Computational membrane remodeling in soft matter and biophysics
Membrane remodelling plays a critical role in many physical and biological/cellular processes including synthetic biology, drug delivery, cellular uptake of nano containers, and self-assembly of nanostructures at membrane interface. The atomistic membrane simulations are however extremely slow to simulate membrane behaviour at large time and length scales. We have developed a triangulated coarse-grained membrane model which is capable of rapid and efficient simulation of membrane remodelling. We performed Monte Carlo simulations of the model to investigate membrane interaction with nanoparticles and proteins. We report tubular membrane structures induced by adsorbed nanoparticles on vesicles and investigate the role of membrane curvature and size and shape of the particles on cellular uptake of the particles. We also show how membrane curvature determines pairwise interactions induced between adsorbed Janus nanoparticles on the vesicles and reveal that the area fraction of the adhesive Janus particle surface is an important control parameter for the assembly of the particles.
We also performed simulations to understand how tubular membrane structures of the Endoplasmic reticulum , Golgi, mitochondria, and other cellular organelles are created and maintained. Our simulations show that the membrane area growth and volume reduction can induce tubular membrane structure in concert with curved proteins previously found to shape these tubules. We use our model to simulate membrane remodelling induced by protein molecules in biological processes. Our simulations reveal the scaffolding role of Atg protein complexes in autophagosome biogenesis in autophagy, a critical physiological process winning the Nobel prize of medicine in 2016. We show that cooperative interaction of aggregates of several protein chains is essential to remodel the membrane appropriately. Our outstanding results, in collaboration with experimental colleagues from Berkeley, indicate how ESCRT (endosomal sorting complex required for transport) machinery can induce membrane remodelling and scission. Our recent simulations reveal spontaneous vesicle constriction by rings of Janus nanoparticles and clusters of curved proteins, relevant for membrane scission by proteins and applicable tosynthetic biology.
About The Speaker
Finishing high school in Tehran, I was ranked in first 500 people amongst almost 600000 participants for general entrance exams of iranian universities and continued my undergraduate studies in mechanical engineering. Ranked 4 amongst 15000 participants in Masters degree entrance exam, I then finished both my Masters and PhD degrees of mechanical engineering in Sharif University of Technology on biomembrane simulation, during which I attended a visiting period in Max Planck Institute of Colloids and Interfaces, Potsdam, Germany. I was then offered a second PhD, before finishing the first one, and ended up earning another PhD in Physics from Technical University of Berlin, spending a 6-month sabbatical period in North Carolina State University. After a successful PhD in computational modelling of vesicle membranes interacting with nanostructures, I joined Max Palnck Institute of Biophysics in 2013 as a postdoctoral researcher. After 6 years of Postdoc, I recently started the group of active membrane dynamics in the department of living matter physics of Max Planck Institute of Dynamics and Self-organisation. I work on computational soft matter and biophysics focusing on membrane remodeling in cellular and biological processes, self organisation of nano-structures, active membrane dynamics, synthetic biology, and protein induced membrane dynamics.