{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/387526"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/387526","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Phase behaviour of multicomponent systems from computer simulations","abstract":"Knowing a material’s thermodynamic stability under different conditions, as summarised in a phase diagram, is of considerable practical importance with numerous technological applications, as well as helping us achieve a fundamental understanding of the chemistry and physics that governs the phase behaviour of a system. In this thesis, we investigate the phase behaviour of different biomolecular solutions and deep eutectic solvents, each having their own distinct characteristics and complexities. Firstly, we explore the process of biomolecular phase separation to form multicomponent biomolecular condensates, which are ubiquitous in cells and are crucial for the organisation and regulation of a range of fundamental biological processes. In particular, we focus on the phase separation of protein and RNA mixtures to form multiphasic condensates, and elucidate the key molecular driving forces for their formation as well as how their properties might be regulated. We propose an evolution approach coupling molecular-dynamics simulations to a genetic algorithm to design multilayered condensates with distinct compositions in each layer. By analysing the features of the sequences that give rise to multiphasic condensates, we find that the correct balance of homo- and heterotypic interactions must be achieved to stabilise the multilayered architecture, through the tuning of a combination of sequence composition, patterning, and/or length. These simple `rules' identified in our work and our approach to understanding the underlying physicochemical driving forces can thus enable the design of synthetic condensates to facilitate further study of their organisation and how their functionality might arise from structure. We also employ a multiscale modelling approach, in combination with experimental biochemical reconstitution and live cell imaging, to study multicomponent condensates of Polycomb proteins. We show that these Polycomb condensates assemble via a scaffold-client model and their stability and properties are sensitively regulated by its composition, as well as identify specific regions and residue pairs within the protein that contribute to their behaviour. Altogether, our results demonstrates the importance of valency and composition, and identifies the key molecular interactions that are essential in driving phase separation in the different systems considered. Lastly, we study the phase behaviour of deep eutectic solvents, an emerging class of green solvents characterised by large melting-point depressions near their eutectic composition. One thing of both fundamental as well as practical interest is predicting the phase diagrams of such eutectic systems, which could give us insight into how changes in the structure and composition of the components can alter phase behaviour and influence solvent properties, as well as guide the development of more transferable models that can be used to make accurate predictions. Here, we use free-energy methods and thermodynamic integration to characterise the liquidus line of the eutectic phase diagram of a mixture of choline chloride and urea, in order to better understand what governs the behaviour of deep eutectic solvents and how solvent properties can be tuned for various applications.","abstract_html":"Knowing a material’s thermodynamic stability under different conditions, as summarised in a phase diagram, is of considerable practical importance with numerous technological applications, as well as helping us achieve a fundamental understanding of the chemistry and physics that governs the phase behaviour of a system. In this thesis, we investigate the phase behaviour of different biomolecular solutions and deep eutectic solvents, each having their own distinct characteristics and complexities. Firstly, we explore the process of biomolecular phase separation to form multicomponent biomolecular condensates, which are ubiquitous in cells and are crucial for the organisation and regulation of a range of fundamental biological processes. In particular, we focus on the phase separation of protein and RNA mixtures to form multiphasic condensates, and elucidate the key molecular driving forces for their formation as well as how their properties might be regulated. We propose an evolution approach coupling molecular-dynamics simulations to a genetic algorithm to design multilayered condensates with distinct compositions in each layer. By analysing the features of the sequences that give rise to multiphasic condensates, we find that the correct balance of homo- and heterotypic interactions must be achieved to stabilise the multilayered architecture, through the tuning of a combination of sequence composition, patterning, and/or length. These simple `rules' identified in our work and our approach to understanding the underlying physicochemical driving forces can thus enable the design of synthetic condensates to facilitate further study of their organisation and how their functionality might arise from structure. We also employ a multiscale modelling approach, in combination with experimental biochemical reconstitution and live cell imaging, to study multicomponent condensates of Polycomb proteins. We show that these Polycomb condensates assemble via a scaffold-client model and their stability and properties are sensitively regulated by its composition, as well as identify specific regions and residue pairs within the protein that contribute to their behaviour. Altogether, our results demonstrates the importance of valency and composition, and identifies the key molecular interactions that are essential in driving phase separation in the different systems considered. Lastly, we study the phase behaviour of deep eutectic solvents, an emerging class of green solvents characterised by large melting-point depressions near their eutectic composition. One thing of both fundamental as well as practical interest is predicting the phase diagrams of such eutectic systems, which could give us insight into how changes in the structure and composition of the components can alter phase behaviour and influence solvent properties, as well as guide the development of more transferable models that can be used to make accurate predictions. Here, we use free-energy methods and thermodynamic integration to characterise the liquidus line of the eutectic phase diagram of a mixture of choline chloride and urea, in order to better understand what governs the behaviour of deep eutectic solvents and how solvent properties can be tuned for various applications.","abstract_has_math":false,"creators":["Chew, Pin Yu"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Reinhardt, Aleks","Collepardo-Guevara, Rosana"],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-04-16","date_published":"2025-04-16","updated_at":"2026-07-22T22:24:16Z","subjects":["Biomolecular phase separation","Deep eutectic solvents","Intrinsically disordered proteins","Molecular simulations","Phase behaviour"],"languages":[],"rights":[],"rights_urls":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/2ee91b9a-404c-46ce-ba39-ec62f71cc700/download","http://purl.org/NET/rdflicense/allrightsreserved"],"identifier_entries":[{"key":"dc:creator.authoridentifier","label":"Author Identifier","values":["0000000264016154"],"render_values":[{"text":"0000-0002-6401-6154","href":"https://orcid.org/0000-0002-6401-6154","code":true}]}]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.120276","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Reinhardt, Aleks","Collepardo-Guevara, Rosana"]},{"key":"dc:contributor.sponsor","label":"Sponsor","values":["Ernest Oppenheimer Studentship Winton Programme for the Physics of Sustainability Scholarship"]},{"key":"dc:creator","label":"Author","values":["Chew, Pin Yu"]},{"key":"dc:creator.authoridentifier","label":"Author Identifier","values":["0000000264016154"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2025-04-16"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/387526"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biomolecular phase separation","Deep eutectic solvents","Intrinsically disordered proteins","Molecular simulations","Phase behaviour"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/2ee91b9a-404c-46ce-ba39-ec62f71cc700/download","http://purl.org/NET/rdflicense/allrightsreserved"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.120276"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/7764839d-228b-4c21-a93b-7944b9eed247/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Knowing a material’s thermodynamic stability under different conditions, as summarised in a phase diagram, is of considerable practical importance with numerous technological applications, as well as helping us achieve a fundamental understanding of the chemistry and physics that governs the phase behaviour of a system. 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By analysing the features of the sequences that give rise to multiphasic condensates, we find that the correct balance of homo- and heterotypic interactions must be achieved to stabilise the multilayered architecture, through the tuning of a combination of sequence composition, patterning, and/or length. These simple `rules' identified in our work and our approach to understanding the underlying physicochemical driving forces can thus enable the design of synthetic condensates to facilitate further study of their organisation and how their functionality might arise from structure. We also employ a multiscale modelling approach, in combination with experimental biochemical reconstitution and live cell imaging, to study multicomponent condensates of Polycomb proteins. We show that these Polycomb condensates assemble via a scaffold-client model and their stability and properties are sensitively regulated by its composition, as well as identify specific regions and residue pairs within the protein that contribute to their behaviour. Altogether, our results demonstrates the importance of valency and composition, and identifies the key molecular interactions that are essential in driving phase separation in the different systems considered. Lastly, we study the phase behaviour of deep eutectic solvents, an emerging class of green solvents characterised by large melting-point depressions near their eutectic composition. One thing of both fundamental as well as practical interest is predicting the phase diagrams of such eutectic systems, which could give us insight into how changes in the structure and composition of the components can alter phase behaviour and influence solvent properties, as well as guide the development of more transferable models that can be used to make accurate predictions. Here, we use free-energy methods and thermodynamic integration to characterise the liquidus line of the eutectic phase diagram of a mixture of choline chloride and urea, in order to better understand what governs the behaviour of deep eutectic solvents and how solvent properties can be tuned for various applications."]},{"key":"dc:format.checksum.md5","label":"Dc Format Checksum Md5","values":["80b563a027517bc8d975ee395aa7fdc7","87eda9de84448d1f82354d60eee3eb5f"]},{"key":"dc:title","label":"Title","values":["Phase behaviour of multicomponent systems from computer simulations"]}]}],"canonical_facts":{"dc:contributor.advisor":["Reinhardt, Aleks","Collepardo-Guevara, Rosana"],"dc:contributor.sponsor":["Ernest Oppenheimer Studentship Winton Programme for the Physics of Sustainability Scholarship"],"dc:creator":["Chew, Pin Yu"],"dc:creator.authoridentifier":["0000000264016154"],"dc:date.issued":["2025-04-16"],"dc:description.abstract":["Knowing a material’s thermodynamic stability under different conditions, as summarised in a phase diagram, is of considerable practical importance with numerous technological applications, as well as helping us achieve a fundamental understanding of the chemistry and physics that governs the phase behaviour of a system. 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By analysing the features of the sequences that give rise to multiphasic condensates, we find that the correct balance of homo- and heterotypic interactions must be achieved to stabilise the multilayered architecture, through the tuning of a combination of sequence composition, patterning, and/or length. These simple `rules' identified in our work and our approach to understanding the underlying physicochemical driving forces can thus enable the design of synthetic condensates to facilitate further study of their organisation and how their functionality might arise from structure. We also employ a multiscale modelling approach, in combination with experimental biochemical reconstitution and live cell imaging, to study multicomponent condensates of Polycomb proteins. We show that these Polycomb condensates assemble via a scaffold-client model and their stability and properties are sensitively regulated by its composition, as well as identify specific regions and residue pairs within the protein that contribute to their behaviour. Altogether, our results demonstrates the importance of valency and composition, and identifies the key molecular interactions that are essential in driving phase separation in the different systems considered. Lastly, we study the phase behaviour of deep eutectic solvents, an emerging class of green solvents characterised by large melting-point depressions near their eutectic composition. One thing of both fundamental as well as practical interest is predicting the phase diagrams of such eutectic systems, which could give us insight into how changes in the structure and composition of the components can alter phase behaviour and influence solvent properties, as well as guide the development of more transferable models that can be used to make accurate predictions. Here, we use free-energy methods and thermodynamic integration to characterise the liquidus line of the eutectic phase diagram of a mixture of choline chloride and urea, in order to better understand what governs the behaviour of deep eutectic solvents and how solvent properties can be tuned for various applications."],"dc:format.checksum.md5":["80b563a027517bc8d975ee395aa7fdc7","87eda9de84448d1f82354d60eee3eb5f"],"dc:identifier.doi":["https://doi.org/10.17863/CAM.120276"],"dc:identifier.uri":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/7764839d-228b-4c21-a93b-7944b9eed247/download"],"dc:publisher.institution":["University of Cambridge"],"dc:relation.isreferencedby.uri":["https://www.repository.cam.ac.uk/handle/1810/387526"],"dc:rights":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/2ee91b9a-404c-46ce-ba39-ec62f71cc700/download","http://purl.org/NET/rdflicense/allrightsreserved"],"dc:subject":["Biomolecular phase separation","Deep eutectic solvents","Intrinsically disordered proteins","Molecular simulations","Phase behaviour"],"dc:title":["Phase behaviour of multicomponent systems from computer simulations"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Doctoral"],"dc:type.qualificationname":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-22T22:24:16Z"}