Complexity via Minimal Building Blocks: Self-organization under Equilibrium and Non-equilibrium Conditions

Reja, Antara (2023) Complexity via Minimal Building Blocks: Self-organization under Equilibrium and Non-equilibrium Conditions. PhD thesis, Indian Institute of Science Education and Research Kolkata.

Text (PhD thesis of Antara Reja (17RS058)) 17RS058.pdf - Submitted Version Restricted to Repository staff only Download (9MB)

Abstract

The present thesis, “Complexity via Minimal Building Blocks: Self-organization under Equilibrium and Non-equilibrium Conditions”, discusses the supramolecular assembly via minimal building blocks, under different thermodynamic regimes within the field of systems chemistry. I explore both traditional equilibrium-driven systems and energy-demanding assemblies, including those that exist in kinetic traps and systems that are in far-from-equilibrium states. Further the functional potentials of these systems are highlighted and how complexity can arise in a system through self-organization of minimal building blocks is discussed. Chapter 1 briefly introduces supramolecular assembly under different thermodynamic regimes and associated up-to-date literature review. In chapter 2 an equilibrium system has been described where a lipidated short peptide-amphiphile forms homogenous nanotubular structure that is stable under equilibrium conditions. The assemblies show excellent selectivity for substrates and drive the formation of a specific aldol adduct from a pool of reactants, signifying the importance of such systems during early evolution. Chapter 3 describes a kinetically trapped system, where light-responsive molecular cofactor bound to short peptide-based assemblies can show proficient C-C bond catalysis (retro-aldolase) under non-equilibrium condition. Further, latent activity of guest bound peptide assemblies is utilized for the in-situ generation of a light-sensitive cofactor that subsequently modulates the retro-aldolase activity, creating a reaction network. Chapter 4 focuses on far-from-equilibrium assemblies, where a single amino acid/dipeptide-based system can self-assemble and oscillate in the absence of evolved biocatalysts. This system exploits pH-driven non-covalent assembly and time-delayed accelerated catalysis from the self-assembled state to install orthogonal feedback loops. In chapter 5 a roadmap towards non-equilibrium to equilibrium assemblies is presented. A peptide amphiphile in the presence of an aldehyde ester leads to the emergence of the non-equilibrium assembly, which eventually collapses to the equilibrium assembly.

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