BE Seminar: Physics of Nuclear Organization

Speaker: Dr. Rakesh Das

Max-Planck-Institute for the Physics of Complex Systems, Germany

Title: Physics of Nuclear Organization

Abstract: Spatiotemporal organization of the subnuclear medium plays a crucial role in genome regulation [1]. However, the effect of active perturbation from various molecular actions in the medium on this organization remains unclear. In this seminar, I will mainly focus on our recent investigations into how such activities influence the coordination of subnuclear compartments (SNCs, such as transcription factories) with chromatin and the compartmentalization of chromatin into eu- and heterochromatic regions, and discuss their biological implications. We have developed a polymer physics-based computational framework where chromatin is perturbed by a non-localized active mechanism mimicking the action of Topoisomerase-II enzyme. Using a self-developed GPU-based parallelized computer code and a newly introduced theoretical model, we demonstrate that SNC dynamics in this complex system can be described by a combination of three modes, each linked to different physical aspects of the embedding medium. Notably, the activity enhances SNC dynamics through a slow mode associated with chromatin-mesh remodeling. This offers new insights into the role of global active perturbations in target-searching processes [2]. Additionally, we report the emergence of characteristic compartmentalization features, viz., wall-like organization of euchromatin with negative nematic ordering of the euchromatic segments due to activity. These features cannot be captured by an equilibrium physics-based theory. This highlights the critical role of such active perturbations in chromatin organization [3]. Given that activity correlates with factors like aging and cell cycle, our studies may shed light on cell state[1]specific genome regulation. I will conclude my seminar with a brief discussion of my future research plan on ‘Integrative Nuclear Architecture’, which investigates the spatiotemporal characteristics of the nucleus as collective features arising from interconnected cellular components.

About The Speaker: Dr. Rakesh Das is a theoretical and computational biophysicist who employs concepts from condensed matter physics and non-equilibrium physics to investigate biological systems. During his Ph.D. at S. N. Bose National Centre for Basic Sciences, he explored collective features in active matter and obtained his degree in 2019. Following that, he joined Mechanobiology Institute at National University of Singapore, Singapore for his first postdoctoral position. Since November 2023, he has held a Postdoctoral Guest Scientist position at Max-Planck-Institute for the physics of Complex Systems in Dresden, Germany. He is interested in the Physics of various cellular systems.