Physical Sciences and Mathematics Commons^™

Toward Scalable Parallel Software: An Active Object Model And Library To Support Von Neumann Languages, George K. Thiruvathukal

George K. Thiruvathukal

Scalable parallel processing has been proposed as the technology scientists and engineers can use today to solve the problems of tomorrow. Many computational Grand Challenge problems require between two and three orders of magnitude than can be provided with the scalable parallel hardware of the early nineteen-nineties. While hardware continues to become more scalable and cheaper, software is not advancing at the same pace and remains a very expensive part of systems development. A great deal of emphasis on software technology to support scalable parallel processing is placed on von Neumann languages. One of two approaches is common: (a) augment …

Java At Middle Age: Enabling Java For Computational Science, George K. Thiruvathukal

George K. Thiruvathukal

Not long after the Mosaic Web browser appeared and Netscape communications formed, Sun Microsystems launched Java in a way that will be forever known as a marketing success story. All across the US, there were many Java Day events. I still have my t-shirts as proof of having been there.

A Java Graphical User Interface For Large-Scale Scientific Computations In Distributed Systems, X Shen, George K. Thiruvathukal, Wei-Keng Liao, Alok Choudhary, A Singh

George K. Thiruvathukal

Large-scale scientific applications present great challenges to computational scientists in terms of obtaining high performance and in managing large datasets. These applications (most of which are simulations) may employ multiple techniques and resources in a heterogeneously distributed environment. Effective working in such an environment is crucial for modern large-scale simulations. In this paper, we present an integrated Java graphical user interface (IJ-GUI) that provides a control platform for managing complex programs and their large datasets easily. As far as performance is concerned, we present and evaluate our initial implementation of two optimization schemes: data replication and data prediction. Data replication …

Wide-Area Implementation Of The Message Passing Interface, Ian Foster, Jonathan Geisler, William Gropp, Nicholas Karonis, Ewing Lusk, George K. Thiruvathukal, Steven Tuecke

George K. Thiruvathukal

The Message Passing Interface (MPI) can be used as a portable, high-performance programming model for wide-area computing systems. The wide-area environment introduces challenging problems for the MPI implementor, due to the heterogeneity of both the underlying physical infrastructure and the software environment at different sites. In this article, we describe an MPI implementation that incorporates solutions to these problems. This implementation has beenconstructed by extending the Argonne MPICH implementation of MPI to use communicationservices provided by the Nexus communication library and authentication, resource allocation, process creation/management, and information services provided by the I-Soft system (initially) and the Globus metacomputing toolkit …

Gentoo Linux: The Next Generation Of Linux, George K. Thiruvathukal

George K. Thiruvathukal

One of the reasons scientific programmers love Linux is its less-is-more philosophy. We can configure it to be anything from a desktop replacement with USB port support to a blade in a large SMP compute engine to a powerful Web server. Although Linux's market penetration in these various sectors remains to be seen, plenty of people are pumping resources into the Linux world. In this article, I?ll explain why Gentoo Linux (www.gentoolinux.org) is a good choice for scientists, and how its structure gives us the flexibility and ease of management we need.

Combining Soa And Bpm Technologies For Cross-System Process Automation, Sebastian Herr, John Shafaee, Konstantin Läufer, George K. Thiruvathukal, Guido Wirtz

George K. Thiruvathukal

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges …

Unit Testing Considered Useful, George K. Thiruvathukal, Konstantin Läufer, Benjamin Gonzalez

George K. Thiruvathukal

Testing is an important part of application development. Hardware engineers, in particular, have a long established history of testing for the obvious reason that it's awfully hard to rebuild a microprocessor every time a bug pops up in the design stage--not to mention the enormous headaches such bugs generate on the software side.

Distributed Memo: A Heterogeneously Distributed And Parallel Software Development Environment, William T. O'Connell, George K. Thiruvathukal, Thomas W. Christopher

George K. Thiruvathukal

Heterogeneously distributed and parallel computing environments are highly dependent on hardware, data migration, and protocols. The result is significant difficulty in software reuse, portability across platforms, and an increased overall development effort. The appearance of a shared directory of unordered queues can be provided by integrating heterogeneous computers transparently. This integration provides a conducive environment for parallel and distributed application development, by abstracting the issues of hardware and communication. Object oriented technology is exploited to provide this seamless environment.

Project Hosting: Expanding The Scientific Programmer's Toolbox, George K. Thiruvathukal

George K. Thiruvathukal

Emerging technologies such as free and open source project hosting will hopefully broaden interest in scientific programming in a business context.

Rest On Routers? Preliminary Lessons For Language Designers, Framework Architects, And App Developers, Joseph P. Kaylor, Konstantin Läufer, George K. Thiruvathukal

George K. Thiruvathukal

In this position paper, we provide a preliminary assessment of hardware and software solution stack choices available to developers of resource-oriented web services on commodity embedded devices. As part of an ongoing interdisciplinary research project on air and water quality in a major urban ecosystem, we are developing an information infrastructure amounting to a role-based hierarchy of individually addressable, interconnected resources, ranging from sensors, analyzers, and other monitoring devices to aggregators and publishers. This infrastructure follows the Representational State Transfer (REST) architectural pattern and integrates non-networked or non-RESTful monitoring devices through RESTful proxy resources running on low-cost, low-energy, possibly wireless, …

Online Layered File System (Olfs): A Layered And Versioned Filesystem And Performance Analysis, Joseph P. Kaylor, Konstantin Läufer, George K. Thiruvathukal

George K. Thiruvathukal

We present a novel form of intra-volume directory layering with hierarchical, inheritance-like namespace unification. While each layer of an OLFS volume constitutes a subvolume that can be mounted separately in a fan-in configuration, the entire hierarchy is always accessible (online) and fully navigable through any mounted layer. OLFS uses a relational database to store its layering metadata and either a relational database or any (virtual) host file system as its backing store, along with metadata and block caching for improved performance. Because OLFS runs as a virtual file system in user-space, its capabilities are available to all existing software without …

Home Networking, George K. Thiruvathukal

George K. Thiruvathukal

My coeditors (Paul Dubois and Konstantin Läufer) and I are among a growing number of individuals who install and maintain a home computer network. When Paul and I first discussed the idea of writing an article about the subject several months ago, my first thought was that you--our cherished readers-might consider this whole notion so trivial as to not be worthy of a column that focuses mostly on scientific programming and software development topics. But based on the realization that we three computer scientists devote a significant part of our time to network and system administration, it almost goes without …

A Computational Framework For Telemedicine, Ian Foster, Gregor Von Laszewski, Brian Toonen, George K. Thiruvathukal

George K. Thiruvathukal

Emerging telemedicine applications require the ability to exploit diverse, geographically distributed resources. These applications use high-speed neworks to integrate supercomputers, large databases, archival storage devices, advanced visualization devices, and/or sophisticated instruments. This form of networked virtual supercomputers is also known as metacomputers and is being used by many other scientific applications areas. In this article, we analyze requirements necessary for a telemedicine computing infrastructure and compare them with requirements found in a typical metacomputing environment. We will show that metacomputing environments can be used to enable a more powerful and unified computational infrastructure for telemedicine. The Globus metacomputing environment can …

A Generic Software Modeling Framework For Building Heterogeneous Distributed And Parallel Software Systems, William T. O'Connell, George K. Thiruvathukal, Thomas W. Christopher

George K. Thiruvathukal

Heterogeneous distributed and parallel computing environments are highly dependent on hardware and communication protocols. The result is significant difficulty in software reuse, portability across platforms, interoperability, and an increased overall development effort. A new systems engineering approach is needed for parallel processing systems in heterogeneous environments. The generic modeling framework de-emphasizes platform- specific development while exploiting software reuse (and platform-specific capabilities) with a simple, well defined, and easily integrated set of abstractions providing a high level of heterogeneous interoperability.

Distributed-Memo: Heterogeneously Concurrent Programming With A Shared Directory Of Unordered Queues, William T. O'Connell, George K. Thiruvathukal, Thomas W. Christopher

George K. Thiruvathukal

Heterogeneously distributed and parallel computing environments are highly dependent on hardware, data migration, and protocols. The result is significant difficulty in software reuse, portability across platforms, and an increased overall development effort. The appearance of a shared directory of unordered queues can be provided by integrating heterogeneous computers transparently. This integration provides a conducive environment for parallel and distributed application development, by abstracting the issues of hardware and communication. Object oriented technology is exploited to provide this seamless environment.

Plone And Content Management, George K. Thiruvathukal, Konstantin Läufer

George K. Thiruvathukal

In this column, the authors look at Plone, which they feel is one of the best content management systems available today. Even better, it?s distributed under a free open-source license: the cost of getting started is only limited to the time you have available to set up the software on a server. Plone is written in Python and uses the Zope application server infrastructure; it runs on most modern operating systems. The authors have even set it up at Loyola University Chicago in the Department of Computer Science. Besides being two faculty members who rely on Plone to host all …

Taming Xml: Objects First, Then Markup, Matt Bone, Peter Nabicht, Konstantin Läufer, George K. Thiruvathukal

George K. Thiruvathukal

Processing markup in object-oriented languages often requires the programmer to focus on the objects generating the markup rather than the more pertinent domain objects. The BetterXML framework aims to improve this situation by allowing the programmer to develop a domain-specific object model as usual and later bind this model to preexisting or newly generated markup. To this end, the framework provides two types of object trees, XElement and NaturalXML, for representing XML documents. XElement goes beyond DOM-like automatic parsing of XML by supporting the custom mapping of elements to domain objects; NaturalXML allows the mapping of existing domain objects to …

Initial Experience In Moving Key Academic Department Functions To Social Networking Sites, David Dennis, George K. Thiruvathukal, Konstantin Läufer

George K. Thiruvathukal

We discuss our initial experience with the transition from conventional technology to social networking sites and other cloud-backed sites for three core business functions of an academic computer science department at a mid-size private university: course management, research collaboration, and community engagement. We first discuss the social/cultural context that informs our technology choices, as well as the evolution of the technology choices themselves. Then, we identify the targeted department functions and their actors. Next, we describe the past and present technical architectures used to support these functions. We conclude with a discussion of our preliminary experience with this transition and …

A Comprehensive Method For Fractionating Soil Organic Matter Not Protected And Protected From Decomposition By Physical And Chemical Mechanisms, César Plaza, José M. Fernández, Engil Isadora Pujol Pereira, Alfredo Polo

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

The objective of this work was to describe a method for isolating meaningful and measurable soil organic matter (SOM) pools that differ in the mechanisms by which they are protected from decomposition. The proposed method is appropriate for soil C stabilization and sequestration studies. Unlike previous fractionation schemes, this procedure allows free SOM located between aggregates (unprotected C pool) and SOM occluded within both macroaggregates and microaggregates (C weakly and strongly protected by physical mechanisms, respectively) to be recovered separately, freed from the soil mineral matrix and the mineral-associated SOM pool (C pool protected by chemical mechanisms) and thus well …

A Critical Study Of Organizational Communication And Organizational Communication Theories- A Historical Perspective, Ratnesh Dwivedi Mr

Ratnesh Dwivedi

Organizational Communication is the study that looks at human communication within and outside the organization. Conrad and Poole (1998) break the definition of organizational communication in parts, by first defining communication and then analyses the organization. These researchers define communication as “a process through which people, acting together, create, sustain, and manage meanings through the use of verbal and nonverbal signs and symbols within a particular context” (Conrad and Poole, 1998, p. 5). In the context of this book, Kenyans and their leaders are communicating their views and final decision through the ballot box to elect their third president, during …

Promise Of Advances In Simulation Methods For Protein Crystallography: Implicit Solvent Models, Time-Averaging Refinement, And Quantum Mechanical Modeling, Celia Schiffer, Jan Hermans

Celia A. Schiffer

No abstract provided.

Competition Between Ski And Creb-Binding Protein For Binding To Smad Proteins In Transforming Growth Factor-Beta Signaling, Weijun Chen, Suvana Lam, Hema Srinath, Celia Schiffer, William Royer, Kai Lin

Celia A. Schiffer

The family of Smad proteins mediates transforming growth factor-beta (TGF-beta) signaling in cell growth and differentiation. Smads repress or activate TGF-beta signaling by interacting with corepressors (e.g. Ski) or coactivators (e.g. CREB-binding protein (CBP)), respectively. Specifically, Ski has been shown to interfere with the interaction between Smad3 and CBP. However, it is unclear whether Ski competes with CBP for binding to Smads and whether they can interact with Smad3 at the same binding surface on Smad3. We investigated the interactions among purified constructs of Smad, Ski, and CBP in vitro by size-exclusion chromatography, isothermal titration calorimetry, and mutational studies. Here, …

Mass Spectrometry Analysis Of Hiv-1 Vif Reveals An Increase In Ordered Structure Upon Oligomerization In Regions Necessary For Viral Infectivity, Jared Auclair, Karin Green, Shivender Shandilya, James Evans, Mohan Somasundaran, Celia Schiffer

Celia A. Schiffer

HIV-1 Vif, an accessory protein in the viral genome, performs an important role in viral pathogenesis by facilitating the degradation of APOBEC3G, an endogenous cellular inhibitor of HIV-1 replication. In this study, intrinsically disordered regions are predicted in HIV-1 Vif using sequence-based algorithms. Intrinsic disorder may explain why traditional structure determination of HIV-1 Vif has been elusive, making structure-based drug design impossible. To characterize HIV-1 Vif's structural topology and to map the domains involved in oligomerization we used chemical cross-linking, proteolysis, and mass spectrometry. Cross-linking showed evidence of monomer, dimer, and trimer species via denaturing gel analysis and an additional …

Viral Protease Inhibitors, Jeffrey Anderson, Celia Schiffer, Sook-Kyung Lee, Ronald Swanstrom

Celia A. Schiffer

This review provides an overview of the development of viral protease inhibitors as antiviral drugs. We concentrate on HIV-1 protease inhibitors, as these have made the most significant advances in the recent past. Thus, we discuss the biochemistry of HIV-1 protease, inhibitor development, clinical use of inhibitors, and evolution of resistance. Since many different viruses encode essential proteases, it is possible to envision the development of a potent protease inhibitor for other viruses if the processing site sequence and the catalytic mechanism are known. At this time, interest in developing inhibitors is limited to viruses that cause chronic disease, viruses …

Mutation Patterns And Structural Correlates In Human Immunodeficiency Virus Type 1 Protease Following Different Protease Inhibitor Treatments, Thomas Wu, Celia Schiffer, Matthew Gonzales, Jonathan Taylor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew Zolopa, W. Jeffrey Fessel, Robert Shafer

Celia A. Schiffer

Although many human immunodeficiency virus type 1 (HIV-1)-infected persons are treated with multiple protease inhibitors in combination or in succession, mutation patterns of protease isolates from these persons have not been characterized. We collected and analyzed 2,244 subtype B HIV-1 isolates from 1,919 persons with different protease inhibitor experiences: 1,004 isolates from untreated persons, 637 isolates from persons who received one protease inhibitor, and 603 isolates from persons receiving two or more protease inhibitors. The median number of protease mutations per isolate increased from 4 in untreated persons to 12 in persons who had received four or more protease inhibitors. …

Curling Of Flap Tips In Hiv-1 Protease As A Mechanism For Substrate Entry And Tolerance Of Drug Resistance, Walter Scott, Celia Schiffer

Celia A. Schiffer

BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) protease is an essential viral protein that is a major drug target in the fight against Acquired Immune Deficiency Syndrome (AIDS). Access to the active site of this homodimeric enzyme is gained when two large flaps, one from each monomer, open. The flap movements are therefore central to the function of the enzyme, yet determining how these flaps move at an atomic level has not been experimentally possible.

RESULTS: In the present study, we observe the flaps of HIV-1 protease completely opening during a 10 ns solvated molecular dynamics simulation starting from …

Exploring The Role Of The Solvent In The Denaturation Of A Protein: A Molecular Dynamics Study Of The Dna Binding Domain Of The 434 Repressor, Celia Schiffer, Volker Dötsch, Kurt Wuthrich, Wilfred Van Gunsteren

Celia A. Schiffer

Molecular dynamics simulations of the DNA binding domain of 434 repressor are presented which aim at unraveling the role of solvent in protein denaturation. Four altered solvent models, each mimicking various possible aspects of the addition of a denaturant to the aqueous solvent, were used in the simulations to analyze their effects on the stability of the protein. The solvent was altered by selectively changing the Coulombic interaction between water and protein atoms and between different water molecules. The use of a modified solvent model has the advantage of mimicking the presence of denaturant without having denaturant molecules present in …

Resilience To Resistance Of Hiv-1 Protease Inhibitors: Profile Of Darunavir, Eric Lefebvre, Celia A. Schiffer

Celia A. Schiffer

The current effectiveness of HAART in the management of HIV infection is compromised by the emergence of extensively cross-resistant strains of HIV-1, requiring a significant need for new therapeutic agents. Due to its crucial role in viral maturation and therefore HIV-1 replication and infectivity, the HIV-1 protease continues to be a major development target for antiretroviral therapy. However, new protease inhibitors must have higher thresholds to the development of resistance and cross-resistance. Research has demonstrated that the binding characteristics between a protease inhibitor and the active site of the HIV-1 protease are key factors in the development of resistance. More …

Structural Analysis Of Human Immunodeficiency Virus Type 1 Crf01_Ae Protease In Complex With The Substrate P1-P6., Rajintha Bandaranayake, Moses Prabu-Jeyabalan, Junko Kakizawa, Wataru Sugiura, Celia Schiffer

Celia A. Schiffer

The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the first crystal structure of the HIV-1 CRF01_AE protease in complex with the p1-p6 substrate to a resolution of 2.8 A. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure.

Stratigraphic Record Of Holocene Coseismic Subsidence, Padang, West Sumatra, Tina Dura, Charles M. Rubin, Harvey M. Kelsey, Benjamin P. Horton, Andrea Hawkes, Christopher H. Vane, Mudrik Daryono, Candace Grand Pre, Tyler Landinsky, Sarah Bradley

All Faculty Scholarship for the College of the Sciences

Stratigraphic evidence is found for two coseismic subsidence events that underlie a floodplain 20 km south of Padang, West Sumatra along the Mentawai segment (0.5°S–0.3°S) of the Sunda subduction zone. Each earthquake is marked by a sharp soil‐mud contact that represents a sudden change from mangrove to tidal flat. The earthquakes occurred about 4000 and 3000 cal years B.P. based on radiocarbon ages of detrital plant fragments and seeds. The absence of younger paleoseismic evidence suggests that late Holocene relative sea level fall left the floodplain too high for an earthquake to lower it into the intertidal zone. Our results …