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Voltage-Driven Polyelectrolyte Complexation Inside a Nanopore
No full textThis thesis investigates how a pair of oppositely charged macromolecules can be driven by an electric field to form a polyelectrolyte complex inside a nanopore. To observe and isolate an individual complex pair, a model protein nanopore, embedded in artificial phospholipid membrane, allowing compartmentalization (cis/trans) is employed. A polyanion in the cis and a polycation in the trans compartments are subjected to electrophoretic capture by the pore. We find that the measured ionic current across the pore has a distinguishable signature of complex formation, which is different from the signature of the passage of individual molecules through the pore. The ionic current signature allows us to detect the interaction between the two oppositely charged macromolecules and thus, enables us to measure the lifetime of the complex inside the nanopore. After showing that we can isolate a complex pair in the nanopore, we studied the effects of molecular identity on the nature of interaction in different complex pairs. In contrast to the irreversible conductance state of the alpha-hemolysin channel in the complexation of poly-styrene-sulfonate (PSS) and poly-L-lysine (PLL), a reversible conductance state is observed during complexation between single stranded DNA (ssDNA) and PLL. This suggests that there is a weak interaction between ssDNA and PLL, when compared to the interaction in a PSS–PLL complex. Analysis of the PSS-PLL complexation events and its lifetime inside the nanopore supports a four step-mechanism: (i) The polyanion is captured by the pore, (ii) the polyanion starts threading through the pore. (iii) The polycation is captured, a complex pair is formed in the pore, and the polyanion slides along the polycation. (iv) The complex pair can be pulled through the pore into the trans compartment or it can dissociate. Additionally, we have developed a simple theoretical model, which describes the lifetime of the complex inside the pore. The observed reversible two-state conductance across the alpha-hemolysin channel during ssDNA-PLL complexation, is described as the binding/unbinding of PLL during the translocation of ssDNA. This enables us to evaluate the apparent rate constants for association/dissociation and equilibrium dissociation constants for the interaction of PLL with ssDNA. This thesis throws light on the behavior of polyelectrolyte complexes in an electric field and enhances our understanding of the electrical aspects of inter-macromolecular interactions, which plays an extremely important role in the organization of macromolecules in the crowded and confined cellular environment.ChemistryDoctor of Philosophy (Ph.D.
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Translocations of Ring and Linear Polymers & Polyelectrolyte Brush in Salty Solution
No full textWe study the electric-field-driven translocation of polymers with ring architecture, i.e. circular polymers, in comparison with their linear counterpart. We construct the free energy landscape for ring and linear polymer translocations respectively, in the context of Fokker-Planck formalism. Non-monotonicity of translocation time as function of polymer length is observed from ring polymer, which is enhanced by pore- polymer attraction. The external electric driving force and pore-polymer interaction are the tuning parameter of relative translocation time of ring and linear polymers. We study the polyelectrolyte brush in monovalent salt using self-consistent-field- theory. We confirmed the step-function polymer profile in strong-stretched state. We examine the ion distribution and assure the trapping counterions by the brush. We also study the polyelectrolyte brush in divalent salt using explicit Donnan equi- librium and free energy minimization. We calculation the brush height and degree of ionization self-consistently as function divalent salt concentration. We explained the non-monotonic behavior of brush height versus salt concentration (observed in experiment) by charge reversal.PhysicsDoctor of Philosophy (Ph.D.
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Phase Transitions and Self-Assembly of Charged Polymer Solutions
Get PDFCharged polymers ubiquitously play a crucial role in numerous biological and synthetic systems, exhibiting diverse phases and self-assembly behaviors due to the entanglement of polymer connectivity and long-range electrostatic interactions. Charged polymer physics delves into understanding their highly coupled and non-linear response, shedding light on comprehending biological systems composed of charged biopolymers. Inspired by biomolecular condensates, membrane-less organelles assembled by intrinsically disordered proteins within cells, we aim to explore the phases and self-assembly in complex charged polymer solutions, where complexities stem from the chemical sequences and physical associations of polymers. These complexities cause difficulties in responding to the growth interest of biomolecular condensates. Employing the field theory formalism and statistical properties of conformations, we address the connectivity and interaction into the spatial correlation of monomer concentration, leading to the Landau free energy predicting the formations of phases and self-assembly. This thesis comprises two works. The first work focuses on predicting the stability, size, and morphology of microphase separation for sequence-specified charged polymers, resulting in machinery for microphases for general sequences. In the second work, utilizing polyzwitterions as a simplified model for associative charged polymers, we explore the thermoreversible behaviors of electric-dipole-driven macrophase separation and gelation. Furthermore, our use of the renormalization group reveals that concentration fluctuations near critical points deviate from the Ising universality class due to the presence of associations. These results can facilitate future investigations on more complex systems in biological and synthetic realms with suitable modifications.Doctor of Philosophy (Ph.D.
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Frontiers in the Self-Assembly of Charged Macromolecules
Get PDFThe self-assembly of charged macromolecules forms the basis of all life on earth. From the synthesis and replication of nucleic acids, to the association of DNA to chromatin, to the targeting of RNA to various cellular compartments, to the astonishingly consistent folding of proteins, all life depends on the physics of the organization and dynamics of charged polymers. In this dissertation, I address several of the newest challenges in the assembly of these types of materials. First, I describe the exciting new physics of the complexation between polyzwitterions and polyelectrolytes. These materials open new questions and possibilities within the context of drug packaging and delivery, a selection of which are addressed in the second chapter. In the third chapter, fundamental questions about the chemical characteristics that influence the phase separation of polyzwitterions and polyelectrolytes are explored systematically. Finally, in the fourth chapter, the phenomenon of coacervation is harnessed in the electrochemical context, and several types of measurements of these properties are described in detail. This work represents the current state-of-the-art in the field of charged systems, and future work to create technologies (in the biomedical context, in particular) can all apply the fundamental results illuminated herein.Polymer Science and EngineeringDoctor of Philosophy (Ph.D.
Applications of Polymer Bioconjugates
No full textInspired by natural functional polymers, which are often very well-defined and bear high-level of information, scientists have undertaken to develop synthetic replicas based on polymer bioconjugates, that can be harnessed for diverse applications. In this regard, excellent strategies that provide the necessary scope for the synthesis and utility of polymer bioconjugates have been developed. Detailed evaluation to determine the influence of chemical factors that impact polymers’ synthesis, alongside physical aspects necessary for their utility have been carried out. In this chapter, we discuss the current methodologies that allow for controlled synthesis of polymer bioconjugates, as their application in the biomedical field.</p
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Dynamics and structure of polyelectrolyte complexes
No full textInteraction of charged macromolecules among themselves and with charged interfaces in salty aqueous medium is a common phenomenon prevalent in biology and synthetic systems. We have addressed several inter-related issues in this general context. First we present a theory of adsorption of polyelectrolytes on the interior and exterior surfaces of a charged spherical vesicle. We derive the critical adsorption condition and the density profile of the polymer in terms of various characteristics of the polymer, vesicle, and the solution, such as the length and charge density of polymer, the radius and charge of the vesicle, the salt concentration of the solution, and the dielectric constant of the solvent. We have used the Wentzel-Kramers-Brillouin (WKB) method to solve the equation for the probability distribution function of the chain. For the polyelectrolyte inside the vesicle, the competition between the loss of conformational entropy and the attractive electrostatic energy between the vesicle and the polyelectrolyte, results in two different encapsulated states. By considering the adsorption from outside, we calculate the entropic and the energetic contributions to the free energy for the polymer being adsorbed in the interior and exterior states and the free energy penalty for the polyelectrolyte being expelled from the vesicle. The kinetics of the polyelectrolyte complexation have been studied using the Smoluchowski equation. We derive the mean distance between two oppositely charged polyelectrolytes and the reaction rate for the complexation in terms of the salt concentration and polyelectrolyte characteristics. We also calculate the half-time for the complexation process at different salt concentrations and initial distances.\\ For a vesicle, we have derived the free energy landscape of translocation through the pore by accounting for the energy penalty of bending and stretching the vesicle from due to deformation by pore. Using the Fokker-Planck formalism, we have calculated the average translocation time corresponding to the various free energy landscapes representing different parameter sets. We also discuss the dependencies of the average translocation time on the strength of the external force, vesicle size, bending and stretching moduli of the vesicle, and the radius and length of the pore. Finally, we formulate a theory of the effects of long-range interactions on surface tension and spontaneous curvature of proteinaceous shells based on the general Deryaguin-Landau-Verwey-Overbeek (DLVO) theory. we have derived the renormalized spontaneous curvature as a function of capsid's inner and outer charge density and solution properties.PhysicsDoctor of Philosophy (Ph.D.
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KINETICS OF THE CRYSTAL-MELT PHASE TRANSFORMATION IN SEMICRYSTALLINE POLYMERS
No full textThe assembly of long-chain polymers into an ordered state is a process that has puzzled polymer scientists for several decades. A process that is largely controlled by the strength of intermolecular attractions in small molecular systems, this crystallization in the case of polymers is controlled by a competition between the aforementioned force of attraction between monomers and the formidable conformational entropy of polymer chains. Any factor that affects this conformational entropy, whether that is an equilibrium thermodynamic factor or a kinetic factor, has the ability to control polymer crystallization. In this thesis, we focus on understanding the underlying kinetic processes that occur during this phase transition from liquid polymer to the solid semicrystalline state using computer simulations and some experiments. We first investigate the effect of chain ends on crystallization by comparing between the crystallization behavior of linear and ring polymers of the same molecular weight using Langevin dynamics simulations. We find single linear polymers to melt at much larger temperatures than single ring polymers, in apparent contradiction of equilibrium thermodynamic arguments. We study several kinetic factors, and find that they explain this discrepancy. We then study the melting of linear polymers by Langevin dynamics simulations to understand the processes occurring during their disassembly. We find that polymer chains go through a globular metastable state at lower melting temperatures before transforming to expanded coils at higher melting temperatures. We also compute a free energy landscape using parallel tempering Langevin dynamics simulations, and confirm the existence of metastable states in the crystalline-amorphous reaction coordinate. We look at the crystallization of triblock copolymers using Langevin dynamics simulations, in which crystallizable blocks are separated by non-crystallizable ones to understand the effect of impurities. We investigate the effects of tailored interblock and solvent-block interactions, and discover a rich system in which the final semicrystalline polymer forms an array of morphologies. We also experimentally investigate the crystallization of calcium oxalate, which is a primary constituent of kidney stones. We crystallize calcium oxalate and show images of crystals obtained from an optical microscope. Lastly, we extend the scope of our studies into the effect of impurities by looking at crystallization of branched polymers. We discover that branches affect the kinetics of crystallization when they are in close proximity with one another.Chemical EngineeringDoctor of Philosophy (Ph.D.
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