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Dynamical Systems and Mathematical Biology Seminar

Fall 2012- Spring 2013

Regular times: every second Friday, 11 am - 12 pm

Location:

Erdos conference room (COE 796), Department of Mathematics and Statistics, 7th floor, College of Education Building, 30 Pryor street, Atlanta

 

Questions or comments?  Please e-mail: Dr. Igor Belykh and Dr. Yi Jiang

 

2012 Fall calendar

Date

Speaker

Title

Host

08/31

Dr. Yuri Bakhtin (Georgia Tech)

"Noisy heteroclinic networks and sequential decision making"

Dr. Belykh

09/11

Dr. Bard Ermentrout (University of Pittsburg)

 

"Oscillations, synchrony, and disease: What can computational models tell us?"

This is a talk in Brains & Behavior Distinguished Lecturer Seminar Series

Dr. Osan

09/14

 

 

 

09/21 Dr. Byoungkoo Lee (Georgia State) "Two- and three-dimensional stochastic off-lattice models of binding chemistry in crowded environments"  

09/28

Dr. Ilya Nemenman (Emory)

"Of exactitude in science:  Coarse-grained models of cellular signaling"

Dr. Jiang

10/05      

10/12

Dr. Vladimir Bondarenko (Georgia State)

“Modeling Pro-arrhythmic Behavior in 1D and 2D Models of Mouse Ventricular Tissues”

 

10/19 Dr. Remus Osan (Georgia State) "Evaluation of Target Search Efficiency for Neurons During Developmental Growth"  

10/26


 

 

11/02      

11/09

Dr. Yi Jiang (Georgia State)

"Blood in the Eye: The Good and the Bad"

 

11/16

Dr. Michele Benzi (Emory)

"Mathematical and Computational Tools for the Analysis of Complex Networks"

Dr. Jiang

11/23

No talks: Thanksgiving

 

 

11/ 30

Dr. Igor Belykh (Georgia State)

TBA

 

12/07

 

 

 

More details (abstracts):


DATE: Friday, October 19, 2012
TIME: : 11:00 am --12:00 pm.
LOCATION: Paul Erdos Room, 796 COE

Speaker: Dr. Remus Osan (Georgia State)

Title: "Evaluation of Target Search Efficiency for Neurons During Developmental Growth"

:Abstract: Regenerative strategies that facilitate the regrowth and reconnection of neurons are some of the most promising methods in spinal cord injury research. An essential part of these strategies is an increased understanding of the mechanisms by which growing neurites seek out and synapse with viable targets. In this paper, we use computational and theoretical tools to examine the targeting efficiency of growing neurites subject to limited resources, such as maximum total neural tree length. We find that in order to efficiently reach a particular target, growing neurites must achieve balance between pruning and branching: rapidly growing neurites that do not prune will exhaust their resources, and frequently pruning neurites will fail to explore space effectively. We also find that the optimal branching/pruning balance must shift as the target distance changes: different strategies are called for to reach nearby vs. distant targets. This suggests the existence of a currently unidentified higher-level regulatory factor to control arborization dynamics. We propose that these findings may be useful in future therapies seeking to improve targeting rates through manipulation of arborization behaviors.


DATE: Friday, October 12, 2012
TIME: : 11:00 am --12:00 pm.
LOCATION: Paul Erdos Room, 796 COE

Speaker: Dr. Vladimir Bondarenko  (Georgia State)

Abstract: A mathematical model for action potential (AP) and calcium dynamics of mouse ventricular cardiac cells (myocytes) is used to study pro-arrhythmic behavior in one-dimensional (1D) and two-dimensional (2D) cardiac tissues. Cellular models are used, which closely reproduce experimental data obtained from the mouse hearts. By today, we have developed experimentally-based models for ventricular cells from four heart regions: apex, septum, epicardium, and endocardium. All model cells reproduce AP shapes and durations; they include comprehensive description of calcium dynamics and predict rate-dependent behavior of calcium transients. Model tissues are composed of isolated cardiac cells: 190 myocytes in 1D tissue and 9100 myocytes in 2D tissue. Both tissue models are stimulated with fast pacing rates to promote pro-arrhythmic behavior. As result, calcium transient alternans and AP propagation block are observed in the tissues. Mechanisms of the development of calcium alternans and AP propagation block in wild type and transgenic TNF-alpha overexpressing mouse cardiac tissues are proposed.

 


DATE: Friday, September 28, 2012
TIME: : 11:00 am --12:00 pm.
LOCATION: Paul Erdos Room, 796 COE

Speaker: Dr. Ilya Nemenman (Emory University)

Title: "Of exactitude in science:  Coarse-grained models of cellular signaling"

Abstract:
…In that Empire, the craft of Cartography attained such Perfection that the Map of a Single province covered the space of an entire City, and the Map of the Empire itself an entire Province. In the course of Time, these Extensive maps were found somehow wanting, and so the College of Cartographers evolved a Map of the Empire that was of the same Scale as the Empire and that coincided with it point for point. Less attentive to the Study of Cartography, succeeding Generations came to judge a map of such Magnitude cumbersome, and, not without Irreverence, they abandoned it to the Rigours of sun and Rain. In the western Deserts, tattered Fragments of the Map are still to be found, Sheltering an occasional Beast or beggar; in the whole Nation, no other relic is left of the Discipline of Geography.

From Travels of Praiseworthy Men (1658) by J. A. Suarez Miranda (a fictional reference). By Jorge Luis Borges and Adolfo Bioy Casares. English translation quoted from J. L. Borges, A Universal History of Infamy, Penguin Books, London, 1975


DATE: Friday, September 21, 2012
TIME: : 11:00 am --12:00 pm.
LOCATION: Paul Erdos Room, 796 COE

Speaker: Dr. Byoungkoo Lee (Georgia State, Dr. Jiang's group)

Title: "Two- and three-dimensional stochastic off-lattice models of binding chemistry in crowded environments"

Abstract: Molecular crowding is one of crucial properties that distinguish the intracellular environment from the well-mixed and diluted in vitro environment. Crowding can significantly alter the rates and equilibria of biochemical reactions, potentially either enhancing or inhibiting a reaction system depending on numerous physical parameters of that system. We have developed stochastic off-lattice models for two and three dimensional spaces based on Green’s function reaction dynamics to better simulate binding chemistry in crowded conditions and to provide a platform for investigating how the crowding effect is influenced by various model assumptions. We have examined a simple homodimerization system to test dependence on seven system parameters: the total concentration of particles; the binding probability between two reactant monomers upon a collision; the mean time until a dissociation event (the inverse of the rate constant); the diffusion coefficient; the ratio of dimer area to monomer area (volume in 3D); the ratio of inert particle area to reactant monomer area (volume in 3D); and the threshold distance, defined as the maximum interaction range between two particles. Results from a two-dimensional variant show that the first four parameters act essentially independently and their joint influences can be accurately modeled by a simple polynomial regression function. The remaining three parameters show more complicated cross-dependencies. Early studies with a three-dimensional model are showing qualitatively similar behaviors to those of the two-dimensional model. Continuing work is aimed at quantitatively accounting for cross-dependent parameters and extending the full results to three-dimensional models. It is hoped that this work will lead to improved corrections for crowding effects in models too large in time or space scale to permit detailed crowding models and ultimately to more realistic general models of assembly chemistry in the cellular environment.

 


DATE: Tuesday, September 11, 2012
TIME: : 10:00 am --11:00 pm.
LOCATION: Petit Science Building , 123 (notice the location and time)

Speaker: Dr. Bard Ermentrout (University of Pittsburg) (http://www.pitt.edu/~phase/)

Title: "Oscillations, synchrony, and disease: What can computational models tell us?"

This is a talk in Brains & Behavior Distinguished Lecturer Seminar Series

http://neuroscience.gsu.edu/lecture_series.html


DATE: Friday, August 31, 2012
TIME: : 11:00 am --12:00 pm.
LOCATION: Paul Erdos Room, 796 COE

Speaker: Dr. Yuri Bakhtin, School of Mathematics, Georgia Institue of Technology (http://people.math.gatech.edu/~bakhtin/)

Title: "Noisy heteroclinic networks and sequential decision making"

Abstract: I will talk about small noisy perturbations of systems with multiple saddle-type equilibrium points connected by heteroclinic orbits. The goal is to give a precise description of the asymptotic behavior in the limit of vanishing noise and interpret the results in terms of sequential decision making. I will discuss applications to neuronal dynamics and psychology.