In this thesis we obtain several interesting algebraic properties of the operations used in the block cipher IDEA which are important for cryptographic analyzes. We view each of these operations as a function from $mathbb Z_{2}^n times mathbb Z_{2}^n to mathbb Z_{2}^n$. By fixing one of variables $v(z)=mathbf Z$ in $mathbb Z_{2}^n times mathbb Z_{2}^n$, we define functions $mathbf {f}_z$ and $mathbf {g}_z$ from $mathbb Z_{2}^n$ to $mathbb Z_{2}^n$ for the addition $BIGboxplus$ and the multiplication $BIGodot$ operations, respectively. We first show that the nonlinearity of $mathbf {g}_z$ remains the same under some transformations of $z$. We give an upper bound for the nonlinearity of $mathbf {g}_{2^k}$, where $2leq k &lt / n-1$. We list all linear relations which make the nonlinearity of $mathbf {f}_z$ and $mathbf {g}_z$ zero and furthermore, we present all linear relations for $mathbf {g}_z$ having a high probability. We use these linear relations to derive many more linear relations for 1-round IDEA. We also devise also a new algorithm to find a set of new linear relations for 1-round IDEA based on known linear relations. Moreover, we extend the largest known linear class of weak keys with cardinality $2^{23}$ to two classes with cardinality $2^{24}$ and $2^{27}$. Finally, we obtain several interesting properties of the set $ { ({mathbf X},{mathbf X} BIGoplus {mathbf A}) in mathbb Z_2^n times mathbb Z_2^n ,|, (mathbf {X}BJoin {mathbf Z})BIGoplus( ({mathbf X} BIGoplus {mathbf A} ) BJoin mathbf {Z} ) = {mathbf B} }$ for varying ${mathbf A}, {mathbf B}$ and ${mathbf Z}$ in $mathbb Z_2^n$, where $BJoin in { BIGodot,BIGboxplus }$. By using some of these properties, we present impossible differentials for 1-round IDEA and Pseudo-Hadamard Transform.

Trapdoor functions, introduced in the seminal paper of Diffie and Hellman, are a fundamental notion in modern cryptography. Informally, trapdoor functions are injective functions that are easy to evaluate but hard to invert unless given an additional input called the trapdoor. Specifically, the classical security notion considered for trapdoor functions is one-wayness, which asks that it be hard to invert (except with very small probability) a uniformly random point in the range without the trapdoor. Motivated by the demands of emerging applications of cryptography as well as stronger security properties desired from higher-level cryptographic primitives constructed out of trapdoor functions, this thesis studies new strengthenings to the classical notion of one-way trapdoor functions and their applications. Our results are organized along two separate threads, wherein we introduce two new cryptographic primitives that strengthen the notion of one-wayness for trapdoor functions in different ways: Deterministic Encryption: Our notion of deterministic (public-key) encryption addresses the weaknesses of using trapdoor functions directly for encryption articulated by Goldwasser and Micali, to the extent possible without randomizing the encryption function (whereas Goldwasser and Micali address them using randomized encryption). Specifically, deterministic encryption ensures no partial information is leaked about a high-entropy plaintext or even multiple correlated such plaintexts. Deterministic encryption has applications to fast search on encrypted data, securing legacy protocols, and ``hedging' randomized encryption against bad randomness. We design a conceptually appealing semantic-security style definition of security for deterministic encryption as well as an easier-to-work-with but equivalent indistinguishability style definition. In the random oracle model of Bellare and Rogaway, we show a secure construction of deterministic encryption for an unbounded number of arbitrarily correlated high-entropy plaintexts based on any randomized encryption scheme, as well as length-preserving such construction based on RSA. In the standard model, we develop a general framework for constructing deterministic encryption schemes based on a new notion of ``robust' hardcore functions. We show a secure construction of deterministic for a single high-entropy plaintext based on exponentially-hard one-way trapdoor functions; single-message security is equivalent to security for an unbounded number of messages drawn from a block-source (where each subsequent message has high entropy conditioned on the previous). We also show a secure construction of deterministic encryption for a bounded number of arbitrarily correlated high-entropy plaintexts based on the notion of lossy trapdoor functions introduced by Peikert and Waters. paragraph*{Adaptive Trapdoor Functions:} Our notion of adaptive trapdoor functions asks that one-wayness be preserved in the presence of an inversion oracle that can be queried on some range points. The main application we give is the construction of black-box chosen-ciphertext secure public-key encryption from weaker general assumptions. (``Black-box' means that the specific code implementing the trapdoor function is not used in the construction, which typically incurs a huge efficiency cost.) Namely, we show such a construction of chosen-ciphertext secure public-key encryption from adaptive trapdoor functions. We then show that adaptive trapdoor functions can be realized from the recently introduced notions of lossy trapdoor functions by Peikert and Waters and correlated-product secure trapdoor functions by Rosen and Segev. In fact, by extending a recent result of Vahlis, we show adaptivity is strictly weaker than the latter notions (in a black-box sense). As a consequence, adaptivity is the weakest security property of trapdoor functions known to imply black-box chosen-ciphertext security. Additionally, by slightly extending our framework and considering ``tag-based' adaptive trapdoor functions, we obtain exactly the chosen-ciphertext secure encryption schemes proposed in prior work, thereby unifying them, although the schemes we obtain via adaptive trapdoor functions are actually more efficient. Finally, we show that adaptive trapdoor functions can be realized from a (non-standard) computational assumption on RSA inversion, leading to a very efficient RSA-based chosen-ciphertext secure encryption scheme in the standard model.

Understanding the molecular basis of protein function is a challenging task that lays the foundation for the pharmacological intervention in many diseases originating in altered structural states of the involved proteins. Dissecting a complex functional machinery into modules is a promising approach to protein function. The motivation for this work was to identify minimal requirements for “local” switching processes in the function of multidomain proteins that can adopt a variety of structural substates of different biological activity or representing intermediates of a complex reaction path. For example, modular switches are involved in signal transduction, where receptors respond to ligand-activation by specific conformational changes that are allosterically transmitted to “effector recognition sites” distant from the actual ligand-binding site. Heptahelical receptors have attracted particular attention due to their ubiquitous role in a large variety of pharmacologically relevant processes. Although constituting switches in their own right, it has become clear through mutagenesis and functional studies that receptors exhibit substates of partial active/inactive structure that can explain biological phenotypes of different levels of activity. Here, the notion that microdomains undergo individual switching processes that are integrated in the overall response of structurally regulated proteins is addressed by studies on the molecular basis of proton-dependent (chemical) and force-dependent (mechanical) conformational transitions. A combination of peptide synthesis, biochemical analysis, and secondary structure sensitive spectroscopy (Infrared, Circular dichroism, Fluorescence) was used to prove the switching capability of putative functional modules derived from three selected proteins, in which conformational transitions determine their function in transmembrane signaling (rhodopsin), transmembrane transport (bacteriorhodopsin) and chemical force generation (kinesin-1). The data are then related to the phenotypes of the corresponding full length-systems. In the first two systems the chemical potential of protons is crucial in linking proton exchange reactions to transmembrane protein conformation. This work addresses the hypothesized involvement of lipid protein interactions in this linkage (1). It is shown here that the lipidic phase is a key player in coupling proton uptake at a highly conserved carboxylic acid (DRY motif located at the C-terminus of helix 3) to conformation during activation of class-1 G protein coupled receptors (GPCRs) independently from ligand protein interactions and interhelical contacts. The data rationalize how evolutionary diversity underlying ligand-specifity can be reconciled with the conservation of a cytosolic ‘proton switch’, that is adapted to the general physical constraints of a lipidic bilayer described here for the prototypical class-1 GPCR rhodopsin (2). Whereas the exact sequence of modular switching events is of minor importance for rhodopsin as long as the final overall active conformation is reached, the related heptahelical light-transducing proton pump bacteriorhodopsin (bR), requires the precise relative timing in coupling protonation events to conformationtional switching at the cytosolic, transmembrane, and extracellular domains to guarantee vectorial proton transport. This study has focused on the cytosolic proton uptake site of this retinal protein whose proton exchange reactions at the cytosolic halfchannel resemble that of rhodopsin. It was a prime task in this work to monitor in real time the allosteric coupling between different protein regions. A novel powerful method based on the correlation of simultaneously recorded infrared absorption and fluorescence emission changes during bR function was established here (3), to study the switching kinetics in the cytosolic proton uptake domain relative to internal proton transfer reactions at the retinal and its counter ion. Using an uptake-impaired bR mutant the data proves the modular nature of domain couplings and shows that the energy barrier of the conformational transition in the cytosolic half but not its detailed structure is under the control of proton transfer reactions at the retinal Schiff base and its counter ion Asp85 (4). Despite the different functions of the two studied retinal proteins, the protonation is coupled to local switching mechanisms studied here at two levels of complexity, [a] a single carboxylic acid side chain acting as a lipid-dependent proton switch [b] a full-length system, where concerted modular regions orchestrate the functional coupling of proton translocation reactions. Switching on the level of an individual amino acid is shown to rely on localizable chemical properties (charge state, hydrophobicity, rotamer state). In contrast, switching processes involving longer stretches of amino acids are less understood, less generalizable, and can constitute switches of mechanical, rather than chemical nature. This applies particularly to molecular motors, where local structural switching processes are directly involved in force generation. A controversy exists with respect to the structural requirements for the cooperation of many molecular motors attached to a single cargo. The mechanical properties of the Hinge 1 domain of kinesin-1 linking the “neck” and motor domain to the “tail” were addressed here to complement single molecule data on torsional flexibility with secondary structure analysis and thermal stability of peptides derived from Hinge 1 (5). It is shown that the Hinge 1 exhibits an unexpected helix-forming propensity that resists thermal forces but unfolds under load. The data resolve the paradox that the hinge is required for motor cooperation, whereas it is dispensable for single motor processivity, clearly emphasizing the modular function of the holoprotein. However, the secondary-structural data reveal the functional importance of providing high compliance by force-dependent unfolding, i.e. in a fundamentally different way than disordered domains that are flexible but yet do not support cooperativity.

<p>The development of improved sequencing technologies hasenabled the field of genomics to evolve. Handling andsequencing of large numbers of samples require an increasedlevel of automation in order to obtain high throughput andconsistent quality. Improved performance has lead to thesequencing of numerous microbial genomes and a few genomes fromhigher eukaryotes and the benefits of comparing sequences bothwithin and between species are now becoming apparent. Thisthesis describes both the development of automated purificationmethods for DNA, mainly sequencing products, and a comparativesequencing project.</p><p>The initially developed purification technique is dedicatedto single stranded DNA containing vector specific sequences,exemplified by sequencing products. Specific capture probescoupled to paramagnetic beads together with stabilizing modularprobes hybridize to the single stranded target. After washing,the purified DNA can be released using water. When sequencingproducts are purified they can be directly loaded onto acapillary sequencer after elution. Since this approach isspecific it can be applied to multiplex sequencing products.Different probe sets are used for each sequencing product andthe purifications are performed iteratively.</p><p>The second purification approach, which can be applied to anumber of different targets, involves biotinylated PCR productsor sequencing products that are captured using streptavidinbeads. This has been described previously, buthere theinteraction between streptavidin and biotin can be disruptedwithout denaturing the streptavidin, enabling the re-use of thebeads. The relatively mild elution conditions also enable therelease of sensitive biotinylated molecules.</p><p>Another project described in this thesis is the comparativesequencing of the 40 kb<i>cag</i>pathogenicity island (PAI) in four<i>Helicobacter pylori</i>strains. The results included thediscovery of a novel gene, present in approximately half of theSwedish strains tested. In addition, one of the strainscontained a major rearrangement dividing the<i>cag</i>PAI into two parts. Further, information about thevariability of different genes could be obtained.</p><p><b>Keywords:</b>DNA sequencing, DNA purification, automation,solid-phase, streptavidin, biotin, modular probes,<i>Helicobacter pylori</i>,<i>cag</i>PAI.</p>

Title from PDF of title page. / Document formatted into pages; contains 83 pages. / Thesis (M.S.I.E.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The need for redesigning existing business processes to improve their efficiency makes it essential to adequately represent, study, and automate them. The WFMC defines "workflow" as computerized facilitation or automation of a business process in whole or part. It is actually a representation of the given process, which is made up of well-defined collection of activities called tasks. Modeling and specification of a workflow involves the following steps: 1) Provide formalism for modeling and specification of workflow 2) specify the tasks together with the associated information and 3) enter the applicable business rules in form of inter-task dependencies. Earlier attempts at modeling of workflows are based on a centralized control approach, has limited applicability for modeling and control of real life workflow due to computational complexity. In this thesis, a distributed supervisory control approach is described and shown to be computationally tractable. / ABSTRACT: The application of such an approach is demonstrated with a case study. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

We compared well known measurement methods for LogGP parameters and discuss their accuracy and network contention. Based on this, a new theoretically exact measurement method that does not saturate the network is derived and explained in detail. The applicability of our method is shown for the low level communication API of Open MPI across several interconnection networks. Based on the LogGP model, we developed a low overhead packet scheduling algorithm. It can handle different types of interconnects with different characteristics. It is able to produce schedules which are very close to the optimum for both small and large messages. The efficiency of the algorithm for small messages is show for a Open MPI implementation. The implementation uses the LogGP benchmark to obtain the LogGP parameters of the available interconnects and can so adapt to any given system.

Thesis (Ph.D)--Computing, Georgia Institute of Technology, 2010. / Committee Chair: Yannis Smaragdakis; Committee Member: Oege de Moor; Committee Member: Richard LeBlanc; Committee Member: Santosh Pande; Committee Member: Spencer Rugaber. Part of the SMARTech Electronic Thesis and Dissertation Collection.

This work describes the design and implementation of a generic lightweight onboard processing system for miniature Unmanned Vehicles (UVs) that is computationally powerful and highly adaptable. First, several classical approaches to giant scale and full size UV onboard processing systems are described along with their corresponding limitations. Second, a detailed study is presented that describes the key characteristics of an onboard system along with associated limitations. Next, an implementation of a generic onboard system capable of vision processing and servo based control is presented along with detailed hardware specifications and implementation software. Last, experimental data, both laboratory and field, are presented to show validation of the onboard processing system design, functionality, and key characteristics presented. Two primary contributions are made in this work. i) Identification of key characteristics of an onboard system allows for a high level validation of the hardware of an onboard system along with a design template for a reconfigurable, platform independent, processing system for UVs. ii) Detailed design and implementation of an adaptable onboard processing system that is both computationally powerful and easily adapted. This system is validated by showing satisfiability of the design characteristics necessary for an adaptable onboard system along with fully operational field test and their corresponding results.

The evolution of human beings is marked by adaptation. The ability to adapt to and manipulate our environment is one definer of intelligence, and ours is unique among life on Earth. Since moving off of the African Continent, humans have migrated to inhabit every part of the Earth. Human existence and perpetuity in the universe depends upon the success of this adaptation, and inevitably, migrating off of this planet. The technological advances being developed today will change our way of life, and enable people to travel to and live permanently on the Moon and Mars. This study involves the architectural design and construction of a completely programmable permanent Martian settlement in the year 2050. Previous studies and proposals for Martian architecture rely mostly on existing technology. The first people are not expected to reach Mars until 2030, and new and emerging technologies will radically affect the designs being considered today. Technical challenges constrain designers of space architecture today, and scientific developments will solve many of these. This study seeks to explore how new technology can positively affect the architecture of the future, affording more comfortable and livable space on Mars. With a construction date of 2050, this project differs from others by benefitting from the next four decades of profound technological advancement. Leading Futurist Raymond Kurzweil predicts that the technological singularity is within this time frame, and that the 21st Century will, “Witness on the order of 20,000 years of progress (at today’s rate of progress) (Kurzweil, Law of Accelerating Change).” This thesis theorizes that nanotechnology will enable the deployment of a completely self-constructing and programmable permanent Martian settlement designed from a series of spatial modules. The anticipated results include a modular system of architectural spaces, and an increased awareness of the architectural benefits of emerging technologies as they relate to future space architecture.

Through the exporting of a portion of site-based work to fabrication shops, modularization (MOD) can enhance efficiency in the construction industry. The industry, however, applies modularization at only a low level. To reach higher levels of modularization, the EPC industry needs new approaches. Previous studies have identified the current trends in and barriers to the industry's application of modularization. Moreover, in 2013, the Construction Industry Institute's (CII) Research Team 283 identified 21 critical success factors (CSFs) that create an optimum environment for a broader and more effective use of modularization. However, the researcher has identified a need to better understand the relative significance of MOD CSFs and their associations with project performance. Thus, the research was conducted to provide recommendations for better project performance by identifying correlations between the accomplishment of MOD CSFs and project performance and examining actual modular projects' MOD CSF accomplishment. This study identified four statistically significant positive correlations. Those are between the accomplishment of MOD CSFs and: 1) cost performance; 2) schedule performance; 3) Construction performance; and 4) Startup performance. In addition to the correlation analysis, the study also identified the CSFs that appear to contribute the most to 1) "Modular Project Success", 2) Construction success, 3) Startup success, 4) Cost performance, and 5) Schedule performance. To collect information on the actual industrial modular projects, the study surveyed industry experts. By using this study, many industrial project stakeholders from owners to fabricators, designers and EPC contractors, will be able to understand the relationships between MOD CSFs and project performance. Such an understanding should motivate them to achieve better project performance through implementing modularization CSFs. / text