Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting

An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the PSII yield, which only emerges on the 100 nm scale of the grana membrane and determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 nm x 200 nm patch of the grana membrane. We demonstrate that single molecule measurements of qE are consistent with a weak-quenching regime. Consequently, excitation transport can be rigorously coarse-grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. A diffusion-corrected lake model substantially improves the PSII yield determined from variable chlorophyll fluorescence measurements and offers an improved model of PSII for photosynthetic metabolism.Comment: 19 pages, 4 figures, 3 supplementary figure

Weak Galerkin finite element methods for elasticity and coupled flow problems

Includes bibliographical references.2020 Summer.We present novel stabilizer-free weak Galerkin finite element methods for linear elasticity and coupled Stokes-Darcy flow with a comprehensive treatment of theoretical results and the numerical methods for each. Weak Galerkin finite element methods take a discontinuous approximation space and bind degrees of freedom together through the discrete weak gradient, which involves solving a small symmetric positive-definite linear system on every element of the mesh. We introduce notation and analysis using a general framework that highlights properties that unify many existing weak Galerkin methods. This framework makes analysis for the methods much more straightforward. The method for linear elasticity on quadrilateral and hexahedral meshes uses piecewise constant vectors to approximate the displacement on each cell, and it uses the Raviart-Thomas space for the discrete weak gradient. We use the Schur complement to simplify the solution of the global linear system and increase computational efficiency further. We prove first-order convergence in the L2 norm, verify our analysis with numerical experiments, and compare to another weak Galerkin approach for this problem. The method for coupled Stokes-Darcy flow uses an extensible multinumerics approach on quadrilateral meshes. The Darcy flow discretization uses a weak Galerkin finite element method with piecewise constants approximating pressure and the Arbogast-Correa space for the weak gradient. The Stokes domain discretization uses the classical Bernardi-Raugel pair. We prove first-order convergence in the energy norm and verify our analysis with numerical experiments. All algorithms implemented in this dissertation are publicly available as part of James Liu's DarcyLite and Darcy+ packages and as part of the deal.II library

Mechanisms of light harvesting by photosystem II in plants

Light harvesting by photosystem II (PSII) in plants is highly efficient and acclimates to rapid changes in the intensity of sunlight. However, the mechanisms of PSII light harvesting have remained experimentally inaccessible. Using a structure-based model of excitation energy flow in 200 nanometer (nm) x 200 nm patches of the grana membrane, where PSII is located, we accurately simulated chlorophyll fluorescence decay data with no free parameters. Excitation movement through the light harvesting antenna is diffusive, but becomes subdiffusive in the presence of charge separation at reaction centers. The influence of membrane morphology on light harvesting efficiency is determined by the excitation diffusion length of 50 nm in the antenna. Our model provides the basis for understanding how nonphotochemical quenching mechanisms affect PSII light harvesting in grana membranes.Comment: 23 pages, 3 figure

Implementing quadratic supergravity inflation

We study inflation driven by a slow-rolling inflaton field, characterised by a quadratic potential, and incorporating radiative corrections within the context of supergravity. In this model the energy scale of inflation is not overly constrained by the requirement of generating the observed level of density fluctuations and can have a physically interesting value, e.g. the supersymmetry breaking scale of $10^{10}$ GeV or the electroweak scale of $10^3$ GeV. In this mass range the inflaton is light enough to be confined at the origin by thermal effects, naturally generating the initial conditions for a (last) stage of inflation of the new inflationary type.Comment: 8 pages, 1 figur

REPRESENTING THE DISPERSION OF EMISSIONS FROM AIRCRAFT ON RUNWAYS

Aircraft in their takeoff ground run constitute an unavoidable strong source of emissions subject to a highly variable motion. The intermittent nature of release makes it difficult to measure the emissions and establish their impact on mean concentrations in the vicinity of airports. Practically, it is also difficult to perform experimental studies near taxiways and runways. Remote observations have nevertheless recently been obtained by a rapidly-swept UV Lidar, and analysis of these has necessitated and informed a parallel modelling effort. Aircraft exhausts disperse in a complex manner, as they are subject not only to transport processes of the ambient atmosphere, but also to those associated with the aircraft itself (with diffusion in ambient turbulence to be expected once turbulence resulting from the aircraft falls to ambient levels). They have a downstream Lagrangian momentum associated with the engine thrust, and steadily acquire a vertical momentum as a result of their buoyancy. Exhaust streams merge and interact strongly with the ground to form a common emission plume within about a wingspan downstream of engines’ exits. Before the aircraft reaches a threshold speed, is rotated upward and lifts off, the downstream (thrust) forcing and upstream source acceleration are approximately constant, and a first-order nonlinear partial differential equation may be expressed capturing the turbulent diffusion of the plume in the reference frame of the source. The downstream forcing exceeds the buoyant forcing, so the plume remains in contact with the ground, but is heightened and narrowed by buoyant rise. During rotation and liftoff, the net downstream forcing declines as a significant airframe drag arises, and the source acceleration plummets. More importantly, lift on the airframe and the associated shed circulation cause exhausts to move downward and, in proximity to ground, outward, so their dynamics decouple from those of exhausts released earlier, with re-coupling unlikely before the aircraft has turned in its flight path. Once rotation is initiated, this argues for a simplifying (and partly analytic) treatment of the exhaust plume generated earlier, such that the turbulent diffusion of a given elemental plume segment is taken to match that of an infinitely long flow tube (with the latter ascribed the same buoyancy density and downstream Lagrangian momentum density – or mass flux – throughout)

A comparison of methods for early prediction of anaerobic biogas potential on biologically treated municipal solid waste

Anaerobic gas production tests, generically Biochemical Methane Potential (BMP) or Biogas Potential (BP) tests, are often used to assess biodegradability, though long duration limits their utility. This research investigated whether simple modelling approaches could provide a reliable earlier prediction of total biogas production. Data were assessed from a non-automated biogas test on a large number of both fresh and processed municipal solid waste (MSW) samples, sourced from a mechanical biological treatment (MBT) plant. Non-linear models of biogas production curves were useful in identifying a suitable test endpoint, supporting a test duration of 50 days. Biogas production at 50 days (B50) was predicted using the first 14 days of test data, using (a) linear correlation, (b) a new linearisation process, and (c) non-linear kinetic models. Prediction errors were quantified as relative root mean squared error of prediction (rRMSEP), and bias. Predictions from most models were improved by removing the initial exponential increase phase. Linear correlation gave the most precise and accurate predictions at 14 days (rRMSEP = 2.8%, bias under 0.05%) and allowed acceptable prediction (rRMSEP 50. These results demonstrate that early prediction of anaerobic gas production is possible for a well-optimised test, using only basic equipment and without recourse to external data sources or complex mathematical modelling

Irreversible Quantum Baker Map

We propose a generalization of the model of classical baker map on the torus, in which the images of two parts of the phase space do overlap. This transformation is irreversible and cannot be quantized by means of a unitary Floquet operator. A corresponding quantum system is constructed as a completely positive map acting in the space of density matrices. We investigate spectral properties of this super-operator and their link with the increase of the entropy of initially pure states.Comment: 4 pages, 3 figures include

The implementation of chlamydia screening: a cross-sectional study in the south east of England

Background England's National Chlamydia Screening Programme (NCSP) provides opportunistic testing for under 25 year-olds in healthcare and non-healthcare settings. The authors aimed to explore relationships between coverage and positivity in relation to demographic characteristics or setting, in order to inform efficient and sustainable implementation of the NCSP. Methods The authors analysed mapped NCSP testing data from the South East region of England between April 2006 and March 2007 inclusive to population characteristics. Coverage was estimated by sex, demographic characteristics and service characteristics, and variation in positivity by setting and population group. Results Coverage in females was lower in the least deprived areas compared with the most deprived areas (OR 0.48; 95% CI 0.45 to 0.50). Testing rates were lower in 20 1324-year-olds compared with 15 1319-year-olds (OR 0.69; 95% CI 0.67 to 0.72 for females and OR 0.67; 95% CI 0.64 to 0.71 for males), but positivity was higher in older males. Females were tested most often in healthcare services, which also identified the most positives. The greatest proportions of male tests were in university (27%) and military (19%) settings which only identified a total of 11% and 13% of total male positives respectively. More chlamydia-positive males were identified through healthcare services despite fewer numbers of tests. Conclusions Testing of males focused on institutional settings where there is a low yield of positives, and limited capacity for expansion. By contrast, the testing of females, especially in urban environments, was mainly through established healthcare services. Future strategies should prioritise increasing male testing in healthcare settings

Bacille Calmette-Guérin vaccine-related disease in HIV-infected children: a systematic review

Objective: To describe the characteristics and risk of bacille Calmette-Gu&eacute;rin (BCG) vaccine related disease in human immunodeficiency virus (HIV) infected infants.Methods: Systematic literature review of articles published from 1950 to April 2009 in the English language. We identified all microbiologically confirmed cases of disseminated BCG disease in vertically HIV-infected children reported in the literature.Results: Sixteen observational studies and 11 case reports/series were included. Observational studies suffered from high rates of loss to follow-up and death. Loco-regional BCG disease was reported in both HIV-infected and non-infected children. Disseminated BCG disease was reported only in children with immunodeficiency and only in studies employing sophisticated laboratory techniques. Sixty-nine cases of disseminated BCG were identified in the literature: 47 cases were reported in six observational studies, the majority (41/47) from the Western Cape of South Africa. A Brazilian cohort study reported no cases of disseminated BCG amongst 66 HIV-infected children observed over a 7-year period. A recent South African surveillance study reported 32 cases of disseminated BCG over a 3-year period, estimating the risk of disseminated BCG to be 992 per 100&thinsp;000 vaccinations in HIV-infected children. Few cases of severe disseminated TB were reported in the cohort studies among HIV-infected children vaccinated with BCG.Conclusion: Data on the risk of BCG vaccination in HIV-infected children are limited. Targeted surveillance for BCG complications employing sophisticated diagnostic techniques is required to inform vaccination policy.<br /

Masticatory musculature of the African mole-rats (Rodentia: Bathyergidae)

The Bathyergidae, commonly known as blesmols or African mole-rats, is a family of rodents well-known for their subterranean lifestyle and tunnelling behaviour. Four of the five extant bathyergid genera (Cryptomys, Fukomys, Georychus and Heliophobius) are chisel-tooth diggers, that is they dig through soil with their enlarged incisors, whereas the remaining genus (Bathyergus) is a scratch-digger, only using its forelimbs for burrowing. Heterocephalus glaber, the naked mole-rat, is also a chisel-tooth digger and was until recently included within the Bathyergidae (as the most basally branching genus), but has now been placed by some researchers into its own family, the Heterocephalidae. Given the importance of the masticatory apparatus in habitat construction in this group, knowledge and understanding of the morphology and arrangement of the jaw-closing muscles in Bathyergidae is vital for future functional analyses. Here, we use diffusible iodine-based contrast-enhanced microCT to reveal and describe the muscles of mastication in representative specimens of each genus of bathyergid mole-rat and to compare them to the previously described musculature of the naked mole-rat. In all bathyergids, as in all rodents, the masseter muscle is the most dominant component of the masticatory musculature. However, the temporalis is also a relatively large muscle, a condition normally associated with sciuromorphous rodents. Unlike their hystricomorphous relatives, the bathyergids do not show an extension of the masseter through the infraorbital foramen on to the rostrum (other than a very slight protrusion in Cryptomys and Fukomys). Thus, morphologically, bathyergids are protrogomorphous, although this is thought to be secondarily derived rather than retained from ancestral rodents. Overall, the relative proportions of the jaw-closing muscles were found to be fairly consistent between genera except in Bathyergus, which was found to have an enlarged superficial masseter and relatively smaller pterygoid muscles. It is concluded that these differences may be a reflection of the behaviour of Bathyergus which, uniquely in the family, does not use its incisors for digging