A structure-preserving approximation of the discrete split rotating shallow water equations

We introduce an efficient split finite element (FE) discretization of a y-independent (slice) model of the rotating shallow water equations. The study of this slice model provides insight towards developing schemes for the full 2D case. Using the split Hamiltonian FE framework [1,2], we result in structure-preserving discretizations that are split into topological prognostic and metric-dependent closure equations. This splitting also accounts for the schemes' properties: the Poisson bracket is responsible for conserving energy (Hamiltonian) as well as mass, potential vorticity and enstrophy (Casimirs), independently from the realizations of the metric closure equations. The latter, in turn, determine accuracy, stability, convergence and discrete dispersion properties. We exploit this splitting to introduce structure-preserving approximations of the mass matrices in the metric equations avoiding to solve linear systems. We obtain a fully structure-preserving scheme with increased efficiency by a factor of two

Energy conserving SUPG methods for compatible finite element schemes in numerical weather prediction

We present an energy conserving space discretisation based on a Poisson bracket that can be used to derive the dry compressible Euler as well as thermal shallow water equations. It is formulated using the compatible finite element method, and extends the incorporation of upwinding for the shallow water equations as described in Wimmer, Cotter, and Bauer (2020). While the former is restricted to DG upwinding, an energy conserving SUPG method for the (partially) continuous Galerkin thermal field space is newly introduced here. The energy conserving property is validated by coupling the Poisson bracket based spatial discretisation to an energy conserving time discretisation. Further, the discretisation is demonstrated to lead to an improved thermal field development with respect to stability when upwinding is included. An approximately energy conserving scheme that includes upwinding for all prognostic fields with a smaller computational cost is also presented. In a falling bubble test case used for the Euler equations, the latter scheme is shown to resolve small scale features at coarser resolutions than a corresponding scheme derived directly from the equations without the Poisson bracket framework

Nickel(II) 3,4;9,10-Perylenediimide bis-Phosphonate Pentahydrate: A Metal−Organic Ferromagnetic Dye

The new metal−organic compound nickel(II) 3,4;9,10- perylenediimide bis-phosphonate pentahydrate, i.e. Ni2[(PDI-BP)- (H2O)2]·3H2O (1), has been synthesized and its structural and magnetic properties have been studied. Reaction of 3,4;9,10-perylenediimide bisphosphonate (PDI-BP, hereafter) ligand and nickel chloride in water resulted in the precipitation of a red and poorly crystalline solid (1). As the solid shows a poor crystalline organization of aggregates, the energy dispersive X-ray diffraction analysis (EDXD) technique has been used to obtain short-range order structural information of the single nanoaggregates by radial distribution function analysis. The overall structure of the compound is characterized by layers containing perylene planes shifted in the direction perpendicular to the stacking axes in such a way that only the outer rings overlap. The edges of the perylene planes are connected to the phosphonate groups through an imido group. The oxygen atoms of the [−PO3]2‑ group and those of the water molecules are bonded to the nickel ions resulting in a [NiO6] octahedral coordination sphere. The Ni−O bond lengths are 0.21 ± 0.08 nm and the Ni−O−Ni angles of aligned moieties are 95 ± 2°. The oxygen atoms of the water molecules and the nickel atoms are nearly planar and almost perpendicular to the perylene planes forming chains of edge-sharing octahedra. The magnetic properties of (1) show the presence of intrachain ferromagnetic Ni−Ni interactions and a long-range ferromagnetic order below 21 K with a canting angle and with a spin glasslike behavior due to disorder in the inorganic layer. Hysteresis cycles show a coercive field of ca. 272 mT at 2 K that decreases as the temperature is increased and vanishes at ca. 20 K

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

Recent technological breakthroughs allow the quantification of hundreds of thousands of genetic interactions (GIs) in Saccharomyces cerevisiae. The interpretation of these data is often difficult, but it can be improved by the joint analysis of GIs along with complementary data types. Here, we describe a novel methodology that integrates genetic and physical interaction data. We use our method to identify a collection of functional modules related to chromosomal biology and to investigate the relations among them. We show how the resulting map of modules provides clues for the elucidation of function both at the level of individual genes and at the level of functional modules

Diagnostic tests for Niemann-Pick disease type C (NP-C): A critical review

Niemann-Pick disease type C (NP-C) is a neurovisceral lysosomal cholesterol trafficking and lipid storage disorder caused by mutations in one of the two genes, NPC1 or NPC2. Diagnosis has often been a difficult task, due to the wide range in age of onset of NP-C and clinical presentation of the disease, combined with the complexity of the cell biology (filipin) laboratory testing, even in combination with genetic testing. This has led to substantial delays in diagnosis, largely depending on the access to specialist centres and the level of knowledge about NP-C of the physician in the area. In recent years, advances in mass spectrometry has allowed identification of several sensitive plasma biomarkers elevated in NP-C (e.g. cholestane-3β,5α,6β-triol, lysosphingomyelin isoforms and bile acid metabolites), which, together with the concomitant progress in molecular genetic technology, have greatly impacted the strategy of laboratory testing. Specificity of the biomarkers is currently under investigation and other pathologies are being found to also result in elevations. Molecular genetic testing also has its limitations, notably with unidentified mutations and the classification of new variants. This review is intended to increase awareness on the currently available approaches to laboratory diagnosis of NP-C, to provide an up to date, comprehensive and critical evaluation of the various techniques (cell biology, biochemical biomarkers and molecular genetics), and to briefly discuss ongoing/future developments. The use of current tests in proper combination enables a rapid and correct diagnosis in a large majority of cases. However, even with recent progress, definitive diagnosis remains challenging in some patients, for whom combined genetic/biochemical/cytochemical markers do not provide a clear answer. Expertise and reference laboratories thus remain essential, and further work is still required to fulfill unmet needs

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcribing. We apply our model to explore the correlation between stress-induced transitions and transcriptional activity in various organisms. In higher eukaryotes we find a strong enhancement of Z-forming regions immediately 5′ to their transcription start sites (TSS), and a depletion of strand separating sites in a broad region around the TSS. The opposite patterns occur around transcript end locations. We also show that susceptibility to each type of transition is different in eukaryotes and prokaryotes. By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downstream of the TSS is not preserved, suggesting it may be under selection pressure

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that occurs among all susceptible Z-forming regions at thermodynamic equilibrium in a superhelically stressed DNA of specified sequence. This method, which we call SIBZ, is similar to the SIDD algorithm that was previously developed to analyze superhelical duplex destabilization. A state of the system is determined by assigning to each base pair either the B- or the Z-conformation, accounting for the dinucleotide repeat unit of Z-DNA. The free energy of a state is comprised of the nucleation energy, the sequence-dependent B-Z transition energy, and the energy associated with the residual superhelicity remaining after the change of twist due to transition. Using this information, SIBZ calculates the equilibrium B-Z transition probability of each base pair in the sequence. This can be done at any physiologically reasonable level of negative superhelicity. We use SIBZ to analyze a variety of representative genomic DNA sequences. We show that the dominant Z-DNA forming regions in a sequence can compete in highly complex ways as the superhelicity level changes. Despite having no tunable parameters, the predictions of SIBZ agree precisely with experimental results, both for the onset of transition in plasmids containing introduced Z-forming sequences and for the locations of Z-forming regions in genomic sequences. We calculate the transition profiles of 5 kb regions taken from each of 12,841 mouse genes and centered on the transcription start site (TSS). We find a substantial increase in the frequency of Z-forming regions immediately upstream from the TSS. The approach developed here has the potential to illuminate the occurrence of Z-form regions in vivo, and the possible roles this transition may play in biological processes

Quantum Tricritical Points in NbFe2_2

Quantum critical points (QCPs) emerge when a 2nd order phase transition is suppressed to zero temperature. In metals the quantum fluctuations at such a QCP can give rise to new phases including unconventional superconductivity. Whereas antiferromagnetic QCPs have been studied in considerable detail ferromagnetic (FM) QCPs are much harder to access. In almost all metals FM QCPs are avoided through either a change to 1st order transitions or through an intervening spin-density-wave (SDW) phase. Here, we study the prototype of the second case, NbFe$_2$. We demonstrate that the phase diagram can be modelled using a two-order-parameter theory in which the putative FM QCP is buried within a SDW phase. We establish the presence of quantum tricritical points (QTCPs) at which both the uniform and finite $q$ susceptibility diverge. The universal nature of our model suggests that such QTCPs arise naturally from the interplay between SDW and FM order and exist generally near a buried FM QCP of this type. Our results promote NbFe$_2$ as the first example of a QTCP, which has been proposed as a key concept in a range of narrow-band metals, including the prominent heavy-fermion compound YbRh$_2$Si$_2$.Comment: 21 pages including S

Exact exchange-correlation potential of a ionic Hubbard model with a free surface

We use Lanczos exact diagonalization to compute the exact exchange-correlation (xc) potential of a Hubbard chain with large binding energy ("the bulk") followed by a chain with zero binding energy ("the vacuum"). Several results of density functional theory in the continuum (sometimes controversial) are verified in the lattice. In particular we show explicitly that the fundamental gap is given by the gap in the Kohn-Sham spectrum plus a contribution due to the jump of the xc-potential when a particle is added. The presence of a staggered potential and a nearest-neighbor interaction V allows to simulate a ionic solid. We show that in the ionic regime in the small hopping amplitude limit the xc-contribution to the gap equals V, while in the Mott regime it is determined by the Hubbard U interaction. In addition we show that correlations generates a new potential barrier at the surface

Improving object segmentation by using EEG signals and rapid serial visual presentation

This paper extends our previous work on the potential of EEG-based brain computer interfaces to segment salient objects in images. The proposed system analyzes the Event Related Potentials (ERP) generated by the rapid serial visual presentation of windows on the image. The detection of the P300 signal allows estimating a saliency map of the image, which is used to seed a semi-supervised object segmentation algorithm. Thanks to the new contributions presented in this work, the average Jaccard index was improved from $0.47$ to $0.66$ when processed in our publicly available dataset of images, object masks and captured EEG signals. This work also studies alternative architectures to the original one, the impact of object occupation in each image window, and a more robust evaluation based on statistical analysis and a weighted F-score