Thesis (Ph.D.) - University of Queensland, 2003. / Includes bibliography.

Polymer thin films with the film thickness (h0) below ~ 100 nm often exhibit physical properties different from the bulk counterparts. In order to make the best use of polymer thin films in applications, it is important to understand the physical origins of these deviations. In this dissertation, I will investigate how different factors influence dynamic properties of polymer thin films upon nano-confinement, including glass transition temperature (Tg), effective viscosity (ηeff) and self-diffusion coefficient (D). The first part of this dissertation concerns the impacts of the molecular weight (MW) and tacticity on the Tg’s of nano-confined polymer films. Previous experiments showed that the Tg of polymer films could be depressed or increased as h0 decreases. While these observations are usually attributed to the effects of the interfaces, some experiments suggested that MW’s and tacticities might also play a role. To understand the effects of these factors, the Tg’s of silica-based poly(α-methyl styrene) (PαMS/SiOx) and poly(methyl methacrylate) (PMMA/SiOx) thin films were studied, and the results suggested that MW’s and tacticities influence Tg in nontrivial ways. The second part concerns an effort to resolve the long-standing controversy about the correlation between different dynamics of polymer thin films upon nano-confinement. Firstly, I discuss the experimental results of Tg, D and ηeff of poly(isobutyl methacrylate) films supported by silica (PiBMA/SiOx). Both Tg and D were found to be independent of h0, but ηeff decreased with decreasing h0. Since both D and ηeff describe transport phenomena known to depend on the local friction coefficient or equivalently the local viscosity, it is questionable why D and ηeff displayed seemingly inconsistent h0 dependencies. We envisage the different h0 dependencies to be caused by Tg, D and ηeff being different functions of the local Tg’s (Tg,i) or viscosities (ηi). By assuming a three-layer model, we were able to account for the experimental data and resolve the inconsistency. By extending the same ideas to the analogous data of silica-based polystyrene films (PS/SiOx), we found a resolution to the inconsistency regarding the effects of nano-confinement on the dynamics of polymer thin films.

Rotational-translational decoupling, in which translational motion is apparently enhanced overrotational motion in violation of Debye-Stokes-Einstein predictions, has been observed in a wide variety of materials near their glass transition temperatures (Tg). This has been posited to result from ensemble averaging in the context of dynamic heterogeneity. In this thesis, single fluorescent probe molecules are tracked rotationally and translationally to interrogate this explanation. In one study, ensemble and single molecule experiments are performed in parallel on the ideal fluorescent probe N,N’-dipentyl-3,4,9,10-perylenedicarboximide (pPDI) in high molecular weight polystyrene near its Tg. Ensemble results show decoupling onset at approximately 1.15Tg, increasing to over three orders of magnitude at Tg. Single molecule measurements also show a high degree of decoupling, with typical molecules at Tg showing translational diffusion coefficients nearly 400 times higher than expected from Debye-Stokes-Einstein predictions. The same experiments were performed on a microscope with somewhat lower spatial resolution to investigate the role of localization accuracy in apparent degree of breakdown. Here similar, though slightly larger, degrees of breakdown were found, consistent with the idea that averaging across heterogeneous regions, even within a single molecule’s trajectory, is the primary driver of rotational-translational breakdown, while the lower degree of localization accuracy of the microscope additionally leads to some sub-ensemble selection that further inflates apparent breakdown. Across all single molecule experiments, higher degree of breakdown is associated with particularly mobile molecules and anisotropic trajectories, providing support for anomalous diffusion as a critical driver of rotational-translational decoupling and Debye-Stokes-Einstein breakdown. In a final study, single molecule translational simulations are performed with varying types (spatial and dynamical) and degrees of heterogeneity to assist in interpreting results of single molecule translation experiments. These reveal that fast portions of translational trajectories inflate diffusion coefficients and that, taken together with experimental results, the majority of rotational- translational decoupling in glassy systems occurs through dynamic exchange consistent with wide underlying distributions of diffusion coefficients and exchange coupled to local spatiotemporal dynamics.

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The optical spectroscopy techniques have been used to investigate left-handed behavior of metamaterials as well as the electron-bosonic spectral functions (or Bosonic spectra) of high-transition-temperature superconductors (or high-Tc superconductors) in the research work of this thesis. The periodic double-ring split-ring resonator (SRR) array was one of the first proposed magnetic metamaterials which could give rise to a negative magnetic permeability (μ<0). In the traditional design of negative index metamaterials, the SRR arrays were combined with continuous metallic wires that provide a negative electric permittivity (∊<0). However, the requirement of an unbroken electrical connection between unit cells would be challenging in building contoured devices. In our study, we carefully examine the electromagnetic properties of the double-ring SRR arrays on silicon substrates in the mid-infrared frequency regime experimentally and numerically. For light at normal incidence, we observe that an electric resonance in the outer ring and a magnetic resonance in the inner ring exist at similar frequencies in one of our samples, which suggests that the double-ring SRR array could have simultaneous a negative permittivity and a negative permeability, or a left-handed behavior. Our conjectures are confirmed by the numerical simulations. We also propose a new left-handed metamaterial composed of two single-ring SRRs in each unit cell. The left-handed behaviors in our designs originate from the SRR structure itself only and therefore, there are no metallic continuous wires involved compared to the conventional left-handed SRR metamaterials. The high-Tc superconductor samples studied here are highly under-doped YBa2Cu3O6.35 (YBCO6.35), nearly optimally doped monolayer HgBa2CuO4+ઠ (Hg1201), Zn- and Ni- doped Bi2Sr2CaCu2O8+ઠ (Bi2212) single crystals. We experimentally determine the optical constants of the samples and numerically extract the electronboson spectral functions from the optical scattering rate by either an analytic formula or a maximum entropy inversion technique. We find that the bosonic mode obtained from the optical data is consistent with a peak in the q-averaged susceptibility seen in the magnetic neutron scattering studies. The comparisons of the bosonic spectra between YBCO6.35 and YBCO6.50, monolayer Hg1201 and trilayer Hg1223 (HgBa2Ca2Cu3O8+ઠ), Zn-doped and Ni-doped Bi2212 characterize the variation of the bosonic spectra with the hole concentration, Tc as well as the magnetic and nonmagnetic atom substitution. / Thesis / Doctor of Philosophy (PhD)

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Polyetherimides are an important class of engineering thermoplastics used in a broad range of industries and applications because of their high heat resistance and stability, high strength and moduli, excellent electrical properties over a wide range of temperatures and frequencies, good processability, good adhesive properties, and chemical stability. All-atom molecular dynamics (MD) simulation is a useful tool to study polymers, but the accessible length and time scales are limited. In this thesis, we explore several computational methods that go beyond all-atom MD simulations to investigate polyetherimides. First, we have developed a transferable coarse-grained MD model of polyetherimides that captures their mechanical and thermal expansion properties. Our results show that in order to make the model transferable, it is critical to include an entropic correction term in the coarse-grained force field and require the coarse-grained model to capture the thermal expansion property of polyetherimides. Secondly, we have constructed a predictive model of the glass transition temperature (Tg) for polyimides by using machine-learning algorithms to analyze existing data on Tg reported in the literature. The predictive model is validated by comparing its predictions to experimental data not used in the training process of the model. We further demonstrate that the diffusion coefficients of small gas molecules can be quickly computed with all-atom MD simulations and used to determine Tg. Finally, we have developed a Monte Carlo (MC) program to model the polymerization process of branched polyetherimides and to compute their molecular weight distribution for a wide range of systems, including fully reacted, partially reacted, stoichiometric, and nonstoichiometric ones. The MC results are compared to the predictions of the Flory-Stockmayer theory of branched polymers and an excellent agreement is found below the gel point of the system under consideration. Above the gel point, the Flory- Stockmayer theory starts to fail but the MC method can still be used to quickly determine the molecular weight distribution of branched polyetherimides under very general conditions. / Doctor of Philosophy / Polyetherimides are an important category of engineering plastics with wide applications in many fields because of their superior mechanical, thermal, chemical, and electrical properties. All-atom molecular dynamics simulations serve as a useful tool to study the properties of polyetherimides in silico. However, such simulations are computationally expensive and therefore limited to small system sizes and short time scales. To overcome these issues, we employed various computational techniques in this thesis to model polyetherimides. First, we have developed a coarse-grained model of polyetherimides where atoms are grouped into beads. We show that molecular dynamics simulations on the basis of the coarse-grained model can be used to provide a reasonable description of the mechanical and thermal expansion properties of polyetherimides. Secondly, we have constructed a predictive model of the glass transition temperature, which is the temperature at which a material enters a glassy state when cooled rapidly, of polyimides using machine-learning algorithms. This model is capable of estimating the glass transition temperature of polyimides within an accuracy of ± 15 K even for those not synthesized yet. We further show that the diffusion coefficients of gas molecules, in addition to the polymer density, can be computed accurately with all-atom molecular dynamics simulations and used to determine the glass transition temperature of polyimides. Finally, we have developed a Monte Carlo scheme to efficiently model the polymerization and compute the chain-length distribution of branched polyetherimides under very general conditions. The results from Monte Carlo simulations are compared to the predictions of the Flory-Stockmayer theory of branched polymers. The range of applicability of the theory is revealed. Overall, we have demonstrated several computational techniques that can be used to efficiently model polyetherimides, potentially other polymers as well, beyond the widely-used all-atom molecular dynamics simulations.

Biomolecular interactions are fundamentally important for a wide variety of biological processes. Understanding the temperature dependence of biomolecular interactions is hence critical for applications in fundamental sciences and drug discovery. Micro-Electro-Mechanical Systems (MEMS) technology holds great potential in facilitating temperature-dependent characterization of biomolecular interactions by providing on-chip microfluidic handling with drastically reduced sample consumption, and well controlled micro- or nanoscale environments in which biomolecules are effectively and efficiently manipulated and analyzed. This dissertation is focused on a high-through and miniaturized differential scanning calorimeter for thermodynamic study of bio-molecules using MEMS techniques. The dissertation firstly introduces the overall design and operation principles. This miniaturized DSC was fabricated based on a polyimide (PI) thin film. Highly temperature sensitive vanadium oxide was used as the thermistor material. A PDMS (Polydimethylsiloxane) microfluidic chamber was separately fabricated and then bonded firmly with the PI substrate by a stamp-and-stick method. Meanwhile, the micro heater design was optimized to reach better uniformity. A heating stage was constructed for fast and reliable scanning. In this study, we used syringes to deliver the 0.63 μL liquid sample into both the sample and reference chambers. All the testing processes were functionalized using the LabVIEW programs. The sensing material was also characterized. To seek a higher temperature coefficient of resistance (TCR) and less resistive behavior, explorations about various PVD (physical vapor deposition) parameters and annealing conditions were conducted for optimization. In this research, we found vanadium oxide deposited under certain conditions leads to the highest TCR value (a maximum of 2.51%/oC). To better understand the material’s property, we also did the XRD (X-ray Diffraction), SEM (Scanning electron microscope). The micro calorimeter was calibrated using a step thermal response. The time constant was around 3s, the thermal conductance was 0.6mW/K, and the sensitivity was 6.1V/W. The static power resolution of the device at equilibrium is 100 nW, corresponding to 250 nJ/K. These performances confirmed the design and material to be appropriate for both good thermal isolation and power sensitivity. We demonstrated the miniaturized DSC’s performance on several different kinds of protein samples: lysozyme, and mAb (monoclonal antibody) and a DVD IgG (double variable domain immunoglobulin G). The results were found to be reasonable by comparing it with the commercial DSC’s tests. Finally, this instrument may be ideal for incorporation into high throughput screening workflows for the relative comparison of thermal properties between large numbers of proteins when only small quantities are available. The micro-DSC has the potential to characterize the thermal stability of the protein sample with significantly higher throughput and less sample consumption, which could potentially reduce the time and cost for the drug formulation in the pharmaceutical industry. / Ph. D. / Virtually all biological phenomena depend on molecular interactions, which is either intra-molecular as protein folding/unfolding or intermolecular as in ligand binding. A basic biology problem is to understand the folding and denaturation processes of a protein: the kinetics, thermodynamics and how a protein unfolds and folds back into its native state. Both folding/unfolding and denaturation processes are associated with enthalpy changes. The thermodynamics of binding compounds helps a great deal to understand the nature and potency of such molecules and is essential in drug discovery. As a label-free and immobilization-free method, calorimetry can evaluate the Gibbs free energy, enthalpy, entropy, specific heat, and stoichiometry, and thus provides a fundamental understanding of the molecular interactions. Calorimetric systems including isothermal titration calorimeters (ITC) and differential scanning calorimeters (DSC) are the gold standard for characterizing molecular interactions. In this research, a micro DSC is developed for direct thermodynamic study of bio-molecules. Compared with the current commercial DSC, it is on a much smaller scale. It consumes much less sample and time in each DSC measurement. It can enable comprehensive high-content thermodynamics study in the early stage of drug discovery and formulation. It also enables direct, precise, and rapid evaluation of the folding and unfolding of the large biomolecules like proteins, DNAs, and enzymes without labeling or immobilization. It can also be used as a powerful tool to study the membrane proteins, which is often impractical or impossible before.

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