Scientific

We discuss deformation theory of rational curves and Mori’s famous Bend and Break techniques as well as their applications to Geometric Manin’s Conjecture. The lecture series contain introductory components as well as problem sessions and they aim for graduate students and postdocs.

During reproduction, viruses manufacture products that diffuse within the host cell. Because a virus does not have exclusive access to its own gene products, coinfection of multiple viruses allows for strategies of cooperation and defection— cooperators produce large amounts of gene product while defectors produce less product but specialize in appropriating a larger share of the common pool. Experimental data shows that, under conditions where coinfection is common, bacteriophage $\Phi$6 becomes trapped in a Prisoner’s dilemma, with defectors spreading to fixation, causing lowered population fitness. However, these experiments did not allow for fluctuation in the density of the external viral population. Here, I’ll discuss a model formulated to see if environmental feedback can free $\Phi$6 from the Prisoner’s dilemma. I’ll also discuss the concept of the Effective Game, which incorporates the frequency and density of different viral types in the environment.

The principal function of the nucleus is to facilitate storage, retrieval, and maintenance of the genetic information encoded into DNA and RNA sequences. A unique feature of nucleoplasm—the fluid of the nucleus—is that it contains chromatin (DNA) and RNA.

In contrast to other important biological polymer hydrogels, such as mucus and extracellular matrix, the nucleic acid polymers have a sequence. Recent experiments have shown that during the growth phase of the cell cycle, chromatin condenses in a sequence specific manner into regions within the nucleoplasm, possibly so that functionally related genes are grouped together spatially even though they might be far apart in terms of sequence distance.

At the same time, we are becoming increasingly aware of the role of liquid-liquid phase separation (LLPS) in cellular processes in the nucleus and the cytoplasm. Complex molecular interactions over a wide range of timescales can cause large biopolymers (RNA, protein, etc) to phase separate from the surrounding nucleoplasm into distinct biocondensates (spherical droplets in the simplest cases).

I will discuss recent work modelling the role of nuclear biocondensates in neurodegenerative disease and several ongoing projects related to
modelling and microscopy image analysis.

Understanding how cells change their identity and behaviour over time in living systems is a key question in many fields of biology. Measurement of cell states is inherently destructive, and so the relationship of the current state of a cell to some future state, or ‘fate’, cannot be observed experimentally. Trajectory inference refers to the general problem of trying to estimate various aspects of the state-fate relationship. We discuss optimal transport as a useful analytical tool for trajectory inference, and we develop a mathematical framework for recovering trajectories in both non-equilibrium as well as equilibrium systems.

A conformal net on $S^1$ is an assignment $\mathcal{A}:\left\{\textrm{open subsets of } S^1\right\} \to \left\{\mbox{von Neumann algebras acting on } \mathcal{F}\right\}$, which satisfies a slew of axioms motivated by quantum field theory. In this talk, I will consider the free fermionic conformal net. In this case, the Hilbert space $\mathcal{F}$ is the Fock space generated by the positive energy modes of square-integrable spinors on the circle $?^2(?^1,\mathbb{S})$; and the von Neumann algebras are Clifford algebras generated by those elements of $?^2(?^1,\mathbb{S})$ whose support lies in $?\subset ?^1$. After going over this construction, I will argue that given an open interval $?\subset ?^1$, one can equip $\mathcal{F}$ with the structure of $\mathcal{A}(I)-\mathcal{A}(I)$-bimodule. I will then outline the construction of a canonical isomorphism of bimodules $\mathcal{F}\boxtimes_{\mathcal{A}(I_\_)}\mathcal{F}\to\mathcal{F}$ where $\boxtimes_{\mathcal{A}(I_\_)}$ stands for the Connes fusion product over the algebra assigned to the lower semi-circle $I_\_$. If time permits, I will discuss some (anticipated) applications of this isomorphism, for example in string geometry, or in the construction of the free fermion extended topological field theory.