Category: James L. Carmon Scholarship Award

James L. Carmon Scholarship Award 2013

Alexander Sokolov, PhD candidate in chemistry, uses mathematics and quantum physics to calculate the chemical and physical properties of molecules. Understanding these basic properties requires a heavy computational burden, even for small molecules, and accurate descriptions of large molecules are exceptionally difficult. As part of his PhD research, Sokolov is searching for mathematical and computational approaches to better understand the properties of large, complex molecules. He is working to refine and optimize the computer code used in a theoretical method known as density cumulant functional theory, or DCFT. Sokolov’s discoveries promise to revolutionize the field of computational quantum chemistry, as his work may one day allow researchers to compute the properties of large molecules without using empirical parameters. That is, researchers could rely completely on computers to conduct “experiments” without ever using a laboratory, which would make experimentation cheaper and would allow researchers to conduct theoretical experiments with large molecules that may be impossible to perform in a lab.

James L. Carmon Scholarship Award 2012

Celine Hong, PhD candidate in the Institute of Bioinformatics, uses innovative ideas and cutting-edge computational methods to address biological problems related to cancer. One of the main topics in Hong’s research is to find a way to enhance cancer diagnosis by identifying biomarkers that can be used to detect the disease at an early stage. Her first project was to develop a computational method for predicting excreted protein to find non-invasive biomarkers in urine. Using experimental techniques to complement her computational prediction, such as western blots and antibody arrays, her work led to the discovery that a protein called endothelial lipase is greatly suppressed in urine from gastric cancer patients versus control. This non-invasive method of testing shows great promise as a diagnostic tool for other types of cancer and a variety of other diseases. Hong has continued her studies with a focus on finding microRNA biomarkers, as well as studying the apoptosis pathways in cancer cells. She is developing and applying novel computational techniques to make meaningful discoveries in her research.

James L. Carmon Scholarship Award (Honorable Mention) 2012

Anirban Mukhopadhyay, PhD candidate in computer science, researches the use of biomedical image analysis, computer vision, pattern recognition and machine learning. He is particularly focused on both functional and structural cardiovascular imaging. For the past year, Mukhopadhyay has been working on the analysis of high-resolution multi-detector computed tomography (MDCT) and intra-vascular ultra-sound-virtual histology (IVUS-VH) images for detection and diagnosis of cardiovascular pathologies. He has designed active contour models for segmentation and 3D visualization of plaque accumulation in an IVUS-VH image sequence of a blood vessel. His recent work has dealt with the characterization of the endocardial surface structure of the left ventricle using high-resolution MDCT images for diagnosis of coronary artery disease. He plans to strengthen his background in the clinical aspects of cardiovascular anatomy, physiology and pathology to enhance his research problem of correlating the morphological analysis of the endocardial surface with functional analysis of CT perfusion data for detection of cardiac ischemia.

James L. Carmon Scholarship Award (Honorable Mention) 2012

Shan Huang, PhD candidate in ecology, developed a creative project for her doctoral research that integrates computer programming with global-scale databases to ask questions about the relationship between evolutionary history and current biodiversity. Huang’s research applies spatial analysis methods, phylogenetic comparative methods using evolutionary “supertrees” and statistical models to analyze data sets compiled across large spatial and taxonomic scales. She hopes to evaluate phylogenetic information as an explanation for global patterns of mammal biodiversity and the diversity of parasites in free-living carnivore populations. Her use of computational methods would expand significantly methods of investigation that have traditionally focused on a few species contained in a small geographic scale. The databases Huang uses span thousands of species and combine data on their geographic ranges, biological traits, evolutionary relatedness and common parasites.

James L. Carmon Scholarship Award 2011

Junqi Yin, a PhD candidate in physics, works on computer simulations of model systems in condensed matter physics. The simulations use algorithms to drive graphics processors to solve problems that can’t be addressed analytically. This enables scientists to study biophysical interactions at extremely small scales. The work has long-range implications in fields as diverse as thermodynamics and biophysics.

Yin’s algorithms and codes take advantage of the platform used in new graphic processing units (GPUs), powerful new tools for supercomputing. Yin’s code, running on a single GPU, outperforms conventional codes of the type running on a 32-CPU cluster by an order of magnitude. Yin’s “Wang-Landau sampling code” provides linear scalability, which extends to large applications. The sheer speed opens up whole new possibilities to run regimes previously considered intractable because of their size and complexity. In fact, Yin’s code has already been used to resolve a longstanding controversy about a specific type of magnetic phase transition.

James L. Carmon Scholarship Award (Honorable Mention) 2011

Michael J. Meindl, an MFA candidate in dramatic media, created a multi-media performance that combines a live actor, a puppet, and a virtual character. The actor wears an iPhone that runs a custom application, communicating its position and orientation to a desktop server, which in turn, communicates with the game engine controlling the virtual character. This enables the character to follow, and even react to, the live actor as he moves. The iPhone, easily concealed in the actor’s pocket, is invisible to the audience — as is the technology. The project combines Meindl’s interests in puppetry, animation, and live performance. It integrates theory and practice by incorporating 3-D animation, interactive programming, sensors, and mobile computing. Meindl is also part of a team producing computer-animated visual effects for an NIH-supported project designed to present difficult concepts of biology to high school students and another to teach students about knot theory in mathematics.

James L. Carmon Scholarship Award 2009

Ming-Hung Kao, a doctoral candidate in statistics, developed sophisticated software that provides optimal experimental designs for event-related functional magnetic resonance imaging (fMRI) studies. This brain-mapping technique, used both in medical practice and scientific research, is one of the most critical tools in neuroscience. Yet its images are expensive, and the signal-to-noise ratio in resulting experimental data is poor. Kao has proposed an efficient knowledge-based algorithm for developing a research design that achieves statistical goals and that, in some sense, does so in the most efficient way. His approach also fulfills the customization requirements for an event-related fMRI study that involves one or more stimulus types. His research won a student-paper award in the Statistical Computing/Statistical Graphics section of the 2008 Joint Statistical Meetings in Denver, Colorado, and a related paper has been accepted for publication in NeuroImage, the leading journal in the field.

James L. Carmon Scholarship Award 2008

Andrew K. Davis, a doctoral candidate in wildlife ecology, studies the health of amphibians in wetlands. Traditional methods for assessing animal population health can be difficult, time-consuming, and for fragile subjects, even fatal. Instead, Davis uses a new approach in wildlife ecology: computer-based image analysis to measure and record subtle variations in coloration and pattern asymmetry. The technique, already proven to be valuable in the lab, has the potential to greatly improve scientists’ ability to track and sample wildlife populations—and to better understand the relationships between environments and animal health. Davis’ work has already resulted in 13 peer-reviewed journal articles, with five more currently under review.

James L. Carmon Scholarship Award 2008

Xiaojia Tang, a doctoral candidate in physics and astronomy, is already a coauthor on three major papers that explain the functioning of biological clocks in governing the behavior of living organisms. Despite the importance of these mechanisms, their molecular underpinnings remained a mystery until last year, when a team of UGA researchers explained how three genes in Neurospora crassa—bread mold—make biological clocks tick. Tang’s main contribution was to adopt and implement an approach from statistical physics, called the ensemble method, which identified working models of the clock. She is now investigating how to expand her working model to demonstrate temperature compensation: the clock’s ability to tell the correct time in both hot and cold.

James L. Carmon Scholarship Award 2007

Chih-Horng Kuo, a doctoral candidate in genetics, is working on computational approaches to address two related but quite different biological systems. One project looks at the mathematical modeling of host-parasite interaction and co-evolution. The second focuses on genome evolution in protozoan parasites. For both projects, Kuo developed novel computational approaches to address questions of biological and evolutionary significance. The innovative tools he developed are directly applicable to genome science, a field of growing importance to all aspects of biology. These tools not only benefit Kuo’s own research but also represent a major advance in computational approaches to study genomes. He published three papers from his master’s work, and in his first three years as a PhD candidate, he published three more and is already writing a fourth.