To this day, there is still no existing quantitative model that can simulate the reaction rates and concentration changes in the comprehensive biochemical reaction network of a cell. Such a simulation model would be useful for understanding the nature of living cells.
A primary barrier is the lack of accurate parameters. Key biochemical parameters are notoriously difficult to measure, with...
Actin assembly drives force generation and membrane remodelling (protrusion, budding, tethering). Many actin kinetic models omit explicit energy accounting with force production \cite{Vavylonis2005,Ditlev2009}, limiting reliable coupling to multiscale models of whole-cell remodelling. Prior efforts linking actin kinetics to continuum mechanics often approximate energy flows and omit explicit...
Cells don’t roll downhill. Waddington’s epigenetic landscape has shaped our thinking about cell fate for decades, inspiring rich mathematical frameworks such as quasi-potential methods, catastrophe theory and energy landscapes. These frameworks share a hidden assumption: that cellular dynamics are gradient systems, derived from a scalar potential.
Whole-cell models (WCMs) allow us to test...
Understanding nutrient transport is essential for mathematically modelling bacterial functions because transport processes govern the rates at which cells acquire substrates that fuel all downstream metabolic activity. Nutrient uptake directly shapes intracellular metabolite levels and thereby constrains metabolic pathway fluxes.
Some data driven mathematical approaches to model membrane...
Genome-scale metabolic models (GEMs) are computable knowledge bases containing information of all biochemical reactions in an organism of interest. Typically, Flux Balance Analysis (FBA) is used to predict intracellular flux distributions corresponding to limiting substrate-efficient metabolic phenotypes. For fast-growing microbes (Escherichia coli, yeasts), alternative efficiency calculi...
Cell migration through extracellular matrix (ECM) is fundamental to many biological processes, including development, immune responses, and cancer metastasis. However, this migration is governed by mechanical interactions that occur at the subcellular scale of individual collagen fibres, and conventional traction‑force methods treat the ECM as a continuum. To move beyond this, we introduce a...
The outer membrane of Gram-negative bacteria is a crucial defensive structure, conferring - among other properties - substantial protection against antibiotics. Decades of high-resolution molecular dynamics modelling has provided powerful insights into the structures of the chemical species that reside in the Gram-negative outer membrane and their chemical and physical interactions. However,...
Mechanistic mathematical models are powerful tools in modern life sciences. Similar to experimental techniques, mechanistic models enable the investigation of biological processes and hypothesis testing. Furthermore, they allow the integrative analysis of multiple datasets as well as the prediction of latent variables and future experimental outcomes.
In this talk, I will outline how...
The landmark first whole-cell model (WCM) – of Mycoplasma genitalium – was published in 2012, offering insight into cellular biology at unprecedented scale and detail \cite{karr_et_al_2012}. The years since have seen WCMs developed by a variety of groups for a range of organisms, and major strides have been made in improving the biological fidelity and analytical power of these models. The...
