5th Semi-Annual Midwest Quantitative Biology Symposium (MidQBio)
University of Notre Dame
Saturday, April 8, 2017
Jordan Hall of Science, Room 105
University of Notre Dame
Notre Dame, IN 46556
The aim of the MidQBio Symposium is to bring together researchers from around the Midwest who share a common interest in quantitative biology, and to help build a community of these researchers. The symposium provides researchers opportunities to: come together to share and disseminate recent results, become familiar with other research groups in the area of quantitative biology, and facilitate potential collaboration. Especially important is the cultivation of early career researchers including graduate students and postdocs whose work is highlighted in lightning presentation sessions.
We are very grateful to the Notre Dame College of Science, the Departments of Applied and Computational Mathematics & Statistics (ACMS), Physics, Chemical and Biomolecular Engineering, Biological Sciences, and Aerospace & Mechanical Engineering for their generous support of this event!
Alexandra Jilkine, ACMS (ajilkine at nd.edu)
Alex Perkins, Biological Sciences (taperkins at nd.edu)
Dervis Can Vural, Physics (dvural at nd.edu)
Jeremiah Zartman, Chemical and Biomolecular Engineering (jzartman at nd.edu)
Pinar Zorlutuna, Aerospace & Mechanical Engineering (pzorlutu at nd.edu)
Research Professor in Materials Sciences & Engineering
University of Delaware
"Nanoscale Characterization of Poly(3-hydroxybutyrate) Fibers"
127 Nieuwland Science Hall – 4 pm
October 29, 2015
Chase's research interests are in the area of structure/property/process relationships in polymeric materials, electrospinning polymer nanofibers, high strength polymeric fibers, IR/Raman spectroscopy, and vibrational sum frequency generation spectroscopy of polymeric films and fibers. In collaboration with Professor John Rabolt, he has developed planar array infrared spectroscopy, a new approach to IR measurements. In collaboration with Professor Matt Doty, he is expanding the use of ultra-fast laser techniques for both time resolved spectroscopy (transient absorption and photoluminescence) and tunable infrared laser measurements. Chase spent 34 years in the Central Research Department at DuPont.
Arey Professor of Chemistry
Director of the Energy Frontier Research Center on Solar Fuels
University of North Carolina at Chapel Hill
Carey Auditorium, Hesburgh Library — 4:00 p.m.
April 16, 2015
The sun could be our ultimate renewable energy source but, as an energy source, suffers from its low intensity, and the massive collection areas required to meet the needs of powering the world’s growing economies. The sun is also intermittent, going down at night, which creates a need for energy storage on massive scales. Inspired by natural photosynthesis, a way to meet the energy storage challenge is by using the energy of the sun to produce “solar fuels” by “Artificial Photosynthesis” with energy stored in the chemical bonds of high energy molecules - hydrogen from water splitting or carbon-based fuels from reduction of CO2.
In this presentation, a hybrid approach to solar fuels is described. It is based on the integration of molecular assemblies for light absorption and catalysis with the band gap and surface properties of mesoscopic, nanoparticle films of inert metal oxides – TiO2, SnO2, NiO. In the resulting Dye Sensitized Photoelectrosynthesis Cells (DSPEC), light absorption by the chromophore and excited state injection into the conduction band of TiO2 initiates a series of electron transfer events. Transfer of the injected electron transfer to a cathode results in H2 evolution. With appropriate design features built in, including surface stabilization of the assembly and use of core/shell structured oxide films, relatively high per photon-absorbed efficiencies for visible light water splitting into hydrogen and oxygen has been achieved.
D.R. Bullard-Welch Foundation Professor of Science, Department of Chemistry, Rice University
"The Protein Folding Problem"
127 Hayes-Healy Center — 4:15 p.m.
October 9, 2014
Protein folding can be understood as a biased search on a funneled but rugged energy landscape. The funneled nature of the protein energy landscape is a consequence of natural selection. Prof. Peter Wolynes of Rice University will discuss how this rather simple picture quantitatively predicts folding mechanism from native structure and sequence. He will also discuss recent advances using energy landscape ideas to create algorithms capable of predicting protein tertiary structure from sequence, protein binding sites and the nature of structurally specific protein misfolding relevant to disease. Finally, he will compare the physical folding energy landscape with the apparent fitness landscape of evolution as inferred from large genomic data sets.
Philip K. Maini
Director of the Centre for Mathematical Biology, Mathematical Institute at Oxford University
Raclin-Charmichael Hall Auditorium — 4:00 p.m.
February 18, 2013
The collective movement of cells in tissue is vital for normal development but also occurs in abnormal development, such as in cancer. We will review three models:
(i) A vertex-based model to describe cell motion in the early mouse embryo
(ii) A individual-based model forneural crest cell invasion
(iii) A model for acid-mediated tumor invasion
In each case we shall use the model to answer important issues concerning biology.
For example, in (i) we shall propose a role for rosette formation. In (ii) we propose that two cell types are necessary for successful invasion. Lastly, in (iii) we shall show how the model suggests possible therapeutic strategies for tumor control.
University of Minnesota
123 Nieuwland Science Hall - 4:30 p.m.
March 3, 2011
Single cell measurements reveal otherwise unobtainable information about how individual biological cells communicate with one another. This talk will focus on the use of single cell microelectrochemical measurements to study (1) blood platelets and (2) immune cell nanoparticle toxicity. Blood platelets are critical players in the process of hemostasis but, based on their small size and propensity to activate, real time single cell measurement of chemical messenger secretion has never been accomplished. Herein, microelectrochemical techniques reveal the concentration of chemical messengers stored in and the kinetics of chemical messenger release from individual platelets, including considerations of how extracellular and membrane manipulations influence platelet behavior. The same electrochemical techniques that reveal fundamental insight about blood platelets can also be used for applied studies of nanoparticle toxicity. In this case, carbon-fiber microelectrochemistry is used to probe critical cell function in immune system cells following exposure to engineered nanoparticles. The insight gained reveals how nanoparticles interact with cells as well as potential avenues to avoid this interaction in next generation nanoparticle-containing products.
Hosted by the University of Notre Dame
October 21-21, 2010 - 2:00 p.m.
- Dimitri Burago (Penn State University)
- Robert Bryant (MSRI, Berkeley)
- Jeff Cheeger (Courant Institute, NYU)
- Toby Colding (MIT)
- Vitali Kapovitch (University of Toronto)
- Bruce Kleiner (Courant Institute, NYU and Yale)
- Peter Petersen (UCLA)
- Anton Petrunin (Penn State University)
- Christina Sormani (CUNY)
- Chuu-Lian Terng (UC-Irvine)
- Gang Tian (Princeton)
- Guofang Wei (UCSB)
- Wolfgang Ziller (University of Pennsylvania)
127 Hayes-Healy Center - 4:30 p.m.
May 25, 2010
Quantum theory, in particular the theory of entanglement, provides a coherent picture of the physical origin of randomness and the growth and decay of correlations, even in macroscopic systems exhibiting few traditional quantum hallmarks. It helps explain why the future is more uncertain than the past, and how correlations can become macroscopic and classical by being redundantly replicated throughout a system's environment. The most private information, exemplified by which path a particle takes through an interferometer, is not replicated, and exists only transiently: after the experiment is over no record remains anywhere in the universe of what ``happened''. At the other extreme is information that has been replicated and propagated so widely as to be infeasible to conceal and unlikely to be forgotten. Modern information technology has caused an explosion of such information, eroding privacy while making it harder for tyrants to rewrite the history of their misdeeds; and it is tempting to believe that all macroscopic information is permanent, making such cover-ups impossible in principle. But we argue, by comparing entropy flows into and out of the Earth with estimates of the planet's storage capacity, that most macroscopic classical information--for example the pattern of drops in last week's rainfall--is impermanent, eventually becoming nearly as ambiguous, from a terrestrial perspective, as the which-path information of an interferometer. Finally, we discuss prerequisites for a system to accumulate and maintain in its present state, as our world does, a complex and redundant record of at least some features of its past. Not all dynamics and initial conditions lead to this behavior, and in those that do, the behavior itself tends to be temporary, with the system losing its memory as it relaxes to thermal equilibrium.
Eric E. Schadt
Chief Science Officer, Pacific Biosciences
Jordan Hall of Science, room 101 - 4:00 p.m.
November 24, 2009
To further our understanding of the complex network of molecular and cellular changes that impact disease risk, disease progression, severity, and drug response, multiple dimensions must be considered together. Schadt presents an approach for integrating a diversity of molecular and clinical data to uncover models that predict complex system behavior. By integrating diverse types of data on a large scale he demonstrates that some forms of common human diseases are most likely the result of perturbations to specific gene networks that in turn cause changes in the states of other gene networks both within and between tissues that drive biological processes associated with disease. His work has significant implications for drug discovery.
Director of Station Q, Microsoft Research, UC Santa Barbara
Jordan Hall of Science, room 105 - 5:00 p.m.
November 16, 2009
The underlying logic of our computers is of the 19th century. Computers might, instead, be designed to “think” in a quantum mechanical way. The tidal wave that brought us quantum mechanics may wash over us again 100 years later. There is reason to believe that quantum computing is the ultimate mode of information processing consistent with physics. So the short answer to, “What will quantum computers do?” is, “Everything possible.” Topology is geometry after you have forgotten local details; it deals with discrete structures. In physics local detail is usually of paramount importance. However one of the key physical ideas of the last 50 years – the “renormalization group” – tells us there are low temperature systems whose most important properties are topological in nature. The discrete nature of topology will allow us to control quantum mechanical evolutions in these systems with amazing precision. This is just what quantum computation requires.
Robert P. Kirshner
Clowes Professor of Science, Harvard University
Hesburgh Library Auditorium, 7:00 p.m.
October 8, 2009
Recent observations of exploding stars located halfway across the Universe reveal an astonishing fact: the expansion of the Universe is speeding up! Apparently, the universe is dominated by a mysterious “dark energy” that drives cosmic acceleration. Robert P. Kirshner, a distinguished astronomer and science educator, explains this astonishing new picture of the universe in a lively, richly illustrated presentation, drawing his own first-hand account of the discovery.