## Arthur Sherman : Diabetes Pathogenesis as a Threshold-Crossing Process

- Mathematical Biology ( 205 Views )It has long been accepted that type 1 diabetes results from a lack of insulin, as the insulin-secreting pancreatic beta cells are destroyed by an autoimmune process. In contrast, the cause of type 2 diabetes (T2D) is less clear. Most people with pre-diabetes or in the early stages of T2D have abnormally high plasma insulin concentrations, and insulin rises before glucose does. We show that these difficulties are resolved by a mathematical model in which the onset of T2D is represented by the crossing of a threshold. The threshold is atypical in some respects and requires consideration of the slow manifolds to avoid incorrect conclusions.

## Cristan Tomasetti : Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

- Mathematical Biology ( 193 Views )Cancers are caused by mutations that may be inherited, induced by environmental factors, or result from DNA replication errors (R). We studied the relationship between the number of normal stem cell divisions and the risk of 17 cancer types in 69 countries throughout the world. The data revealed a strong correlation (median = 0.80) between cancer incidence and normal stem cell divisions in all countries, regardless of their environment. The major role of R mutations in cancer etiology was supported by an independent approach, based solely on cancer genome sequencing and epidemiological data, which suggested that R mutations are responsible for two-thirds of the mutations in human cancers. All of these results are consistent with epidemiological estimates of the fraction of cancers that can be prevented by changes in the environment. Moreover, they accentuate the importance of early detection and intervention to reduce deaths from the many cancers arising from unavoidable R mutations.

## Michael Mackey : Understanding, treating and avoiding hematological disease

- Mathematical Biology ( 158 Views )This talk will trace many years of work mathematical modeling hematological diseases. The Â?understandÂ? part talks about the use of mathematical to figure out what causes cyclical neutropenia, and the Â?treatÂ? part refers to work on treating cyclical neutropenia using recombinant cytokines. The Â?avoidÂ? part deals with current ongoing work trying to obviate the deleterious effects of chemotherapy on blood cell productionÂ?one of the major negative side effects of chemotherapy.

## Nick Moore : How focused flexibility maximizes the thrust production of flapping wings

- Mathematical Biology ( 154 Views )Birds, insects, and fish all exploit the fact that flexible wings or fins generally perform better than their rigid counterparts. Given the task of designing an optimal wing, though, it is not clear how to best distribute the flexibility: Should the wing be uniformly flexible along its length, or could some advantage be gained by making certain sections more rigid than others? I will discuss this question by using a 2D small-amplitude model for the fluid-structure interaction combined with an efficient Chebyshev PDE solver. Numerical optimization shows that concentrating flexibility near the leading edge of the wing maximizes thrust production, an arrangement that resembles the torsional-joint flexibility mechanism found in insect wings. I will discuss the possibility of extending into three dimensions to address the question of optimal wing architecture more generally.

## Adriana Dawes : Protein localization at the single cell level: Interplay between biochemistry, mechanics and geometry

- Mathematical Biology ( 153 Views )Cells are highly organized and complex structures, with the capacity to segregate specific factors to spatially disjoint regions in a process called polarization. Polarization, which specifies a spatial axis in the cell, is a highly conserved biological process and is required for proper embryonic development, wound healing, and many other normal and pathological biological functions. Despite the importance of polarization, we do not fully understand how this protein segregation is initiated and maintained. In this talk, I will show how we can use numerical and analytical approaches to investigate how symmetry breaking begins the process of polarization, and how the geometry of the cell may play a role in the establishment and maintenance of spatial patterns associated with polarization.

## Tom Kepler : Microevolution in the Immune System: A Computational Systems Approach--second lecture

- Mathematical Biology ( 149 Views )Vaccines protect their recipients by inducing long-term structural changes in populations of immune cells. Part of that restructuring is exactly analogous to Darwinian Selection. New antibody molecules are created by somatic mutation of existing antibody genes. Subsequently, the immune cell populations that possess these mutated receptors overtake the "wild-type" immune cells due to the selective advantage they have acquired. Thus the immune system is vastly better prepared to recognize and eliminate the eliciting pathogen the next time around. New sequencing and biosynthesis technologies, together with mathematical and computational tools, now allow us to investigate this fascinating and important phenomenon more deeply than ever before. I will illustrate this development with examples from the immune response to HIV infection. Second lecture will focus on specifically mathematical questions.

## Mainak Patel : Temporal Binding Emerges as a Rapid and Accurate Encoding Tool Within a Network Model of the Locust Antennal Lobe

- Mathematical Biology ( 143 Views )The locust olfactory system interfaces with the external world through antennal receptor neurons (ORNs), which represent odors in a distributed, combinatorial manner. ORN axons bundle together to form the antennal nerve, which relays sensory information centrally to the antennal lobe (AL). Within the AL, an odor produces a stimulus-specific temporal progression of neuronal spiking, inspiring the hypothesis that the AL encodes odors through dynamically evolving ensembles of active cells. Such a coding strategy, however, requires higher olfactory centers to integrate a prolonged dynamic profile of AL signals prior to stimulus assessment, a process that is likely to be slow and inconsistent with the generation of quick behavioral responses. Our modeling work has led us to propose an alternate hypothesis: the dynamical interplay of fast and slow inhibition within the locust AL induces transient correlations in the spiking activity of an odor-dependent neural subset, giving rise to a temporal binding code and allowing rapid stimulus detection by downstream elements.

## Rodica Curtu : Mixed-Mode Activity Patterns in Neuronal Networks with Lateral Inhibition

- Mathematical Biology ( 141 Views )Stimulus tuning in a reduced model for neural competition leads to

## Cecilia Clementi : A multiscale approach to characterize macromolecular dynamics and functions

- Mathematical Biology ( 140 Views )A multiscale approach to characterize macromolecular dynamics and functions The understanding of emerging collective behaviors in biomolecular complexes represents a major challenge in modern biophysics. As a first step toward the study of such processes we have applied multi-resolution nonlinear dimensionality reduction and diffusion analysis to obtain reliable low-dimensional representations and models for the dynamics of apparently high-dimensional complex systems such as proteins in a biological environment. The results clearly show that the proposed methods can efficiently find low dimensional representations of a complex process such as protein folding.

## Franziska Michor : Evolutionary dynamics of cancer

- Mathematical Biology ( 135 Views )Cancer emerges due to an evolutionary process in somatic tissue. The fundamental laws of evolution can best be formulated as exact mathematical equations. Therefore, the process of cancer initiation and progression is amenable to mathematical investigation. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and represent promising targets for therapeutic intervention. Here we describe a mathematical approach, called Retracing the Evolutionary Steps in Cancer (RESIC), to deduce the temporal sequence of genetic events during tumorigenesis from crosssectional genomic data of tumors at their fully transformed stage. When applied to a dataset of 70 advanced colorectal cancers, our algorithm accurately predicts the sequence of APC, KRAS, and TP53 mutations previously defined by analyzing tumors at different stages of colon cancer formation. We further validate the method with glioblastoma and leukemia sample data and then apply it to complex integrated genomics databases, finding that high-level EGFR amplification appears to be a late event in primary glioblastomas. RESIC represents the first evolutionary mathematical approach to identify the temporal sequence of mutations driving tumorigenesis and may be useful to guide the validation of candidate genes emerging from cancer genome surveys.

## Jill Galagher : Targeting the phenotype: Treatment strategies for heterogeneous cancer

- Mathematical Biology ( 133 Views )Targeted cancer drugs attack pathway specific phenotypes and can lead to very positive outcomes when a particular phenotype dominates the population of a specific tumor. However, these drugs often fail because not all cells express the targeted phenotype to the same degree. This leads to a heterogeneous response to treatment, and ultimate recurrence of the cancer as sensitive cells die off and resistant cells take over. We explore how treatment strategies informed by a tumorÂ?s phenotypic mix, can help slow the emergence of resistance and stave off tumor recurrence. We use an off-lattice agent-based model that incorporates inheritance of two phenotypes Â? proliferation rate and migration speed Â? and is modulated by a space limiting selection force. We find how and when distinct distributions of phenotypes require different treatment strategies.

## Anita Layton : Myogenic Response to Systolic Pressure in the Afferent Arteriole

- Mathematical Biology ( 133 Views )Elevations in systolic blood pressure are believed to be closely linked to the pathogenesis and progression of renal diseases. It has been hypothesized that the afferent arteriole (AA) protects the glomerulus from the damaging effects of hypertension by sensing increases in systolic blood pressure and responding with a compensatory vasoconstriction. To investigate this hypothesis, we developed a mathematical model of the myogenic response of an AA smooth muscle cell, based on an arteriole model by Gonzalez-Fernandez and Ermentrout (Math Biosci 1994). renal hemodynamic regulation. The model incorporates ionic transport, cell membrane potential, contraction of the AA smooth muscle cell, and the mechanics of a thick-walled cylinder. The model represents a myogenic response based on a pressure-induced shift in the voltage dependence of calcium channel openings: with increasing transmural pressure, model vessel diameter decreases; and with decreasing pressure, vessel diameter increases. Further, the model myogenic mechanism includes a rate-sensitive component that yields constriction and dilation kinetics similar to behaviors observed in vitro. A parameter set is identified based on physical dimensions of an AA in a rat kidney. Model results suggest that the interaction of Ca2+ and K+ fluxes mediated by voltage-gated and voltage-calcium-gated channels, respectively, gives rise to periodicity in the transport of the two ions. This results in a time-periodic cytoplasmic calcium concentration, myosin light chains phosphorylation, and crossbridges formation with the attending muscle stress. Further, the model predicts myogenic responses that agree with experimental observations, most notably those which demonstrate that the renal AA constricts in response to increases in both steady and systolic blood pressures. The myogenic model captures these essential functions of the renal AA, and it may prove useful as a fundamental component in a multi-scale model of the renal microvasculature suitable for investigations of the pathogenesis of hypertensive renal diseases.

## Mark Alber : Modeling elastic properties of cells and fibrin networks

- Mathematical Biology ( 131 Views )Viscoelastic interactions of Myxococcus xanthus cells in a low-density domain close to the edge of a swarm have been recently studied in [1] using a combination of a cell-based three-dimensional Subcellular Element (SCE) model [1,2] and cell-tracking experiments. The model takes into account the flexible nature of M. xanthus as well as the effects of adhesion between cells arising from the interaction of the capsular polysaccharide covering two cells in contact with each other. New image and dynamic cell curvature analysis algorithms were used to track and measure the change in cell shapes that occur as flexible cells undergo significant bending during collisions resulting in direct calibration of the model parameters. It will be shown in this talk that flexibility of cells and the adhesive cellÃ¢Â?Â?cell and cellÃ¢Â?Â?substrate interactions of M. xanthus together with cell to aspect-ratio and directional reversals [3], play an important role in smooth cell gliding and more efficient swarming. In the second part of the talk results of the analysis of the three dimensional structures of fibrin networks, with and without cells, reconstructed from two-dimensional z-stacks of confocal microscopy sections using novel image analysis algorithms, will be presented. These images were used to establish microstructure-based models for studying the relationship between the structural features and the mechanical properties of the fibrin networks in blood clots. The change in the fibrin network alignment under applied strain and the elastic modulus values will be shown to agree well with the experimental data [4]. 1. C.W. Harvey, F. Morcos, C.R. Sweet, D. Kaiser, S. Chatterjee, X. Lu, D. Chen and M. Alber [2011], Study of elastic collisions of M. xanthus in swarms, Physical Biology 8, 026016. 2. C.R. Sweet, S. Chatterjee, Z. Xu, K. Bisordi, E.D. Rosen and M. Alber [2011], Modeling Platelet-Blood Flow Interaction Using Subcellular Element Langevin Method, J R Soc Interface, 2011 May 18. [Epub ahead of print], doi: 10.1098/rsif.2011.0180. 3. Y. Wu, Y. Jiang, D. Kaiser and M. Alber [2009], Periodic reversal of direction allows Myxobacteria to swarm, Proc. Natl. Acad. Sci. USA 106 4 1222-1227. 4. E. Kim, O.V. Kim, K.R. Machlus, X. Liu, T. Kupaev, J. Lioi, A.S. Wolberg, D.Z. Chen, E.D. Rosen, Z. Xu and M. Alber [2011], Soft Matter 7, 4983-4992.

## Aaron Fogelson : Two Examples of Chemical Modulation of the Properties and Dynamics of Physiological Gels: Fibrin Formation and Mucin Swelling

- Mathematical Biology ( 129 Views )Gels formed from mixtures of polymers and solvent are ubiquitous in physiological systems. The structure and properties of a gel can change dramatically in response to chemical modulation. Two examples of the influence of chemistry on gel properties will be discussed. The structure of fibrin gels that form during blood clotting is strongly influenced by the concentration of the enzyme thrombin that produces the fibrin monomers from which the gel is built. Presumably at higher thrombin concentrations, fibrin monomers are produced more rapidly from the precursor fibrinogen molecules. I will present an analysis of a possible mechanism of fibrin branching that can explain the sensitivity of fibrin structure to the rate of supply of monomers. Mucin gel is released from vesicles in goblet cells. During this exocytotic process, the polyelectrolyte mucin gel swells to many times its original volume at a very rapid rate. I will present a model in which this swelling is triggered by an exchange of divalent calcium ions in the vesicle and monovalent sodium ions in the extracellular space, and in which the ion concentrations and the rheological properties of the mucin gel determine its equilibrium size and the dynamics of its swelling.

## Elizabeth Bouzarth : Using Regularized Stokeslets to Model Immersed Biological Fibers

- Mathematical Biology ( 128 Views )The behavior of inextensible fibers immersed in a fluid is of interest in a variety of applications ranging from polymer suspensions to actin filament transport. In these cases, the dynamics of an immersed fiber can play a large role in the observed macroscale fluid dynamics. The method of regularized Stokeslets provides a way to calculate fluid velocities in the Stokes fluid flow regime due to a collection of regularized point-forces without computing fluid velocities on an underlying grid. In this discussion, the method of Regularized Stokeslets will be used to model the dynamics of an inextensible flexible fiber immersed in a two-dimensional cellular background flow in comparison with results found in the experimental and mathematical literature. Studying this scenario with regularized Stokeslets provides insight into the documented stretch-coil transition and macroscale random walk behavior supported by mathematical models and experimental results.

## Yuan Lou : Finding Evolutionarily Stable Strategies

- Mathematical Biology ( 126 Views )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 Â?optimallyÂ? in heterogeneous environments? I will discuss some recent development on the evolution of dispersal, focusing on evolutionarily stable strategies (ESS) for dispersal.

## Leonid Berlyand : PDE/ODE models of motility in active biosystems

- Mathematical Biology ( 124 Views )In the first part of the talk we present a review of our work on PDE models of swimming bacteria. First we introduce a stochastic PDE model for a dilute suspension of self-propelled bacteria and obtain an explicit asymptotic formula for the effective viscosity (E.V.) that explains the mechanisms of the drastic reduction of E.V.. Next, we introduce a model for semi-dilute suspensions with pairwise interactions and excluded volume constraints. We compute E.V. analytically (based on a kinetic theory approach) and numerically. Comparison with the dilute case leads to a phenomenon of stochasticity arising from a deterministic system. We develop a ODE/PDE model that captures the phase transition, an appearance of correlations and large scale structures due to interbacterial interactions. Collaborators: S. Ryan, B. Haines, (PSU students); I. Aronson, A. Sokolov, D. Karpeev (Argonne); In the second part of the talk we discuss a system of two parabolic PDEs arising in modeling of motility of eukaryotic cells on substrates. The two key properties of this system are (i) presence of gradients in the coupling terms (gradient coupling) and (ii) mass (volume) preservation constraints. We derive the equation of the motion of the cell boundary, which is the mean curvature motion perturbed by a novel nonlinear term and prove that the sharp interface property of initial conditions is preserved in time. This novel term leads to surprising features of the motion of the interface such as discontinuities of the interface velocity and hysteresis. This is joint work with V. Rybalko and M. Potomkin.

## Avner Friedman : Conservation laws in mathematical biology

- Mathematical Biology ( 123 Views )Many mathematical models in biology can be described by a system of hyperbolic conservation laws with nonlinear and nonlocal coefficients. In order to determine these coefficients one needs to solve auxiliary systems of equations, for example elliptic or parabolic PDEs, which are coupled to the hyperbolic equations. In this talk we give several examples: The growth of tumors, the shrinking of dermal wounds, T cell differentiation, the growth of drug resistant bacteria in hospitals, and the transport of molecules along microtubules in axon. In these examples, the auxiliary systems range from elliptic-parabolic free boundary problems to nonlocal ODEs. Motivated by biological questions, we shall describe mathematical results regarding properties of the solutions of the conservation laws. For example, we shall determine the stability of spherical tumors and the growth of Â?fingers;Â? we shall discuss conditions for shrinking of the wound; suggest how to reduce the growth of drug resistant bacteria, and derive biologically motivated asymptotic behavior of solutions.

## Susan Holmes : Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

- Mathematical Biology ( 122 Views )Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and `generalizability' of these summaries. I will present applications of the Billera, Holmes, Vogtman (2001) distance to inferential problems both in the frequentist (bootstrap) and Bayesian contexts. I will compare the tree of trees representation to the Euclidean approximations of treespace made available through Multidimensional Scaling of the matrix of distances between trees. We also provide applications of the distances between trees to hierarchical clustering trees constructed from microarrays and phylogenetic trees of metagenomic data of bacteria in the gut. This talk contains joint work with John Chakerian and Alfred Spormann.

## Tom Kepler : Microevolution in the Immune System: A Computational Systems Approach

- Mathematical Biology ( 122 Views )Vaccines protect their recipients by inducing long-term structural changes in populations of immune cells. Part of that restructuring is exactly analogous to Darwinian Selection. New antibody molecules are created by somatic mutation of existing antibody genes. Subsequently, the immune cell populations that possess these mutated receptors overtake the "wild-type" immune cells due Â to the selective advantage they have acquired. Thus the immune system is vastly better prepared to recognize and eliminate the eliciting pathogen the next time around.

New sequencing and biosynthesis technologies, together with mathematical and computational tools, now allow us to investigate this fascinating and important phenomenon more deeply than ever before. I will illustrate this development with examples from the immune response to HIV infection.

## Katarzyna Rejniak : Fluid dynamics in cancer cell biology

- Mathematical Biology ( 120 Views )Eukaryotic cell microenvironment (inner and outer) is composed in large parts from fluids that interact with solid and elastic bodies, whereas it is the cell cytoplasm, cytoskeleton and basal membrane; the interstitial fluid interpenetrating the stroma and tumor cells; or blood flow carrying the immune or circulating tumor cells. I will discuss the use of two fluid-structure interactions methods, the immersed boundary and the regularized Stokeslets, in applications dealing with the tumor development and treatment. First model operates on the cellular scale and will be used to model various cell processes, such as cell growth, division or death, during the cellular self-organization into a normal mammary acinus, a 3D in vitro structure recapitulating the morphology of breast cysts (acini). I will discuss model development, parameterization and tuning with the experimental data, as well as their subsequent use to investigate the link between morphogenesis of epithelial mutants and molecular alterations of tumor cells. Second model acts on the tissue level, and will be used to investigate the relation between tumor tissue structure and efficacy of anticancer drugs in the context of interstitial fluid flow. I will present simulation results showing non-linear relation between tumor tissue structure and effectiveness of drug penetration. I will also discuss how tumor tissue metabolic state(its oxygenation and acidity) becomes modified due to actions of chemotherapeutic drugs leading to the emergence of tumor zones with potentially drug-resistant cells and/or to tumor areas that are not exposed to drugs at all. Both of these phenomena can contribute to the moderateclinical success of many anticancer drugs.

## Joshua Goldwyn : Analysis of stochastic auditory nerve models with applications to cochlear implant psychophysics

- Mathematical Biology ( 120 Views )Cochlear implants are neural prostheses that restore a sense of hearing to individuals with severe to profound deafness. Two fundamental theoretical questions that we face are: How does the auditory nerve respond to electrical stimulation? And how is sound information represented in the spike trains of auditory nerve fibers? We will discuss model-based efforts to investigate these questions. I will focus on the development of reduced models that incorporate essential biological features of this complicated system, and remain useful tools for analyzing neural coding.

Using a point process model of the auditory nerve, I simulate amplitude modulation detection, a common test of temporal resolution. I find that the temporal information in the simulated spike trains does not limit modulation sensitivity in cochlear implant users, and discuss how the point process framework can be extended to include additional biophysical mechanisms. Next, I illustrate how spatial spread of excitation and neural degeneration can lead to of within- and across-patient variability in listening outcomes. This points toward an important goal of computational modeling: to develop patient-specific models that can be used to optimize stimulation strategies for individual cochlear implant users.

## Andrew Gillette : Multiscale Diffusion Modeling in Charged and Crowded Biological Environments

- Mathematical Biology ( 116 Views )The macroscopic diffusion constant for small ions in biological environments is in part dependent on the volume excluded by diffusional barriers and by long-range interactions between those barriers and the ion. Increasing excluded volume reduces diffusive transport of the solute, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. My colleagues and I have developed a computational methodology for studying these effects via a homogenized finite element method for the Smoluchowski equation. I will introduce the relevant background, both biological and mathematical, and present our recent results. This work is joint with Peter Kekenes-Huskey (U. Kentucky) and J. Andrew McCammon (UC San Diego).

## Harsh Jain : A delay differential equation model of cancer chemotherapy, with applications to ovarian carcinoma treatment

- Mathematical Biology ( 114 Views )The use of delay differential equations (DDEs) to study biological phenomena has a long history, when the rate of change of model variables depends their previous history. Today, DDEs occupy a central place in models of infectious disease dynamics, epidemiology, ecology and tumor growth. In this talk, I will present a delayed partial differential equation (PDE) model of tumor growth and treatment. The model accounts for cell cycle arrest and cell death induced by chemotherapy, and explicitly includes intracellular signaling pathways relevant to drug action. The model is simplified to give a 1D hyperbolic PDE, which is further reduced to a nonlinear, non-autonomous DDE by projecting along characteristics. Necessary and sufficient conditions for the global stability of the cancer-free equilibrium are derived and conditions under which the system evolves to periodic solutions are determined. This has clinical implications since it leads to a lower bound for the amount of therapy required to affect a cure. Finally, I will present a clinical application of the model, by applying it to the treatment of ovarian cancers. Two types of drugs are considered Â? platinum-based chemotherapeutic agents that are the current standard of care for most solid tumors, and small molecule cell death inducers that are currently under development. The model is calibrated versus in vitro experimental results, and is then used to predict optimal doses and administration time scheduling for the treatment of a tumor growing in vivo.

## David Anderson : Stochastic models of biochemical reaction systems: network structure and qualitative dynamics

- Mathematical Biology ( 113 Views )Biochemical reaction networks can be represented as graphs, with chemical complexes serving as vertices and reaction channels serving as directed edges. To each such network there is an associated stochastic process that models the behavior of the underlying system of interest. In this talk I will present results that relate the structure of the reaction network to the possible dynamics of the model. I will pay particular attention to how the results pertaining to the stochastic models compare and contrast with similar results pertaining to deterministic models.

## Chia Lee : Stochastic simulation of biochemical systems with randomly fluctuating rate constants

- Mathematical Biology ( 110 Views )In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate constants, it is necessary to investigate how one can simulate such a biochemical system. To do this, we will take the Gillespie's stochastic simulation algorithm for simulation the evolution of the state of a chemical system, and study a modification of the algorithm that incorporates the random rate constants, using in part the Metropolis-Hastings algorithm to enact the distribution on the random rate constants. This modified algorithm, when applied to the single enzyme reaction system, produces simulation outputs that are corroborated by the experimental results. This project is in its early stages, and it is hoped that it can subsequently be used as a tool for the estimation or calibration of parameters in the system using experimental data.