Scholarly Works, Computer Science

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Research articles, presentations, and other scholarship

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Memetic algorithms for Spatial Partitioning problems
Biswas, Subhodip; Chen, Fanglan; Chen, Zhiqian; Lu, Chang-Tien; Ramakrishnan, Naren (ACM)
Spatial optimization problems (SOPs) are characterized by spatial relationships governing the decision variables, objectives, and/or constraint functions. In this article, we focus on a specific type of SOP called spatial partitioning, which is a combinatorial problem due to the presence of discrete spatial units. Exact optimization methods do not scale with the size of the problem, especially within practicable time limits. This motivated us to develop population-based metaheuristics for solving such SOPs. However, the search operators employed by these population-based methods are mostly designed for real-parameter continuous optimization problems. For adapting these methods to SOPs, we apply domain knowledge in designing spatially-aware search operators for efficiently searching through the discrete search space while preserving the spatial constraints. To this end, we put forward a simple yet effective algorithm called SPATIAL and test it on the school (re)districting problem. Detailed experimental investigations are performed on real-world datasets to evaluate the performance of SPATIAL. Besides, ablation studies are performed to understand the role of the individual components of SPATIAL. Additionally, we discuss how SPATIAL is helpful in the real-life planning process, its applicability to different scenarios, and motivate future research directions.
Deceleration of a Rotating Disk in a Viscous Fluid
Watson, Layne T.; Wang, Chang Y. (AIP Publishing, 1979)
A disk rotating in a viscous fluid decelerates with an angular velocity inversely proportional to time. It is found that the unsteady Navier–Stokes equations admit similarity solutions which depend on a nondimensional parameter S =α/Ω0, measuring unsteadiness. The resulting set of nonlinear ordinary differential equations is then integrated numerically. The special case of S =−1.606 699 corresponds to the decay of rotation of a free, massless disk in a viscous fluid.
The Evolution of Longwave Solutions to the Nonlinear Schrödinger Equation
Cramer, Mark S.; Watson, Layne T. (AIP Publishing, 1984)
In water of moderate depth, the behavior of small perturbations superimposed on Stokes wave trains is described by the nonlinear (cubic) Schrödinger equation. In the present study wave‐like solutions to this equation are examined, and it is shown that when these perturbations are neutrally stable and sufficiently long, solutions to the Schrödinger equation may be approximated by the well‐known Korteweg–deVries equation. As a result, sufficiently long perturbations to Stokes wave trains may be regarded as mathematically analogous to those imposed on a free surface separating two fluids of different densities. This result is established independently by singular perturbation techniques, numerical computation, and comparison of exact stationary wave solutions.
Maintaining Spatial Orientation during Travel in an Immersive Virtual Environment
Bowman, Douglas A.; Davis, Elizabeth T.; Hodges, Larry F.; Badre, Albert N. (MIT Press, 1999-12-01)
An experiment is presented comparing the effects of various virtual travel techniques in an immersive virtual environment (VE) on the spatial orientation of users. The experiment was designed and implemented in the context of a formal framework for the design and evaluation of VE travel techniques. Subjects traveled through virtual corridors, noting the location of objects along the way, and were asked to point in the direction of one of these objects when the end of the corridor was reached. Results indicate that virtual travel techniques, in which users do not physically translate their bodies, can allow the maintenance of a user's spatial orientation as measured by a pointing task. The experiment also replicates an earlier result, showing that path dimension significantly affects user performance. Finally, the strategies used by subjects to perform the task were shown to be significant, indicating that performance depends not only on the technique, environment, and task, but also on the sophistication of the user.
The simple virtual environment library: An extensible framework for building VE applications
Kessler, G. D.; Bowman, Douglas A.; Hodges, Larry F. (MIT Press, 2000-04-01)
As virtual environment (VE) technology becomes accessible to (and affordable for) an ever-widening audience of users, the demand for VE applications will increase. Tools that assist and facilitate the development of these applications, therefore, will also be in demand. To support our efforts in quickly designing and implementing VE applications, we have developed the Simple Virtual Environment (SVE) library. In this article, we describe the characteristics of the library that support the development of both simple and complex VE applications. Simple applications are created by novice programmers or for rapid prototyping. More-complex applications incorporate new user input and output devices, as well as new techniques for user interaction, rendering, or animation. The SVE library provides more-comprehensive support for developing new VE applications and better supports the various device configurations of VE applications than current systems for 3-D graphical applications. The development of simple VE applications is supported through provided default interaction, rendering, and user input and output device handling. The library's framework includes an execution framework that provides structure for incrementally adding complexity to selected tasks of an application, and an environment model that provides a layer of abstraction between the application and the device configuration actually used at runtime. This design supports rapid development of VE applications through incremental development, code reuse, and independence from hardware resources during the development.
Testbed evaluation of virtual environment interaction techniques
Bowman, Douglas A.; Johnson, D. B.; Hodges, Larry F. (MIT Press, 2001-02-01)
As immersive virtual environment (VE) applications become more complex, it is clear that we need a firm understanding of the principles of VE interaction. In particular, designers need guidance in choosing three-dimensional interaction techniques. In this paper, we present a systematic approach, testbed evaluation, for the assessment of interaction techniques for VEs. Testbed evaluation uses formal frameworks and formal experiments with multiple independent and dependent variables to obtain a wide range of performance data for VE interaction techniques. We present two testbed experiments, covering techniques for the common VE tasks of travel and object selection/manipulation. The results of these experiments allow us to form general guidelines for VE interaction and to provide an empirical basis for choosing interaction techniques in VE applications. Evaluation of a real-world VE system based on the testbed results indicates that this approach can produce substantial improvements in usability.
An introduction to 3-d user interface design
Bowman, Douglas A.; Kruijff, E.; LaViola, Joseph J., Jr.; Poupyrev, I. (MIT Press, 2001-02-01)
Three-dimensional user interface design is a critical component of any virtual environment (VE) application. In this paper, we present a broad overview of 3-D interaction and user interfaces. We discuss the effect of common VE hardware devices on user interaction, as well as interaction techniques for generic 3-D tasks and the use of traditional 2-D interaction styles in 3-D environments. We divide most user-interaction tasks into three categories: navigation, selection/manipulation, and system control. Throughout the paper, our focus is on presenting not only the available techniques but also practical guidelines for 3-D interaction design and widely held myths. Finally, we briefly discuss two approaches to 3-D interaction design and some example applications with complex 3-D interaction requirements. We also present an annotated online bibliography as a reference companion to this article.
Studying the Functional Genomics of Stress Responses in Loblolly Pine With the Expresso Microarray Experiment Management System
Heath, Lenwood S.; Ramakrishnan, Naren; Sederoff, Ronald R.; Whetten, Ross W.; Chevone, Boris I.; Struble, Craig A.; Jouenne, Vincent Y.; Chen, Dawei; van Zyl, Leonel; Grene, Ruth (Hindawi, 2002-01-01)
Conception, design, and implementation of cDNA microarray experiments present avariety of bioinformatics challenges for biologists and computational scientists. The multiplestages of data acquisition and analysis have motivated the design of Expresso, asystem for microarray experiment management. Salient aspects of Expresso includesupport for clone replication and randomized placement; automatic gridding, extraction ofexpression data from each spot, and quality monitoring; flexible methods of combiningdata from individual spots into information about clones and functional categories; and theuse of inductive logic programming for higher-level data analysis and mining. Thedevelopment of Expresso is occurring in parallel with several generations of microarrayexperiments aimed at elucidating genomic responses to drought stress in loblolly pineseedlings. The current experimental design incorporates 384 pine cDNAs replicated andrandomly placed in two specific microarray layouts. We describe the design of Expresso aswell as results of analysis with Expresso that suggest the importance of molecularchaperones and membrane transport proteins in mechanisms conferring successfuladaptation to long-term drought stress.
A Survey of Usability Evaluation in Virtual Environments: Classification and Comparison of Methods
Bowman, Douglas A.; Gabbard, Joseph L.; Hix, Deborah (MIT Press, 2002-08-01)
Virtual environments (VEs) are a relatively new type of human-computer interface in which users perceive and act in a three-dimensional world. The designers of such systems cannot rely solely on design guidelines for traditional two-dimensional interfaces, so usability evaluation is crucial for VEs. This paper presents an overview of VE usability evaluation to organize and critically analyze diverse work from this field. First, we discuss some of the issues that differentiate VE usability evaluation from evaluation of traditional user interfaces such as GUIs. We also present a review of some VE evaluation methods currently in use, and discuss a simple classification space for VE usability evaluation methods. This classification space provides a structured means for comparing evaluation methods according to three key characteristics: involvement of representative users, context of evaluation, and types of results produced. Finally, to illustrate these concepts, we compare two existing evaluation approaches: testbed evaluation (Bowman, Johnson, & Hodges, 1999) and sequential evaluation (Gabbard, Hix, & Swan, 1999).
BSML: A Binding Schema Markup Language for Data Interchange in Problem Solving Environments
Verstak, Alex; Ramakrishnan, Naren; Watson, Layne T.; He, Jian; Shaffer, Clifford A.; Bae, Kyung Kyoon; Jiang, Jing; Tranter, William H.; Rappaport, Theodore S. (Hindawi, 2003-01-01)
We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with a PSE or application composition system that views model specification and execution as a problem of managing semistructured data. The data interchange problem is addressed by three techniques for processing semistructured data: validation, binding, and conversion. We present BSML and describe its application to a PSE for wireless communications system design.
DIVERSE: A Framework for Building Extensible and Reconfigurable Device-Independent Virtual Environments and Distributed Asynchronous Simulations
Kelso, John; Satterfield, Steven G.; Arsenault, Lance E.; Ketchan, Peter M.; Kriz, Ronald D. (MIT Press, 2003-02-01)
We present DIVERSE, a highly modular collection of complimentary software packages designed to facilitate the creation of device-independent virtual environments and distributed asynchronous simulations. DIVERSE is free/open source software, containing both end-user programs and C++ application programming interfaces (APIs). DPF is the DIVERSE graphics interface to OpenGL Performer. A program using the DPF API can run without modification on platforms ranging from fully immersive systems such as CAVEs to generic desktop workstations. The DIVERSE toolkit (DTK) contains all the nongraphical components of DIVERSE, such as networking utilities, hardware device access, and navigational techniques. It introduces a software implementation of networks of replicated noncoherent shared memory. It also introduces a method that seamlessly extends hardware drivers into interprocess and Internet hardware services. We will describe the design of DIVERSE and present a specific example of how it is being used to aid researchers.
The Catchment Feature Model: A Device for Multimodal Fusion and a Bridge between Signal and Sense
Quek, Francis (2004-09-18)
The catchment feature model addresses two questions in the field of multimodal interaction: how we bridge video and audio processing with the realities of human multimodal communication, and how information from the different modes may be fused. We argue from a detailed literature review that gestural research has clustered around manipulative and semaphoric use of the hands, motivate the catchment feature model psycholinguistic research, and present the model. In contrast to “whole gesture” recognition, the catchment feature model applies a feature decomposition approach that facilitates cross-modal fusion at the level of discourse planning and conceptualization. We present our experimental framework for catchment feature-based research, cite three concrete examples of catchment features, and propose new directions of multimodal research based on the model.
Induced nanoscale deformations in polymers using atomic force microscopy
Lyuksyutov, S. F.; Paramonov, P. B.; Sharipov, R. A.; Sigalov, G. (American Physical Society, 2004-11-19)
An exact analytical solution, based on the method of images, is obtained for the description of the electric field between an atomic force microscope (AFM) tip and a thin dielectric polymer film (30 nm thick) spin coated on a conductive substrate. Three different tip shapes are found to produce electrostatic pressure above the plasticity threshold in the polymers up to 50 MPa. It is shown experimentally that a strong nonuniform electric field (5x10(8)-5x10(9) V m(-1)) between the AFM tip and polymer substrate produces nanodeformations of two different kinds in planar polymer films. Nanostructures (lines and dots) 10-100 nm wide and 0.1-5 nm high are patterned in the polymer films by using two different experimental techniques. The first technique relies on electric breakdown in the film leading to polymer heating above the glass transition point followed by mass transport of softened polymer material towards the AFM tip. The second technique is believed to be associated with plastic deformation of the polymer surface at the nanoscale. In this case the nanostructures are experimentally patterned in the films with no external biasing of the AFM tip, and using only the motion of the tip. This suggests an additional nanomechanical approach for nanolithography in polymer films of arbitrary thickness.
Protecting the communication structure in sensor networks
Olariu, S.; Xu, Q.; Eltoweissy, M.; Wadaa, A.; Zomaya, A. Y. (Hindawi Publishing Corporation, 2005)
In the near future wireless sensor networks will be employed in a wide variety of applications establishing ubiquitous networks that will pervade society. The inherent vulnerability of these massively deployed networks to a multitude of threats, including physical tampering with nodes exacerbates concerns about privacy and security. For example, denial of service attacks (DoS) that compromise or disrupt communications or target nodes serving key roles in the network, e.g. sink nodes, can easily undermine the functionality as well as the performance delivered by the network. Particularly vulnerable are the components of the communications or operation infrastructure. Although, by construction, most sensor network systems do not possess a built-in infrastructure, a virtual infrastructure, that may include a coordinate system, a cluster structure, and designated communication paths, may be established post-deployment in support of network management and operation. Since knowledge of this virtual infrastructure can be instrumental for successfully compromising network security, maintaining the anonymity of the virtual infrastructure is a primary security concern. Somewhat surprisingly, in spite of its importance, the anonymity problem has not been addressed in wireless sensor networks. The main contribution of this work is to propose an energy-efficient protocol for maintaining the anonymity of the virtual infrastructure in a class of sensor network systems. Our solution defines schemes for randomizing communications such that the cluster structure, and coordinate system used remain undetectable and in visible to an observer of network traffic during both the setup and operation phases of the network.
H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules
Gordon, John C.; Myers, Jonathan B.; Folta, Timothy; Shoja, Valia; Heath, Lenwood S.; Onufriev, Alexey V. (2005-07-01)
The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants of macromolecules based upon their atomic resolution Protein Data Bank (PDB) structures; the calculations are often performed within the framework of the continuum electrostatics model. Unfortunately, these methodologies are complex, involve multiple steps and require considerable investment of effort. Our web server http://biophysics.cs.vt.edu/H++ provides access to a tool that automates this process, allowing both experts and novices to quickly obtain estimates of pKs as well as other related characteristics of biomolecules such as isoelectric points, titration curves and energies of protonation microstates. Protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH; the output is in the PQR (PDB + charges + radii) format. In addition, corresponding coordinate and topology files are generated in the format supported by the molecular modeling package AMBER. The server is intended for a broad community of biochemists, molecular modelers, structural biologists and drug designers; it can also be used as an educational tool in biochemistry courses.
Learning When Less is More: “Bootstrapping” Undergraduate Programmers as Coordination Designers
Lin, Strong; Tatar, Deborah; Harrison, Steve; Roschelle, Jeremy; Patton, Charles (Computer Professionals for Social Responsibility, 2006)
In this paper, we describe an undergraduate computer science class in the United States that we started with the intention of creating a participatory design experience to create distributed mobile collaborative technologies for education. The case highlights the ways in which programmer understanding of an innovative new technology can depend on understanding the context of use. The students were to use Tuple-spaces, a language for coordination. However, it soon became clear that while the coordination of machines may be thought of as a computer science problem, the students could not understand the technical system without richer models of how, why, or when coordination is desirable. We were in the ironic position of teaching human coordination at the same time as describing the technical properties of a system to support it. To “bootstrap” the learning process, we asked the students to draw on their own coordination expertise by implementing familiar coordinative games. We propose games as an addition to the PD toolkit when implementers need help in stepping outside their everyday mindset.
VMD: a community annotation database for oomycetes and microbial genomes
Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (2006-01-01)
The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae and Phytophthora ramorum. With the completion of the draft genome sequences of these pathogens in collaboration with the DOE Joint Genome Institute (JGI), we have created this resource to make the sequences publicly available. The genome sequences ( 95 MB for P. sojae and 65 MB for P. ramorum) were annotated with similar to 19 000 and similar to 16 000 gene models, respectively. We used two different statistical methods to validate these gene models, Fickett's and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, we could assign putative functions to 17 694 genes in P. sojae and 14 700 genes in P. ramorum. We created an easy-to-use genome browser to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are similar to 1600 gene models for P. sojae and similar to 700 models for P. ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. The database is publicly available at http://phytophthora.vbi.vt.edu/.
Technical note: Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1
Sandu, Adrian; Sander, Rolf (Copernicus Publications, 2006-01-01)
This paper presents the new version 2.1 of the Kinetic PreProcessor (KPP). Taking a set of chemical reactions and their rate coefficients as input, KPP generates Fortran90, Fortran77, Matlab, or C code for the temporal integration of the kinetic system. Efficiency is obtained by carefully exploiting the sparsity structures of the Jacobian and of the Hessian. A comprehensive suite of stiff numerical integrators is also provided. Moreover, KPP can be used to generate the tangent linear model, as well as the continuous and discrete adjoint models of the chemical system.
The Effects of Text Drawing Styles, Background Textures, and Natural Lighting on Text Legibility in Outdoor Augmented Reality
Gabbard, Joseph L.; Swan, J. Edward; Hix, Deborah (MIT Press, 2006-02-01)
A challenge in presenting augmenting information in outdoor augmented reality (AR) settings lies in the broad range of uncontrollable environmental conditions that may be present, specifically large-scale fluctuations in natural lighting and wide variations in likely backgrounds or objects in the scene. In this paper, we motivate the need for research on the effects of text drawing styles, outdoor background textures, and natural lighting on user performance in outdoor AR. We present a pilot study and a follow-on user-based study that examined the effects on user performance of outdoor background textures, changing outdoor illuminance values, and text drawing styles in a text identification task using an optical, see-through AR system. We report significant effects for all these variables, and discuss user interface design guidelines and ideas for future work.
Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes
Lawson, Mark J.; Zhang, Liqing (2006-02-21)
Background Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic development, and regulation of gene expression. We have performed a detailed comparative study of the distribution of SSRs in the sequenced genomes of Arabidopsis thaliana and rice. Results SSRs in different genic regions - 5'untranslated region (UTR), 3'UTR, exon, and intron - show distinct patterns of distribution both within and between the two genomes. Especially notable is the much higher density of SSRs in 5'UTRs compared to the other regions and a strong affinity towards trinucleotide repeats in these regions for both rice and Arabidopsis. On a genomic level, mononucleotide repeats are the most prevalent type of SSRs in Arabidopsis and trinucleotide repeats are the most prevalent type in rice. Both plants have the same most common mononucleotide (A/T) and dinucleotide (AT and AG) repeats, but have little in common for the other types of repeats. Conclusion Our work provides insight into the evolution and distribution of SSRs in the two sequenced model plant genomes of monocots and dicots. Our analyses reveal that the distributions of SSRs appear highly non-random and vary a great deal in different regions of the genes in the genomes.

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