- ItemDynamical large deviations of diffusions(Stellenbosch : Stellenbosch University, 2023-03) Du Buisson, Johannes Petrus; Touchette, Hugo; Muller-Nedebock, Kristian K.; Stellenbosch University. Faculty of Science. Dept. of Physics.ENGLISH ABSTRACT: We solve two problems related to the fluctuations o f t ime-integrated function- als of Markov diffusions, u sed i n p hysics t o m odel n onequilibrium s ystems. In the first w e d erive a nd i llustrate t he a ppropriate b oundary c onditions o n the spectral problem used to obtain the large deviations of current-type observables for reflected d iffusions. Fo r th e se cond pr oblem we st udy li near di ffusions and obtain exact results for the generating function associated with linear additive, quadratic additive and linear current-type observables by using the Feynman- Kac formula. We investigate the long-time behavior of the generating function for each of these observables to determine both the so-called rate function and the form of the effective p rocess r esponsible f or m anifesting t he fl uctuations of the associated observable. It is found that for each of these observables, the effective p rocess i s a gain a l inear d iffusion. We ap ply ou r ge neral re sults fo r a variety of linear diffusions i n R ², w ith p articular e mphasis o n i nvestigating the manner in which the density and current of the original process are modified in order to create fluctuations.
- ItemResonant ionization spectroscopy for laser isotope separation of zinc isotopes(Stellenbosch : Stellenbosch University, 2021-12) De Bruyn, Andre; Steenkamp, Christine M.; Rohwer, Erich G.; Du Plessis, Anton; Stellenbosch University. Faculty of Science. Dept. of Physics.ENGLISH ABSTRACT: The vast zinc (Zn) reserves in South Africa are currently being underutilized, as the Zn ore refinement and isotope enrichment occurs abroad. The enrichment process most commonly used thus relies only on mass separation techniques and is therefore limited when separating isotopes of similar masses like 68Zn and 67Zn. Pure 68Zn and 67Zn are important stable nuclides in the medical industry as these isotopes are used for production of gallium-based radiopharmaceuticals used in positron emission tomography (PET) and single-photon emission computerised tomography (SPECT) scans. Additionally, depleted 64Zn is used in the cooling water of nuclear reactors for the prevention of stress corrosion cracking as well as limiting the formation of cobalt radioisotopes. This study aimed to investigate, model and optimize resonant ionization spectroscopy (RIS) schemes for the Zn isotopes 68Zn and 67Zn that are suitable for laser-based enrichment of these isotopes from natural Zn. This study reports on the development and implementation of the first experimental RIS system combined with a time-of-flight mass spectrometer at Stellenbosch University. This system was used to investigate a resonance ionization scheme that has potential for laser-based enrichment of Zn isotopes from a natural Zn sample. The ionization scheme was chosen by considering transition wavelengths, the hyper fine splitting of 67Zn, and transition strengths of intermediate levels. The effect of physical conditions and laser parameters was experimentally investigated. The experimental results were complemented by a rate equation model of the RIS scheme developed in this study. The experimental measurements included laser induced fluorescence (LIF) from both the first and second intermediate levels in the RIS scheme. The experimental LIF results contributed to optimization of the experiment and refining the rate equation model by confirming the laser bandwidth and helping to estimate an unknown transition probability. The experimental RIS measurements confirmed the model results for the existing experimental conditions, including the effects of laser tuning, pulse timing and laser pulse energy. The limiting factor to the isotope selectivity of the RIS experiment was the bandwidth of the dye laser used for the first excitation step. The simulated results of the rate equation model that was developed in this study was tested against experimental results and was found to be in good agreement. The model was also applied to conditions which could be found in industrial scenarios. The results indicated that when using a commercially available narrow bandwidth Ti:sapphire laser ( 300 MHz) it is possible to achieve 85% enrichment of 67Zn if the Zn vapour is suffciently cooled ( 100 K).
- ItemThe Structure of 33Si,35S and the magicity of the N = 20 gap at Z = 14; 16(Stellenbosch : Stellenbosch University, 2021-12) Jongile, Sandile; Wiedeking, Mathis; Wyngaart, S.; Sorlin, O.; Lemasson, A.; Papka, Paul; Stellenbosch University. Faculty of Science. Dept. of Physics.ENGLISH ABSTRACT: Nuclei along N = 20 provide an excellent region to investigate nuclear structure and interactions, with their evolution from the doubly magic nucleus 40Ca through the Z = 16 and Z = 14 nuclei 36S and 34Si, respectively, to 32Mg with a deformed 2p 2h intruder ground state. This study is motivated by and focuses on: i) The robustness of the N = 20 shell gap from 40Ca (studied previously by Matoba et al., ) to 36S and 34Si, after removing 4 and 6 protons, respectively. A strong sd-shell closure would lead to a fully occupied neutron d3=2 orbital and no, or little occupancy, neutrons in the p3=2 and f7=2 orbitals located above N = 20. With the deformed 32Mg having only 2 protons removed from 34Si it is an interesting question if the magicity is somewhat gradually or abruptly eroded below Z = 14. ii) A significant reduction of the neutron 1d5=2 and 1d3=2 spin-orbit splitting between 40Ca and 36S, as protons are removed from the 1d3=2 orbital, would be indicative of the effect of proton-neutron tensor force. By comparing the neutron 1d5=2 hole strength between these nuclei, the strength of the tensor force can be probed in an unprecedented manner. Two separate studies were carried out to address the aforementioned motivations. Firstly, an inverse kinematics experiment with the 9Be(34Si,33Si+ )X and 9Be(36S,35S+ )X reactions which was performed at the National Superconducting Cyclotron Laboratory (NSCL) with 98.5 MeV/u 34Si and 88 MeV/u 36S secondary beams produced in the fragmentation of a 48Ca primary beam has been reanalysed. Reaction products were detected with the Gamma-Ray Energy Tracking In-beam Nuclear Array (GRETINA) coupled to the S800 magnetic spectrometer. This measurement focused on probing the Fermi surface in 34Si and 36S, and locating the strength of the neutron d5=2 orbital. From the spectroscopic factor values, which are derived from observed -ray decays, the neutron 1d3=2 appears to be fully occupied, while some fraction of the 1d5=2 orbital is observed only as the states lie above the neutron emission energy threshold. Secondly, the 36S(p; d)35S reaction is a useful tool to probe the change in neutron spinorbit splitting between 34Si and 36S. The 36S(p; d)35S reaction allows for an investigation into the 36S Fermi surface stiffness and the neutron d3=2 d5=2 spin-orbit reduction. It also serves to probe the magicity of 36S through its Fermi surface, complementary to the (d; p) reaction previously performed, reported in Ref. . Of course all this depends on the availability of a reliable 36S target. This was achieved by specifically developing a new target system at iThemba LABS which allows for a cost effective 36S target without heavy contaminants to be used. This novel target, which is in motion and encapsulates sulfur between two Mylar foils, has been shown to be an effective way to produce targets with a significant amount of material (0.5-1 mg/cm2) . Using the developed moving 36S target system with 66 MeV incident protons, states in 35S were populated and studied with the K600 magnetic spectrometer at iThemba LABS. States up to 9 MeV are observed, identifying the neutron single-particle strength below and above the Fermi surface using the detection of the deuterons at the focal plane of the K600 spectrometer with an energy resolution of approximately FWHM = 30 keV in the center of mass.
- ItemVibrational spectroscopy for characterisation of a cyclic antimicrobial peptide(Stellenbosch : Stellenbosch University, 2021-12) Pfukwa, Ngaatendwe Buhle Cathrine; Neethling, Pieter H.; Rautenbach, Marina; Parker, Anthony W.; Rohwer, Erich G.; Stellenbosch University. Faculty of Science. Dept. of Physics.ENGLISH ABSTRACT: In order to understand antimicrobial peptide action towards membrane surfaces it is imperative to first understand the structure and conformational behaviour of the antimicrobial in solution environments representative of the target membrane. Information on conformational behaviour can be extracted in more detail from analysis of the peptide secondary structure using the structural sensitivity afforded by two dimensional infrared (2D-IR) spectroscopy with which subtle details of peptide structure, which may not be well resolved with one dimensional infrared (1D-IR) spectroscopy, can be obtained. With 2D-IR spectroscopy spectral content is spread over two frequency axes and the high time resolution on femtosecond and picosecond timescales for transient processes provides an advantage over conventional techniques such as X-ray diffraction, circular dichroism (CD) or Ultraviolet spectroscopy. In this study the aims were to evaluate the adaptability of two-dimensional infrared (2D-IR) spectroscopy, together with multivariate data analysis methods such as principal component analysis (PCA), to provide and extract spectral details which can be correlated to changes in structure of a cationic antimicrobial peptide (CAMP) gramicidin S (GS). GS was selected as prototype as it is a well characterised anti-parallel β-sheet peptide, active by disrupting bacterial membranes, consequently causing membrane penetration. Furthermore, a qualitative working relationship between 1D and 2D IR and Raman spectroscopy in corroboration with quantum mechanical (QM) simulations was established towards correlating GS spectral features to conformational secondary structural changes. The structural changes were used to elucidate the conformational behaviour of GS in selected solvent environments which are representative of GS target membrane lipid bilayers. The solvent environments were an aqueous ubiquitous environment (H2O/D2O), a membrane mimetic partially polar environment (1-octanol) and a membrane mimetic strongly H-bonded environment (TFE). Self-association of GS was promoted in H2O/D2O and 1-octanol forming aggregates which persisted in solution at increasing peptide concentration, as revealed from increase in the β-sheet content and loss in β-turns. While in TFE, a strong H-bonding solvent, the GS aggregates were molecularly solvated. These changes were correlated to occur in the residues which contribute greatly to the amphiphilic nature of GS. Further solvent effects on the structural factors contributing to GS bioactivity are discussed. The thermostability of GS was investigated for the temperature range 20-80 ℃. The dissociation of GS aggregates/small oligomers to monomeric structures in 1-octanol was favoured at elevated temperatures. Thermodynamic parameters were extracted and the dissociation process was described by a bimodal profile with two identified melting transitions at Tm1 = 45 oC and Tm2 = 57 oC. Results obtained confirmed that both IR and Raman can provide complementary results as evidenced by their sensitivity towards hydrophilic and hydrophobic structures is GS. Further providing insight towards the type of residue substituents which can be interchanged in future synthesis of GS derivatives, with the aim of increasing the bioactivity of GS whilst lowering its haemolytic effects. The significance of SERS using silver nanoparticles in detection of low peptide concentrations is reported and a GS concentration of 1x10-5 M was detected. Information in thesis demonstrates the novelty and broad use of 1D and 2D IR, RS and SERS techniques in understanding the solvent and temperature induced conformational changes which occur in GS, which provides information on GS structure towards generation of more bioactive GS derivatives for therapeutic purposes.
- ItemSingle-beam coherent anti-Stokes Raman scattering combining polarization shaping with spectral focusing(Stellenbosch : Stellenbosch University, 2021-03) Viljoen, Ruan; Rohwer, Erich G.; Neethling, Pieter H.; Stellenbosch University. Faculty of Science. Dept. of Physics.ENGLISH ABSTRACT: Single-beam coherent anti-Stokes Raman scattering (SB-CARS is a compact approach to CARS which employs a single broadband laser source to probe molecular vibrations. A variety of light sources can be used, one of which is a photonic crystal fibre (PCF pumped by a femtosecond laser. The SB-CARS setup presented herein utilises a polarization main-taining all-normal dispersion PCF (PM-ANDi-PCF pumped by a femtosecond oscillator. The oscillator produces 80 fs pulses with a low average power of 1W at a repetition rate of 80 MHz. When these pulses are used to pump the PM-ANDi-PCF, supercontinuum pulses are produced with a much broader bandwidth (150 nm at the same repetition rate. The supercontinuum pulses are pulse-to-pulse phase stable with high peak intensi-ties, perfect for fast acquisition of spectra in applications of non-linear spectroscopy and microscopy. As a result of using a broadband laser source, the produced CARS spectrum is also broad and dominated by a non-resonant background which is generated by a four-wave mixing non-linear process. The SB-CARS setup utilises an active shaping approach which allows for a multitude of approaches, that can reduce the non-resonant background, to be implemented within the same setup. A spatial light modulator in a 4-f shaper affords the ability to shape the supercontinuum pulses at will and also enables the integration of pulse characterisation techniques into the same SB-CARS setup. Implementation of a phase-only temporal ptychography technique, i2PIE, in a SB-CARS setup is reported on for the first time. Pulse characterisation is a vitally important component of this setup, as produced supercontinuum pulses are initially temporally broad, because of dispersion in the optical fibre, and need to be compressed for applications in spectroscopy. Comparison of i2PIE to another phase-only technique, multiphoton intrapulse interference phase scan (MIIPS, shows remarkable improvements in compression. Second harmonic spectra generated in a beta-barium borate crystal when the supercontinuum pulses are compressed using phase reconstructed with i2PIE and MIIPS, showed an increase of integrated spectral intensity by a factor of 4. When applied to SB-CARS measurements, the integrated intensity of SB-CARS spectra increased by a factor 6.5 when i2PIE was used. The improvement was not limited to spectral intensity yield, but also showed an improvement of signal-to-background in extracted CARS spectra by a factor of 4 when i2PIE was used. Different SB-CARS strategies were implemented in the same setup and evaluated through simulation and experimentation to illustrate the versatility of the SB-CARS apparatus. A new spectral focusing SB-CARS approach that utilises the polarization shaping and phase shaping capabilities of an SLM, is introduced and compared to other SF techniques. Non-resonant background is reduced in this technique by using a narrow probe decoupled from the pump and Stokes fields. Spectral focusing is achieved with phase shaping of the pump which focuses the bandwidth to mostly target a single Raman resonance. Results from spectral measurements demonstrate that the new technique (PP-QPSF) yields spectra with an overall increased S:B. This new technique is evaluated spectroscopically and shows promise for an application in SB-CARS microscopy.