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Organic semiconductors : optical amplification, lasing and soft lithography
Full text linkThis thesis presents an investigation of optical amplification and lasing in con jugated polymers and novel dendritic organic semiconductors. Novel methods of producing useful wavelength scale microstructure in these materials are also examined. Conjugated materials are a new class of semiconductors that show great potential for tuneable lasers, displays and photovoltaics.
Conjugated polymers have received interest as novel laser gain media be cause they exhibit optical gain over broad spectral ranges and are easy to process. However, there had been no demonstration of an polymer optical amplifier. A broadband solution based optical amplifier is demonstrated. The effect of pump energy, probe energy and solution concentration are examined. Progress towards a solid state polymer amplifier is discussed. Such devices would be useful in ultrafast data communications due to the possibility of gain over a broad spectral range.
Wavelength scale microstructure can be used to control and manipulate light. To realise microstructured organic semiconductor devices, complex fabrication methods are used which remove the ease of processability that is a key advantage of organic materials. Simple techniques to pattern organic semiconductors directly are demonstrated. Solvent assisted micromoulding is used to fabricate polymer distributed feedback lasers in less than two minutes.
Recently a new class of materials have been developed called dendrimers. Their branched modular architecture allows for the independent tuning of the electrical, optical and processing properties. Strong amplification in both solutions and thin films of a bis-fluorene cored dendrimer have been demonstrated. DFB lasers were also fabricated and lower threshold and higher output power were achieved by increasing the dendrimer generation and by changing from etched silica substrates to directly imprinted DFB structures. These advances in organic semiconductor materials and device fabrication should lead to new applications in optoelectronics
DEER measurements of calmodulin : novel spin labels and structural insights
No full textDouble electron-electron resonance (DEER) spectroscopy is a biophysical technique used in structural biology. It allows nanometre scale distance measurements between spin labels containing unpaired electrons. In this thesis, DEER was employed to investigate the structure and behaviour of calmodulin, a calcium binding protein with significant functional and physiological importance.
Following an introduction to the theoretical background and methodologies, the experimental work is organised around three main research questions. The first experimental chapter explores the use of bifunctional spin labelling of vicinal cysteines with a next-generation maleimide spin label. This approach aimed to reduce linker flexibility and to establish a viable labelling strategy for cysteine rich proteins.
The second experimental section investigates the DEER characteristics of five Gd(III) spin labels, both well established and new molecules, measured on two calmodulin mutants, engineered to yield a short and respectively a long distance distribution. This study also compares sensitivity between two home-built W-band spectrometers and a commercial Q-band instrument.
The final part examines the behaviour of calmodulin in a synthetic macromolecular crowding environment, combining DEER measurements of four apo and holo calmodulin mutants with computational modelling to assess the structural changes."The work presented in this thesis was funded by Engineering and Physical Sciences Research Council (EPSRC) EP/ N509759/1. The part of work conducted in collaboration with Weizmann Institute of Science, Israel was sponsored by the Bluston Making Connections (UK-WIS) scheme, The Royal Society (International Exchanges) and the Carnegie Trust."--Fundin
Machine learning whole slide image analysis for the prediction of colorectal cancer biomarkers
No full textColorectal cancer (CRC) is the second leading cause of cancer death worldwide, and incidence is predicted to rise sharply in the next decade. Precision oncology requires the identification of clinically actionable biomarkers such as MMR/MSI status and KRAS, NRAS and BRAF mutations, however immunohistochemistry and sequencing are slow and costly. This thesis shows that machine learning algorithms can rapidly and inexpensively predict these biomarkers directly from routine haematoxylin and eosin whole slide images (WSI), potentially accelerating triage for confirmatory testing and shortening the route to targeted therapy.
Baseline tissue segmentation and slide-level tumour detection are established using fully supervised convolutional networks. A data constrained experiment then evaluates three foundation models (CTransPath, Phikon and UNI) on 423 CRC slides, confirming that self-supervised representations support reliable biomarker prediction when data are scarce. Next, the thesis introduces SurGen, a public dataset of 1020 slides from 843 patients with genetic and survival annotations, released with fully reproducible code exemplars, lowering the barrier to entry for future researchers.
An extensive generalisation study trains transformer aggregators on embeddings from UNI, UNI2-h and Virchow2 across five cohorts: TransSCOT, SurGen, TCGA-CRC, CPTAC-COAD and ORION. Models achieve state-of-the-art AUROC of 0.81778 for KRAS, 0.72108 for NRAS 0.92828 for BRAF, and 0.9559 for MSI within individual cohorts, and retain high accuracy when applied to unseen datasets. A two stage hyper-parameter search reduces computation by a factor of twenty without sacrificing performance.
The thesis supplies the first openly accessible large scale CRC WSI resource with genomics and outcomes, rigorous baselines for both data-rich and data-scarce settings, and the most extensive evaluation to date of foundation model transfer in colorectal pathology. Combining open data with extensive experimentation and thorough benchmarking, this thesis advances WSI biomarker detection towards clinical triage workflow, potentially expediting access to personalised care for colorectal cancer patients."I would like to thank NHS Lothian for funding the work carried out in this thesis. This work is supported in part by the Industrial Centre for AI Research in Digital Diagnostics (iCAIRD) which is funded by Innovate UK on behalf of UK Research and Innovation (UKRI) (project number 104690)."--Fundin
An investigation into some characteristics of the rainfall-subsurface runoff system in an upland catchment : Glendevon, Scotland
Full text linkThe study was aimed at investigating certain aspects of the subsurface hydrology in the Upper Frandy Catchment, Glendevon, Scotland. Examination was directed towards an understanding of the rainfall- throughflow and overlandflow processes as they operate upon the undisturbed slopes of this area.
From a review of the pertinent literature two forms of theoretical analysis were considered. Queueing theory was found to provide a useful conceptualisation of the processes included, but the underlying assumptions of this form of analysis could not be satisfied. Spectral analysis of time series was carried out using the B.M.D. package; however, although the technique appeared a priori to be appropriate, the extremely long runs of observations with value zero which occured in the data undermined its validity.
Data loggers and their ancillary computer programs were developed. Data collection was frought with problems and only one month of usable data was finally available. Due to the discrete nature of the process as recorded, time-series analysis was found to be inappropriate, but even with the underlying unstationarity certain tentative conclusions as to the relative importance of the processes and the delays incorporated in these processes could be drawn.
The spatial makeup of the Upper Frandy was also investigated with an aim to the extension of any models developed for the point process studies. It was shown that this area possesses a highly variable hydrologic space and that any models developed would have to encompass this.
The main aim of the thesis was not met, but instead various forms of analysis have been examined and their limitations to this type of study demonstrated with better data collection techniques, the principles laid down in this study should go a long way to answering the questions posed
Spectroscopy of free-floating planetary-mass objects and their disks with JWST
No full textFunding: B.D. and A.S. acknowledge support from the UKRI Science and Technology Facilities Council through grant ST/Y001419/1/. R.J. and L.F. acknowledge support for the JWST-GO-04583.008 program provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–03127. V.A.-A. acknowledges support from the INAF grant 1.05.12.05.03. K.M. acknowledges support from the Fundação para a Ciância e a Tecnologia (FCT) through the grant 2022.03809.CEECIND, and the Scientific Visitor Programme of the European Southern Observatory (ESO) in Chile. P.P. acknowledges funding from the UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee from ERC (under grant agreement No 101076489).Free-floating planetary-mass objects (FFPMOs) are known to harbor disks at young ages. Here, we present 1–13 μm spectra for eight young FFPMOs with masses of 5–10 MJup (at ages of 1–5 Myr), using the NIRSpec and MIRI instruments on the James Webb Space Telescope. We derive fundamental properties of these targets, and find spectral types of M9.5 to L4, with effective temperatures of 1600–1900 K. The photospheric spectra of our targets show a clear diversity at similar temperatures, especially in the 3–5 μm range, unaccounted for by existing atmospheric models. We find a silicate absorption feature in the photosphere of one of our targets, the first such detection in very young FFPMOs, indicating silicate clouds in their cool atmospheres. Six of our objects show mid-infrared excess emission above the photosphere, as well as silicate emission features, demonstrating the presence of disks. The shape and strength of the latter features constitute strong evidence of grain growth and crystallization, similar to what is seen in more massive brown dwarfs and stars. We also detect emission lines from hydrocarbon molecules in the disks of several targets. These are the lowest-mass isolated objects found so far with silicate and hydrocarbon emission features arising in their disks. The presence of disks and their characteristics point to the potential for the formation of rocky companions around free-floating planetary-mass objects.Peer reviewe
Tropical temperature distributions over a wide range of climates : theory and idealized simulations
No full textFunding: J. A. M. D. is supported by a St Leonard’s College Doctoral Scholarship awarded by the University of St Andrews, and M. P. B. is supported by the UKRI Frontier Research Guarantee scheme (Grant EP/Y027868/1).Understanding future changes in temperature variability and extremes is an important scientific challenge with societal impacts. Here, the responses of daily near-surface temperature distributions to climate warming are explored using an idealized GCM. Simulations of a wide range of climate states are performed using both a slab-ocean aquaplanet configuration and a simple continental configuration with a bucket-style model for land hydrology. In the tropics, the responses of extreme temperatures to climate change contrast strongly over land and ocean. Over land, warming is amplified for hot days relative to the average summer day. But over ocean, warming is suppressed for hot days, implying a narrowing of the temperature distribution. Previous studies have developed theories based on convective coupling to interpret changes in extreme temperatures over land. Building on that work, the contrasting temperature distribution responses over land and ocean are investigated using a novel theoretical framework based on local convective coupling. The theory highlights five physical mechanisms with the potential to drive differential warming across temperature percentiles: free-tropospheric temperature change, relative humidity change, convective available potential energy (CAPE) change, the hot-get-hotter mechanism, and the drier-get-hotter mechanism. Hot days are relatively dry over land due to limited moisture availability, which drives the drier-get-hotter mechanism and amplified warming of the warm tail of the distribution. This mechanism is the primary factor explaining the contrasting responses of hot days over land and ocean to climate change, but other mechanisms also contribute to changing the temperature distribution, with changes in free-tropospheric temperature and surface relative humidity having large influences (which partially cancel).Peer reviewe
Resonant interlayer coupling in NbSe2-graphite epitaxial moiré superlattices
No full textFunding: The authors gratefully acknowledge support from the UK Engineering and Physical Sciences Research Council (Grants Nos. EP/X015556/1 and EP/M023958/1). M.S.B. acknowledges support from Leverhulme Trust (Grant No. RPG-2023-253). K. K. was supported by the CDT in Graphene NOWNANO. A.A. had support from the Indonesia Endowment Fund for Education (LPDP), NIB/202209223311735. R.V.B. and M.S.B. are grateful to E-IMR center at the Institute for Materials Research, Tohoku University, for continuous support.Moiré heterostructures, created by stacking 2D materials together with a finite lattice mismatch or rotational twist, represent a new frontier of designer quantum materials. Typically, however, this requires the painstaking manual assembly of heterostructures formed from exfoliated materials. Here, clear spectroscopic signatures of moiré lattice formation in epitaxial heterostructures of monolayer (ML) NbSe2 grown on graphite substrates are observed. Angle-resolved photoemission measurements and theoretical calculations of the resulting electronic structure reveal moiré replicas of the graphite π states forming pairs of interlocking Dirac cones. Interestingly, these intersect the NbSe2 Fermi surface at the k-space locations where NbSe2's charge-density wave (CDW) gap is maximal in the bulk. This provides a natural route to understand the lack of CDW enhancement for ML-NbSe2/graphene as compared to a more than fourfold enhancement for NbSe2 on insulating support substrates, and opens new prospects for using moiré engineering for controlling the collective states of 2D materials.Peer reviewe
The substellar population in Corona Australis
No full textFunding: KM and AdB-dV acknowledges support from the Fundação para a Ciência e a Tecnologia (FCT) through the CEEC-individual contract 2022.03809.CEECIND (DOI 10.54499/2022.03809.CEECIND/CP1722/CT0001), and the project 2023.01915.BD (DOI 10.54499/2023.01915.BD). KM also acknowledges support from the Scientific Visitor Programme of the European Southern Observatory (ESO) in Chile. BD and AS acknowledge support from the UKRI Science and Technology Facilities Council through grant ST/Y001419/1/. VA-A acknowledges support from the INAF grant 1.05.12.05.03.Context . The substellar initial mass function (IMF) and the formation mechanisms of brown dwarfs (BDs) remain key open questions in star formation theory. A detailed census and characterization of the IMF in a large number of star-forming regions are essential for constraining these processes. Aims . We identify and spectroscopically confirm very low-mass members of the Corona Australis (CrA) star-forming region to refine its substellar census, determine its low-mass IMF, and compare it to other clusters. Methods . Using deep I-band photometry from Suprime-Cam/Subaru and data from the VISTA Hemisphere Survey (VHS), we identified low-mass BD candidates in CrA. We subsequently conducted near-infrared spectroscopic follow-up of 173 of these candidates with KMOS/VLT, and we also obtained optical spectra for eight kinematic candidate members identified via Gaia data using FLOYDS/LCO. Results . The kinematic candidates observed with optical spectroscopy are confirmed as low-mass stellar members with spectral types M1 to M5. In contrast, all 173 BD candidates observed with KMOS are identified as contaminants. Although the follow-up yielded no new substellar members, it places strong constraints on the number of undetected substellar objects in the region. Combined with literature data, this enables us to derive the substellar IMF, which is consistent with a single power-law slope of α = 0.95 ± 0.06 in the range 0.01–1 M⊙ or α = 0.33 ± 0.19 in the range 0.01–0.1 M⊙. The star-to-BD ratio in CrA is ∼2. We also provide updated IMFs and star-to-BD ratios for Lupus 3 and Cha I from the SONYC survey, reflecting revised distances from Gaia. Finally, we estimate surface densities and median far-ultraviolet fluxes for six star-forming regions and clusters to characterize their environments and compare their substellar populations as a function of environmental properties. Conclusions . The IMF and star-to-BD ratio show no clear dependence on stellar density or ionizing flux from the massive stars. A combined effect in which one factor enhances and the other suppresses BD formation also appears unlikely.Peer reviewe
A search for transit-timing variations in the transiting hot-Jupiter systems HIP 65, NGTS-6, NGTS-10, and WASP-173
No full textFunding: JS acknowledges support from STFC under grant no. ST/Y002563/1. FA, MA, and UGJ acknowledge funding from the Novo Nordisk Foundation Interdisciplinary Synergy Programme grant no. NNF19OC0057374. VB and PR are supported by PRIN 2022 CUP D53D23002590006. RFJ acknowledges the support provided by the GEMINI/ANID project under grant no. 32240028, by ANID’s Millennium Science Initiative through grant ICN12_009, awarded to the Millennium Institute of Astrophysics (MAS), and by ANID’s Basal project FB210003. EK is supported by the National Research Foundation of Korea 2021M3F7A1082056. LM acknowledges the financial contribution from PRIN MUR 2022 project 2022J4H55R.Hot Jupiters are Jupiter-mass planets with orbital periods of less than 10 d. Their short orbital separations make tidal dissipation within the stellar host especially efficient, potentially leading to a measurable evolution of the orbit. One possible manifestation of this is orbital decay, which presents itself observationally through variations in the orbital period and thus times of transit. Here, we select four promising exoplanetary systems for detecting this effect: HIP 65, NGTS-6, NGTS-10, and WASP-173. We present 33 new transit light curves taken with the 1.54 m Danish Telescope, and analyse these alongside photometric data from the Transiting Exoplanet Survey Satellite and transit-timing data from the literature. We construct two ephemeris models for each target: a linear ephemeris and a shrinking orbital period due to tidal decay. The linear ephemeris is preferred for three of the four models – the highest significance for the quadratic ephemeris is over 3σ for WASP-173. We compare these results to theoretical predictions for tidal dissipation of gravity waves in radiation zones, and find that wave breaking is predicted only in WASP-173, making rapid decay plausible in this system but unclear in the other three. The sensitivity of transit timings to orbital decay depends on the square of the time interval covered by available observations, so our results establish a useful baseline against which future measurements can be compared. NGTS-6 and NGTS-10 are important objects for future study as they are in the first field to be observed by the upcoming PLATO mission.Peer reviewe
Longest common subsequence with gap constraints
No full textFunding: The work on the current article was partly supported by the German Research Foundation (DFG) [project numbers 389613931 (research grant); 466789228 (Heisenberg grant)]. Open Access funding enabled and organized by Projekt DEAL.We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. (2022), we consider the setting when the distance (i. e., the gap) between two consecutive symbols of the subsequence has to be between a lower and an upper bound (which may depend on the position of those symbols in the subsequence or on the symbols bordering the gap) as well as the case where the entire subsequence is found in a bounded range (defined by a single upper bound), considered by Kosche et al. (2022). In all these cases, we present efficient algorithms for determining the length of the longest common constrained subsequence between two given strings, and discuss lower bounds for the respective problems.Peer reviewe
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