The Numerical Initial Boundary Value Problem for the Generalised Conformal Field Equations in General Relativity

The purpose of this work is to develop for the first time a general framework for the Initial Boundary Value Problem (IBVP) of the Generalised Conformal Field Equations (GCFE). At present the only investigation toward obtaining such a framework was given in the mid 90's by Friedrich at an analytical level and is only valid for Anti-de Sitter space-time. There have so far been no numerical explorations into the validity of building such a framework. The GCFE system is derived in the space-spinor formalism and Newman and Penrose's eth-calculus is imposed to obtain proper spin-weighted equations. These are then rigorously tested both analytically and numerically to confirm their correctness. The global structure of the Schwarzschild, Schwarzschild-de Sitter and Schwarzschild-Anti-de Sitter space-times are numerically reproduced from an IVP and for the first time, numerical simulations that incorporate both the singularity and the conformal boundary are presented. A framework for the IBVP is then given, where the boundaries are chosen as arbitrary time-like conformal geodesics and where the constraints propagate on (at least) the numerical level. The full generality of the framework is verified numerically for gravitational perturbations of Minkowski and Schwarzschild space-times. A spin-frame adapted to the geometry of future null infinity is developed and the expressions for the Bondi-mass and the Bondi-time given by Penrose and Rindler are generalised. The Bondi-mass is found to equate to the Schwarzschild-mass for the standard Schwarzschild space-time and the famous Bondi-Sachs mass loss is reproduced for the gravitationally perturbed case

Dynamics of chromosome organization in a minimal bacterial cell

Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM. </p

Molecular dynamics simulation of an entire cell

The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell’s components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell’s spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future

STROBE-X: X-ray Timing & Spectroscopy on Dynamical Timescales from Milliseconds to Years

We describe a probe-class mission concept that provides an unprecedented view of the X-ray sky, performing timing and 0.2-30 keV spectroscopy over timescales from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) comprises three primary instruments. The first uses an array of lightweight optics (3-m focal length) that concentrate incident photons onto solid state detectors with CCD-level (85-130 eV) energy resolution, 100 ns time resolution, and low background rates to cover the 0.2-12 keV band. This technology is scaled up from NICER [1], with enhanced optics to take advantage of the longer focal length of STROBE-X. The second uses large-area collimated silicon drift detectors, developed for ESA's LOFT [2], to cover the 2-30 keV band. These two instruments each provide an order of magnitude improvement in effective area compared with its predecessor (NICER and RXTE, respectively). Finally, a sensitive sky monitor triggers pointed observations, provides high duty cycle, high time resolution, high spectral resolution monitoring of the X-ray sky with approx. 20 times the sensitivity of the RXTE ASM, and enables multi-wavelength and multi-messenger studies on a continuous, rather than scanning basis. For the first time, the broad coverage provides simultaneous study of thermal components, non-thermal components, iron lines, and reflection features from a single platform for accreting black holes at all scales. The enormous collecting area allows detailed studies of the dense matter equation of state using both thermal emission from rotation-powered pulsars and harder emission from X-ray burst oscillations. The combination of the wide-field monitor and the sensitive pointed instruments enables observations of potential electromagnetic counterparts to LIGO and neutrino events. Additional extragalactic science, such as high quality spectroscopy of clusters of galaxies and unprecedented timing investigations of active galactic nuclei, is also obtaine

STROBE-X: X-ray Timing & Spectroscopy on Dynamical Timescales from Milliseconds to Years

We describe a probe-class mission concept that provides an unprecedented view of the X-ray sky, performing timing and 0.2-30 keV spectroscopy over timescales from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) has three key science drivers: (1) measuring the spin distribution of accreting black holes, (2) understanding the equation of state of dense matter, and (3) exploring the properties of the precursors and electromagnetic counterparts of gravitational wave sources. To perform these science investigations, STROBE-X comprises three primary instruments. The first uses an array of lightweight optics (3-m focal length) that concentrate incident photons onto solid state detectors with CCD-level (85-130 eV) energy resolution, 100 ns time resolution, and low background rates to cover the 0.2-12 keV band. This technology is scaled up from NICER, with enhanced optics to take advantage of the longer focal length of STROBE-X. The second uses large-area collimated silicon drift detectors, developed for ESA's LOFT, to cover the 2-30 keV band. These two instruments each provide an order of magnitude improvement in effective area compared with its predecessor (NICER and RXTE, respectively). Finally, a sensitive sky monitor triggers pointed observations, provides high duty cycle, high time resolution, high spectral resolution monitoring of the X-ray sky with ~20 times the sensitivity of the RXTE ASM, and enables multi-wavelength and multi-messenger studies on a continuous, rather than scanning basis. The STROBE-X mission concept is a rapidly repointable observatory in low-Earth orbit, similar to RXTE or Swift, and will be presented to the 2020 Astrophysics Decadal Survey for consideration as a probe-class mission

STROBE-X: A probe-class mission for x-ray spectroscopy and timing on timescales from microseconds to years

We describe the Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X), a probeclass mission concept that will provide an unprecedented view of the X-ray sky, performing timing and spectroscopy over both a broad energy band (0.2-30 keV) and a wide range of timescales from microseconds to years. STROBE-X comprises two narrow-field instruments and a wide field monitor. The soft or low-energy band (0.2-12 keV) is covered by an array of lightweight optics (3-m focal length) that concentrate incident photons onto small solid-state detectors with CCD-level (85-175 eV) energy resolution, 100 ns time resolution, and low background rates. This technology has been fully developed for NICER and will be scaled up to take advantage of the longer focal length of STROBE-X. The higher-energy band (2-30 keV) is covered by large-area, collimated silicon drift detectors that were developed for the European LOFT mission concept. Each instrument will provide an order of magnitude improvement in effective area over its predecessor (NICER in the soft band and RXTE in the hard band). Finally, STROBE-X offers a sensitive wide-field monitor (WFM), both to act as a trigger for pointed observations of X-ray transients and also to provide high duty-cycle, high time-resolution, and high spectral-resolution monitoring of the variable X-ray sky. The WFM will boast approximately 20 times the sensitivity of the RXTE All-Sky Monitor, enabling multi-wavelength and multi-messenger investigations with a large instantaneous field of view. This mission concept will be presented to the 2020 Decadal Survey for consideration

Genes, gene flow and adaptation of Diabrotica virgifera virgifera

Diabrotica virgifera virgifera has emerged as a major pest of cultivated maize, due to a combination of its high capacity to inflict economic damage, adaptability to pest management techniques and invasiveness. This review presents a survey of the current state of knowledge about the genetics of D. v. virgifera. In addition, the tools and resources currently available to Diabrotica geneticists are identified, as are areas where knowledge is lacking and research should be prioritized. A substantial amount of information has been published concerning the molecular phylogenetic relationships of D. v. virgifera to other chrysomelids. There is a growing literature focused on the population genetics and evolution of the species. Several adaptations to anthropogenic selection pressure have been studied, with resistance to synthetic insecticides providing some particularly well-characterized examples. A notable deficiency is a lack of studies directed toward the formal genetics of D. v. virgifera

Global causes of blindness and distance vision impairment 1990–2020: a systematic review and meta-analysis

Background: Contemporary data on causes of vision impairment and blindness form an important basis for recommendations in public health policies. Refreshment of the Global Vision Database with recently published data sources permitted modeling of cause of vision loss data from 1990 to 2015, further disaggregation by cause, and forecasts to 2020. Methods: Published and unpublished population-based data on the causes of vision impairment and blindness from 1980 to 2015 were systematically analysed. A series of regression models were fit to estimate the proportion of moderate and severe vision impairment (MSVI; defined as presenting visual acuity <6/18 but ≥3/60 in the better eye) and blindness (presenting visual acuity <3/60 in the better eye) by cause by age, region, and year. Findings: Among the projected global population with MSVI (216.6 million; 80% uncertainty intervals [UI] 98.5-359.1), in 2015 the leading causes thereof are uncorrected refractive error (116.3 million; UI 49.4-202.1), cataract (52.6 million; UI 18.2-109.6), age-related macular degeneration (AMD; 8.4 million; UI 0.9-29.5), glaucoma (4.0 million; UI 0.6-13.3) and diabetic retinopathy (2.6 million; UI 0.2-9.9). In 2015, the leading global causes of blindness were cataract (12.6 million; UI 3.4-28.7) followed by uncorrected refractive error (7.4 million; UI 2.4-14.8) and glaucoma (2.9 million; UI 0.4-9.9), while by 2020, these numbers affected are anticipated to rise to 13.4 million, 8.0 million and 3.2 million, respectively. Cataract and uncorrected refractive error combined contributed to 55% of blindness and 77% of MSVI in adults aged 50 years and older in 2015. World regions varied markedly in the causes of blindness, with a relatively low prevalence of cataract and a relatively high prevalence of AMD as causes for vision loss in the High-income subregions. Blindness due to cataract and diabetic retinopathy was more common among women, while blindness due to glaucoma and corneal opacity was more common among men, with no gender difference related to AMD. Conclusions: The numbers of people affected by the common causes of vision loss have increased substantially as the population increases and ages. Preventable vision loss due to cataract and refractive error (reversible with surgery and spectacle correction respectively), continue to cause the majority of blindness and MSVI in adults aged 50+ years. A massive scale up of eye care provision to cope with the increasing numbers is needed if one is to address avoidable vision loss