Emergence of Non-equilibrium Self-assembly of Simple Building Blocks via Negative Feedback

Afrose, Syed Pavel (2023) Emergence of Non-equilibrium Self-assembly of Simple Building Blocks via Negative Feedback. PhD thesis, Indian Institute of Science Education and Research Kolkata.

Text (PhD thesis of Syed Pavel Afrose (17RS017)) 17RS017.pdf - Submitted Version Restricted to Repository staff only Download (10MB)

Abstract

The present thesis, “Emergence of Non-equilibrium Self-assembly of Simple Building Blocks via Negative Feedback” deals with the design of non-equilibrium catalytic self-assemblies using simple building blocks based on amino acids and a heterocycle argued to be a plausible protonucleobase. Non-equilibrium generation of catalytic microphases has been achieved by the addition of simple molecules as chemical fuels. The self-assembled states show emergent properties along with augmentation of catalytic activity which provide negative feedback towards the assembly process by degrading the molecule that drives the assembly, reminiscent of the mechanism underlying the dynamic instability of microtubules. Further, the non-equilibrium assemblies have been utilized for temporal control over complex properties. Chapter 1 briefly introduces non-equilibrium self-assemblies with examples from Nature where non-equilibrium self-assemblies are generated when driven by activated substrates. The chapter also introduces the underlying mechanism behind the augmentation of catalytic activities in the substrate driven self-assembled state that leads to the coupling of self-assembly process with the substrate to product conversion for the realisation of non-equilibrium self-assembly. It also presents associated up-to-date literature review. Chapter 2 presents non-equilibrium self-assembly of a simple amino acid containing amphiphile driven by another amino acid based activated substrate. The substrate induced helical self-assembled state displays emergent catalytic property to degrade the substrate predominantly from the self-assembled state which provides negative feedback towards the stability of the assembled microphases, similar to the cytoskeleton proteins. Chapter 3 demonstrates the generation of nonequilibrium catalytic supramolecular assemblies of a simple heterocycle melamine, argued to be a plausible protonucleobase, driven by a thermodynamically activated ester. Formation of a reversible covalent linkage with an imidazole moiety installed negative feedback pathway and rendered the assemblies catalytic, realising a transient state that dissipated energy via accelerated hydrolysis of the activated ester. The nonequilibrium assemblies were further capable of temporally binding to hydrophobic guests for temporal modulation of photophysical properties and for control over release of the guest in bulk solution. Chapter 4 shows the non-equilibrium generation of microphases of a simple heterocycle argued to be a candidate for primitive protonucleobase, driven by a simple aromatic substrate. Notably, the assemblies could bind an amino acid building block which rendered the assemblies capable of activating a cofactor towards the oxidative degradation of the substrate which results in disassembly. The collaboration of the protonucleobase and amino acid building blocks results in the emergence of catalytic activity. Chapter 5 presents an overall summary of the work and describes the significant findings of these studies. In addition, a broad overview of the possible future directions has been discussed.

Actions (login required)

View Item