Patterns of past and recent conversion of indigenous grasslands in the South Island, New Zealand

We used recent satellite imagery to quantify the extent, type, and rate of conversion of remaining indigenous grasslands in the inland eastern South Island of New Zealand in recent years. We describe the pattern of conversion in relation to national classifications of land use capability and land environments, and ecological and administrative districts and regions. We show that although large areas of indigenous grasslands remain, grassland loss has been ongoing. Indigenous grassland was reduced in the study area by 3% (70 200 ha) between 1990 and 2008. Almost two-thirds of post-1990 conversion occurred in threatened environments with less than 30% of indigenous cover remaining, primarily in the Waitaki, Mackenzie and Central Otago administrative districts. This conversion occurred primarily on non-arable land. In the Mackenzie and Waitaki districts the rate of conversion in 2001-2008 was approximately twice that in 1990-2001. Opportunities to protect more of the full range of indigenous grasslands lie with the continuing tenure review process in these districts

Density fluctuations and the structure of a nonuniform hard sphere fluid

We derive an exact equation for density changes induced by a general external field that corrects the hydrostatic approximation where the local value of the field is adsorbed into a modified chemical potential. Using linear response theory to relate density changes self-consistently in different regions of space, we arrive at an integral equation for a hard sphere fluid that is exact in the limit of a slowly varying field or at low density and reduces to the accurate Percus-Yevick equation for a hard core field. This and related equations give accurate results for a wide variety of fields

Orbital-Free Density Functional Theory: Kinetic Potentials and Ab-Initio Local Pseudopotentials

In the density functional (DF) theory of Kohn and Sham, the kinetic energy of the ground state of a system of noninteracting electrons in a general external field is calculated using a set of orbitals. Orbital free methods attempt to calculate this directly from the electron density by approximating the universal but unknown kinetic energy density functional. However simple local approximations are inaccurate and it has proved very difficult to devise generally accurate nonlocal approximations. We focus instead on the kinetic potential, the functional derivative of the kinetic energy DF, which appears in the Euler equation for the electron density. We argue that the kinetic potential is more local and more amenable to simple physically motivated approximations in many relevant cases, and describe two pathways by which the value of the kinetic energy can be efficiently calculated. We propose two nonlocal orbital free kinetic potentials that reduce to known exact forms for both slowly varying and rapidly varying perturbations and also reproduce exact results for the linear response of the density of the homogeneous system to small perturbations. A simple and systematic approach for generating accurate and weak ab-initio local pseudopotentials which produce a smooth slowly varying valence component of the electron density is proposed for use in orbital free DF calculations of molecules and solids. The use of these local pseudopotentials further minimizes the possible errors from the kinetic potentials. Our theory yields results for the total energies and ionization energies of atoms, and for the shell structure in the atomic radial density profiles that are in very good agreement with calculations using the full Kohn-Sham theory.Comment: To be published in Phys. Rev.

From Discrete Hopping to Continuum Modeling on Vicinal Surfaces with Applications to Si(001) Electromigration

Coarse-grained modeling of dynamics on vicinal surfaces concentrates on the diffusion of adatoms on terraces with boundary conditions at sharp steps, as first studied by Burton, Cabrera and Frank (BCF). Recent electromigration experiments on vicinal Si surfaces suggest the need for more general boundary conditions in a BCF approach. We study a discrete 1D hopping model that takes into account asymmetry in the hopping rates in the region around a step and the finite probability of incorporation into the solid at the step site. By expanding the continuous concentration field in a Taylor series evaluated at discrete sites near the step, we relate the kinetic coefficients and permeability rate in general sharp step models to the physically suggestive parameters of the hopping models. In particular we find that both the kinetic coefficients and permeability rate can be negative when diffusion is faster near the step than on terraces. These ideas are used to provide an understanding of recent electromigration experiment on Si(001) surfaces where step bunching is induced by an electric field directed at various angles to the steps.Comment: 10 pages, 4 figure

Central spindle self-organization and cytokinesis in artificially activated sea urchin eggs

Author Posting. © Marine Biological Laboratory, 2016. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 230, no.2 (2016): 85-95.The ability of microtubules of the mitotic apparatus to control the positioning and initiation of the cleavage furrow during cytokinesis was first established from studies on early echinoderm embryos. However, the identity of the microtubule population that imparts cytokinetic signaling is unclear. The two main––and not necessarily mutually exclusive–– candidates are the central spindle and the astral rays. In the present study, we examined cytokinesis in ammonia-activated sea urchin eggs, which lack paternally derived centrosomes and undergo mitosis mediated by unusual anastral, bipolar mini-spindles. Live cell imaging and immunolabeling for microtubules and the centralspindlin constituent and kinesin-related protein, MKLP1, demonstrated that furrowing in ammonia-activated eggs was associated with aligned arrays of centralspindlin-linked, opposed bundles of antiparallel microtubules. These autonomous, zipper- like arrays were not associated with a mitotic apparatus, but did possess characteristics similar to the central spindle region of control, fertilized embryos. Our results highlight the self-organizing nature of the central spindle region and its ability to induce cytokinesis-like furrowing, even in the absence of a complete mitotic apparatus.This research was supported by student/faculty summer research grants from the Dickinson College Research and Development Committee to JHH; Laura and Arthur Colwin Summer Research Fellowships from the MBL to JHH and CBS; a National Science Foundation Major Research Instrumentation grant to JHH (MRI-0320606); and a NSF collaborative research grant to JHH (MCB-1412688) and to CBS (MCB- 1412734)

Current-Induced Step Bending Instability on Vicinal Surfaces

We model an apparent instability seen in recent experiments on current induced step bunching on Si(111) surfaces using a generalized 2D BCF model, where adatoms have a diffusion bias parallel to the step edges and there is an attachment barrier at the step edge. We find a new linear instability with novel step patterns. Monte Carlo simulations on a solid-on-solid model are used to study the instability beyond the linear regime.Comment: 4 pages, 4 figure

A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

<p>Abstract</p> <p>Background</p> <p>The ability to differentiate a bioterrorist attack or an accidental release of a research pathogen from a naturally occurring pandemic or disease event is crucial to the safety and security of this nation by enabling an appropriate and rapid response. It is critical in samples from an infected patient, the environment, or a laboratory to quickly and accurately identify the precise pathogen including natural or engineered variants and to classify new pathogens in relation to those that are known. Current approaches for pathogen detection rely on prior genomic sequence information. Given the enormous spectrum of genetic possibilities, a field deployable, robust technology, such as a universal (any species) microarray has near-term potential to address these needs.</p> <p>Results</p> <p>A new and comprehensive sequence-independent array (Universal Bio-Signature Detection Array) was designed with approximately 373,000 probes. The main feature of this array is that the probes are computationally derived and sequence independent. There is one probe for each possible 9-mer sequence, thus 4⁹(262,144) probes. Each genome hybridized on this array has a unique pattern of signal intensities corresponding to each of these probes. These signal intensities were used to generate an un-biased cluster analysis of signal intensity hybridization patterns that can easily distinguish species into accepted and known phylogenomic relationships. Within limits, the array is highly sensitive and is able to detect synthetically mixed pathogens. Examples of unique hybridization signal intensity patterns are presented for different <it>Brucella </it>species as well as relevant host species and other pathogens. These results demonstrate the utility of the UBDA array as a diagnostic tool in pathogen forensics.</p> <p>Conclusions</p> <p>This pathogen detection system is fast, accurate and can be applied to any species. Hybridization patterns are unique to a specific genome and these can be used to decipher the identity of a mixed pathogen sample and can separate hosts and pathogens into their respective phylogenomic relationships. This technology can also differentiate between different species and classify genomes into their known clades. The development of this technology will result in the creation of an integrated biomarker-specific bio-signature, multiple select agent specific detection system.</p