Mathematics

On growth and form: geometry, physics and biology

Speaker: 
Lakshminarayanan Mahadevan
Date: 
Thu, May 24, 2012
Location: 
PIMS, University of British Columbia
Conference: 
2012 Niven Lecture
Abstract: 
The diversity of form in living beings led Darwin to state that it is "enough to drive the sanest man mad". How can we describe this variety? How can we predict it? Motivated by biological observations on different scales from molecules to tissues, I will show how a combination of biological and physical experiments, mathematical models and simple computations allow us to begin to unravel the physical basis for morphogenesis.

Mathematical Cell Biology Summer Course Lecture 36

Speaker: 
Dimitrios Vavylonis
Date: 
Thu, May 24, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
TBA

Mathematical Cell Biology Summer Course Lecture 35

Speaker: 
Dimitrios Vavylonis
Date: 
Thu, May 24, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
  • Regulatory circuits in Bacterial Chemotaxis and motility
  • Introduction to molecular motors, porters vs rowers and cooperativity of myosin in muscle
  • Microtubule dynamics
  • Cytokinesis
  • FRAP studies of microtubule dynamics in the mitotic spindle

Cell Polarity Models & Simulating Cell Motility Using the Cellular Potts Model (CPM)

Speaker: 
Leah Edelstein-Keshet
Date: 
Wed, May 23, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
First, the universal features of polarizing cells are listed, and details of the Mori-Jilkine wave-pinning model are assembled and discussed biologically and mathematically. A short review of thelocal pulse analysis is provided to indicate the usefulness of this method of analysis. Then, I discuss the survey of polarizing cells from a paper by Jilkine and LEK (2011) that appeared in PLoS Comput Biol 7(4): e1001121. Here, common and distinct attributes of different cell types and of several models for cell polarization are compared. The responses of models to a set of computational perturbations mimicking stimuli protocols are described. This lecture introduces the topic of 2D cell motility simulations, but focuses on one specific method, the CPM (as implemented by Maree et al in Bull Math Biol (2006), 68(5):1169-1211 and PLoS Comput Biol (2012) 8(3): e1002402). I explain the details of the method, the biological facts that were included (signaling from GTPases and phosphoinositides to actin assembly and myosin contraction). I illustrate typical results, and then discuss some of the technical aspects of the method, emphasizing its link to the (previously discussed) Metropolis-Hastings algorithm. I also show how Stan Maree was able to chose CPM parameters to phenomenologically mimic the known relationship between actin filament ends and cell protrusion speed.

Mathematical Cell Biology Summer Course Lecture 33

Speaker: 
Dimitrios Vavylonis
Date: 
Wed, May 23, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
Introduction to molecular motors, porters vs rowers and cooperativity of myosin in muscle

Models for Cell Shape and Actin Filament Distributions

Speaker: 
Leah Edelstein-Keshet
Date: 
Tue, May 22, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
In this lecture I describe a model by Grimm et al (2003) Eur Biophys J 32: 563-577. The authors ask what processes might account for a parabolic density profile of actin seen across the front edge of a keratocyte. In an elegant coupled PDE model, they show that right and left growing actin filaments, competing for the actin branching complex Arp2/3 have solutions with the appropriate profile. I here consider one of the cases, that of local competition and slow capping of filaments, where the equations are fully analytically solvable in closed form.

Mathematical Cell Biology Summer Course Lecture 31

Speaker: 
Dimitrios Vavylonis
Date: 
Tue, May 22, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
  • Diffusion-controlled processes in the cell and sensing in bacterial chemotaxis
    • Compact vs non-Compact Exploration [deGennes, Macromolecules 1982]
    • Bacterial Chemotaxis [Berg and Purcell Biophys J 1977]
    • Reduction of Dimensionality [Philips, Kondev and Theriot, Physical Biology of the Cell]
    • Formins and Tip-tracking

Mathematical Cell Biology Summer Course Lecture 30

Speaker: 
Hildor
Date: 
Fri, May 18, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
TBA

Mathematical Cell Biology Summer Course Lecture 29

Speaker: 
William Holmes
Date: 
Fri, May 18, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
  • Local Pulse Analysis for RD equations
  • Actin Waves
  • Matlab examples and exercises

Mathematical Cell Biology Summer Course Lecture 28

Speaker: 
Raibatak (Dodo) Das
Date: 
Fri, May 18, 2012
Location: 
PIMS, University of British Columbia
Conference: 
Mathematical Cell Biology Summer Course
Abstract: 
Data Analysis Methods
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