-studies-of-oligosaccharides-and-other-natural-products(7420df81-3623-497b-825c-09fa6e29c7db).html"><span>NMR structural studies of oligosaccharides and other natural products</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/louise-kjaerulff(840d3acf-77d5-4323-84ed-14a6ff8aabfc).html"><span>Kjærulff, L.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/charlotte-held-gotfredsen(1cf4df84-2d0e-4693-bf47-e9932e3bf0e3).html"><span>Gotfredsen, C. H.</span></a> <span class="date">2014</span> <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">311 p.</span><p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">NMR spectroscopy is an important tool in chemical analysis and for structural studies in various research areas. The subject of this thesis is liquid state NMR spectroscopy for structural analysis of small molecules, both regarding method development and structure elucidation by NMR spectroscopy.<br />HMBC+ is a new pseudo-3D NMR experiment for measurement of long-range homonuclear JHH coupling constants in small molecules. Based on two existing experiments, multiplicity edited HMBC and HAT HMBC by Benie, Nyberg, and Sørensen, the new HMBC+ experiment takes advantage of a π phase difference with respect to n+1JHH between these two experiments, observed in the nJCH HMBC cross peak. Through a double editing procedure this enables straightforward determination of both sign and magnitude of n+1JHH, including for very small coupling constants. Excellent results were obtained for the natural product strychnine, and 28 n+1JHH coupling constants were determined, of which 10 had not previously been measured due to their small sizes. By comparing to calculated coupling constants, an RMSD of 0.28 Hz was obtained, all coupling constant signs fit with the calculations, and all errors were below 1 Hz, also when comparing the absolute values to experimental coupling constants measured by Carter et al. using 1D 1H NMR on deuterated strychnine analogues. Providing an excellent tool for measurement of long-range JHH with the extra convenience of labeling the coupling constant information to the 13C chemical shift through the nJCH correlation, this experiment has exciting applications for configurational assignment of e.g. carbohydrates and for residual dipolar couplings.<br />Identification of known molecules and discovery of novel molecules are other important applications of NMR spectroscopy. Bacteria and fungi produce secondary metabolites for signaling and competing against other organisms, and these molecules are important in drug discovery due to their inherent biological activities. From a marine Photobacterium (P. halotolerans) we isolated the solonamides and the ngercheumicins, two families of cyclic depsipeptides capable of attenuating virulence in S. aureus by quorum sensing inhibition through the accessory gene regulator agr. This is likely due to their structural similarities with the auto-inducing peptides of S. aureus, controlling quorum sensing in bacterial populations. A filamentous fungus, A. fijiensis, was also investigated for production of novel secondary metabolites, and a new pyranonigrin (E) was isolated and structure elucidated by NMR spectroscopy along with JBIR-74 and decumbenone A, two known metabolites previously isolated from Aspergillus and Penicillium species.<br />Oligosaccharides found in human milk are important for infant nutrition, and a collaborative effort of university and industry partners was aimed at establishing methods for production of human milk oligosaccharides. Two different bioenzymatic methods for production of 3’-sialyllactose were investigated, and a screening of trans-fucosidases enabled the NMR spectroscopic identification of three pNP-fucosylfucopyranosides as major reaction products.</div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>311</td></tr><tr class="status"><th>State</th><td>Published</td></tr></tbody></table></div></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/nmr-structural-studies-of-oligosaccharides-and-other-natural-products(7420df81-3623-497b-825c-09fa6e29c7db).html2013-12-31T23:00:00ZAvailability by Design - A Complementary Approach to Denial-of-Service
http://orbit.dtu.dk/en/publications/availability-by-design--a-complementary-approach-to-denialofservice(d1ea8614-836f-4f8e-a6e8-f594f316aaab).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/availability-by-design--a-complementary-approach-to-denialofservice(d1ea8614-836f-4f8e-a6e8-f594f316aaab).html"><span>Availability by Design - A Complementary Approach to Denial-of-Service</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/roberto-vigo(30a191fc-d2a3-4401-a0d9-41c4ab54de7c).html"><span>Vigo, R.</span></a>, <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/hanne-riis-nielson(44a7d08e-b083-4419-a466-8f4392a7112f).html"><span>Nielson, H. R.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/flemming-nielson(f63ba194-185f-465d-9b2b-1f6ff489bc3d).html"><span>Nielson, F.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">190 p.</span> (DTU Compute PHD-2014; No. 353).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">In computer security, a Denial-of-Service (DoS) attack aims at making a resource unavailable. DoS attacks to systems of public concern occur increasingly and have become infamous on the Internet, where they have targeted major corporations and institutions, thus reaching the general public. There exist various practical techniques to face DoS attacks and mitigate their effects, yet we witness the successfulness of many.<br />The need for a renewed investigation of availability gains in relevance when considering that our life is more and more dominated by Cyber-Physical Systems (CPSs), large-scale network of sensors that interact with the physical environment. CPSs are increasingly exploited in the realisation of critical infrastructure, from the power grid to healthcare, traffic control, and defence applications. Such systems are particularly prone to DoS attacks: in addition to classic communication-based attacks, their components can be subject to physical capture. Moreover, sensors are often powered by batteries, and time-limited unavailability is usually a stage planned to prolong their life span.<br />This dissertation argues that techniques rooted in the theory and practice of programming languages, language-based techniques, offer a unifying framework to deal with the consequences of DoS, thereby encompassing inadvertent and malicious sources of unavailability in a uniform manner.<br />In support to this claim we develop a family of process calculi, the Quality Calculi, where availability considerations are promoted to be first-class object of the language domain. Moreover, these modelling tools are complemented by static analyses that pinpoint where and why unavailability may occur, levering the enhanced expressiveness of the language.<br />The ultimate aim of the framework is to foster the development of systems resilient to DoS by means of a principled design process, in which formal models allow, and verification tools enforce, the production of such robust code.<br /></div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>190</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>353</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/availability-by-design--a-complementary-approach-to-denialofservice(d1ea8614-836f-4f8e-a6e8-f594f316aaab).html2013-12-31T23:00:00ZCUDArray: CUDA-based NumPy
http://orbit.dtu.dk/en/publications/cudarray-cudabased-numpy(1e806793-a31e-4a87-bc14-7d389f0a2d57).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/cudarray-cudabased-numpy(1e806793-a31e-4a87-bc14-7d389f0a2d57).html"><span>CUDArray: CUDA-based NumPy</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/anders-boesen-lindbo-larsen(e16ce50c-66b8-488b-b2bd-36c64f111f76).html"><span>Larsen, A. B. L.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">5 p.</span> (DTU Compute-Technical Report-2014; No. 21).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Report – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">This technical report introduces CUDArray – a CUDA-accelerated subset of the NumPy library. The goal of CUDArray is to combine the ease of development from NumPy with the computational power of Nvidia GPUs in a lightweight and extensible framework. Since the motivation behind CUDArray is to facilitate neural network programming, CUDArray extends NumPy with a neural network submodule. This module has both a CPU and a GPU back-end to allow for experiments without requiring a GPU.</div><div class="scientificreport"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>5</td></tr><tr class="status"><th>State</th><td>Published</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute-Technical Report-2014</td></tr><tr><th>Number</th><td>21</td></tr><tr><th>ISSN (print)</th><td>1601-2321</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/cudarray-cudabased-numpy(1e806793-a31e-4a87-bc14-7d389f0a2d57).html2013-12-31T23:00:00ZAn algebraic approach to graph codes
http://orbit.dtu.dk/en/publications/an-algebraic-approach-to-graph-codes(bb4e0715-71b9-406f-bf7e-84ccf1441b87).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/an-algebraic-approach-to-graph-codes(bb4e0715-71b9-406f-bf7e-84ccf1441b87).html"><span>An algebraic approach to graph codes</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/fernando-pinero(3f66e5f4-861e-4384-89ad-fddfc12127a2).html"><span>Pinero, F.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/peter-beelen(da3e5b30-4aed-4f4f-9e17-3fda35fb6788).html"><span>Beelen, P.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">94 p.</span> (DTU Compute PHD-2014; No. 352).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">This thesis consists of six chapters. The first chapter, contains a short introduction to coding theory in which we explain the coding theory concepts we use. In the second chapter, we present the required theory for evaluation codes and also give an example of some fundamental codes in coding theory as evaluation codes. Chapter three consists of the introduction to graph based codes, such as Tanner codes and graph codes. In Chapter four, we compute the dimension of some graph based codes with a result combining graph based codes and subfield subcodes. Moreover, some codes in chapter four are optimal or best known for their parameters. In chapter five we study some graph codes with Reed–Solomon component codes. The underlying graph is well known and widely used for its good characteristics. This helps us to compute the dimension of the graph codes. We also introduce a combinatorial concept related to the iterative encoding of graph codes with MDS component code. The last chapter deals with affine Grassmann codes and Grassmann codes. We begin with some previously known codes and prove that they are also Tanner codes of the incidence graph of the point–line partial geometry of the Grassmannian. We expect that the techniques exposed in chapter six are also applicable to other codes as well.</div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>94</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>352</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/an-algebraic-approach-to-graph-codes(bb4e0715-71b9-406f-bf7e-84ccf1441b87).html2013-12-31T23:00:00ZOn the use of functional calculus for phase-type and related distributions
http://orbit.dtu.dk/en/publications/on-the-use-of-functional-calculus-for-phasetype-and-related-distributions(6a1a9683-151c-46f9-9f89-d5ca1ac9ca47).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/on-the-use-of-functional-calculus-for-phasetype-and-related-distributions(6a1a9683-151c-46f9-9f89-d5ca1ac9ca47).html"><span>On the use of functional calculus for phase-type and related distributions</span></a></h2>Bladt, M., Campillo Navarro, A. & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/bo-friis-nielsen(364b98b5-e608-4186-a566-62fa91a37d59).html"><span>Nielsen, B. F.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">25 p.</span> (DTU Compute-Technical Report-2014; No. 18).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Report – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">The area of phase-type distributions is renowned for its ability to obtain closed form formulas or algorithmically exact solutions to many complex stochastic models. The method of functional calculus will provide an additional tool along these lines for establishing results in terms of functions of matrices. Functional calculus, which is a branch of operator theory frequently associated with complex analysis, can be applied to phase-type and matrix-exponential distributions in a rather straightforward way. In this paper we provide a number of examples on how to execute the formal arguments.<br /></div><div class="scientificreport"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>25</td></tr><tr class="status"><th>State</th><td>Published</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute-Technical Report-2014</td></tr><tr><th>Number</th><td>18</td></tr><tr><th>ISSN (print)</th><td>1601-2321</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/on-the-use-of-functional-calculus-for-phasetype-and-related-distributions(6a1a9683-151c-46f9-9f89-d5ca1ac9ca47).html2013-12-31T23:00:00ZCombined Shape and Topology Optimization
http://orbit.dtu.dk/en/publications/combined-shape-and-topology-optimization(7b49dbcb-17e4-425c-8ca8-a1553f95b884).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/combined-shape-and-topology-optimization(7b49dbcb-17e4-425c-8ca8-a1553f95b884).html"><span>Combined Shape and Topology Optimization</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/asger-nyman-christiansen(d2eae353-75aa-49dd-b0dd-6e91b18610e9).html"><span>Christiansen, A. N.</span></a>, <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/jakob-andreas-baerentzen(f0d1a57d-f173-4c59-87ad-b554b3678a8c).html"><span>Bærentzen, J. A.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/ole-sigmund(cefe1d93-608f-4ebc-823e-e776210cc1e1).html"><span>Sigmund, O.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">131 p.</span> (DTU Compute PHD-2014; No. 350).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">Shape and topology optimization seeks to compute the optimal shape and topology of a structure such that one or more properties, for example stiffness, balance or volume, are improved. The goal of the thesis is to develop a method for shape and topology optimization which uses the Deformable Simplicial Complex (DSC) method. Consequently, we present a novel method which combines current shape and topology optimization methods. This method represents the surface of the structure explicitly and discretizes the structure into non-overlapping elements, i.e. a simplicial complex. An explicit surface representation usually limits the optimization to minor shape changes. However, the DSC method uses a single explicit representation and still allows for large shape and topology changes. It does so by constantly applying a set of mesh operations during deformations of the structure. Using an explicit instead of an implicit representation gives rise to several advantages including straightforward modeling of the surface, improved scalability and ability to optimize multiple materials. <br /><br />This dissertation describes the essential parts of the novel method for combined shape and topology optimization. This includes the structural analysis in Chapter 2, the optimization in Chapter 3 and the Deformable Simplicial Complex method in Chapter 4. Finally, four applications of the developed method are presented in the included papers and summarized in Chapter 5.</div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>131</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>350</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/combined-shape-and-topology-optimization(7b49dbcb-17e4-425c-8ca8-a1553f95b884).html2013-12-31T23:00:00ZTowards Theory-of-Mind agents using Automated Planning and Dynamic Epistemic Logic
http://orbit.dtu.dk/en/publications/towards-theoryofmind-agents-using-automated-planning-and-dynamic-epistemic-logic(d676ba55-6834-4ccc-8ab7-8b9f39a895df).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/towards-theoryofmind-agents-using-automated-planning-and-dynamic-epistemic-logic(d676ba55-6834-4ccc-8ab7-8b9f39a895df).html"><span>Towards Theory-of-Mind agents using Automated Planning and Dynamic Epistemic Logic</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/mikkel-birkegaard-andersen(5264cada-012e-4a54-b77e-cd80df5bdd05).html"><span>Andersen, M. B.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/thomas-bolander(c99c0e8e-86ba-44df-98df-7c5c926d803b).html"><span>Bolander, T.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">193 p.</span> (DTU Compute PHD-2014; No. 351).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">This thesis is part of a growing body of work in what we call epistemic planning. Epistemic planning is situated at the intersection of automated planning and what can broadly be called dynamic logics. Both are part of the much larger field of Artificial Intelligence.<br /><br />Automated Planning has been around since at least the 1970s. It is a diverse collection of methods, models, algorithms and specification languages for giving autonomous agents the ability to come up with plans for proactively achieving goals. Autonomous agents can be understood as independent actors, given a purpose by their designer. Whether they are in a software system, connected to the real world with sensors and actuators, or used as a tool for modelling people, for instance in economics, they need to be able to imagine (or predict) outcomes of actions in order to form plans.<br /><br />The feature that most distinguishes planning from other decision making methods, is that the planner does not know the full system from the beginning. Most of the time it would simply be too big to store in memory! Instead of being given the entire “game”, they use a specification of actions and the initial state to generate only a fraction of the full search space. This means that what an agent can plan for depends crucially on what domains we can describe. This is where logic comes into the picture.<br /><br />For most of its more than 2500 year long history, logic has been mostly interested in the study of valid reasoning. In later years (in the scheme of things), more attention has been given to studying when reasoning fails in humans. Like using differential equations to analyse and simulate both when a bridge holds and when it collapses, we can use logic to analyse and simulate reasoning both when it is sound and when it isn’t.<br /><br />The subbranch of logic applied in this work is Dynamic Epistemic Logic. The epistemic part concerns the formalisation of knowledge and belief (mainly) in multi-agent settings. We can describe situations in which many agents are present and have different knowledge and beliefs about the world and each others’ knowledge and belief. Adding the dynamic part of Dynamic Epistemic Logic to our arsenal, we can describe how situations change when, broadly speaking, things happen. In the application to Automated Planning, we let these things be actions of the agents in the system. In doing so we derive new planning formalisms that allow agents to plan under consideration of how what they do changes both the world and knowledge and belief about the world.<br /><br />In this thesis we give new planning formalisms for single-agent planning and new results for the model theory of multi-agent models. The first of the two fully developed planning formalisms is conditional (single-agent) epistemic planning, allowing an agent to plan with what it knows now and what it knows it will come to know. Though this is nothing new in Automated Planning, it sets the stage for later work.<br /><br />The second planning formalism extends conditional epistemic planning with beliefs, letting the agent have expectations, without probabilities, of how things will turn out. Our radically different notions of bisimulation for the multi-agent versions of these models are particularly interesting for logicians, as are surprising expressivity results for well known logics on such models. <br /><br />The final part of the thesis describes ideas on extending the second formalism to a multi-agent setting. With a view towards the practical implementation of agents, we shall also see how an agent can discard the parts of its model that it does not believe to be the case. While this is not necessary for analysing reasoning agents, it does seem a requirement for practical implementations. There are simply too many possibilities for a resource-bounded agent to keep track of. If the agent does discard unlikely possibilities, it must be able to do belief revision if it later turns out to be wrong. Such a procedure is also described.<br /><br />The long term potential of multi-agent aware planning algorithms is that agents that can predict and understand others in order to plan cooperation, communication, and/or competition. It is the slow edging towards a general framework for multi-agent planning that is the underlying motivation, and some of the main results, of this thesis. While regrettably we haven’t gotten there yet, we’re considerably closer than when we started.<br /></div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>193</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>351</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/towards-theoryofmind-agents-using-automated-planning-and-dynamic-epistemic-logic(d676ba55-6834-4ccc-8ab7-8b9f39a895df).html2013-12-31T23:00:00ZOn the Impact of Energy Harvesting on Wireless Sensor Network Security
http://orbit.dtu.dk/en/publications/on-the-impact-of-energy-harvesting-on-wireless-sensor-network-security(55504a70-d478-4d56-8ef6-ce0a893cef00).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/on-the-impact-of-energy-harvesting-on-wireless-sensor-network-security(55504a70-d478-4d56-8ef6-ce0a893cef00).html"><span>On the Impact of Energy Harvesting on Wireless Sensor Network Security</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/alessio-di-mauro(871ecd8a-a186-438b-85d3-81867b027395).html"><span>Di Mauro, A.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/nicola-dragoni(d3e23247-b383-48bc-a5c1-f5de69fc9834).html"><span>Dragoni, N.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">144 p.</span> (DTU Compute PHD-2014; No. 349).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">Given the continuous advancements in the technology of energy harvesting over the last few years, we are now starting to see wireless sensor networks (WSNs) powered by scavenged energy. This change in paradigm has major repercussions not only on the hardware engineering aspects, but also on the software side. The first protocols specifically designed to take advantage of the energy harvesting capabilities of a network have just recently appeared. At the same time, security remains one of the central points of WSNs development, because of their intrinsically<br />unreliable nature that combines a readily accessible communication infrastructure such as wireless data exchange, to an often likewise readily accessible physical deployment. This dissertation provides a comprehensive look at how security can be improved by what energy harvesting has to offer. The main question asked is whether or not it is possible to provide better security in a WSN, by being aware of the fact that the amount of available energy is not going to monotonically decrease over time. The work covers different aspects and components of a WSN and focuses on what is arguably one the most important ones, medium access control (MAC) protocols. An energy-harvesting specific MAC protocol is introduced together with a related security suite. A new attack relevant to a whole class of MAC protocols is also introduced, along with a scheme that defeats it. A security approach for MAC protocols is discussed to provide an energy-aware solution. In order to address security bootstrapping, a new energy-adaptive key reinforcement scheme is presented. Finally an implementation and some experimental results are provided.<br /></div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>144</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>349</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/on-the-impact-of-energy-harvesting-on-wireless-sensor-network-security(55504a70-d478-4d56-8ef6-ce0a893cef00).html2013-12-31T23:00:00ZTopics in combinatorial pattern matching
http://orbit.dtu.dk/en/publications/topics-in-combinatorial-pattern-matching(645fcd6e-ba1d-48b8-bc3d-04f90e14dce0).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/topics-in-combinatorial-pattern-matching(645fcd6e-ba1d-48b8-bc3d-04f90e14dce0).html"><span>Topics in combinatorial pattern matching</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/hjalte-wedel-vildhoej(7bac41cb-80f9-4c7e-9053-b5c740a9537a).html"><span>Vildhøj, H. W.</span></a>, <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/inge-li-goertz(08da98e0-b1f4-492e-94e7-15083cc40701).html"><span>Gørtz, I. L.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/philip-bille(81ad6edf-aa11-47bc-adaf-227fe7e6963e).html"><span>Bille, P.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">111 p.</span> (DTU Compute PHD-2014; No. 348).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">This dissertation studies problems in the general theme of combinatorial pattern matching. More specifically, we study the following topics:<br /><br />Longest Common Extensions. We revisit the longest common extension (LCE) problem, that is, preprocess a string T into a compact data structure that supports fast LCE queries. An LCE query takes a pair (i, j) of indices in T and returns the length of the longest common prefix of the suffixes of T starting at positions i and j. Such queries are also commonly known as longest common prefix (LCP) queries. We study the time-space trade-offs for the problem, that is, the space used for the data structure vs. the worst-case time for answering an LCE query. Let n be the length of T. Given a parameter τ , 1 ≤ τ ≤ n, we show how to achieve either O(n/√τ ) space and O(τ) query time, or O(n/τ) space and O(τ log (|LCE(i, j)|/τ)) query time, where ?LCE(i, j)| denotes the length of the LCE returned by the query. These bounds provide the first smooth trade-offs for the LCE problem and almost match the previously known bounds at the extremes when τ = 1 or τ = n. We apply the result to obtain improved bounds for several applications where the LCE problem is the computational bottleneck, including approximate string matching and computing palindromes. We also present an efficient technique to reduce LCE queries on two strings to one string. Finally, we give a lower bound on the time-space product for LCE data structures in the non-uniform cell probe model showing that our second trade-off is nearly optimal.<br /><br />Fingerprints in Compressed Strings. The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. We show how to construct a data structure for a string S of size N compressed by a context-free grammar of size n that supports fingerprint queries. That is, given indices i and j, the answer to a query is the fingerprint of the substring S[i, j]. We present the first O(n) space data structures that answer fingerprint queries without decompressing any characters. For Straight Line Programs (SLP) we get O(log N) query time, and<br />for Linear SLPs (an SLP derivative that captures LZ78 compression and its variations) we get O (log log N) query time. Hence, our data structures has the same time and space complexity as for random access in SLPs. We utilize the fingerprint data structures to solve the longest common extension problem in query time O(log N log e) and O(log e log log e+log log N) for SLPs and Linear SLPs, respectively. Here, e = |LCE(i, j)| denotes the length of the LCE.<br /><br />Sparse Text Indexing. We present efficient algorithms for constructing sparse suffix trees, sparse suffix arrays and sparse positions heaps for b arbitrary positions of a text T of length n while using only O(b) words of space during the construction. Our main contribution is to show that the sparse suffix tree (and array) can be constructed in O(n log² b) time. To achieve this we develop a technique, that allows to efficiently answer b longest common prefix queries on suffixes of T, using only O(b) space. Our first solution is Monte-Carlo and outputs the correct tree with high probability. We then give a Las-Vegas algorithm which also uses O(b) space and runs in the same time bounds with high probability when b = O(√n). Furthermore, additional tradeoffs between the space usage and the construction time for the Monte-Carlo algorithm are given. Finally, we show that at the expense of slower pattern queries, it is possible to construct sparse position heaps in O(n + b log b) time and O(b) space.<br /><br />The Longest Common Substring Problem. Given m documents of total length n, we consider the problem of finding a longest string common to at least d ≥ 2 of the documents. This problem is known as the longest common substring (LCS) problem and has a classic O(n) space and O(n) time solution (Weiner [FOCS’73], Hui [CPM’92]). However, the use of linear space is impractical in many applications. We show several time-space trade-offs for this problem. Our main result is that for any trade-off parameter 1 ≤ τ ≤ n, the LCS problem can be solved in O(τ) space and O(n²/τ) time, thus providing the first smooth deterministic time-space trade-off from constant to linear space. The result uses a new and very simple algorithm, which computes a τ-additive approximation to the LCS<br />in O(n²/τ) time and O(1) space. We also show a time-space trade-off lower bound for deterministic branching programs, which implies that any deterministic RAM algorithm solving the LCS problem on documents from a sufficiently large alphabet in O(τ) space must use Ω (n√log(n/(τ log n))/ log log(n/(τ log n)) time.<br /><br />Structural Properties of Suffix Trees. We study structural and combinatorial properties of suffix trees. Given an unlabeled tree T on n nodes and suffix links of its internal nodes, we ask the question “Is T a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as T ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol. This corresponds to considering the more general definition of implicit or extended suffix trees. Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online. We prove that T is a suffix tree if and only if it is realized by a string S of length n – 1, and we give a linear-time algorithm for inferring S when the first letter on each edge is known.</div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>111</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>348</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/topics-in-combinatorial-pattern-matching(645fcd6e-ba1d-48b8-bc3d-04f90e14dce0).html2013-12-31T23:00:00ZA Probabilistic Approach for the System-Level Design of Multi-ASIP Platforms
http://orbit.dtu.dk/en/publications/a-probabilistic-approach-for-the-systemlevel-design-of-multiasip-platforms(60b4a2db-15f6-42d6-9e06-88af5edc0d5f).html
<div style='font-size: 9px;'><div class="rendering rendering_publication rendering_publication_short rendering_bookanthology rendering_short rendering_bookanthology_short"><h2 class="title"><a class="link" rel="BookAnthology" href="http://orbit.dtu.dk/en/publications/a-probabilistic-approach-for-the-systemlevel-design-of-multiasip-platforms(60b4a2db-15f6-42d6-9e06-88af5edc0d5f).html"><span>A Probabilistic Approach for the System-Level Design of Multi-ASIP Platforms</span></a></h2><a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/laura-micconi(56a260fb-3d5f-425f-a2bf-e1ff437ac861).html"><span>Micconi, L.</span></a>, <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/jan-madsen(5f89e4ed-9ff8-43d2-add5-a5182f0e1268).html"><span>Madsen, J.</span></a> & <a class="link person" rel="Person" href="http://orbit.dtu.dk/en/persons/paul-pop(9ae8b873-7735-48b5-8b97-9fedf1891f0f).html"><span>Pop, P.</span></a> <span class="date">2014</span> Kgs. Lyngby: <a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a>. <span class="numberofpages">176 p.</span> (DTU Compute PHD-2014; No. 347).<p class="type"><span class="type_family">Publication<span class="type_family_sep">: </span></span><span class="type_classification_parent">Research<span class="type_parent_sep"> › </span></span><span class="type_classification">Ph.D. thesis – Annual report year: 2014</span></p></div><div class="rendering rendering_publication rendering_publication_detailsportal rendering_bookanthology rendering_detailsportal rendering_bookanthology_detailsportal"><div class="textblock">Application Specific Instruction-set Processors (ASIPs) offer a good trade off between performance and flexibility when compared to general purpose processors or ASICs. Additionally, multiple ASIPs can be included in a single platform and they allow the generation of customized heterogeneous MPSoC with a relatively short time-to-market. While there are several commercial tools for the design of a single ASIP, there is still a lack of automation in the design of multi-ASIP platforms. <br /><br />In this thesis we consider multi-ASIP platforms for real-time applications. Each ASIP is designed to run a specific group of tasks that we identifies as a task cluster. With realtime applications, to decide how the tasks should be clustered, we perform a schedulability analysis of the system to verify if the deadlines of the applications can be met. However, to run a schedulability analysis, we need to know the WCET of each task that is available only after an ASIP is designed. Therefore, there is a circular dependency between the definition of the task clusters and the impossibility of defining them without knowing the WCET of the tasks as the ASIPs have not been defined yet. <br /><br />Many approaches available in the literature break this circular dependency considering pre-defined task clusters or considering a small set of micro-architecture configurations for each ASIP. We propose an alternative approach that uses a probabilistic model to consider the design space of all possible micro-architecture configurations. We introduce a system-level Design Space Exploration (DSE) for the very early phases of the design that automatizes part of the multi-ASIP design flow. Our DSE is responsible for assigning the tasks to the different ASIPs exploring different platform alternatives. We perform a schedulability analysis for each solution to determine which one has the highest chances of meeting the deadlines of the applications and that should be considered in the next stages of the multi-ASIP design flow.</div><div class="phddissertation"><table class="properties"><tbody><tr class="language"><th>Original language</th><td>English</td></tr><tr><th>Publication date</th><td><span class="date">2014</span></td></tr></tbody></table><table class="properties"><tbody><tr><th>Place of publication</th><td>Kgs. Lyngby</td></tr><tr><th>Publisher</th><td><a class="link" rel="Publisher" href="http://orbit.dtu.dk/en/publishers/technical-university-of-denmark-dtu(f7c040ab-194a-4da4-b458-670da24b2a08).html"><span>Technical University of Denmark (DTU)</span></a></td></tr><tr><th>Number of pages</th><td>176</td></tr><tr class="status"><th>State</th><td>Submitted</td></tr></tbody></table></div> <table class="properties"><tbody><tr><th>Name</th><td>DTU Compute PHD-2014</td></tr><tr><th>Number</th><td>347</td></tr><tr><th>ISSN (print)</th><td>0909-3192</td></tr></tbody></table></div></div>Tue, 31 Dec 2013 23:00:00 GMThttp://orbit.dtu.dk/en/publications/a-probabilistic-approach-for-the-systemlevel-design-of-multiasip-platforms(60b4a2db-15f6-42d6-9e06-88af5edc0d5f).html2013-12-31T23:00:00Z