Department of Computer Science

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https://hdl.handle.net/10919/19035
The Department of Computer Science has an accredited undergraduate program that offers specialized ‘tracks’ of study in key areas. Undergraduates are prepared by graduation for pursuing a computing career or for graduate study. Our active corporate partners program offers internships and permanent employment to our students. Students are encouraged to participate in research experiences during their studies. Capstone courses provide significant team project experiences. The graduate program offers M.S. and Ph.D. degrees, emphasizing thesis work both at the main campus in Blacksburg and at the Northern Virginia Center. About two-thirds of the graduate students are pursuing the Ph.D. degree. The faculty, among whom there are 12 NSF or DOE CAREER Award winners, are active researchers who are visible contributors to the profession and have achieved significant honors.

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Browsing Department of Computer Science by Department "Biomedical Engineering and Mechanics"

Now showing 1 - 6 of 6
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    Bare-hand volume cracker for raw volume data analysis
    Socha, John J.; Laha, Bireswar; Bowman, Douglas A. (2016-09-28)
    Analysis of raw volume data generated from different scanning technologies faces a variety of challenges, related to search, pattern recognition, spatial understanding, quantitative estimation, and shape description. In a previous study, we found that the volume cracker (VC) 3D interaction (3DI) technique mitigated some of these problems, but this result was from a tethered glove-based system with users analyzing simulated data. Here, we redesigned the VC by using untethered bare-hand interaction with real volume datasets, with a broader aim of adoption of this technique in research labs. We developed symmetric and asymmetric interfaces for the bare-hand VC (BHVC) through design iterations with a biomechanics scientist. We evaluated our asymmetric BHVC technique against standard 2D and widely used 3DI techniques with experts analyzing scanned beetle datasets. We found that our BHVC design significantly outperformed the other two techniques. This study contributes a practical 3DI design for scientists, documents lessons learned while redesigning for bare-hand trackers and provides evidence suggesting that 3DI could improve volume data analysis for a variety of visual analysis tasks. Our contribution is in the realm of 3D user interfaces tightly integrated with visualization for improving the effectiveness of visual analysis of volume datasets. Based on our experience, we also provide some insights into hardware-agnostic principles for design of effective interaction techniques.
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    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.
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    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.
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    Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator
    Xiong, Yeyue; Onufriev, Alexey V. (PLOS, 2019-11-14)
    Rigid n-point water models are widely used in atomistic simulations, but have known accuracy drawbacks. Increasing the number of point charges, as well as adding electronic polarizability, are two common strategies for accuracy improvements. Both strategies come at considerable computational cost, which weighs heavily against modest possible accuracy improvements in practical simulations. In an effort to provide guidance for model development, here we have explored the limiting accuracy of “electrostatically globally optimal” npoint water models in terms of their ability to reproduce properties of water dimer—a mimic of the condensed state of water. For a given n, each model is built upon a set of reference multipole moments (e.g. ab initio) and then optimized to reproduce water dimer total dipole moment. The models are then evaluated with respect to the accuracy of reproducing the geometry of the water dimer. We find that global optimization of the charge distribution alone can deliver high accuracy of the water model: for n = 4 or n = 5, the geometry of the resulting water dimer can be almost within 50 of the ab initio reference, which is half that of the experimental error margin. Thus, global optimization of the charge distribution of classical n-point water models can lead to high accuracy models. We also find that while the accuracy improvement in going from n = 3 to n = 4 is substantial, the additional accuracy increase in going from n = 4 to n = 5 is marginal. Next, we have explored accuracy limitations of the standard practice of adding electronic polarizability (via a Drude particle) to a “rigid base”—pre-optimization rigid n-point water model. The resulting model (n = 3) shows a relatively small improvement in accuracy, suggesting that the strategy of merely adding the polarizability to an inferior accuracy water model used as the base cannot fix the defects of the latter. An alternative strategy in which the parameters of the rigid base model are globally optimized along with the polarizability parameter is much more promising: the resulting 3-point polarizable model out-performs even the 5-point optimal rigid model by a large margin. We suggest that future development efforts consider 3- and 4-point polarizable models where global optimization of the “rigid base” is coupled to optimization of the polarizability to deliver globally optimal solutions.
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    iBLAST: Incremental BLAST of new sequences via automated e-value correction
    Dash, Sajal; Rahman, S. R.; Hines, H. M.; Feng, Wu-chun (PLoS, 2021-04-01)
    Search results from local alignment search tools use statistical scores that are sensitive to the size of the database to report the quality of the result. For example, NCBI BLAST reports the best matches using similarity scores and expect values (i.e., e-values) calculated against the database size. Given the astronomical growth in genomics data throughout a genomic research investigation, sequence databases grow as new sequences are continuously being added to these databases. As a consequence, the results (e.g., best hits) and associated statistics (e.g., e-values) for a specific set of queries may change over the course of a genomic investigation. Thus, to update the results of a previously conducted BLAST search to find the best matches on an updated database, scientists must currently rerun the BLAST search against the entire updated database, which translates into irrecoverable and, in turn, wasted execution time, money, and computational resources. To address this issue, we devise a novel and efficient method to redeem past BLAST searches by introducing iBLAST. iBLAST leverages previous BLAST search results to conduct the same query search but only on the incremental (i.e., newly added) part of the database, recomputes the associated critical statistics such as e-values, and combines these results to produce updated search results. Our experimental results and fidelity analyses show that iBLAST delivers search results that are identical to NCBI BLAST at a substantially reduced computational cost, i.e., iBLAST performs (1 + δ)/δ times faster than NCBI BLAST, where δ represents the fraction of database growth. We then present three different use cases to demonstrate that iBLAST can enable efficient biological discovery at a much faster speed with a substantially reduced computational cost.
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    Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions
    Anandakrishnan, Ramu; Baker, Charles; Izadi, Saeed; Onufriev, Alexey V. (PLOS, 2013-07-04)
    We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior of the approximate potential. A general framework for numerically computing OPCA, for any given number of approximating charges, is described. We then derive a 2-charge practical point charge approximation, PPCA, which approximates the 2-charge OPCA via closed form analytical expressions, and test the PPCA on a set of charge distributions relevant to biomolecular modeling. We measure the accuracy of the new approximations as the RMS error in the electrostatic potential relative to that produced by the original charge distribution, at a distance the extent of the charge distribution–the mid-field. The error for the 2-charge PPCA is found to be on average 23% smaller than that of optimally placed point dipole approximation, and comparable to that of the point quadrupole approximation. The standard deviation in RMS error for the 2-charge PPCA is 53% lower than that of the optimal point dipole approximation, and comparable to that of the point quadrupole approximation. We also calculate the 3-charge OPCA for representing the gas phase quantum mechanical charge distribution of a water molecule. The electrostatic potential calculated by the 3-charge OPCA for water, in the mid-field (2.8 Å from the oxygen atom), is on average 33.3% more accurate than the potential due to the point multipole expansion up to the octupole order. Compared to a 3 point charge approximation in which the charges are placed on the atom centers, the 3-charge OPCA is seven times more accurate, by RMS error. The maximum error at the oxygen-Na distance (2.23 Å ) is half that of the point multipole expansion up to the octupole order.