Physical Sciences and Mathematics Commons^™

Fibonacci Or Quasi-Symmetric Phyllotaxis. Part Ii: Botanical Observations, Stéphane Douady, Christophe Golé

Mathematics Sciences: Faculty Publications

Historically, the study of phyllotaxis was greatly helped by the simple description of botanical patterns by only two integer numbers, namely the number of helices (parastichies) in each direction tiling the plant stem. The use of parastichy num- bers reduced the complexity of the study and created a proliferation of generaliza- tions, among others the simple geometric model of lattices. Unfortunately, these simple descriptive method runs into difficulties when dealing with patterns pre- senting transitions or irregularities. Here, we propose several ways of addressing the imperfections of botanical reality. Using ontogenetic analysis, which follows the step-by-step genesis of the pattern, …

Fibonacci Or Quasi-Symmetric Phyllotaxis. Part I: Why?, Christophe Golé, Jacques Dumais, Stéphane Douady

Mathematics Sciences: Faculty Publications

The study of phyllotaxis has focused on seeking explanations for the occurrence of consecutive Fibonacci numbers in the number of helices paving the stems of plants in the two opposite directions. Using the disk-accretion model, first introduced by Schwendener and justified by modern biological studies, we observe two dis- tinct types of solutions: the classical Fibonacci-like ones, and also more irregular configurations exhibiting nearly equal number of helices in a quasi-square pack- ing, the quasi-symmetric ones, which are a generalization of the whorled patterns. Defining new geometric tools allowing to work with irregular patterns and local transitions, we provide simple …

A Survey Of Visual Analytics Tools For Effective Decision-Making, R. Jordan Crouser, Erina Fukuda, Subashini Sridhar

Computer Science: Faculty Publications

Over the past decade, the visualization for cybersecurity (VizSec) research community has adapted many information visualization techniques to support the critical work of cyber analysts. While these efforts have yielded many specialized tools and platforms, the community lacks a unified approach to the design and implementation of these systems. In this work, we provide a retrospective analysis of the past decade of VizSec publications, with an eye toward developing a more cohesive understanding of the emerging patterns of design:

• We identify common thematic groupings among existing work, as well as interesting patterns of design around the utilization of various …

Looking Into The Crystal Ball: Requirements Evolution Over Time, Alicia M. Grubb, Marsha Chechik

Computer Science: Faculty Publications

Goal modeling has long been used in the literature to model and reason about system requirements, constraints within the domain and environment, and stakeholders' goals. Goal model analysis helps stakeholders answer 'what if' questions enabling them to make tradeoff decisions about their project requirements. However, questions concerning the evolution over time of stakeholder requirements or changes in actor intentionality are not explicitly addressed by current approaches. In this paper, we tackle this problem by presenting a method for specifying changes in intentions over time, and a technique that uses simulation for asking a variety of 'what if' questions about such …

Pushback: Critical Data Designers And Pollution Politics, Kim Fortun, Lindsay Poirier, Alli Morgan, Brandon Costelloe-Kuehn, Mike Fortun

Statistical and Data Sciences: Faculty Publications

In this paper, we describe how critical data designers have created projects that ‘push back’ against the eclipse of environmental problems by dominant orders: the pioneering pollution database Scorecard, released by the US NGO Environmental Defense Fund in 1997; the US Environmental Protection Agency’s EnviroAtlas that brings together numerous data sets and provides tools for valuing ecosystem services; and the Houston Clean Air Network’s maps of real-time ozone levels in Houston. Drawing on ethnographic observations and interviews, we analyse how critical data designers turn scientific data and findings into claims and visualisations that are meaningful in contemporary political terms. The …

Tracing Slow Winds From T Tauri Stars Via Low-Velocity Forbidden Line Emission, M. N. Simon, I. Pascucci, Suzan Edwards, W. Feng, U. Gorti, D. Hollenbach, E. Rigliaco, J. T. Keane

Astronomy: Faculty Publications

Using Keck/HIRES spectra (Δ v ∼ 7 km s−1) we analyze forbidden lines of [O I] 6300 Å, [O I] 5577 Å and [S II] 6731 Å from 33 T Tauri stars covering a range of disk evolutionary stages. After removing a high-velocity component (HVC) associated with microjets, we study the properties of the low-velocity component (LVC). The LVC can be attributed to slow disk winds that could be magnetically (magnetohydrodynamic) or thermally (photoevaporative) driven. Both of these winds play an important role in the evolution and dispersal of protoplanetary material. LVC emission is seen in all 30 stars with …

Unfolding Genus-2 Orthogonal Polyhedra With Linear Refinement, Mirela Damian, Erik Demaine, Robin Flatland, Joseph O'Rourke

Mathematics Sciences: Faculty Publications

We show that every orthogonal polyhedron of genus g ≤ 2 can be unfolded without overlap while using only a linear number of orthogonal cuts (parallel to the polyhedron edges). This is the first result on unfolding general orthogonal polyhedra beyond genus- 0. Our unfolding algorithm relies on the existence of at most 2 special leaves in what we call the “unfolding tree” (which ties back to the genus), so unfolding polyhedra of genus 3 and beyond requires new techniques.

Hard-Wall And Non-Uniform Lattice Monte Carlo Approaches To One-Dimensional Fermi Gases In A Harmonic Trap, Casey E. Berger, Joaquín E. Drut, William J. Porter

Physics: Faculty Publications

We present in detail two variants of the lattice Monte Carlo method aimed at tackling systems in external trapping potentials: a uniform-lattice approach with hard-wall boundary conditions, and a non-uniform Gauss–Hermite lattice approach. Using those two methods, we compute the ground-state energy and spatial density profile for systems of N=4–8 harmonically trapped fermions in one dimension. From the favorable comparison of both energies and density profiles (particularly in regions of low density), we conclude that the trapping potential is properly resolved by the hard-wall basis. Our work paves the way to higher dimensions and finite temperature analyses, as calculations with …

The “Phunger Games”: Manuscript Review To Assess Graduating Chemistry Majors, David J. Gorin, Elizabeth R. Jamieson, Kate Queeny, Kevin M. Shea, Carrie G. Read Spray

Chemistry: Faculty Publications

Numerous options exist to assess student performance using standardized, multiple-choice exams at the course and department levels. This paper describes the development and implementation of an alternative department-level assessment for graduating chemistry majors. The assessment detailed here evaluates students’ ability to transfer chemical knowledge from their classes to a real life application, namely the review of a scientific paper. Working in groups of three with full access to reference materials, students review a paper intentionally doctored by the faculty to contain a variety of errors. Student groups identify and correct mistakes in a paper with content spanning numerous chemistry subdisciplines. …

Slip Distribution Of The 2014 Mw=8.1 Pisagua, Northern Chile, Earthquake Sequence Estimated From Coseismic Fore-Arc Surface Cracks, John P. Loveless, Chelsea P. Scott, Richard W. Allmendinger, Gabriel González

Geosciences: Faculty Publications

The 2014 Mw = 8.1 Iquique (Pisagua), Chile, earthquake sequence ruptured a segment of the Nazca-South America subduction zone that last hosted a great earthquake in 1877. The sequence opened >3700 surface cracks in the fore arc of decameter-scale length and millimeter-to centimeter-scale aperture. We use the strikes of measured cracks, inferred to be perpendicular to coseismically applied tension, to estimate the slip distribution of the main shock and largest aftershock. The slip estimates are compatible with those based on seismic, geodetic, and tsunami data, indicating that geologic observations can also place quantitative constraints on rupture properties. The earthquake sequence …

Neilson Library Final Charter, Smith College

The New Neilson Library

Final charter for the New Neilson Library project.

Segmentation-Free Spotting Of Cuneiform Using Part-Structured Models, Bartosz Bogacz, Nicholas Howe, Mara Mara

Computer Science: Faculty Publications

Cuneiform scripts constitute an immense source of information about ancient history, dating back almost four thousand years. Documents were written by imprinting wedgeshaped impressions into wet clay tablets, and current scholarly practice typically transcribes the resulting markings by hand with ink on paper. This work develops algorithmic methods for cuneiform script, combining feature extraction for cuneiform wedges with prior work on segmentation-free word spotting using part-structured models. We adapt the inkball model used for word spotting to treat wedge features as individual parts arranged in a tree structure. The geometric relationship between query and target is measured by the energy …

Interseismic Deformation And Moment Deficit Along The Manila Subduction Zone And The Philippine Fault System, Ya-Ju Hsu, Shui-Beih Yu, John P. Loveless, Teresito Bacolcol, Renato Solidum, Artemio Luis Jr., Alfie Pelicano, Jochen Woessner

Geosciences: Faculty Publications

We examine interseismic coupling of the Manila subduction zone and fault activity in the Luzon area using a block model constrained by GPS data collected from 1998 to 2015. Estimated long-term slip rates along the Manila subduction zone show a gradual southward decrease from 90–100 mm/yr at the northwest tip of Luzon to 65–80 mm/yr at the southern portion of the Manila Trench. We provide two block models (models A and B) to illustrate possible realizations of coupling along the Manila Trench, which may be used to infer future earthquake rupture scenarios. Model A shows a low coupling ratio …

Extinction Intensity, Selectivity And Their Combined Macroevolutionary Influence In The Fossil Record, Jonathan L. Payne, Andrew M. Bush, Ellen T. Chang, Noel A. Heim, Matthew L. Knope, Sara B. Pruss

Geosciences: Faculty Publications

The macroevolutionary effects of extinction derive from both intensity of taxonomic losses and selectivity of losses with respect to ecology, physiology and/or higher taxonomy. Increasingly, palaeontologists are using logistic regression to quantify extinction selectivity because the selectivity metric is independent of extinction intensity and multiple predictor variables can be assessed simultaneously. We illustrate the use of logistic regression with an analysis of physiological buffering capacity and extinction risk in the Phanerozoic marine fossil record. We propose the geometric mean of extinction intensity and selectivity as a metric for the influence of extinction events. The end-Permian mass extinction had the largest …

Smoothness Of Subriemannian Isometries, Luca Capogna, Enrico Le Donne

Mathematics Sciences: Faculty Publications

We show that the group of isometries (i.e., distance-preserving homeomorphisms) of an equiregular subRiemannian manifold is a finite-dimensional Lie group of smooth transformations. The proof is based on a new PDE argument, in the spirit of harmonic coordinates, establishing that in an arbitrary subRiemannian manifold there exists an open dense subset where all isometries are smooth.

Inkball Models As Features For Handwriting Recognition, Nicholas Howe, Andreas Fischer, Baptiste Wicht

Computer Science: Faculty Publications

Inkball models provide a tool for matching and comparison of spatially structured markings such as handwritten characters and words. Hidden Markov models offer a framework for decoding a stream of text in terms of the most likely sequence of causal states. Prior work with HMM has relied on observation of features that are correlated with underlying characters, without modeling them directly. This paper proposes to use the results of inkball-based character matching as a feature set input directly to the HMM. Experiments indicate that this technique outperforms other tested methods at handwritten word recognition on a common benchmark when applied …

Synthetic And Computational Studies On The Rhodium-Catalyzed Hydroamination Of Aminoalkenes, Alexandra E. Strom, David Balcells, John F. Hartwig

Chemistry: Faculty Publications

The influence of ligand structure on rhodium-catalyzed hydroamination has been evaluated for a series of phosphinoarene ligands. These catalysts have been evaluated in a set of catalytic intramolecular Markovnikov hydroamination reactions. The mechanism of hydroamination catalyzed by the rhodium(I) complexes in this study was examined computationally, and the turnover-limiting step was elucidated. These computational studies were extended to a series of theoretical hydroamination catalysts to compare the electronic effects of the ancillary ligand substituents. The relative energies of intermediates and transition states were compared to those of intermediates in the reaction catalyzed by the unsubstituted catalyst. The experimental difference in …

Bayesian Peer Calibration With Application To Alcohol Use, Miles Q. Ott, Joseph W. Hogan, Krista J. Gile, Crystal Linkletter, Nancy P. Barnett

Statistical and Data Sciences: Faculty Publications

Peers are often able to provide important additional information to supplement self-reported behavioral measures. The study motivating this work collected data on alcohol in a social network formed by college students living in a freshman dormitory. By using two imperfect sources of information (self-reported and peer-reported alcohol consumption), rather than solely self-reports or peer-reports, we are able to gain insight into alcohol consumption on both the population and the individual level, as well as information on the discrepancy of individual peer-reports. We develop a novel Bayesian comparative calibration model for continuous, count and binary outcomes that uses covariate information to …

Modeling Internet Traffic Generations Based On Users And Activities For Telecommunication Applications, Sara Stoudt, Pamela Badian-Pessot, Blanche Ngo Mahop, Erika Earley, Jordan Menter, Yadira Flores, Danielle Williams, Weijia Zhang, Liza Maharjan, Yixin Bao, Laura Rosenbauer, Van Nguyen, Veena Mendiratta, Nessy Tania

Mathematics Sciences: Faculty Publications

A traffic generation model is a stochastic model of the data flow in a communication network. These models are useful during the development of telecommunication technologies and for analyzing the performance and capacity of various protocols, algorithms, and network topologies. We present here two modeling approaches for simulating internet traffic. In our models, we simulate the length and interarrival times of individual packets, the discrete unit of data transfer over the internet. Our first modeling approach is based on fitting data to known theoretical distributions. The second method utilizes empirical copulae and is completely data driven. Our models were based …

Unfolding Convex Polyhedra Via Radially Monotone Cut Trees, Joseph O'Rourke

Computer Science: Faculty Publications

A notion of "radially monotone" cut paths is introduced as an effective choice for finding a non-overlapping edge-unfolding of a convex polyhedron. These paths have the property that the two sides of the cut avoid overlap locally as the cut is infinitesimally opened by the curvature at the vertices along the path. It is shown that a class of planar, triangulated convex domains always have a radially monotone spanning forest, a forest that can be found by an essentially greedy algorithm. This algorithm can be mimicked in 3D and applied to polyhedra inscribed in a sphere. Although the algorithm does …

Splines In Geometry And Topology, Julianna Tymoczko

Mathematics Sciences: Faculty Publications

This survey paper describes the role of splines in geometry and topology, emphasizing both similarities and differences from the classical treatment of splines. The exposition is non-technical and contains many examples, with references to more thorough treatments of the subject.

Regularity For Subelliptic Pde Through Uniform Estimates In Multi-Scale Geometries, Luca Capogna, Giovanna Citti

Mathematics Sciences: Faculty Publications

We aim at reviewing and extending a number of recent results addressing stability of certain geometric and analytic estimates in the Riemannian approximation of subRiemannian structures. In particular we extend the recent work of the the authors with Rea (Math Ann 357(3):1175–1198, 2013) and Manfredini (Anal Geom Metric Spaces 1:255–275, 2013) concerning stability of doubling properties, Poincare’ inequalities, Gaussian estimates on heat kernels and Schauder estimates from the Carnot group setting to the general case of Hörmander vector fields.

Programming Molecular Association And Viscoelastic Behavior In Protein Networks, Lawrence J. Dooling, Maren E. Buck, Wen Bin Zhang, David A. Tirrell

Chemistry: Faculty Publications

No abstract provided.

Plants' Native Distributions Do Not Reflect Climatic Tolerance, Tierney Bocsi, Jenica M. Allen, Jesse Bellemare, John Kartesz, Misako Nishino, Bethany A. Bradley

Biological Sciences: Faculty Publications

Aim: Biogeographers have long known that plant species do not fully encompass their fundamental niche. Nonetheless, in practice, species distribution modelling assumes that plant distributions represent a reasonable approximation of their environmental tolerance. For ecological forecasting, projections of habitat loss due to climate change assume that many species will be unable to tolerate climate conditions outside of those found within their current distributional ranges. We aim to test how well occurrences in the native range approximate the climatic conditions in which plant species can survive.

Location: Continental USA. Methods: We compared the climatic conditions between occurrences in the US native …

Contrasting Sediment Melt And Fluid Signatures For Magma Components In The Aeolian Arc: Implications For Numerical Modeling Of Subduction Systems, Denis Zamboni, Esteban Gazel, Jeffrey G. Ryan, Claudia Cannatelli, Federico Lucchi, Zachary D. Atlas, Jarek Trela, Sarah E. Mazza, Benedetto De Vivo

Geosciences: Faculty Publications

The complex geodynamic evolution of Aeolian Arc in the southern Tyrrhenian Sea resulted in melts with some of the most pronounced along the arc geochemical variation in incompatible trace elements and radiogenic isotopes worldwide, likely reflecting variations in arc magma source components. Here we elucidate the effects of subducted components on magma sources along different sections of the Aeolian Arc by evaluating systematics of elements depleted in the upper mantle but enriched in the subducting slab, focusing on a new set of B, Be, As, and Li measurements. Based on our new results, we suggest that both hydrous fluids and …

A Bayesian Method For Cluster Detection With Application To Five Cancer Sites In Puget Sound, Albert Y. Kim, Jon Wakefield

Mathematics Sciences: Faculty Publications

Cluster detection is an important public health endeavor and in this paper we describe and apply a recently developed Bayesian method. Commonly-used approaches are based on so-called scan statistics and suffer from a number of difficulties including how to choose a level of significance and how to deal with the possibility of multiple clusters. The basis of our model is to partition the study region into a set of areas which are either “null” or “non-null”, the latter corresponding to clusters (excess risk) or anti-clusters (reduced risk). We demonstrate the Bayesian method and compare with a popular existing approach, using …

Effect Of The Spiroiminodihydantoin Lesion On Nucleosome Stability And Positioning, Erika Norabuena, Sara Barnes Williams, Margaret A. Klureza, Liana J. Goehring, Brian Gruessner, Mala L. Radhakrishnan, Elizabeth R. Jamieson, Megan E. Núñez

Chemistry: Faculty Publications

DNA is constantly under attack by oxidants, generating a variety of potentially mutagenic covalently modified species, including oxidized guanine base products. One such product is spiroiminodihydantoin (Sp), a chiral, propeller-shaped lesion that strongly destabilizes the DNA helix in its vicinity. Despite its unusual shape and thermodynamic effect on double-stranded DNA structure, DNA duplexes containing the Sp lesion form stable nucleosomes upon being incubated with histone octamers. Indeed, among six different combinations of lesion location and stereochemistry, only two duplexes display a diminished ability to form nucleosomes, and these only by ∼25%; the other four are statistically indistinguishable from the control. …

Generalized Splines On Arbitrary Graphs, Simcha Gilbert, Julianna Tymoczko, Shira Viel

Mathematics Sciences: Faculty Publications

Let G be a graph whose edges are labeled by ideals of a commutative ring. We introduce a generalized spline, which is a vertex labeling of G by elements of the ring so that the difference between the labels of any two adjacent vertices lies in the corresponding edge ideal. Generalized splines arise naturally in combinatorics (algebraic splines of Billera and others) and in algebraic topology (certain equivariant cohomology rings, described by Goresky, Kottwitz, and MacPherson, among others). The central question of this paper asks when an arbitrary edge-labeled graph has nontrivial generalized splines. The answer is “always”, and we …

Deep Learning For Population Genetic Inference, Sara Sheehan, Yun S. Song

Computer Science: Faculty Publications

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statis- tics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on …

Sticky Seeding In Discrete-Time Reversible-Threshold Networks, Gwen Spencer

Mathematics Sciences: Faculty Publications

When nodes can repeatedly update their behavior (as in agent-based models from computational social science or repeated-game play settings) the problem of optimal network seeding becomes very complex. For a popular spreading-phenomena model of binary-behavior updating based on thresholds of adoption among neighbors, we consider several planning problems in the design of Sticky Interventions: when adoption decisions are reversible, the planner aims to find a Seed Set where temporary intervention leads to long-term behavior change. We prove that completely converting a network at minimum cost is Ω(ln(OP T ))-hard to approximate and that maximizing conversion subject to a budget is …