Helium Cone Research Articles

Long-wavelength native SAD phasing at BL13-XALOC enabled by the presence of a helium cone

Long-wavelength native SAD phasing at BL13-XALOC enabled by the presence of a helium cone

A simple adaptation to a protein crystallography station to facilitate difference X-ray scattering studies.

The X-ray crystallography station I911-2 at MAXLab II (Lund, Sweden) has been adapted to enable difference small- and wide-angle X-ray scattering (SAXS/WAXS) data to be recorded. Modifications to the beamline included a customized flow cell, a motorized flow cell holder, a helium cone, a beam stop, a sample stage and a sample delivery system. This setup incorporated external devices such as infrared lasers, LEDs and reaction mixers to induce conformational changes in macromolecules. This platform was evaluated through proof-of-principle experiments capturing light-induced conformational changes in phytochromes. A difference WAXS signature of conformational changes in a plant aqua-porin was also demonstrated using caged calcium.

On the influence of crystal size and wavelength on native SAD phasing.

Native SAD is an emerging phasing technique that uses the anomalous signal of native heavy atoms to obtain crystallographic phases. The method does not require specific sample preparation to add anomalous scatterers, as the light atoms contained in the native sample are used as marker atoms. The most abundant anomalous scatterer used for native SAD, which is present in almost all proteins, is sulfur. However, the absorption edge of sulfur is at low energy (2.472 keV = 5.016 Å), which makes it challenging to carry out native SAD phasing experiments as most synchrotron beamlines are optimized for shorter wavelength ranges where the anomalous signal of sulfur is weak; for longer wavelengths, which produce larger anomalous differences, the absorption of X-rays by the sample, solvent, loop and surrounding medium (e.g. air) increases tremendously. Therefore, a compromise has to be found between measuring strong anomalous signal and minimizing absorption. It was thus hypothesized that shorter wavelengths should be used for large crystals and longer wavelengths for small crystals, but no thorough experimental analyses have been reported to date. To study the influence of crystal size and wavelength, native SAD experiments were carried out at different wavelengths (1.9 and 2.7 Å with a helium cone; 3.0 and 3.3 Å with a helium chamber) using lysozyme and ferredoxin reductase crystals of various sizes. For the tested crystals, the results suggest that larger sample sizes do not have a detrimental effect on native SAD data and that long wavelengths give a clear advantage with small samples compared with short wavelengths. The resolution dependency of substructure determination was analyzed and showed that high-symmetry crystals with small unit cells require higher resolution for the successful placement of heavy atoms.

EMBL beamlines for macromolecular crystallography at PETRA III

Since 2012, EMBL Hamburg operates two new beamlines for macromolecular crystallography - P13 and P14 - at PETRA III at DESY (Hamburg, Germany). We exploit the high brilliance and the wide energy range offered by PETRA III to offer a wide range of conditions to fit the experimental conditions to the challenges posed by the samples. P13 provides high photon flux down to 4 keV. With a helium cone and a kappa goniostat, this allows optimized data collection for SAD phasing. Using adaptive mirrors, the focus size (H x V) can be adjusted between 30 x 20 μm^2 and 150 x 100 μm^2 to match the size of the sample. A MARVIN sample changer is in operation for rapid loading and unloading of samples. P14 offers a high photon flux (>10^12 ph/sec at 12 keV into 5 x 5 µm^2). The beamsize can be varied between 1 x 1.5 mm^2 (unfocused) and 5 x 5 µm^2 (fully focused) in less than a minute by moving the KB mirrors in and out of the beam. For small crystals, an MD3 vertical diffractometer with a sphere of confusion smaller than 100 nm offers excellent conditions. Both beamlines are equipped with PILATUS 6M-F detectors for shutter-less data collection and dedicated data processing computers. The beamlines are embedded into the 'Integrated Facility for Structural Biology' offering facilities for sample preparation and characterization, a laboratory specifically equipped for the preparation of heavy atom derivatives, and downstream facilities for data evaluation We will report about the status of the beamlines and describe typical experimental situations (small crystals, large unit cells, serial crystallography, low-energy phasing, small molecules and others).

Helium pickup ion focusing cone as an indicator of the interstellar flow direction

Abstract The spatial distribution of pickup He+ in the helium focusing cone during the most recent very quiet solar minimum is studied numerically by solving the transport equation for the anisotropic velocity distribution function of the ions, which takes into account pitch-angle scattering, adiabatic cooling, and focusing in the interplanetary magnetic field. It is shown that the pickup He+ focusing cone observed with the STEREO spacecraft can be shifted in ecliptic longitude relative to the neutral helium cone, and thus can be considered as an indicator of the interstellar flow direction only in the case if all relevant transport effects are taken into account. The value of the shift depends on the mean free path of pickup ions. The larger is the mean free path, the larger is the shift. Under unusually quiet solar wind conditions during the recent solar minimum the shift can reach 5°.

EMBL beamlines for macromolecular crystallography at PETRA III

Since 2012, EMBL Hamburg operates two new beamlines for macromolecular crystallography - P13 and P14 - at PETRA III at DESY (Hamburg, Germany). We exploit the high brilliance and the wide energy range offered by PETRA III to offer a wide range of conditions to fit the experimental conditions to the challenges posed by the samples. P13 provides high photon flux down to 4 keV. With a helium cone and a kappa goniostat, this allows optimized data collection for SAD phasing. Using adaptive mirrors, the focus size (H x V) can be adjusted between 30 x 20 μm^2 and 150 x 100 μm^2 to match the size of the sample. A MARVIN sample changer is in operation for rapid loading and unloading of samples. P14 offers a high photon flux (>10^12 ph/sec at 12 keV into 5 x 5 µm^2). The beamsize can be varied between 1 x 1.5 mm^2 (unfocused) and 5 x 5 µm^2 (fully focused) in less than a minute by moving the KB mirrors in and out of the beam. For small crystals, an MD3 vertical diffractometer with a sphere of confusion smaller than 100 nm offers excellent conditions. Both beamlines are equipped with PILATUS 6M-F detectors for shutter-less data collection and dedicated data processing computers. The beamlines are embedded into the 'Integrated Facility for Structural Biology' offering facilities for sample preparation and characterization, a laboratory specifically equipped for the preparation of heavy atom derivatives, and downstream facilities for data evaluation We will report about the status of the beamlines and describe typical experimental situations (small crystals, large unit cells, serial crystallography, low-energy phasing, small molecules and others). http://www.eiseverywhere.com/image.php?acc=4087&id=283682

Pickup interstellar helium ions in the region of the solar gravitational cone

Our numerical analyses of the velocity and spatial distributions of pickup interstellar helium ions in the region of the solar gravitational cone in the ecliptic plane at a distance of 1 AU show that the ion density maximum must be displaced relative to the neutral helium cone axis in the direction of the Earth’s revolution around the Sun. The solar wind parameters in the numerical model correspond to their observed values during the crossing of the helium cone by the ACE spacecraft in 1998. At these parameters, the calculated angular displacement is 5°. The absence of a similar displacement in the ACE measurements is shown to stem from the fact that the spectrometer onboard ACE records and identifies only a fraction of the pickup helium ions with fairly high magnitudes and certain directions of the velocities.

Observation of the interstellar helium cone by the NOZOMI spacecraft

‘The Japanese Mars probe, NOZOMI, is staying in the interplanetary space (1–1.5 AU) until its Mars’ orbit insertion scheduled in early 2004. Every 16 months on this interplanetary orbit the spacecraft crosses around 1 AU the ‘gravitational focusing cone’ of the interstellar helium, which are penetrating into the inner heliosphere under the solar gravity. During the first crossing of the cone in the season of March–May 2000, we observed these helium particles after the solar wind pickup process with an E/q type ion detector aboard NOZOMI. We have estimated the original temperature of the interstellar helium as 11 000 K.

Signatures of the Interplanetary Helium Cone Reflected by Pick-up Ions

As known for a long time, interstellar wind neutral helium atoms deeply penetrate into the inner heliosphere and, when passing through the solar gravity field, form a strongly pronounced helium density cone in the downwind direction. Helium atoms are photoionized and picked-up by the solar wind magnetic field, but as pick-up ions they are not simply convected outwards with the solar wind in radial directions as assumed in earlier publications. Rather they undergo a complicated diffusion-convection process described here by an appropriate kinetic transport equation taking into account adiabatic cooling and focusing, pitch angle scattering and energy diffusion. In this paper, we solve this equation for He+pick-up ions which are injected into the solar wind mainly in the region of the helium cone. We show the resulting He+pick-up ion density profile along the orbit of the Earth in many respects differs from the density profile of the neutral helium cone: depending on solar-wind-entrained Alfvenic turbulence levels, the density maximum when looking from the Earth to the Sun is shifted towards the right side of the cone, the ratio of peak-densities to wing-densities varies and a left-to-right asymmetry of the He+-density profile is pronounced. Derivation of interstellar helium parameters from these He+-structures, such as the local interstellar medium (LISM) wind direction, LISM velocity and LISM temperature, are very much impeded. In addition, the pitch-angle spectrum of He+pick-up ions systematically becomes more anisotropic when passing from the left to the right wing of the cone structure. All effects mentioned are more strongly pronounced in high velocity solar wind compared to the low velocity solar wind.

Interplanetary Pick-Up Ion Acceleration A Study of Anisotropic Phase-Space Diffusion

Interplanetary pick-up ions originate from ionizations of neutral interstellar atoms in the heliosphere. Over the past periods it was generally expected that after pick-up by the frozen-in solar wind magnetic fields these ions quickly isotropize in velocity space by strong pitch- angle scattering, they do, however, not assimilate to the ambient solar wind ions. Meanwhile careful investigations of pick-up ion data obtained with the plasma analyzers on AMPTE and ULYSSES could clearly reveal that, especially at periods of flow-aligned fields, noticeably anisotropic distributions must prevail. To better understand the evolutionary tracks of pick-up ions in interplanetary phase-space we carried out an injection study which takes into account all relevant convection and diffusion processes, i.e. describing pitch angle scattering, adiabatic cooling, drifts and energy diffusion. As demonstrated here particles injected at 1 AU establish a distribution function with substantial anisotropies up to distances beyond 6 AU. Only under the action of fairly strong isotropic turbulence levels a trend towards isotropy can be recognized. The bulk velocity of the injected pick-up ions turns out to be remarkably smaller than the solar wind velocity. It also is obvious that pick-ups are strongly spread out from that solar wind plasma parcel into which they were originally implanted. As one consequence it must be concluded that the derivation of interstellar He gas parameters, using He pick-up ion flux data, require appreciable caution. Due to anisotropic spatial diffusion the location of the LISM helium cone axis, i.e. the LISM wind vector, and the LISM helium temperature are hidden in the associated He+pick-up ion flux patterns.

Determination of interstellar helium parameters from the ULYSSES-NEUTRALGAS experiment: Method of data analysis

The GAS instrument on board the ULYSSES spacecraft has, for the first time, measured directly the interstellar flux of helium atoms in the inner solar system. From the locally measured angular distribution of the flux, the task is to derive the five parameters of the Maxwellian distribution function: density, bulk velocity vector, and temperature describing the state of the interstellar helium outside of the heliosphere, “at infinity. To accomplish this, a new method for the data analysis has been developed that employs Tarantola's approach. In the inverse problem considered a solution is found by optimizing (minimizing) the sum of squared residuals between the measured counts and the count numbers derived from a computer simulation. The mathematical formulation of this method is described in detail. The method proved to be reliable and robust in that it always finds a solution. In two extreme, but still typical cases of actual measurements the power but also the limitations of the method are demonstrated. The solution obtained can either be unique, e.g. for measurements taken in the helium cone at 1.5 AU, or belongs, in cases of larger heliocentric distances and outside of the cone, to a one-dimensional family of equally acceptable helium parameters. To obtain a unique solution in the latter, ill-determined problem, further information is required, which can be achieved by combining measurements that are taken during sufficiently different conditions, e.g. downwind or crosswind with respect to the helium flow (comparable to the tomography problem). Three different approaches to this problem have been investigated. The confidence factor of a solution is estimated by a standard test and the error bars are determined from the covariance matrix. Also, the dependence of the solutions on systematic errors in a number of input parameters, such as background level, ionization rate, spacecraft attitude and efficiency function of the detector is studied.

Broadening of the Interplanetary Helium Cone Structure Due to Elastic Collisions of LISM Helium Atoms with Solar Wind Ions

AbstractNeutral interstellar particles penetrating into the heliosphere, besides being subject there to specific loss processes, suffer elastic collisions with KeV-solar wind ions. The momentum transfer to the neutrals connected with these collisions leads to a loss of angular momentum with respect to the sun and to a fractional compensation of the effective solar gravity. The dynamical particle trajectories hence are changed into non-Keplerians leading to density and temperature distributions differing from those calculated in the past. This is found from a solution of the Boltzmann equation that linearizes the effect of this additional force. It is shown here that the HeI-584A resonance glow of the heliospheric helium cone lead to substantially lower interstellar helium temperatures if re-interpreted on the basis of this revised theory. These temperatures now seem to be in accordance with the derived temperatures for interstellar hydrogen.

An interpretation of Mariner 10 helium (584 A) and hydrogen (1216 A) interplanetary emission observations

Measurements of the interplanetary emissions of both He(584 A) and H(1216 A) on January 28, 1974, a time of solar minimum, are reported and discussed. An analysis of the Mariner 10 ultraviolet spectrometer data shows that a simultaneous measurement of both emissions results in a self-consistent determination of the physical properties of the interstellar wind. With the aid of a model the number densities of helium and hydrogen outside the solar system were found to be 0.008 + or - 0.003/cu cm and 0.04 (+0.03, -0.02)/cu cm, respectively, which indicates a He/H ratio of 0.20 (+0.30, -0.13). Values characterizing the helium cone, interstellar wind temperature, effective lifetime of hydrogen atoms in the solar system, and downstream direction of the interstellar wind are presented.