Digital Commons Network^™

Resonant Emergence Of Global And Local Spatiotemporal Order In A Nonlinear Field Model, Marcelo Gleiser, Rafael C. Howell

Dartmouth Scholarship

We investigate the nonequilibrium evolution of a scalar field in (2+1) dimensions. The field is set in a double-well potential in contact (open) or not (closed) with a heat bath. For closed systems, we observe the synchronized emergence of coherent spatiotemporal configurations, identified with oscillons. This initial global ordering degenerates into localized order until all oscillons disappear. We show that the synchronization is driven by resonant parametric oscillations of the field’s zero mode and that local ordering is only possible outside equipartition. None of these orderings occur for open systems.

Experimenting With Tcpa/Tcg Hardware, Or: How I Learned To Stop Worrying And Love The Bear, John Marchesini, Sean Smith, Omen Wild, Rich Macdonald

Computer Science Technical Reports

Over the last few years, our group has been working on applications of secure coprocessors---but has been frustrated by the limited computational environment and high expense of such devices. Over the last few years, the TCPA (now TCG) has produced a specification for a trusted platform module (TPM)---a small hardware addition intended to improve the overall security of a larger machine (and tied up with a still-murky vision of Windows-based trusted computing). Some commodity desktops now come up with these TPMs. Consequently, we began an experiment to see if (in the absence of a Non-Disclosure Agreement) we could use this …

A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald

Computer Science Technical Reports

Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function to identify model orientations consistent with non-crystallographic symmetry (NCS), and to generate NCS-consistent orientations missing from the list of cross-rotation peaks. Our algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups of NCS. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct NCS. The CRANS algorithm was first tested using cross-rotation peaks …

Antipredator Behavior And Physiology Determine Lestes Species Turnover Along The Pond-Permanence Gradient, Robby Stoks, Mark A. Mcpeek

Dartmouth Scholarship

Identifying key traits that shape trade-offs that restrict species to only a subset of environmental gradients is crucial to understanding and predicting species turnover. Previous field experiments have shown that larvae of Lestes damselfly species segregate along the entire gradient of pond permanence and predator presence and that differential predation risk and life history constraints together shape their distribution. Here, we report laboratory experiments that identify key differences in behavior and physiology among species that structure their distributions along this gradient. The absence of adaptive antipredator behavioral responses against large dragonfly larvae and fish of Lestes dryas, the only species …

Objectivity, Information, And Maxwell's Demon, Steven Weinstein

Dartmouth Scholarship

This paper examines some common measures of complexity, structure, and information, with an eye toward understanding the extent to which complexity or information‐content may be regarded as objective properties of individual objects. A form of contextual objectivity is proposed which renders the measures objective, and which largely resolves the puzzle of Maxwell's Demon.

Interleukin-10 And Pathogenesis Of Murine Ocular Toxoplasmosis, Fangli Lu, Shiguang Huang, Lloyd H. Kasper

Dartmouth Scholarship

To understand the role of interleukin-10 (IL-10) in ocular toxoplasmosis, we compared C57BL/6 (B6) and BALB/c background mice lacking a functional IL-10 gene (IL-10(-/-)) and B6 transgenic mice expressing IL-10 under the control of the IL-2 promoter. Increased cellular infiltration and necrosis were observed in the eye tissue of IL-10(-/-) mice of both the B6 and BALB/c backgrounds with associated changes in the levels of cytokines in serum. In contrast, there was no evidence of necrosis in the eye tissue from IL-10 transgenic mice following parasite exposure. Our results demonstrate that IL-10 is important in the regulation of inflammation during …

Disulfide Bond Formation Involves A Quinhydrone-Type Charge–Transfer Complex, James Regeimbal, Stefan Gleiter, Bernard L. Trumpower, Chang-Ang Yu

Dartmouth Scholarship

The chemistry of disulfide exchange in biological systems is well studied. However, the detailed mechanism of how oxidizing equivalents are derived to form disulfide bonds in proteins is not clear. In prokaryotic organisms, it is known that DsbB delivers oxidizing equivalents through DsbA to secreted proteins. DsbB becomes reoxidized by reducing quinones that are part of the membrane-bound electron-transfer chains. It is this quinone reductase activity that links disulfide bond formation to the electron transport system. We show here that purified DsbB contains the spectral signal of a quinhydrone, a charge-transfer complex consisting of a hydroquinone and a quinone in …

Incommensurate Spin Density Waves In Iron Aluminides, D. R. Noakes, A. S. Arrott, M. G. Belk, S. C. Deevi

Dartmouth Scholarship

Neutron diffraction in Fe(Al) reveals incommensurate spin density waves (SDWs) in alloys known to be spin glasses. The wave vectors for crystals of Fe(34Al), Fe(40Al), and Fe(43Al) show n varying from 11 to 6 for →q=2π(h±1/n,k±1/n,l±1/n)/a0, where (h,k,l) and a0 characterize the parent bcc lattice of the CsCl structure. The magnetic reflections are present far above the spin-glass freezing temperatures. These SDWs keep the spins on nearest-neighbor Fe atoms close to parallel, in contrast with SDWs in Cr, which keep nearest-neighbor spins close to antiparallel.

On The Complexity Of Implementing Certain Classes Of Shared Objects, King Yang Tan

Dartmouth College Ph.D Dissertations

We consider shared memory systems in which asynchronous processes cooperate with each other by communicating via shared data objects, such as counters, queues, stacks, and priority queues. The common approach to implementing such shared objects is based on locking: To perform an operation on a shared object, a process obtains a lock, accesses the object, and then releases the lock. Locking, however, has several drawbacks, including convoying, priority inversion, and deadlocks. Furthermore, lock-based implementations are not fault-tolerant: if a process crashes while holding a lock, other processes can end up waiting forever for the lock.

Wait-free linearizable implementations were conceived …

Redshift-Distance Survey Of Early-Type Galaxies: Spectroscopic Data, G. Wegner, M. Bernardi, C. N. A. Willmer, L. N. Da Costa

Dartmouth Scholarship

We present central velocity dispersions and Mg₂ line indices for an all-sky sample of ~1178 elliptical and S0 galaxies, of which 984 had no previous measures. This sample contains the largest set of homogeneous spectroscopic data for a uniform sample of elliptical galaxies in the nearby universe. These galaxies were observed as part of the ENEAR project, designed to study the peculiar motions and internal properties of the local early-type galaxies. Using 523 repeated observations of 317 galaxies obtained during different runs, the data are brought to a common zero point. These multiple observations, taken during the many runs …

Converting Plant Biomass To Fuels And Commodity Chemicals In South Africa: A Third Chapter?, L R. Lynd, H H Von Blottnitz, B Tait, J De Boer, I S. Pretorius, K Rumbold, W H. Van Zyl

Dartmouth Scholarship

There have been two distinct chapters in the history of converting cellulosic biomass to fuels and commodity chemicals in South Africa. The first chapter, fromthe late 1970s to the early 1990s, involved some of the most active research and development efforts of their kind anywhere in the world. Thereafter, during the second chapter, there has been very little activity in the field in South Africa while there has been an unprecedented awakening to the potential of biomass conversion elsewhere. This paper considers the rationale and possible benefits of a potential third chapter based on a revitalized effort on biomass conversion …

A Probability-Based Similarity Measure For Saupe Alignment Tensors With Applications To Residual Dipolar Couplings In Nmr Structural Biology, Anthony K. Yan, Christopher J. Langmead, Bruce Randall Donald

Computer Science Technical Reports

High-throughput NMR structural biology and NMR structural genomics pose a fascinating set of geometric challenges. A key bottleneck in NMR structural biology is the resonance assignment problem. We seek to accelerate protein NMR resonance assignment and structure determination by exploiting a priori structural information. In particular, a method known as Nuclear Vector Replacement (NVR) has been proposed as a method for solving the assignment problem given a priori structural information [24,25]. Among several different kinds of input data, NVR uses a particular type of NMR data known as residual dipolar couplings (RDCs). The basic physics of residual dipolar couplings tells …

Il-23 Produced By Cns-Resident Cells Controls T Cell Encephalitogenicity During The Effector Phase Of Experimental Autoimmune Encephalomyelitis, Burkhard Becher, Brigit G. Durell, Randolph J. Noelle

Dartmouth Scholarship

CNS-resident cells, in particular microglia and macrophages, are a source of inflammatory cytokines during inflammation within the CNS. Expression of IL-23, a recently discovered cytokine, has been shown to be critical for the development of experimental autoimmune encephalomyelitis (EAE) in mice. Expression of the p40 subunit of IL-12 and IL-23 by microglia has been shown in situ and in vitro, but direct evidence for a functional significance of p40 expression by CNS cells during an immune response in vivo is still lacking. Here we report that p40 plays a critical role in maintaining encephalitogenicity during the disease course. By using …

Interpreting Hemoglobin And Water Concentration, Oxygen Saturation, And Scattering Measured In Vivo By Near-Infrared Breast Tomography, Subhadra Srinivasan, Brian W. Pogue, Shudong Jiang, Hamid Dehghani, Christine Kogel, Sandra Soho, Jennifer J. Gibson, Tor D. Tosteson, Steven P. Poplack, Keith D. Paulsen

Dartmouth Scholarship

Near-infrared spectroscopic tomography was used to measure the properties of 24 mammographically normal breasts to quantify whole-breast absorption and scattering spectra and to evaluate which tissue composition characteristics can be determined from these spectra. The absorption spectrum of breast tissue allows quantification of (i) total hemoglobin concentration, (ii) hemoglobin oxygen saturation, and (iii) water concentration, whereas the scattering spectrum provides information about the size and number density of cellular components and structural matrix elements. These property data were tested for correlation to demographic information, including subject age, body mass index, breast size, and radiographic …

A Role For Yip1p In Copii Vesicle Biogenesis, Matthew Heidtman, Catherine Z. Chen, Ruth N. Collins, Charles Barlowe

Dartmouth Scholarship

Yeast Ypt1p-interacting protein (Yip1p) belongs to a conserved family of transmembrane proteins that interact with Rab GTPases. We encountered Yip1p as a constituent of ER-derived transport vesicles, leading us to hypothesize a direct role for this protein in transport through the early secretory pathway. Using a cell-free assay that recapitulates protein transport from the ER to the Golgi complex, we find that affinity-purified antibodies directed against the hydrophilic amino terminus of Yip1p potently inhibit transport. Surprisingly, inhibition is specific to the COPII-dependent budding stage. In support of this in vitro observation, strains bearing the temperature-sensitive yip1-4 allele accumulate ER membranes …

Stellar Pollution And [Fe/H] In The Hyades, Aaron Dotter, Brian Chaboyer

Dartmouth Scholarship

The Hyades open cluster presents a unique laboratory for planet formation and stellar pollution studies because all of the stars have essentially the same age and were born from the same cloud of gas. Furthermore, with an age of ~650 Myr, most of the intermediate- and low-mass stars are on the main sequence. Given these assumptions, the accretion of metal-rich material onto the surface of a star during and shortly after the formation of planetary systems should be evident via the enhanced metallicity of the star. Building on previous work, stellar evolution models that include the effects of stellar pollution …

Mobicom Poster: Evaluating Location Predictors With Extensive Wi-Fi Mobility Data, Libo Song, David Kotz, Ravi Jain, Xiaoning He

Dartmouth Scholarship

A fundamental problem in mobile computing and wireless networks is the ability to track and predict the location of mobile devices. An accurate location predictor can significantly improve the performance or reliability of wireless network protocols, the wireless network infrastructure itself, and many applications in pervasive computing. These improvements lead to a better user experience, to a more cost-effective infrastructure, or both. Location prediction has been proposed in many areas of wireless cellular networks as a means of enhancing performance, including better mobility management, improved assignment of cells to location areas, more efficient paging, and call admission control. To the …

Gauge-Invariant Initial Conditions And Early Time Perturbations In Quintessence Universes, Michael Doran, Christian M. Müller, Gregor Schäfer, Christof Wetterich

Dartmouth Scholarship

We present a systematic treatment of the initial conditions and evolution of cosmological perturbations in a universe containing photons, baryons, neutrinos, cold dark matter, and a scalar quintessence field. By formulating the evolution in terms of a differential equation involving a matrix acting on a vector comprised of the perturbation variables, we can use the familiar language of eigenvalues and eigenvectors. As the largest eigenvalue of the evolution matrix is fourfold degenerate, it follows that there are four dominant modes with a nondiverging gravitational potential at early times, corresponding to adiabatic, cold dark matter isocurvature, baryon isocurvature and neutrino isocurvature …

Impact Of Frustrated Singularities On Magnetic Island Evolution, B. D. Jemella, M. A. Shay, J. F. Drake, B. N. Rogers

Dartmouth Scholarship

The growth of magnetic islands is explored using the magnetohydrodynamic model in a simple slab system in which the value of the tearing mode stability parameter Δ′ can be varied continuously. Unless the system is close to marginal stability reconnection is controlled by Sweet-Parker current layers, whose formation is a consequence of the inherent singular structure of magnetic island equilibria.

On Friction And Surface Cracking During Sliding Of Ice On Ice, Maurine Montagnat, Erland M. Schulson

Dartmouth Scholarship

As a complement to earlier measurements on the friction of both granular fresh-water ice and S2 columnar salt-water ice, new experiments were performed on the friction of S2 columnar fresh-water ice sliding against itself at low velocities (5 × 10−7 to 5 × 10−1 m s−1) and at −10°C, using the same double-shear device as was used earlier. The results showed that under a given set of experimental conditions the kinetic coefficient of friction of S2 fresh-water ice compares favorably with that of the other two variants.The experiments also revealed friction-induced surface cracks and recrystallized grains.These deformation features are explained, …

High-Throughput 3d Homology Detection Via Nmr Resonance Assignment, Christopher James Langmead, Bruce Randall Donald

Computer Science Technical Reports

One goal of the structural genomics initiative is the identification of new protein folds. Sequence-based structural homology prediction methods are an important means for prioritizing unknown proteins for structure determination. However, an important challenge remains: two highly dissimilar sequences can have similar folds --- how can we detect this rapidly, in the context of structural genomics? High-throughput NMR experiments, coupled with novel algorithms for data analysis, can address this challenge. We report an automated procedure, called HD, for detecting 3D structural homologies from sparse, unassigned protein NMR data. Our method identifies 3D models in a protein structural database whose geometries …

An Improved Nuclear Vector Replacement Algorithm For Nuclear Magnetic Resonance Assignment, Christopher James Langmead, Bruce Randall Donald

Computer Science Technical Reports

We report an improvement to the Nuclear Vector Replacement (NVR) algorithm for high-throughput Nuclear Magnetic Resonance (NMR) resonance assignment. The new algorithm improves upon our earlier result in terms of accuracy and computational complexity. In particular, the new NVR algorithm assigns backbone resonances without error (100% accuracy) on the same test suite examined in [Langmead and Donald J. Biomol. NMR 2004], and runs in $O(n^{5/2} \log {(cn)})$ time where $n$ is the number of amino acids in the primary sequence of the protein, and $c$ is the maximum edge weight in an integer-weighted bipartite graph.

Sart Influences Sars Expression In Staphylococcus Aureus, Katherine A. Schmidt, Adhar C. Manna, Ambrose L. Cheung

Dartmouth Scholarship

Staphylococcus aureus is a gram-positive pathogen that is capable of expressing a variety of virulence proteins in response to environmental signals. Virulence protein expression in S. aureus is controlled by a network of regulatory loci including sarA and agr. The sarA/agr network is associated with the expression of cell wall-associated adhesins during exponential growth and the expression of secreted enzymes and toxins in the transition to post-exponential growth. A number of sarA homologs, including sarT and sarS, have been identified in the S. aureus genome. Previous studies have shown that sarA influences expression of both sarT and sarS in the …

A Model Of Zebra Emission In Solar Type Iv Radio Bursts, J. Labelle, R. A. Treumann, P. H. Yoon, M. Karlicky

Dartmouth Scholarship

Solar type IV radio bursts present a theoretical challenge because they are composed of both continuum emission and fine structures. The latter include "zebra bursts," which appear as harmonically spaced multiplets that shift in frequency with time. Similarities between these features and terrestrial auroral emissions suggest a new model to explain zebra-structured type IV emissions. In this model, the basic generation mechanism is identical with that proposed by Winglee and Dulk: mode conversion of Z-mode waves generated by the cyclotron maser mechanism under the condition fuh = Nfce, with N an integer; however, we propose a twist …

Bear: An Open-Source Virtual Secure Coprocessor Based On Tcpa, Rich Macdonald, Sean Smith, John Marchesini, Omen Wild

Computer Science Technical Reports

This paper reports on our ongoing project to use TCPA to transform a desktop Linux machine into a virtual secure coprocessor: more powerful but less secure than higher-end devices. We use TCPA hardware and modified boot loaders to protect fairly static components, such as a trusted kernel; we use an enforcer module---configured as Linux Security Module---to protected more dynamic system components; we use an encrypted loopback filesystem to protect highly dynamic components. All our code is open source and available under GPL from http://enforcer.sourceforge.net/

Phantom Energy: Dark Energy With W < − 1 Causes A Cosmic Doomsday, Robert R. Caldwell, Marc Kamionkowski, Nevin N. Weinberg

Dartmouth Scholarship

We explore the consequences that follow if the dark energy is phantom energy, in which the sum of the pressure and energy density is negative. The positive phantom-energy density becomes infinite in finite time, overcoming all other forms of matter, such that the gravitational repulsion rapidly brings our brief epoch of cosmic structure to a close. The phantom energy rips apart the Milky Way, solar system, Earth, and ultimately the molecules, atoms, nuclei, and nucleons of which we are composed, before the death of the Universe in a “big rip.”

Formal Properties Of Linear Memory Types, Heng Huang, Lea Wittie, Chris Hawblitzel

Computer Science Technical Reports

Efficient low-level systems need more control over memory than safe high-level languages usually provide. As a result, run-time systems are typically written in unsafe languages such as C. This report describes an abstract machine designed to give type-safe code more control over memory. It includes complete definitions and proofs of preservation, progress, strong normalization, erasure, and translation correctness.

Ccr5 Mediates Specific Migration Of Toxoplasma Gondii—Primed Cd8+ Lymphocytes To Inflammatory Intestinal Epithelial Cells, Souphalone Luangsay, Lloyd H. Kasper, Nicolas Rachinel, Laurie A. Minns

Dartmouth Scholarship

Toxoplasma gondii, an obligate intracellular parasite, can invade intestinal epithelial cells and elicit a robust Th1 immune response. In this model of intestinal inflammation, CD8⁺ intraepithelial lymphocytes (IELs) secrete transforming growth factor (TGF)-β, which appears necessary for the maintenance of homeostasis in the intestine. However, the mechanism responsible for the IEL migration to the inflamed intestine is still unclear.An in vitro coculture cell system was used to quantify the IEL attraction by an infected intestinal epithelial cell line (m-IC_cl2). We used CCR5-deficient mice to determine which chemokine receptor—chemokine interaction could be responsible for the recruitment of …

The Virulence Activator Apha Links Quorum Sensing To Pathogenesis And Physiology In Vibrio Cholerae By Repressing The Expression Of A Penicillin Amidase Gene On The Small Chromosome, Gabriela Kovacikova, Wei Lin, Karen Skorupski

Dartmouth Scholarship

Activation of the tcpPH promoter on the Vibrio pathogenicity island by AphA and AphB initiates the Vibrio cholerae virulence cascade and is regulated by quorum sensing through the repressive action of HapR on aphA expression. To further understand how the chromosomally encoded AphA protein activates tcpPH expression, site-directed mutagenesis was used to identify the base pairs critical for AphA binding and transcriptional activation. This analysis revealed a region of partial dyad symmetry, TATGCA-N6-TNCNNA, that is important for both of these activities. Searching the V. cholerae genome for this binding site permitted the identification of a second one upstream of a …

Using Caching For Browsing Anonymity, Anna M. Shubina, Sean W. Smith

Computer Science Technical Reports

Privacy-providing tools, including tools that provide anonymity, are gaining popularity in the modern world. Among the goals of their users is avoiding tracking and profiling. While some businesses are unhappy with the growth of privacy-enhancing technologies, others can use lack of information about their users to avoid unnecessary liability and even possible harassment by parties with contrary business interests, and to gain a competitive market edge. Currently, users interested in anonymous browsing have the choice only between single-hop proxies and the few more complex systems that are available. These still leave the user vulnerable to long-term intersection attacks. In this …