Modelling of plant light-harvesting spectra

Thesis (PhD (Physics))--University of Pretoria, 2022.In plants, the life-sustaining process of photosynthesis begins when molecular light-harvesting complexes capture sunlight. In order to understand the role and function of these complexes, they are often characterised with the powerful technique of linear optical spectroscopy. Modelling linear optical spectra allows researchers to improve their understanding of the design principles and quantum mechanical processes in light-harvesting complexes, extract molecular parameters quantitatively, and test new methods for calculating spectra or molecular parameters. In this thesis, we consider various methods for the exact and approximate calculation of absorption- and fluorescence-type linear spectra. We discuss the Exact Stochastic Path Integral Evaluation (PI) method, and several approximate methods—including the Full Cumulant Expansion (FCE), complex time-dependent Redfield (ctR), and Redfield and modified Redfield methods. We systematically describe the accuracy of the approximate methods for calculating the spectra of a chlorophyll dimer system with molecular parameters and system–environment interaction similar to that of plant light-harvesting complexes. From this analysis we found the FCE method to perform best for the calculation of absorption-type spectra and for fluorescence-type spectra when the interpigment coupling is not very strong (we regard couplings greater than 300 per cm as very strong). The ctR method generally performs well for couplings smaller than about 100 per cm, except for the calculation of circular dichroism spectra, and outperforms FCE for the calculation of fluorescence-type spectra when the coupling is very strong. Spectra calculated with the Redfield or modified Redfield methods are often inaccurate—especially when the interpigment couplings are strong or site energy gaps are small. We also found that the quality of fluorescence-type spectra depends crucially on the accurate modelling of the Stokes shift and the equilibrium state. We calculate spectra with the ctR method in order to compare literature Hamiltonians of the light-harvesting complex CP29, and we use particle swarm optimisation (PSO) to determine an improved set of energies (and additional molecular parameters) for this complex. Finally, we show that artificial neural networks can be used to accurately predict linear spectra from molecular parameters, and vice versa.South African National Research Foundation (Grant No. 101404); South African Quantum Technology Initiative (Grant No. SAQuTI03/2021)PhysicsPhD (Physics)Unrestricte

Optimisation of Microfluidic Flow Systems

This project investigates the fluid flow and heat transfer in microfluidic flow systems using Computational Fluid Dynamics (CFD) and experiments. The first part of this work focuses on developing a CFD - enabled optimisation methodology of the geometrical features of i) a microfluidic heatsink design and ii) a single-phase (SP) continuous-flow (CF) Polymerase Chain Reaction (PCR) Device. This is achieved using COMSOL Multiphysics 5.4 ®to simulate the fluid flow, heat transfer (and PCR kinetics for the case of the microfluidic PCR device). Optimisation problems are then formed, selecting objective functions related to the performance of the devices. Design of Experiments is then used together with COMSOL Multiphysics 5.4 ® to collect the values of the objective functions over the design domain. Matlab© is then used to generate the response surfaces of the objective functions, using different techniques, locate the optimum design solutions (genetic algorithm, multi-level coordinate search method) and obtain the Pareto front for the cases of multi-objective optimisation problems. Results of this work indicate the possibility of significantly enhancing the performance of SP-CF-PCR devices in terms of the DNA amplification, device volume, total operating time and total pressure drop by up to 16.4%, 43.2%, 17.8% and 80.5% respectively, after applying the appropriate design modifications for each objective. The increase in the DNA amplification is achieved by increasing the channel width and residence times while minimising the channel height. The reduction in the device volume, total operating time and total pressure drop are achieved when using the smallest residence times and higher channel width. According to this investigation, the DNA amplification appears to be linked to the temperature uniformity and to the residence time in the extension zone. The second part of this work focuses on i) obtaining a better understanding of the role that the concentration and presence of droplets play in conjugate heat transfer phenomena in droplet-laden flows, ii) creating and optimising a reusable, cheap and easy-to-fabricate device that can perform Melting Curve Analysis (MCA), in order to facilitate the work of a group of biologists at the University of Leeds. More specifically, this device aims to check for the presence of rare DNA species and possible contaminations in their collected samples in a fast, robust and cheap way, by testing if the DNA product has a unique melting temperature. The experimental setup is designed after performing a series of simulations using COMSOL Multiphysics 5.4 ®, considering different potential designs while at the same time simulating the energy requirements of the system. After finalising the design, a PID temperature controller is implemented on the Arduino Platform, achieving the required temperature difference between the two ends of the device. The results obtained during the experiments demonstrate a successful temperature control that is robust and does not require the adjustment of the PID parameters for the performance of similar experiments in the different temperature ranges tested

Numerical and experimental investigation of novel materials for laser and amplifier operations

One of the most exciting areas of research in optics is rare-earth doped glasses and fibres with capacity for near-infrared to mid-infrared operations. In particular, there is great interest in optimising parameters like ion concentration, fibre length/geometry, and pump conditions for applications in photoluminescence, amplification and lasing. Round trip investigation from material fabrication, experimental setup and actual device can be laborious, expensive and come with some uncertainties. Some of these uncertainties are accurate identification of ion-ion interactions, impact of such interactions on device performance, correct extraction of phenomenological material properties and the prediction of combination of properties with numerical methods. In this thesis, the spectroscopic behaviour of rare-earth doped materials are theoretically studied via numerical simulations and experimentally verified. The models developed are applicable to steady-state and transient behaviour of rare-earths under different excitation conditions. For the simulation, a couple of spectroscopic parameters are needed which have to be obtained in advance from bulk glasses. Parameters like radiative and non-radiative lifetimes are calculated by complementing theoretical analysis with a few experimental measurements. The first part of the research concentrates on the study of ion-ion interactions in different concentrations of erbium doped sol-gel SiO2 prepared by the sol-gel method. The work includes continuous-wave (CW) and pulsed excitation spectroscopic measurement on the glasses that provide data for the model. These measurements together with the rate-equation modelling are used to obtain a physical understanding of the processes responsible for the fluorescence features observed. A particle swarm optimisation technique was used to predict the values of the ion-ion interactions. The behaviour of the 488 nm and 800 nm excitations were consistent with the predictions of the model. Indeed, the agreement between the calculated photoluminescence and the measured emission indicates that the six important processes that influence the ion-ion interactions in the bulk material have been correctly identified and included. With this model of photoluminescence at hand, it was possible to extend it to laser or amplifier configurations. Subsequently, erbium doped ZBLAN glass fibre with lower phonon energy were explored for lasing in the mid-infrared for application to 2.73 µm high-power delivery for tissue surgery. Accurate laser characteristics were predicted for two different designs, including the ultimate thermal designs. Optimum boundary conditions of mirror end-facet reflectivity, fibre length and effects of modelling parameters were addressed. The study is complimented with experimental data of double-clad fibre and the results reported were a clear documentation of the design of erbium doped ZBLAN fiber laser. Finally, the potential of P r3+ doped chalcogenide (GeAs(Ga/In)Se) glass for photoluminescence and lasing at 4.73 µm is studied. This is to answer the research question - Can we extract the spectroscopic parameters and also model the superior property of these novel glasses?. The laboratory facilities and availability of experimental data were decisive in the choice of praseodymium ions as well as inclusion of Gallium or Indium for this part of the research. The superior characteristics of Indium over Gallium for hotoluminescence and consequently device characteristics were studied with the aid of a rate equation model. The phenomenon of photon reabsorption in the chalcogenide fibres were also simulated and verified with experiment. The work has produced a comprehensive numerical model for the simulation of photoluminescence in P r3+doped selenide based chalcogenide glass and fibre from NIR to mid-IR especially in the Gallium and Indium based analogues

ReSCon '09, Research Student Conference: Book of Abstracts

The second SED Research Student Conference (ReSCon2009) was hosted over three days, 22-24 June 2009, in the Lecture Centre at Brunel University. The conference consisted of technical presentations, a poster session and social events. The abstracts and presentations were the result of ongoing research by postgraduate research students from the School of Engineering and Design at Brunel University. The conference is held annually, and ReSCon plays a key role in contributing to research and innovations within the School

Numerical and experimental investigation of novel materials for laser and amplifier operations

One of the most exciting areas of research in optics is rare-earth doped glasses and fibres with capacity for near-infrared to mid-infrared operations. In particular, there is great interest in optimising parameters like ion concentration, fibre length/geometry, and pump conditions for applications in photoluminescence, amplification and lasing. Round trip investigation from material fabrication, experimental setup and actual device can be laborious, expensive and come with some uncertainties. Some of these uncertainties are accurate identification of ion-ion interactions, impact of such interactions on device performance, correct extraction of phenomenological material properties and the prediction of combination of properties with numerical methods. In this thesis, the spectroscopic behaviour of rare-earth doped materials are theoretically studied via numerical simulations and experimentally verified. The models developed are applicable to steady-state and transient behaviour of rare-earths under different excitation conditions. For the simulation, a couple of spectroscopic parameters are needed which have to be obtained in advance from bulk glasses. Parameters like radiative and non-radiative lifetimes are calculated by complementing theoretical analysis with a few experimental measurements. The first part of the research concentrates on the study of ion-ion interactions in different concentrations of erbium doped sol-gel SiO2 prepared by the sol-gel method. The work includes continuous-wave (CW) and pulsed excitation spectroscopic measurement on the glasses that provide data for the model. These measurements together with the rate-equation modelling are used to obtain a physical understanding of the processes responsible for the fluorescence features observed. A particle swarm optimisation technique was used to predict the values of the ion-ion interactions. The behaviour of the 488 nm and 800 nm excitations were consistent with the predictions of the model. Indeed, the agreement between the calculated photoluminescence and the measured emission indicates that the six important processes that influence the ion-ion interactions in the bulk material have been correctly identified and included. With this model of photoluminescence at hand, it was possible to extend it to laser or amplifier configurations. Subsequently, erbium doped ZBLAN glass fibre with lower phonon energy were explored for lasing in the mid-infrared for application to 2.73 µm high-power delivery for tissue surgery. Accurate laser characteristics were predicted for two different designs, including the ultimate thermal designs. Optimum boundary conditions of mirror end-facet reflectivity, fibre length and effects of modelling parameters were addressed. The study is complimented with experimental data of double-clad fibre and the results reported were a clear documentation of the design of erbium doped ZBLAN fiber laser. Finally, the potential of P r3+ doped chalcogenide (GeAs(Ga/In)Se) glass for photoluminescence and lasing at 4.73 µm is studied. This is to answer the research question - Can we extract the spectroscopic parameters and also model the superior property of these novel glasses?. The laboratory facilities and availability of experimental data were decisive in the choice of praseodymium ions as well as inclusion of Gallium or Indium for this part of the research. The superior characteristics of Indium over Gallium for hotoluminescence and consequently device characteristics were studied with the aid of a rate equation model. The phenomenon of photon reabsorption in the chalcogenide fibres were also simulated and verified with experiment. The work has produced a comprehensive numerical model for the simulation of photoluminescence in P r3+doped selenide based chalcogenide glass and fibre from NIR to mid-IR especially in the Gallium and Indium based analogues

Autonomous Monitoring of Contaminants in Fluids

The litigation and mitigation of maritime incidents suffer from a lack of information, first at the incident location, then throughout the evolution of contaminants such as spilled oil through the surrounding environment. Prior work addresses this through ocean and oil models, model directed sensor guidance and other observation methods such as satellites. However, each of these approaches and research fields have short-comings when viewed in the context of fast-response to an incident, and of constructing an all-in-one framework for monitoring contaminants using autonomous mobile sensors. In summary, models often lack consideration of data-assimilation or sensor guidance requirements, sensor guidance is specific to source locating, oil mapping, or fluid measuring and not all three, and data assimilation methods can have stringent requirements on model structure or computation time that may not be feasible. This thesis presents a model-based adaptive monitoring framework for the estimation of oil spills using mobile sensors. In the first of a four-stage process, simulation of a combined ocean, wind and oil model provides a state trajectory over a finite time horizon, used in the second stage to solve an adjoint optimisation problem for sensing locations. In the third stage, a reduced-order model is identified from the state trajectory, utilised alongside measurements to produce smoothed state estimates in the fourth stage, which update and re-initialise the first-stage simulation. In the second stage, sensors are directed to optimal sensing locations via the solution of a Partial Differential Equation (PDE) constrained optimisation problem. This problem formulation represents a key contributory idea, utilising the definition of spill uncertainty as a scalar PDE to be minimised subject to sensor, ocean, wind and oil constraints. Spill uncertainty is a function of uncertainty in (i) the bespoke model of the ocean, wind and oil spill, (ii) the reduced order model identified from sensor data, and (iii) the data assimilation method employed to estimate the states of the environment and spill. The uncertainty minimisation is spatio-temporally weighted by a function of spill probability and information utility, prioritising critical measurements. In the penultimate chapter, numerical case-studies spanning a 2500 km2 coastal area are presented. Here the monitoring framework is compared to an industry standard method in three scenarios: A spill monitoring and prediction problem, a retrodiction and monitoring problem and a source locating problem