Francesco Avanzini, Timur Aslyamov, Étienne Fodor, Massimiliano Esposito
{"title":"非理想反应-扩散系统的非平衡热力学:主动自组织的意义","authors":"Francesco Avanzini, Timur Aslyamov, Étienne Fodor, Massimiliano Esposito","doi":"arxiv-2407.09128","DOIUrl":null,"url":null,"abstract":"We develop a framework describing the dynamics and thermodynamics of open\nnon-ideal reaction-diffusion systems, which embodies Flory-Huggins theories of\nmixtures and chemical reaction network theories. Our theory elucidates the\nmechanisms underpinning the emergence of self-organized dissipative structures\nin these systems. It evaluates the dissipation needed to sustain and control\nthem, discriminating the contributions from each reaction and diffusion process\nwith spatial resolution. It also reveals the role of the reaction network in\npowering and shaping these structures. We identify particular classes of\nnetworks in which diffusion processes always equilibrate within the structures,\nwhile dissipation occurs solely due to chemical reactions. The spatial\nconfigurations resulting from these processes can be derived by minimizing a\nkinetic potential, contrasting with the minimization of the thermodynamic free\nenergy in passive systems. This framework opens the way to investigating the\nenergetic cost of phenomena such as liquid-liquid phase separation,\ncoacervation, and the formation of biomolecular condensates.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"6 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Nonequilibrium Thermodynamics of Non-Ideal Reaction-Diffusion Systems: Implications for Active Self-Organization\",\"authors\":\"Francesco Avanzini, Timur Aslyamov, Étienne Fodor, Massimiliano Esposito\",\"doi\":\"arxiv-2407.09128\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"We develop a framework describing the dynamics and thermodynamics of open\\nnon-ideal reaction-diffusion systems, which embodies Flory-Huggins theories of\\nmixtures and chemical reaction network theories. Our theory elucidates the\\nmechanisms underpinning the emergence of self-organized dissipative structures\\nin these systems. It evaluates the dissipation needed to sustain and control\\nthem, discriminating the contributions from each reaction and diffusion process\\nwith spatial resolution. It also reveals the role of the reaction network in\\npowering and shaping these structures. We identify particular classes of\\nnetworks in which diffusion processes always equilibrate within the structures,\\nwhile dissipation occurs solely due to chemical reactions. The spatial\\nconfigurations resulting from these processes can be derived by minimizing a\\nkinetic potential, contrasting with the minimization of the thermodynamic free\\nenergy in passive systems. This framework opens the way to investigating the\\nenergetic cost of phenomena such as liquid-liquid phase separation,\\ncoacervation, and the formation of biomolecular condensates.\",\"PeriodicalId\":501325,\"journal\":{\"name\":\"arXiv - QuanBio - Molecular Networks\",\"volume\":\"6 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-07-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"arXiv - QuanBio - Molecular Networks\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/arxiv-2407.09128\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - QuanBio - Molecular Networks","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2407.09128","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Nonequilibrium Thermodynamics of Non-Ideal Reaction-Diffusion Systems: Implications for Active Self-Organization
We develop a framework describing the dynamics and thermodynamics of open
non-ideal reaction-diffusion systems, which embodies Flory-Huggins theories of
mixtures and chemical reaction network theories. Our theory elucidates the
mechanisms underpinning the emergence of self-organized dissipative structures
in these systems. It evaluates the dissipation needed to sustain and control
them, discriminating the contributions from each reaction and diffusion process
with spatial resolution. It also reveals the role of the reaction network in
powering and shaping these structures. We identify particular classes of
networks in which diffusion processes always equilibrate within the structures,
while dissipation occurs solely due to chemical reactions. The spatial
configurations resulting from these processes can be derived by minimizing a
kinetic potential, contrasting with the minimization of the thermodynamic free
energy in passive systems. This framework opens the way to investigating the
energetic cost of phenomena such as liquid-liquid phase separation,
coacervation, and the formation of biomolecular condensates.