Conveners
Multiscale modelling and simulation: Part A
- Mark Flegg (Monash University)
Multiscale modelling and simulation: Part B
- Mark Flegg (Monash University)
Description
One of the most controversial and difficult problems regarding the mathematical modelling of biological systems is determination of the appropriateness of the choice of mathematical framework and the implementation of scale in any given model. Concentration scales, spatial scales and temporal scales characteristic of models in biology, more so than any other application, are highly varied and structured even in regards to a single process. In this minisymposium we will be hearing from speakers working on the forefront of foundations in multiscale modelling in biology. It is best to keep an open mind in these talks about the fundamental choice of the methodology which is appropriate to a system and how these methodologies relate to each other. You will be stimulated with ideas regarding discrete versus continuous and stochastic versus deterministic modelling, as well as more general discussion about the nature and treatment of multiscale frameworks in biology.
In many biological applications, it is useful to model chemical reactions at the level of individual molecules whilst not running costly Brownian dynamics models. Modelling chemical reactions as interactions at a distance can lead to errors if multiple species and time scales are important to the kinetics (for example, catalytic reactions). Multiple time scale analysis of equivalent mean-field...
I will discuss mathematical and computational methods for spatio-temporal modelling in molecular and cell biology, including all-atom and coarse-grained molecular dynamics (MD), Brownian dynamics (BD), stochastic reaction-diffusion models and macroscopic mean-field equations.
Microscopic (BD, MD) models are based on the simulation of trajectories of individual molecules and their localized...
Patch dynamics is a numerical multiscale solver which constructs a macroscale solution of a microscale system by solving the original microscale problem, but only within discrete patches. These patches are spread across the domain of the system and are separated by the desired macroscale spacing, thus providing a description of the system at the macroscale. The space between the patches is...
Stochastic simulations are essential to the study of biological cells, yet there is no computational framework allowing for detailed spatial simulations of genetic regulatory network within large populations of cells.
We fill this gap by developing a parallel simulation framework capable of spatially resolved stochastic simulation of cell-cell signalling in multicellular systems. We use an...
The three-dimensional structure of eukaryotic genomes is non-random, dynamic, highly regulated, and can be observed to change according to external signals and differentiation state. Disruptions can lead to disease, in which incorrect genomic contacts are responsible for mis-regulation of gene expression. However, the underlying mechanisms that organise the genome are still largely unknown....
Many T cell receptors have long, unstructured cytoplasmic tails that contain tyrosine sites. These sites can serve as regulators of receptor activation when phosphorylated or dephosphorylated, while also serving as docking sites for cytosolic enzymes. We coarse-grain the effective interaction between two tails, and develop a mesoscopic particle-based stochastic reaction-diffusion model to...