Quantitative Biology Institute

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"

Abstract:

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"

Abstract:

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"

Abstract

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 k_BT 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"

Abstract

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

STOCHASTIC PHENOMENA IN BIOLOGY

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

Abstract

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.