gradstud

Graduate Students

		Scott Christley Graduate Student Department of Computer Science and Engineering 206 Cushing 574-631-7596 schristl@nd.edu http://www.nd.edu/~schristl/
		Research interests: My primary research interests include bioinformatics, computational biology, and formal methods for representing and reasoning about biological systems. Recent work includes the implementation of a discrete, multi-scale stochastic model for the behavior of limb bud precartilage mesenchymal cells in vitro. The model employs a biologically motivated reaction-diffusion process and cell-matrix adhesion as the basis of self-organizing pattern formation of precartilage condensations. Future enhancements to the model include incorporating the TGF-beta and Notch gene regulatory network for the reaction-diffusion process and representing the model using a formal method that allows reasoning about the properties of the model.

		Trevor Cickovski Graduate Student Department of Computer Science and Engineering 325 Cushing Hall 574-631-3906 tcickovs@nd.edu http://www.nd.edu/~tcickovs/
		Research interests: My research involves programming languages and their application to computational biology. I specifically am studying domain-specific languages and their implementation scientific processes using stochastic methods. Some of these processes include scripted parallel molecular dynamics, microtubule modeling, reaction-diffusion equations, and cell-centered approaches to morphogenesis modeling like the Cellular Potts Model. My research also involves scientific software engineering, including the incorporation of domain-specific languages into larger frameworks.

		Richard Gejji Graduate Student Department of Mathematics 237 Hayes-Healy 574-631-3741 rgejji@nd.edu
		Research interests: My research interest lies in using mathematical analysis and computer simulations to model and understand complex dynamics. My current research project is using computer simulations to model how global warming influences the evolution of the Colias butterfly and other butterflies whose flight is weather dependent. Using the results of the computation model, we can build a continuum model and make predictions on the spatial patterns of butterfly populations.

		Ivan Gregoretti Graduate Student Department of Chemistry and Biochemistry 251 Nieuwland Science Hall 574-631-8512 igregore at nd.edu http://www.nd.edu/~igregore/
		Research interests: I started studying the cytoskeleton experimentally followed by studies of the molecular evolution of the histone deacetilases. My primary research focus currently is the application of mathematical tools to understanding the microtubule cytoskeleton. My major interest is applying mathematical and computational approaches to obtain answers to the biologically most relevant questions.

		Tanya Kazakova Graduate Student Department of Mathematics 237 Hayes-Healy 574-631-3741 tkazakov@nd.edu http://www.nd.edu/~tkazakov/
		Research interests: My primary research interest is mathematical and computational modeling of somite formation in vertebrates. In particular, I am looking at somite formation using three different approaches: the Cellular Potts model, differential equations with delays and nonlinear partial differential equations. Another research interest I have is mathematical education. I am currently involved in designing and building online tutorials for high school and undergraduate students to encourage them to explore the interrelationships between the sciences and mathematics.

		Fang Qi Graduate Student Department of Mathematics 253B Hayes-Healy 574-631-5459 fqi@nd.edu http://www.nd.edu/~fqi/
		Research interests: My research interests involve running mathematical simulations of problems in biology and comparing the simulation outcomes to the experimental results. I am currently working on modeling aggregation of platelets in order to analyze the rules governing the blood clot formation. I use two models: discrete and continuous. The discrete model uses Monte-Carlo and energy methods, while my continuous model involves numerical solution of partial differential equation.

		Matt Rissler Graduate Student Department of Mathematics 235 Hayes-Healy 574-631-3221 mrissler@nd.edu http://www.nd.edu/~mrissler/
		Research interests: My current interests are in the area of collective motion exhibited by swarming Myxococcus Xanthus, and statistical and imaging tools to collect data on the motion of individual cells in a swarm. My current work involves collecting phase contrast images of M. Xanthus on agar, and developing processing tools and methods to extract data about individual cells.

		Yilin Wu Graduate Student Department of Physics 336 Nieuwland Science Hall 574-631-6590 ywu1@nd.edu http://www.nd.edu/~ywu1
		Research interests: I use statistical physics and computational tools to study the self-organization and non-equilibrium behavior in biological systems. My current research work involves the pattern formation and collective motion of Myxobacteria, a type of soil microbe.

		Jianfeng Zhu Graduate Student Department of Mathematics 217 Hayes-Healy 574-631-4861 zhu.17@nd.edu
		Research interests: My research involves numerical analysis of reaction-diffusion systems and their application to the pattern formation in the biological system. I am interesting in the analysis of Turing parameter space, the simulation of some pattern formation, such as dissipative structures, the spiral and scroll waves, and the biological system with growing domain.