Digital Commons Network^™

Meld Application On Refining Dock Results, Cong Liu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In order to bridge the computational gap between DOCK and MD-based methods, a pipeline was designed to combine external information derived from DOCK with replica exchange molecular dynamics using MELD, an algorithm recently developed by our lab. Our goal was to predict the lowest free energy binding pose within the DOCK ensemble, therefore enabling us to refine DOCK results in cases where the correct structure is incorrectly scored. Our method was tested on 8 such ‘scoring failures’ found in the DOCK database SB2012. Three protocols of extracting structural information from DOCK ensembles were designed and tested. Crystal-like poses were correctly …

Risk Assessment In Intraday Trading, Fangfei Dong

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In these days, high frequency hedge funds have developed as a new and successful category of hedge funds. Accordingly, risk management is now obliged to keep pace with this market and takes intraday-risk management into consideration. To aim to contribute on answering questions on intraday risk management, the dissertation consists of three parts. In first part, an intraday risk assessment model incorporating long-range dependence and heavy-tailness is suggested. Fractional integrated time series model with nearly elliptical distributed innovations are used to compute more accurate intraday level value at risk. Second part investigates the market efficiency by analyzing the relation between …

A New Stochastic Regime Switching Model With Time-Varying Regression Coefficients And Error Variances, Xiaojin Dong

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Since the publication of Hamilton’s (1989) seminal work on Markov switching model, a large number of applications have been found in economics and finance. The classical Markov switching models characterize the estimation of parameters in finite state, limited by the pre-specified number of regimes, thus it is restrictive in empirical studies. In this thesis, we develop a stochastic regime switching model, where the model parameters are both categorical and continuous. By assuming conjugate priors and defining stochastic regime switching variables, we derive recursive filtering and smoothing algorithms to estimate the regimes and develop closed-form recursive Bayes estimates of the regression …

Automatic Discovery Of Efficient Divide-&-Conquer Algorithms For Dynamic Programming Problems, Pramod Ganapathi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation is an excursion into computer-discovered algorithms and computer-aided algorithm design. In our vision of the not-so-distant future of computing, machines will take the responsibility of designing and implementing most, if not all, machine-specific highly efficient nontrivial algorithms with provable correctness and performance guarantees. Indeed, as the complexity of computing hardware grows and their basic architectures keep changing rapidly, manually redesigning and reimplementing key algorithms for high performance on every new architecture is quickly becoming an impossible task. Automation is needed. We design algorithms that can design other algorithms. Our focus is on auto-generating algorithms for solving dynamic programming …

The Computational Complexity Of The Provision-After-Wait Problem In Healthcare, Gowtham Srinivasan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In Provision-after-Wait in Healthcare (PaW), a social planner operating on a constrained budget is required to sponsor medical treatments to a population of patients. Specifically, each patient is allocated to any of the k hospitals to receive a single unit of medical treatment. The cost of treatment depends upon the hospital and is paid for by the planner. Associated with every patient is a set of k non-negative numbers which denote the patients’ preference or intrinsic value towards getting treated in each of the k hospitals. Since the patients do not pay for the treatment and the planner cannot afford …

Novel Spectral Representations And Sparsity-Driven Algorithms For Shape Modeling And Analysis, Ming Zhong

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this dissertation, we focus on extending classical spectral shape analysis by incorporating spectral graph wavelets and sparsity-seeking algorithms. Defined with the graph Laplacian eigenbasis, the spectral graph wavelets are localized both in the vertex domain and graph spectral domain, and thus are very effective in describing local geometry. With a rich dictionary of elementary vectors and forcing certain sparsity constraints, a real life signal can often be well approximated by a very sparse coefficient representation. The many successful applications of sparse signal representation in computer vision and image processing inspire us to explore the idea of employing sparse modeling …

Moving Mountains, Desert Sea, Victoria Hortensia Febrer

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

I consider the role of not just the act of painting and the act of remembering, but the sea, the desert, the wind, the salt, the earth, and the light in this process—the way that non-human elements exert their existence and connect us to history, time, and geography. I use the term “painting†broadly here, to consider any act of placing color onto a surface, which in my case includes the use of acrylic, red wine (vinography), and projected light. The primary manifestation of this investigation is a still ongoing series of over 400 paintings and vinographs of landmasses seen …

Persistent Organic Chemicals In The Pacific Basin Countries: An Overview, Bommanna G. Loganathan

Faculty & Staff Research and Creative Activity

The Pacific Basin is a unique geographical region representing tropical, temperate and polar zones. This region is home to 2/3 of world’s population and consists of rapidly growing economies (countries) and highly developed countries. The Pacific Basin countries have had a history of use of persistent organic chemicals (POCs) at varying proportions during the last five decades. Due to diverse climatic and socio-economic conditions, the environment and biota in different countries in this basin have varying degrees of environmental contamination and effects on wildlife and humans. In this chapter, the historical background of POCs including, discovery, production, use, regulations/restrictions imposed, …

Environmental Emission Of Pharmaceuticals From Wastewater Treatment Plants In The Usa, Bikram Subedi, Bommanna G. Loganathan

Faculty & Staff Research and Creative Activity

The residual drugs, drug bioconjugates, and their metabolites, mostly from human and veterinary usage, are routinely flushed down the drain, and enter wastewater treatment plants (WWTP). Increasing population, excessive use of allopathic medicine, continual introduction of novel drugs, and existing inefficient wastewater treatment processes result in the discharge of large volumes of pharmaceuticals and their metabolites from the WWTPs into the environment. The effluent from the WWTPs globally contaminate ~25% of rivers and the lakes. Pharmaceuticals in the environment, as contaminants of emerging concerns, behave as pseudo-persistent despite their relatively short environmental half-lives in the environment. Therefore, residual levels of …

Could ‘Doctor Who’ Time Travel Really Work?, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

A Non-Traditional Approach To Synthesizing Aryl Vinyl Sulfides Is Described. 2,2-Diphenyl-1,3-Oxathiolane Slowly Liberates Vinyl Sulfide Anion Under Basic Conditions. Using A Pd/Xantphos Catalyst System To Activate A Wide Range Of Aryl Bromides, This Transient Sulfide Species Can Be Effectively Trapped And Fed Into A Traditional Pd0/Pdii Catalytic Cycle. Scope And Limitations Of The Methodology Are Presented Along With Significant Discussion Of A Competitive C–S Bond Activation By This Catalyst System., Jason R. Schmink, Summer A. Baker Dockrey, Tianyi Zhang, Naomi Chebet, Alexis Van Venrooy, Mary Sexton, Sarah I. Lew, Steffany Chou, Ami Okazaki

Chemistry Faculty Research and Scholarship

A non-traditional approach to synthesizing aryl vinyl sulfides is described. 2,2-diphenyl-1,3-oxathiolane slowly liberates vinyl sulfide anion under basic conditions. Using a Pd/Xantphos catalyst system to activate a wide range of aryl bromides, this transient sulfide species can be effectively trapped and fed into a traditional Pd⁰/Pd^II catalytic cycle. Scope and limitations of the methodology are presented along with significant discussion of a competitive C–S bond activation by this catalyst system.

Huntsman Alumni Magazine, Fall 2016, Usu Jon M. Huntsman School Of Business

Huntsman Business Magazine

Alumni magazine for the Jon M. Huntsman School of Business at Utah State University.

Understanding How Algorithms Work Persuasively Through The Procedural Enthymeme, Kevin Brock, Dawn Shepherd

English Literature Faculty Publications and Presentations

Procedure, when discussed in regards to rhetoric, and to “digital rhetoric” in particular, is framed overwhelmingly in regards to game play (and to video games most frequently). We argue that this view needs to be expanded if scholars of rhetoric are to realize how complex human-computer rhetor systems function in diverse contexts. Such systems do so through procedural enthymemes, which persuade audience agents to action through the apparent logic of a given system. Procedural persuasion occurs most often via strategies that facilitate the agent to assume an active role in “self-persuasion” in order to complete a given enthymeme. In …

Stony Brook Press, V. 38, N. 05, Stony Brook University. Stony Brook Press.

Stony Brook Press

v. 36,n. 4, v.:ill. ; 38 cm (original analog pub.)

The Transition Experiences Of International Graduate Students In Clark University School Of Professional Studies, Xuesong Huang, Mingyang Lian, Dang Trung, Jay Sheth, Yuwei Yang, Irina Klimenko

School of Professional Studies

In the last decade, the School of Professional Studies at Clark University has witnessed a sharp increase in international students. More and more international students in the millennial generation have entered the School of Professional Studies pursuing one of the two-year graduate programs: Master of Science in Professional Studies, Master of Science in Public Administration, and Master of Science in Information Technology. In the past, working adult student dominant the program. These students already had a career outside the classrooms before them came to study. The millennial international students have generated new adjustment problems. Some of the transition issues of …

Investigating The Practices And Needs Of Agricultural Researchers At The University Of Nebraska-Lincoln, Leslie M. Delserone, Andrea L. Dinkelman

University of Nebraska-Lincoln Libraries: Faculty Publications

University of Nebraska-Lincoln (UNL) Libraries was one of 19 libraries participating in a national study, initiated by Ithaka S+R, of the research practices and needs of agricultural researchers. Two UNL Libraries faculty members participated in this study by interviewing 11 UNL agricultural scholars during the summer of 2016. The ethnographic research approach revealed four core themes explored in this UNL-specific report: interdisciplinarity and collaborations; scientific communication practices; scientific research data; and challenges and opportunities. Illustrated by the sample of faculty comments presented here, the themes have direct implications for the UNL Libraries, while in other cases these point to concerns …

Wave Propagation And Imaging In Structured Optical Media, Zun Huang

Open Access Dissertations

Structured optical media, usually characterized by periodic patterns of inhomogeneities in bulk materials, provide a new approach to ultimate control of wave propagation with possible practical applications: from distributed feedback lasers by diffraction gratings, to highly nonlinear performance for super-continuum generation, to fiber-optic telecommunications by microstructured photonic crystal fibers, to invisibility cloaking, to super-resolution imaging with metamaterials etc.

In particular, structured optical media allow to manipulate the wave propagation and dispersion. In this thesis, we focus on engineering the propagation phase dispersion by modulating the compositions and dimensions of the periodic elements. By tailoring the dispersion in momentum space, we …

Ole Miss Engineer 2016-2017

Ole Miss Engineer

No abstract provided.

Reduction Of A Nilpotent Intuitionistic Fuzzy Matrix Using Implication Operator, Riyaz A. Padder, P. Murugadas

Applications and Applied Mathematics: An International Journal (AAM)

A problem of reducing intuitionistic fuzzy matrices is examined and some useful properties are obtained with respect to nilpotent intutionistic fuzzy matrices. First, reduction of irreflexive and transitive intuitionistic fuzzy matrices are considered, and then the properties are applied to nilpotent intutionistic fuzzy matrices. Nilpotent intuitionistic fuzzy matrices are intuitionistic fuzzy matrices which signify acyclic graphs, and the graphs are used to characterize consistent systems. The properties are handy for generalization of various systems with intuitionistic fuzzy transitivity.

Hydromagnetic Peristaltic Transportation With Porous Medium Through An Asymmetric Vertical Tapered Channel And Joule Heating, S. R. Kumar

Applications and Applied Mathematics: An International Journal (AAM)

The present paper deals with a theoretical investigation of the hydromagnetic peristaltic transportation with porous medium through coaxial asymmetric vertical tapered channel and joule heating which has been studied under the assumption of long wavelength approximations. Exact analytical expressions of axial velocity, volume flow rate, pressure gradient, temperature and heat transfer coefficient at both walls were calculated. The effects of various emerging parameters, Hartmann number, Non-uniform parameter, Prandtl number, Heat generator parameter, Brinkman number, Porous parameter are discussed through the use of graphs. We notice from the figures that the temperature of the fluid increases in the entire vertical tapered …

Solution Of A Cauchy Singular Fractional Integro-Differential Equation In Bernstein Polynomial Basis, Avipsita Chatterjee, Uma Basu, B. N. Mandal

Applications and Applied Mathematics: An International Journal (AAM)

This article proposes a simple method to obtain approximate numerical solution of a singular fractional order integro-differential equation with Cauchy kernel by using Bernstein polynomials as basis. The fractional derivative is described in Caputo sense. The properties of Bernstein polynomials are used to reduce the fractional order integro-differential equation to the solution of algebraic equations. The numerical results obtained by the present method compares favorably with those obtained earlier for the first order integro-differential equation. Also the convergence of the method is established rigorously.

Non-Inflationary Bianchi Type Vi0 Model In Rosen’S Bimetric Gravity, M. S. Borkar, N. P. Gaikwad

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, we have present the solution of Bianchi type VI₀ space-time by solving the Rosen’s field equations with massless scalar field φ and with constant scalar potential V(φ) for flat region. It is observed that the scalar field φ is an increasing function of time and affects the physical parameters of the model and leads to non-inflationary type solution of model, which contradicts the inflationary scenario. Other geometrical and physical properties of the model in relation to this non-inflationary model are also studied.

Density-Dependent Leslie Matrix Modeling For Logistic Populations With Steady-State Distribution Control, Bruce Kessler, Andrew Davis

Mathematics Faculty Publications

The Leslie matrix model allows for the discrete modeling of population age-groups whose total population grows exponentially. Many attempts have been made to adapt this model to a logistic model with a carrying capacity (see [1], [2], [4], [5], and [6]), with mixed results. In this paper we provide a new model for logistic populations that tracks age-group populations with repeated multiplication of a density-dependent matrix constructed from an original Leslie matrix, the chosen carrying capacity of the model, and the desired steady-state age-group distribution. The total populations from the model converge to a discrete logistic model with the same …

Moderating “Cry Wolf” Events With Excess Mad In Benford's Law Research And Practice, Bradley J. Barney, Kurt S. Schulzke

Accountancy Faculty Publications

False positives or “Type I errors,” wherein test results indicate fraud where none actually exists, have been described as a costly “cry wolf problem” in auditing practice. Benford's Law, which is used as one tool among many in screening for financial statement manipulation, is especially prone to false positives when applied to small and moderately sized datasets. Relying in part on Monte Carlo simulations, we describe with greater precision than extant literature the mathematical correlation between N and Mean Absolute Deviation (MAD), a statistic increasingly used for assessing deviation from Benford's Law. We recommend replacing MAD with an alternative, Excess …

Curriculum Subcommittee Agenda, December 1, 2016, Utah State University

Educational Policies Committee

Program Proposals

• Offering a Sociology-Criminal Justice Major with emphases
• Changing the name from PhD in Sociology; doctoral specialization in States & Markets to PhD in Sociology; doctoral specialization in Social Inequality
• Offering a Master of Science in Data Science
• Offering a Computer Science Teaching Minor
• Offering a PhD in Landscape Architecture
• Offering a Bachelor of Science in Technology Systems

Semester Course Approval Reviews

Other

• Curriculog updates

Stronger Together: The Reality Of Humanities Curriculum In A Stem Focused Era, Morgan Dalton

Honors Theses

The world of education is constantly changing. However, the way the pendulum is currently swinging has placed the Humanities, what has been seen as the framework since ancient times, under attack. Currently, that pendulum has become predominately focused on STEM education, and many budget cuts are being made to any part of the curriculum that does not fall under that category. This is not only seen in college and the job market, but in K-12 education. Pre-service teachers focusing on a STEM subject are often offered more incentives. Many college bound students are also shying away from the arts, especially …

Cgils Phase 2 Les Intercomparison Of Response Of Subtropical Marine Low Cloud Regimes To Co2 Quadrupling And A Cmip3 Composite Forcing Change, Peter N. Blossey, Christopher S. Bretherton, Anning Cheng, Satoshi Endo, Thijs Heus, Adrian P. Lock, Johan J. Van Der Dussen

Physics Faculty Publications

© 2016. The Authors. Phase 1 of the CGILS large-eddy simulation (LES) intercomparison is extended to understand if subtropical marine boundary-layer clouds respond to idealized climate perturbations consistently in six LES models. Here the responses to quadrupled carbon dioxide (“fast adjustment”) and to a composite climate perturbation representative of CMIP3 multimodel mean 2×CO2 near-equilibrium conditions are analyzed. As in Phase 1, the LES is run to equilibrium using specified steady summertime forcings representative of three locations in the Northeast Pacific Ocean in shallow well-mixed stratocumulus, decoupled stratocumulus, and shallow cumulus cloud regimes. The results are generally consistent with a single-LES …

What Determines The Fate Of Rising Parcels In A Heterogeneous Environment?, Maren Brast, Roel A.J. Neggers, Thijs Heus

Physics Faculty Publications

© 2016. The Authors. We investigate the potential impact of the local environment on rising parcels in a convective boundary layer. To this end, we use data from an LES simulation of a shallow convective cloud field to feed a parcel model with a range of different local environments, representative of the heterogeneous environment inside a shallow cumulus cloud layer. With this method we can study the statistics of an ensemble of rising parcels, but also the behavior of individual parcels. Through the use of a heterogeneous environment, the interactions between different parcels are indirectly represented. The method, despite its …

A Heuristic Solution Of The Toll Optimal Problem With Congestion Affected Costs, Vyacheslav Kalashnikov, José Guadalupe Flores Muñiz, Nataliya Kalashnykova

Departmental Technical Reports (CS)

An important problem concerning the toll roads is the setting of appropriate costs for driving along paid arcs of a transportation network. Our paper treats this problem as a bilevel programming model. At the upper level, decisions are made by a public regulator/private company that administers the toll roads endeavoring to elevate their benefits. At the lower level, several transportation companies/individual users appease the existing demand for transportation of goods or passengers while selecting the routes that would minimize their total travel costs. In contrast to the previous models, here the lower level problem assumes quadratic costs implied by the …

A Formative Experiment To Align Middle-School History Instruction With Literacy Goals, Jamie Colwell, David Reinking

Publications

Background/Context

Recent curricular trends based on new standards emphasize the centrality of reading and studying texts in history instruction. That trend suggests a closer alignment between middle-school history instruction and goals for developing literacy. Yet potential obstacles identified in the literature, particularly a teacher's stance toward teaching history, imply challenges to instantiating that alignment. Relatively little research has addressed how relevant conceptual positions such as disciplinary literacy might be realized in authentic practice.

Purpose/Objective

The objective was to investigate how middle-school history instruction could be transformed to align with the literacy goals addressed in new curricular standards and to better …