J- and Ks-band Galaxy Counts and Color Distributions in the AKARI North Ecliptic Pole Field

We present the J- and Ks-band galaxy counts and galaxy colors covering 750 square arcminutes in the deep AKARI North Ecliptic Pole (NEP) field, using the FLoridA Multi-object Imaging Near-ir Grism Observational Spectrometer (FLAMINGOS) on the Kitt Peak National Observatory (KPNO) 2.1m telescope. The limiting magnitudes with a signal-to-noise ratio of three in the deepest regions are 21.85 and 20.15 in the J- and Ks-bands respectively in the Vega magnitude system. The J- and Ks-band galaxy counts in the AKARI NEP field are broadly in good agreement with those of other results in the literature, however we find some indication of a change in the galaxy number count slope at J~19.5 and over the magnitude range 18.0 < Ks < 19.5. We interpret this feature as a change in the dominant population at these magnitudes because we also find an associated change in the B - Ks color distribution at these magnitudes where the number of blue samples in the magnitude range 18.5 < Ks < 19.5 is significantly larger than that of Ks < 17.5

Inelastic Quantum Transport

We solve a Schrodinger equation for inelastic quantum transport that retains full quantum coherence, in contrast to previous rate or Boltzmann equation approaches. The model Hamiltonian is the zero temperature 1d Holstein model for an electron coupled to optical phonons (polaron), in a strong electric field. The Hilbert space grows exponentially with electron position, forming a non-standard Bethe lattice. We calculate nonperturbatively the transport current, electron-phonon correlations, and quantum diffusion. This system is a toy model for the constantly branching ``wavefunction of the universe''.Comment: revtex, 13 pages, 4 figure

Local Electronic Structure of a Single Magnetic Impurity in a Superconductor

The electronic structure near a single classical magnetic impurity in a superconductor is determined using a fully self-consistent Koster-Slater algorithm. Localized excited states are found within the energy gap which are half electron and half hole. Within a jellium model we find the new result that the spatial structure of the positive-frequency (electron-like) spectral weight (or local density of states), can differ strongly from that of the negative frequency (hole-like) spectral weight. The effect of the impurity on the continuum states above the energy gap is calculated with good spectral resolution for the first time. This is also the first three-dimensional self-consistent calculation for a strong magnetic impurity potential.Comment: 13 pages, RevTex, change in heuristic picture, no change in numerical result

Local Electronic Structure of Defects in Superconductors

The electronic structure near defects (such as impurities) in superconductors is explored using a new, fully self-consistent technique. This technique exploits the short-range nature of the impurity potential and the induced change in the superconducting order parameter to calculate features in the electronic structure down to the atomic scale with unprecedented spectral resolution. Magnetic and non-magnetic static impurity potentials are considered, as well as local alterations in the pairing interaction. Extensions to strong-coupling superconductors and superconductors with anisotropic order parameters are formulated.Comment: RevTex source, 20 pages including 22 figures in text with eps

Advances in ab-initio theory of Multiferroics. Materials and mechanisms: modelling and understanding

Within the broad class of multiferroics (compounds showing a coexistence of magnetism and ferroelectricity), we focus on the subclass of "improper electronic ferroelectrics", i.e. correlated materials where electronic degrees of freedom (such as spin, charge or orbital) drive ferroelectricity. In particular, in spin-induced ferroelectrics, there is not only a {\em coexistence} of the two intriguing magnetic and dipolar orders; rather, there is such an intimate link that one drives the other, suggesting a giant magnetoelectric coupling. Via first-principles approaches based on density functional theory, we review the microscopic mechanisms at the basis of multiferroicity in several compounds, ranging from transition metal oxides to organic multiferroics (MFs) to organic-inorganic hybrids (i.e. metal-organic frameworks, MOFs)Comment: 22 pages, 9 figure

Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (,23%) than the other two, COPI (,9%) and COPII (,8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

<p>Abstract</p> <p>Background</p> <p>In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions.</p> <p>Results</p> <p>To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of <it>Escherichia coli </it>(931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state.</p> <p>Conclusion</p> <p>Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered.</p

Beyond the black box: Promoting mathematical collaborations for elucidating interactions in soil ecology

© 2019 The Authors. Understanding soil systems is critical because they form the structural and nutritional foundation for plants and thus every terrestrial habitat and agricultural system. In this paper, we encourage increased use of mathematical models to drive forward understanding of interactions in soil ecological systems. We discuss several distinctive features of soil ecosystems and empirical studies of them. We explore some perceptions that have previously deterred more extensive use of models in soil ecology and some advances that have already been made using models to elucidate soil ecological interactions. We provide examples where mathematical models have been used to test the plausibility of hypothesized mechanisms, to explore systems where experimental manipulations are currently impossible, or to determine the most important variables to measure in experimental and natural systems. To aid in the development of theory in this field, we present a table describing major soil ecology topics, the theory previously used, and providing key terms for theoretical approaches that could potentially address them. We then provide examples from the table that may either contribute to important incremental developments in soil science or potentially revolutionize our understanding of plant-soil systems. We challenge scientists and mathematicians to push theoretical explorations in soil systems further and highlight three major areas for the development of mathematical models in soil ecology: Theory spanning scales and ecological hierarchies, processes, and evolution

Beyond the black box: promoting mathematical collaborations for elucidating interactions in soil ecology

This work is licensed under a Creative Commons Attribution 4.0 International License.Understanding soil systems is critical because they form the structural and nutritional foundation for plants and thus every terrestrial habitat and agricultural system. In this paper, we encourage increased use of mathematical models to drive forward understanding of interactions in soil ecological systems. We discuss several distinctive features of soil ecosystems and empirical studies of them. We explore some perceptions that have previously deterred more extensive use of models in soil ecology and some advances that have already been made using models to elucidate soil ecological interactions. We provide examples where mathematical models have been used to test the plausibility of hypothesized mechanisms, to explore systems where experimental manipulations are currently impossible, or to determine the most important variables to measure in experimental and natural systems. To aid in the development of theory in this field, we present a table describing major soil ecology topics, the theory previously used, and providing key terms for theoretical approaches that could potentially address them. We then provide examples from the table that may either contribute to important incremental developments in soil science or potentially revolutionize our understanding of plant–soil systems. We challenge scientists and mathematicians to push theoretical explorations in soil systems further and highlight three major areas for the development of mathematical models in soil ecology: theory spanning scales and ecological hierarchies, processes, and evolution

Evidence for a Massive Post-Starburst Galaxy at z ~ 6.5

We present results from a search for high-redshift J--band ``dropout'' galaxies in the portion of the GOODS southern field that is covered by extremely deep imaging from the Hubble Ultradeep Field (HUDF).Using observations at optical, near-infrared and mid-infrared wavelengths from the Hubble and Spitzer Space Telescopes and the ESO-VLT, we search for very massive galaxies at high redshifts and find one particularly remarkable candidate. Its spectral energy distribution is consistent with a galaxy at z ~ 6.5 and a stellar mass of 6x10e11 M(sun) (for a Salpeter IMF). We interpret a prominent photometric break between the near-infrared and Spitzer bandpasses as the 3646A Balmer discontinuity. The best-fitting models have low reddening and ages of several hundred Myr, placing the formation of the bulk of the stars at z > 9. Alternative models of dusty galaxies at z ~ 2.5 are possible but provide significantly poorer fits. The object is detected with Spitzer at 24 micron. This emission originats from an obscured active nucleus or star formation. We present optical and near-infrared spectroscopy which has, thus far, failed to detect any spectral features. This helps limit the solution in which the galaxy is a starburst or active galaxy at z ~ 2.5. If the high-redshift interpretation is correct, this object would be an example of a galaxy that formed by a process strongly resembling traditional models of monolithic collapse, in a way which a very large mass of stars formed within a remarkably short period of time, at very high redshift.Comment: Accepted for publication in Ap.J. 31 pages, 6 diagram