The present thesis is devoted to theoretical studies of pulse propagation of light through linear and nonlinear media, and of light-induced nuclear dynamics. The first part of the thesis addresses propagation of light pulses in linear periodical media - photonic crystals. The main accent was put on studies of the angular properties of two qualitatively different types of photonic crystals: holographic photonic crystals, and impurity band based photonic crystals. The anisotropy of band structure, group velocity and pulse delay with respect to the light polarization are analyzed. In the second part of the thesis a strict theory of nonlinear propagation of a few strong interacting light beams is presented. The key idea of this approach is a self-consistent solution of the nonlinear wave equation and the density matrix equations of the material. This technique is applied to studies of dynamics of cavityless lasing generated by ultra-fast multi-photon excitation. It is shown that interaction of co- and counter-propagating pulses of amplified spontaneous emission (ASE) affects the dynamics and efficiency of nonlinear conversion. Our dynamical theory allows to explain the asymmetric spectral properties of the forward and backward ASE pulses, which were observed in recent experiment with different dye molecules. It is shown that the ASE spectral profile changes drastically when the pump intensity approaches the threshold level. The effect of the temporal self-pulsation of ASE is studied in detail. The third part of the thesis is devoted to light-induced nuclear dynamics. Time- and frequency-resolved X-ray spectroscopy of molecules driven by strong and coherent infrared (IR) pulses shows that the phase of the IR field strongly influences the trajectory of the nuclear wave packet, and hence, the X-ray spectrum. Such a dependence arises due to the interference of one (X-ray) and two-photon (X-ray + IR) excitation channels. The phase of the light influences the dynamics also when the Rabi frequency approaches the vibrational frequency, breaking down the rotating-wave approximation. The probe X-ray spectra are also sensitive to the delay time, the duration, and the shape of the pulses. The evolution of the nuclear wave packets in the dissociative core-excited state affects the dynamics of resonant Auger scattering from fixed-in-space molecules. One of the important dynamical effects is the atomic-like resonance which experiences electronic Doppler shift. We predict that the scattering of the Auger electrons by nearby atoms leads to new Doppler shifted resonances. These extra resonances show sharp maxima in the bond directions, which makes them very promising as probes for local molecular structure using energy and angular resolved electron-ion coincidence techniques. Our theory provides prediction of several new effects, but also results that are in good agreement with the available experimental data. / QC 20100906

Thesis(M.S.)--Auburn University, 2005. / Abstract. Includes bibliographic references (leaves 61-68).

Conjugated Polymers have attracted a great deal of research interest in recent years due to their optoelectronic properties which makes them suitable for applications in organic light-emitting devices (OLEDs) and organic photovoltaics. Their properties are strongly dependent on the electron-electron and electron-nuclear interactions as well as the disorder which is present in almost all systems at finite temperatures. In this thesis the optical properties of electronically neutral conjugated polymers will be investigated. The results obtained are general and applicable to a wide range of parameters. In order to compare these to experiment the optical properties of poly( paraphenylene), poly(para-phenylene vinylene), and derivatives have been calculated. In these polymers the primary photoexcitations are Frenkel excitons which can be described by the Frenkel-Holstein Hamiltonian, which explicitly takes into account the exciton-nuclear coupling. Disorder can be introduced into this model both as diagonal and off-diagonal disorder within the Hamiltonian. First the optical transitions in ordered, linear conjugated polymers are investigated. It is found that the length of the polymer has a direct spectroscopic signature in the emission spectrum. When off-diagonal disorder is introduced the excitons localise on portions of the chain and the length of these portions, the conjugation length, then shows a clear emission signature. As such, a disordered polymer can be described theoretically as a chain of shorter segments, which define chromophores in a polymer context. Following from these calculations the role of conformation was investigated and effects were observed that greatly determine the optical properties of non-linear polymers. Most notable the Herzberg-Teller effect, which renders symmetrically forbidden transitions weakly allowed and greatly affects the absorption and emission spectra. The signatures observed in these spectra allow the determination of the (coarse grained) conformation of the polymer, something that has been difficult to measure directly.

The study of supercooled liquids and glasses remains one of the most divisive and divided fields in modern physics. Despite a vast amount of effort and research time invested in this topic, the answers to many central questions remain disputed and incomplete. However, the link between the behaviour of supercooled liquids and their energy landscapes is well established and widely accepted. Understanding this link would be a key step towards resolving many of the mysteries and controversies surrounding the glass transition. Therefore the study of glassy energy landscapes is an important area of research. In this thesis, I report some of the most detailed computational studies of glassy potential energy landscapes ever performed. Using geometry optimisation techniques, I have sampled the local minima and saddle points of the landscapes for several supercooled liquids to analyse their dynamics and thermodynamics. Some of my analysis follows previous work on the binary Lennard-Jones fluid (BLJ), a model atomic liquid. BLJ is a fragile glass former, meaning that its transport coefficients have super-Arrhenius temperature dependence, rather than the more usual Arrhenius behaviour exhibited by strong liquids. The difference in behaviour between these two classes of liquid has previously been attributed to differing degrees of structure in the relevant energy landscapes. I have studied models for both fragile and strong glass formers: the molecular liquid ortho-terphenyl (OTP) and viscous silica (SiO$_{2}$) respectively. My results for OTP agree closely with trends observed for BLJ, suggesting that the same diffusion mechanism is applicable to fragile molecular liquids as well as to atomic. However, the dynamics and energy landscape of OTP are made complicated by the molecular orientational degrees of freedom, making the analysis more challenging for this system. Dynamics of BLJ, OTP and silica are all dominated by cage-breaking events: structural rearrangements in which atoms change their nearest neighbours. I propose a robust and general method to identify cage breaks for small rigid molecules, and compare some properties of cage breaks between strong and fragile systems. The energy landscapes of BLJ and OTP both display hierarchical ordering of potential energy minima into metabasins. These metabasins can be detected by the cage-breaking method. It has previously been suggested that metabasins are responsible for super-Arrhenius behaviour, and are absent from the landscapes of strong liquids such as SiO2. My results indicate that metabasins are present on the silica landscape, but that they each contain fewer minima than metabasins in BLJ or OTP. Metabasins are associated with anticorrelated particle motion, mediated by reversed transitions between minima of the potential energy landscape. I show that accounting for time-correlation of particle displacement vectors is essential to describe super-Arrhenius behaviour in BLJ and OTP, but also required to reproduce strong behaviour in silica. I hypothesise that the difference between strong and fragile liquids arises from a longer correlation timescale in the latter case, and I suggest a number of ways in which this proposition could be tested. I have investigated the effect on the landscape of freezing the positions of some particles in a BLJ fluid. This “pinning” procedure induces a dynamical crossover that has been described as an equilibrium “pinning transition”, related to the hypothetical ideal glass transition. I show that the pinning transition is related to (and probably caused by) a dramatic change in the potential energy landscape. Pinning a large fraction of the particles in a supercooled liquid causes its energy landscape to acquire global structure and hence structure-seeking behaviour, very different from the landscape of a typical supercooled liquid. I provide a detailed description of this change in structure, and investigate the mechanism underlying it. I introduce a new algorithm for identifying hierarchical organisation of a landsape, which uses concepts related to the pinning transition but is applicable to unpinned liquids as well. This definition is complementary to metabasins, but the two methods often identify the same higher-order structures. The new “packings” algorithm offers a route to test thermodynamic theories of the glass transition in the context of the potential energy landscape. Over the course of this thesis, I discuss several different terms and methods to identify higher-order structures in the landscapes of model glass formers, and investigate how this organisation varies between different systems. Although little variation is immediately apparent between most glassy landscapes, deeper analysis reveals a surprising diversity, which has important implications for dynamical behaviour in the vicinity of the glass transition.

X-ray photoelectron spectroscopy (XPS) of ionic liquids (ILs) has become a valuable tool for the investigations of IL interfacial and physicochemical properties. The complex signals that result from elements which occupy a variety of chemical states, for example the C 1s photoemission, are often interpreted through chemical intuition and peak fitting parameters. This Thesis will present a new method to determine exact photoemission binding energies (B.E.s), through the comparison of multiple spectra. The designer aspect of ILs has been exploited in order to produce salts with small structural modifications. By comparing the C 1s and N 1s photoemissions of the structurally related samples, difference spectra have been produced. These spectra show the relative shifting of electron density between the two signals, revealing the initial and final locations of the changing photoemission. Using this technique, the current C 1s peak fitting models of imidazolium and pyridinium ILs have been examined. A variety of 4,4’-bipyridinium salts have also been used as a structural variation of pyridinium ILs to show how molecular symmetry and normalisation may be utilised in order to produce photoemissions equivalent to fragments of molecules. The subsequent C 1s difference spectra have provided carbon peak fitting models for mono- and di-alkylated 4,4’-bipyridinium salts. Without the use of XP difference spectra, these known fitting models would be almost impossible to determine. Finally, multiple complex difference spectra have been used to identify the exact B.E.s of C 1s photoemissions from a series of nitrile functionalised ILs. The complex difference spectra have also been analysed by inverse Gaussian fittings to show how additional information may be extracted from the characteristic shapes. The ‘construction’ of photoemissions is also demonstrated, whereby known B.E. peaks are assembled to accurately reproduce experimentally determined XP spectra.

Radioisotopes of caesium (Cs) and strontium (Sr) have been distributed in the environment due to weapons testing, nuclear power production and accidents at nuclear facilities. Radiocaesium and radiostrontium are of major concern in the medium to long term following accidental releases as they have high energies, long half lives (137Cs≈30 years; 90Sr≈29 years) and their easy assimilation into biological systems due to their similarity to the biologically important elements potassium (K) and calcium (Ca), respectively. Radio-caesium and -strontium are transferred to humans primarily via plant root uptake, and therefore minimising this uptake has been the focus of a number of remediation strategies, such as ploughing and fertiliser application. Species or cultivar substitution, where a species/cultivar that has higher uptake is replaced by a species/cultivar that has lower uptake, has been proposed as an effective and socially acceptable remediation strategy for contaminated agricultural land, but not enough is known about its efficacy for it to be recommended internationally. The aim of this thesis is to evaluate the potential of species or cultivar substitution as a remediation strategy for contaminated agricultural areas. Chapter 2 consists of meta-analysis of the available data (115 experiments) on the inter-cultivar variation in Cs and Sr accumulation by 27 plant species. Chapter 3 includes experiments conducted in the laboratory (UK) and two experiments in the field (Ukraine) investigating inter-cultivar variation in radiocaesium and radiostrontium accumulation in Brassica oleracea, and whether consistently lower-accumulating cultivars could be identified. Chapter 4 details analysis of samples from grass breeding experiments in Aberystwyth and Edinburgh (UK) from four forage grass species; hybrid ryegrass (Lolium perenne L. x Lolium multiflorum Lam.), L. perenne, L.multiflorum and Festuca arundinacea Shreb., and investigates inter-species and inter-cultivar variation in uptake of stable Cs and Sr. Hybrid ryegrass cultivars that were lower-accumulating in Cs and/or Sr were also identified. Chapter 5 compares the stable Cs and Sr uptake in six L. perenne and two F. arundinacea cultivars grown in Aberystwyth and Narodychi (Ukraine). Chapter 6 compares the performance in terms of yield and forage quality (elemental concentrations, digestibility and water soluble carbohydrate content) of six hybrid ryegrass cultivars and ten F. arundinacea cultivars identified as consistently lower-accumulating in Cs and/or Sr against the performance of two commercial hybrid ryegrass cultivars. The mean inter-cultivar variation in Cs and Sr was 1.8-fold and 2.0-fold,respectively when 27 plant species were studied. Thirty-five-fold variation in radiocaesium and 23-fold variation in radiostrontium was found between c.70 Brassica oleracea cultivars. In two field experiments in Ukraine, five cultivars had consistently lower radiocaesium concentration ratios and two cultivars consistently lower radiostrontium concentration ratios. One cultivar had lower radiocaesium and radiostrontium concentration ratios. Festuca arundinacea cultivars had lower Cs and Sr concentration ratios than cultivars of hybrid ryegrass, L. perenne and L. multiflorum. Three out of 17 hybrid ryegrass cultivars had consistently lower Cs concentration ratios, two cultivars consistently lower Sr and one consistently lower Cs and Sr. Despite differences in soil properties and environmental conditions, F. arundinacea cultivars grown in Aberystwyth and Narodychi accumulated less stable and radioactive Cs and Sr than L. perenne cultivars. One L. perenne cultivar also accumulated less Cs and Sr at both sites. F. arundinacea cultivars accumulated less Cs and Sr than commercial hybrid ryegrass cultivars, but alsohad up to 59% lower yield and a reduction of up to 19% in K accumulation, up to 46% in Ca accumulation, up to 7% in dry matter digestibility and up to 17% in water soluble carbohydrate content. Selecting lower accumulating cultivars was found to reduce Cs and Sr accumulation less, but with a smaller yield penalty and a smaller reduction in digestibility and water soluble carbohydrate content. It is concluded that species and cultivar substitution could be an effective remediation strategy in contaminated agricultural land provided implications for yield and quality are considered.

Tandem dye-sensitised solar cells, which contain two dye-sensitized electrodes (one p-type and one n-type), are often cited as a way of improving upon the standard devices, in which only the n-type electrode is photoactive. However, the p-type component of these devices suffers from very poor photocurrents, limiting the overall performance of the tandem cell. This Thesis aims to improve the performance of p-type dye-sensitised solar cells. An emphasis is made on tuning the energy levels of the different components of the device to ensure that the charge transfer processes which dictate the current and voltage are efficient. Chapters 1 & 2: A brief introduction to p-type and tandem dye-sensitised solar cells. The dye characterisation methods and techniques used to test complete devices are also discussed. Chapter 3: Dye synthesis and characterisation methods are presented as well as the apparatus used to characterise complete DSC devices. Material characterisation methods used in Chapter 6 are also discussed. Chapter 4: Novel dye structures were investigated for their use in p-type dye-sensitised solar cells. The optical and electrochemical properties of these dyes were investigated experimentally and by computational methods. It was found that the energies of the frontier orbitals of these dyes had a profound effect on charge transfer processes within p-DSCs. Charge recombination was investigated using small square wave modulated photovoltage and charge extraction measurements, this demonstrated that blocking units can be employed to inhibit this process. Transient absorption and time resolved infrared spectroscopies are employed to investigate the excited and charge separated state lifetimes of a number of these dyes. The dye CAD3 in this Chapter generated a record breaking photocurrent. This dye absorbed towards the red region (> 600 nm) of the visible spectrum, which made it ideal for use in tandem-DSCs in which red light is absorbed at the photocathode. Chapter 5: Three dyes, including CAD3 from Chapter 4 were used on the photocathode in tandem-DSCs. The photocurrent generated was largely dependent on the degree of spectral overlap between these dyes and the dye on the photoanode. CAD3, which absorbed at longer wavelengths than the other dyes, generated a record breaking photocurrent when paired with the literature n-type dye D35. However, these devices suffered from poor photovoltages as result of using an electrolyte solution optimised for p-DSCs. Chapter 6: Mg2+ doping studies were performed on the NiO films used in p-DSCs. It was found that higher concentrations of MgO improved the photovoltage of these devices. However, there was a notable drop in photocurrent with increasing Mg2+. From charge extraction experiments it was revealed that the cause of this was a positive shift in the energy of the valence band. This decreased the driving force for electron transfer from the NiO film to the dye and therefore the photocurrent. The MgO also had a profound effect on the morphology of the films. The larger pore volume in the 150-500 nm range lead to an improvement in dye adsorption, despite the overall surface area being slightly decreased. Chapter 7: Based on work by O’Regan et al., the effect of free iodine on p-DSCs was investigated. In this Chapter it was demonstrated that increased concentration of free iodine reduced the photovoltage obtained by a p-DSC. This was confirmed to be a result of increased charge recombination using small square wave modulated photovoltage and charge extraction measurements. The fact that increasing concentration of free iodine increased the rate of recombination so significantly indicates an alternate main pathway for recombination. This study was then repeated with increasing concentrations of triiodide, which was found to have little or no effect on the performance of the p-DSCs. Chapter 8: A concluding summary of the work presented in this Thesis. Future work is also discussed in this Chapter.

Over the last decade the beneficial properties of hydrogels as artificial cell culture supports have been extensively investigated. Certain synthetic hydrogels have been proposed to be similar in composition and structure to the native extracellular matrix of the stem cell niche, their in vivo cell habitat, which is a powerful component in controlling stem cell fate. The stem cell differentiation pathway taken is influenced by many factors. When culturing cells within or upon hydrogels the choice can be strongly dependent on the underlying 3D hydrogel chemistry which strongly influences hydrogel-cell interactions. The interrelationship between hydrogel chemistry and that of biomolecules in controlling cellular response ideally requires analysis methods to characterise the chemistry without labels and normally in 3D. Time-of-flight secondary ion mass spectrometry (ToF SIMS) has the potential to be utilised for through thickness characterisation of hydrogels. The frozen-hydrated sample format is well suited to minimise changes associated with dehydration or the complication of chemical ‘fixation’. There is however significant challenges associated with this sample format. Frost formation occurs on cold samples in the ambient atmosphere affecting the quality of chemical information acquired from depth profiling frozen hydrogel samples. We develop a simple method to remove this frost by blowing with gas prior to entry into the instrument which is shown to produce remarkably good profiles on a poly(2-hydroxyethyl methacrylate) (pHEMA) hydrogel film where a model protein, lysozyme, is incorporated to demonstrated how biomolecule distribution within hydrogels can be determined. A comparison of lysozyme incorporation is made between the situation where the protein is present in the polymer dip coating solution and lysozyme is a component of the incubation medium. It is shown that protonated water clusters H(H2O)n+ where n=5-11 that are indicative of ice are detected through the entire thickness of the pHEMA and the lysozyme distribution through the pHEMA hydrogel films can be determined using the intensity of characteristic fragment secondary ions. Quantitative TOF-SIMS analysis is highly desirable in biomaterial analysis as the amount and type of molecule in the material analysed may be determined. This has significant interest in hydrogel chemical analysis as cellular development on or within hydrogels may be highly influenced by the concentration and type of soluble molecule. Unfortunately, the matrix effect in SIMS changes the measured signal intensity of the analyte, preventing accurate quantitation. For this reason, we apply X-Ray Photoelectron Spectroscopy (XPS) on the equivalent samples as the ToF-SIMS in an attempt to correlate molecular ion yields to exact elemental concentrations. Similarly to ToF-SIMS the frozen-hydrated format in XPS is however still relatively unexplored. We apply the developed preparatory procedure in 3D XPS analysis of pHEMA/lysozyme hydrogel films in a hydrated state. We show that this format is suitable for alternative high vacuum analysis techniques. Furthermore, we show that lysozyme ingression and concentration can be determined through XPS. This work describes the first example of the characterisation of a hydrogel by ToF-SIMS and XPS in a frozen hydrated format, characterising hydrogels in a format most reflecting its native hydrated state at culture conditions. The described procedure allows for the mapping of biomolecules in a label free manner in 3D, furthermore allowing quantitative determination of biomolecule concentrations in hydrogels.

Gas phase metal-containing complexes provide suitable systems in which to study fundamental binding motifs between a metal ion and molecules in the absence of any solvent, support or competing charge effects. In this thesis, metal-containing species are explored experimentally using infrared resonance enhanced photodissociation (IR-REPD) spectroscopy and velocity map imaging (VMI). The experimental results are further interpreted with the aid of spectral simulations based on density functional theory (DFT). These are the first studies reported using a newly built IR-REPD spectrometer equipped with a purpose-built laser ablation source to allow for the study of single metal ion-molecule complexes. The laser ablation source is shown to efficiently produce various complexes including Rh⁺(CO₂)_n, VO₂⁺(N₂O)_n and Au⁺(CH₄)_n and the IR-REPD spectrometer has been characterised against a well-studied system of V⁺(CO₂)_n complexes. In order to record the IR-REPD spectra for small metal ion-molecule complexes, an argon atom is employed as the inert messenger. A combined IR-REPD spectroscopy and DFT investigation of M⁺(CO₂)_n complexes (where M = Co⁺, Rh⁺ and Ir⁺) reveals a common [M⁺(CO₂)₂] core structure for all three considered metal ions. Additional ligands, which are not directly bound to the central metal ion, experience lower perturbation as evident in the reduced blue-shift for the ligand in the outer coordination shells. A further IR-REPD/DFT study involving CO₂ complexation around NbO₂⁺ and TaO₂⁺ ions reveals a strongly-bound core of four CO₂ ligands around the MO₂⁺ ion (M = Nb, Ta). A significant increase in the intermolecular bond distances for the second coordination sphere ligands coincides with a decrease in the calculated binding energies. Velocity map imaging is employed to explore the rich photodissociation dynamics of VO in the vicinity of C⁴Σ- - X⁴Σ-(v',0) vibronic transitions in VO. The final quantum state distribution was observed to be strongly dependent on the intermediate vibronic state of VO via which the dissociation threshold is reached. This work provides a refined value for the VO dissociation energy of D₀(VO) = 53190 ± 261 cm^-1 in excellent agreement with available literature.

The technology employed by human beings for the generation, storage and usage of energy is presently undergoing the fastest and most profound change since the industrial revolution. The changes in the generation and usage of energy necessitate the development of new methods of energy storage. In these systems, electrochemical energy storage will play a crucial role and to this end new electrolytes need to be explored to complement these changes. One such class of liquids is ionic liquids, a class of salts that are molten at room temperature. These liquids have a broad applicability to batteries and supercapacitors. This thesis details work where molecular dynamics simulations have been used to explore the nanostructure of ionic liquids and their mixtures with various molecular solvents at simplistic electrodes. The thesis has two broad sections. The first is covered in Chapter 3, and explores the nanostructure of ionic liquid propylene carbonate solutions, developing a framework through which these nanostructures can be understood. The section concludes that the increasing dilution of ionic liquids decreases the surface charge at which the characteristic ionic liquid oscillatory interfacial structure gives way to a different structure featuring monotonic charge decay. The behaviour of ionic liquids at interfaces is found to be correlated to ion size and type, as well as concentration. A wide divergence in the observed behaviour is shown at positive and negative electrodes due to the asymmetry of propylene carbonate. The second section, consisting of two chapters, explores the interfacial nanostructure of solvate ionic liquids using two different boundary conditions to model the electrode. This work is the first simulation of solvate ionic liquids at electrified interfaces. This section will explore the effect of electrode model on the behaviour of these ionic liquids at the electrode. Chapter 4 uses a fixed charge electrode, whereas Chapter 5 uses one with a fixed potential. The section concludes that regardless of electrode model, the idealised portrait of a solvate ionic liquid - one where the liquid behaves exactly as an aprotic ionic liquid - is not applicable. In Chapter 4's exploration of fixed charged electrodes, the formation of 2 glyme to lithium complexes contradicts the idealised portrait of the liquid. A different change is observed in Chapter 5's exploration of fixed potential electrodes, with both lithium glyme and lithium anion clusters forming at the interface. The key difference between the two studies is that lithium does not coordinate to the electrode in the fixed charge simulations, while in the fixed potential case it does. At the end of Chapter 5 the results are compared against experimental data, with the efficacy of the two models discussed. The aim of both studies is to look at the nanostructure of ionic liquids, when the symmetry between co-ion and cation repulsion - and related effects - is broken by the presence of a non ionic constituent in the liquid.