L4

Our visual perception of the world heavily relies on sophisticated and delicate biological mechanisms, and any disruption to these mechanisms negatively impacts our lives. Age-related macular degeneration (AMD) affects the central field of vision and has become increasingly common in our society, thereby generating a surge of academic and clinical interest. I will present some recent developments in the mathematical modeling of the retinal pigment epithelium (RPE) in the retina in the context of AMD; the RPE cell layer supports photoreceptor survival by providing nutrients and participating in the visual cycle and “cellular maintenance". Our objectives include modeling the aging and degeneration of the RPE with a mechanistic approach, as well as predicting the progression of atrophic lesions in the epithelial tissue. This is a joint work with the research team of Prof. M. Paques at Hôpital National des Quinze-Vingts.

The rheological (deformation and flow) properties of biological tissues  are important in processes such as embryo development, wound healing and 
tumour invasion. Indeed, processes such as these spontaneously generate  stresses within living tissue via active process at the single cell level. 
Tissues are also continually subject to external stresses and deformations  from surrounding tissues and organs. The success of numerous physiological 
functions relies on the ability of cells to withstand stress under some conditions, yet to flow collectively under others. Biological tissue is 
furthermore inherently viscoelastic, with a slow time-dependent mechanics.  Despite this rich phenomenology, the mechanisms that govern the 
transmission of stress within biological tissue, and its response to bulk deformation, remain poorly understood to date.

This talk will describe three recent research projects in modelling the rheology of biological tissue. The first predicts a strain-induced 
stiffening transition in a sheared tissue [1]. The second elucidates the interplay of external deformations applied to a tissue as a whole with 
internal active stresses that arise locally at the cellular level, and shows how this interplay leads to a host of fascinating rheological 
phenomena such as yielding, shear thinning, and continuous or discontinuous shear thickening [2]. The third concerns the formulation of 
a continuum constitutive model that captures several of these linear and nonlinear rheological phenomena [3].

[1] J. Huang, J. O. Cochran, S. M. Fielding, M. C. Marchetti and D. Bi, 
Physical Review Letters 128 (2022) 178001

[2] M. J. Hertaeg, S. M. Fielding and D. Bi, Physical Review X 14 (2024) 
011017.

[3] S. M. Fielding, J. O. Cochran, J. Huang, D. Bi, M. C. Marchetti, 
Physical Review E (Letter) 108 (2023) L042602.

Circadian clocks generate autonomous daily rhythms of gene expression in anticipation of daily sunlight and temperature cycles in a variety of organisms. The simples and best characterised of all circadian clocks in nature is the cyanobacterial clock, the core of which consists of just 3 proteins - KaiA, KaiB and KaiC - locked in a 24-h phosphorylation-dephosphorylation loop. Substantial progress has been made in understanding how cells generate and sustain this rhythm, but important questions remain: how does the clock maintain resilience in the face of internal and external fluctuations, how is the clock coupled to other cellular processes and what dynamics arise from this coupling? We address these questions using an interdisciplinary approach combining time-lapse microscopy and modelling. In this talk, I will first characterise the clock's free-running robustness and explore how the clock buffers environmental noise and genetic mutations. Our stochastic model predicts how the clock filters out such noise, including fast light fluctuations, to keep time while remaining responsive to environmental shifts, revealing also that the wild-type operates at a noise optimum. Next, I will focus on how the clock interacts with the other major cellular cycle, the cell division cycle. Our single-cell data shows that the clock couples to the division rate and expression of cell cycle-dependent factors using both frequency modulation and amplitude modulation strategies, with implications for cell growth and cell size control. Our findings illustrate how simple systems can exhibit complex dynamics, advancing our understanding of the interdependency between gene circuits and cellular physiology.  
 

The question can be formulated as a statistical hypothesis asserting that the distribution of the shapes of closed curves representing outlines of cell nuclei in a spatial domain is independent of the distribution of their locations. The key challenge in developing a procedure to test the hypothesis from a sample of spatially indexed curves (e.g. from an image) lies in how symmetries in the data are accounted for: shape of a curve is a property that is invariant to similarity transformations and reparameterization, and the shape space is thus an infinite-dimensional quotient space. Starting with a convenient geometry for the shape space developed over the last few years, I will discuss dependence measures and their estimates for spatial point processes with shape-valued marks, and demonstrate their use in testing for spatial independence of marks in a breast cancer application.  

The class of $t$-perfect graphs consists of graphs whose stable set polytopes are defined by their non-negativity, edge inequalities, and odd circuit inequalities. These were first studied by Chvátal in 1975, motivated by the related and well-studied class of perfect graphs. While perfect graphs are easy to colour, the same is not true for $t$-perfect graphs; numerous questions and conjectures have been posed, and even the most basic, on whether there exists some $k$ such that every $t$-perfect graph is $k$-colourable, has remained open since 1994. I will talk about joint work with Maria Chudnovsky, Linda Cook, James Davies, and Sang-il Oum in which we establish the first finite bound and show that a little less than 200 000 colours suffice.

Multiparameter persistent homology is a generalization of persistent homology that allows for more than a single filtration function. Such constructions arise naturally when considering data with outliers or variations in density, time-varying data, or functional data. Even though its algebraic roots are substantially more complicated, several new invariants have been proposed recently. In this talk, I will go over such invariants, as well as their stability, vectorizations and implementations in statistical machine learning.

In this talk, I will discuss Figalli and Gigli’s formulation of optimal transport between non-negative Radon measures in the setting of metric pairs. This framework allows for the comparison of measures with different total masses by introducing an auxiliary set that compensates for mass discrepancies. Within this setting, classical characterisations of optimal transport plans extend naturally, and the resulting spaces of measures are shown to be complete, separable, geodesic, and non-branching, provided the underlying space possesses these properties. Moreover, we prove that the spaces of measures 
equipped with the $L^2$-optimal partial transport metric inherit non-negative curvature in the sense of Alexandrov. Finally, generalised spaces of persistence diagrams embed naturally into these spaces of measures, leading to a unified perspective from which several known geometric properties of generalised persistence diagram spaces follow. These results build on recent work by Divol and Lacombe and generalise classical results in optimal transport.

We are going to study the Ginzburg-Landau energy for two specific geometries, related to the very experiments on fermionic condensates: annuli and strips 

The specific geometry of a strip provides connections between solitons and vortices, called solitonic vortices, which are vortices with a solitonic behaviour in the infinite direction of the strip. Therefore, they are very different from classical vortices which have an algebraic decay at infinity. We show that there exist stationary solutions to the Gross-Pitaevskii equation with k vortices on a transverse line, which bifurcate from the soliton solution as the width of the strip is increased. This is motivated by recent experiments on the instability of solitons by imposing a phase shift in an elongated condensate for bosonic or fermionic atoms.

For annuli, we prescribe a very large degree on the outer boundary and find that either there is a transition from a giant vortex to vortices also in the bulk but tending to the outer boundary.

This is joint work with Ph. Gravejat and E.Sandier for solitonice vortices and Remy Rodiac for annuli.
 

In this talk we consider the four-waves spatially homogeneous kinetic equation arising in weak wave turbulence theory from the microscopic Fermi-Pasta-Ulam-Tsingou (FPUT) oscillator chains.  This equation is sometimes referred to as the Phonon Boltzmann Equation. I will discuss the global existence and stability of solutions of the kinetic equation near the Rayleigh-Jeans (RJ) thermodynamic equilibrium solutions. This is a joint work with Pierre Germain (Imperial College London) and Joonhyun La (KIAS).