Mathematical Biology and Physiology Seminar

Spring 2013 Full Schedule

Date: Tuesday, February 12, 2013

Location: McAllister 216 (1-time location)

Speaker: John Fricks, Penn State Stats

Title: Stochastic Limits and Computation for Multiple Molecular Motors

Abstract: Limit theorems for multiple molecular motors from a path perspective are presented. By carefully considering appropriate scale separation of the biochemical and physical mechanisms underlying kinesin and dynein stepping, we derive limit theorems that reveal important biological phenomena and simplify computation in multi-motor systems.

Date: Tuesday, February 19, 2013

Speaker: Jessica Conway, Los Alamos National Lab

Title: Stochastic model of HIV prevention using anti-retroviral drugs

Abstract: Drug treatments for HIV very effectively control chronic infection. They can also be used to prevent the initiation of HIV infection, either in advance of risky exposure (termed pre-exposure prophylaxis, PrEP), or very shortly after accidental exposure (termed post-exposure prophylaxis, PEP), to the virus. To investigate this use of HIV treatments, we developed a multi-type, continuous-time branching process model of the very early stages of HIV infection within-host. We extract extinction probabilities for HIV from equations for the probability generating function, derived from the related Chapman-Kolmogorov equation. We will discuss model predictions regarding the effectiveness of PrEP/PEP depending on clinically-relevant factors such as drug type, post-exposure initiation time, and duration of treatment

Date: Tuesday, March 5 2013

Spring Break, no talk

Date: Tuesday, March 12, 2013

Speaker: Nikolaos Mykoniatis, Department of Agricultural Economics, Penn State

Title: Efficient harvest regimes for a sedentary fishery: The case of Eastern Oyster in Chesapeake Bay

Abstract: We investigate optimal area allocation, combination and significance of simultaneous existence of four management systems: permanent no-harvest areas, pulsed harvest and continuous harvest, from both private and public grounds. An optimal control bioeconomic model applied to native oysters in Chesapeake Bay incorporating environmental, stock and biodiversity externalities is developed. We consider two cases: a) harvest effort in public grounds can be controlled and b) open access. Results in both cases show that it is not socially optimal for all four management systems to coexist simultaneously. Under the first case, the system that generates the highest benefits is public harvest in the entire area. If some portion of the system is to be managed as pulsed or no-harvest, the first generates higher social welfare. Under the second case, the first-best outcome is pulsed harvest. When this outcome cannot be attained no-harvest zones become more important relative to public grounds.

Date: Tuesday, March 19, 2013

Speaker: Steven Pressé from Indiana University-Purdue University Indianapolis (IUPUI).

Title: Practical Guide to Information Theory in Biophysics: how single molecule experiments challenge what we know about finding models from data

Abstract: Single molecule experiments probe biophysical systems at just the time and length scale relevant to biology. There is a catch: single molecule data is notoriously difficult to interpret and turn into a story (i.e. a model) with mechanochemical and biological insight. Traditional model-building approaches have relied on fitting the data to a pre-conceived model. We are developing methods, grounded in information theory, for doing almost exactly the opposite. That is, we want to start from a very general model class and ask the data to guide us towards the correct model. In this context, I will discuss our work in extracting conformational memory from single molecule experiments on large biomolecules. I will show that the dynamical model emerging from this analysis is often more textured and complex than could otherwise come from fitting. If time allows I will discuss our data-driven approach as it relates to maximum entropy for dynamical systems and discuss some of our recent efforts in trying to transform PALM spectroscopy into a quantitative tool for enumerating tightly co-localized proteins.

Date: Thursday, March 21, 2013

Time: In weekly Math Colloquium, 3:35 - 4:35 pm

Where: McAllister 114

Speaker: Yuan Lou, Ohio State University

Title: Evolutionarily stable strategies for dispersal in heterogeneous environments

Abstract: From habitat degradation and climate change to spatial spread of invasive species, dispersal plays a central role in determining how organisms cope with a changing environment. How should organisms disperse "optimally" in heterogeneous environments? In this talk I will discuss some recent development of game theoretic approach on the evolution of dispersal via Lotka-Volterra competition models.

Date: Tuesday, March 26, 2013

Speaker: Anita Layton, Duke University

Title: Mathematical modeling of renal hemodynamics: Feedback dynamics and coupled oscillators

Abstract: We have formulated a mathematical model for the rat afferent arteriole (AA), glomerulus, and short loop of Henle, and used that model to study the interactions between the tubuloglomerular feedback (TGF) and myogenic mechanism, the two key mechanisms that mediate renal autoregulation. Blood flow is described by Poiseuille flow. The AA model consists of a series of arteriolar smooth muscle cells, each of which represents ion transport, cell membrane potential, cellular contraction, gap junction coupling, and wall mechanics. The myogenic response representation is based on the hypothesis that the voltage dependence of calcium channel openings responds to transmural pressure so that the vessel constricts when pressure increases. The glomerular filtration model is based on the model by Deen et al. (AJP 1972). The TGF model represents the pars recta, descending limb, and thick ascending limb, and predicts tubular fluid flow rate and [Cl-] along the loop. The model can be used as a fundamental component in a multi-scale renal microvasculature model for investigations of pathogenesis of hypertensive renal diseases. This research was supported in part by NIH grant DK-89066 and NSF grants DMS-0715021 and DMS-0943760.

Date: Tuesday, April 2, 2013

Speaker: TBD

Date: Tuesday, April 9, 2013

Speaker: Eunha Shim, University of Pittsburgh

Date: Tuesday, April 16, 2013

Speaker: David Koslicki

Title: Quikr: a Compressive Sensing Approach to Bacterial Community Reconstruction

Abstract: Many metagenomic studies compare hundreds to thousands of environmental and health-related samples by extracting and sequencing their 16S rRNA amplicons and measuring their similarity using beta-diversity metrics. However, one of the first steps - to classify the operational taxonomic units withing the sample - can be a computationally time-consuming task since most methods rely on computing the taxonomic assignment of each individual read out of tens to hundreds of thousands of reads. This talk will introduce Quikr: a QUadratic, K-mer based, Iterative, Reconstruction method which computes a vector of taxonomic assignments and their proportions in the sample using an optimization technique motivated from the mathematical theory of compressive sensing. On both simulated and actual biological data, Quikr is demonstrated to be typically more accurate as well as typically orders of magnitude faster than the most commonly utilized taxonomic assignment technique (the Ribosomal Database Project's Naive Bayesian Classifier). Furthermore, the technique is shown to be unaffected by the presence of chimeras thereby allowing for the circumvention of the time-intensive step of chimera filtering.

Date: Tuesday, April 23, 2013

Speaker: Julia Chifman, Department of Cancer Biology, Wake Forest University School of Medicine

Title: Intracellular model of iron homeostasis

Abstract: The importance of iron to almost all leaving organisms is undeniable; iron is required for oxygen transport, energy production, DNA synthesis and cellular respiration. At the same time, excess iron can be toxic due to the possibility of various oxidation states that can facilitate the formation of hydroxyl or lipid radicals, which damage proteins, DNA, cellular membranes, and can even kill the cell. Dysregulation of iron homeostasis has been linked to a wide range of diseases, e.g. hemochromatosis, iron-refractory iron-deficiency anemia, aceruloplasminemia and cancer. To balance iron homeostasis on both the systemic and the cellular levels, human organism has developed elaborate machinery to control iron intake, storage, utilization, and recycling. Our understanding of diseases associated with iron depends on our knowledge of iron homeostasis.

This talk will describe part of a complex cellular iron network that consists of multiple feedback loops as well as a mathematical model intended to help shed light on key regulatory nodes of iron metabolism dynamics. This model is specific to normal breast epithelial cells and represents the core control system of iron metabolism focused on iron import, export, sequestration, and regulation. There are a variety of mathematical formalisms one can use. A common approach is through a system of differential equations. Alternatively, one can view the network in terms of a collection of logical rules: rather than varying continuously, the species might take on categorical values, such as LOW or HIGH. This presentation will focus on both continuous and discrete modeling approaches.