Solar variability, weather, and climate

Advances in the understanding of possible effects of solar variations on weather and climate are most likely to emerge by addressing the subject in terms of fundamental physical principles of atmospheric sciences and solar-terrestrial physis. The limits of variability of solar inputs to the atmosphere and the depth in the atmosphere to which these variations have significant effects are determined

Knots, Trees, and Fields: Common Ground Between Physics and Mathematics

One main theme of this thesis is a connection between mathematical physics (in particular, the three-dimensional topological quantum field theory known as Chern-Simons theory) and three-dimensional topology. This connection arises because the partition function of Chern-Simons theory provides an invariant of three-manifolds, and the Wilson-loop observables in the theory define invariants of knots. In the first chapter, we review this connection, as well as more recent work that studies the classical limit of quantum Chern-Simons theory, leading to relations to another knot invariant known as the A-polynomial. (Roughly speaking, this invariant can be thought of as the moduli space of flat SL(2,C) connections on the knot complement.) In fact, the connection can be deepened: through an embedding into string theory, categorifications of polynomial knot invariants can be understood as spaces of BPS states. We go on to study these homological knot invariants, and interpret spectral sequences that relate them to one another in terms of perturbations of supersymmetric theories. Our point is more general than the application to knots; in general, when one perturbs any modulus of a supersymmetric theory and breaks a symmetry, one should expect a spectral sequence to relate the BPS states of the unperturbed and perturbed theories. We consider several diverse instances of this general lesson. In another chapter, we consider connections between supersymmetric quantum mechanics and the de Rham version of homotopy theory developed by Sullivan; this leads to a new interpretation of Sullivan's minimal models, and of Massey products as vacuum states which are entangled between different degrees of freedom in these models. We then turn to consider a discrete model of holography: a Gaussian lattice model defined on an infinite tree of uniform valence. Despite being discrete, the matching of bulk isometries and boundary conformal symmetries takes place as usual; the relevant group is PGL(2,Qp), and all of the formulas developed for holography in the context of scalar fields on fixed backgrounds have natural analogues in this setting. The key observation underlying this generalization is that the geometry underlying AdS3/CFT2 can be understood algebraically, and the base field can therefore be changed while maintaining much of the structure. Finally, we give some analysis of A-polynomials under change of base (to finite fields), bringing things full circle.</p

Indices and Applications in High-Throughput Sequencing

Recent advances in sequencing technology allow to produce billions of base pairs per day in the form of reads of length 100 bp an longer and current developments promise the personal $1,000 genome in a couple of years. The analysis of these unprecedented amounts of data demands for efficient data structures and algorithms. One such data structures is the substring index, that represents all substrings or substrings up to a certain length contained in a given text. In this thesis we propose 3 substring indices, which we extend to be applicable to millions of sequences. We devise internal and external memory construction algorithms and a uniform framework for accessing the generalized suffix tree. Additionally we propose different index-based applications, e.g. exact and approximate pattern matching and different repeat search algorithms. Second, we present the read mapping tool RazerS, which aligns millions of single or paired-end reads of arbitrary lengths to their potential genomic origin using either Hamming or edit distance. Our tool can work either lossless or with a user-defined loss rate at higher speeds. Given the loss rate, we present a novel approach that guarantees not to lose more reads than specified. This enables the user to adapt to the problem at hand and provides a seamless tradeoff between sensitivity and running time. We compare RazerS with other state-of-the-art read mappers and show that it has the highest sensitivity and a comparable performance on various real-world datasets. At last, we propose a general approach for frequency based string mining, which has many applications, e.g. in contrast data mining. Our contribution is a novel and lightweight algorithm that is faster and uses less memory than the best available algorithms. We show its applicability for mining multiple databases with a variety of frequency constraints. As such, we use the notion of entropy from information theory to generalize the emerging substring mining problem to multiple databases. To demonstrate the improvement of our algorithm we compared to recent approaches on real-world experiments of various string domains, e.g. natural language, DNA, or protein sequences

Space Mechanisms Lessons Learned Study. Volume 1: Summary

Hundreds of satellites have been launched to date. Some have operated extremely well and others have not. In order to learn from past operating experiences, a study was conducted to determine the conditions under which space mechanisms (mechanically moving components) have previously worked or failed. The study consisted of: (1) an extensive literature review that included both government contractor reports and technical journals; (2) communication and visits (when necessary) to the various NASA and DOD centers and their designated contractors (this included contact with project managers of current and prior NASA satellite programs as well as their industry counterparts); (3) requests for unpublished information to NASA and industry; and (4) a mail survey designed to acquire specific mechanism experience. The information obtained has been organized into two volumes. Volume 1 provides a summary of the lessons learned, the results of a needs analysis, responses to the mail survey, a listing of experts, a description of some available facilities and a compilation of references. Volume 2 contains a compilation of the literature review synopsis