Digital Commons Network^™

Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis

Chemistry Faculty Publications

New RNA interaction interfaces are reported for designing RNA modules for directional supramolecular self-assembly. The new interfaces are generated from existing ones by inserting C-loops between the interaction motifs that mediate supramolecular assembly. C-Loops are new modular motifs recently identified in crystal structures that increase the helical twist of RNA helices in which they are inserted and thus reduce the distance between pairs of loop or loop-receptor motifs from 11 to 9 base-stacking layers while maintaining correct orientation for binding to cognate interaction interfaces. Binding specificities of C-loop-containing molecules for cognate molecules that also have inserted C-loops were found to …

Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa

Chemistry Faculty Publications

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more R helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. …

Iron In Hot Da White Dwarfs, Stéphane Vennes, Pierre Chayer, Jean François Dupuis, Thierry M. Lanz

Aerospace, Physics, and Space Science Faculty Publications

We present a study of the iron abundance pattern in hot, hydrogen-rich (DA) white dwarfs. The study is based on new and archival far-ultraviolet spectroscopy of a sample of white dwarfs in the temperature range 30,000 K ≲ Teff ≲ 64,000 K. The spectra obtained with the Far Ultraviolet Spectroscopic Explorer, along with spectra obtained with the Hubble Space Telescope Imaging Spectrograph and the International Ultraviolet Explorer, sample Fe III-Fe VI absorption lines, enabling a detailed iron abundance analysis over a wider range of effective temperatures than previously afforded. The measurements reveal abundance variations in excess of 2 orders of …

Some Issues In The Art Image Database Systems, Peter L. Stanchev, David Green Jr., Boyan N. Dimitrov

Mathematics Publications

In this paper we illustrate several aspects of art databases, such as: the spread of the multimedia art images; the main characteristics of art images; main art images search models; unique characteristics for art image retrieval; the importance of the sensory and semantic gaps. In addition, we present several interesting features of an art image database, such as: image indexing; feature extraction; analysis on various levels of precision; style classification. We stress color features and their base, painting analysis and painting styles. We study also which MPEG-7 descriptors are best for fine painting images retrieval. An experimental system is developed …

Asymptotic Sign-Solvability, Multiple Objective Linear Programming, And The Nonsubstitution Theorem, L Clayton, R Herring, Allen G. Holder, J Holzer, C Nightingale, T Stohs

Mathematics Faculty Research

In this paper we investigate the asymptotic stability of dynamic, multiple-objective linear programs. In particular, we show that a generalization of the optimal partition stabilizes for a large class of data functions. This result is based on a new theorem about asymptotic sign-solvable systems. The stability properties of the generalized optimal partition are used to extend a dynamic version of the Nonsubstitution Theorem.

Partitioning Multiple Objective Optimal Solutions With Applications In Radiotherapy Design, Allen G. Holder

Mathematics Faculty Research

The optimal partition for linear programming is induced by any strictly complementary solution, and this partition is important because it characterizes the optimal set. However, constructing a strictly complementary solution in the presence of degeneracy was not practical until interior point algorithms became viable alternatives to the simplex algorithm. We develop analogs of the optimal partition for linear programming in the case of multiple objectives and show that these new partitions provide insight into the optimal set (both pareto optimality and lexicographic ordering are considered). Techniques to produce these optimal partitions are provided, and examples from the design of radiotherapy …

Interview With Carol Mayer-Reed, Mayer/Reed, 2006 (Audio), Carol Mayer-Reed

All Sustainability History Project Oral Histories

Interview of Carol Mayer-Reed by Robyn Russnogle at on December 1st, 2006.

The interview index is available for download.

Association Between Fire Return Interval And Population Dynamics In Four California Populations Of Tecate Cypress (Cupressus Forbesii), Roland C. De Gouvenain, Ali M. Ansary

Faculty Publications

The Tecate cypress (Cupressus forbesii) is a tree species associated with chaparral ecosystems in southern California and northern Baja California, Mexico. It is fire-adapted, its regeneration triggered by the opening of serotinous cones when adult trees are burned. Surveys made in the 1980s by others suggested that some Tecate cypress populations were declining, and some authors suggested that increased fire frequency in southern California was a major factor for this decline. We asked whether current population trends were still negative for Tecate cypress 20 years later, and whether population growth was associated with fire return interval length. Based on demographic, …

Synthesis And Characterization Of Complex Polymer Architectures, Brandon Scott Farmer

Doctoral Dissertations

Anionic polymerization based upon high vacuum technique has been used to synthesize different star polymers using varying linking techniques. In particular chlorosilanes, divinylbenzene, and polyhedral oligomeric silsesquioxane (POSS) chlorosilane derivatives were used in the synthesis of star polymers. These polymers, along with polymers synthesized by others, have been characterized by a range of methods in this work.

A series of polyisoprene (PI) stars were synthesized from dimethylaminopropyllithium (DMAPLi) and subsequently hydrogenated to form poly (ethylene-co-propylene) (PEP) these were characterized by size exclusion chromatography (SEC) coupled with online two angle laser light scattering (TALLS). These polymers were synthesized in an attempt …

Cheating To Get Better Roommates In A Random Stable Matching, Chien-Chung Huang

Computer Science Technical Reports

This paper addresses strategies for the stable roommates problem, assuming that a stable matching is chosen at random. We investigate how a cheating man should permute his preference list so that he has a higher-ranking roommate probabilistically. In the first part of the paper, we identify a necessary condition for creating a new stable roommate for the cheating man. This condition precludes any possibility of his getting a new roommate ranking higher than all his stable roommates when everyone is truthful. Generalizing to the case that multiple men collude, we derive another impossibility result: given any stable matching in which …

Evaluating Next Cell Predictors With Extensive Wi-Fi Mobility Data, Libo Song, David Kotz, Ravi Jain, Xiaoning He

Dartmouth Scholarship

Location is an important feature for many applications, and wireless networks can better serve their clients by anticipating client mobility. As a result, many location predictors have been proposed in the literature, though few have been evaluated with empirical evidence. This paper reports on the results of the first extensive empirical evaluation of location predictors, using a two-year trace of the mobility patterns of over 6,000 users on Dartmouth's campus-wide Wi-Fi wireless network. The surprising results provide critical evidence for anyone designing or using mobility predictors. \par We implemented and compared the prediction accuracy of several location predictors drawn from …

An Eccentric Hot Jupiter Orbiting The Subgiant Hd 185269, John Asher Johnson, Geoffrey W. Marcy, Debra A. Fischer, Gregory W. Henry, Jason T. Wright, Howard Isaacson, Chris Mccarthy

Information Systems and Engineering Management Research Publications

We report the detection of a Jupiter-mass planet in a 6.838 day orbit around the 1.28 M☉ subgiant HD 185269. The eccentricity of HD 185269b (e = 0.30) is unusually large compared to other planets within 0.1 AU of their stars. Photometric observations demonstrate that the star is constant to ±0.0001 mag on the radial velocity period, strengthening our interpretation of a planetary companion. This planet was detected as part of our radial velocity survey of evolved stars located on the subgiant branch of the H-R diagram—also known as the Hertzsprung gap. These stars, which have masses between 1.2 and …

Historical Lessons On Id Technology And The Consequences Of An Unchecked Trajectory, Katina Michael, M G. Michael

Faculty of Informatics - Papers (Archive)

This paper traces the use of identification techniques throughout the ages and focuses on the growing importance of citizen identification by governments. The paper uses a historical approach beginning with manual techniques such as tattoos, through to more recent automatic identification (auto-ID) techniques such as smart cards and biometrics. The findings indicate that identification techniques born for one purpose have gradually found their way into alternate applications, and in some instances have been misused altogether. There is also strong evidence to suggest that governments are moving away from localized identification schemes to more global systems based on universal lifetime identifiers.

Hclp Based Service Composition, Ying Guan, Aditya K. Ghose, Zheng Lu

Faculty of Informatics - Papers (Archive)

A key impediment to the widespread adoption of web services is the relatively limited set of tools available to deal with Quality-of-Service (QoS) factors. QoS factors pose several difficult challenges in how they may be articulated. While the functional requirements of a service can be represented as predicates to be satisfied by the target system, QoS factors are effectively statements of objectives to be maximized or minimized. QoS requirements occur naturally as local specifications of preference. Dealing with QoS factors is therefore a multi-objective optimization problem. In effect, these objectives are never fully satisfied, but satisficed to varying degrees. In …

Facilitating Universal Multimedia Adaptation (Uma) In A Heterogeneous Peer-To-Peer Network, L. Rong, I. Burnett

Faculty of Informatics - Papers (Archive)

This paper proposes a P2P architecture which uses MPEG-21 as a standard based technique to dynamically adapt resources according to various usage environment attributes such as terminal capabilities and user preferences. In the architecture, a super peer based approach is used to cluster peers, store peer information, perform searches and instruct peers to adapt/send resources. Pull and push-based adaptation methods are introduced to adapt search results and resources in an intelligent manner based on the usage environment attributes. Simulation results show that the proposed architecture reduces download time while increasing resource availabilities and download speed in the network when compared …

Co-Evolution Of Agent-Oriented Conceptual Models And Caso Agent Programs, A. Dasgupta, Aneesh Krishna, Aditya K. Ghose

Faculty of Informatics - Papers (Archive)

Agent-Oriented conceptual modelling notations are highly effective in representing requirements from an intentional stance and answering questions such as what goals exist, how key actors depend on each other and what alternatives must be considered. In this paper, we suggest an approach to executing i* models by translating these into set of interacting agents implemented in the CASO language. In addition, we suggest a hybrid modelling, or co-evolution, approach in which i* models and CASO agent programs are concurrently maintained and updated, while retaining some modicum of loose consistency between the two. This allows us to benefit from the complementary …

Enhancing Interoperability Via Generic Multimedia Syntax Translation, Joseph Thomas-Kerr, I. Burnett, C. H. Ritz

Faculty of Informatics - Papers (Archive)

The Bitstream Binding Language (BBL) is a new technology developed by the authors and being standardized by MPEG, which describes how multimedia content and metadata can be mapped onto streaming formats. This paper describes how BBL can be used to enhance the interoperability of multimedia content by providing a generic mechanism for the translation of content between formats. As new content formats are developed, BBL can be used to describe how to translate the content into a form that existing devices are able to render. This consequently simplifies the adoption of new multimedia content forms because existing devices are able …

Adopting Default Reasoning In Service Composition Context, Zheng Lu, Aditya K. Ghose, Peter Hyland

Faculty of Informatics - Papers (Archive)

Web Service composition is the ability of one business to provide value-added services to its customers through the composition of basic Web services, possibly offered by different companies [12]. Because of distributed responsibilities, ownership and control, it is often not feasible to acquire all information needed for service composition. These characteristics are fundamental to service oriented computing but make it inherently difficult to avoid service conflicts. To reason about and adapt to a changing environment, in this work, we will extend current OWL-S by introducing the concept of service assumptions which allow reasoning with incomplete information. Furthermore, together with the …

Uv-B Screening Potential Is Higher In Two Cosmopolitan Moss Species Than In A Co-Occurring Antarctic Endemic Moss – Implications Of Continuing Ozone Depletion, J. L. Dunn, Sharon A. Robinson

Faculty of Science - Papers (Archive)

Concentrations of UV-B absorbing pigments and anthocyanins were measured in three moss species, over a summer growing season in Antarctica. Pigment concentrations were compared with a range of climatic variables to determine if there was evidence that pigments were induced by UV-B radiation, or other environmental parameters, and secondly if there were differences between species in their pigment responses. Significant seasonal differences in the potential UV-B screening pigments were found, with the two cosmopolitan species Bryum pseudotriquetrum and Ceratodon purpureus appearing better protected from the potentially damaging effects of ozone depletion than the Antarctic endemic Schistidium antarctici. Bryum pseudotriquetrum accumulated …

Explicit Symmetries Of Strict Feedforward Control Systems, Issa Amadou Tall, Witold Respondek

Miscellaneous (presentations, translations, interviews, etc)

We show that any symmetry of a smooth strict feedforward system is conjugated to a scaling translation and any 1-parameter family of symmetries to a family of scaling translations along the first variable. We compute explicitly those symmetries by finding the conjugating diffeomorphism. We deduce, in accordance with our previous work, that a smooth system is feedback equivalent to a strict feedforward form if and only if it gives rise to a sequence of systems, such that each element of the sequence, firstly, possesses an infinitesimal symmetry whose flow is conjugated to a 1- parameter families of scaling translations and, …

Data Management Plans: Stages, Components, And Activities, Abbas S. Tavakoli, Kirby Jackson, Linda Moneyham, Kenneth D. Phillips, Carolyn Murdaugh, Gene Meding

Applications and Applied Mathematics: An International Journal (AAM)

Data management strategies have become increasingly important as new computer technologies allow for larger and more complex data sets to be analyzed easily. As a consequence, data management has become a specialty requiring specific skills and knowledge. Many new investigators have no formal training in management of data sets. This paper describes common basic strategies critical to the management of data as applied to a data set from a longitudinal study. The stages of data management are identified. Moreover, key components and strategies, at each stage are described.

Oscillations Of Hyperbolic Systems With Functional Arguments, Yutaka Shoukaku, Norio Yoshida

Applications and Applied Mathematics: An International Journal (AAM)

Hyperbolic systems with functional arguments are studied, and sufficient conditions are obtained for every solution of boundary value problems to be weakly oscillatory (that is, at least one of its components is oscillatory) in a cylindrical domain. Robin-type boundary condition is considered. The approach used is to reduce the multi-dimensional oscillation problems to one-dimensional oscillation problems by using some integral means of solutions.

Stability Analysis For An Seir Age-Structured Epidemic Model Under Vaccination, M. El-Doma

Applications and Applied Mathematics: An International Journal (AAM)

An SEIR age-structured epidemic model is investigated when susceptible and immune individuals are vaccinated indiscriminately and the force of infection of proportionate mixing type. We determine the steady states and obtain an explicitly computable threshold condition, and then study the stability of the steady states.

An Ocean View Of The Early Cenozoic Greenhouse World, Ellen Thomas, Henk Brinkhuis, Matthew Huber, Ursula Röhl

Department of Earth, Atmospheric, and Planetary Sciences Faculty Publications

No abstract provided.

Physics Department News, December 2006, College Of Arts And Sciences

Physics Newsletter

Contents from Volume 5, Issue 2:

• Editor’s Note
• From the Chair
• What’s New at the University
• Faculty Highlights
• Staff Highlights
• PhysTEC
• International Week
• ICPEAC Program Meeting
• Student News
• Annual Student Awards
• Recent Graduates
• Department Roster
• Photo Gallery
• Feedback/Update Reply Form

The Proteomics Of N-Terminal Methionine Cleavage, Frédéric Frottin, Aude Martinez, Philippe Peynot, Sanghamitra Mitra, Richard C. Holz, Carmela Giglione, Thierry Meinnel

Chemistry Faculty Research and Publications

Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1′), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (>120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1′ were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues …

National Security: The Social Implications Of The Politics Of Transparency, M G. Michael, Katina Michael

Faculty of Informatics - Papers (Archive)

This special issue of Prometheus is dedicated to the theme of the Social Implications of National Security Measures on Citizens and Business. National security measures can be defined as those technical and non-technical measures that have been initiated as a means to curb breaches in national security, irrespective of whether these might occur by nationals or aliens in or from outside the sovereign state. National security includes such government priorities as maintaining border control, safeguarding against pandemic outbreaks, preventing acts of terror, and even discovering and eliminating identification fraud. Governments worldwide are beginning to implement information and communication security techniques …

Extending Semantic Web Service Description By Service Assumption, Zheng Lu, Shiyan Li, Aditya K. Ghose, Peter Hyland

Faculty of Informatics - Papers (Archive)

Unlike a traditional software module, which runs within a predictable domain, Web Services are autonomous software agents running in a heterogeneous execution environment. Because of distributed responsibilities, ownership and control, it is often not feasible to acquire all information needed for the service composition. These characteristics of autonomy and heterogeneity are fundamental to service oriented computing but make it inherently difficult to avoid service conflicts. To reason about and adapt to a changing environment, in this work, we will extend current OWL-S by introducing the concept of service assumptions which allow reasoning with incomplete information. Furthermore, together with the proposed …

Detecting Policy Violations Through Traffic Analysis, J. Horton, R. Safavi-Naini

Faculty of Informatics - Papers (Archive)

Restrictions are commonly placed on the permitted uses of network protocols in the interests of security. These restrictions can sometimes be difficult to enforce. As an example, a permitted protocol can be used as a carrier for another protocol not otherwise permitted. However, if the observable behaviour of the protocol exhibits differences between permitted and non-permitted uses, it is possible to detect inappropriate use. We consider SSH, the Secure Shell protocol. This is an encrypted protocol with several uses. We attempt firstly to classify SSH sessions according to some different types of traffic for which the sessions have been used, …

Differential Electron Emission For Single And Multiple Ionization Of Argon By 500 Ev Positrons, Jared M. Gavin, Robert D. Dubois, O. G. De Lucio

Physics Faculty Research & Creative Works

Triply differential electron emission cross sections are measured for single ionization of argon by 500 eV positrons. Data are presented for coincidences between projectiles scattered into angles of 3° and electrons with emission energies less than 10 eV that are observed between 45 and 135° along the beam direction. For interpretation, these are compared to cosine squared representations of the binary and recoil lobes which are convoluted over experimental parameters. Singly differential electron emission data for double and triple ionization by positrons are also presented.