Seminar

Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions such as signaling and trafficking. However, physical principles governing their function is not well understood, as their nanoscopic and highly dynamic nature limit both direct experimental measurements and their interpretation [1]. In this context, computer simulation holds immense potential to investigate their molecular origin and the mechanisms that govern their functions.  Taking inspiration from the physics of amorphous systems [2], we characterize membrane order using a non-affine deformation frame-work [3]. Further, as a conjugate of this order, we probe the packing defects or membrane free volume [4]. We use this connection to explore generic mechanistic principles behind peptide localization and membrane permeability of small molecules [5].

Internal packing can also indicate the physical mechanisms that drive functional motions in proteins. Toward this, we represent protein as an abstract elastic network, where the nodes represent amino acids and the bonds indicate their interactions. By evolving the network against specific fitness, we study the emergence of various functional motions such as, allosteric regulation and hinge joint. We observe that the characteristic features in the fit networks are associated with specific geometries of 'liquid-like' regions embedded in an amorphous solid.  Our analysis provides insight into the architectural demands on proteins that enable prescribed functions [6].
I will present some of our recent works along these lines and discuss their scope and implications.