Physical Sciences and Mathematics | Open Access Articles

Numerical Analysis - Final Report, John Rice

John R Rice

No abstract provided.

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Speedup In Parallel Algorithms For Adaptive Quadratures, James Lemme, John Rice

John R Rice

No abstract provided.

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The Ellpack Performance Evaluation System, John Bonomo, Wayne Dyksen, John Rice

John R Rice

No abstract provided.

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Gas Turbine Engine Compressor- Combustor Dynamics Simulation Design, Sanford Fleeter, Elias Houstis, John Rice, Chem Zhou

John R Rice

No abstract provided.

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Composition Of Libraries, Software Parts And Problem Solving Environments, John Rice

John R Rice

No abstract provided.

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Ellpack Project Status Report, John Rice, Wayne Dyksen, Elias Houstis, Calvin Ribbens

John R Rice

No abstract provided.

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Ellpack '78 User's Guide-Preliminary Version, John Rice

John R Rice

No abstract provided.

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Solving Elliptic Problems Using Ellpack Part 1: Ellpack User's Guide; Part 2: The Problem Solving Modules, John Rice, Ronald Boisvert

John R Rice

No abstract provided.

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Computing About Physical Objects, Chanderjit Bajaj, Christoph Hoffmann, Elias Houstis, John Korb, John Rice

John R Rice

No abstract provided.

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Convergence Analysis Of A Non-Overlapping Domain Decomposition Method For Elliptic Pdes, John Rice, E. Vavalis, D. Yang

John R Rice

No abstract provided.

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On The Effects Of Synchronization In Parallel Computing, Dan Marinescu, John Rice

John R Rice

No abstract provided.

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Books And Our Human Stories, Paul Benson

Paul H. Benson

An essay on the impact of the works in the Imprints and Impressions: Milestones in Human Progress, an exhibition of rare books from the collection of Stuart Rose. Exhibition was held Sept. 29-Nov. 9, 2014, at the University of Dayton.

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Optical Switching And Routing Architectures For Fiber-Optic Computer Communication Networks, Alok Choudhary, Salim Hariri, Wang Song, Partha Banerjee, Sanjay Ranka

Partha Banerjee

Optical technology has become a significant part of communication networks. We propose an Optical Interface Message Processor (OPTIMP) that exploits high-bandwidth, parallelism, multi-dimensional capability, and high storage density offered by optics. The most time consuming operations such as switching and routing in communication networks are performed in optical domain in the proposed system. Our design does not suffer from the optical/electrical conversion bottlenecks and can perform switching and routing in the range of Gigabits/s. The proposed design can have significant impact in high-speed communication networks as well as high-speed interconnection networks for parallel computers. The source-destination (S-D) information from a …

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The Extended Tracking Network And Indications Of Baseline Precision And Accuracy In The North Andes, Jeffrey Freymueller, James Kellogg

James N Kellogg

The CASA UNO Global Positioning System (GPS) experiment (January-February 1988) included an extended tracking network which covered three continents in addition to the network of scientific interest in Central and South America. The repeatability of long baselines (400-1000 km) in South America is improved by up to a factor of two in the horizontal vector baseline components by using tracking stations in the Pacific and Europe to supplement stations in North America. In every case but one, the differences between the mean solutions obtained using different tracking networks was equal to or smaller than day-to-day rms repeatabilities for the same …

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Reply To Comment On "Subduction Of The Caribbean Plate And Basement Uplifts In The Overriding South American Plate", James Kellogg, William Bonini

James N Kellogg

No abstract provided.

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Central And South America Gps Geodesy- Casa Uno, James Kellogg, Timothy Dixon

James N Kellogg

In January 1988, scientists from over 25 organizations in 13 countries and territories cooperated in the largest Global Positioning System (GPS) campaign in the world to date (Table 1). 43 GPS receivers collected approximately 590 station-days of data in America, Samoa, Australia, Canada, Colombia, Costa Rica, Ecuador, New Zealand, Norway, Panama, Sweden, United States, West Germany, and Venezuela. The experiment was entitled CASA UNO, an acronym for Central and South America -- and uno is the Spanish word for one, designating first epoch measurements. The CASA UNO experiment was the first civilian effort implementing a global GPS satellite tracking network. …

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A 3-D Gravity Tectonic Study Of Ita Mai Tai Guyot: An Uncompensated Seamount In The East Mariana Basin, Bruce Wedgeworth, James Kellogg

James N Kellogg

Ita Mai Tai is a large, locally uncompensated seamount on the eastern edge of the East Mariana Basin. A large positive gravity anomaly of 254 mgal characterizes the summit and a low of -69 mgal, the surrounding moat. Using polygonal prisms to approximate the bathymetry, the observed gravity was inverted to calculate an average density of 2.59 g/ems for the seamount. Observed-calculated gravity residuals are reduced by including the flanking sedimentary basins and a dense volcanic conduit. The drill sites from DSDP Legs 20 and 89 describe a volcanic edifice formed in the Aptian!Albian on Jmassic/Cretaceous crust. The volcanism is …

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Seismic Evidence For Blind Thrusting Of The Northwestern Flank Of The Venezuelan Andes, Bruno De Toni, James Kellogg

James N Kellogg

Surface geology and seismic and well data from the northwestern flank of the Venezuelan Andes indicate overthrusting of Andean basement rocks toward the adjacent Maracaibo Basin along a blind thrust fault. The frontal monocline is interpreted as the forelimb of a northwestward verging fault-related fold deformed over a crustal-scarle map. The Andean block has been thrust 20 km to the northwest and uplifted 10 km on a ramp that dips about 20o-30o southeastward. The thrust fault ramps up through crystalline basement rocks to a decollement horizon within the shaly units of the Cretaceous Colon-Mito Juan formations. Backthrusts in the monocline …

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First Gps Baseline Results From The North Andes, James Kellogg, Jeffrey Freymueller, Timothy Dixon, Ruth Neilan, Clemente Ropain U., Sergio Camargo M., Benjamin Fernandez Ch., James Stowell, Anibal Salazar, Jaime Mora V., Luis Espin, Vernon Perdue, Leonard Leos

James N Kellogg

The CASA UNO GPS (Global Positioning System) experiment (January-February 1988) has provided the first epoch baseline measurements for the study of plate motions and crustal deformation in and around the North Andes. Two dimensional horizontal baseline repeatabilities are as good as 5 parts in 10⁸ for short baselines (100-1000km), and better than3 parts in 10⁸ for long baselines (>1000km). Vertical repeatabilities are typically 4 -6 cm, with a weak dependence on baseline length. The expected rate of plate convergence across the Colombia Trench is 6-8 cm/yr, which should be detectable by the repeat experiment planned for 1991. …

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Isostatic Compensation And Conduit Structures Of Western Pacific Seamounts: Results Of Three-Dimensional Gravity Modeling, James Kellogg, Bruce Wedgeworth, Jeffrey Freymueller

James N Kellogg

Detailed three-dimensional polygonal prism models of two large western Pacific seamounts show that the 135 mgal difference in the observed sea surface gravity over the two can be best explained by similar mean densities (2.6 gjcm3) and crustal thickening under one seamount (Airy isostatic compensation). Observed calculated residuals are further reduced by including dense (2.9 gjcm3) vertical feeder pipes or volcanic conduits in the models. Dense conduits or fracture zones 5 to 17 km in diameter are located under many, if not all, craters on volcanic islands and seamounts. Results from the detailed seamount studies can be generalized using exact …

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New Standards For Reducing Gravity Data: The North American Gravity Database, William Hinze, Carlos Aiken, John Brozena, Bernard Coakley, David Dater, Guy Flanagan, Rene Forsberg, Thomas Hildenbrand, G. Keller, James Kellogg, Robert Kucks, Xiong Li, Andre Mainville, Robert Morin, Mark Pilkington, Donald Plouff, Dhananjay Ravat, Daniel Roman, Jamie Urrutia-Fucugauchi, Marc Veronneau, Michael Webring, Daniel Winester

James N Kellogg

The North American gravity database as well as databases from Canada, Mexico, and the United States are being revised to improve their coverage, versatility, and accuracy. An important part of this effort is revising procedures for calculating gravity anomalies, taking into account our enhanced computational power, improved terrain databases and datums, and increased interest in more accurately defining long-wavelength anomaly components. Users of the databases may note minor differences between previous and revised database values as a result of these procedures. Generally, the differences do not impact the interpretation of local anomalies but do improve regional anomaly studies. The most …

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Crystal Structure Of (Pyridine-[Kappa]N)Bis(Quinolin-2-Olato-[Kappa]2n,O)Copper(Ii) Monohydrate, Shawn Burdette, B. Hawks, J. Yan, P. Basa

Shawn C. Burdette

The title complex, [Cu(C9H6NO)2(C5H4N)]·H2O, adopts a slightly distorted square-pyramidal geometry in which the axial pyridine ligand exhibits a long Cu-N bond of 2.305 (3) Å. The pyridine ligand forms dihedral angles of 79.5 (5) and 88.0 (1)° with the planes of the two quinolin-2-olate ligands, while the dihedral angle between the quinoline groups of 9.0 (3)° indicates near planarity. The water molecule connects adjacent copper complexes through O-H...O hydrogen bonds to phenolate O atoms, forming a network interconnecting all the complexes in the crystal lattice.

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Marginal Structural Models: An Application To Incarceration And Marriage During Young Adulthood, Valerio Bacak, Edward Kennedy

Edward H. Kennedy

Advanced methods for panel data analysis are commonly used in research on family life and relationships, but the fundamental issue of simultaneous time-dependent confounding and mediation has received little attention. In this article the authors introduce inverse-probability-weighted estimation of marginal structural models, an approach to causal analysis that (unlike conventional regression modeling) appropriately adjusts for confounding variables on the causal pathway linking the treatment with the outcome. They discuss the need for marginal structural models in social science research and describe their estimation in detail. Substantively, the authors contribute to the ongoing debate on the effects of incarceration on marriage …

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Structural Basis And Distal Effects Of Gag Substrate Coevolution In Drug Resistance To Hiv-1 Protease, Aysegul Ozen, Kuan-Hung Lin, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease-substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease-substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate …

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Structural Analysis Of Asunaprevir Resistance In Hcv Ns3/4a Protease, Djade Soumana, Akbar Ali, Celia Schiffer

Celia A. Schiffer

Asunaprevir (ASV), an isoquinoline-based competitive inhibitor targeting the hepatitis C virus (HCV) NS3/4A protease, is very potent in vivo. However, the potency is significantly compromised by the drug resistance mutations R155K and D168A. In this study three crystal structures of ASV and an analogue were determined to analyze the structural basis of drug resistance susceptibility. These structures revealed that ASV makes extensive contacts with Arg155 outside the substrate envelope. Arg155 in turn is stabilized by Asp168, and thus when either residue is mutated, the enzyme's interaction with ASV's P2* isoquinoline is disrupted. Adding a P1-P3 macrocycle to ASV enhances the …

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Improving The Resistance Profile Of Hepatitis C Ns3/4a Inhibitors: Dynamic Substrate Envelope Guided Design, Aysegul Ozen, Woody Sherman, Celia Schiffer

Celia A. Schiffer

Drug resistance is a principal concern in the treatment of quickly evolving diseases. The viral protease NS3/4A is a primary drug target for the hepatitis C virus (HCV) and is known to evolve resistance mutations in response to drug therapy. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition by NS3/4A; the drug resistant protease variants are no longer effectively inhibited by the competitive active site inhibitors but can still process the natural substrates with enough efficiency for viral survival. In previous works we have developed the "substrate envelope" hypothesis, which posits that …

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Efficient Computation Of Small-Molecule Configurational Binding Entropy And Free Energy Changes By Ensemble Enumeration, Nathaniel Silver, Bracken King, Madhavi Nalam, Hong Cao, Akbar Ali, G. S. Kiran Kumar Reddy, Tariq Rana, Celia Schiffer, Bruce Tidor

Celia A. Schiffer

Here we present a novel, end-point method using the dead-end-elimination and A* algorithms to efficiently and accurately calculate the change in free energy, enthalpy, and configurational entropy of binding for ligand-receptor association reactions. We apply the new approach to the binding of a series of human immunodeficiency virus (HIV-1) protease inhibitors to examine the effect ensemble reranking has on relative accuracy as well as to evaluate the role of the absolute and relative ligand configurational entropy losses upon binding in affinity differences for structurally related inhibitors. Our results suggest that most thermodynamic parameters can be estimated using only a small …

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Drug Resistance Conferred By Mutations Outside The Active Site Through Alterations In The Dynamic And Structural Ensemble Of Hiv-1 Protease, Debra Ragland, Ellen Nalivaika, Madhavi Nalam, Kristina Prachanronarong, Hong Cao, Rajintha Bandaranayake, Yufeng Cai, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

HIV-1 protease inhibitors are part of the highly active antiretroviral therapy effectively used in the treatment of HIV infection and AIDS. Darunavir (DRV) is the most potent of these inhibitors, soliciting drug resistance only when a complex combination of mutations occur both inside and outside the protease active site. With few exceptions, the role of mutations outside the active site in conferring resistance remains largely elusive. Through a series of DRV-protease complex crystal structures, inhibition assays, and molecular dynamics simulations, we find that single and double site mutations outside the active site often associated with DRV resistance alter the structure …

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Testing The Substrate-Envelope Hypothesis With Designed Pairs Of Compounds, Yang Shen, Michael Altman, Akbar Ali, Madhavi Nalam, Hong Cao, Tariq Rana, Celia Schiffer, Bruce Tidor

Celia A. Schiffer

Acquired resistance to therapeutic agents is a significant barrier to the development of clinically effective treatments for diseases in which evolution occurs on clinical time scales, frequently arising from target mutations. We previously reported a general strategy to design effective inhibitors for rapidly mutating enzyme targets, which we demonstrated for HIV-1 protease inhibition [Altman et al. J. Am. Chem. Soc. 2008, 130, 6099-6113]. Specifically, we developed a computational inverse design procedure with the added constraint that designed inhibitors bind entirely inside the substrate envelope, a consensus volume occupied by natural substrates. The rationale for the substrate-envelope constraint is that it …

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Development Of A Novel Screening Strategy Designed To Discover A New Class Of Hiv Drugs, Nancy Cheng, Sook-Kyung Lee, P. Donover, Mel Reichman, Celia Schiffer, Emily Hull-Ryde, Ronald Swanstrom, William Janzen

Celia A. Schiffer

Current antiretroviral treatments target multiple pathways important for human immunodeficiency virus (HIV) multiplication, including viral entry, synthesis and integration of the DNA provirus, and the processing of viral polyprotein precursors. However, HIV is becoming increasingly resistant to these "combination therapies." Recent findings show that inhibition of HIV Gag protein cleavage into its two structural proteins, matrix (MA) and capsid (CA), has a devastating effect on viral production, revealing a potential new target class for HIV treatment. Unlike the widely used HIV protease inhibitors, this new class of inhibitor would target the substrate, not the protease enzyme itself. This approach offers …

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Full-Text Articles in Physical Sciences and Mathematics

Numerical Analysis - Final Report, John Rice

John R Rice

Speedup In Parallel Algorithms For Adaptive Quadratures, James Lemme, John Rice

John R Rice

The Ellpack Performance Evaluation System, John Bonomo, Wayne Dyksen, John Rice

John R Rice

Gas Turbine Engine Compressor- Combustor Dynamics Simulation Design, Sanford Fleeter, Elias Houstis, John Rice, Chem Zhou

John R Rice

Composition Of Libraries, Software Parts And Problem Solving Environments, John Rice

John R Rice

Ellpack Project Status Report, John Rice, Wayne Dyksen, Elias Houstis, Calvin Ribbens

John R Rice

Ellpack '78 User's Guide-Preliminary Version, John Rice

John R Rice

Solving Elliptic Problems Using Ellpack Part 1: Ellpack User's Guide; Part 2: The Problem Solving Modules, John Rice, Ronald Boisvert

John R Rice

Computing About Physical Objects, Chanderjit Bajaj, Christoph Hoffmann, Elias Houstis, John Korb, John Rice

John R Rice

Convergence Analysis Of A Non-Overlapping Domain Decomposition Method For Elliptic Pdes, John Rice, E. Vavalis, D. Yang

John R Rice

On The Effects Of Synchronization In Parallel Computing, Dan Marinescu, John Rice

John R Rice

Books And Our Human Stories, Paul Benson

Paul H. Benson

Optical Switching And Routing Architectures For Fiber-Optic Computer Communication Networks, Alok Choudhary, Salim Hariri, Wang Song, Partha Banerjee, Sanjay Ranka

Partha Banerjee

The Extended Tracking Network And Indications Of Baseline Precision And Accuracy In The North Andes, Jeffrey Freymueller, James Kellogg

James N Kellogg

Reply To Comment On "Subduction Of The Caribbean Plate And Basement Uplifts In The Overriding South American Plate", James Kellogg, William Bonini

James N Kellogg

Central And South America Gps Geodesy- Casa Uno, James Kellogg, Timothy Dixon

James N Kellogg

A 3-D Gravity Tectonic Study Of Ita Mai Tai Guyot: An Uncompensated Seamount In The East Mariana Basin, Bruce Wedgeworth, James Kellogg

James N Kellogg

Seismic Evidence For Blind Thrusting Of The Northwestern Flank Of The Venezuelan Andes, Bruno De Toni, James Kellogg

James N Kellogg

First Gps Baseline Results From The North Andes, James Kellogg, Jeffrey Freymueller, Timothy Dixon, Ruth Neilan, Clemente Ropain U., Sergio Camargo M., Benjamin Fernandez Ch., James Stowell, Anibal Salazar, Jaime Mora V., Luis Espin, Vernon Perdue, Leonard Leos

James N Kellogg

Isostatic Compensation And Conduit Structures Of Western Pacific Seamounts: Results Of Three-Dimensional Gravity Modeling, James Kellogg, Bruce Wedgeworth, Jeffrey Freymueller

James N Kellogg

James N Kellogg

Crystal Structure Of (Pyridine-[Kappa]N)Bis(Quinolin-2-Olato-[Kappa]2n,O)Copper(Ii) Monohydrate, Shawn Burdette, B. Hawks, J. Yan, P. Basa

Shawn C. Burdette

Marginal Structural Models: An Application To Incarceration And Marriage During Young Adulthood, Valerio Bacak, Edward Kennedy

Edward H. Kennedy

Structural Basis And Distal Effects Of Gag Substrate Coevolution In Drug Resistance To Hiv-1 Protease, Aysegul Ozen, Kuan-Hung Lin, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

Structural Analysis Of Asunaprevir Resistance In Hcv Ns3/4a Protease, Djade Soumana, Akbar Ali, Celia Schiffer

Celia A. Schiffer

Improving The Resistance Profile Of Hepatitis C Ns3/4a Inhibitors: Dynamic Substrate Envelope Guided Design, Aysegul Ozen, Woody Sherman, Celia Schiffer

Celia A. Schiffer

Efficient Computation Of Small-Molecule Configurational Binding Entropy And Free Energy Changes By Ensemble Enumeration, Nathaniel Silver, Bracken King, Madhavi Nalam, Hong Cao, Akbar Ali, G. S. Kiran Kumar Reddy, Tariq Rana, Celia Schiffer, Bruce Tidor

Celia A. Schiffer

Drug Resistance Conferred By Mutations Outside The Active Site Through Alterations In The Dynamic And Structural Ensemble Of Hiv-1 Protease, Debra Ragland, Ellen Nalivaika, Madhavi Nalam, Kristina Prachanronarong, Hong Cao, Rajintha Bandaranayake, Yufeng Cai, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

Testing The Substrate-Envelope Hypothesis With Designed Pairs Of Compounds, Yang Shen, Michael Altman, Akbar Ali, Madhavi Nalam, Hong Cao, Tariq Rana, Celia Schiffer, Bruce Tidor

Celia A. Schiffer

Development Of A Novel Screening Strategy Designed To Discover A New Class Of Hiv Drugs, Nancy Cheng, Sook-Kyung Lee, P. Donover, Mel Reichman, Celia Schiffer, Emily Hull-Ryde, Ronald Swanstrom, William Janzen

Celia A. Schiffer