All-atom and coarse-grained molecular dynamics (MD), Langevin dynamics (LD) and Brownian dynamics (BD) are computational methodologies, which have been applied to spatio-temporal modelling of a number of intracellular processes. I will discuss connections between MD, LD and BD, with a focus on the development, analysis and applications of multi-resolution methods, which use (detailed) MD...
My research is focused on the mathematical and computational modeling of cell regulatory processes. We and others have developed an approach to modeling the reaction kinetics of biochemical systems that allows detailed knowledge about protein-protein interactions to be encoded as rules that generalize the standard reaction network formulation and enables the building, simulation, and analysis...
The inositol-requiring enzyme 1 (IRE1) serves as a highly conserved stress sensor within the endoplasmic reticulum (ER), crucial for mitigating the cytotoxic effects resulting from the accumulation of unfolded proteins. Dysregulation of the unfolded protein response (UPR), a network of signaling pathways aimed at alleviating ER stress, is implicated in various human pathologies including...
Biological movement patterns are sometimes quasi linear with abrupt changes in direction and speed, as in movements of plastids in root cells of plants. We discuss random walk (RW) models suggesting that modelling absolute movement direction can be advantageous as compared to relative direction as assumed in the widely used correlated RWs. A new stochastic model called linear walk is proposed...
Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a central challenge in developmental biology. This is particularly intriguing in early mammalian development, where early cell-lineage differentiation arises from processes that initially appear cell-autonomous but later materialize reliably at the tissue level. In this study, we develop a multi-scale,...
Precise spatial patterning of cell fate during morphogenesis requires accurate inference of cellular position. In making such inferences from morphogen profiles, cells must contend with inherent stochasticity in morphogen production, transport, sensing and signalling. Motivated by the multitude of signalling mechanisms in various developmental contexts, we show how cells may utilise multiple...
