Abstract

The physics of Topologically Modified polymers (ToMo polymers) is of interest because of its direct relevance to understand chromosome organization in cells. We have been investigating ToMo ring polymers, which have internal loops along the chain contour, and its emergent organization inside cylindrical confinement. We used these localization properties of suitably “designed” polymer topologies to understand the underlying spatio-temporal dynamics of chromosomes in the bacterial cell E. coli [1,2,3]. In this presentation, I will be focusing on the principles of entropic organization of some segments of the polymer along the long axis of the cylinder. Further investigations show how (i) we can modulate entropic interactions between internal loops to induce alignment of polymers segments along the cylinder long-axis, reminiscent of Ising like interactions of magnetic spin and (ii) how suitably “designed” topological modifications can be used to localize certain sections of a polymers to the regions closer to the surface of a sphere [4].  [1] D. Mitra, Shreerang Pande, A. Chatterji. Phys. Rev.E, 106, 054502 (2022).  [2] D. Mitra, Shreerang Pande, A. Chatterji. Soft Matter, 18, 5615 (2022).  [3] Shreerang Pande, D. Mitra, A. Chatterji. Phys. Rev E, 110, 054401 (2024).  [4] K. Roychoudhury, Shreerang Pande, Indrakanty S.S., D. Mitra, A. Chatterji, arXiv:2501.02276 – Undergoing review in Phys. Rev E