NIMBioS Calendars: Events Seminars Live Streaming Visitors Working Groups Workshops Tutorials Other
2015 Archive: NIMBioS Seminars
In conjunction with the interdisciplinary activities of the National Institute for Mathematical and Biological Synthesis (NIMBioS), a seminar series on topics in mathematical biology is hosted at NIMBioS every other Tuesday at 3:30 p.m. (unless otherwise noted) in Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Seminar speakers focus on their research initiatives at the interface of mathematics and many areas of the life sciences. Light refreshments are served in the 1st floor visitor breakroom beginning 30 minutes before each talk. Faculty and students from across the UT community are welcome to join us.
Video Archive of NIMBioS Seminars
Archived Seminar Calendars:
2020
2019
2018
2017
2016
2015
2014
2013
2012
2011
2010
2009
**NIMBioS Special Seminar
NIMBioS Seminar Abstracts
Time/Date: 3:30 p.m. Tuesday, November 10Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Richard Schugart, Mathematics, Western Kentucky Univ.; NIMBioS Sabbatical Fellow
Topic: Can mathematics heal all wounds?
Abstract: In this talk, I will present multiple wound-healing problems. The first problem uses optimal control theory to analyze the treatment of a bacterial infection in a wound with oxygen therapy. Two types of oxygen therapies (hyperbaric and topical) will be presented and preliminary results will be presented. The second problem uses patient data to formulate a mathematical model for proteolytic enzyme interactions and their effects on the healing response of a wound. Curve fitting of the model and sensitivity analyses will be presented with some interesting results when comparing different sensitivity analyses. Extensions of both problems will also be discussed. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m. Tuesday, November 3Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Steven Wise, Mathematics, Univ. of Tennessee
Topic: Some mixture models for tissue growth with applications in spatiotemporal cancer modeling
Abstract: In this talk, I will describe some PDE and IPDE models of tissue dynamics, mainly with applications in tumor growth problems. We will examine the details of the model formulations, some issues of well-posedness, and aspects of efficient numerical approximation. Some of the work is a few years old, some is preliminary, but the discussion will at all times be informal. Click here for more information. Seminar flyer (pdf)
Time/Date: 3:30 p.m. Tuesday, October 20Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Quentin Johnson, NIMBioS postdoctoral fellow
Topic: Utilizing computational methods to predict allosteric networks in protein complexes
Abstract: Allostery is a fundamental control mechanism used to regulate many biological processes that range from ligand binding to transcriptional activation. In the context of proteins and protein complexes, allostery is the ability of one binding site to influence another distant site. This means that proteins can self-regulate or be regulated by other macromolecules without the need for proximity. This type of distal signaling is used as the basis for molecular switches, cellular signaling, and oxygen transport. While the importance of allostery is well appreciated, a clear understanding of the process still eludes modern science. This is chiefly due to the fact that the residual networks involved in this process are vast and complex, also the physical interactions that sustain these networks occur on an atomistic level and a picosecond timescale. Therefore, it can be quite vexing to study allostery using traditional methods. Still, the rewards far outweigh the frustrations, as an understanding of allostery can lead to the physical control of molecular switches and downstream cellular responses. Here, I discuss a novel computational approach for the detection of allostery in protein complexes by way of molecular dynamics simulation and advanced data reduction protocols. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m. Tuesday, October 13Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Megan Rúa, NIMBioS postdoctoral fellow
Topic: Fantastic Fungi! Exploring the ecological and evolutionary forces which shape host-microbe interactions
Abstract: Coevolution describes evolutionary change in which two or more interacting species reciprocally drive each other's evolution. The strength of this selection process may vary spatially and temporally due to abiotic and biotic contextual factors. Interactions among plant hosts and their microbes may provide an ecologically unique arena in which to examine the nature of selection in multispecies interactions. In particular, interactions between coniferous plants and their microbes provide a good system for experiments exploring the relative importance of biotic versus abiotic sources of selection, as conifers interact with a suite of microorganisms including mutualistic ectomycorrhizal fungi (ECM), and these interactions vary along environmental gradients. In one of the first thorough explorations of multi-species interactions, I used observational, experimental, and theoretical approaches to investigate the interaction between plants and their microbes. Preliminary work examining the co-evolutionary relationship between plant hosts and their microbial mutualists indicate that not only fungal species identity but host genetic background play a significant component in shaping host-microbe-microbe relationships. Overall, this work demonstrates that mutualists can have important impacts on not only the host but also on the success of each other and highlights the importance of considering both ecological and evolutionary perspectives when examining the plant microbiome. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Tuesday, October 6Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Charles "Chuck" Price, Biology, Univ. of Western Australia
Topic: Flow similarity, stochastic branching, and quarter power scaling in plants
Abstract: The origin of allometric scaling patterns that are multiples of one-fourth has long fascinated biologists. Several models have been advanced to explain the underlying principles of such patterns, but questions regarding the disconnect between model structures and empirical data have limited their widespread acceptance. I show that quarter power scaling can be derived using only the preservation of volume flow rate and velocity as constraints. Applying the model to the specific case of land plants, I show that incorporating biomechanical principles and allowing different parts of plant branching networks to be optimized to serve different functions predicts non-linearity in allometric relationships, and helps explain why interspecific scaling exponents covary along a fractal continuum. Data from numerous sources at the level of plant shoots, stems, petioles, and leaves show strong agreement with model predictions. This novel theoretical framework provides an easily testable alternative to current general models of plant metabolic allometry. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Monday, September 28Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Stuart Pimm, Doris Duke Professor of Conservation, Nicholas School of the Environment, Duke Univ.
Topic: The laws of biodiversity and what we do not understand about them
Abstract: The practice of conservation biodiversity starts with understanding which species and which places are priorities in preventing species decline and extinction. A minority are obvious and familiar: large bodied vertebrates, especially predators, are hunted or persecuted over their large geographical ranges. The large majority of threatened vertebrates have small geographical ranges leading them to be vulnerable to habitat destruction. Armed with where these species live, we can make strategic choices of which places are world priorities – the "biodiversity hotspots" – and downscale to tactical decisions on exactly where and how to protect them. There's an obvious problem. We are protecting biodiversity based on 0.1% of species. Taxonomists are not going to name, let alone map, the remaining 99.9% anytime soon. This motivates a search for general patterns of biodiversity – I call them "laws" – and an understanding of them that might help address whether they are likely to apply equally to known and unknown taxa. Wallace promulgated the most famous law of biodiversity: "Every species has come into existence coincident both in space and time with a pre-existing closely allied species." A simple enough pair of observations, yet ones with profound implications. There are others. The sizes of species ranges have consistent log-normal distributions. Widespread species are locally common, whereas local species are generally rare. Species densities vary greatly from place to place. Species with small geographical ranges are geographically concentrated and generally not in the places where the largest numbers of species live. There is the familiar species-area relationship and there is a distinctive pattern of species loss where habitats are destroyed. To be credible, the theories to explain these laws need to be mechanistically credible, testable against new data, and make hitherto unexpected predictions. Most theories fail these criteria, suggesting considerable effort is needed to understand biodiversity patterns. Click here for more information. Seminar flyer (pdf).
For more information about this seminar, contact Sergey Gavrilets at gavrila@utk.edu.
Time/Date: 3:30 p.m. Tuesday, September 22Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Elizabeth Bradley, Computer science, Univ. of Colorado; NIMBioS Postdoctoral Fellows Invited Distinguished Visitor
Topic: Chaos and control
Abstract: Understanding and exploiting the special properties of chaos can lead to designs that vastly improve the performance of many practical and useful systems — spacecraft trajectories that require less fuel, for example, or tracking circuitry with broader capture ranges and fuel injectors that mix gasoline and air more effectively. Control strategies that leverage chaos's characteristic geometry, ergodicity, and sensitivity to attain such improvements rely on powerful computational tools that use a combination of quantitative and qualitative reasoning to work with the special properties involved. This talk will begin with a review of the mathematical theory and computational techniques that are used in the control of chaos, and then cover a variety of interesting examples ranging from science and engineering to dance. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Tuesday, September 8Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Nels Johnson, NIMBioS postdoctoral fellow
Topic: Nonparametric Bayesian functional equivalence models for community data
Abstract: Ecological community data frequently contain large numbers of sparsely observed species. Reducing the number of species used in a community analysis can make model estimation and interpretation much easier. However, choosing this reduction is non-trivial. Important species can be left out of the analysis or combined inappropriately. We introduce a nonparametric Bayesian model to simultaneously learn about the groups of functionally equivalent species and the corresponding parameter values of each group for describing an ecosystem function. We motivate this work using a community of methane-consuming soil-bacteria from across the North American Great Plains. Click here for more information.
Time/Date: 3:30 p.m., Tuesday, October 6Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Charles "Chuck" Price, Biology, Univ. of Western Australia
Topic: Flow similarity, stochastic branching, and quarter power scaling in plants
Abstract: The origin of allometric scaling patterns that are multiples of one-fourth has long fascinated biologists. Several models have been advanced to explain the underlying principles of such patterns, but questions regarding the disconnect between model structures and empirical data have limited their widespread acceptance. I show that quarter power scaling can be derived using only the preservation of volume flow rate and velocity as constraints. Applying the model to the specific case of land plants, I show that incorporating biomechanical principles and allowing different parts of plant branching networks to be optimized to serve different functions predicts non-linearity in allometric relationships, and helps explain why interspecific scaling exponents covary along a fractal continuum. Data from numerous sources at the level of plant shoots, stems, petioles, and leaves show strong agreement with model predictions. This novel theoretical framework provides an easily testable alternative to current general models of plant metabolic allometry. Click here for more information. Seminar flyer (pdf)
Time/Date: 3:30 p.m., Tuesday, August 25Location: Hallam Auditorium, Room 105, Claxton Building, 1122 Volunteer Blvd.
Speaker: Anthony Mezzacappa, Director, Joint Institute for Computational Sciences
Topic: The Joint Institute for Computational Sciences: The Skinny
Abstract: The Joint Institute for Computational Sciences (JICS) was first established in 1991 and has been through several critical phases in the more than two decades since, including the award by DOE to UT-Battelle of the management of the Oak Ridge National Laboratory, the award by NSF to the University of Tennessee (UT) of the Kraken supercomputer, which was the nation's first academic petaflop supercomputer, and the award by NSF to the University of Illinois of the eXtreme Science and Engineering Discovery Environment (XSEDE), of which JICS is a leading partner, to support NSF's national cyberinfrastructure. As a result, JICS and, within it, the National Institute for Computational Sciences (NICS), one of NSF's five supercomputing centers, took on a national focus, supporting thousands of users and projects across all scientific and engineering domains. Within the past two years, we have focused on bringing JICS expertise and resources, and its overall unparalleled NSF track record of user support, to campus. During this time, we have established a significant number of new, single- and multiple-investigator collaborations with campus faculty. Our desire is to continue this growth and, most important, bring the best of what the University has to offer in computing to its faculty and the research frontiers they wish to advance. I will give an overview of JICS, focusing on its unique aspects, particularly as they pertain to their potential utility to campus faculty and the opportunities they may afford faculty. I will discuss some of our ongoing collaborations with campus, and discuss ways we can, and hope to, engage other faculty in the future. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m. p.m., Tuesday, April 21Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Mats Gyllenberg, Mathematics and Statistics, Centre of Excellence in Analysis and Dynamics, Univ. of Helsinki
Topic: Functional responses and how they evolve by natural selection
Abstract: The functional response is a fundamental concept in theoretical biology. By definition, it is the number of prey eaten by a predator per unit of time. Most often, as in the pioneering work by Holling and co-workers in the 1950s, the functional response is a function of prey density, but in the mid 1970s DeAngelis and Beddington et al. independently put forward the idea that it could depend on the predator density as well. The purpose of this talk is twofold: Firstly, I present a mechanistic derivation, based on assumptions concerning individual behaviour of predator and prey, of the DeAngelis-Beddington functional response. Surprisingly, it turns out that the dependence on the predator density in the DeAngelis-Beddington functional response is a consequence of prey behaviour and not of predator behaviour. Proponents of the functional response have previously argued that competition among predators should be reflected in the functional response. A great advantage of the mechanistic derivation is that all parameters in the functional response reflect individual traits that are subject to natural selection. In the second part of my talk I use adaptive dynamics to investigate possible evolutionary outcomes of natural selection on one of the parameters, viz. "timidity" of the prey, that is, its readiness to seek refuge. It turns out that the results depend on whether the predator-prey system remains at equilibrium or whether it exhibits cycles. As a matter of fact, typical predator-prey cycles that can be observed in nature could be the result of natural selection. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Tuesday, April 7Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Caroline Farrior, NIMBioS postdoctoral fellow
Topic: Plant traits and the importance of competition among individuals
Abstract: Plant communities are complex systems. The success of an individual depends not only on that individual's strategy and its match to the environment, but also on the strategies of other individuals within the community. One of the most noticeable structures in forests, wood, is a great example of this. Wood itself is not a productive tissue, but aids plants in competition with one another for light. So, in order to understand and predict changes in allocation to wood, we must scale from the environment and plant physiology, through individual-level competition, and up to population dynamics and finally landscape-level properties. I will present a model that makes these scale transitions for plants in competition for light, water, and nutrients, and use it to explain empirical phenomena including (1) dominant tradeoffs in allocation patterns in forests and (2) complex plant responses to simple resource addition experiments. In addition, I will introduce plans for expanding this framework to incorporate the pressure of rare disturbances as a potential driver of coexistence of important plant traits. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Tuesday, March 31Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Xiaopeng Zhao, Mechanical, Aerospace, & Biomedical Engineering Univ. of Tennessee, Knoxville
Topic: Multiscale Modeling of Complex Parasitic Transmission Mechanisms
Abstract: Parasitic pathogens often have complicated life cycles, making it hard to identify the right antigens for vaccine development. Using Toxoplasma gondii (T. gondii) as an example, this talk will discuss modeling approaches on understanding parasitic transmission mechanisms, including cellular-level kinetics, host-pathogen interaction, and population dynamics of complex parasitic infections. T. gondii is globally distributed and infects 30% of the world's population. Yet, the critical determinants that underlie the pathogen's ability to disseminate and establish chronic infection in the brain, smooth muscle and other tissues as well as to transmit between hosts remain poorly understood. Much work has been done on modeling the life cycle of T. gondii through an investigative workshop and a working group at NIMBioS. Results from the workshop and the working group will be reported and future research will be discussed. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m. p.m., Wednesday, March 25Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Kehinde R. Salau, Alliance Postdoctoral Research Fellow, Mathematics, Univ. of Arizona
Topic: Taking a moment to measure networks - A hierarchical approach
Abstract: Network-theoretic tools contribute to understanding real-world system dynamics, e.g., in epidemics, power outages, and wildlife conservation. Network visualization helps illustrate structural heterogeneity; however, details about heterogeneity are lost when summarizing networks with a single mean-style measure. Researchers have indicated that a hierarchical system composed of multiple metrics may be a more useful determinant of structure, but a formal method for grouping metrics is still lacking. We develop a hierarchy using the statistical concept of moments and systematically test the hypothesis that simple metrics are sufficient to explain the variation in processes that take place on networks, using an ecological systems example. Results indicate that the moments approach outperforms single summary metrics and accounts for a majority of the variation in process outcomes. The hierarchical measurement scheme is helpful for indicating when additional structural information is needed to describe system process outcomes. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m. p.m., Tuesday, March 10Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Laurent Excoffier, Population Genetics CMPG Lab, Institute of Ecology and Evolution, Univ. of Bern; NIMBioS Postdoctoral Fellows Invited Distinguished Visitor
Co-author: Stephan Peischl, Population Genetics CMPG Lab, Institute of Ecology and Evolution, Univ. of Bern
Topic: Consequences of spatial expansions on population functional diversity
Abstract: It is known that spatial expansions have had a major influence on population genetic diversity: some neutral variants can increase in frequency and spread over large areas in newly occupied territories. This is the phenomenon of gene surfing. However, selected variants can also surf and thus modify the fitness of expanding populations. We have studied this phenomenon by simulations and by analytical derivations in relatively simple models of expansions in homogeneous environments. Very generally, we find that the fitness of populations located on the expansion front decreases proportionally to their distance from the origin of the expansion. The creation of this expansion load happens in 1D or 2D expansions, in case of hard or soft selection, in presence or absence of recombination and for different distribution of fitness effects. The evolutionary dynamics of this expansion load differs between cases, and also depends on the level of dominance between variants. All these cases will be briefly presented, and we will conclude by showing some evidence that this phenomenon also occurred in human populations. Click here for more information. Seminar flyer (pdf).
Time/Date: 9:00 a.m., Wednesday, February 25Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Julio Ramirez, Chief, Division of Infectious Diseases, Univ. of Louisville
Topic: Clinical and translational research at the University of Louisville
Abstract: The objectives of this Special Seminar at NIMBioS are to review current research projects in the field of pulmonary infections; to describe the pathogenesis of pneumonia in relation to pathogen, host, and antimicrobial therapy; to explain the role of lung and systemic inflammatory response in lung injury and lung repair; and to review clinical outcomes in patients with pneumonia. Click here for more information. Seminar flyer (pdf).
Time/Date: 10:30 a.m., Tuesday, February 10Location: Room 105, Claxton Building, 1122 Volunteer Blvd.
Speaker: Stacy Krueger-Hadfield, Grice Marine Laboratory, College of Charleston
Topic: Brokedown life cycles: Implications of the haploid-diploid life cycle on macroalgal population genetics
Abstract: Many macroalgal life cycles alternate between free-living diploid and haploid stages. Very few studies have addressed population genetic structure and mating systems of macroalgae in native habitats. Thus, it is unclear what impacts biological invasions have on different processes during the haploid-diploid life cycle. I will present part of my dissertation and postdoctoral research on haploid-diploid red seaweed genetic structure and mating systems in order to illustrate the need for a framework with which to design efficient sampling strategies. Better sampling methodology is sorely needed in order to address the impacts of different factors, ranging from the intertidal shorescape to inbreeding depression, on haploid-diploid life cycles. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Tuesday, February 10Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Michael Lynch, Biology, Indiana Univ., Bloomington; NIMBioS Postdoctoral Fellows Invited Distinguished Visitor
Topic: Mutation, Drift and the Origin of Subcellular Features
Abstract: Understanding the mechanisms of evolution and the degree to which phylogenetic generalities exist requires information on the rate at which mutations arise and their effects at the molecular and phenotypic levels. Although procuring such data has been technically challenging, high-throughput genomic sequencing is rapidly expanding our knowledge in this area. Most notably, information on spontaneous mutations, now available in a wide variety of organisms, implies an inverse scaling of the mutation rate (per nucleotide site) with the effective population size of a lineage. The argument will be made that this pattern naturally arises as natural selection pushes the mutation rate down to a lower limit set by the power of random genetic drift rather than by intrinsic molecular limitations on repair mechanisms. This drift-barrier hypothesis has general implications for all aspects of evolution, including the performance of enzymes and the stability of proteins. The fundamental assumption is that as molecular adaptations become more and more refined, the room for subsequent improvement becomes diminishingly small. If this hypothesis is correct, the population-genetic environment imposes a fundamental constraint on the level of perfection that can be achieved by any molecular adaptation, and indeed all adaptations. Additional examples consistent with this hypothesis will be drawn from recent observations on the transcription error rate and on the evolution of the oligomeric states of proteins. Click here for more information. Seminar flyer (pdf).
Time/Date: 3:30 p.m., Tuesday, January 27Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Suzanne O'Regan, NIMBioS postdoctoral fellow
Topic: Detecting critical transitions in infectious disease dynamics
Abstract: Predicting abrupt shifts in state ("critical transitions") of complex systems is a key research topic in a variety of scientific domains. Small smooth changes in underlying drivers leading to a sudden change in system behavior, mathematically described as a bifurcation, is a mechanism for critical transitions of considerable interest. Bifurcations may be detectable because prior to reaching the dynamical threshold, the system may exhibit "critical slowing down." Statistical signatures of critical slowing down have been detected from temporal and spatial data in biological systems ranging from the global climate system, ecosystems, experimental microcosms and physiological systems. Anticipating infectious disease emergence and documenting progress in disease elimination are important applications for the theory of critical transitions. A key problem is the development of theory relating the dynamical processes of transmission to observable phenomena. In this talk, I consider compartmental epidemiological SIS and SIR models that are slowly forced through a critical transition. I develop expressions for the behavior of several candidate indicators during the approach to emergence or elimination. I show that moving-window estimates of the candidate indicators may be used for anticipating critical transitions in infectious disease systems. Although leading indicators of elimination were highly predictive, I found the approach to emergence to be much more difficult to detect. It is hoped that these results, which show the anticipation of critical transitions in infectious disease systems to be theoretically possible, may be used to guide the construction of online algorithms for processing surveillance data. Click here for more information. Seminar flyer (pdf).
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From 2008 until early 2021, NIMBioS was supported by the
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through NSF Award #DBI-1300426, with additional support from
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