L1

Please see http://www.cs.ox.ac.uk/seminars/CompBioPublicSeminars/

Mechanics plays an important role during several biological phenomena such as morphogenesis,

wound healing, bone remodeling and tumorogenesis. Each one of these events is triggered by specific

elementary cell deformations or movements that may involve single cells or populations of cells. In

order to better understand how cell behave and interact, especially during degenerative processes (i.e.

tumorogenesis and metastasis), it has become necessary to combine both numerical and experimental

approaches. Particularly, numerical models allow determining those parameters that are still very

difficult to experimentally measure such as strains and stresses.

During the last few years, I have developed new finite element models to simulate morphogenetic

movements in Drosophila embryo, limb morphogenesis, bone remodeling as well as single and

collective cell migration. The common feature of these models is the multiplicative decomposition of

the deformation gradient which has been used to take into account both the active and the passive

deformations undergone by the cells. I will show how this mechanical approach, firstly used in the

seventies by Lee and Mandel to describe large viscoelastic deformations, can actually be very

powerful in modeling the biological phenomena mentioned above.

There are many recent points of contact of model theory and other 
parts of mathematics: o-minimality and Diophantine geometry, geometric group 
theory, additive combinatorics, rigid geometry,...  I will probably 
emphasize  long-standing themes around stability, Diophantine geometry, and 
analogies between ODE's and bimeromorphic geometry.

Several recent works by D. Tamarkin, D. Nadler, E. Zaslow make use of the microlocal theory of sheaves of M. Kashiwara and P. Schapira to obtain results in symplectic geometry. The link between sheaves on a manifold $M$ and the symplectic geometry of the cotangent bundle of $M$ is given by the microsupport of a sheaf, which is a conic co-isotropic subset of the cotangent bundle. In the above mentioned works properties of a given Lagrangian submanifold $\Lambda$ are deduced from the existence of a sheaf with microsupport $\Lambda$, which we call a quantization of $\Lambda$.

In the second talk we will introduce a stack on $\Lambda$ by localization of the category of sheaves on $M$. We deduce topological obstructions on $\Lambda$ for the existence of a quantization.

In this talk I will discuss recent developments in information theoretical approaches to fundamental

molecular processes that affect the cellular decision making processes. One of the challenges of applying

concepts from information theory to biological systems is that information is considered independently from

meaning. This means that a noisy signal carries quantifiably more information than a unperturbed signal.

This has, however, led us to consider and develop new approaches that allow us to quantify the level of noise

contributed by any molecular reactions in a reaction network. Surprisingly this analysis reveals an important and hitherto

often overlooked role of degradation reactions on the noisiness of biological systems. Following on from this I will outline

how such ideas can be used in order to understand some aspects of cell-fate decision making, which I will discuss with

reference to the haematopoietic system in health and disease.