Electron Density Data Research Articles

From Data or Dogma? The Myth of the Ideal Helix

In the course of building detailed surface representations for peptidomimetics, we were motivated to analyze the detailed surfaces of helices in proteins. Unexpectedly, we observed few ideal helical forms in high-resolution protein structures. Instead of a bimodal distribution matching the well-known alpha and 3(10) helical forms, we observed a smooth, single-peaked population, characterized by intermediate helices with shared hydrogen bonds. Bifurcated, or three-center hydrogen bonds, have been well-documented in small molecules and peptides, but they're rarely highlighted in the context of folded proteins. The data suggests shared hydrogen bonds are a major component of helices in proteins.Contrary to the Pauling-Corey-Branson models, we did not restrict our analysis to single hydrogen bonds--shared three-center hydrogen bonds were included. High resolution (<2.0 A), electron density data is sharp enough that a helical structure should be unambiguous and accurately modeled. These helices are centered on an intermediate helical form. At poorer resolutions (2.0-5.0 A), electron density is ambiguous; refinement fitting methods are employed to model ideal structures into the data. Here there is an enriched population of ideal structures. A structurally representative subset of proteins reveals the same trends as the whole PDB. The data support the observation that ideal helical parameters do not accurately describe the distribution of real helices in proteins.Hydrogen bonds are a polar (and polarizable) moiety and an accurate model must account for this. We present data comparing molecular dynamics simulations using popular monopole force fields (OPLS-AA and CHARMM) with a next generation force field (AMOEBA) implementing polarizability and multipole electrostatics. AMOEBA simulations are shown to quantitatively reproduce the experimentally observed trends in helical populations. These results emphasize the importance of using appropriate force field potential models when simulating hydrogen bonded structures in proteins.

Seasonal variations of the electron density distribution in the polar region during geomagnetically quiet periods near solar maximum

Meridional electron density distributions above 45° invariant latitude (ILAT) during geomagnetically quiet periods are statistically studied. Electron density data were obtained from plasma waves observed by the Akebono satellite from March 1989 to February 1991 (near solar maximum) in an altitude range of 274–10,500 km. Field‐aligned electron density profiles were fitted by the sum of exponential and power law functions. The transition height, where the power law term equals the exponential term, is highest in the summer (at low solar zenith angle (SZA)) at ∼4000 km and lowest in the winter (at high SZA) at ∼1800 km in a region of ILAT ≥ 70°; this is caused by the larger scale height in the summer (∼550 km) than that in the winter (∼250 km). The largest seasonal variation and SZA dependence of the electron density are found at an altitude of ∼2000 km with a factor of ∼50 (∼104 /cc in the summer, ∼103 /cc in the winter) in the trough, auroral, and polar cap regions. The seasonal variation and SZA dependence are smaller, about a factor of 5–10, above ∼5000 km. Day‐night asymmetries in each season (within a factor of 5) are smaller than the seasonal variation. The scale height is larger in the dayside than in the nightside in each season. These results indicate that photoionization processes in the ionosphere strongly control electron density distributions up to at least ∼5000 km in the trough, auroral, and polar cap regions.

Height profiles of OI 630 nm and OI 557.7 nm airglow intensities measured via rocket-borne photometers and estimated using electron density data: a comparison

Fotómetros y sensores para medidas de densidad electrónica a bordo de cohetes de sondeo brasileños Sonda III fueron lanzados desde Natal (5.8º S, 35.2º W), Brasil. El primero en 11 de Diciembre de 1985 (20:30 hora local) y el otro en 31 de Octubre de 1986 (22:59 hora local). La carga científica consistió de fotómetros para medir emisiones de oxígeno atómico OI 557.7 nm (línea verde) y OI 630 nm (línea roja) en la ionosfera nocturna, dispuestos paralelamente al eje de giro del cohete, y dos sondas de densidad electrónica: una sonda de Langmuir y la otra tipo capacitiva de alta frecuencia, utilizadas para medir la densidad electrónica ionosférica y la presencia de fluctuaciones espaciales. Los valores de densidad electrónica medidos desde esos vuelos de cohetes y otros parámetros obtenidos en los modelos IRI-2001 y MSIS-E 90 han sido utilizados para obtener perfiles de tasa de emisión volumétrica de los oxígenos atómicos OI 557.7 nm y OI 630 nm. Esos datos son comparados con perfiles de altitud obtenidos a partir de los datos de los fotómetros. Tomando como base este estudio comparativo, realizamos una discusión.

Calculation of electronic stopping power along glancing swift heavy ion tracks inperovskites using ab initio electron density data

In recent experiments the irradiation of insulators of perovskite type with swift(E∼100 MeV) heavy ions under glancing incidence has been shown to provide a unique means togenerate periodically arranged nanodots at the surface. The physical origin of thesepatterns has been suggested as stemming from a highly anisotropic electron densitydistribution within the bulk. In order to show the relevance of the electron densitydistribution of the target we present a model calculation for the system that is known to produce the aforementioned surface modifications. On the basis of theLindhard model of electronic stopping, we employ highly-resolved ab initio electron densitydata to describe the conversion of kinetic energy into excitation energy along the ion track.The primary particle dynamics are obtained via integration of the Newtonian equations ofmotion that are governed by a space- and time-dependent frictional force originating fromLindhard stopping. The analysis of the local electronic stopping power along the ion trackreveals a pronounced periodic structure. The periodicity length varies strongly withthe particular choice of the polar angle of incidence and is directly correlated tothe experimentally observed formation of periodic nanodots at insulator surfaces.

A steady-state model for the D- to F-region of the polar cap

For obvious reasons the ionosphere of the polar cap, surrounded by the auroral zone, is only poorly investigated. Even ionosonde data are very scant from geomagnetic latitudes beyond 70°. Since 1997 the European incoherent scatter radar facility EISCAT has an additional installation on Svalbard and has been providing electron density data nearly continuously ever since. These measurements which mainly cover the E- and F-regions are supplemented by rocket data from Heiss Island at a comparable magnetic latitude; these data are more sporadic, but cover lower altitudes and densities. A provisional, steady-state, neural network-based model is presented which uses the data of both sites.

A neural network-based ionospheric model for Arecibo

The Arecibo Observatory (18°N, 66°W) has the world’s largest single dish antenna (300 m diameter). Beyond radio astronomy it can also operate as an incoherent scatter radar and in that mode its figure-of-merit makes it also one of the most powerful world-wide. For the present purpose all electron density data available on the web, from the beginning with the first erratic measurements in 1966 up to 2004 inclusive, were downloaded. The measurements range from about 100 km to beyond 700 km and are essentially evenly distributed, i.e. not dedicated to measure specific geophysical events. From manually edited/inspected data a neural network (NN) was established with season, hour of the day, solar activity and Kp as the input parameters. The performance of this model is checked against a – likewise NN based – global model of foF2, a measure of the maximum electron density of the ionosphere. Considering the diverse data sources and assumptions of the two models it can be concluded that they agree remarkably well.

Least-squares gradient calculation from multi-point observations of scalar and vector fields: methodology and applications with Cluster in the plasmasphere

Abstract. This paper describes a general-purpose algorithm for computing the gradients in space and time of a scalar field, a vector field, or a divergence-free vector field, from in situ measurements by one or more spacecraft. The algorithm provides total error estimates on the computed gradient, including the effects of measurement errors, the errors due to a lack of spatio-temporal homogeneity, and errors due to small-scale fluctuations. It also has the ability to diagnose the conditioning of the problem. Optimal use is made of the data, in terms of exploiting the maximum amount of information relative to the uncertainty on the data, by solving the problem in a weighted least-squares sense. The method is illustrated using Cluster magnetic field and electron density data to compute various gradients during a traversal of the inner magnetosphere. In particular, Cluster is shown to cross azimuthal density structure, and the existence of field-aligned currents in the plasmasphere is demonstrated.

Regional 4-D modeling of the ionospheric electron density

The knowledge of the electron density is the key point in correcting ionospheric delays of electromagnetic measurements and in studying the ionosphere. During the last decade GNSS, in particular GPS, has become a promising tool for monitoring the total electron content (TEC), i.e., the integral of the electron density along the ray-path between the transmitting satellite and the receiver. Hence, geometry-free GNSS measurements provide informations on the electron density, which is basically a four-dimensional function depending on spatial position and time. In addition, these GNSS measurements can be combined with other available data including nadir, over-ocean TEC observations from dual-frequency radar altimetry (T/P, JASON, ENVISAT), and TECs from GPS-LEO occultation systems (e.g., FORMOSAT-3/COSMIC, CHAMP) with heterogeneous sampling and accuracy. In this paper, we present different multi-dimensional approaches for modeling spatio-temporal variations of the ionospheric electron density. To be more specific, we split the target function into a reference part, computed from the International Reference Ionosphere (IRI), and an unknown correction term. Due to the localizing feature of B-spline functions we apply tensor-product spline expansions to model the correction term in a certain multi-dimensional region either completely or partly. Furthermore, the multi-resolution representation derived from wavelet analysis allows monitoring the ionosphere at different resolutions levels. For demonstration we apply three approaches to electron density data over South America.

Can electromagnetic disturbances related to the recent great earthquakes be detected by satellite magnetometers?

On December 26, 2004 the world's fourth largest earthquake since 1900 and the largest since the 1964 Prince William Sound, Alaska earthquake, occurred off the west coast of northern Sumatra with a magnitude of 9.3. On March 28, 2005 another event of magnitude 8.7 took place in the same region. The December 26, 2004 earthquake has prompted scientists to investigate possible electromagnetic signatures of this event, using ground magnetic observations. Iyemori et al. [Iyemori, T. et al., 2005. Geomagnetic pulsations caused by the Sumatra earthquake on December 26, 2004. Geophys. Res. Lett., 32, L20807, doi:10.1029/2005GL024083.] have suggested that a 3.6 min long geomagnetic pulsation, observed shortly after this event, was generated by the earthquake. They have speculated that a 30 s magnetic pulsation was also caused by the earthquake. Here for the first time, CHAMP satellite magnetic and electron density data are examined to find out if electromagnetic signatures which are possibly related to these recent megathrust earthquakes are observed in satellite magnetic data. We have shown that some specific features are observed after the two earthquakes, with periods of about 16 and 30 s. Our results favor an external source origin for the 30 s pulsation. Moreover, after more than 1 h, CHAMP magnetic data indicate the existence of a feature characterized by the same parameters (duration, amplitude, and frequency content), which could be associated with each earthquake, respectively. Further investigations are required in order to answer the question of whether these signals can be associated with earthquakes and to assign their possible usefulness with respect to earthquake development.

Theoretical study of hydrogen bond interactions of felodipine with polyvinylpyrrolidone and polyethyleneglycol

The hydrogen bonding in solid dispersions of the antihypertension and antianginal drug felodipine, ethylmethyl-4-(2,3-dichlorophenyl)-1,4-dihydro-2,6-dimethyl-3,5-pyridine-dicarboxylate, with the polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) water soluble polymers, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Six low energy conformers of felodipine have been located. The vibrational as well as the 1H and 13C NMR spectroscopic properties calculated for the most stable isomer were in satisfactory agreement with the experimental data. The hydrogen bonded complexes of felodipine conformers with low molecular weight models of the polymers have been fully optimized. In all cases a N–H⋯O hydrogen bond is formed. The BSSE and ZPE corrected interaction energies were estimated of 30–36 kJ/mol for PVP and 19–21 kJ/mol for PEG complexes. The electron density ( ρ b) and Laplacian (∇ 2 ρ b) properties at critical points of the relevant bonds, estimated by AIM calculations, showed that N–H⋯O have low and positive character (∇ 2 ρ b > 0), consistent with electrostatic character of the hydrogen bond. The vibrational study of the hydrogen bonded complexes showed negative (red) shifts for the ν(N–H) stretching mode. Interaction energies, electron density, Laplacian and vibrational data showed a stronger hydrogen bond of felodipine with PVP polymer in comparison to that with PEG, in agreement with experimental data concerning the dissolution rates of the corresponding solid dispersions.

ALTAIR incoherent scatter observations of the equatorial daytime ionosphere

The first high‐resolution electron density maps of the low‐latitude D‐ and E‐region ionosphere in the Pacific sector acquired with ALTAIR UHF measurements are presented. The electron density data were collected in connection with a rocket based common volume experiment described by Friedrich et al. (2006). The observed phenomena in the density maps include E‐region density layers of tidal origin, shorter lived layers with small vertical scales, and lower E‐region electron density enhancement in response to enhanced X‐ray flux.

In situ observation atL= 2.3–5 by the Akebono satellite of the plasmaspheric depletion during the September 1998 magnetic storm

[1] From ground-based observations at L = 2.07 of the field line resonance (FLR) during an intense magnetic storm on 25 September 1998, Chi et al. (2000) estimated that the equatorial plasma density at L = 2.07 dropped to 25% of the prestorm value. Such depletion very close to the Earth is unusual. Two possible interpretations of the result are: (1) the plasmapause moved inward past L = 2.07, and (2) the plasmapause remained outside L = 2.07, but the density within the plasmasphere decreased. To distinguish between these possibilities, we examine in situ observations of the electron density made by the Akebono satellite at L = 2.3–5 on four passes during the same storm. The electron density measured by Akebono at a reference L shell of L ∼2.5 changed with time in a manner consistent with the FLR-based estimates. On three of these passes, the plasmapause was located at L > 3, and if the plasmaspheric L profile of the Akebono density data is extrapolated inward, for each pass, its value at L = 2.07 matches the FLR-based estimates. However, on the pass at 2323–2351 UT on 25 September that corresponded to the severe density decrease detected at L = 2.07, Akebono did not detect a plasmapause in the L range (>2.3) for which the electron density data were available. For the same pass, inward extrapolation of the density measured at L > 2.3 was a factor of ∼5 smaller than the FLR-based estimate. This implies that there was a sharp density inward gradient (the plasmapause) at 2.07 < L < 2.3, supporting the second interpretation.

Topside electron density in IRI and NeQuick: Features and limitations

The topside ionosphere modeling suffers from the relative scarcity of experimental electron density data. Different modeling approaches have been applied in empirical models, like IRI, and profilers, like NeQuick. Comparing ISIS-2 topside electron density profiles with IRI and NeQuick models weak points in their topside formulation are identified and analysed. The IRI topside consists in two constant gradient sections, with a transition height kept at a fixed height in its domain. Tests of transition height and gradient modifications are presented, based on experimental evidences and model efforts. NeQuick model has a topside formulation based on a semi-Epstein layer, governed by an empirical shape parameter k. An alternative formulation is presented based on k values derived from experimental profiles.

DETERMINING RELEVANT FEATURES TO RECOGNIZE ELECTRON DENSITY PATTERNS IN X-RAY PROTEIN CRYSTALLOGRAPHY

High-throughput computational methods in X-ray protein crystallography are indispensable to meet the goals of structural genomics. In particular, automated interpretation of electron density maps, especially those at mediocre resolution, can significantly speed up the protein structure determination process. TEXTAL(TM) is a software application that uses pattern recognition, case-based reasoning and nearest neighbor learning to produce reasonably refined molecular models, even with average quality data. In this work, we discuss a key issue to enable fast and accurate interpretation of typically noisy electron density data: what features should be used to characterize the density patterns, and how relevant are they? We discuss the challenges of constructing features in this domain, and describe SLIDER, an algorithm to determine the weights of these features. SLIDER searches a space of weights using ranking of matching patterns (relative to mismatching ones) as its evaluation function. Exhaustive search being intractable, SLIDER adopts a greedy approach that judiciously restricts the search space only to weight values that cause the ranking of good matches to change. We show that SLIDER contributes significantly in finding the similarity between density patterns, and discuss the sensitivity of feature relevance to the underlying similarity metric.

The Cassini solar Faraday rotation experiment

The Cassini Faraday rotation experiment improves the current understanding of the coronal magnetic field by making the first measurements of the magnetic field within two solar radii of the south pole and by allowing the separation of the changing electron density from the magnetic field during transient crossings of the line of sight. Simultaneous ranging data to Cassini also contributes to the growing body of empirical electron density models by providing electron density data at solar maximum at varying latitudes including over the poles. Faraday rotation data in the solar corona were collected in 2002 and 2003 using the Cassini spacecraft in cruise to Saturn. Although Cassini primarily transmits in right-hand polarization, enough left-hand is produced to enable polarization measurements. We show that during solar conjunction Faraday rotation is measurable with Cassini. In the X- and Ka-bands both datasets currently show an asymmetric diurnal pattern in polarization not associated with the ionosphere. The Ka-band is much more sensitive to pointing accuracy and experienced periods of power drop outs which caused the left-circularly polarized signal to drop into the noise on occasion during the 2003 conjunction. Interpretation of the dataset is deferred to future papers.

Application and Limitations of X‐Ray Crystallographic Data in Structure‐Based Ligand and Drug Design.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Application and limitations of X-ray crystallographic data in structure-based ligand and drug design.

Structure-based design usually focuses upon the optimization of ligand affinity. However, successful drug design also requires the optimization of many other properties. The primary source of structural information for protein-ligand complexes is X-ray crystallography. The uncertainties introduced during the derivation of an atomic model from the experimentally observed electron density data are not always appreciated. Uncertainties in the atomic model can have significant consequences when this model is subsequently used as the basis of manual design, docking, scoring, and virtual screening efforts. Docking and scoring algorithms are currently imperfect. A good correlation between observed and calculated binding affinities is usually only observed only when very large ranges of affinity are considered. Errors in the correlation often exceed the range of affinities commonly encountered during lead optimization. Some structure-based design approaches now involve screening libraries by using technologies based on NMR spectroscopy and X-ray crystallography to discover small polar templates, which are used for further optimization. Such compounds are defined as leadlike and are also sought by more traditional high-throughput screening technologies. Structure-based design and HTS technologies show important complementarity and a degree of convergence.

Combining ionosonde with ground GPS data for electron density estimation

Dual frequency Global Positioning System (GPS) receivers provide integrated total electron content (TEC) along the ray path (slant TEC, affected by a bias). By inverting this observable, it is possible to obtain the vertical total electron content with some assumptions about the horizontal structure of the ionosphere. The large number of permanent receivers distributed around the world provide enough information to obtain such TEC observables with high spatial and temporal resolutions. Nevertheless, the geometry (mainly vertical) of the ground GPS observations does not allow to solve the vertical structure of electron density of the ionosphere. Mixing different kinds of complementary data in a tomographic context helps to overcome this problem. Several works have obtained successful results achieved by combining occultation and ground GPS data to estimate the local three-dimensional structure of ionospheric electron density. This paper proposes the use of just ground data to obtain similar or better results. To do this, the ground GPS data are mixed with vertical profiles of electron density derived from ionosonde data instead of GPS occultation observations. In this paper, the complementarity between vertical profiles of electron density (estimated using the NeQuick model) and ground GPS data (from GPS IGS permanent network) are shown as well as the performance of the resulting combination.

Some features of electron density behaviour in the high latitude D-region derived from in situ measurements

A large database of rocket measurements of the D-region electron concentration has been studied. The data were obtained at four sites in the Antarctic (Molodezhnaya and Syowa) and Arctic (Heiss Island, and Andøya/Kiruna). The electron densities were analysed in terms of their variations with solar zenith angle, geomagnetic activity and atmospheric temperature. We found that there is a particle ionisation source in the auroral oval even in quiet conditions. The energy of the particles is such, that they penetrate down to 85 km , are partially absorbed between 85 and 80 km but do not penetrate (are completely absorbed) below 75 km . Analysis of the dependence of the electron concentration [e] on the daily sum of Kp indices, ∑Kp, shows that at all heights considered there is an increase of [e] with ∑Kp up to some saturation value of ∑Kp and beyond this level [e] is either constant (with large scatter of the data) or even decreases. This indicates that when the auroral oval expands with increasing geomagnetic activity, a particular station may move from a position outside or at the boundary of the oval, to a position inside the polar cap. An attempt is made to find the temperature dependence of the electron concentration. It is found that [e] at 75 and 80 km increases with temperature T. Analysis of the flights conducted during noctilucent cloud (NLC) events at Andøya/Kiruna reveals a strong dependence of [e] on ∑Kp at 80 and 85 km . This dependence is stronger and better defined than that for the entire data set. This may be explained by the low mesopause temperatures observed in summer when NLC occur. A comparison of the electron density data sets with empirical and theoretical models is presented and during quiet magnetic conditions a good agreement with mid-latitude models is found.

Comparisons of IRI model and electron density data for the sub-equatorial station, Natal

Database from CADI (Canadian Digital Ionosonde) recorded at Natal (5.2° S, 36° W) near solar maximum are used to compare with the International Reference Ionosphere (IRI) predictions. Such comparison is done using vertical profiles of electron density and F region peak parameters, the maximum electron density ( NmF2) and its corresponding height ( HmF2), for geomagnetically quiet and disturbed conditions. The mean behavior of the observed vertical electron density profiles at 0300, 0900, 1500 and 2100 UT (UT = LT + 2.4 hr) for quiet and disturbed periods was compared with IRI profiles. Generally, good agreement between the two sets is noted, but IRI underestimates the heights of the bottomside F region at 0900 and 2100 UT. Also, discrepancies are found between the observed values of NmF2 and HmF2 and those obtained from IRI using URSI coefficients during evening-nighttime period.