Theme Semester on Discrete Networks

Paper for Assaf Naor's colloquium on September 19th

Background links for Robert Connelly's lectures:

  • Presentation on basics of rigidity
  • Presentation on prestress stability
  • Paper on Tensegrities for Discussion on September 18th at noon in Thackeray 704
  • Existence problem paper
  • Universal rigidity paper
  • Reference to a pebble game paper: Jacobs, Donald J.; Hendrickson, Bruce An algorithm for two-dimensional rigidity percolation: the pebble game. J. Comput. Phys. 137 (1997), no. 2, 346-365.

  • Complex Biological Systems Group

    Department of Mathematics, University of Pittsburgh


    About Us






    Theme Days 2012
    Theme Days 2011
    Theme Days 2010
    Theme Days 2009

    Complex Biological Systems Group
    University of Pittsburgh
    Department of Mathematics
    301 Thackeray Hall
    Pittsburgh, PA 15260
    Tel: (412) 624-6157
    Fax: (412) 624-8397

    Our group is supported in part by the National Science Foundation, Award EMSW21-RTG 0739261.

    Award period: June 2008 - May 2013.

    News and Events

    • May 2013 — Seeing double: Another paper from a former RTG undergraduate has been accepted. This one is by Jonathan Rubin, Jonathan Rubin, and Bard Ermentrout, is titled "Analysis of synchronization in a slowly changing environment: how slow coupling becomes weak coupling", and will appear soon in Physical Review Letters. The lead author is Jonathan J., who now works in information technology for the Grant Street Group in Pittsburgh, while the second author is Math Department faculty member Jonathan E. The two are not related, other than by name and by authorship. A write-up about the article is available online.

    • January 2013 — Our weekly meetings this semester will focus on the theme of networks in mathematical biology. We will read papers from the literature and trainees will take turns presenting overviews and commentary on these works.

    • December 2012 — Congratulations to former undergraduate Steven Reich and postdoc Robert Rosenbaum on the acceptance of their paper, "The impact of short term synaptic depression and stochastic vesicle dynamics on neuronal variability", in Journal of Computational Neuroscience. Nothing depressing about that!

    • Fall 2012 — This fall, our trainees will present their latest research results in our weekly group meetings. Come check out what these hard working folks have been up to.

    • August 2012 — Welcome to graduate student Jeffrey Dunworth. Jeff is joining us from The Ohio State University and is interested in a variety of areas of mathematical biology.

    • March 2012 — JOBS! Congratulations to graduate student Lucy Spardy on being hired as a postdoc at MBI at Ohio State, starting at the end of the summer. Congratulations to postdoc Stefanos Folias for being hired into a tenure-track position at U. Alaska, Anchorage. And congratulations to postdoc Jared Barber for being hired here in Pittsburgh at Alcoa.

    • January 2012 — CBSG undergraduate researcher Suren Jayasuriya and his advisor, postdoc Zachary Kilpatrick, have had a paper on their research accepted for publication in Bulletin of Mathematical Biology! See our publications list for examples of other papers we have published, including several involving undergraduates.

    • December 2011 — Best wishes for the holidays!

    • November 2011 — Check out a Pitt Chronicle article on the work by some CBSG group members and their collaborators on Parkinson's disease.

    • October 2011 — Check out our new CBSG logo!! This logo is an update, due to postdoc Stefanos Folias, on our previous design put together by undergraduate David Gau.

    • September 2011 — It's a new semester! Welcome new graduate students David Burstein, Jeremy Harris, and Lisa Mathis! This fall the RTG seminar will concentrate on the research of graduate students and postdocs. See the schedule for speakers and titles.

    • July, 2011 — On to the next level: We give our best wishes to postdoc Julia Arciero as she embarks on her new job as a tenure-track Assistant Professor of Mathematics at IUPUI and to graduate student Justin Dunmyre as he starts a postdoc position in the Department of Mathematics at University of Michigan! They will both be missed.

    • summer, 2011 — Congratulations to graduate students Aushra Abouzeid and Justin Dunmyre for successfully defending their Ph.D. dissertations: "Stochastic Neural Oscillators: Theory, Simulation, and Experiment" (A. Abouzeid) and "A Study of Synchronous Bursting in the PreBotzinger Complex" (J. Dunmyre)!

    • May 9-10, 2011 CBSG Theme Days 2011 — We will have our annual Theme Days Meeting in Thackeray 704 on Monday, May 9 - Tuesday, May 10. The meeting themes include mathematical modeling and experimental approaches to studying inflammation/immune response, neurodegenerative diseases, and human intestinal diseases. Outside speakers include Stephen Eubank (Virginia Tech), R. Lee Mosley (University of Nebraska), Leonid Rubchinsky (IUPUI), and Anna Maria Spagnuolo (Oakland University). Speakers from Pitt include Joanne Flynn, David Hackam, Rob Turner, Yoram Vodovotz, James Bales, and Jared Barber.

      More information, including titles and abstracts of the talks during this 2–day event, may be found at CBSG Theme Days 2011.

    • It's a new semester! We look forward to seeing everyone at our first group meeting, during the week of August 30-September 3, and to welcoming new graduate students Abigail Snyder, Shelby Stanhope, and Glenn Young.

    • December 8, 2010 Julia Arciero will present her research on "Using a Two-dimensional Continuum Mechanical Model to Predict Collective Cell Migration" at the Biophysical Theory Club today. The seminar is in 307 Eberly Hall at 4:00 pm.

    • August 4, 2010 -- Master's Thesis! -- Congratulations to Pamela Reitsma on defending her Master's Thesis, "Correlation Transfer from Basal Ganglia to Thalamus in Parkinson's Disease"! Pam's work was completed under the supervision of Profs. Doiron and Rubin and is now being prepared for publication.

    • July 12-15, 2010 -- Poster Prizes! -- At the SIAM Conference on the Life Sciences here in Pittsburgh, three RTG/former RTG students were among the 8 poster prize winners! Congratulations to Callie Johnson (first prize winning graduate student), Pam Reitsma (second prize winning graduate student) and Helen Parks (first prize winning undergraduate student) on their success.

    • May 7–8, 2010 -- CBSG THEME DAYS SYMPOSIUM -- The theme this year is the interface between experimental and theoretical neuroscience. Outside speakers will be Steven Schiff (Penn State), Jaime de la Rocha (Rutgers), and Tay Netoff (U. of Minnesota). Additionally, we will have local speakers including Nathan Urban (Carnegie Mellon), Satish Iyengar (Pitt), Thanos Tzounopoulos (Pitt), Brent Doiron (Pitt), and Stefanos Folias (Pitt). The 2–day symposium will be an opportunity for graduate students, postdocs, and faculty members to interact and discuss problems and ideas at the interface of experimental and theoretical neuroscience, with subtopics covering control theory, neural activity in pathological states, and sensory coding.

      More information, including titles and abstracts of the talks during this 2–day event, may be found at CBSG Theme Days 2010.

    • March 20, 2010 -- Several CBSG graduate students (Justin Dunmyre, Ian Price, Pamela Reitsma, Tracy Stepien) will be participating in and presenting their research at the SIAM/MAA Mid-Atlantic Regional Applied Mathematics Student Conference on Saturday, March 20 in Shippensburg, PA. The conference was co-organized by Julia Arciero and Jonathan Rubin, along with faculty members from Shippensburg University, George Mason University, and the University of Delaware

    • March 2010 -- Paper accepted! Congratulations to postdoc Julia Arciero (with G. Bard Ermentrout, Jeffrey Upperman, Yoram Vodovotz, Jonathan Rubin) on the acceptance of the paper, "Using a Mathematical Model to Analyze the Role of Probiotics and Inflammation in Necrotizing Enterocolitis" for publication in PLoS ONE            

    • Upcoming meeting deadlines: Feb. 2 is the deadline for poster submission for the SIAM Conference on the Life Sciences, to be held in Pittsburgh, July 12-15, 2010. Feb. 14 is the deadline for submissions for the CNS*2010 Annual Computational Neuroscience Meeting, to be held in San Antonio, TX, July 24-30, 2010.
    • Math bio seminars Jan-May, 2010: This semester, students and postdocs will be presenting their research results Thursdays 12:30-1:30 in Thackeray 704. Schedule.
    • December 8, 2009 -- Special math neuro seminar: Visit and seminar by Michael Buice from the National Institutes of Health.
    • November, 2009 -- Paper accepted! Congratulations to graduate student Justin Dunmyre on the acceptance of his paper, "Optimal intrinsic dynamics for bursting in a three-cell network" (with J. Rubin) for publication in SIAM Journal on Applied Dynamical Systems.
    • October 27, 2009 -- Special math neuro seminar: Visit and seminar by Jianzhong Su from University of Texas, Arlington.
    • August, 2009 -- New postdoc arrives We welcome postdoc Jared Barber, from University of Arizona, to our group.
    • August, 2009 -- Preliminary exam success: Congratulations to graduate student Pamela Reitsma on passing the Preliminary Examinations! Way to go, Pam!
    • Summer, 2009 -- Summer research by undergraduates: Our CBSG summer research undergraduate students for 2009 are Chris Horvat (Pitt), Michaelangelo Tabone (Pitt), Hannah Vogel (CMU), and Christian Woods (Pitt).
    • May 7-8, 2009 -- CBSG Theme Days: The first CBSG Theme Days was a great success! In May 2009, the CBSG had the pleasure of hosting Leah Edelstein-Keshet (University of British Columbia), Hong Qian (University of Washington), Rebecca Segal (Virginia Commonwealth University), Lance Davidson (Pitt), and Jim Faeder (Pitt) at the University of Pittsburgh for a 2-day meeting on cell motility, wound healing, and cell signaling. The meeting provided an environment in which graduate students, postdocs, and faculty members could interact and discuss signaling, rule-based, and mechanical modeling approaches for cell migration. Experimental observations and findings were also presented and provided useful insight into the study of large scale movements of cells and tissues.
    • April 3, 2009 -- MAA Sectional Meeting: Undergraduates Kevin Kroll and Dan Vargo traveled with Dr. Rubin, graduate student Justin Dunmyre, and several other undergraduates to the MAA Allegheny Section Meeting at Wheeling Jesuit University, where they will gave talks on their research projects.
    • March 31, 2009 -- New Publication: Congratulations to graduate student Tracy Stepien on the publication of her paper, Tubuloglomerular Feedback-Mediated Dynamics in Three Coupled Nephrons, in the journal SIAM Undergraduate Research Online! The paper is available online. See our publications link on the sidebar for a complete listing of publications by group members.
    • February 21, 2009 -- Regional conference: Undergraduates Marissa Goldrich, Chris Horvat, Kristen Pueschel, Vikram Raghu, Michaelangelo Tabone, and Christian Woods will travel with Dr. Swigon to Youngstown State University, where they will give talks on their research projects at the Pi Mu Epsilon Regional Conference.
    • January 5, 2009 -- Welcome back! Our winter/spring semester started January 5th. We will be having 2 seminar/journal clubs this semester: Mathematical Neuroscience on Tuesdays, 11:45 - 12:45, and Parameter Estimation Methods on Wednesdays, 1:00 - 2:00, both in Thackeray 703. The general Math Neuro topic for this semester is oscillations and rhythms in pathology or altered brain states. Follow the Seminars link on the side tab for weekly updates on these seminars.
    • September 12, 2008 -- David Swigon and Anna Vainchtein are organizing a conference on Constitutive Properties of Biomaterials that will take place on September 19-21 at the Frick Fine Arts building on Oakland Campus. The conference is sponsored by the Society for Natural Philosophy, the Institute for Mathematics and its Applications and the University of Pittsburgh. The goal of the meeting is to facilitate interaction between experts in experimental study of biomaterials on one hand and mathematical modeling and nonlinear continuum mechanics on the other, that will promote the exchange of ideas while enabling new interdisciplinary collaborations advancing understanding of the role of mechanics in biology.

      Among the invited speakers are Davide Ambrosi (Politecnico di Torino), Bernard Coleman (Rutgers University), Stephen Cowin (City College of NY), John Criscione (Texas A&M), Roger Fosdick (University of Minnesota) and Larry Taber (Washington University). For more information see the conference website.

    • August 29, 2008: The weekly meetings of the Mathematical Neuroscience Journal Club will be held on Tuesdays in Thackeray Hall 703 at 12pm. Lunch will be provided. This semester's theme is the visual system. The first meeting will be on September 2, the reading can be found on the Seminars page.

      The weekly meetings of Inflammation Journal Club will be held on Thursdays in Thackeray Hall 704 at 12:30pm. Lunch will be provided. This semester's theme is modeling infectious diseases. The first meeting is September 4, the reading can be found on the Seminars page.

    • August 23, 2008 Our welcome orientation was held today and overall it was a success. The session was attended by about 30 people, including the faculty and postdocs, some of our senior graduate students, all of our incoming graduate students, and some undergraduate students eager to learn about the group . We were especially happy to welcome among us two new postdocs Julia Arciero (coming from University of Arizona) and Stefanos Folias (from Boston University) and four new graduate students: Callie Johnson, Sherry Linn, Pamela Reitsma, and Tracy Stepien.

      After breakfast we moved to Room 704 where Jon Rubin began the orientation with an overview of this year's activities and organizational matters. (The notes can be found here.) Then the faculty members of the program, David Swigon, Ivan Yotov, Gilles Clermont, Yoram Vodovotz, Jon Rubin, Brent Doiron, and Bard Ermentrout presented overviews of their research activities, slides of which you can find under the links. We finished with a tasty lunch organized by our helpful staff of Judith Kampert and Melissa Weidman, to whom we hereby thank. For pictures from the event see Photos page.

    • May 17, 2008 The first RTG activity will be a welcome/orientation session to be held Saturday, August 23, starting at 9 AM, in Thackeray Hall rooms 704-5. The agenda for this session will be to provide an overview of the group's research activities, of what's in store for the year ahead, and of relevant resources on campus, as well as for all of us to meet in person and get to know each other a little better. All PI's and training faculty are welcome to give an overview of the relevant research projects with which they are involved. There will not be a precise timetable for the session but we'll aim to have lunch, which will be provided, around noon.
    • April 5, 2008 We have kicked off the RTG program with a party organized by Bard Ermentrout and attended by most of our faculty, postdocs, and graduate students. The food was spectacular and entertainment even better. For incriminating pictures see our Photos page.