Basis set dependence of the molecular electrostatic potential topography. A case study of substituted benzenes

The basis set dependence of the topographical structure of the molecular electrostatic potential (MESP), as well as the effect of substituents on the MESP distribution, has been investigated with substituted benzenes as test cases. The molecules are studied at HF-SCF 3�21G and 6�31G** levels, with a further MESP topographical investigation at the 3�21G, double-zeta, 6�31G*, 6�31G**, double-zeta polarized and triple-zeta polarized levels. The MESP critical points for a 3�21G optimized/6�31G** basis are similar to the corresponding 6�31G** optimized/6�31G** ones. More generally, the qualitative features of the MESP topography computed at the polarized level are independent of the level at which optimization is carried out. For a proper representation of oxygen lone pairs, however, optimization using a polarized basis set is required. The nature of the substituent drastically changes the MESP distribution over the phenyl ring. The values and positions of MESP minima indicate the most active site for electrophilic attack. This point is strengthened by a study of disubstituted benzenes.

Recent advances in engineering topography mediated antibacterial surfaces

The tendency of bacterial cells to adhere and colonize a material surface leading to biofilm formation is a fundamental challenge underlying many different applications including microbial infections associated with biomedical devices and products. Although, bacterial attachment to surfaces has been extensively studied in the past, the effect of surface topography on bacteria-material interactions has received little attention until more recently. We review the recent progress in surface topography based approaches for engineering antibacterial surfaces. Biomimicry of antibacterial surfaces in nature is a popular strategy. Whereas earlier endeavors in the field aimed at minimizing cell attachment, more recent efforts have focused on developing bactericidal surfaces. However, not all such topography mediated bactericidal surfaces are necessarily cytocompatible thus underscoring the need for continued efforts for research in this area for developing antibacterial and yet cytocompatible surfaces for use in implantable biomedical applications. This mini-review provides a brief overview of the current strategies and challenges in the emerging field of topography mediated antibacterial surfaces.

An alternative approach to study nonlinear inviscid flow over arbitrary bottom topography

This paper deals with a new approach to study the nonlinear inviscid flow over arbitrary bottom topography. The problem is formulated as a nonlinear boundary value problem which is reduced to a Dirichlet problem using certain transformations. The Dirichlet problem is solved by applying Plemelj-Sokhotski formulae and it is noticed that the solution of the Dirichlet problem depends on the solution of a coupled Fredholm integral equation of the second kind. These integral equations are solved numerically by using a modified method. The free-surface profile which is unknown at the outset is determined. Different kinds of bottom topographies are considered here to study the influence of bottom topography on the free-surface profile. The effects of the Froude number and the arbitrary bottom topography on the free-surface profile are demonstrated in graphical forms for the subcritical flow. Further, the nonlinear results are validated with the results available in the literature and compared with the results obtained by using linear theory. (C) 2015 Elsevier Inc. All rights reserved.

Quantitative characterization of adhesion and stiffness of corneal lens of Drosophila melanogaster using atomic force microscopy

Atomic force Microscopy (AFM) has become a versatile tool in biology due to its advantage of high-resolution imaging of biological samples close to their native condition. Apart from imaging, AFM can also measure the local mechanical properties of the surfaces. In this study, we explore the possibility of using AFM to quantify the rough eye phenotype of Drosophila melanogaster through mechanical properties. We have measured adhesion force, stiffness and elastic modulus of the corneal lens using AFM. Various parameters affecting these measurements like cantilever stiffness and tip geometry are systematically studied and the measurement procedures are standardized. Results show that the mean adhesion force of the ommatidial surface varies from 36 nN to 16 nN based on the location. The mean stiffness is 483 +/- 5 N/m, and the elastic modulus is 3.4 +/- 0.05 GPa (95% confidence level) at the center of ommatidia. These properties are found to be different in corneal lens of eye expressing human mutant tau gene (mutant). The adhesion force, stiffness and elastic modulus are decreased in the mutant. We conclude that the measurement of surface and mechanical properties of D. melanogaster using AFM can be used for quantitative evaluation of `rough eye' surface. (C) 2015 Elsevier Ltd. All rights reserved.

Toward a High-Resolution Monitoring of Continental Surface Water Extent and Dynamics, at Global Scale: from GIEMS (Global Inundation Extent from Multi-Satellites) to SWOT (Surface Water Ocean Topography)

Up to now, high-resolution mapping of surface water extent from satellites has only been available for a few regions, over limited time periods. The extension of the temporal and spatial coverage was difficult, due to the limitation of the remote sensing technique e.g., the interaction of the radiation with vegetation or cloud for visible observations or the temporal sampling with the synthetic aperture radar (SAR)]. The advantages and the limitations of the various satellite techniques are reviewed. The need to have a global and consistent estimate of the water surfaces over long time periods triggered the development of a multi-satellite methodology to obtain consistent surface water all over the globe, regardless of the environments. The Global Inundation Extent from Multi-satellites (GIEMS) combines the complementary strengths of satellite observations from the visible to the microwave, to produce a low-resolution monthly dataset () of surface water extent and dynamics. Downscaling algorithms are now developed and applied to GIEMS, using high-spatial-resolution information from visible, near-infrared, and synthetic aperture radar (SAR) satellite images, or from digital elevation models. Preliminary products are available down to 500-m spatial resolution. This work bridges the gaps and prepares for the future NASA/CNES Surface Water Ocean Topography (SWOT) mission to be launched in 2020. SWOT will delineate surface water extent estimates and their water storage with an unprecedented spatial resolution and accuracy, thanks to a SAR in an interferometry mode. When available, the SWOT data will be adopted to downscale GIEMS, to produce a long time series of water surfaces at global scale, consistent with the SWOT observations.

Rossby Waves With Linear Topography In Barotropic Fluids

Rossby waves are the most important waves in the atmosphere and ocean, and are parts of a large-scale system in fluid. The theory and observation show that, they satisfy quasi-geostrophic and quasi-static equilibrium approximations. In this paper, solitary Rossby waves induced by linear topography in barotropic fluids with a shear flow are studied. In order to simplify the problem, the topography is taken as a linear function of latitude variable y, then employing a weakly nonlinear method and a perturbation method, a KdV (Korteweg-de Vries) equation describing evolution of the amplitude of solitary Rossby waves induced by linear topography is derived. The results show that the variation of linear topography can induce the solitary Rossby waves in barotropic fluids with a shear flow, and extend the classical geophysical theory of fluid dynamics.

Atomic force microscopy observations of the topography of regenerated silk fibroin aggregations

How fibroin molecules fold themselves and further self-assemble into aggregations with specific structures when the solution concentration increases is the key to understanding the natural silk-forming process of the silkworm. A regenerated Bombyx mori silk fibroin solution was prepared, and serially diluted solutions were coated on aminated coverslips. Atomic force microscopy (AFM) observations of the topography of fibroin molecules revealed a transformation from rodlike aggregations 100-200 nm long to small globules 50 mn in diameter with decreasing concentrations. When the incubation duration increased, the aggregations of fibroin molecules showed a self-assembling process, which was measured with AFM. In particular, after the molecules were incubated for more than 20 min, rodlike micelles formed and were distributed evenly on the surface of the aminated slides. Flow chamber technology was used to study the effect of the shear loading on the topography of the fibroin molecular aggregations. After a shear loading was applied, larger rodlike particles formed at a higher incubation concentration in comparison with those at a lower concentration and were obviously oriented along the direction of fluid flow.

Thermocline topography, horizontal currents and “ridging” in the Eastern Tropical Pacific

ENGLISH: A primary objective of the Inter-American Tropical Tuna Commission is a knowledge of the ecology of tunas which inhabit the Eastern Tropical Pacific. This paper presents some results of the work in physical oceanography, which, it is hoped, will be useful to the biological work and at the same time of interest to physical oceanographers. The work presented here was begun in connection with simple observable facts; the thermocline is very close to the sea surface in a region off Costa Rica (Wooster and Cromwell, 1958), and this region is biologically productive (Holmes, et al. 1957; Brandhorst, 1958). It is the main object of this study to describe and explain these facts, insofar as possible. SPANISH: Uno de los principales objetivos de la Comisión Interamericana del Atún Tropical es el conocimiento de la ecología de los atunes que viven en el Pacífico Oriental Tropical. Este informe presenta algunos de los resultados del estudio en oceanografía física, los cuales se espera que serán útiles en la investigación biológica y, al mismo tiempo, de interés para los oceanógrafos físicos. El trabajo presentado aquí se inició en conexión con sencillos hechos observables; mar afuera de Costa Rica, la termoclina queda muy cerca de la superficie del mar (Wooster y Cromwell, 1958) y esta región es biológicamente productiva (Holmes, el al., 1957; Brandhorst, 1958). El objeto principal de este estudio es describir y explicar estos hechos, hasta donde sea posible. (PDF contains 32 pages.)

Aspects of quality control of wind profiler measurements in complex topography

It is well known in the scientific community that some remote sensing instruments assume that sample volumes present homogeneous conditions within a defined meteorological profile. At complex topographic sites and under extreme meteorological conditions, this assumption may be fallible depending on the site, and it is more likely to fail in the lower layers of the atmosphere. This piece of work tests the homogeneity of the wind field over a boundary layer wind profiler radar located in complex terrain on the coast under different meteorological conditions. The results reveal the qualitative importance of being aware of deviations in this homogeneity assumption and evaluate its effect on the final product. Patterns of behavior in data have been identified in order to simplify the analysis of the complex signal registered. The quality information obtained from the homogeneity study under different meteorological conditions provides useful indicators for the best alternatives the system can offer to build wind profiles. Finally, the results are also to be considered in order to integrate them in a quality algorithm implemented at the product level.

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Interpretation of lunar topography : impact cratering and surface roughness

This work seeks to understand past and present surface conditions on the Moon using two different but complementary approaches: topographic analysis using high-resolution elevation data from recent spacecraft missions and forward modeling of the dominant agent of lunar surface modification, impact cratering. The first investigation focuses on global surface roughness of the Moon, using a variety of statistical parameters to explore slopes at different scales and their relation to competing geological processes. We find that highlands topography behaves as a nearly self-similar fractal system on scales of order 100 meters, and there is a distinct change in this behavior above and below approximately 1 km. Chapter 2 focuses this analysis on two localized regions: the lunar south pole, including Shackleton crater, and the large mare-filled basins on the nearside of the Moon. In particular, we find that differential slope, a statistical measure of roughness related to the curvature of a topographic profile, is extremely useful in distinguishing between geologic units. Chapter 3 introduces a numerical model that simulates a cratered terrain by emplacing features of characteristic shape geometrically, allowing for tracking of both the topography and surviving rim fragments over time. The power spectral density of cratered terrains is estimated numerically from model results and benchmarked against a 1-dimensional analytic model. The power spectral slope is observed to vary predictably with the size-frequency distribution of craters, as well as the crater shape. The final chapter employs the rim-tracking feature of the cratered terrain model to analyze the evolving size-frequency distribution of craters under different criteria for identifying "visible" craters from surviving rim fragments. A geometric bias exists that systematically over counts large or small craters, depending on the rim fraction required to count a given feature as either visible or erased.