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Energy landscape exploration and global optimisation of hydrated molecular clusters
Get PDFThe Hofmeister series is a ranking of ions based on their ability to affect various properties of proteins and other biological macro-molecules in aqueous solutions. Initially described by Franz Hofmeister in the late 19 century, the series categorises ions according to their effects on the solubility, stability, and activity of proteins. It is often used to understand and predict the behaviour of proteins in different ionic environments, particularly in the context of protein precipitation, folding, and stability. In this thesis I present a systematic study of the stepwise hydration of simple ions within the Hoffmeister series with the aim of elucidating both their structures and their energy landscapes. This study was undertaken using parallel basin hopping global optimisation with a hybrid of potentials, a cheap OPLS-like (Optimised Potentials for Liquid Simulations) potential was used to generate large databases of candidate minima. These putative minima were then reoptimised to a much tighter tolerance using a dispersion-corrected DFT scheme, to yield good minima that are shown to reproduce various experimental results. This technique has allowed us to provide good putative minima to larger sizes of clusters in a systematic manner than would otherwise be available. We establish common structural motifs across a variety of ions from across the Hoffmeister series, and show the effects of interpolating charges between two candidate ions has on the structural motifs present.
We then extend this study to encompass metal ions. We study the stepwise hydration of AuAg nanoclusters as cations, anions and uncharged clusters. This part of the study was conducted using the MEGA/GIGA genetic algorithms, directly at the DFT level. I reproduce some previous experimental infrared spectra for the anionic clusters, and then go on to present novel structures for the cationic system and the neutral system. I then categorise the structural motifs present in the clusters and compare these to those seen in the Hoffmeister ion study and present some computed infrared spectra.
Finally, I present a novel fusion of a parallel pool genetic algorithm with a Thresholding Algorithm I am calling BMPGA. The genetic algorithm is an entirely new implementation of the old BPGA written specifically with the optimisation of molecular clusters in mind. BMPGA implements a modified Deavan and Ho crossover scheme optimised for molecular systems, has massive thread-safe parallelism built-in by design, and implements a number of common and less common mutation schemes.1 The mutation schemes include the old classics such as single and multiple translations and rotations, as well as some more computationally demanding mutations such as short, high temperature Monte Carlo and molecular dynamics simulations. The hybridisation with the Thresholding scheme comes in to play in two different ways; it is available as an optional mutation scheme in the form of Threshold Monte Carlo. These mutations allow for the system to undergo infinite-temperature MC runs with a total-system energy cap applied the final configuration obtained is then subjected to a number of stochastic quenches. The other way that Thresholding is incorporated into the GA is that it can be applied to the population of minima within the GA itself, this leads to ensemble Thresholding and I show that this method allows for very rapid exploration of the landscape by allowing the population to escape wells that it may otherwise become trapped in. By lowering the energy cap over the course of the optimisation, good performance of this method is seen. I present benchmark results for this new GA using a variety of systems and potentials, from simple Lennard-Jones clusters, through some DFTB results to direct landscape exploration at the DFT level. I show that the parallel performance of this method is extremely good, and scales very well to a large number of CPU cores. This new GA method shows promise for allowing very large-scale optimisations to be performed on a large range of systems, only limited by the availability of HPC resources
Composite thermochemical energy storage materials for building applications
No full textNo abstract available
Colonisation of the gut microbiome by Escherichia coli during international travel
Get PDFThere is a high risk of acquiring extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), predominantly Escherichia coli, among international travellers visiting antimicrobial resistance hotspots. Although factors that drastically perturb the gut microbiome — e.g. antibiotic use and travellers’ diarrhoea — have been shown to influence the risk of ESBL-E acquisition, it remains largely unknown whether successful colonisation of ESBL-E during travel is associated with the composition, functional capacity and resilience of the traveller’s microbiome. Strains of E. coli often vary by geography and pathogenicity and it is unknown how their inter- and intra-species interactions associate with the acquisition of ESBL-E. The research in this thesis aims to address these problems by determining how involved the entire gut microbiome is in resisting colonisation from invading ESBL-E, or if species interactions are more important. Faecal samples from before travel and immediately upon return from Africa or Asia of 179 Dutch travellers had previously been collected and whole metagenome shotgun sequenced. Here, the gut microbiome was profiled with a metagenomics species concept approach and the microbial composition, population diversity and functional capacity were determined and how these associate with the acquisition of ESBL-E during travel was calculated. None of the measurements in pre-travel samples were predictive of risk of acquiring ESBL-E. When compared to post-travel measurements, there were also no longitudinal changes specific to acquiring ESBL-E, instead only significantly associating with the onset of travellers’ diarrhoea. How individual taxa are associated was then determined, where it was discovered that the prevalence and abundance of Citrobacter freundii and two members of the genus Bacteroides increased in those remaining uncolonised by ESBL-E, suggesting that these taxa may have some capability of outcompeting ESBL-E. This was tested by growing both commensal and ESBL-producing E. coli in nutrient broth in the presence of travel-acquired Citrobacter, but Citrobacter could not outcompete E. coli in a direct manner in nutrient rich media.
As the longitudinal change to E. coli was not significantly associated with the acquisition of ESBL-producing E. coli, it was hypothesised that strain replacement was occurring. Individual strains were assembled into metagenome assembled genomes (MAGs) and compared to reference genomes that represent the total E. coli strain diversity. The population of E. coli strains was drastically altered during travel, but this was independent from the factors driving the acquisition of ESBL-E (and perturbing the gut microbiome). The results from this thesis highlight the potential of individual species to interact with invading ESBL-E, but most importantly focusses future research towards avenues of altering a person’s colonisation resistance as an intervention strategy to minimise the spread of multidrug resistant bacteria
Muslim perceptions of biblical lore narratives: between tentative acceptance and total rejection (7th- 14th century)
No full textThis research demonstrates that isrāʾīliyyāt category has not been theorised by early Muslims to denote biblical lore. Rather, the theorisation of isrāʾīliyyāt category started with the fourteenth- century Ḥanbalī scholar Ibn Taymiyya who outlined the appropriate methodology for dealing with such narratives. Ibn Taymiyya's theoretical framework was subsequently embraced and put into practice by his dedicated student Ibn Kathīr.
This dissertation argues that before the theoretical formulation of the term, early Muslims engage with biblical lore without subjecting it to any critical examination. It was Ibn Taymiyya and Ibn Kathīr who utilised ḥadīth methodology to assess the biblical lore embedded in Islamic literature. While this work aims firstly to examine the validity of biblical lore within Islamic literature, it aims secondly to question the concept of taḥrīf (scriptural falsification) and investigate whether it poses an impediment to Muslims to engage with biblical lore
An exploratory qualitative study of patients’ perceptions of material risks for Orthognathic Surgery
Get PDFAbstract
Aim: There are a limited number of publications which have qualitatively investigated the treatment journey and the risk based decision-making process of patients undergoing orthognathic surgery following the Montgomery versus Lanarkshire Health Board (2015) legal ruling. Therefore, the aim of the study is to carry out qualitative research to ascertain the perception of risks during decision-making in a group of patients who have undergone orthognathic surgery. The goal is to improve the consent process of this elective procedure and better tailor this for each individual patient and improve their overall experience.
Design: The aims of this study were to evaluate patients’ perception and their lived experiences qualitatively, using focus groups and one to one interviews.
Methods: Patients who had undergone bimaxillary orthognathic surgery were recruited from review clinics at Birmingham Dental Hospital and School. Recruitment began in September 2021 and was completed by December 2021. All patients were approached by an orthodontic registrar (SMS). Twenty-three participants were initially identified and of those fifteen were interviewed. Ten of the participants interviewed were female and five were male. Ages ranged from twenty-three years to forty-three years old. The range of surgery dates was from October 2017 to December 2019.
Results: Two domains were identified, the first domain investigated perceptions of risk involved in orthognathic surgery. The second domain looked at the impact of orthognathic surgery on patients’ psychosocial well-being and considerations during the consent process. The first domain based on three main themes were identified from the interviews centring on the patient’s perceived risks to orthognathic surgery: sources of information about orthognathic surgery, surgical risk and setting and format of how risks should be presented. For the second domain, again three themes; physical effects of surgery and its impact on patients' psychosocial well-being, non-physical effects of surgery and its impact on patients' psychosocial well-being, and impact of surgery necessitating support.
Conclusions: This study has found that patients need to be informed of the overall experience of the treatment journey, providing realistic and accurate information prior to starting treatment. Previous patients are a valuable source in supporting future patients in the consent process. Clinicians should be aware that what may seem of importance to them may not be the same for patients. Patients should be aware of the pain, swelling, nerve injury, difficulty eating and drinking, and the difficulties that may arise in the initial postoperative recovery period. They should also be given a realistic idea of their final facial appearance. This knowledge may lead to greater patient satisfaction and most importantly mentally prepare these patients to reduce the negative implications on their psychosocial well-being. This research has identified the importance of the patient’s social network, dieticians, and psychologists in the treatment pathway. The findings of this study can inform future quantitative studies in which further research is required to look at how this new setting and format should be employed to improve the consent process for these patients as well as developing a comprehensive list of risks from both a clinicians and patient perspective
Improving the interpretability of machine learning approaches with user-generated data
Get PDFGiven the increasing deployment of automatic decision systems in many critical scenarios, understanding and explaining machine-based decision systems has become an important problem to be solved. For this reason, recently, there has been an increasing interest in what we commonly call Explainable AI (XAI). In this thesis, starting from an overview of the inner mechanisms of deep neural networks, we will tackle the problem of interpretability from two different perspectives.
First, considering that neural networks usually encode the input features as numerical vector representations hardly understandable by humans, we propose new approaches to learning interpretable numerical vectors. In view of the availability of large collections of textual data in different scenarios, we intend to exploit the natural language information to generate vectors with intrinsic interpretability. In this way, the new numerical vectors will have the capacity of being effectively used by neural algorithms while also providing human-understandable information. The proposed methodologies are evaluated on e-commerce data with textual reviews. In this context, given the so-called neural hype, we also critically analyze whether the use of complicated and deep architectures is fully motivated in recommender systems scenarios.
Second, given the inscrutability of the inner reasoning of neural architectures, we develop a new approach capable of highlighting the portion of input information effectively used by the model for its predictions. The methodology is based on the so-called learning to explain paradigm and is applied to graph-based models. The proposed method learns to select subgraphs that are used in all the computational operations until prediction. The inherent interpretability of the model overcomes the limitations of common post-hoc explanation techniques. Furthermore, since the resulting explanations are faithful to the model reasoning, the results can also be used for model debugging and hyperparameter tuning
Strangers and strange spaces: land, people, and power in the Medieval Gawain romances
No full textThis thesis discusses ecology and sovereignty in nine Middle English and Older Scots Arthurian romances preserved in manuscripts produced between 1400 and 1650. It draws on Timothy Morton’s discussion of ‘strange strangers’ in a ‘mesh’ (The Ecological Thought, 40-41)—all human and non-human beings within the environment—to examine the Arthurian knight Gawain as he interacts with various outsiders: the Green Knight, the giant Carl, the Loathly Lady, a Ghost, a Turk, and several enemy knights. The outsiders challenge Arthur’s authority and right to rule over conquered lands, channelling concerns about land ownership, violence, and the relationship between a king and the people and land under his control. Though strange and frightening to Arthur and the Round Table, these characters cannot be rejected. To do so would be to diminish Arthur’s sovereignty, his influence over all human and non-human elements within his empire. Instead, they must be accepted with ‘radical openness’ (Morton, 81), a process that reveals the strangeness inherent in the court.
This process occurs through a series of romance motifs: the hunt, feast, bedroom, and beheading. Through these scenes, Gawain meets strange strangers, integrates them into the court, and eliminates difference between opposing sides. These interactions alter the familiar motifs, demonstrating how the inclusion of strange strangers complicates established conventions of behaviour and nobility. The Gawain romances thus exploit the conventions of romance into a complex study of the governance, land management, and cooperation needed to sustain an empire
Design and modelling of the clean energy router with advanced adiabatic compressed air energy storage system
Get PDFThe advanced adiabatic compressed air energy storage (AA-CAES) technology naturally has the flexibility of multi-energy storage and supply, which is discussed in this doctoral study as a demand for the current power system to provide more flexibility under the high proportion of sustainable consumption of renewable energy. The clean energy router (CER) can be suggested as a scheme based on the properties of AA-CAES. This thesis systematically studies the design, modelling, and operation methods of AA-CAES typical application forms, providing technical support for the operation control optimization planning of modern power systems (MPSs).
An overall architecture scheme of the CER based on AA-CAES is constructed to store and convert abandoned wind and solar energy to heating, cooling, and electricity, it offered a crucial technical solution for coordinating and fully utilizing a variety of clean energy sources. The thermodynamic model of AA-CAES can also be used to examine the CER scheme efficiency and transformation mechanism.
Based on the CER with high-temperature medium thermal storage and high-speed turbine power generation, a solar thermal collection and storage (STC) can be integrated to use the natural solar energy to further improve the overall efficiency. Combining the STC technology with AA-CAES, it can improve the capacity of multi-energy storage and supply. From the aspect of system design, it can ensure the flexible multi-energy storage joint supply capacity and high energy conversion efficiency of the system. Exergy efficiency can be applied to reflect the efficiency of the system to further analyze the performance of each subsystem and the overall system. For the economy of the system, an artificial intelligence algorithm – particle swarm optimization algorithm (PSO) is applied to obtain the minimum cost of the system through multi-objective optimization of heat and power supply units
What is Anxiety?
Get PDFIn psychology, anxiety is used as an umbrella category term to refer to three distinct phenomena: transitory episodes of anxiety (‘state anxiety’); a more stable disposition to experience these episodes (‘trait anxiety’); and the ‘anxiety disorders’. Although anxiety is widely used across psychology, our current understanding of this category is based on unsupported assumptions. Therefore, the aim of this thesis is to provide a novel, interdisciplinary understanding of the psychological category of anxiety.
The prevailing view in psychology is that anxiety forms a disunified and heterogenous category. However, in Chapter 1, I reject this prevailing assumption by arguing that anxiety forms a unified kind. To do this, I argue there is a set of distinctive reliably projectable properties that can be found across the category of anxiety. In Chapter 2, I argue that the constituents of anxiety (state anxiety, trait anxiety, and the anxiety disorders) can also be categorised together in virtue of a shared biological function. This function is the detection of and response to uncertain threats in our environment. In this way, I argue that anxiety forms not only a unified kind, but a biological functional kind. In Chapter 3, I argue that anxiety is also a strong candidate for natural kindhood. However, I argue that more empirical work must be done to firmly establish anxiety as a natural kind category. While taxonomizing anxiety is key to our metaphysical understanding of it, to provide a full picture, we must also consider its constituent parts in more detail. Therefore, in Chapter 4, I turn to consider normal and abnormal episodes of anxiety. I argue that the two lay on a multidimensional spectrum and can be delineated by four independent, but often co-occurring properties. These are: how proportionate the episode is to the objective threat that has provoked it; how physically and socially disabling the episode is; how mentally manageable the episode is; and lastly, how phenomenologically intense the episode is. In Chapter 5, I introduce a sub-category of anxiety in the form of medicalized anxiety which is comprised of both abnormal episodes of anxiety and the anxiety disorders. The development of this sub-category means that in folk psychology, a dichotomy emerges between normal anxiety and medicalized anxiety. In Chapter Six, I employ corpus linguistics to analyse our expressions of normalised and medicalized anxiety. I show that, generally, we use ‘to be anxious’ to convey normalised experiences of anxiety. Contrastingly, to convey medicalized experiences, we objectify our anxiety, using the phrase ‘to have anxiety’. To conclude the thesis, in Chapter 7, I argue that while using this objectified language to describe our medicalized experiences of anxiety may be beneficial to reduce our feelings of blame, it may also stand as an obstacle to treatment and reduce our sense of agency
Development of far-ir ultrafast time-resolved and polarization dependent techniques for investigation the charge carriers dynamics in topological insulators
Get PDFThis thesis investigates the ultrafast dynamics of photo-excited carriers on the surface of a topological insulator sample Bi2Te3. The work involves two parts. The first part of this work describes the use of time resolved spectroscopy as a technique with an infrared probe
being used in conjunction with a visible pump. An ultrafast laser system was employed in this work and shows the advantage of using an infrared probe to investigate the dynamics of free carriers on the surface. We studied the reflectance of the probe with different pump power and different probe polarization states. It was found that reflectance signals indicated the surface plasma wave generated by a visible pump that excited the surface. A surprising �finding is that the decay time of the surface wave increases as pump fluence increases. The results showed that Bi2Te3 can be employed for high-speed switching in infrared devices and optical communication.
The second part of this work is devoted to the development and application of the time resolved ellipsometry method to investigate how the refractive index of the topological insulator surface evolves in time. We developed an ellipsometry set-up by using a visible pump and an infrared probe. We have demonstrated how the complex refractive index changed following excitation. The results indicate that the refractive index reduced after excitation, while the extinction coefficient increased. In addition, the complex refractive index is recovered in a few picoseconds. From our results, we suggest that, by combining ultrafast surface plasma generated on the metallic surfaces with highly tunable refractive
index in the infrared region, Bi2Te3 thin �films can be used efficiently in optical devices for light control
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