Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

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Systems known as complex materials have key attributes that contribute to their designation as "complex''. For example, evolving dynamical properties add complexity, as is observed in supercooled liquids. Polymers and proteins are structurally complex as they can fold in different conformations, with these different conformations affecting different biological functions or physical properties. Complex materials generally have interesting macroscopic properties that are difficult to predict from their microscopic (molecular) constituents. The connection between microscopic features and macroscopic properties in these materials has been a subject of study for decades, yet the ability to wield strong predictive power in these materials remains elusive. Imaging can provide information in both space and time necessary to understand how the microscopic details in these materials yield the observed macroscopic properties. Moreover, time-sequenced imaging allows one to understand how these properties might evolve. To image these details however, requires high resolution in both time and space. Unfortunately, obtaining images and extracting information from these images becomes quite difficult as the length scales of interest become small, especially when signal-to-background ratios are low. My dissertation work addresses the challenge of extracting such information by developing quantitative methods to circumvent obstacles related to obfuscation from low signal as well as the diffraction limit, with high-throughput and high-resolution. I apply these techniques towards the study of the following complex materials via imaging: (1) single molecules rotating in a supercooled liquid (2) conjugated polymers containing multiple emitters within the diffraction limit (3) solvent vapor annealing mediated conjugated polymer aggregation and (4) collagen gels during their formation and perturbation. The first chapter describes how the local dynamics in a supercooled liquid may be assessed by the rotations of single-molecule probes. To resolve rotations however, requires splitting the fluorescence signal from single-molecules into orthogonal polarizations thereby reducing the already low signal-to-background ratio (SBR) expected from single-molecule experiments. The data is further complicated by instances of photoblinking and out-of-plane rotation, when only background signal is present. A convenient method for excluding background signal was developed via a Monte Carlo simulation for discriminating points in the trajectory composed only of background signal that is robust to SBR. These simulations also showed an SBR dependance for the accuracy of the values extracted from rotational autocorrelation functions. This method was used experimentally to directly demonstrate ergodicity in supercooled liquids. The next chapter focuses on conjugated polymers, which display a complex relationship between chain conformation and photophysics. This conformational complexity exists even at the single-chain level, obscuring the understanding of how excitons behave in the bulk, such as in a device. Understanding this relationship however, is difficult as conformation and photophysics are hard to access in operando not only because a single conjugated polymer chain is smaller than the diffraction limit, but also because a fluorescing conjugated polymer emits light from many locations. The overall conformation is typically assessed using polarization modulation measurements, which only provide mesoscale information about a chain's conformation. A super-resolution method was developed to map the distribution of emitters and trace out single-chain conformation. The extracted radii of gyration for these single-chains matched well with polymer theory. Chapter three describes the development of experimental and image analytical tools to bridge single-chain studies of photophysics in conjugated polymer, to the photophysics that might be observed in a conjugated polymer device where chain-chain contacts and high levels of local ordering may be present. It has been shown previously that solvent vapor annealing can be used to prepare conjugated polymer aggregates of various levels of internal ordering. However, solvent vapor annealing is a process that is difficult to control and difficult to evaluate. Therefore, a first-of-its-kind apparatus was constructed that can generate and deliver solvent vapor in a controlled fashion to swell polymer films while monitoring both film dynamics by fluorescence imaging as well as swelling extent via a quartz crystal microbalance. Fluorescent images acquired during aggregation showed heterogeneous diffusion among aggregates, possibly indicating heterogeneous sizing. Fluorescent characterization of presumably differently sized aggregates indicates a possible emergent quenching phenomenon in a bulk conjugated polymer material. The final chapter of this dissertation describes an effort to characterize dynamics in collagen gels. Collagen gels form through a complex sol-gel process precipitated by nucleation and growth fibrillogenesis. To probe the long length scales of interest here, single-molecule methods were not practical. Instead, an optical flow algorithm was explored to detect key physical events in the evolving system. One effort aims to characterize the dynamics of the early gelation process. In particular, the optical flow measurements provide a high-resolution measure for the moment at which the sol-gel transition occurs. Another application involves the use of optical flow to observe distortions in the collagen network while it is undergoing strain stiffening. Preliminary studies show that at critical strain, local breaks in the gel propagate throughout the gel until the gel completely loses its ability to sustain stress. In general, the ability to quantify details about complex materials from imaging data can be quite a complex endeavor itself, requiring awareness of the physical phenomena of interest, how said phenomena manifests optically, and the use and development of appropriate algorithms. As described in this dissertation, the proper use and/or development of the proper image analysis methods allow for extraction of key information from dense data.

Static measures such as density and entropy, which are intimately connected to structure, have featured prominently in modern thinking about the dynamics of the liquid state. In this dissertation, we explore the connections between self-diffusivity, density, available space, and excess entropy in two non-trivial problems in liquid state theory, confined and supercooled liquids. We present exact simulation data for the relationship between self-diffusivity and excess entropy for a wide range of simple of simple fluids (i.e. hard-sphere, Lennard-Jones and square-well) confined to pores with a variety of different sizes and fluid-wall interations. Our main finding is that, at a given temperature, self-diffusivity of the confined fluids collapses onto the bulk behavior when plotted versus excess entropy. In other words, the only information required to "predict" the implications of confinement for the single-particle dynamics is the bulk fluid behavior at a given temperature and the excess entropy of the confined fluid. This should prove practically useful given that the bulk behavior is well known for these fluid systems, and the excess entropy of the confined fluids can be readily estimated from classical density functional theory. We also show that the self-diffusivity of the confined fluids approximately collapses onto the data for the corresponding bulk fluid when plotted versus the average packing fraction (which is based on total, rather than center accessible volume). For continuous interaction potentials such as Lennard-Jones, calculation of effective packing fraction requires knowledge of both the number density of the fluid and a temperature-dependent Boltzmann diameter associated with the repulsive part of the interparticle interactions. We suggest a way to calculate this effective diameter, which to a very good approximation, collapse the temperature- and density-dependent data for the self-diffusivity of the bulk Lennard-Jones fluid onto hard-sphere fluid data plotted versus the fluid's effective packing fraction. Finally, we found that the self-diffusivities of several model systems in their supercooled state also scale exponentially not only with the excess entropy, but also with the two-body contribution to the excess entropy obtained from the pair correlation function of the fluid. The latter observation is particularly interesting because it provides direct evidence of a quantitative link between the dynamics and the average structural order of supercooled liquids. Whether such a connection could indeed be discovered is part of a long-standing question in the study of liquids. / text

Thesis advisor: Udayan Mohanty / The stabilization of particular conformations of protein and nucleic acid structure is believed to play an important role in many important biological functions. In chapter one, the α -helical conformation and structural stability of single and double stapled all- hydrocarbon cross-linked p53 peptides when bound and unbound to MDM2 are investigated. Our study provides a comprehensive rationalization of the relationship between peptide stapling strategy, the secondary structural stability, and the binding affinity of p53-MDM2 complex. In chapter two, we study counterion-mediated collapse of a strongly charged model polyelectrolyte chain by Group-II divalent metal cations using coarse-grained Brownian dynamics simulations. Polyelectrolyte effects govern the association of counterions with the chain. Large ions are less effective in counterion condensation than small ions. However, upon counterion condensation, the reduction of the backbone charge is independent of size of the metal cations. Above a threshold value of Coulomb strength parameter, counterion release entropy drives the formation of counterion-induced compact states. In chapter three, the nature of surface tension in the random first order theory of supercooled liquid is analyzed within the framework of Landau-Lifshitz fluctuation theory. We show that the surface tension of a droplet satisfies the differential equation 4πr2(dσ)+ 8πrσ(r)− Br1/2 = 0 , where B/ T = 12πkBcv , T is temperature, kB is dr Boltzmann constant, and cv is heat capacity. A consequence is that the slope of the relaxation time at the glass transition temperature, i.e., the fragility index, is expressed as the square of the ratio of heat capacity and configurational entropy of the supercooled liquid. When backbone extended nucleosides are incorporated into a double helix, a unique helical structure is formed. In chapter four, we find that the predicted stability of modified backbone DNA strands in aqueous solution is in good agreement with experimental melting temperature data. The incorporation of extended backbone nucleosides into a duplex results in elongation of the end-to-end chain distance due to the distortion of the B-DNA conformation at the mutated base-pair insertion. We also find that the modified backbone helical twist is approximately 40 degrees, larger than B-DNA helical twist and closer to the twist angle predicted for D-form DNA. The folding of RNA tertiary structure has been described as an equilibrium between partially folded I (intermediate) states, and the fully folded native conformation, or N state. RNA is highly sensitive to the ionic environment due to its negative charge, and tertiary structures tend to be strongly stabilized by Mg2+. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. In chapter 5, we present a generalized Manning condensation model of RNA electrostatics for studying the Mg2+-induced RNA folding of the 58mer ribosomal fragment. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Doctor of Philosophy (PhD) / The glass-transition traverses continuously from liquid to solid behaviour, yet the role of structure in this large and gradual dynamic transition is poorly understood. This thesis presents a theoretical study of the relationship between structure and dynamics in two-dimensional glass-forming alloys, and provides new tools and real-space insight into the relationship at a microscopic level. The work is divided into two parts. Part I is concerned with the role of structure in the appearance of spatially heterogeneous dynamics in a supercooled glass-forming liquid. The isoconfigurational ensemble method is introduced as a general tool for analysing the effect that a configuration has on the subsequent particle motion, and the dynamic propensity is presented as the aspect of structural relaxation that can be directly related to microscopic variations in the structure. As the temperature is reduced, the spatial distribution of dynamic propensity becomes increasingly heterogeneous. This provides the first direct evidence that the development of spatially heterogeneous dynamics in a fragile glass-former is related to spatial variations in the structure. The individual particle motion also changes from Gaussian to non- Gaussian as the temperature is reduced, i.e. the configuration expresses its character more and more intermittently. The ability of several common measures of structure and a measure of structural ‘looseness’ to predict the spatial distribution of dynamic propensity are then tested. While the local coordination environment, local potential energy, and local free volume show some correlation with propensity, they are unable to predict its spatial variation. Simple coarse-graining does not help either. These results cast doubt on the microscopic basis of theories of the glass transition that are based purely on concepts of free volume or local potential energy. In sharp contrast, a dynamic measure of structural ‘looseness’ - an isoconfigurational single-particle Debye-Waller (DW) factor - is able to predict the spatial distribution of propensity in the supercooled liquid. This provides the first microscopic evidence for previous correlations found between short- and long-time dynamics in supercooled liquids. The spatial distribution of the DW factor changes rapidly in the supercooled liquid and suggests a picture of structural relaxation that is inconsistent with simple defect diffusion. Overall, the work presented in Part I provides a real-space description of the transition from structure-independent to structure-dependent dynamics, that is complementary to the configuration-space description provided by the energy landscape picture of the glass transition. In Part II, an investigation is presented into the effect of varying the interparticle potential on the phase behaviour of the binary soft-disc model. This represents a different approach to studying the role of structure in glass-formation, and suggests many interesting directions for future work. The structural and dynamic properties of six different systems are characterised, and some comparisons are made between them. A wide range of alloy-like structures are formed, including substitutionally ordered crystals, amorphous solids, and multiphase materials. Approximate phase diagrams show that glass-formation generally occurs between competing higher symmetry structures. This work identifies two new glass-forming systems with effective chemical ordering and substantially different short- and medium-range structure compared to the glassformer studied in Part I. These represent ideal candidates for extending the study presented in Part I. There also appears to be a close connection between quasicrystal and glass-formation in 2D via random-tiling like structures. This may help explain the experimental observation that quasicrystals sometimes vitrify on heating. The alignment of asymmetric unit cells is found to be the rate-limiting step in the crystal nucleation and growth of a substitutionally ordered crystal, and another system shows amorphous-crystal coexistence and appears highly stable to complete phase separation. The generality of these results and their implications for theoretical descriptions of the glass transition are also discussed.

It has been reported that the Zr-based amorphous alloys exhibit high corrosion resistance, good mechanical properties, better thermal stability and good glass-forming ability. The thermal properties of the Zr-Al-Cu-Ni amorphous alloys could be improved by adding boron and silicon that also has been reported. Therefore, the Zr-Al-Cu-Ni amorphous alloys are chosen as the base materials for investigating the effect of the thermal properties by adding boron and silicon at the same time. According to the results of the experiment, the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons with the highest GFA index (g value) and the value is 0.42; the maximum supercooled liquid region (DTx) is about 85 K for the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons. For the isothermal analysis or non-isothermal analysis, the Avrami index (n value) is not constant, and the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons with the largest activation energy which was more than 300 kJ/mol. When the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons were heated to 721 K and held for 4000 seconds, the crystallized phases were ZrO2 with orthorhombic structure and Zr2Ni with tetragonal structure. When the Zr62Al7.5Cu17.5Ni10B2Si1 amorphous alloy ribbons were heated to 724 K and held for 4000 seconds, besides the ZrO2 phase with orthorhombic structure and the Zr2Ni phase with tetragonal structure, a Zr2Ni crystallized phase with cubic structure is also included. According to the observation of the TEM image for heating Zr62Al7.5Cu17.5Ni10B2Si1 amorphous alloy ribbons to 694 K and held for 4000 seconds, there are many grains distribute in the amorphous matrix, and the grain size is about 20 ~40 nm.

Water is abundant on earth and in the atmosphere and the most crucial liquid for life as we know it. It has been subject to rather intense research since more than a century and still holds secrets about its molecular structure and dynamics, particularly in the supercooled state, i. e. the metastable liquid below its melting point.  This thesis is concerned with different aspects of water and is written from a theoretical perspective. Simulation techniques are used to study structures and processes on the molecular level and to interpret experimental results. The evaporation kinetics of tiny water droplets is investigated in simulations with focus on the cooling process associated with evaporation. The temperature evolution of nanometer-sized droplets evaporating in vacuum is well described by the Knudsen theory of evaporation. The principle of evaporative cooling is used in experiments to rapidly cool water droplets to extremely low temperatures where water transforms into a highly structured low-density liquid in a continuous and accelerated fashion. For water at ambient conditions, a structural standard is established in form of a high precision radial distribution function as a result of x-ray diffraction experiments and simulations. Recent data even reveal intermediate range molecular correlations to distances of up to 17 Å in the bulk liquid. The barium fluoride (111) crystal surface has been suggested to be a template for ice formation because its surface lattice parameter almost coincides with that of the basal plane of hexagonal ice. Instead, water at the interface shows structural signatures of a high-density liquid at ambient and even at supercooled conditions. Inelastic neutron scattering experiments have shown a feature in the vibrational spectra of supercooled confined and protein hydration water which is connected to the so-called Boson peak of amorphous materials. We find a similar feature in simulations of bulk supercooled water and its emergence is associated with the transformation into a low-density liquid upon cooling. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.</p>

A new technique, named Vertical Profile Indicator (VPI), which uses the vertical structure of the reflectivity profile to delineate regions most likely to have supercooled liquid water content (SCLWC) within the precipitation field, was developed. When the aircraft flew in the "active regions" (as defined by the VPI technique) it was found that 90% of the time significant amounts of SCLWC were observed. / Using Doppler and "Quasi-Doppler" radar data, high convergence cores (> 3.0 x 10('-3) s('-1)) and updraft activity were observed to occur preferentially in the "active regions". During the 1981 winter-spring period of the Precipitation Enhancement Project in the Duero Basin of Spain percentages of "active regions" in relation to the whole precipitation field, and in relation to the total radar observation area, did not exceed 47% and 18% respectively. / The VPI technique provides information which may be used to direct research aircraft to cloud regions containing SCLWC to allow measurements of the time evolution of their microphysical state. These measurements would permit a better estimation of the residence time of the SCLWC and its removal rates. This is a key parameter for better understanding the microphysical properties of clouds and consequently the possibility of artificial modification of precipitation.