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APRIL 19, 2016  QBI Seminar

Irvine 159 3:00-3:55 PM


Maxim Bazhenov

Division of Pulmonary, Critical Care and Sleep Medicine

UC San Diego, School of Medicine

“Role of Sleep in Memory Consolidation”  


Abstract:  Memory depends on three general processes: encoding, consolidation and retrieval. Although the vast majority of research has been devoted to understanding encoding and retrieval, recent novel approaches have been developed in both human and animal research to probe mechanisms of consolidation. A story is emerging in which important functions of consolidation occur during sleep and that specific features of sleep appear critical for successful retrieval across a range of memory domains, tasks, and species. In my talk I will first discuss the neuronal and network level mechanisms behind major sleep EEG rhythms and experimental data on memory consolidation. I will then present our new results, obtained in computer simulations with large-scale network models, to reveal the neural substrates of memory consolidation involving preferential replay of memory specific sequences of spikes.



NOVEMBER 20, 2014  QBI Seminar

Morton 219 5:00-5:45 PM

Kie Van Ivanky Saputra

Visiting Fullbright Scholar, partially supported by QBI

Head of Dept. of Mathematics, University of Pelita Harapan, Indonesia
“Dynamics of an HIV-1 infection model with Cytotoxic T-Lymphocytes (CTL) responses”


Abstract:  As an example of dynamical systems having a co-dimension one invariant manifold, this talk will discuss the dynamics of an HIV-1 infection model with CTL responses. Detailed analysis will show that the system has three equilibrium solutions, namely the disease-free equilibrium, an endemic equilibrium without CTL response, and an endemic equilibrium with CTL response. The model exhibits transcritical and Hopf bifurcations. The model also addresses how treatment is related to varying model parameters. The findings show how treatment would allow our immune system to control the virus in the long run.


SEPTEMBER 15, 2014  QBI Seminar

Morton 318 4:10-5:10 PM


Joan Saldańa

Dept. Informŕtica, Matemŕtica Aplicada i Estadística 
Edifici P-IV, Campus de Montilivi
Universitat de Girona

“Analysis of a class of epidemic models with awareness”  


Abstract:  Recent formulations of epidemic models consider human behavioral responses. In the analysis of these models, the influence of these responses on the prevention of epidemic spreading is measured from the stability analysis of the disease-free equilibrium. One of these works considers a network epidemic model where individuals are classified as susceptible (S), aware (A), and infectious (I), and assumes no decay in awareness. For this SAIS model, it was proven the existence of a die-out threshold (different from the classic disease-invasion one) defining a region of slow epidemic extinction.


By means of an equivalent mean-field model defined on regular random networks, we analyze the dynamics of this network model, especially for very low values of the awareness decay, and show that the continuum of equilibria arising from the absence of awareness decay collapses into a unique equilibrium when awareness decay is assumed. For this modified model, the resulting bifurcation from the disease-free equilibrium turns out to be equivalent to that of classic epidemic models and those minor outbreaks observed in the slow die-out epidemic regime are now replaced by dumped oscillations around an endemic equilibrium. Continuous-time stochastic simulations are carried out on networks of size 1000 for both models. They show good agreement with the mean-field predictions when the network degree is not very low.


MAY 12, 2014  Dynamics Seminar

Morton 326 4:10-5:10 PM


Sebastian van Strien

Department of Mathematics, Imperial College, London


 "Dynamics of expanding maps in heterogeneous networks"


Abstract: We study expanding circle maps interacting in a heterogeneous random network. Heterogeneity means that some nodes in the network are massively connected, while the remaining nodes are only poorly connected. We provide a probabilistic approach which enables us to describe the effective dynamics of the massively connected nodes when taking a weak interaction limit. More precisely, we show that for almost every random network and almost all initial conditions the high dimensional network governing the dynamics of the massively connected nodes can be reduced to a few macroscopic equations. Such reduction is intimately related to the ergodic properties of the expanding maps. This reduction allows one to explore the coherent properties of the network.


APRIL 21, 2014  QBI Seminar

Morton 326 4:10-5:10 PM


Valentin Afraimovich

Glidden Visiting Professor


 " Heteroclinic Sequences and Neuronal Networks"


Abstract:  Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this talk we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional LotkaVolterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network and generalizations that we have been pursuing this year at Ohio.


APRIL 9, 2014  Undergraduate Seminar

Morton 318 2:10-3:00 PM


Nathan Breitsch 

Honors Tutorial College Math Undergraduate student

Ohio University


 "Techniques for the Study of Coupled Biological Oscillators"


Abstract:    For over forty years, biologists have observed oscillating oxygen consumption in dense cultures of yeast.  The period of the oxygen oscillations divides the period of the yeast cell cycle suggesting that the cell cycle drives oxygen consumption and that the distribution of cell cycle phases is not uniform.  Non-uniform phase distributions can be reproduced by ordinary differential equations models in which cells progress through the cell cycle at rates dependent on the phases of other cells.  The model predicts that after a long time, cells will segregate into two or more synchronized cohorts.  What phase distributions are possible?  How does synchrony emerge from arbitrary distributions?  We will answer these questions using techniques from linear algebra, dynamical systems, and computational geometry.


MARCH 17, 2014  QBI Seminar

Morton 326 4:10-5:10 PM


Igor Belykh

Department of Mathematics, Neurosciences Institute

Georgia State University


 "When repulsive inhibition induces synchrony in excitatory networks of bursting neurons"


Abstract:  Synchrony has been broadly observed in pathological brain states, especially during epilepsy and Parkinson's tremors. In this talk, we will discuss the influence of coupling strength and network topology on synchronization in neuronal networks with fast excitatory and inhibitory connections. We will show that the addition of repulsive inhibition to excitatory networks induces bursting synchrony, in contrast to one's expectations.  We will discuss the mechanism of this purely synergetic phenomenon and show that it originates from the transition between two distinct types of bursting. Our study suggests that promoting inhibition in an attempt to destabilize the abnormal synchronous state can have a counterproductive effect.


FEBRUARY 28, 2014  Physics Colloquium

Walter 245 4:10-5:10 PM


John Wikswo

Gordon A. Cain University Professor of Physics, Professor of Molecular Physiology and Biophysics, and Professor of Biomedical Engineering

Vanderbilt University


“A physicist's perspective on the complexity of biology”


Abstract:  The complexity of biological systems arises from highly nonlinear structural, metabolic, and signaling networks that span multiple spatiotemporal scales. Massively parallel systems-biology experiments provide ever more dynamic data. As we acquire complete, reductionist parts list for simple biological systems, we must ascertain how these pieces interact – a mathematical model of a functioning animal might require Avogadro’s number of partial differential equations, termed a Leibnitz. One might worry about the limitations of the human mind in designing and interpreting multivariable experiments on complex, non-linear systems, particularly humans. The key could be robot scientists that independently design and conduct experiments to infer automatically models describing the dynamics of simultaneous interactions between hundreds of biological variables. This presents significant challenges: three-dimensional bioreactors that recapitulate organ microenvironments; sensors and actuators with adequate spatial and temporal resolution to acquire the necessary data from living cells and organisms; computer algorithms that specify initial conditions, the variables to measure for each experiment, and the desired perturbations/actuations; and bioinformatics tools to explain moles of data. We are developing an integrated measurement and modeling system in which a computer specifies an experiment on organs-on-chips, the dynamic responses of the cells to a controlled stimulus are recorded using multiple real-time analytical techniques, and the computer then uses these data to select among possible models of the system and propose the next experiment for further model refinement. Preliminary results are encouraging – we only need to expand the approach by 23 orders of magnitude.


JANUARY 31, 2014  Math Colloquium

Morton 318 4:10-5:10 PM


Alexander Nepomnyashch

Technion University, Israel


 "Dynamics of liquid membranes"


Abstract:  It is known that vesicles formed by lipid bilayer membranes, which are permeable for water and small molecules but impermeable for large molecules, can be used for transportation of a toxic drug to a target, where the drug is released through created pores. A lipid membrane can be considered as a two-dimensional liquid medium surrounded by a three-dimensional medium of the ambient liquid. The dynamics of a liquid membrane includes a viscous or viscoelastic two-dimensional flow inside the membrane and an elastic deformation of the membrane itself.  We consider a mathematical model that describes the membrane dynamics. An instability of a lipid vesicle, which leads to the change of its shape, is discussed. A special attention is paid to the dynamics of a pore in a stretched membrane.



OCTOBER 29, 2013  QBI/CMSS Seminar

Walter Hall 245 4:10-5:10 PM


Hans Braun

Neurodynamics Group, Institute of Physiology, Philipps University, Marburg, Germany


“Nonlinear Dynamics, Oscillations, Chaos and Noise:

From Shark Electroreceptors to Mental Disorders


Abstract:  Biological functions typically include nonlinearities and time delays and often are organized in circular, positive and negative feedback loops which easily can lead to oscillations and even chaotic behvior. Moreover, biological systems are notoriously noisy which can induce significant alterations of the system dynamics compared to the deterministic situation.


Consequences of these particular properties will be illustrated by experimental recording from hypothalamic neurons and sensory receptors of the skin with focus on temperature sensitive electroreceptors of sharks that are endowed with a most exquisite stimulus sensitivity. The experimental data will be accomplished by computer simulations for the elucidation of the underlying dynamics.


Remarkably, similar functional principles can be applied to model the time course of manic-depressive disorders - in this case, however, with rather detrimental than beneficial effects: sensitivity turns into vulnerability. Implications of these apparently general principles of biological functions will be discussed, - also in comparison to technical systems. The question arises whether biological systems are still more flexible and adaptable then any technical system not despite but because of these technically mostly undesired properties. 



OCTOBER 23, 2013  Applied Math and QBI Seminar

Morton Hall 122 4:10-5:10 PM


Kendrick Shaw

MD-PhD Medical Scientist Training Program, Case Western Reserve University


“Dynamical Architectures for Controlling Feeding in Aplysia californica


Abstract:  For behaviors such as swallowing, walking, and swimming, the nervous system must reliably generate sequences of motor behavior.  Two competing models have been proposed for how this task is accomplished - chain reflex theory and central pattern generator theory.  Chain reflex theory posits that the nervous system contains a sequence of reflexes, so that the action of one reflex creates the sensory input required to trigger the next.  In contrast, central pattern generator theory posits that the nervous system is capable, in the absence of sensory input, of generating motor patterns that closely resemble the motor patterns during behavior.  When modeling these behaviors with systems of differential equations, these two ideas correspond to a collection of stable nodes, in the case of the chain reflex theory, and a stable limit cycle, in the case of central pattern generator theory.  Many systems can exhibit motor patterns in the absence of sensory input, violating the predictions of chain reflex theory, but those patterns are very distorted compared to in vivo behaviors, violating the assumptions of central pattern generator theory.  In this talk, we will explore a third hypothesis, known as a heteroclinic channel, where a trajectory slows dramatically in small regions as it passes near saddle points, creating local regions of sensitivity.  We explore the implications of these dynamics by building a neuromechanical model of swallowing in Aplysia californica which can be changed from a stable heteroclinic channel to a limit cycle by changing a single parameter, and then compare the behavior within these two regimes to the behavior seen in vivo.  The stable heteroclinic channel provides a better match for what is seen in vivo, seemingly due to its timing sensitivity.  We then analytically explored the basis for this sensitivity by studying a tractable heteroclinic channel and deriving a closed-form expression for its infinitesimal phase response curve. The qualitative behavior of the tractable model is present in more complex models, including the Morris-Lecar neuron model as it approaches the homoclinic bifurcation.


APRIL 19, 2013  Physics Colloquium

Walter Hall 245  4:10-5:00 PM


Michal Zochowski, University of Michigan


"Understanding Brain Function and Pathology through Network Dynamics"


Abstract: Brain is a complex and evolving network. While a lot is known about its biology, the dynamical principles underlying information processing in the brain remain elusive. Collective network dynamics seems the natural substrate on which this problem can be elucidated, as it becomes apparent that to understand dynamics of brain function one has not only understand dynamical properties of individual cells, but also of the whole networks. In this talk I will use example of various cognitive processes to highlight the link between evolving network dynamics and the brain function. At the same time, I will use experimental and theoretical results obtained in my laboratory to underscore the role physics can play in understanding the brain function as well as its pathologies.


MARCH 11, 2013  Applied Math and QBI Seminar

Morton Hall 226 4:10-5:10 PM


S. Lee Hong
Department of Biomedical Sciences, Ohio University


“Entropy Conservation in Brain and Behavior”



Patterns of brain activity as well as cognitive and motor behavior are known to be highly variable.  Despite being variable, behavioral patterns are extremely flexible and adaptable to different task demands and environmental conditions.  This prompts a question of whether “rules” exist to guide the process of adaptation.  In this talk, I will present results from a range of different experiments that test the hypothesis of “entropy conservation” in brain and behavior.  First, we will explore the phenomenon of entropy conservation in task, behavior, and environment during adaptations of muscle force control under different conditions.  Next, we will examine the effects of stimulus uncertainty on visual search strategies and cognitive responses.  Finally, I will present data from a study of neural activity obtained from mice actively exploring a maze.  The common finding across all of these studies was compensatory tradeoffs in entropy:  whenever there is an increase in entropy in one dimension, there are observed decreases in others.  The results of all of these studies provide initial evidence that entropy conservation guides the process of harnessing variability for functional adaptation in brain and behavior.



OCTOBER 1, 2012  Differential Equations and Dynamics Seminar

Morton 122 4:10-5:05 PM

L. Schimansky-Geier

Institute of Physics and Bernstein Center for Computational Neuroscience, Humboldt-University at Berlin


“Synchronization of stochastic oscillators in networks”



Synchronization is a universal phenomenon in networks of coupled neuronal units and induces a large scaled coherent rhythmic spiking. I will concentrate in my talk on the influence of noise in the dynamics, on effects of network-disorder and network-correlations on the neural activity, and on modifications arising from delayed interactions between the stochastic neurons. For all these topics paradigmatic models for phases of the neurons are introduced and will be investigated. Outgoing from the stochastic dynamics of the ensemble of neurons, I formulate nonlinear balance equations for the mean phases and study them by bifurcation theory. In dependence on noise intensity, strength of disorder and of correlations and mean delay time conditions for synchronizations are elaborated. Computer simulations support the findings, but show also the limitations of the made approximations in certain cases as will be discussed in the talk.


T. Prager,  M. Falcke, L. Schimansky-Geier,  and M. A. Zaks Phys. Rev.  E 76, 011118 (2007). “Non-Markovian approach to globally coupled excitable systems”


Nikos Kouvaris, Felix Müller and Lutz Schimansky-Geier, Phys. Rev. E  82, 061124 (2010). “Ensembles of excitable two-state units with delayed feedback”


Bernard Sonnenschein and Lutz Schimansky-Geier Phys. Rev  E 85,  051116 (2012).  “Onset of synchronization in complex networks of noisy oscillators”



AUGUST 24, 2012  QBI Seminar

Clippinger 259 12:00-1:00 PM

Benjamin Lindner

Bernstein Center for Computational Neuroscience, Berlin and Physics Department of the Humboldt University Berlin


“Neural information transmission with dynamic synapses”


Abstract: Many synapses display short-term plasticity (STP): upon repetitive stimulation, synaptic efficacies can either increase (facilitation) or decrease (depression). In my talk I discuss the effect of STP on the neural encoding of information about time-dependent stimuli. Specifically, I address under which conditions integrate-and-fire neurons with dynamic synapses encode preferentially slow components (low-pass information filter) or fast components (high-pass information filter) of one or more signals. Considered are a homogeneous setup, in which all synapses of the postsynaptic cell are of the same kind and a heterogeneous setup, in which facilitating and depressing synapses coexist and are driven by distinct signals.


APRIL 6, 2012  Physics colloquium

Walter 245  4:10-5:00 PM

Dolores Bozovic



“Nonlinear dynamics and bifurcations in hair cells of the inner ear”


Abstract.  The inner ear constitutes a remarkable biological sensor that exhibits nanometer-scale sensitivity of mechanical detection. The first step in auditory processing is performed by hair cells, which transduce displacements into electrical signals via opening of mechanically sensitive channels. In 1940s, Thomas Gold first proposed that hair cells must contain an active process that pumps energy into the system, since they operate in a viscous medium, but can nevertheless sustain oscillations, amplify incoming signals, and even exhibit spontaneous motility. Theoretical models have proposed that a hair cell constitutes a nonlinear system with an internal feedback mechanism that can drive it across a bifurcation and into an unstable regime. Latest results will be presented, showing phase-locking dynamics of hair bundles exhibiting spontaneous oscillations. A simple dynamic systems framework will be discussed, that captures the main features of the experimentally observed behavior in the form of an Arnold Tongue. We observe multiple bifurcations in our system, including a saddle-node bifurcation on an invariant circle and a supercritical Andronov-Hopf bifurcation. Secondly, dynamic self-tuning by hair cells exposed to mechanical over-stimulation will be presented and discussed in the context of nonlinear dynamics.



MARCH 28, 2012  QBI Seminar

ARC 102  4:10-5:00 PM

Gabor Balazsi

Department of Systems Biology

The University of Texas, MD Anderson Cancer Center


“Networks, noise and fitness: Lessons from synthetic gene circuits”


Abstract.  Genes are templates for protein synthesis. Proteins determine how cells behave. Therefore, genes should determine how cells behave. However, genes do not act in isolation: they alter each other’s protein producing capacity through complex regulatory networks. Moreover, genes and proteins are present in small numbers and move around stochastically inside minuscule cellular volumes, giving rise to stochastic reactions. These reactions can affect cell division rates, thereby modulating fitness. Therefore, the connection between genes and cell behavior is complex and non-deterministic. I will illustrate how we apply mathematical and computational methods to design synthetic gene networks that control biological noise, providing insights into microbial drug resistance.



JANUARY 19, 2012  QBI Seminar

Irvine Hall 159  4:10-5:00 PM

Bard Ermentrout

Department of Mathematics

University of Pittsburgh


“Flicker Phosphenes: How to get your visual kicks in a drug free world”


Abstract.  When the human visual system is subjected to diffuse flickering light in the range of 5-25 Hz, many subjects report beautiful swirling colorful geometric patterns. In the years since Jan Purkinje first described them, there have been many qualitative and quantitative analyses of the conditions in which they occur. Here, we use a simple excitatory-inhibitory neural network to explain the dynamics of these fascinating patterns. We employ a combination of computational and mathematical methods to show why these patterns arise. We demonstrate that the geometric forms of the patterns are intimately tied to the frequency of the flickering stimulus.


Bard is the author/developer of the free differential equations solving software XPP/XPPAUT, which runs on many platforms, including the iPad  ( .  Bard is also the co-author (with David Terman) of the book “Mathematical Foundations of Neuroscience”. 



OCTOBER 6, 2011  Math seminar

Baker 218, 4:10-5:00 PM

Andrey Shilnikov

Neuroscience Institute, Georgia State University, Atlanta

“Painting chaos using symbolic approach”



SEPTEMBER 26, 2011  QBI Seminar

Morton Hall 218  4:10-5:00 PM

Valentin Afraimovich

Universidad Autónoma de San Luis Potosí, S.L.P., México.

“Transient Dynamics in Neural Networks”



The observed forms of electrical activity in neural systems are quite varied. Neurophysiological experiments show that some neural processes are accompanied by short-time activity of individual neurons or small groups of neurons. For some models, for instance the generalized Lotka-Volterra systems, a mathematical description of such a transient activity is based on the existence of a collection of metastable invariant sets joined by heteroclinic trajectories in the phase space, the heteroclinic network. So, the motion can be thought of a process of successive switchings among these metastable sets. In the simple situation when these sets are just saddle equilibrium points, the full description of transient behavior can be adequately described, including a mechanism of binding between different information modalities. However, sequential activity is not always directly related to the existence of heteroclinic networks. For such situations an approach suggested by D. Terman et al (2008) appeared that allows us to reduce the study of some neural networks to a simple discrete dynamics in the form of cellular automata. V. Nekorkin et al (2011) have applied this approach to networks of Morris-Lecar and Hodgkin-Huxley neurons joint by chemical synapses possessing the short-term plasticity property.  In the present talk, we suppose to discuss all these problems.


Two seminars by QBI folk.


APRIL 27, 2011  New Professor Lecture Series

Baker 242, 4-5 PM

Todd Young, Department of Mathematics


“Clustering in the Cell Cycle of Yeast.  How a Dynamical Systems Viewpoint can be Useful for Biology”



APRIL 28, 2011 Math Awareness Month

Morton 115, 4:10-5:00 PM

Winfried Just, Department of Mathematics


Unraveling Complex systems: What do brains, the internet, and ant colonies have in common?


ABSTRACT:  We are surrounded by complex systems: Power grids, transportation systems, administrative structures, hurricanes, biological systems from cells through organs to ecosystems. The list goes on.  Scientists from a variety of disciplines are trying to understand and predict the behavior of such systems.  How can mathematics contribute to these efforts?  Which mathematical tools are needed for the study of complex systems?  Will existing mathematical tools give us the answers we are seeking, or do we need to develop  new areas of mathematics?  The talk will address these questions at a level accessible to a general audience.



FEBRUARY 18, 2011 QBI Seminar

Morton Hall 318, 4-5 PM

Horst Malchow

Institute of Environmental Systems Research, Department of Mathematics and Computer Science, University of Osnabrück, 49069 Osnabrück, Germany


“Noise and Diffusion in Models of Population Dynamics”


Abstract.   The dynamics of spatial and spatiotemporal pattern formation in nonlinear systems far from equilibrium are of continuous interest and many mechanisms of structure generation are not known yet.  Here, the fascinating variety of spatiotemporal patterns in such systems and the governing mechanisms of their generation and further dynamics are described and related to plankton communities.  The formation and spread of spatiotemporal structures in a simple predation-diffusion model with Holling type II or III predator is demonstrated.  The analysis of the local system yields a number of stationary and/or oscillatory regimes.  Correspondingly interesting is the spatiotemporal behaviour, modeled by reaction-diffusion equations.  Spatial spread will be presented as well as competition of concentric and/or spiral population waves with non-oscillatory subpopulations for space, and long transients to spatially homogeneous population distributions.  Environmental fluctuations are modeled as parametric as well as external multiplicative noise, using stochastic partial differential equations.  The noise can enhance the survival of a population that would go extinct in a deterministic environment. In the parameter range of excitability and slow-fast dynamics of prey and predator, respectively, noise can induce local and global oscillations as well as local coherence resonance and global synchronization.  Stationary patterns have been observed, too.  Furthermore, it is shown that noise can suppress periodic travelling waves and the onset of chaos.  The results are related to plankton dynamics, partly with viral infections of the prey population [1–4].



[1] H. Malchow, S.V. Petrovskii, E. Venturino, Spatiotemporal patterns in ecology and epidemiology:  Theory, models, simulations,  CRC Mathematical and Computational Biology Series, CRC Press, Boca Raton, 2008.

[2] M. Sieber, H. Malchow, S.V.Petrovskii, Noise-induced suppression of periodic travelling waves in oscillatory reaction-diffusion systems, Proceedings of the Royal Society A466(2010) 1903-1917.

[3] M. Sieber, H. Malchow, Oscillations vs. chaotic waves: Attractor selection in bistable stochastic reaction-diffusion systems, The European Physical Journal–Special Topics 187(2010) 95-99.

[4] S. Petrovskii, A. Morozov, H. Malchow, M. Sieber, Noise can prevent onset of chaos in spatiotemporal population dynamics, The European Physical Journal B78(2010) 253–264.



JANUARY 19, 2011 QBI Seminar

Irvine Hall 159, 4-5 PM

 Angela Blisset

Biophysics Program, Ohio State University


“Extracellular Matrix Regulation by Discoidin Domain Receptors (DDR1 and DDR2)”


Abstract: Bone strength is dependent upon the material composition and the microarchitectural structure of bone tissue. The underlying mechanisms that regulate bone material composition and microarchitectural structure are not well understood. Since collagen type 1 is the major component of bone, it is evident that processes regulating collagen deposition and structure are bound to impact bone quality. Discoidin domain receptors (DDRs) are ubiquitously expressed, unique tyrosine kinase receptors that bind to and get activated by collagens, including collagen type I.  Our lab has recently discovered a novel mechanism of collagen regulation by the extracellular domain (ECD) of DDR1 and DDR2 in an in vitro study.  Using stably transfected MC 3T3 pre-osteoblast cell lines, transfected with DDR1 and DDR2 protein constructs absent of the kinase domain, we have elucidated that expression of DDR ECDs results in alterations of endogenous matrix laid down by cells.  Evaluation by transmission electron microscopy (TEM) analysis revealed that expression of DDR ECDs results in collagen fibers with smaller fiber diameters, disrupted banded structures, reduced matrix deposition, delayed rate of fibrillogenesis and increased amount of matrix mineralization.  The goal of our current study is to elucidate the role of DDR1 in bone morphology to elucidate its effect on mechanical integrity of bone. Using bone tissue from DDR1 knock out mice and their wildtype littermates we assess both cortical and trabecular bone morphology in the adult mouse by µ-CT analysis.  Further, using isolated monocytes cultured in the presence of differentiation media we aim to elucidate the role of DDR1 in osteoclast differentiation and function in-vitro via various cell based techniques.  This pilot study on adult DDR1 knockout mice will pave the way for further studies to understand how the DDR1 receptor is involved in matrix remodeling events in different pathological situations and aging.


OCTOBER 7, 2010 QBI Colloquium

Morton 322, 2:10-3:00 PM
Valentin Afraimovich

Universidad Autónoma de San Luis Potosí, S.L.P., México.

“Modeling of sequential dynamics in networks of active elements.”

Abstract:  In neural networks, central pattern generators, cognitive systems, etc. people have been observing a special kind of dynamics that is characterized by an alternate activation of different elements or clusters of elements. Such dynamics is said to be sequential. In the phase space of a mathematical model it corresponds to a successive switching among metastable states along heteroclinic trajectories joining the metastable sets. In this talk we present some theoretical and numerical results related to the case where the mathematical image of a metastable state is just a saddle equilibrium point.



MAY 6, 2010  Distinguished Lecture in Quantitative Biology

Morton Hall 115 4:10-5:00 PM

Martin Golubitsky

Distinguished Professor of Mathematics and Physical Sciences, Director of the Mathematical Biosciences Institute, Ohio State University


”Symmetry-Breaking; Synchrony Breaking"


Abstract:  A coupled cell system is a network of interacting dynamical systems.  Coupled cell models assume that the output from each cell is important and that signals from two or more cells can be compared so that patterns of synchrony can emerge.  We ask: which part of the qualitative dynamics observed in coupled cells is the product of network architecture and which part depends on the specific equations?


In our theory, local network symmetries replace symmetry as a way of organizing network dynamics, and synchrony-breaking replaces symmetry-breaking as a basic way in which transitions to complicated dynamics occur. Background on symmetry-breaking and pattern formation will be presented.



Dr. Golubitsky is a Fellow of the American Academy of Arts and Sciences, the American Association for the Advancement of Science (AAAS), and the Society for Industrial and Applied Mathematics (SIAM). He is also the 1997 recipient of the University of Houston Esther Farfel Award, the 2001 co-recipient of the Ferran Sunyer i Balaguer Prize (for / The Symmetry Perspective/) and the recipient of the 2009 Moser Lecture Prize of the SIAM Dynamical Systems Activity Group. He has been elected to the Councils of the Society for Industrial and Applied Mathematics (SIAM), AAAS, and the American Mathematical Society. Dr. Golubitsky was the founding Editor-in-Chief of the /SIAM Journal on Applied Dynamical Systems/ and has served as President of SIAM (2005-06).  He has co-authored four graduate texts, one undergraduate text, and two nontechnical trade books, (/Fearful Symmetry: Is God a Geometer/ with Ian Stewart and / Symmetry in Chaos/ with Michael Field) and over 100 research papers.


MARCH 4, 2010

Walter Hall 245 4:10-5:00 PM

Jianwei Shuai

Department of Physics

Xiamen University, China

"The stochastic dynamics of hierarchical intracellular calcium signals"



NOVEMBER 18, 2009

Morton Hall 318 4:10-5:00 PM

Edy Soewono

Department of Mathematics

Institut Teknologi Bandung

"A harm reduction model for controlling the spread of HIV/AIDS among injecting drug users"


The spread of HIV/AIDS, especially among injecting drug users (IDUs), has becomes an alarming issue all over the world in the last few decades. One of the recommended programs believed to be safe and effective in controlling the spread of HIV/AIDS is called Harm Reduction Program. In this program, two strategic methods are implemented. The first method is called the Needle and Syringe Program, in which syringes and needles are distributed for free among IDUs upon the return of used needles. The second program is Methadone Therapy, in which methadone is given at a reduced price in several designated hospitals and clinics. Due to limited government budgets, a practical question to be answered is how one can determine the size of action such that the Harm Reduction Program is still effective within a given period. Here in this presentation a new mathematical model for controlling the spread of HIV/AIDS among IDUs is considered. Basic reproduction ratios for both actions and for a combination of the two actions are obtained. Optimum portions of treated compartments which give the largest harm reduction are shown.


MARCH 11, 2009

Walter Hall 245 4:10-5:00 PM

Brent Doiron

Department of Mathematics

University of Pittsburgh

"Unlocking temporal rhythms with spatial keys"


Stimulus evoked rhythms in neural populations are observed in many sensory systems.  The basic interactions between populations of excitatory and inhibitory cells that subtend network rhythms are somewhat understood.  In contrast, the mechanisms by which stimuli modulate rhythms are virtually unknown.  Using characterized circuitry in both the electrosensory system and the auditory cortex I show how the spatial extent of a driving input can gate rhythmic activity.  In both cases mean field theory for populations of simple integrate-and-fire neurons is developed and captures the essential mechanisms.  Overall the work points to a general theory whereby the spatial structure of sensory networks into feature-based topologies permits select stimuli to recruit network oscillations. This suggests that neural rhythms may be useful in sensory coding, consistent with their frequent occurrence in sensory evoked neural dynamics.


FEBRUARY 9, 2009 Joint QBI and Applied Math Seminar 

Irvine 159  4:10-5:00PM

Erik Boczko

Vanderbilt University

"Talking Yeast"

Cell cycle position and age are often dispersed in a culture of budding yeast and can confound measured population averages. We have been exploring methods to describe and to manipulate the population structure of different yeast strains with modeling and data. Our work has resulted in a filtration protocol to extend the maintenance of cell cycle synchrony, and a model of the population structure that develops under autonomous oscillations. We will describe the development and application of these ideas and their relation to quorum sensing.

SEPTEMBER 11, 2008 Mathematics Colloquium Morton Hall 318 4:10-5:00PM

Todd Young, Department of Mathematics

Ohio University

"ODE Models of Cell Cycle Dynamics and Clustering"



Biologists have long observed periodic-like oxygen consumption oscillations in yeast populations under certain conditions and several unsatisfactory explanations for this phenomenon have been proposed. We hypothesize that these oscillations could be caused by cell cycle weak synchronization or clustering. We develop some novel ODE models of the cell cycle. We give proofs and simulations showing that both positive and negative feedback are possible agents that can cause clustering of populations within the cell cycle for these models. Furthermore, this clustering phenomenon is seen to be robust; it occurs for a variety of models, a broad selection of parameter values in those models and even for random perturbations of the models. Since there are necessarily an integer number of clusters, clustering can lead to periodic-like behavior with periods that are nearly integer divisors of the period of the cell cycle. Related experiments have shown conclusively that cell cycle clustering occurs in oscillating cultures.

MAY 28, 2008 QBI seminar

Irvine 159 4:10-5:00PM

Sonya Bahar, Center for Neurodynamics, Department of Physics & Astronomy

University of Missouri at St. Louis

"Synchronization in the brain: from epilepsy to traumatic brain injury"



I will discuss the application of stochastic phase synchronization analysis to two pathological situations: (1) neural synchronization imaged in the rat cortex in vivo during focal seizures, and (2) synchronization between eye and target in human traumatic brain injury.  In the first study, we perform in vivo voltage sensitive dye imaging of the rat cortex during 4-aminopyridine induced seizures. We find a sharp increase in synchronization between all areas of seizure activity during the duration of the seizure, supporting the hypothesis that seizure activity correlates with massive over-synchronization of neural firing in the affected brain area. In the traumatic brain injury study, we investigate the effect of brain injury on smooth pursuit eye movement, in which human subjects are asked to visually track a target moving in a circular path. We find that age, injury, and cognitive load all affect the subject's ability to track the target.


MAY 23, 2008 Physics Colloquium

Walter Hall 245, 4:10-5:00 PM

Dan Hammer, Department of Bioengineering, University of Pennsylvania

(no title yet but area is Cell adhesion and has published with Goetz and Tees)


MAY 22, 2008 Physics Special Colloquium

Walter Hall 245, 4:10-5:00 PM

Venki Ramakrishnan, College of Arts and Sciences Outstanding Alumnus 2006

MRC Laboratory of Molecular Biology, University of Cambridge

"The Ribosome: The cell's protein factory and how antibiotics sabotage it."


MAY 21, 2008 Applied and Computational Mathematics Seminar

Morton Hall 320, 4:10-5:00 PM

Anastasios Matzavinos, Department of Mathematics, The Ohio State University

"Theoretical approaches to actin filament dynamics"


MAY 19, 2008 Biological and Biomedical Sciences seminar

Irvine Hall 159, 4:10-5:00 PM

David M Senseman, Department of Biology, University of Texas at San Antonio

Title: "Turtles Making Waves: Cortical Processing of Visual Information"


MAY 16, 2008 seminar

Irvine Hall 159, 2:10-3:00 PM

Jeffrey R Groff, College of William and Mary

Title: "Markov chain model of calcium puffs and sparks" 


Abstract. Localized cytosolic Ca2+ elevations known as puffs and sparks are important regulators of cellular function that arise due to the cooperative activity of Ca2+-regulated inositol 1,4,5-trisphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) co-localized at Ca2+ release sites on the surface of the endoplasmic reticulum or sarcoplasmic reticulum. Theoretical studies have demonstrated that the cooperative gating of a cluster of Ca2+-regulated Ca2+ channels modeled as a continuous-time discrete-state Markov chain may result in dynamics reminiscent of Ca2+ puffs and sparks. In such simulations, individual Ca2+-release channels are coupled via a mathematical representation of the local [Ca2+] and exhibit “stochastic Ca2+ excitability” where channels open and close in a concerted fashion.


In this seminar, I will present results of simulations involving Markov chain models of Ca2+ release sites composed of channels that are both activated and inactivated by Ca2+. These simulations help to clarify the role of Ca2+ inactivation in the generation and termination of puffs and sparks. It is found that when the average fraction of inactivated channels is significant, puffs and sparks are often less sensitive to variations in the number of channels at release sites and the strength of Ca2+ coupling between channels. Importantly, we found that Ca2+ inactivation may be an important negative feedback mechanism contributing to puff/spark termination even when its time constant is much greater than the duration of puffs and sparks. I will also present results of simulations that investigate the dynamics of puffs and sparks exhibited by release site models that include both Ca2+ coupling and nearest-neighbor allosteric coupling between channels. It is observed that allosteric interactions that energetically stabilize neighboring channel pairs (when both channels are in the same state) often promote puffs and sparks. Interestingly, the dynamics of puffs and sparks are somewhat insensitive to the spatial aspect of allosteric interactions leading to a computationally efficient “mean-field” approximation to the full spatially explicit release site model.



April, 2008.   Grant Award to Peter Jung from NSF.  Peter Jung received a grant award from the National Science Foundation for the project “Modeling of Calcium Signaling Differentiation During Oocyte Maturation”, $165,813.


MARCH 13, 2008 seminar (Joint CMMS/QBI)

Walter Hall 245, 4:10-5:00 PM

Ulrike Feudal, UC Santa Barbara and Carl von Ossietyky University,Oldenburg, Germany


Title: "Spatio-temporal patterns in simple models of marine systems" 

Abstract. Spatio-temporal patterns in marine systems are a result of the interaction of population dynamics with physical transport processes.  These physical transport processes can be either diffusion processes in marine sediments or advection of biological species in the water column. We study in a simplified model the dynamics of one population of bacteria and its nutrient in sediments, taking into account that the considered bacteria possess an active as well as an inactive state, where activation is processed by signal molecules. Furthermore the nutrients are transported actively by bioirrigation and passively by diffusion. It is shown that under certain conditions Turing patterns can occur which yield heterogeneous spatial patterns of species.  The influence of bioirrigation on Turing patterns leads to the emergence of "hot spots," i.e. localized regions of enhanced bacterial activity. In the water column advection is the dominant physical process. We study the influence of mesoscale hydrodynamic structures on biological growth processes in the wake of an island.  Using a stream function approach for the velocity field we show how the upwelling of nutrients away from the island affects the evolution of plankton close to it. In particular we show that mesoscale vortices act as incubators for planktongrowth leading to localized plankton blooms within vortices. 

FEBRUARY 6, 2008 seminar

Irvine Hall 159, 4:10-5:00 PM

Greg Smith, Department of Applied Science,  The College of William and Mary.

"Modeling local control of calcium-induced calcium release in cardiac myocytes"


Abstract.  I will present a probability density approach to modeling localized Ca influx via L-type Ca channels and Ca-induced Ca release mediated by clusters of ryanodine receptors during excitation-contraction coupling in cardiac myocytes. Coupled advection-reaction equations are derived relating the time-dependent probability density of subsarcolemmal subspace and junctional sarcoplasmic reticulum [Ca] conditioned on "Ca release unit" state. When these equations are solved numerically using a high-resolution finite difference scheme and the resulting probability densities are coupled to ordinary differential equations for the bulk myoplasmic and sarcoplasmic reticulum [Ca], a realistic but minimal model of cardiac excitation-contraction coupling is produced. Modeling Ca release unit activity using this probability density approach avoids the computationally demanding task of resolving spatial aspects of global Ca signaling, while accurately representing heterogeneous local Ca signals in a population of diadic subspaces and junctional sarcoplasmic reticulum depletion domains. The probability density approach is validated for a physiologically realistic number of Ca release units and benchmarked for computational efficiency by comparison to traditional Monte Carlo simulations. [This is joint work with George S. B. Williams, Marco A. Huertas, Eric A. Sobie, and M. Saleet Jafri.]


NOVEMBER 1, 2007 Mathematics Snapshots Lecture

Morton Hall 222, 4:10-5:00 PM.

Winfried Just, Department of Mathematics, Ohio University

"Mathematical Tools for the Understanding of Life"


Abstract.  Students often ask: “What do I need to know to become a successful user of mathematics?  This talk will illustrate how tools from different areas of mathematics may be put to work in building mathematical models and making inferences about the real world from these models.  The speaker works on applications of mathematics to biology. In the talk, he will give some simple examples of questions that biologists try to answer with the help of mathematical models. He will illustrate the process of mathematical modeling, and will briefly introduce some tools from different areas of mathematics, such as linear algebra, differential equations, stochastic processes, and dynamical systems that can be used to answer these questions. No prior knowledge of biology or the areas of mathematics mentioned above will be assumed in the talk.


OCTOBER 30, 2007 seminar

Irvine Hall 159, 4:10-5:00 PM.

Visiting Professor Fabio Marchesoni, Dipartimento di Fisica, Universita' di Camerino, Italy will give the third of three seminars on "STOCHASTIC PHENOMENA IN BIOLOGY" on "SINGLE MOLECULE EXPERIMENTS: A physicist’s interpretation"


Single molecule experiments are a valuable source of knowledge and information even from a physicist’s viewpoint. We discuss how RNA folding-unfolding experiments can greatly contribute to elucidate the role of large fluctuations in non-equilibrium statistical physics. Non-equilibrium thermodynamics of small systems describes energy exchange processes between a system and its environment in the low energy range of a few kBT where Brownian fluctuations are dominant. This new approach to the notion of fluctuation is aimed to identify the building blocks of a general theory describing energy fluctuations in non-equilibrium processes occurring in systems ranging from condensed matter physics to biophysics. In particular, recently formulated fluctuation theorems and path thermodynamics can be used to extract information from current single-molecule experiments.


OCTOBER 23, 2007 seminar

Irvine Hall 159, 4:10-5:00 PM.

Robin Snyder, Department of Biology, Case Western Reserve University

"Duration and behavior of transient dynamics in a spatially extended system: plant population responses to altered disturbance regimes"


Abstract.  The disturbance regimes on which many plant communities depend can be changed by, e.g., changes in fire suppression or grazing practices or alterations in weather patterns due to climate change. Most work on environmental variation has focused on populations' ultimate fates via their long-run growth rates, implicitly assuming that transient dynamics are short-lived. I present an analytic study of transient dynamics in a spatial model of competing annual plants. I find that the traits which promote species segregation also increase reactivity (the tendency for perturbations to grow initially) and transient duration.


OCTOBER 16, 2007 seminar

Irvine Hall 159, 4:10-5:00 PM.

Visiting Professor Fabio Marchesoni, Dipartimento di Fisica, Universita' di Camerino, Italy will give the second of three seminars on "STOCHASTIC PHENOMENA IN BIOLOGY" on "The Physics of Molecular Motors"


Our physical intuition, based on everyday observation of large machines, fails when we consider the world of the small. It is a capricious world, ruled by thermal and quantum fluctuations. This applies in particular to the molecular machinery of the cell: How effectively it works against the 2nd Law of Thermodynamics has kept puzzling statistical physicists for decades.

We discuss how thermal Brownian motion coupled to an unbiased, non-equilibrium environment can be used to control the operation of both biological and artificial systems characterized by spatial or dynamical symmetry breaking at the micro- or even on the nano-scale. This mechanism is known in the physics literature as “Brownian motor” or “noise rectification”. The constructive role of Brownian motion is exemplified for the case of noise-induced transport in one-dimensional channels. We present the working principles and characteristics of the most common stylized Brownian motors. Such devices are particularly simple to implement experimentally in order to optimize and selectively control a rich variety of directed transport behaviors.


October, 2007


Visiting Professor Fabio Marchesoni from the Department of Physics at the University of Camerino, Italy will give a series of three seminars on "STOCHASTIC PHENOMENA IN BIOLOGY" on alternate Tuesdays in October in Irvine 159 at 4:10 PM. Topics are:

"Stochastic Resonance" (October 2)

"Molecular Motors" (October 16) and

"Extracting Information from Biological Data" (October 30).

OCTOBER 2, 2007 Stochastic Resonance


Conventional wisdom teaches us that the transmission and detection of signals is hindered by noise. However, during the last two decades, the paradigm of stochastic resonance (SR) proved this assertion wrong: indeed, addition of the appropriate amount of noise can boost a signal and hence facilitate its detection in a noisy environment. Due to its simplicity and robustness, SR can work on almost every scale, thus attracting interdisciplinary interest from physicists, geologists, engineers, biologists and medical doctors, who nowadays use it as an instrument for their specific purposes.

At the present time, there exist a lot of diversified models of SR. Moreover, different characterizations of SR have been proposed in order to make such a mechanism more accessible to experimenters. This presentation relies mostly on the two-state model of SR, which is general enough to exhibit the main features of SR. Finally, we also discuss some situations that go beyond the generic SR scenario but are still characterized by a constructive role of noise.

(Abstracts for October 16 and October 30 seminars will follow later).


May 30, 2007 seminar

(Applied Math seminar)

Morton 320 4:10-5:00 PM

German Enciso, Ohio State University, MBI will speak on: “Moving in the right direction: A model of direction selectivity in the retina


May 16, 2007 seminar

(Joint with Biophysics Seminar Series)

Clippinger 259 4:10-5:00 PM

Andrey Shilnikov, Dept. Mathematics, Georgia State University, will speak on:  “Routes to bursting in neuronal models”


May 9, 2007 seminar

(Joint with Biophysics Seminar Series)

Clippinger 259 4:10-5:00 PM

Tatiana Engel, Dept. Physics, Humboldt University, Berlin will speak on:  “Firing statistics in neurons as non-Markovian first passage time problem”


February 28, 2007 seminar

(Joint with Biophysics Seminar Series)

Grosvenor West 111  4:10-5:00 PM

Jong-Hoon Nam, University of Wisconsin-Madison, Dept. of Physiology will speak on:  “A virtual hair cell: computational study on the structure, dynamics and mechanoelectric transduction of vestibular hair cell”


February 21, 2007 seminar

(Jointly sponsored with Applied Math)

Morton 320 2:10-3:00 PM

German Enciso, Ohio State University, MBI will speak on: “Monotone systems: stability and oscillations”


February 20, 2007 QBI seminar

Baker Center 239  4:10-5:00 PM

Gregg Hartvigsen, Biology Department, SUNY Geneseo (currently on sabbatical at MBI), will present a talk entitled "How I learned to stop worrying and love influenza"

 January 12, 2007  QBI Seminar

(Jointly sponsored with the Mathematics dept.)

Morton 126 4:10-5:00 PM

Avner Friedman, Ohio State University.  Dr. Friedman is President-elect of the Society for Mathematical Biology, a member of the National Academy of Sciences, and Director of the Mathematical Biosciences Institute.  He will speak on:  “Mathematical Models of Tumor Growth”


December, 2006.   Grant Award to Ellengene Peterson, Michael Rowe and Alexander Neiman from NIH. 

Ellengene Peterson, Michael Rowe and Alexander Neiman received a grant award from National Institutes of Health for the project “Biomechanics of vertebrate hair cells”, $2,827,313, 12/2006-11/2011.


November 8, 2006  seminar

(Joint with EEB colloquium)

Irvine 114 12:10-1:00 PM

Will Wilson, Duke University, will speak on:  “Ecological Patterns for Mechanistic Processes”


October 25, 2006 seminar

(Mathematics colloquium)

Morton 322 3:00-4:00 PM

Martin Feinburg, Chemical Engineering and Mathematics, Ohio State, will present a seminar:  “Understanding Bistability in Complex Enzyme-Driven Reaction Networks”


October 18, 2006 QBI Seminar

(Joint with Applied Math/Computational Math)

Morton 320 3:10-4:00 PM

Brandilyn Stigler, MBI, Ohio State University, will present a seminar “Reverse engineering of network topology”

September 27, 2006 QBI Seminar

Morton 320 3:10-4:10 PM

Andrew Nevai, MBI, Ohio State University, will present a seminar “A mathematical model of plant competition for sunlight”

February, 2006. Grant Award to David Tees from NSF

David Tees received a CAREER grant award from the National Science Foundation for the project “Leukocyte adhesion and mechanical arrest in a model capillary,” $432,986, 07/2006 – 06/2010.

September, 2005.  Grant Award to Kim Cuddington from NSF

Kim Cuddington received a grant award from the National Science Foundation, Division of Ecology, for the project “Predicting the effects of diffusion-limitation in a model predator-prey system,” $378,978, 09/2005 – 08/2009.





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