{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/150761"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/150761","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Topology, Symmetry and Mechanics: Deciphering and Controlling information flows in a living cell","abstract":"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.","abstract_html":"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.","abstract_has_math":false,"creators":["Liu, Jinghui"],"institution":"Massachusetts Institute of Technology","degree_name":"Doctoral","degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Physics","school":null,"contributors":[],"advisors":["Fakhri, Nikta"],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-09","date_published":"2022-09","updated_at":"2026-07-22T22:21:12Z","subjects":[],"languages":[],"rights":["In Copyright - Educational Use Permitted","Copyright MIT"],"rights_urls":["http://rightsstatements.org/page/InC-EDU/1.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/1721.1/150761","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Fakhri, Nikta"]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. 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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."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Ph.D."]},{"key":"dc:title","label":"Title","values":["Topology, Symmetry and Mechanics: Deciphering and Controlling information flows in a living cell"]}]}],"canonical_facts":{"dc:contributor.advisor":["Fakhri, Nikta"],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Physics"],"dc:creator":["Liu, Jinghui"],"dc:date.accessioned":["2023-05-17T17:40:52Z"],"dc:date.available":["2023-05-17T17:40:52Z"],"dc:date.issued":["2022-09"],"dc:description.abstract":["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."],"dc:description.degree":["Ph.D."],"dc:identifier.uri":["https://hdl.handle.net/1721.1/150761"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["In Copyright - Educational Use Permitted","Copyright MIT"],"dc:rights.uri":["http://rightsstatements.org/page/InC-EDU/1.0/"],"dc:title":["Topology, Symmetry and Mechanics: Deciphering and Controlling information flows in a living cell"],"dc:type":["Thesis"],"thesis:degree_name":["Doctoral","Doctor of Philosophy"]},"updated_at":"2026-07-22T22:21:12Z"}