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Prof. Mark Alber
Email: malber@nd.edu
Modeling Microtubules Dynamic Instability
Mark Alber (Departments of Mathematics and Physics) and Holly Goodson (Department of Chemistry and Biochemistry)
Microtubules (MTs) are long proteinaceous tubular polymers found in all eukaryotes. MTs perform important cellular processes such as providing the cell with a scaffold for organization acting as tracks for vesicle transport, establishing cell polarization and segregating the chromosomes during cell division. A key property for their function is their high dynamicity evidenced by their ability to quickly elongate or shorten as they exchange materials with the cytosol. Elongation is achieved by incorporation of their building units while shortening occurs by unit detachment. Both processes occur exclusively at the MT tip and the units are alpha-beta tubulin heterodimers. MTs are well known to display dynamic instability behavior. Under certain conditions individual MT can switch between the phases of growth and shortening (even being in a steady state). The length of a MT fluctuates significantly on order of its total length. The project will focus on development of a Monte Carlo computational model and testing its ability to explain dilusion experiment.
Study of Swarming in Myxobacteria
Mark Alber (Departments of Mathematics and Physics), Jesus Izaguirre (Department of
Computer Science and Engineering), Yi Jiang (Los Alamos National Laboratory) and Dale Kaiser (Biochemistry Department, Stanford University)
Swarming, the coordinated motion of many cells, facilitates their spread on the surface of a suitably moist solid medium. As a result of evolution the use of energy is optimized by swarming in order for bacterial colonies to expand and cover the largest possible area, allowing individual cells maximal access to nutrients and oxygen. When the surface is a living tissue, many pathogenic bacteria swarm to facilitate infection. Swarming also speeds the formation of biofilms and fruiting bodies. Swarming is observed in cells that are propelled by rotating flagella, by the secretion of slime, and by retracting type IV pili. To study swarming we chose to examine Myxococcus xanthus, because it swarms rapidly, exhibits typical type IV pili-mediated motility, and also has slime secretion engines at the rear. It has been studied for decades; numerous swarming mutants have been identified and characterized. Myxobacteria are commonly found in cultivated soils, where they feed on other bacteria. The project will focus on studying the role of social interactions between cells, including the interaction mediated by type IV pili, in myxobateria swarming.
Prof.
Howard Blackstead
Email: blackstd@nd.edu
We are studying novel high temperature superconductors in an effort
to determine which layers of the oxide structures participate in the
superconductivity. In order to reduce the complexity of the several
issues, we are focussing on materials which have only two distinct
chemical layers.The materials in which we have the greatest interest
are double Perovskites of the form A2LnRu1-uCuuO6 where A is an alkaline earth, either Sr or Ba, and Ln is any of the
lanthanides or Y. This class of materials has two distinct chemical
layers, LnRuO4 (which is hole doped by partial replacement
of Ru by lower valence Cu) and SrO or BaO. We carry out a variety
of characterizations including: x-ray diffraction, microwave resonance
and surface resistance studies, as well as resistivity and magnetization
measurements as functions of temperature and applied magnetic field.
Collaborators carry out neutron diffraction and muon spin rotation
studies.
Prof.
Bruce Bunker
Email: bunker@nd.edu
This project involves designing and coding a data simulation program
for x-ray absorption spectroscopy utilizing x-ray fluorescence detection.
We currently have codes that will reliable calculate the x-ray absorption
coefficient for x-ray absorption fine structure, but need a program
that will generate "fake" data which includes instrumental effects
such as dead-time corrections, self-absorption effects, x-ray harmonic
contamination, etc. To code this, the student will work closely
with others in the group to understand both the basic physics and
the instrumentation used for our experiments. We hope the student
can also accompany us on an experimental run to the Advanced
Photon Source to see the experiments in action.
Prof.
Margaret Dobrowolska-Furdyna
Email: mdobrowo@nd.edu
The available projects involve the study of properties of ferromagnetic
semiconductors. GaAs, where some of the Ga atoms are substituted
by a magnetic ion Mn, would be the example of this class of materials.
We have the Molecular Epitaxy Machine where we can grow this materials
in a very controllable way. Some projects concentrate on the optical
properties of the samples. We can do magneto-luminescence, micro-luminescence,
absorption and/or reflection of circularly polarized light where
we study what happens to the polarization after light interacts
with the sample. We also study magneto-transport. One of the students
is involved in achieving a light emitting diode based on this class
of materials.
Prof. Morten Eskildsen
Email: meskilds@nd.edu
The research of my group is focused on the study of vortices in superconductors and how they reflect on the detailed nature of the superconducting state (for more information see: www.nd.edu/~vortex). The REU project includes participation in a small-angle neutron scattering experiment at an international neutron facility, and responsibility for the subsequent data analysis. For more information see e.g L. DeBeer-Schmitt, Phys. Rev. Lett. 97, 127001 (2006).
Prof. Kathie Newman, Physics
Email: newman@nd.edu
Prof. Steven Corcelli, Chemistry and Biochemistry
Email: scorcell@nd.edu
In this project, the student will work with theorists from physics and chemistry on a problem related to developing renewable energy resources. The long-term goal of the project is understanding the mechanism for the photocatalytic production of hydrogen from aqueous methanol solutions with titanium dioxide as a catalyst. A number of research methodologies from chemistry and physics are to be brought together to address the problem including using density-functional tight-binding method to compute the interatomic forces in the problem. A physics REU student could help advance this project by comparing results from different electronic structure techniques. This represents a chance to learn electronic structure methodologies as well as how to validate and improve existing computer code. An alternative or second project would be to help develop visualization programs to use in future computer simulations. The student would join a lively research group that includes one postdoc, two graduate students, and two undergraduate students and would have the opportunity to work closely with both faculty and the graduate students and to run code in a top 500 research computer facility. Fortran programming experience and/or a desire to learn programming quickly is required.
Prof. Zoltan Toroczkai
Email: toro@nd.edu
My group focuses on a number of projects: 1) modeling real-world networks (such as Internet, www, metabolic nets, epidemic contacts, etc.) using graph-theoretic methods, 2) correlations between persistence of fluctuations of flows on networks and network topology, 3) modeling plasticity in large-scale brain-like neuronal networks and 4) studying the relationship between steric constraints in a protein and the funnel character of its free-energy landscape. All projects require intermediate or higher level numerical programming.
Dr.
Igor Veretennikov
Email: ivereten@nd.edu
This project involves the Magnetic Resonance Imaging (MRI) of granular
media, i.e. materials, which are composed of collections of separated
solid grains. Such granular media (e.g. sand) display a variety
of complex dynamic and static properties, which distinguish them
from materials in bulk solid or liquid phases. We are focusing on
visualization of the local rearrangements of grains caused by the
motion of small disk and how grains rearrangements depend on the
disk displacement. The student will perform the experiments using
state of the art 7 Tesla MRI imager and process the MRI data using
already available codes. |
