Physical Sciences and Mathematics Commons^™

A Bayesian Model For Pooling Gene Expression Studies That Incorporates Co-Regulation Information, Erin M. Conlon, Bradley L. L. Postier, Barbara A. Methé, Kelly P. Nevin, Derek R. Lovley

Erin M. Conlon

Current Bayesian microarray models that pool multiple studies assume gene expression is independent of other genes. However, in prokaryotic organisms, genes are arranged in units that are co-regulated (called operons). Here, we introduce a new Bayesian model for pooling gene expression studies that incorporates operon information into the model. Our Bayesian model borrows information from other genes within the same operon to improve estimation of gene expression. The model produces the gene-specific posterior probability of differential expression, which is the basis for inference. We found in simulations and in biological studies that incorporating co-regulation information improves upon the independence model. …

Assessment Of Regional Climate Model Simulation Estimates Over The Northeast United States, M. A. Rawlins, Raymond S. Bradley, H. F. Diaz

Raymond S Bradley

Given the coarse scales of coupled atmosphere-ocean global climate models, regional climate models (RCMs) are increasingly relied upon for studies at scales appropriate for many impacts studies. We use outputs from an ensemble of RCMs participating in the North American Regional Climate Change Assessment Program (NARCCAP) to investigate potential changes in seasonal air temperature and precipitation between present (1971–2000) and future (2041–2070) time periods across the northeast United States. The models show a consistent modest cold bias each season and are wetter than observations in winter, spring, and summer. Agreement in spatial variability and pattern correlation is good for air …

The Shape And Mechanics Of Curved Fold Origami Structures, Marcelo A. Dias, Christian Santangelo

Christian Santangelo

We develop recursion equations to describe the three-dimensional shape of a sheet upon which a series of concentric curved folds have been inscribed. In the case of no stretching outside the fold, the three-dimensional shape of a single fold prescribes the shape of the entire origami structure. To better explore these structures, we derive continuum equations, valid in the limit of vanishing spacing between folds, to describe the smooth surface intersecting all the mountain folds. We find that this surface has negative Gaussian curvature with magnitude equal to the square of the fold's torsion. A series of open folds with …

Climate Change Adaptation Chapter: Marshfield, Massachusetts, Joshua H. Chase, Jonathan G. Cooper, Rory Elizabeth Fitzgerald, Filipe Antunes Lima, Sally R. Miller, Toni Marie Pignatelli

Landscape Architecture & Regional Planning Studio and Student Research and Creative Activity

Climate change, understood as a statistically significant variation in the mean state of the climate or its variability, is the greatest environmental challenge of this generation (Intergovernmental Panel on Climate Change, 2001). Marshfield is already being affected by changes in the climate that will have a profound effect on the town’s economy, public health, coastal resources, natural features, water systems, and public and private infrastructure. Adaptation strategies have been widely recognized as playing an important role in improving a community’s ability to respond to climate stressors by resisting damage and recovering quickly.

Based on review of climate projections for the …

Statics And Dynamics Of Atomic Dark-Bright Solitons In The Presence Of Impurities, V. Achilleos, Panos Kevrekidis, V. M. Rothos, D. J. Frantzeskakis

Panos Kevrekidis

Adopting a mean-field description for a two-component atomic Bose-Einstein condensate, we study the statics and dynamics of dark-bright solitons in the presence of localized impurities. We use adiabatic perturbation theory to derive an equation of motion for the dark-bright soliton center. We show that, counterintuitively, an attractive (repulsive) delta-like impurity, acting solely on the bright-soliton component, induces an effective localized barrier (well) in the effective potential felt by the soliton; this way, dark-bright solitons are reflected from (transmitted through) attractive (repulsive) impurities. Our analytical results for the small-amplitude oscillations of solitons are found to be in good agreement with results …

Transfer And Scattering Of Wave Packets By A Nonlinear Trap, Kai Li, Panos Kevrekidis, Boris A. Malomed, D. J. Frantzeskakis

Panos Kevrekidis

In the framework of a one-dimensional model with a tightly localized self-attractive nonlinearity, we study the formation and transfer (dragging) of a trapped mode by “nonlinear tweezers,” as well as the scattering of coherent linear wave packets on the stationary localized nonlinearity. The use of a nonlinear trap for dragging allows one to pick up and transfer the relevant structures without grabbing surrounding “radiation.” A stability border for the dragged modes is identified by means of analytical estimates and systematic simulations. In the framework of the scattering problem, the shares of trapped, reflected, and transmitted wave fields are found. Quasi-Airy …

On Hilbert Modular Threefolds Of Discriminant 49, Lev A. Borisov, Paul E. Gunnells

Paul Gunnells

Let K be the totally real cubic field of discriminant 49 , let \fancyscriptO be its ring of integers, and let p⊂\fancyscriptO be the prime over 7 . Let Γ(p)⊂Γ=SL2(\fancyscriptO) be the principal congruence subgroup of level p . This paper investigates the geometry of the Hilbert modular threefold attached to Γ(p) and some related varieties. In particular, we discover an octic in P3 with 84 isolated singular points of type A2 .

Modular Forms And Elliptic Curves Over The Cubic Field Of Discriminant - 23, Paul E. Gunnells, Dan Yasaki

Paul Gunnells

Let F be the cubic field of discriminant –23 and let O Ϲ F be its ring of integers. By explicitly computing cohomology of congruence subgroups of 〖GL〗_2(O) , we computationally investigate modularity of elliptic curves over F.

Vortex–Bright-Soliton Dipoles: Bifurcations, Symmetry Breaking, And Soliton Tunneling In A Vortex-Induced Double Well, M. Pola, J. Stockhofe, P. Schmelcher, Panos Kevrekidis

Panos Kevrekidis

The emergence of vortex-bright soliton dipoles in two-component Bose-Einstein condensates through bifurcations from suitable eigenstates of the underlying linear system is examined. These dipoles can have their bright solitary structures be in phase (symmetric) or out of phase (anti-symmetric). The dynamical robustness of each of these two possibilities is considered and the out-of-phase case is found to exhibit an intriguing symmetry-breaking instability that can in turn lead to tunneling of the brightwave function between the two vortex “wells.” We interpret this phenomenon by virtue of a vortex-induced double-well system, whose spontaneous symmetry breaking leads to asymmetric vortex-bright dipoles, in addition …

Evidence Of Non-Mean-Field-Like Low-Temperature Behavior In The Edwards-Anderson Spin-Glass Model, B. Yucesoy, Helmut G. Katzgraber, Jonathan Machta

Jonathan Machta

The three-dimensional Edwards-Anderson and mean-field Sherrington-Kirkpatrick Ising spin glasses are studied via large-scale Monte Carlo simulations at low temperatures, deep within the spin-glass phase. Performing a careful statistical analysis of several thousand independent disorder realizations and using an observable that detects peaks in the overlap distribution, we show that the Sherrington-Kirkpatrick and Edwards-Anderson models have a distinctly different low-temperature behavior. The structure of the spin-glass overlap distribution for the Edwards-Anderson model suggests that its low-temperature phase has only a single pair of pure states.

Nonlinear Pt-Symmetric Plaquettes, Kai Li, Panos Kevrekidis, Boris A. Malomed, Uwe Günther

Panos Kevrekidis

We introduce four basic two-dimensional (2D) plaquette configurations with onsite cubic nonlinearities, which may be used as building blocks for 2D PT -symmetric lattices. For each configuration, we develop a dynamical model and examine its PT symmetry. The corresponding nonlinear modes are analyzed starting from the Hamiltonian limit, with zero value of the gain-loss coefficient, . Once the relevant waveforms have been identified (chiefly, in an analytical form), their stability is examined by means of linearization in the vicinity of stationary points. This reveals diverse and, occasionally, fairly complex bifurcations. The evolution of unstable modes is explored by means of …

Borexino Calibrations: Hardware, Methods, And Results, H. Back, G. Bellini, J. Benziger, D. Bick, G. Bonfini, D. Bravo, M. Buizza Avanzini, B. Caccianiga, L. Cadonati, F. Calaprice, C. Carraro, P. Cavalcante, A. Chavarria, D. D'Angelo, S. Davini, A. Derbin, A. Etenko, F. Von Feilitzsch, G. Fernandes, K. Fomenko, D. Franco, C. Galbiati, S. Gazzana, C. Ghiano, M. Giammarchi, M. Goeger-Neff, A. Goretti, L. Grandi, E. Guardincerri, S. Hardy, Aldo Ianni, Andrea Ianni, A. Kayunov, S. Kidner, V. Kobychev, D. Korablev, G. Korga, Y. Koshio, D. Kryn, M. Laubenstein, T. Lewke, E. Litvinovich, B. Loer, F. Lombardi, P. Lombardi, L. Ludhova, I. Machulin, S. Manecki, W. Maneschg, G. Manuzio, Q. Meindl, E. Meroni, L. Miramonti, M. Misiaszek, D. Montanari, P. Mosteiro, V. Muratova, L. Oberauer, M. Obolensky, F. Ortica, K. Otis, M. Pallavicini, L. Papp, L. Perasso, S. Perasso, Andrea Pocar, R. S. Raghavan, G. Ranucci, A. Razeto, A. Re, A. Romani, N. Rossi, D. Rountree, A. Sabelnikov, R. Saldanha, C. Salvo, S. Schönert, H. Simgen, M. Skorokhvatov, O. Smirnov, A. Sotnikov, S. Sukhotin, Y. Suvorov, R. Tartaglia, G. Testera, D. Vignaud, R. B. Vogelaar, J. Winter, M. Wojcik, A. Wright, M. Wurm, J. Xu, O. Zaimidoroga, S. Zavatarelli, G. Zuzel

Andrea Pocar

Borexino was the first experiment to detect solar neutrinos in real-time in the sub-MeV region. In order to achieve high precision in the determination of neutrino rates, the detector design includes an internal and an external calibration system. This paper describes both calibration systems and the calibration campaigns that were carried out in the period between 2008 and 2011. We discuss some of the results and show that the calibration procedures preserved the radiopurity of the scintillator. The calibrations provided a detailed understanding of the detector response and led to a significant reduction of the systematic uncertainties in the Borexino …

Angular Tension Of Black Holes, David Kastor, Jennie Traschen

David Kastor

Angular tension is an Arnowitt-Deser-Misner charge that contributes a work term to the first law of black hole mechanics when the range of an angular coordinate is varied and leads to a new Smarr formula for stationary black holes. A phase diagram for singly spinning D=5 black holes shows that angular tension resolves the degeneracies between spherical black holes and (dipole) black rings and captures the physics of the black ring balance condition. Angular tension depends on the behavior of the metric at rotational axes and we speculate on its relation to rod/domain structure characterizations of higher-dimensional black holes and …

Hierarchical Fractional-Step Approximations And Parallel Kinetic Monte Carlo Algorithms, Giorgos Arampatzis, Markos Katsoulakis, Petr Plechac, Michela Taufer, Lifan Xu

Markos Katsoulakis

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. Rather than focusing on constructing exactly the stochastic trajectories, our approach relies on approximating the evolution of observables, such as density, coverage, correlations and so on. More specifically, we develop a spatial domain decomposition of the Markov operator (generator) that describes the evolution of all observables according to the kinetic Monte Carlo algorithm. This domain decomposition …

Crystallization And Polymerization, Otto Vogl, Frank T. Traceski, Eric G. Vogl

Otto Vogl

No abstract provided.

Slack Dynamics On An Unfurling String, J. A. Hanna, Christian Santangelo

Christian Santangelo

An arch will grow on a rapidly deployed thin string in contact with a rigid plane. We present a qualitative model for the growing structure involving the amplification, rectification, and advection of slack in the presence of a steady stress field, validate our assumptions with numerical experiments, and pose new questions about the spatially developing motions of thin objects.

There Is No Triangulation Of The Torus With Vertex Degrees 5, 6, . . ., 6, 7 And Related Results: Geometric Proofs For Combinatorial Theorems, Ivan Izmestiev, Robert B. Kusner, Günter Rote, Boris Springborn, John M. Sullivan

Robert Kusner

There is no 5,7-triangulation of the torus, that is, no triangulation with exactly two exceptional vertices, of degree 5 and 7. Similarly, there is no 3,5-quadrangulation. The vertices of a 2,4-hexangulation of the torus cannot be bicolored. Similar statements hold for 4,8-triangulations and 2,6-quadrangulations. We prove these results, of which the first two are known and the others seem to be new, as corollaries of a theorem on the holonomy group of a euclidean cone metric on the torus with just two cone points. We provide two proofs of this theorem: One argument is metric in nature, the other relies …

Finite-Temperature Dynamics Of Matter-Wave Dark Solitons In Linear And Periodic Potentials: An Example Of An Antidamped Josephson Junction, Y. Shen, Panos Kevrekidis, N. Whitaker, N. I. Karachalios, D. J. Frantzeskakis

Panos Kevrekidis

We study matter-wave dark solitons in atomic Bose-Einstein condensates (BECs) at finite temperatures, under the effect of linear and periodic potentials. Our model, namely, a dissipative Gross-Pitaevskii equation, is treated analytically by means of dark-soliton perturbation theory and the Landau dynamics approach, which result in a Newtonian equation of motion for the dark-soliton center. This reduced model, which incorporates an effective washboard potential and an antidamping term accounting for finite-temperature effects, constitutes an example of an antidamped Josephson junction. We perform a qualitative (local and global) analysis of the equation of motion. We present results of systematic numerical simulations for …

Proceedings Of The Oss 2012 Doctoral Consortium, Klaas-Jan Stol, Charles M. Schweik, Imed Hammouda

Charles M. Schweik

Papers accepted (and revised) by doctoral students who participated in the Open Source Systems (OSS) 2012 Doctoral Consortium, Hammamet, Tunisia

Quantum Corrections To The Gravitational Interaction Of Massless Particles, Thomas J. Blackburn Jr.

Open Access Dissertations

Donoghue's effective field theory of quantum gravity is extended to include the interaction of massless particles. The collinear divergences which accompany massless particles are examined first in the context of QED and then in quantum gravity. A result of Weinberg is extended to show how these divergences vanish in the case of gravity. The scattering cross section for hypothetical massless scalar particles is computed first, because it is simpler, and the results are then extended to photons. Some terms in the cross section are shown to correspond to the Aichelburg-Sexl metric surrounding a massless particle and to quantum corrections to …

Breaking The Barriers Of All-Polymer Solar Cells: Solving Electron Transporter And Morphology Problems, Nagarjuna Gavvalapalli

Open Access Dissertations

All-polymer solar cells (APSC) are a class of organic solar cells in which hole and electron transporting phases are made of conjugated polymers. Unlike polymer/fullerene solar cell, photoactive material of APSC can be designed to have hole and electron transporting polymers with complementary absorption range and proper frontier energy level offset. However, the highest reported PCE of APSC is 5 times less than that of polymer/fullerene solar cell. The low PCE of APSC is mainly due to: i) low charge separation efficiency; and ii) lack of optimal morphology to facilitate charge transfer and transport; and iii) lack of control over …

New Bilinear Estimates For Quadratic-Derivative Nonlinear Wave Equations In 2+1 Dimensions, Allison J. Tanguay

Open Access Dissertations

This thesis is concerned with the Cauchy problem for the quadratic derivative nonlinear wave equation in two spatial dimensions. Using standard techniques, we reduce local well-posedness in Fourier Lebesgue spaces to bilinear estimates in associated wave Fourier Lebesgue spaces, for which we prove new product estimates. These estimates then allow us to establish local well-posedness in a parameter range that gives improvement over previously known results on the Sobolev scale.

Allosteric Regulation Of Caspase-6 Proteolytic Activity, Elih M. Velazquez-Delgado

Open Access Dissertations

Caspases are cysteine proteases best known for their controlling roles in apoptosis and inflammation. Caspase-6 has recently been shown to play a key role in the cleavage of neurodegenerative substrates that causes Huntington and Alzheimer's Disease, heightening interest in caspase-6 and making it a drug target. All thirteen human caspases have related specificities for binding and cleaving substrate, so achieving caspase-specific regulation at the active site has been extremely challenging if not impossible. We have determined the structures of four unliganded forms of caspase-6, which attain a novel helical structure not observed in any other caspases. In this conformation, rotation …

Information Retrieval With Query Hypergraphs, Michael Bendersky

Open Access Dissertations

Current information retrieval models are optimized for retrieval with short keyword queries. In contrast, in this dissertation we focus on longer, verbose queries with more complex structure that are becoming more common in both mobile and web search. To this end, we propose an expressive query representation formalism based on query hypergraphs. Unlike the existing query representations, query hypergraphs model the dependencies between arbitrary concepts in the query, rather than dependencies between single query terms. Query hypergraphs are parameterized by importance weights, which are assigned to concepts and concept dependencies in the query hypergraph, based on their contribution to the …

Swelling And Folding As Mechanisms Of 3d Shape Formation In Thin Elastic Sheets, Marcelo A. Dias

Open Access Dissertations

We work with two different mechanisms to generate geometric frustration on thin elastic sheets; isotropic differential growth and folding. We describe how controlled growth and prescribing folding patterns are useful tools for designing three-dimensional objects from information printed in two dimensions. The first mechanism is inspired by the possibility to control shapes by swelling polymer films, where we propose a solution for the problem of shape formation by asking the question, ``what 2D metric should be prescribed to achieve a given 3D shape?'', namely the reverse problem. We choose two different types of initial configurations of sheets, disk-like with one …

Studies In The Atomic Spectrometric Determination Of Selenium, Mercury, And Rare Earth Elements, Lindsay Rhae Harris

Open Access Dissertations

The field of analytical chemistry is very important to today's society as more and more regulations and legislations emerge regarding trace elements in food, consumer products, medicines, and the environment. Like many areas of science, the current goals of trace elemental measurements and speciation are to increase knowledge on the subject and to improve upon current techniques by enhancing the figures of merit, such as accuracy and reproducibility, meanwhile balancing with the cost and time of analysis.

The topics covered in this work were investigated primarily through the use of inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma …

The Assembly Of Galaxies Over Cosmic Time, Yicheng Guo

Open Access Dissertations

To Understand how galaxies were assembled across the cosmic time remains one of the most outstanding questions in astronomy. The core of this question is how today's Hubble Sequence, namely the differentiation of galaxy morphology and its correlation to galaxy physical properties, is formed. In this thesis, we investigate the origin of the Hubble Sequence through galaxies at z~2, an epoch when the cosmic star formation activity reaches its peak and the properties of galaxies undergo dramatic transitions. Galaxies at z~2 have two important features that are distinct from nearby galaxies: much higher frequency of clumpy morphology in star-forming systems, …

Searches For Gravitational Waves From Binary Black Hole Coalescences With Ground-Based Laser Interferometers Across A Wide Parameter Space, Satyanarayan Ray Pitambar Mohapatra

Open Access Dissertations

This is an exciting time for Gravitational Wave (GW) theory and observations. From a theoretical standpoint, the grand-challenge problem of the full evolution of a Binary Black Hole (BBH) system has been solved numerically, and a variety of source simulations are made available steadfastly. On the observational side, the first generation of state-of-the-art GW detectors, LIGO and Virgo, have achieved their design goal, collected data and provided astrophysically meaningful limits. The second generation of detectors are expected to start running by 2015. Inspired by this zeitgeist, this thesis focuses on the detection of potential GW signatures from the coalescence of …

Retrieval And Evaluation Techniquesfor Personal Information, Jinyoung Kim

Open Access Dissertations

Providing an effective mechanism for personal information retrieval is important for many applications, and requires different techniques than have been developed for general web search. This thesis focuses on developing retrieval models and representations for personal search, and on designing evaluation frameworks that can be used to demonstrate retrieval effectiveness in a personal environment.

From the retrieval model perspective, personal information can be viewed as a collection of multiple document types each of which has unique metadata. Based on this perspective, we propose a retrieval model that exploits document metadata and multi-type structure. Proposed retrieval models were found to be …

Towards Large-Scale Validation Of Protein Flexibility Using Rigidity Analysis, Filip Jagodzinski

Open Access Dissertations

Proteins are dynamic molecules involved in virtually every chemical process in our bodies. Understanding how they flex and bend provides fundamental insights to their functions. At the atomic level, protein motion cannot be observed using existing experimental methods. To gain insights into these motions, simulation methods are used. However such simulations are computationally expensive.

Rigidity analysis is a fast, alternative graph-based method to molecular simulations, that gives information about the flexibility properties of molecules modeled as mechanical structures. Due to the lack of convenient tools for curating protein data, the usefulness of rigidity analysis has been demonstrated on only a …