Permanent geological carbon storage will reduce greenhouse gas emissions and help mitigate climate change. Storage security is increased by CO₂ capillary trapping in cm-to-m scale, layered rock heterogeneities; features that are ubiquitous across storage sites worldwide. This talk will outline the challenges associated with modelling the impact of small-scale heterogeneity on large scale saturation distributions and trapping during geological CO₂ storage, including the difficulties in incorporating petrophysical and geological uncertainty into field-scale numerical models. Experimental results demonstrate the impact of cm-scale heterogeneity on pore-scale processes, which in turn influence large scale behaviour. Heterogeneity is shown to have a leading order impact on saturation distribution and storage capacity during geological CO₂ storage.

We study the positional information conferred by the morphogens Sonic Hedgehog and BMP in neural tube patterning. We use the mathematics of information theory to quantify the information that cells use to decide their fate. We study the encoding, recoding and decoding that take place as the morphogen gradient is formed, triggers a nuclear response and determines cell fates using a gene regulatory network.

When a biological system is modelled using a mathematical process, the next step is often to estimate the system parameters. Although computational and statistical techniques have been developed to estimate parameters for complex systems, this can be a difficult task. As a result, researchers have focused on revealing parameter-independent dynamical properties of a system. In this talk, we will discuss the study of qualitative behaviors of stochastic biochemical systems using reaction networks, which are graphical configurations of biochemical systems. The goal of this talk is to (1) introduce the basic modelling aspects of stochastically-modelled reaction networks and (2) discuss important results in this literature, including the random time representation, relationships between stochastic and deterministic models, and derivation of stability via network structures.

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.

Image-based readouts of biology are information-rich and inexpensive. Yet historically, bespoke data collection methods and the intrinsically unstructured nature of image data have made these assays difficult to work with at scale. This presentation will discuss advances made at Recursion to industrialise the use of cellular imaging to decode biology and drive drug discovery. First, the use of deep learning allows the transformation of unstructured images into biologically meaningful representations, enabling a 'map of biology' relating genetic and chemical perturbations to scale drug discovery. Second, building such a map at whole-genome scale led to the discovery of a "proximity bias" globally confounding CRISPR-Cas9-based functional genomics screens. Finally, I will discuss how publicly-shared resources from Recursion, including the RxRx3 dataset and MolRec application, enable downstream research both on cellular images themselves and on deep learning-derived embeddings, making advanced image analysis more accessible to researchers worldwide.