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College of Arts & Sciences
Computing and Information Technology

User Research

The Research Computing Center together with previous CC-RCI supports the research of many researchers, including faculty, postdocs, and students. This support includes joint scientific and engineering research collaborations, HPC computational resources at USC, middleware support for cluster and large scale computing, instructional tutorials, access to TeraGrid/XSEDE national supercomputer sites through the NSF Campus Champions program, software and systems support, and Desktop to TeraGrid HPC tools. RCC participants include researchers both within the University of South Carolina system and neighboring institutions. Here we briefly describe several research projects conducted by the USC researchers.

Dynamic 3D modeling of biofilms using GPU computing

Prof. Qi Wang (Mathematics, University of South Carolina)

We study complex phenomena in nanoscience research through an integrated program of theory, modeling, and computational simulations. The current research activities in the group include: quantum chemistry, algorithm development and analysis, pattern recognition and visualization, Monte Carlo, molecular dynamics, Ab initio simulation of complex material systems, multiscale modeling and simulation of molecular structures, self-assembly phenomena, mesoscale structure in complex fluids/soft matter, high performance computing, and GPU computing. We seek interdisciplinary interaction with other researchers within the USC and outside groups. [read more]


Nanomaterials and Catalysis, Multi-Scale Modeling

Prof. Andreas Heyden (Chemical Engineering, University of South Carolina)

To enable simulations of complex systems that accurately reflect experimental observations, continued advances in modeling potential energy surfaces and statistical mechanical sampling are necessary. While studying systems relevant for catalysis, we develop new theoretical and computational tools for the investigation of these complex chemical systems. Our tool development efforts are at the interface between engineering, chemistry, and physics, and are rooted in classical, statistical, and quantum mechanics with a special focus on novel multiscale methods. [read more]


Quantum chemistry, electron correlation effects in molecules

Vitaly Rassolov (Chemistry and Biochemistry, University of South Carolina)

It is well known to theorists that most chemical reactions require quantum description of nuclei due to the effects of tunneling, zero point energy, and non-adiabatic phenomena. It is appealing to describe quantum effects using semiclassical methods. The problem is that modern semiclassical methods are often more expensive than full quantum treatment, and their error is difficult to assess. My group develops a method based on Bohmian trajectories that is very inexpensive at the semiclassical limit, favorably compares to other semiclassical methods (such as Herman-Kluk), and is systematically improvable. [read more]


Development of approximate quantum potential method applicable to large molecular systems and studies of reactivity of hyperthermal oxygen

Sophya Garashchuk (Chemistry and Biochemistry, University of South Carolina)

For general problems, the exact determination of the quantum potential is at least as difficult as the solution of the standard Schrodinger equation, but the quantum trajectory formulation provides a convenient starting point for approximation of the "quantum'' quantities which are small in the semiclassical limit of heavy particles such as nuclei. We develop global approximations to the quantum potential, which capture dominant quantum effects, such as zero-point energy, tunneling, wavepacket bifurcation, in a computationally efficient manner (currently tested for up to 40 degrees of freedom). [read more]


Spin photovoltaic effects in quantum wires

Yuriy Pershin (Physics and Astronomy, University of South Carolina)

We consider the current induced in quantum wire by external electromagnetic radiation. The photocurrent is caused by the interplay of spin-orbit interaction and external in plane magnetic field. We calculate this current using a Wigner function approach taking into account radiation-induced transitions between transverse subbands. [read more]

Electron Microscopy and Nano Imaging Reconstruction

Douglas Blom (Electron Microscopy Center, University of South Carolina)

A systematic approach is being developed to extract high resolution information from HAADF-STEM images which will be beneficial to the characterization of beam sensitive materials. The idea is to treat several, possibly many, low electron dose images with specially adapted digital image processing concepts applied to the raw STEM data at minimum allowable spatial resolution. We are refining the main conceptual imaging concepts and restoration methods that are suitable for carrying out such a program and, in particular, allow one to correct special acquisition artifacts. This project is in a collaboration with members of the Interdisciplinary Mathematics Institute here at the University of South Carolina. [read more]


2012 Pilot Training Program: Middleware for Research

EPSCoR RII Track I & II assistantship support was provided for 13 graduate and 5 undergraduate students in the Middleware Training Program for Spring/Summer 2012. Student participants in the program were nominated by selected faculty mentors drawn from a wide variety of disciplines, ranging from tissue fabrication, geonomics, fuel cells, computational biology, electrical engineering, analysis of sensor data, and digital humanities. The faculty researchers were identified based both upon the quality of their research and as being strong candidates for HPC enhancement by middleware support.


Thermo-mechanical Modeling of SiC/SiC Nuclear Fuel Cladding Test Assembly

Luis Alva-Solari (Mechanical Engineering, University of South Carolina) mentored by Prof. Xinyu Huang

The objective of this modeling study is to simulate temperature distribution and mechanical stress/strain state in a SiC/SiC composite cladding under simulated thermo-mechanical loading. A Zirconia tube will be inserted in the SiC/SiC tube with a predetermined radial interference between them and an intense heat source, placed inside the Zirconia tube (inner tube), will heat the inner tube up to a target temperature. The hot and expanding Zirconia tube will subsequently heat up and pressure the SiC/SiC composite tube. The set of tubes will be isolated from the surrounding air by thermal insulation. (more)



Electron Microscopy Image De-Noising using Fourier Analysis (Undergraduate Project)

Charles Arnold (Mathematics, University of South Carolina) mentored by Prof. Benjamin Berkels

Electron microscopy requires a high density of electrons per square nanometer in order to have images with high resolution and an acceptable signal-to-noise ratio. The environment in which an electron microscope is used must be very stable. Ambient vibrations, temperature fluctuations, acoustic waves, and electromagnetic waves can all add unwanted information, or noise, into the electron microscope readings. When analyzing soft materials one must use a smaller dose of electrons per square nanometer, for the standard dose can damage or destroy the material. However, this can cause the readings to have low resolution and an unacceptable signal-to-noise ratio. (more)



Enhancing Computational Science Curriculum to Include Key Concepts of Parallelism  (Undergraduate Project)

Trent Edwards and James Sweeney (Mathematics and Computer Science, Coker College) mentored by Prof. Paul Dostert

The Coker College research team focused their efforts on implementing parallel structure and high performance computing into the computer science and mathematics curriculum at not only their own school but any school that is looking to introduce a more updated computer science and mathematics program. These courses offer all beginning computer science majors with the basic essentials necessary to understand and utilize parallel computing in their programs throughout the duration of their career. Parallel computing is essential in this age, with large data sets and a hefty weight put on speed. (more)



Effects of polymer structure and composition on fully resorbable endovascular scaffold performance

Jahid Ferdous (Biomedical Engineering, University of South Carolina) mentored by Prof. Tarek Shazly

Fully-erodible endovascular scaffolds are increasingly considered for the treatment of ischemic artery disease owing to their potential to mitigate long-term risks associated with permanent devices. While complete scaffold erosion facilitates vessel healing, the generation and release of material degradation by-products may elicit a local inflammatory response that limits implant efficacy. Poly-L-lactide (PLLA) is candidate material for a variety of erodible implants due to generally acceptable biocompatibility and the tunable physical, chemical, and mechanical properties. (more)



GPU acceleration of pyrosequencing noise removal

Yang Gao (Computer Science and Engineering, University of South Carolina) mentored by Prof. Jason Bakos

AmpliconNoise , an updated version of Pyronoise , is a tool for removing noise from metagenomic data recorded by a 454 pyrosequencer. AmpliconNoise has shown to be effective in reducing overestimation of operational taxonomic units (OTUs) and chimera detection. AmpliconNoise’s noise removal method relies on clustering a large set of short sequences read by the sequencer. The DNA sequencing algorithm requires the computation of O(n2) pairwise distances using a global sequence alignment method. Each sequence consists of a few hundred base pairs and a typical dataset contains 104 sequences, making the clustering computation extremely expensive. (more)



Agent-based Simulations of Casualties Incurred by Invasion of Japan

Michael Helms (Center for Digital Humanities, University of South Carolina) mentored by Profs. John Bonnet (Brock Univ.) and David Miller (USC)

The atomic bombings of Hiroshima and Nagasaki remain one of the most contested areas of debate in the literatures devoted to the conclusion of World War II and the beginning of the Cold War. One important point of contention is the issue of the cost of the bombings. We know that more than 200,000 people died as a result of the bombings. How many would have died if the bombs had not been used, or if they had not worked and the U.S. and its allies had been forced to invade Japan proper in late 1945 and early 1946? In their post-war defenses of the bombings, members of the Truman administration argued that they had expected anywhere between half a million to two million casualties on the allied side alone. (more)



Using the Lefkovitch Matrix to examine long-term population projections of island populations of the Eastern Diamondback Rattlesnake, Crotalus adamanteus

Mike Martin (Biology, University of South Carolina) mentored by Prof. Tim Mousseau

Demographic information for wildlife populations is important in helping wildlife managers make appropriate management decisions. However, detailed information for populations is often lacking. The Eastern Diamondback Rattlesnake (Crotalus adamanteus; EDB) is currently under review for listing as a federally threatened species, yet studies have not focused on survival with respect to life history for this long-lived species. Pressure from loss of habitat and persecution are thought to be primary drivers of the decline of populations of this species. (more)



Multislice Frozen Phonon HAADF-STEM Image Simulation of Important Inorganic Materials

Sonali Mitra (Chemistry, University of South Carolina) mentored by Dr. Doug Blom

The Multislice Frozen Phonon High Angle Annular Dark Field (HAADF)-STEM (Scanning Transmission Electron Microscopy) image simulation on various intergrowth and grain boundary of orthorhombic M1-type phase and trigonal Mo3VOx phase of industrially important molybdenum-vanadium bronze based selective oxidation catalysts will be carried out using High-Performance Cluster Computing. The “autostem” code written in C language developed by E.J. Kirkland and freely downloadable from the site is used for Multislice Frozen Phonon simulation. (more)



Building a middleware cybersecurity interface for cloud supercomputing  (Undergraduate Project)

Loodwing Murillo (Methematics and Computer Science, Benedict College) mentored by Prof. Shahadat Kowuser

Cloud Computing has been envisioned as the next generation architecture of IT Enterprise. In contrast to traditional solutions, where the IT services are under proper physical, logical and personnel controls, Cloud Computing moves the application software and databases to the large data centers, where the management of the data and services may not be fully trustworthy. This unique attribute, however, poses many new security challenges which have not been well understood. In our research, we focus on cloud data storage security, which has always been an important aspect of quality of service. To ensure the correctness of users’ data in the cloud, we propose an effective and flexible distributed scheme with two salient features, opposing to its predecessors. (more)



Utilizing bioinformatics and geographical tools to correlate spatial and genetic distance in the malaria parasite, Plasmodium falciparum

Chase Nelson (Biology, University of South Carolina) mentored by Prof. Austin L. Hughes

This project studied genetic variation in the C-terminal non-repetitive (CTNR) region of the circumsporozoite protein (CSP) of Plasmodium falciparum, the most virulent human malaria parasite (Hughes 1991). The CTNR region contains T cell epitopes that are enriched in radical nonsynonymous (amino acid-altering) changes, indicative of positive (Darwinian) diversifying selection for immune evasion (Hughes & Hughes 1995). Previous attempts have been made at a geographical analysis, showing that levels of polymorphism differ between different regions of Thailand under differing levels of pest control (Jongwutiwes et al. 2010). Here, a more thorough geographical analysis was undertaken. First, the entire CTNR region was obtained for the 7G8 sequence (Dame et al. 1984). (more)



Comparative metagenomic and transciptomic analysis of the microbial community living in hypersaline mats in San Salvador

Eva Preisner (Environmental Health Sciences, University of South Carolina) mentored by Prof. Sean Norman

For this project we conduct comparative metagenomic and transcriptomic analysis to investigate the variety of bacteria (using 16S rRNA gene sequences), and active bacteria (16S rRNA transcript sequences) in microbial mats. The objective is to develop computational procedures that are able to help us perform the corresponding bioinformatic analysis. That analysis must first trim the sequences to remove primers. The next step is to process transcripts data. The Pipeline procedure (i.e. percent recovery of internal control transcripts) aligns all sequences to the internal control sequence to see how many contiqs are formed, and further remove the internal control sequence from the sequence data. (more)



Multiple object tracking with occlusion handling using Average Longest Path framework

Dhaval Salvi (Computer Science and Engineering, University of South Carolina) mentored Prof. Song Wang

We formulate the tracking as a graph problem. Starting from a set of candidate detected boxes on each video frame, we construct initial "tracklets." Tracklets are coherent sub-portions of an entire track, computed using simple heuristic like distance between the detection boxes between consecutive frames etc. We then combine these tracklets in a hierarchical manner to obtain the complete tracks. At each level of the hierarchy we construct a directed graph, where each tracklet is represented by a node, together with two additional nodes: enter node S and exit node T. (more)



Applications of Compressed Sensing to Electron Tomography

Toby Sanders (Mathematics, University of South Carolina) mentored by Prof. Peter Binev

The analysis of biological and soft materials comes from images formed by electron microscopes. Unfortunately, obtaining a quality image of these materials can require high density sampling which can damage the material under investigation. Therefore, we need the use of special reconstruction techniques such as compressed sensing (CS) for the under sampled set of data that comes from electron tomography (ET). The process of ET involves scanning the material with an electron beam along a grid at several different angles. For each scan we obtain a value which corresponds to the integral of the intersection of the area of the material and the electron beam. This can be mathematically represented as a matrix multiplication with our material x, i.e. Ax = b, where b is a vector containing the values of the integrals. (more)



An Algorithm to quickly compute the approximate distance field in a proximity to a point cloud

Jenny Tabat (Mathematics, University of South Carolina) mentored by Prof. Peter Binev

My research project is to create an algorithm to quickly compute the approximate distance field in a proximity to a point cloud. The goal is to implement this algorithm in parallel on GPUs so the distances can be quickly generated for a large point cloud. An octree is used to sort the points into cubes by using several dyadic splits until the cubes are the required size. For each vertex in the domain, Principal Component Analysis will be used on the local point cloud to find the rectangle that approximates the point cloud. The distance will then be found from the vertex to the rectangle. This algorithm can then be used to initialize an Eikonal equation solver to generate a distance field on the entire domain. See Mentor's website for more details.



Mechanical Behavior of the Heart Post-Myocardial Infarction  (Undergraduate Project)

Lauren Wolf (Biomedical Engineering, University of South Carolina) mentored by Prof. Tarek Shazly

A myocardial infarction is caused by inadequate perfusion to an area of the myocardium, and produces lasting changes in the material behavior of the heart. At the epicenter of the damage lies the zone of infarct/necrosis, at which tissue function cannot be recovered. A zone of ischemia surrounds the zone of infarct and consists of tissue that is damaged and may not function optimally; the necrotic zone may expand into the ischemic zone if the mechanism of myocardial injury is not corrected. (more)



Accelerating simulation of Virtual Test Bed software by adopting the Latency Insertion Method in a high performance computing environment

Huaxi Zheng (Electrical Engineering, University of South Carolina) mentored by Prof. Roger Dougal

The Latency Insertion Method (LIM) is adopted to accelerate simulation of the Virtual Test Bed (VTB) software in a high performance computing environment at USC. VTB is a multi-discipline simulation tool currently being developed at USC. VTB utilizes matrix operations in order to solve sets of simultaneous equations. Matrix operations do not scale linearly and so as the size of the system increases, the required time to solve for the solution to the system increases as a cubic operation O(N3). (more)