** 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.

** 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

** 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.

** Speaker: **
Steven PressÃ© 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.

** 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.

** 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.

** 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.

** 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.