Simulating hydrates in shallow marine sediments

With global energy needs growing alongside a drive to reduce carbon emissions, there is a demand for cleaner, alternative energy. Methane hydrates are one such resource that is being investigated with the goal of future potential exploitation. 99 % of this resource is found within marine environments where, particularly in shallow marine sediments, there is a concern that rising ocean temperatures may lead to widespread methane release as hydrate dissociates. Multi-component, multi-phase (MCMP) modelling can be used to forecast the behaviour of methane hydrate dissociation in these contexts. However, there is a lack of agreement across literature on how best to numerically solve and mathematically describe the hydrate dissociation problem. The objective of this PhD is to develop new numerical models from first principles using the Method of Lines (MOL) approach. The MOL is attractive because it takes advantage of widely available high quality, ordinary differential equation solvers. However, a significant challenge is that the MOL requires formulating the problem in terms of persistent primary dependent variables. A kinetic model was developed and used to simulate experimental data from a well studied hydrate dissociation experiment. This study improved on previous work by reconciling more of the dataset. A three-phase permeability model was developed for this purpose, which invokes a critical threshold whereby permeability is dramatically reduced in the presence of very small hydrate saturations. Due to numerical instability associated with upscaling the hydrate kinetics, the MOL is challenging to solve for regional scale problems using the kinetic model. An alternative model which maintains phases in equilibrium by removing the hydrate kinetics was therefore developed. Preliminary work applied this equilibrium model to a regional scale ocean warming driven hydrate dissociation problem. Permeability in the presence of hydrate is a strong function of pore morphology as hydrate grows within porous media. Constraining this relationship can lead to better estimations of methane emissions driven by ocean warming and methane recovery in economically attractive hydrate deposits

2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis

Funding: Engineering and Physical Sciences Research Council [EP/M019195/1]; Engineering and Physical Sciences Research Council Studentship (to J.S.H.); Biotechnology and Biological Sciences Research Council [BB/J001694/2, BB/R021848/1]; ADTBio; University of Kentucky and NCI Cancer Center Support Grant [P30 CA177558]; The Carmen L. Buck Endowment; Emerging Fields Initiative of the Friedrich-Alexander-University of Erlangen-Nuremberg [Grant title ‘Chemistry in Live Cells’]; Wellcome Trust [099149/Z/12/Z]; Royal Society, University Research Fellowship (to J.E.L.). Funding for open access charge: University of Oxford.The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2–10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2′ position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2′-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation.Publisher PDFPeer reviewe

Sn 5 s 2 lone pairs and the electronic structure of tin sulphides: A photoreflectance, high-energy photoemission, and theoretical investigation

The effects of Sn 5 s lone pairs in the different phases of Sn sulphides are investigated with photoreflectance, hard x-ray photoemission spectroscopy (HAXPES), and density functional theory. Due to the photon energy-dependence of the photoionization cross sections, at high photon energy, the Sn 5 s orbital photoemission has increased intensity relative to that from other orbitals. This enables the Sn 5 s state contribution at the top of the valence band in the different Sn-sulphides, SnS, Sn 2 S 3 , and SnS 2 , to be clearly identified. SnS and Sn 2 S 3 contain Sn(II) cations and the corresponding Sn 5 s lone pairs are at the valence band maximum (VBM), leading to ∼ 1.0 –1.3 eV band gaps and relatively high VBM on an absolute energy scale. In contrast, SnS 2 only contains Sn(IV) cations, no filled lone pairs, and therefore has a ∼ 2.3 eV room-temperature band gap and much lower VBM compared with SnS and Sn 2 S 3 . The direct band gaps of these materials at 20 K are found using photoreflectance to be 1.36, 1.08, and 2.47 eV for SnS, Sn 2 S 3 , and SnS 2 , respectively, which further highlights the effect of having the lone-pair states at the VBM. As well as elucidating the role of the Sn 5 s lone pairs in determining the band gaps and band alignments of the family of Sn-sulphide compounds, this also highlights how HAXPES is an ideal method for probing the lone-pair contribution to the density of states of the emerging class of materials with n s 2 configuration

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function

SummaryCondensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation

Mapping the Scope of Software Interventions for Moderate Internet Use on Mobile Devices

ICT is expected to form 21% of global electricity demand in 2030, and history has shown that efficiency gains in Internet infrastructure aiming to curtail such impacts are far outstripped by the growth in data traffic. We need to reduce demand for Internet connectivity, yet encouraging moderate interactions with digital devices and online services could potentially benefit users. HCI designs have been suggested for moderate interactions and Internet usage, most commonly on smartphones - but it's currently unclear whether these interventions can actually be implemented and tested to understand the user and environmental impacts. In this paper, we review features for understanding and manipulating data traffic in accordance with the stock Android and iOS development libraries to better scope the potential for implementing moderate and sustainable digital experiences. Specifically, we outline the intervention features plausible for Android implementation, and we provide reasoning for why iOS is currently too restrictive

Great expectations or small country living? Enabling small rural creative businesses with ICT.

Small businesses are prototypical rural business, but limited by distance. However, creative businesses are less constrained by space and hold great promise for rural development. Indeed, the rural is an attractive creative aesthetic milieu. Moreover, new broadband technologies seem to offer a solution to address connectivity; the social and spatial problem of being rural. Consequently, we ask how does broadband enable small rural creative firms. We sought out the practices and experiences of creative business owners, finding that broadband offered useful technical, creative, and business linking. However many were frustrated by poor technical performance. Furthermore, the accelerating pace of ICT worried respondents, who feared being left behind. Nonetheless for most-without broadband their rural location would have been impossible. We found that broadband has fostered creative rural businesses, but as new ways of making a small country living rather than stimulating a rural creative milieu. The digital promise of a creative transformation of the rural has not been realised in Scotland

Consensus Paper: Cerebellum and Social Cognition.

The traditional view on the cerebellum is that it controls motor behavior. Although recent work has revealed that the cerebellum supports also nonmotor functions such as cognition and affect, only during the last 5 years it has become evident that the cerebellum also plays an important social role. This role is evident in social cognition based on interpreting goal-directed actions through the movements of individuals (social "mirroring") which is very close to its original role in motor learning, as well as in social understanding of other individuals' mental state, such as their intentions, beliefs, past behaviors, future aspirations, and personality traits (social "mentalizing"). Most of this mentalizing role is supported by the posterior cerebellum (e.g., Crus I and II). The most dominant hypothesis is that the cerebellum assists in learning and understanding social action sequences, and so facilitates social cognition by supporting optimal predictions about imminent or future social interaction and cooperation. This consensus paper brings together experts from different fields to discuss recent efforts in understanding the role of the cerebellum in social cognition, and the understanding of social behaviors and mental states by others, its effect on clinical impairments such as cerebellar ataxia and autism spectrum disorder, and how the cerebellum can become a potential target for noninvasive brain stimulation as a therapeutic intervention. We report on the most recent empirical findings and techniques for understanding and manipulating cerebellar circuits in humans. Cerebellar circuitry appears now as a key structure to elucidate social interactions