Numerical impacts on tracer transport: A proposed intercomparison test of Atmospheric General Circulation Models

The transport of trace gases by the atmospheric circulation plays an important role in the climate system and its response to external forcing. Transport presents a challenge for Atmospheric General Circulation Models (AGCMs), as errors in both the resolved circulation and the numerical representation of transport processes can bias their abundance. In this study, two tests are proposed to assess transport by the dynamical core of an AGCM. To separate transport from chemistry, the tests focus on the age‐of‐air, an estimate of the mean transport time by the circulation. The tests assess the coupled stratosphere–troposphere system, focusing on transport by the overturning circulation and isentropic mixing in the stratosphere, or Brewer–Dobson Circulation, where transport time‐scales on the order of months to years provide a challenging test of model numerics. Four dynamical cores employing different numerical schemes (finite‐volume, pseudo‐spectral, and spectral‐element) and discretizations (cubed sphere versus latitude–longitude) are compared across a range of resolutions. The subtle momentum balance of the tropical stratosphere is sensitive to model numerics, and the first intercomparison reveals stark differences in tropical stratospheric winds, particularly at high vertical resolution: some cores develop westerly jets and others easterly jets. This leads to substantial spread in transport, biasing the age‐of‐air by up to 25% relative to its climatological mean, making it difficult to assess the impact of the numerical representation of transport processes. This uncertainty is removed by constraining the tropical winds in the second intercomparison test, in a manner akin to specifying the Quasi‐Biennial Oscillation in an AGCM. The dynamical cores exhibit qualitative agreement on the structure of atmospheric transport in the second test, with evidence of convergence as the horizontal and vertical resolution is increased in a given model. Significant quantitative differences remain, however, particularly between models employing spectral versus finite‐volume numerics, even in state‐of‐the‐art cores

A standard test case suite for two-dimensional linear transport on the sphere

It is the purpose of this paper to propose a standard test case suite for two-dimensional transport schemes on the sphere intended to be used for model development and facilitating scheme intercomparison. The test cases are designed to assess important aspects of accuracy in geophysical fluid dynamics such as numerical order of convergence, "minimal" resolution, the ability of the transport scheme to preserve filaments, transport "rough" distributions, and to preserve pre-existing functional relations between species/tracers under challenging flow conditions. <br><br> The experiments are designed to be easy to set up. They are specified in terms of two analytical wind fields (one non-divergent and one divergent) and four analytical initial conditions (varying from smooth to discontinuous). Both conventional error norms as well as novel mixing and filament preservation diagnostics are used that are easy to implement. The experiments pose different challenges for the range of transport approaches from Lagrangian to Eulerian. The mixing and filament preservation diagnostics do not require an analytical/reference solution, which is in contrast to standard error norms where a "true" solution is needed. Results using the CSLAM (Conservative Semi-Lagrangian Multi-tracer) scheme on the cubed-sphere are presented for reference and illustrative purposes

Learning Conditional Distributions using Mixtures of Truncated Basis Functions

Mixtures of Truncated Basis Functions (MoTBFs) have recently been proposed for modelling univariate and joint distributions in hybrid Bayesian networks. In this paper we analyse the problem of learning conditional MoTBF distributions from data. Our approach utilizes a new technique for learning joint MoTBF densities, then propose a method for using these to generate the conditional distributions. The main contribution of this work is conveyed through an empirical investigation into the properties of the new learning procedure, where we also compare the merits of our approach to those obtained by other proposals

Self-consistent quantal treatment of decay rates within the perturbed static path approximation

The framework of the Perturbed Static Path Approximation (PSPA) is used to calculate the partition function of a finite Fermi system from a Hamiltonian with a separable two body interaction. Therein, the collective degree of freedom is introduced in self-consistent fashion through a Hubbard-Stratonovich transformation. In this way all transport coefficients which dominate the decay of a meta-stable system are defined and calculated microscopically. Otherwise the same formalism is applied as in the Caldeira-Leggett model to deduce the decay rate from the free energy above the so called crossover temperature $T_0$.Comment: 17 pages, LaTex, no figures; final version, accepted for publication in PRE; e-mail: [email protected]

iPSC-derived liver organoids and inherited bleeding disorders : potential and future perspectives

Funding: This work was made possible with funding from the Norwegian Research Council (325869) and the South-Eastern Norway Regional Health Authority (2019071).The bleeding phenotype of hereditary coagulation disorders is caused by the low or undetectable activity of the proteins involved in hemostasis, due to a broad spectrum of genetic alterations. Most of the affected coagulation factors are produced in the liver. Therefore, two-dimensional (2D) cultures of primary human hepatocytes and recombinant overexpression of the factors in non-human cell lines have been primarily used to mimic disease pathogenesis and as a model for innovative therapeutic strategies. However, neither human nor animal cells fully represent the hepatocellular biology and do not harbor the exact genetic background of the patient. As a result, the inability of the current in vitro models in recapitulating the in vivo situation has limited the studies of these inherited coagulation disorders. Induced Pluripotent Stem Cell (iPSC) technology offers a possible solution to overcome these limitations by reprogramming patient somatic cells into an embryonic-like pluripotent state, thus giving the possibility of generating an unlimited number of liver cells needed for modeling or therapeutic purposes. By combining this potential and the recent advances in the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology, it allows for the generation of autologous and gene corrected liver cells in the form of three-dimensional (3D) liver organoids. The organoids recapitulate cellular composition and organization of the liver, providing a more physiological model to study the biology of coagulation proteins and modeling hereditary coagulation disorders. This advanced methodology can pave the way for the development of cell-based therapeutic approaches to treat inherited coagulation disorders. In this review we will explore the use of liver organoids as a state-of-the-art methodology for modeling coagulation factors disorders and the possibilities of using organoid technology to treat the disease.Peer reviewe

Likelihood Geometry

We study the critical points of monomial functions over an algebraic subset of the probability simplex. The number of critical points on the Zariski closure is a topological invariant of that embedded projective variety, known as its maximum likelihood degree. We present an introduction to this theory and its statistical motivations. Many favorite objects from combinatorial algebraic geometry are featured: toric varieties, A-discriminants, hyperplane arrangements, Grassmannians, and determinantal varieties. Several new results are included, especially on the likelihood correspondence and its bidegree. These notes were written for the second author's lectures at the CIME-CIRM summer course on Combinatorial Algebraic Geometry at Levico Terme in June 2013.Comment: 45 pages; minor changes and addition

Energy-conserving physics for nonhydrostatic dynamics in mass coordinate models

Motivated by reducing errors in the energy budget related to enthalpy fluxes within the Energy Exascale Earth System Model (E3SM), we study several physics–dynamics coupling approaches. Using idealized physics, a moist rising bubble test case, and the E3SM's nonhydrostatic dynamical core, we consider unapproximated and approximated thermodynamics applied at constant pressure or constant volume. With the standard dynamics and physics time-split implementation, we describe how the constant-pressure and constant-volume approaches use different mechanisms to transform physics tendencies into dynamical motion and show that only the constant-volume approach is consistent with the underlying equations. Using time step convergence studies, we show that the two approaches both converge but to slightly different solutions. We reproduce the large inconsistencies between the energy flux internal to the model and the energy flux of precipitation when using approximate thermodynamics, which can only be removed by considering variable latent heats, both when computing the latent heating from phase change and when applying this heating to update the temperature. Finally, we show that in the nonhydrostatic case, for physics applied at constant pressure, the general relation that enthalpy is locally conserved no longer holds. In this case, the conserved quantity is enthalpy plus an additional term proportional to the difference between hydrostatic pressure and full pressure.</p

Complex Periodic Orbits and Tunnelling in Chaotic Potentials

We derive a trace formula for the splitting-weighted density of states suitable for chaotic potentials with isolated symmetric wells. This formula is based on complex orbits which tunnel through classically forbidden barriers. The theory is applicable whenever the tunnelling is dominated by isolated orbits, a situation which applies to chaotic systems but also to certain near-integrable ones. It is used to analyse a specific two-dimensional potential with chaotic dynamics. Mean behaviour of the splittings is predicted by an orbit with imaginary action. Oscillations around this mean are obtained from a collection of related orbits whose actions have nonzero real part

Three disks in a row: A two-dimensional scattering analog of the double-well problem

We investigate the scattering off three nonoverlapping disks equidistantly spaced along a line in the two-dimensional plane with the radii of the outer disks equal and the radius of the inner disk varied. This system is a two-dimensional scattering analog to the double-well-potential (bound state) problem in one dimension. In both systems the symmetry splittings between symmetric and antisymmetric states or resonances, respectively, have to be traced back to tunneling effects, as semiclassically the geometrical periodic orbits have no contact with the vertical symmetry axis. We construct the leading semiclassical ``creeping'' orbits that are responsible for the symmetry splitting of the resonances in this system. The collinear three-disk-system is not only one of the simplest but also one of the most effective systems for detecting creeping phenomena. While in symmetrically placed n-disk systems creeping corrections affect the subleading resonances, they here alone determine the symmetry splitting of the 3-disk resonances in the semiclassical calculation. It should therefore be considered as a paradigm for the study of creeping effects. PACS numbers: 03.65.Sq, 03.20.+i, 05.45.+bComment: replaced with published version (minor misprints corrected and references updated); 23 pages, LaTeX plus 8 Postscript figures, uses epsfig.sty, espf.sty, and epsf.te