Event type: Seminar
(Ohio State University)
Mathematical models in biological pattern formationShow/Hide Abstract
I will discuss two mathematical problems in biological pattern formation. The first is on modeling concentric ring patterns formed in engineered bacterial colonies. I will first present a hybrid model that incorporates a detailed description of cell movement and cell signaling and explains the underlying mechanism of the ring pattern. I will then present a PDE model derived from the hybrid model that captures the biological phenomena equally well. The second concerns spatial pattern formation in reaction-diffusion systems. I will discuss a computational method that can be used to discover potentially all nonuniform steady states of the PDE system, describing the structure of the spatial patterns. The method uses techniques from numerical algebraic geometry. This talk is based on joint work with Min Tang from Shanghai Jiaotong University and Wenrui Hao from Penn State University.
Feb 7, 2020 Online Seminar
(Fred Hutchinson Cancer Research Center)
Making Bayesian phylogenetics like training a neural networkShow/Hide Abstract
Bayesian posterior distributions on phylogenetic trees remain difficult to sample despite decades of effort. The complex discrete and continuous model structure of trees means that recent inference methods developed for Euclidean space are not easily applicable to the phylogenetic case. Thus, we are left with random-walk Markov Chain Monte Carlo (MCMC) with uninformed tree modification proposals; these traverse tree space slowly because phylogenetic posteriors are concentrated on a small fraction of the very many possible trees. In this talk, I will describe our wild adventure developing efficient alternatives to random-walk MCMC, which has concluded successfully with the development of a variational Bayes formulation of Bayesian phylogenetics. This formulation leverages a “factorization
Feb 14, 2020 Online Seminar
Ultrastructural 3D simulations of electrical and calcium dynamics in neurons and networksShow/Hide Abstract
Neurons make use of their complex cellular and intracellular architecture to process and guide electrical and biochemical signals. To study this structure-function interplay, computational methods are detremental, since many parameters are not directly accessible in an experimental setting. This also means that the detailed three-dimensional morphology of cells and organelles needs to be included in modeling and simulation, which results in complex-domain problems, described by systems of coupled, nonlinear, partial differential equations. We have developed numerical discretization methods and fast solvers to address this general type of biological problem set, with a focus on optimal weak scalability on High Performance Computing infrastructures. We present some of the important biological problems revolving around cellular calcium signaling, coupled to electrical models, and the use of our NeuroBox Toolbox and the multiphysics platform uG4 to solve such ultrastructural 3D neuron models. Selected results show how neurons are capable of using their (intra)cellular architecture to fine-tune their response to exterior/network input.
Feb 28, 2020 Online Seminar
(University of British Columbia)
From Cell polarity to intracellular networks in single and collective cell motilityShow/Hide Abstract
Cell migration plays a central role in embryonic development, wound healing and immune surveillance. In 2008, Yoichiro Mori, Alexandra Jilkine and I published a model for the initial step of cell migration, the front-back chemical polarization that sets a cell’s directionality. (More detailed mathematical properties of this model were described by the same group in 2011.) Since then, progress has been made in investigating how that simple “wave-pinning" mechanism is shaped and tuned by feedback from other proteins, such as actin, from the cell’s environment (extracellular matrix), from interplay with larger signaling networks, and from cell-cell interactions. In this talk I will describe some of this progress, with emphasis on links to experiments on melanoma cell motility. If time permits, I will also briefly describe more recent work on collective cell migration that we are currently undertaking.
Sep 22, 2020 Online Seminar
Opinion Dynamics with Tunable SensitivityShow/Hide Abstract
I will present a general model of continuous-time opinion dynamics for an arbitrary number of agents that sense or communicate over a network and form real-valued opinions about an arbitrary number of options. Drawing from biology, physics, and social psychology, an attention parameter is introduced to modulate social influence and a saturation function to bound inter-agent and intra-agent opinion exchanges. This yields simply parameterized dynamics that exhibit the range of opinion formation behaviors predicted by model-independent bifurcation theory but not exhibited by linear models or existing nonlinear models. Behaviors include rapid and reliable formation of multistable consensus and dissensus states, even in homogeneous networks, as well as ultra-sensitivity to inputs, robustness to uncertainty, flexible transitions between consensus and dissensus, and opinion cascades. Augmenting the opinion dynamics with feedback dynamics for the attention parameter results in tunable thresholds that govern sensitivity and robustness. The model provides new means for systematic study of dynamics on natural and engineered networks, from information spread and political polarization to collective decision making and dynamic task allocation. This is joint work with Alessio Franci (UNAM, Mexico) and Anastasia Bizyaeva (Princeton). The talk is based on version 2 of the paper “A General Model of Opinion Dynamics with Tunable Sensitivity”, which will be available on Tuesday October 13, 2020 here: https://arxiv.org/abs/2009.04332v2
Oct 13, 2020 Online Seminar
(University of Washington)
Constraints on the dimensionality of neural representationsShow/Hide Abstract
In the domain of computational/theoretical neuroscience a recently revived question is about the complexity of neural data. This question can be tackled by studying the dimensionality of such data: is neural activity high or low dimensional? How does the geometrical structure of neural activity depend on behavior, learning or the underlying connectivity? In my talk I will show how it is possible to link these three aspects (animal behavior, learning and underlying network connectivity) to the geometrical properties of neural data, with an emphasis on dimensionality phenomena. My results depart from neural recordings and aim at building understanding of neural dynamics by means of theoretical and computational tools. Such tools are mainly borrowed from the domain of neural networks dynamics, using a blend of large scale dynamical systems and statistical physics approaches.
Oct 20, 2020 Online Seminar
Modeling and measuring pattern formation in zebucturesShow/Hide Abstract
Wild-type zebrafish (Danio rerio) are characterized by black and yellow stripes, which form on their body and fins due to the self-organization of thousands of pigment cells. Mutant zebrafish and sibling species in the Danio genus, on the other hand, feature altered, variable patterns, including spots and labyrinth curves. The longterm goal of my work is to better link genotype, cell behavior, and phenotype by helping to identify the specific alterations to cell interactions that lead to these different fish patterns. Using a phenomenological approach, we develop agent-based models to describe the behavior of individual cells and simulate pattern formation on growing domains. In this talk, I will overview our models and highlight how topological techniques can be used to quantitatively compare our simulations with in vivo images. I will also discuss future directions related to taking a more mechanistic approach to modeling cell behavior in zebrafish.
Oct 27, 2020 Online Seminar