Topology, Symmetry and Mechanics: Deciphering and Controlling information flows in a living cell

Living organisms collect, preserve and transform information on complex spatiotem­poral bases. Take a living cell for instance, the signaling proteins are capable of forming patterns on lengths that are tens of thousands the molecular size. During force-generating processes such as cell divisions, both the spatial and temporal aspects of protein patterning convey essential physiology outcomes. While many advances focusing on the molecular complexity of such chemomechan­ical interactions have been made in recent years, it remains unclear to what extent they can be described and even predicted with the language of a physicist. That is, to decipher the structure and dynamics of the cellular information flows focusing on system-level topology and symmetry signatures, rather than the molecular and kinetic specificities. Taking a step further, with emerging experimental tools that allow for quantitative controls over the molecular interactions, the engineering of information flows towards violation of system-level physical symmetry remains an open pursuit. In this thesis, I present a series of studies in the chemomechanical Rho-actomyosin signaling process that takes place in P. Miniata starfish egg cells. In Chapter 1, I review this model system for its molecular components and physiological functions, highlighting the need of novel order parameters for characterizing the complex bio­chemical and biochemical changes. In Chapter 2, I show that the statistics and dynamics of topological defects embedded in Rho chemical patterns can be drawn an unexpected parallel to classical and quantum turbulent fluids. In Chapter 3, I further demonstrate a Bosonic symmetry between braided topological defects as well as the emergence of pair-scattering virtual particles on the cell membrane during sig­naling. In Chapter 4, I develop an optogenetic-based tool recruiting Rho-activating enzyme and use light to quantitatively control surface contraction waves that override wild type guiding cues and violate pole symmetry. In Chapter 5, I discuss the use of vibrational sound microscopy on non-invasively probing active fluctuations in the force-generating cell cortex. Finally, I conclude in Chapter 6 by discussing investi­gation of room-temperature novel physics in biological systems combining advanced biological tools and a condensed-matter theoretical approach.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Physics

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2022

Author dc:creator

• Liu, Jinghui

Advisor dc:contributor.advisor

• Fakhri, Nikta

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright MIT

Licence dc:rights.uri

• http://rightsstatements.org/page/InC-EDU/1.0/

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/150761

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/150761