This thesis focuses on the security of Short Message Service (SMS) and the Global System for Mobile communication (GSM) network and the use of encryption to protect SMS messages. A detailed study of the GSM network and SMS protocol, and encryption schemes was conducted to understand the properties of different encryption schemes and their applicability to SMS messages. An experiment was conducted to measure the actual performance of various encryption schemes on a modern smart phone device. An analysis of the encryption scheme properties and the performance measurement was then conducted to select a suitable scheme for SMS encryption. The selected scheme was implemented in the form of a Secure SMS Chat application to validate the viability of the selected encryption scheme. Potential applications of secure SMS in military settings are also discussed.

Mobile IP defines the mechanisms and protocol behaviors necessary to facilitate the seamless flow of traffic to a mobile host that roams from its normal home network. Of particular interest in this research, is how this capability might support the relatively rapid roaming of a wirelessly connected host. This research is focused on isolating and analyzing the constituent components of the Mobile IP protocol for the purpose of identifying any component(s) that may be improved upon, or may be exploited by an attacker intent on denying or delaying proper handoff service.

IPv6, the successor of IPv4, introduces the stateless autoconfiguration feature as a convenient alternative to the Dynamic Host Configuration Protocol (DHCP). However, the security implications of this new approach have only been discussed at the conceptual level. This thesis research develops software based on the open-source packet capture library Jpcap to capture and build appropriate ICMPv6 autoconfiguration messages. The developed Java software is used to implement two DoS threats to the IPv6 autoconfiguration procedure in a laboratory IPv6 network. The results indicate that these threats are real and further studies are required to identify suitable countermeasures. During this work compliance defects are also identified for the Linux Operating System's IPv6 implementation.

Approved for public release, distribution unlimited / This thesis explores ways of using probe packets to identify the type and version of OS that is run by a remote IPv6 host. Such a probing technique can be effective because developers of different OSes often interpret the guidance provided by the RFCs slightly differently, and consequently their network protocol stack implementation may generate responses bearing unique markers to certain probing packets. The key challenge is to find suitable probing packets for different OSes. Using a real IPv6 test bed, this thesis has evaluated both existing UDP-or-TCP-based and new IPv6-extension-header-based probing packets against a selected set of eight popular OSes. The results show that the UDP/TCP methods are also effective in an IPv6 environment and the extension header approach is worthy further study. There are evidences that OS fingerprinting is harder with IPv6. It might be due to the fact that given the experimental nature of IPv6, similar OSes tend to reuse IPv6 code. This conjecture requires further study. Finally, the thesis has also developed a method of crafting arbitrary IPv6 packets using the SmartBits system.

The research presented in this thesis provides the reader with a set of algorithms and techniques that enable the user to remotely determine what chipset and device driver an 802.11 device is using. The work details both passive and active approaches, and quantitatively gauges the effectiveness of various techniques. The implications of this are far ranging. On one hand, the techniques can be used to implement innovative new features in Wireless Intrusion Detection Systems (WIDS). On the other, they can be used to target link layer device driver attacks with much higher precision.

Approved for public release, distribution unlimited / Current chat and instant messaging (IM) solutions within the DoD have created problems with information security and interoperability. Though Extensible Message and Presence Protocol (XMPP) is the only mandated chat and IM protocol in the DoD, the majority of the military still operates alternate nonstandard solutions that prevent interoperability and lack appropriate security assurances. XMPP is a streaming XML protocol used for multi-user text chat and Instant Messaging (IM). XMPP supports a large set of administrative and user features, valuable to military chat and IM users. As an open standard, XMPP is also extensible to allow for development of military-specific chat and IM requirements. XMPP protocol also provides significant extensibility to allow for greater command and control and other operational capabilities. This work demonstrates the use of XMPP to route XML-expressed Distributed Interactive Simulation (DIS-XML) data to conduct distributed modeling and simulation. This work also demonstrates the use of XMPP as a generalized XML message-routing framework in conjunction with XML-expressed military data models, such as the Joint Consultation Command and Control Information Exchange Data Model. Also presented in this thesis is an XML document based chat data logger, designed to support persistent operations using distributed chat architecture. Experiments conducted with Navy Exercise Trident Warrior 2006 demonstrate the value of such a framework, as well as the value of XML document-based chat data logging. Results indicate that implementation and extension of XMPP has significant value for enhancing command and control. These features, along with the benefits of the adoption of open standard solutions, make XMPP an essential technology for adoption in todayâ s operational command and control suites.

<p>A molecule's biological function is determined by its chemical structure and its three dimensional (3D) shape. While a molecule's chemical structure is fairly static its physical 3D structure is typically very dynamic and thus more difficult to determine. A protein's 3D structure is actually an ensemble of shapes that it can assume depending on its immediate surroundings. The two main methods of determining a protein's 3D structure at high resolution are X-ray crystallography and nuclear magnetic resonance (NMR). These two methods complement each other by allowing for a protein's 3D shape to be studied in a wider variety of environments than either one alone can do. We are working to develop new methods for determining the 3D structures of proteins in solution by NMR, with and without ligands present that may bind to them. In particular we are developing NMR methods for studying the solution-phase 3D structures of large, biologically important, enzymes. </p><p>We are interested in determining the solution-phase 3D structures of enzymes at the atomic level so that we can understand their biological functions and how they accomplish them, and thus how to control them in order to treat diseases and improve human health. We are also interested in using high resolution structures of enzymes to do structure-based reengineering of them. Redesigning enzymes enhances our understanding of how they function in their native environment and leads to redesigned</p><p>versions of them that can be used to chemoenzymatically synthesize clinically important drugs. </p><p>This dissertation begins with our studies, by NMR, of the solution-phase structures of two bacterial enzymes involved in the biosynthesis of antibiotics. In particular we studied the solution-phase structures of the adenylation domain responsible for selectively activating the amino acid phenylalanine in the biosynthetic pathway for the antibiotic gramicidin S. Next, we present our studies of two glycosylation enzymes involved in the final phase of biosynthesis of the antibiotic vancomycin. We compared two approaches to determine the amino acids involved in substrate binding by these two enzymes, a solution-phase NMR approach and an in silico protein modeling, with ligand docking, approach. These enzymes are each quite large for current NMR solution-phase techniques and we present the lessons we learned from studying them and our plans for future work. Finally, we present a review of the use of small-molecule inhibitors and enzyme redesign in the study of the function of glycosyltransferases, with applications in the treatment of glycosylation disorders in humans and the chemoenzymatic synthesis of homogeneously glycosylated molecules.</p> / Dissertation

<p> In this work, a systematic method based on graph theoretic concepts is presented that allows setting up a general mechanism's governing equations and analyzing transmission performance for a wide range of parametric and topological variations. The algorithms and methods described in this work are designed to be both fully automatic &mdash; requiring minimal supervision from an analyst for successful execution, robust &mdash; capable of handling instantaneous bifurcations and end-of-stroke conditions, and numerically efficient &mdash; through the application of numerical reduction strategies, custom sparse matrix methods and vectorization. </p><p> In the first primary section, the focus is on automatic, graph-theoretic methods for setting up a mechanism's constraint equations and solving the dynamic equations of motion. A multibody system's constraint equations, i.e. the Jacobian matrix, plays a central role in the equations of motion, and is almost never full-rank, which complicates the solution process even for relatively simple systems. Therefore, Generalized Coordinate Partitioning (GCP), a numerical method based on LU decomposition applied to the Jacobian matrix is applied to find the optimal set of independent, generalized coordinates to describe the system. To increase the efficiency of the GCP algorithm, a new general purpose graph-partitioning algorithm, referred to as "Kinematic Substructuring" is introduced and numerical results are provided. Furthermore, a new numerical implementation of solving the equations of motion, referred to as the "Preconditioned Spatial Equations of Motion" is presented and new sparse matrix solver is described and demonstrated in several numerical examples. </p><p> In the second primary section, it is shown how a simple numerical procedure applied to a mechanism's constraint equations can be used as a measure of transmission performance. The metric, referred to as "mobility numbers" provides an indication of a joint's ability to affect a change on a mechanism's overall configuration and is directly related to a mechanism's instantaneous mobility. The relationship between mobility, transmission and manipulability is discussed. Unlike many other measures of transmission performance, mobility numbers are normalized and bound between 0 and 1, and can be computed simply and efficiently from the Jacobian matrix using LU and QR matrix decomposition methods. Examples of applications of mobility numbers are provided. </p><p> Finally, in the last section, aspects of software design, including external and internal storage formats and memoization programming methods are discussed. </p>

<p> In this dissertation, we describe our research contributions for a novel approach to the application of machine learning for the automatic detection of anomalous events. We work in two different domains to ensure a robust data-driven workflow that could be generalized for monitoring other systems. Specifically, in our first domain, we begin with the identification of internal erosion events in earth dams and levees (EDLs) using geophysical data collected from sensors located on the surface of the levee. As EDLs across the globe reach the end of their design lives, effectively monitoring their structural integrity is of critical importance. The second domain of interest is related to mobile telecommunications, where we investigate a system for automatically detecting non-commercial base station routers (BSRs) operating in protected frequency space. The presence of non-commercial BSRs can disrupt the connectivity of end users, cause service issues for the commercial providers, and introduce significant security concerns. We provide our motivation, experimentation, and results from investigating a generalized novel data-driven workflow using several machine learning techniques. </p><p> In Chapter 2, we present results from our performance study that uses popular unsupervised clustering algorithms to gain insights to our real-world problems, and evaluate our results using internal and external validation techniques. Using EDL passive seismic data from an experimental laboratory earth embankment, results consistently show a clear separation of events from non-events in four of the five clustering algorithms applied. </p><p> Chapter 3 uses a multivariate Gaussian machine learning model to identify anomalies in our experimental data sets. For the EDL work, we used experimental data from two different laboratory earth embankments. Additionally, we explore five wavelet transform methods for signal denoising. The best performance is achieved with the Haar wavelets. We achieve up to 97.3% overall accuracy and less than 1.4% false negatives in anomaly detection. </p><p> In Chapter 4, we research using two-class and one-class support vector machines (SVMs) for an effective anomaly detection system. We again use the two different EDL data sets from experimental laboratory earth embankments (each having approximately 80% normal and 20% anomalies) to ensure our workflow is robust enough to work with multiple data sets and different types of anomalous events (e.g., cracks and piping). We apply Haar wavelet-denoising techniques and extract nine spectral features from decomposed segments of the time series data. The two-class SVM with 10-fold cross validation achieved over 94% overall accuracy and 96% F1-score. </p><p> Our approach provides a means for automatically identifying anomalous events using various machine learning techniques. Detecting internal erosion events in aging EDLs, earlier than is currently possible, can allow more time to prevent or mitigate catastrophic failures. Results show that we can successfully separate normal from anomalous data observations in passive seismic data, and provide a step towards techniques for continuous real-time monitoring of EDL health. Our lightweight non-commercial BSR detection system also has promise in separating commercial from non-commercial BSR scans without the need for prior geographic location information, extensive time-lapse surveys, or a database of known commercial carriers. (Abstract shortened by ProQuest.) </p>

<p>In this dissertation, we emphasize productiveness not just undecidability since pro- ductiveness implies constructive incompleteness. Analogues of Rice?s Theorem for different classes of languages are investigated, refined and generalized. In particular, several sufficient but general conditions are presented for predicates to be as hard as some widely discussed predicates such as ?= ?? and ?= {0,1}??. These conditions provide several general methods for proving complexity/productiveness results and apply to a large number of simple and natural predicates. As the first step in apply- ing these general methods, we investigate the complexity/productiveness of the pred- icates ?= ??, ?= {0,1}?? and other predicates that can be useful sources of many- one reductions for different classes of languages. Then we use very efficient many- one reductions of these basic source predicates to prove many new non-polynomial complexity lower bounds and productiveness results. Moreover, we study the com- plexity/productiveness of predicates for easily recognizable subsets of instances with important semantic properties. Because of the efficiency of our reductions, intuitively these reductions can preserve many levels of complexity. We apply our general methods to pattern languages [1] and multi-pattern lan- guages [2]. Interrelations between multi-pattern languages (or pattern languages) and standard classes of languages such as context-free languages and regular languages are studied. A way to study the descriptional complexity of standard language descriptors (for examples, context-free grammars and regular expressions) and multi-patterns is illustrated. We apply our general methods to several generalizations of regular ex- pressions. A productiveness result for the predicate ?= {0,1}?? is established for synchronized regular expressions [3]. Because of this, many new productiveness re- sults for synchronized regular expressions follow easily. We also apply our general methods to several classes of Lindenmayer systems [4] and of cellular automata [5]. A way of studying the complexity/productiveness of the 0Lness problem is developed and many new results follow from it. For real time one-way cellular automata, we observe that the predicates ?= ?? and ?= {0,1}?? are both productive. Because vi of this, many more general results are presented. For two-way cellular automata, we prove a strong meta-theorem and give a complete characterization for testing containment of any fixed two-way cellular automaton language. Finally, we generalize our methods and apply them to the theory of functions of real variables. In rings, the equivalence to identically 0 function problem which is an analogue of ?= ?? is studied. We show that the equivalence to identically 0 function problem for some classes of elementary functions is productive for different domains including open and closed bounded intervals of real numbers. Two initial results for real fields are also presented.