L3

The Omicron BA.1 variant of SARS-CoV-2 was more transmissible and less severe than the preceding Delta variant, including in hosts without previous infection or vaccination.  To investigate why this was the case, we conducted in vitro replication experiments in human nasal and lung cells, then constructed and fitted ODE models of varying levels of complexity to the data, using Markov chain Monte Carlo methods.  Our results fitting a simple model suggest that the basic reproduction number and growth rate are higher for Omicron in nasal cells, and higher for Delta in lung cells. As growth in nasal cells is thought to correspond to transmissibility and growth in lung cells is thought to correspond to severity, these results are consistent with epidemiological and clinical observations.  We then fitted a more complex model, including different virus entry pathways and the immune response, to the data, to understand the mechanisms leading to higher infectivity for Omicron in nasal cells. This work paves the way for using within-host mathematical models to analyse experimental data and understand the transmission potential of future variants. 

While presenting the results of this study, I will use them to open a wider discussion on common problems in mathematical biology, such as the situations in which complex models are preferable to simpler models; when it is appropriate to fix model parameters; and how to present results which are contingent on unidentifiable parameters.

Abstract: Neurotransmission at chemical synapses relies on the calcium-induced fusion of synaptic vesicles with the presynaptic membrane. The distance of the vesicle to the calcium channels determines the fusion probability and consequently the postsynaptic signal. After a fusion event, both the release site and the vesicle undergo a recovery process before becoming available for reuse again. For all these process components, stochastic effects are widely recognized to play an important role. In this talk, I will present our recent efforts on how to describe and structurally understand neurotransmission dynamics using stochastic modeling approaches. Starting with a linear reaction scheme, a method to directly compute the exact first- and second-order moments of the filtered output signal is proposed. For a modification of the model including explicit recovery steps, the stochastic dynamics are compared to the mean-field approximation in terms of reaction rate equations. Finally, we reflect on spatial extensions of the model, as well as on their approximation by hybrid methods.

References:

- A. Ernst, C. Schütte, S. Sigrist, S. Winkelmann. Mathematical Biosciences, 343, 108760, 2022.

- A. Ernst, N. Unger, C. Schütte, A. Walter, S. Winkelmann. Under Review. https://arxiv.org/abs/2302.01635

The Stokes–Onsager–Stefan–Maxwell (SOSM) equations model the flow of concentrated mixtures of distinct chemical species in a common thermodynamic phase. We derive a novel variational formulation of these nonlinear equations in which the species mass fluxes are treated as unknowns. This new formulation leads to a large class of high-order finite element schemes with desirable linear-algebraic properties. The schemes are provably convergent when applied to a linearization of the SOSM problem.

We propose a nematic model for polyatomic gas, intending to study anisotropic phenomena. Such phenomena stem from the orientational degree of freedom associated with the rod-like molecules composing the gas. We adopt as a primer the Curitss-Boltzmann equation. The main difference with respect to Curtiss theory of hard convex body fluids is the fact that the model here presented takes into account the emergence of a nematic ordering. We will also derive from a kinetic point of view an energy functional similar to the Oseen-Frank energy. The application of the Noll-Coleman procedure to derive new expressions for the stress tensor and the couple-stress tensor will lead to a model capable of taking into account anisotropic effects caused by the emergence of a nematic ordering. In the near future, we hope to adopt finite-element discretisations together with multi-scale methods to simulate the integro-differential equation arising from our model.

Toward a characterization of modularity using shatter functions, we show that an o-minimal expansion of the  real ordered additive group $(\mathbb{R}; 0, +,<)$ does not define restricted multiplication if and only if the shatter function of every definable family is asymptotic to a polynomial. Our result implies that vc-density can only take integer values in $(\mathbb{R}; 0, +,<)$ confirming a special case of a conjecture by Chernikov. (Joint with Abdul Basit.)

We will define a notion of a semi-retraction between two first-order structures introduced by Scow. We show how a semi-retraction encodes Ramsey problems of finitely-generated substructes of one structure into the other under the most general conditions. We will compare semi-retractions to a category-theoretic notion of pre-adjunction recently popularized by Masulovic. We will accompany the results with examples and questions. This is a joint work with Lynn Scow.

Hitchin's equations are a system of gauge theoretic equations on a Riemann surface that are of interest in many areas including representation theory, Teichmüller theory, and the geometric Langlands correspondence. The Hitchin moduli space carries a natural hyperkähler metric.  An intricate conjectural description of its asymptotic structure appears in the work of Gaiotto-Moore-Neitzke and there has been a lot of progress on this recently.  I will discuss some recent results using tools coming out of geometric analysis which are well-suited for verifying these extremely delicate conjectures. This strategy often stretches the limits of what can currently be done via geometric analysis, and simultaneously leads to new insights into these conjectures.

The equivalence of NSOP${}_1$ and NSOP${}_3$, two model-theoretic complexity properties, remains open, and both the classes NSOP${}_1$ and NSOP${}_3$ are more complex than even the simple unstable theories. And yet, it turns out that classical geometric stability theory, in particular the group configuration theorem of Hrushovski (1992), is capable of controlling classification theory on either side of the NSOP${}_1$-SOP${}_3$ dichotomy, via the expansion of stable theories by generic predicates and equivalence relations. This allows us to construct new examples of strictly NSOP${}_1$ theories. We introduce generic expansions corresponding, though universal axioms, to definable relations in the underlying theory, and discuss the existence of model companions for some of these expansions. In the case where the defining relation in the underlying theory $T$ is a ternary relation $R(x, y, z)$ coming from a surface in 3-space, we give a surprising application of the group configuration theorem to classifying the corresponding generic expansion $T^R$. Namely, when $T$ is weakly minimal and eliminates the quantifier $\exists^{\infty}$, $T^R$ is strictly NSOP${}_4$ and TP${}_2$ exactly when $R$ comes from the graph of a type-definable group operation; otherwise, depending on whether the expansion is by a generic predicate or a generic equivalence relation, it is simple or NSOP${}_1$.

In his pioneering and celebrated 1968 paper on the elementary theory of finite fields Ax asked if the theory of the class of all the finite rings $\mathbb{Z}/m\mathbb{Z}$, for all $m>1$, is decidable. In that paper, Ax proved that the existential theory of this class is decidable via his result that the theory of the class of all the rings $\mathbb{Z}/p^n\mathbb{Z}$ (with $p$ and $n$ varying) is decidable. This used Chebotarev’s Density Theorem and model theory of pseudo-finite fields.

I will talk about a recent solution jointly with Angus Macintyre of Ax’s Problem using model theory of the ring of adeles of the rational numbers.