Framework for setting up a Hydro-JULES perturbed parameter ensemble (PPE)

Land surface and hydrological processes and feedbacks that act at sub-grid scales need to be parameterised within models. These parameterisation schemes are an important source of uncertainty in model simulations. One of the aims of Hydro- JULES (HJ) is to quantify uncertainties in river flows induced by land surface and hydrological model parameterisations

Mergers of black hole binaries driven by misaligned circumbinary discs

With hydrodynamical simulations we examine the evolution of a highly misaligned circumbinary disc around a black hole binary including the effects of general relativity. We show that a disc mass of just a few percent of the binary mass can significantly increase the binary eccentricity through von-Zeipel–Kozai–Lidov (ZKL) like oscillations provided that the disc lifetime is longer than the ZKL oscillation timescale. The disc begins as a relatively narrow ring of material far from the binary and spreads radially. When the binary becomes highly eccentric, disc breaking forms an inner disc ring that quickly aligns to polar. The polar ring drives fast retrograde apsidal precession of the binary that weakens the ZKL effect. This allows the binary eccentricity to remain at a high level and may significantly shorten the black hole merger time. The mechanism requires the initial disc inclination relative to the binary to be closer to retrograde than to prograde

Relativistic Effects on Circumbinary Disk Evolution: Breaking the Polar Alignment around Eccentric Black Hole Binary Systems

We study the effects of general relativity (GR) on the evolution and alignment of circumbinary disks around binaries on all scales. We implement relativistic apsidal precession of the binary into the hydrodynamics code phantom. We find that the effects of GR can suppress the stable polar alignment of a circumbinary disk, depending on how the relativistic binary apsidal precession timescale compares to the disk nodal precession timescale. Studies of circumbinary disk evolution typically ignore the effects of GR, which is an appropriate simplification for low-mass or widely separated binary systems. In this case, polar alignment occurs, provided that the disks initial misalignment is sufficiently large. However, systems with a very short relativistic precession timescale cannot polar align and instead move toward coplanar alignment. In the intermediate regime where the timescales are similar, the outcome depends upon the properties of the disk. Polar alignment is more likely in the wavelike disk regime (where the disk viscosity parameter is less than the aspect ratio, α < H/r), since the disk is in good radial communication. In the viscous disk regime, disk breaking is more likely. Multiple rings can destructively interact with one another, resulting in short disk lifetimes and the disk moving toward coplanar alignment. Around main-sequence star or stellar mass black hole binaries, polar alignment may be suppressed far from the binary, but in general, the inner parts of the disk can align to polar. Polar alignment may be completely suppressed for disks around supermassive black holes for close binary separations

Deceleration and trapping of heavy diatomic molecules using a ring-decelerator

We present an analysis of the deceleration and trapping of heavy diatomic molecules in low-field seeking states by a moving electric potential. This moving potential is created by a 'ring-decelerator', which consists of a series of ring-shaped electrodes to which oscillating high voltages are applied. Particle trajectory simulations have been used to analyze the deceleration and trapping efficiency for a group of molecules that is of special interest for precision measurements of fundamental discrete symmetries. For the typical case of the SrF molecule in the (N,M) = (2, 0) state, the ring-decelerator is shown to outperform traditional and alternate-gradient Stark decelerators by at least an order of magnitude. If further cooled by a stage of laser cooling, the decelerated molecules allow for a sensitivity gain in a parity violation measurement, compared to a cryogenic molecular beam experiment, of almost two orders of magnitude

Empirical Determination of Bang-Bang Operations

Strong and fast "bang-bang" (BB) pulses have been recently proposed as a means for reducing decoherence in a quantum system. So far theoretical analysis of the BB technique relied on model Hamiltonians. Here we introduce a method for empirically determining the set of required BB pulses, that relies on quantum process tomography. In this manner an experimenter may tailor his or her BB pulses to the quantum system at hand, without having to assume a model Hamiltonian.Comment: 14 pages, 2 eps figures, ReVTeX4 two-colum

Quantum walks: a comprehensive review

Quantum walks, the quantum mechanical counterpart of classical random walks, is an advanced tool for building quantum algorithms that has been recently shown to constitute a universal model of quantum computation. Quantum walks is now a solid field of research of quantum computation full of exciting open problems for physicists, computer scientists, mathematicians and engineers. In this paper we review theoretical advances on the foundations of both discrete- and continuous-time quantum walks, together with the role that randomness plays in quantum walks, the connections between the mathematical models of coined discrete quantum walks and continuous quantum walks, the quantumness of quantum walks, a summary of papers published on discrete quantum walks and entanglement as well as a succinct review of experimental proposals and realizations of discrete-time quantum walks. Furthermore, we have reviewed several algorithms based on both discrete- and continuous-time quantum walks as well as a most important result: the computational universality of both continuous- and discrete- time quantum walks.Comment: Paper accepted for publication in Quantum Information Processing Journa

A standard protocol to report discrete stage‐structured demographic information

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

The role of bats as reservoir hosts of emerging neurological viruses

Introduction It is now well-recognized that more than 75% of emerging diseases over the past 2 decades have been zoonoses. Many of these zoonotic viruses have caused neurological disease, especially those emerging during this period in the South-East Asian and Western Pacific regions [1, 2]. Most of the diseases emerging from wildlife have been from bats and rodents. Bats are only second to rodents in terms of mammalian species richness [3] and constitute about 20% of all mammalian species. Thus, with their wide distribution and abundance, it is not surprising that there is growing awareness that bats are the reservoir hosts for a number of these emerging viruses [4, 5, 6, 7] and suspected of being associated with many others on serological grounds. Not only have they been shown to be the reservoir hosts for rabies and related lyssaviruses but also for other human pathogens, or potential pathogens, such as SARS-coronavirus-like viruses [8, 9, 10], Ebola virus [11, 12], Menangle virus [13], and Hendra and Nipah viruses [14, 15, 16]. This brief review looks at the biological features that make bats good reservoir hosts, and the more important neurological viruses associated with bats that are, or have the potential to be, transmitted to humans. Bats as reservoir hosts: Implications for virus transmission The order chiroptera, their diversity, evolution, abundance, and social behavior The mammalian Order Chiroptera is divided into two suborders, the Megachiroptera, or Old World fruit- and nectar-feeding bats, including flying foxes, and the Microchiroptera, or echolocating bats [17]