Preferential Orientation Of Particles Research Articles

Thicker Ice Improves the Integrity and Angular Distribution of CDC48A Hexamers on Cryo-EM Grids.

Many cryogenic electron microscopy (cryo-EM) single particle analyses are constrained by the sample preparation step upon which aggregation, dissociation, and/or preferential orientation of particles can be introduced. Here, we report how we solved these problems in the case of CDC48A, a hexameric AAA ATPase from Arabidopsis thaliana. CDC48A hexamers are well preserved under negative staining conditions but disassemble during grid freezing using the classical blotting method. Vitrification of grids using the blot-free Chameleon method preserved the integrity of particles but resulted in their strong preferential orientation. We then used a strategy where we improved in parallel the purification of CDC48A and the conditions for cryo-EM data acquisition. Indeed, we noted that images taken from thicker ice presented an even distribution of intact particles with random orientations, but resulted in a lower image resolution. Consequently, in our case, distribution, orientation, image resolution, and the integrity of particles were tightly correlated with ice thickness. By combining the more homogeneous and stable CDC48A hexamers resulting from our improved purification protocol with an iterative search across different ice thicknesses, we identified an intermediate thickness that retained sufficiently high-resolution structural information while maintaining a complete distribution of particle orientations. Our approach may provide a simple, fast, and generally applicable strategy to record data of sufficient quality under standard laboratory and microscope settings. This method may be of particular value when time and resources are limited.

Orientation of non spherical prolate dust particles moving vertically in the Earth’s atmosphere

Preferential particle orientation has been previously reported for desert dust and attributed on atmospheric electricity (Ulanowski et al., 2007). Depending on its strength, the total electric field within the dust layer can: (a) counteract the gravitational settling of large particles and (b) cause a preferential orientation of the non-spherical particles along the vertical direction (Fucks, 1958; Ulanowski et al., 2007). Both effects change the particle aerodynamics and impact radiative transfer. Here, we quantify the electrical and aerodynamic torques on the non-spherical prolate model that is frequently assumed for dust particles. The transport of these particles is assumed to only depend on the influence of electric and gravitational fields. We provide an analytical approximation for the calculation of the mean orientation angle of both charged and uncharged dust particles. We find that electric fields with strength greater than 60 kV/m are required for the alignment of particles up to 20 μm in diameter, with the electric field lines. If the particles are moving with the same speed and in the same direction with the wind, the aerodynamic torque is zero and particle orientation along the electric field requires 1–2 orders of magnitude lower electric field strengths.

Stiff, strong and ductile heterostructured aluminum composites reinforced with oriented nanoplatelets

In this study, we report a liquid-solid reaction method combined with preferential particle orientation for fabricating a heterostructured Al3BC/6061 composite with ultrahigh Young's modulus (105 GPa), high tensile strength (495 MPa) and reasonable ductility (6.2%). The preferential orientation of Al3BC nanoplatelets contributes to the ultrahigh stiffness, and heterogeneous grain structure of the Al matrix facilitates the development of hetero-deformation induced stress and extra strain hardening, giving rise to high strength and good ductility. These results shed new sights into the untapped potential in improving the mechanical properties of metal matrix composites.

Method for the determination of preferential orientation of marine particles from laser diffraction measurements.

In situ laser diffractometry (LD) is increasingly used in oceanographic studies to estimate sediment transport, particle fluxes and to assess the concentration of marine phytoplankton. It enables an accurate characterization of the size distribution of suspended particles from the scattering signal produced by their interaction with a collimated laser beam. LD reliably reflects the sizes of suspensions dominated by nearly spherical particles; however, when complex particle morphologies dominate the suspension (e.g. phytoplankton) the resulting particle size distribution (PSD) may present significant variations attributed to different factors. In particular, the orientation of non-spherical particles - which abound in the sea - modifies LD measurements of PSDs. While this may be interpreted as a drawback for some studies (i.e. when precise measurement of the volume concentration is required), we propose that detailed analysis of this signal provides information on particle orientation. We use PDMS micropillars with prescribed elliptical cross-sections to experimentally determine the dependence between the spatial orientation of elongated particles and changes in the PSD measured with a LISST laser diffractometer. We show that LD can be used to adequately characterize the different dimensions of the non-spherical particles at specific orientations. Using this property, we describe and validate a method to infer the preferential orientation of particles in the sea. Our study opens new perspectives in the use of in-situ LD in ocean research.

Cryo-EM Structure of BIVV001 Reveals Coagulation Factor VIII-Von Willebrand Factor D'D3 Interaction Mode

Introduction Coagulation Factor VIII (FVIII) is a serine protease cofactor that directly interacts with coagulation factors IXa and X on activated platelets, and enhances FIXa activity toward FX by 105. von Willebrand Factor (VWF), via its D'D3 domains, interacts with FVIII and prevents premature deposition on phospholipids until activation by thrombin. Thrombin cleavage at Arg1689 of FVIII promotes VWF dissociation by disrupting the FVIII a3 high affinity interaction with the VWF D' domain. VWF extends the half-life of circulating FVIII from less than 3 hours to ~11 hours in humans. While crystal structures of FVIII and VWF D'D3 alone have been solved, the atomic details of a formed complex are unknown. We sought to determine the FVIII-VWF D'D3 complex structure by using BIVV001, our investigational new drug currently in clinical trials for the treatment of Hemophilia A. BIVV001 (rFVIIIFc-VWF-XTEN) is a novel fusion protein consisting of single chain B-domain deleted (BDD) human FVIII, the Fc domain of human immunoglobulin G1 (IgG1), the FVIII-binding D'D3 domain of human von Willebrand factor, and 2 XTEN polypeptide linkers. The Fc, VWF, and XTEN linker portions of the molecule are each designed to extend the half-life of FVIII. We anticipated that the tethering of FVIII to D'D3 through the Fc dimer in BIVV001 would stabilize the complex for structural studies. Given the large size of BIVV001, at 312 kDa, we thought it an ideal target for structure determination by single particle cryo-EM. Methods We collected a total of 3955 micrographs of BIVV001 embedded in vitreous ice at 81,000x magnification using a Titan Krios electron microscope equipped with a Gatan BioQuantum K3 energy filter and camera operating in super-resolution mode. Preferential particle orientation was a major challenge that was overcome through a variety of methods. Micrograph movies were motion-corrected and summed, and over 2 million candidate particle coordinates were extracted. Repeated rounds of reference-free 2D classification resulted in a set of 1.2 million particles that generated a reasonable ab initio/de novo 3D model. Initial full 3D refinements of this model produced a map at approximately 5 Å resolution, into which available crystal structures can be readily fit. Subsequent iterative 3D refinement and 3D classification resulted in a final map at high resolution, into which an atomic model was built. Results The structure of BIVV001 was solved by single particle cryo-EM. D' of VWF interacts with the front face of the C1 and A3 domains of FVIII, consistent with a lower resolution, negative stain EM map (Yee et al. 2015. Blood). Interface residues on FVIII identified in an HDX-MS dataset (Chiu et al. 2015. Blood.) largely correspond to this high affinity interaction. D' protrudes upward from the VWF D3 domain, which sits centrally located between the C1 and C2 domains of FVIII at a 45° tilt. By occupying this position, D3 likely sterically blocks the FVIII C domains from binding to membrane. The VWD3 module of the D3 domain contacts the base of the C1 domain, whereas C8-3 binds to the bottom of the C2 domain. The conserved Ca2+ site in VWD3 identified previously (Dong et al. 2019. Blood.) is in the interface with C1. This is consistent with Yee et al., where docking placed D3 below the C domains. In that study, a lack of density between FVIII and VWF D3 in the 3D reconstruction, due to flexibility, prevented the detailed analysis that is possible here. In this study, flexibility in this region is also apparent, as C2 is less well ordered than the rest of FVIII and VWF D3 is the least well-ordered portion of the resolved structure. The XTEN linkers are not visible in the final map and were not apparent in any 2D class averages. The Fc is absent in most 2D class averages, due to a lack of consistent positioning relative to FVIII. In the rare cases where the Fc is visible, it adopts a preferred position on the back side of FVIII below the A3 protrusion. Conclusions The structure of BIVV001 has been solved by cryo-electron microscopy to high resolution. Alignment with previous results and the averaging out of BIVV001 elaborations suggests the structure obtained here likely represents WT FVIII-D'D3. This structure demonstrates how VWF D'D3 prevents premature FVIII deposition on phospholipids. The structural basis of type 2N von Willebrand Disease mutations in D'D3 can be readily interpreted. Next steps include solving a FVIII-D'D3 dimer structure at high resolution. Disclosures Fuller: Sanofi: Employment. Batchelor:Sanofi: Employment. Knockenhauer:Sanofi: Employment. Biemann:Sanofi: Employment. Peters:Sanofi: Employment.

Streptavidin Affinity Grids for cryo-EM

The preparation of specimen grids for cryo-EM often proves to be difficult because of unwanted factors such as preferential orientation of particles, too few particles being seen within holes, particle disruption occurring within thin aqueous films, and unexpected aggregation of sample material. In instances where it is suspected that those difficulties might be caused by interaction with the air-water interface, a possible solution is to immobilize particles on a structure-friendly support film, thus preventing diffusion to the air-water interface of the thin aqueous film that remains after blotting away excess sample. We have developed a form of EM grid on which streptavidin-monolayer crystals serve as an affinity support-film. A thin covering of trehalose is used to embed the streptavidin monolayers during storage, thereby preserving the crystalline structure and biotin-binding function of the streptavidin. These affinity grids can thus be prepared in any desired quantity and stored for future use. Many strategies are possible for immobilizing particles by affinity-binding to the streptavidin monolayer after washing off the protective layer of trehalose. One of the simplest is to randomly biotinylate one or two surface-lysine residues on particles of interest. Advantages of these grids include: (1) a good surface density of immobilized particles is obtained rapidly at sample concentrations as low as 50 nM; (2) the streptavidin component of the image serves as an internal standard to verify sample preservation and image quality; and (3) the streptavidin “background” in the image can be removed, whenever desired, by Fourier filtering.

Evidence for ubiquitous preferential particle orientation in representative oceanic shear flows.

In situ measurements were undertaken to characterize particle fields in undisturbed oceanic environments. Simultaneous, co‐located depth profiles of particle fields and flow characteristics were recorded using a submersible holographic imaging system and an acoustic Doppler velocimeter, under different flow conditions and varying particle concentration loads, typical of those found in coastal oceans and lakes. Nearly one million particles with major axis lengths ranging from ∼14 μm to 11.6 mm, representing diverse shapes, sizes, and aspect ratios were characterized as part of this study. The particle field consisted of marine snow, detrital matter, and phytoplankton, including colonial diatoms, which sometimes formed “thin layers” of high particle abundance. Clear evidence of preferential alignment of particles was seen at all sampling stations, where the orientation probability density function (PDF) peaked at near horizontal angles and coincided with regions of low velocity shear and weak turbulent dissipation rates. Furthermore, PDF values increased with increasing particle aspect ratios, in excellent agreement with models of spheroidal particle motion in simple shear flows. To the best of our knowledge, although preferential particle orientation in the ocean has been reported in two prior cases, our findings represent the first comprehensive field study examining this phenomenon. Evidence of nonrandom particle alignment in aquatic systems has significant consequences to aquatic optics theory and remote sensing, where perfectly random particle orientation and thus isotropic symmetry in optical parameters is assumed. Ecologically, chain‐forming phytoplankton may have evolved to form large aspect ratio chains as a strategy to optimize light harvesting.

Ellipsoidal Janus Nanoparticles Assembled at Spherical Oil/Water Interfaces

The equilibrium behavior of ellipsoidal Janus nanoparticles adsorbed at spherical oil/water interfaces was investigated using dissipative particle dynamics simulations. Several phenomena were documented that were not observed on similar simulations for planar oil/water interfaces. The nanoparticles were found to yield isotropic, radial nematic phases, and axial nematic domains, depending on the nanoparticle characteristics (aspect ratio and surface chemistry), particle density at the interface, and droplet properties (curvature of the interface, and surprisingly, liquid type). When adsorbed on water droplets, the nanoparticles with high aspect ratio and few nonpolar beads on their surface can show two preferred orientation angles. Only one equilibrium orientation was found for such nanoparticles adsorbed on oil droplets. These observations might help explain a discrepancy previously reported between experimental and simulation results concerning the preferential orientation of particles at liquid-liquid interfaces. Different driving forces are responsible for the phenomena just summarized, including nanoparticle-nanoparticle and nanoparticle-solvent interactions, nanoparticle density at the interface, and droplet curvature via the Laplace pressure. The simulation results we present could be useful for engineering Pickering emulsions toward practical applications, and perhaps also for guiding new technologies for material synthesis.

Detection of preferential particle orientation in the atmosphere: Development of an alternative polarization lidar system

Increasing interest in polarimetric characterization of atmospheric aerosols has led to the development of complete sample-measuring (Mueller) polarimeters that are capable of measuring the entire backscattering phase matrix of a probed volume. These Mueller polarimeters consist of several moving parts, which limit measurement rates and complicate data analysis. In this paper, we present the concept of a less complex polarization lidar setup for detection of preferential orientation of atmospheric particulates. On the basis of theoretical considerations of data inversion stability and propagation of measurement uncertainties, an optimum optical configuration is established for two modes of operation (with either a linear or a circular polarized incident laser beam). The conceptualized setup falls in the category of incomplete sample-measuring polarimeters and uses four detection channels for simultaneous measurement of the backscattered light. The expected performance characteristics are discussed through an example of a typical aerosol with a small fraction of particles oriented in a preferred direction. The theoretical analysis suggests that achievable accuracies in backscatter cross-sections and depolarization ratios are similar to those with conventional two-channel configurations, while in addition preferential orientation can be detected with the proposed four-channel system for a wide range of conditions.

Characterization of textured ceramics containing mullite from phyllosilicates

Abstract Organized ceramics are obtained from kaolinite and muscovite suspensions and shaped by aqueous tape casting or centrifugation. These processes favor the preferential orientation of particles in the powder compact. After sintering at 1400 °C, this study analyzed sample microstructures using QTA to determine the degree of the mullite orientation. The analyses revealed two main texture components, a planar texture along the c -axis of the mullite and a preferred orientation along the a -axis, which were aligned parallel and perpendicular to the casting plane, respectively. The important role of processing parameters in the organization degree of the mullite was apparent during the study. The elastic properties at different measurement scales were obtained using US echography and nanoindentation and were closely related to the organization degree of the mullite crystals obtained from the QTA analyses that were consistent with the development of an interconnected mullite network. The Young's moduli due to the nanoindentations were also determined parallel and perpendicular to the layers, and indicated the samples' anisotropic behavior. Both the Young's modulus and the anisotropy of the Young's modulus were correlated with the texture index. In particular, the anisotropy of the Young's moduli was linearly related to the overall texture index, highlighting the microstructures' anisotropic nature.

Elliptical pollen corona from North American boreal paper birch trees (Betula papyrifera): strong fall orientations for near-spherical particles

It has only recently been realized that solar corona can be generated by dispersions of tree pollen grains suspended in the atmosphere, and these studies have come almost exclusively from Scandinavia. Using corona photographic and surface pollen analyses, it is shown here that paper birch trees in the interior of Alaska regularly generate solar corona during the boreal green-out in mid-May. Although near-spherical in shape, these ~27 μm average diameter particles have three surface protrusions involved in germination that are indicated to aid in the generation of elliptical corona, for which a strong preferential particle orientation is needed. For observations at solar elevation angles of ~35°-40°, an axis ratio of about 1.2 and average radius of 2.5° (for the second-order red band) are found. Because oriented particles of a particular shape tend to fall slower than randomly oriented ones, this microdesign promotes the lateral spread of pollen and enhances tree reproductive opportunities, an especially important trait for pioneering species.

Water‐worked gravel beds in laboratory flumes – a natural analogue?

AbstractAn investigation has been conducted to identify the key parameters that are likely to scale laboratory sediment deposits to the field scale. Two types of bed formation were examined: one where sediment is manually placed and screeded and the second where sediment is fed into a running flume. This later technique created deposits through sequential cycles of sediment transport and deposition. Detailed bed surface topography measurements have been made over a screeded bed and three fed beds. In addition, bulk subsurface porosity and hydraulic conductivity have been measured. By comparing the four beds, results revealed that certain physical properties of the screeded bed were clearly different from those of the fed beds. The screeded bed had a random organization of grains on both the surface and within the subsurface. The fed beds exhibited greater surface and subsurface organization and complexity, and had a number of properties that closely resembled those found for water‐worked gravel beds. The surfaces were water‐worked and armoured and there was preferential particle orientation and direction of imbrication in the subsurface. This suggested that fed beds are able to simulate, in a simplified manner, both the surface and subsurface properties of established gravel‐bed river deposits. The near‐bed flow properties were also compared. It revealed that the use of a screeded bed will typically cause an underestimation in the degree of temporal variability in the flow. Furthermore, time‐averaged streamwise velocities were found to be randomly organized over the screeded bed but were organized into long streamwise flow structures over the fed beds. It clearly showed that caution should be taken when comparing velocity measurements over screeded beds with water‐worked beds, and that the formation of fed beds offers an improved way of investigating intragravel flow and sediment–water interface exchange processes in gravel‐bed rivers at a laboratory scale. Copyright © 2008 John Wiley & Sons, Ltd.

112] Oriented Terfenol-D Composites

This paper describes the manufacture and testing of polymer matrix Terfenol-D particulate composites fabricated with a [112] preferred crystal orientation. The results demonstrate that crystal orientation permits higher saturation strain than previously obtained in particulate composites. Oriented particle composites were fabricated using needle shaped Terfenol-D particulate made from commercially available [112] textured polycrystals. A magnetic field applied during manufacture oriented the particles along their longest dimension. Three materials of 22, 36, and 49% particulate volume fraction, were produced and tested to obtain the magnetostriction at constant mechanical loads from 0.5 to 16 MPa. Results demonstrate that crystallographically oriented particle composites saturate at 1475 microstrain whereas the previous non-oriented particle composite saturates at 1150 microstrain. The authors attribute the increased magnetostriction to a predominance of particle orientation along the [112] crystal direction. Modulus measurements indicate that the composites can be described using an upper bound 1–3 composite model. Upper bound rule of mixtures models show that the 36% and 49% oriented particle composites exhibit 94% and 90% respectively of the predicted upper bound magnetostriction. Further rule of mixtures models are used to illustrate how applied stress increases the effective anisotropy in composites as a function of particulate volume fraction. The results demonstrate that by preferential orientation of particles, Terfenol-D particulate composite materials may be fabricated with magnetostriction properties close to that of bulk Terfenol-D.

Strength of one dimensionally consolidated clays : SAADA, AS BIANCHINI, GF 11F, 3T, 13R J. GEOTECH. ENGNG DIV., ASCE. V101, GT11, NOV. 1975, P1151–1164

The discussers note the authors' failure to consider recent developments in this field, and comment on the authors consideration of stress-strain anisotropy with preferential orientation of particles. It has been shown that undrained strength and stress-strain anisotropy in cohesive soils are essentially influence by the anisotropic stresses experienced by the soil in situ, even though fabric anisotropy also does contribute independently to a small extent to the observed gross anisotropic response. This fact explains why significant anisotropy is not observed in the strength parameters adopting the conventional isotropically consolidated triaxial compression test on specimens at different orientations. It has also been suggested that a more appropriate way to obtain the strength parameters (and pore pressure parameters) would be to adopt the truly triaxial apparatus. Reexamination is urged of the authors' method to evaluate anisotropic responses using hollow cylindrical samples subjected to axial and torsional stress. Attention is drawn to a standard procedure for evaluating strength anisotropy consisting of a triaxial extension compression test and direct simple shear test. It is also noted that because soils do possess different strengths in different directions, there cannot be a unique relationship between water content and strength.