Voronoi diagram-based compensation of preferred particle orientations in cryo-EM 3D reconstructions

Influence of preferred orientation of clay particles on the diffusion of water in kaolinite porous media at constant porosity

The effects of tableting procedures on the preferred orientation of phenacetin and aspirin crystals in a tablet were investigated. Among aspects of tableting procedures which might affect the preferred crystal orientation, the granulation process, the shape of the punch and the addition of magnesium stearate were investigated. A wet granulation method decreased the mobility of crystals during compression, and thus reduced the degree of preferred orientation. This phenomenon was considered to be one of reasons for the improved lamination properties seen with the granulation method. The shape of the punch affected the preferred orientation ; a concave punch caused a more complex preferred orientation pattern than a flat punch. The preferred orientation was considered to correspond to the stress distribution in a tablet. Magnesium stearate reduced the interparticle friction and facilitated the attainmnet of preferred orientation. The characteristic preferred orientation of crystals in the neighborhood of the upper surface and side surface of a tablet was investigated. The broadest faces of crystals were aligned in parallel to the upper punch face and the die wall.

Forces related to clay-mineral surfaces ________________ _ Forces between clay-mineral particles

The loading conditions of pebbles in fluvial gravel deposits were studied with different degrees of preferred particle orientation. Sediments that are comprised of non-spherical particles often show a preferred particle orientation, due to dynamic sedimentation. Here, the impact of this effect on the loading conditions of the particles and its implication on particle breakage was investigated by using discrete element simulations in three dimensions. The numerical models are based on the size and shape distribution of pebbles from a natural gravel sample. In addition, the particle size in some of the models was chosen to be uniform, to study the influence of the particle size distribution on the loading condition. Fluvial pebbles, whose shapes can be at best approximated by ellipsoids, were efficiently simulated in the discrete element models by the use of clumps. The results show that a preferred orientation of approximate ellipsoidal sedimentary particles has only a minor effect on the number and the position of particle contacts but leads to a significant load transfer from the rim to the centre of the oblate sides of the ellipsoidal particles, in comparison to an assembly of arbitrarily oriented particles. The comparison of the different particle size models indicates that the influence of the particle size distribution on the loading condition is relatively low. The results have significant implications for the breakage rate of non-spherical particles in sediments under load.

Mud volcano is a unique geological formation that constantly ejects clay-rich fluids and gases to the surface. These fluids is generally formed due to the mixing and heating process between rock or sediment layers and subsurface water. Over time clay-rich fluids can become overpressured and be forced upward through fractures in the overlying rocks when experience extremely high pressure from tectonic activities in the area. Despite the abundance of sedimentary rocks formed by mud volcano activities worldwide, their physical and chemical properties are still poorly understood. This is mainly due to the extremely fine grain size of clay minerals, which cannot be effectively characterized by classical methods. This study thus aims to determine mineral compositions, crystallographic preferred orientation (CPO), and microstructures of 2 sedimentary samples obtained from mud volcano near the Salton Sea in California, USA by using synchrotron X-ray techniques. Results from synchrotron X-ray diffraction show that both samples have high clay content approximately 69 – 75wt.%, including illite-mica, smectite, and kaolinite as major phases. A small amount of calcite and dolomite are only observed in Sample B, indicating a compositional variation of fluids ejected from different periods of the same mud volcano. Despite a slight compositional difference, these samples have a noticeable variation of microstructures. Sample A has very weak degrees of clay preferred orientation (1-2 m.r.d.) while Sample B has moderate degrees of preferred orientation (~3 m.r.d.). These results are consistent with three-dimensional morphology and distribution of clay minerals obtained from synchrotron x-ray microtomography measurement as most of clay particles in sample B are very fine and preferentially align parallel to sub-parallel to the horizontal direction. On the contrary, clay particles in sample A are mostly randomly orientated. Due to the grain size effect. Sand- or silt-size particles in the matrix play a major role in controlling the preferred orientation of sheet-like clay particles during sedimentation.

Activation of Anaplastic lymphoma kinase (ALK) and leukocyte tyrosine kinase (LTK) by their cognate cytokines ALKAL2 and ALKAL1 plays important roles in development, metabolism, and cancer. Recent structural studies revealed ALK/LTK-cytokine assemblies with distinct stoichiometries. Structures of ALK-ALKAL2 and LTK-ALKAL1 complexes with 2:1 stoichiometry determined by X-ray crystallography contrasted the 2:2 ALK-ALKAL2 complexes determined by cryo-EM and X-ray crystallography. Here, we show based on reanalysis of the cryo-EM data deposited in EMPIAR-10930 that over half of the ALK-ALKAL2 particles in the dataset are classified into 2D and 3D classes obeying a 2:1 stoichiometry besides the originally reported structure displaying 2:2 stoichiometry. Unlike particles representing the 2:2 ALK-ALKAL2 complex, particles for the 2:1 ALK-ALKAL2 complex suffer severely from preferred orientations that resulted in cryo-EM maps displaying strong anisotropy. Here, we show that extensive particle orientation rebalancing in cryoSPARC followed by 3D refinement with Blush regularization in RELION constitutes an effective strategy for avoiding map artifacts relating to preferred particle orientations and report a 3D reconstruction of the 2:1 ALK-ALKAL2 complex to 3.2 Å resolution from EMPIAR-10930. This new cryo-EM structure together with the crystal structures of ALK-ALKAL2 and LTK-ALKAL1 complexes with 2:1 stoichiometry reconciles a common receptor dimerization mode for ALK and LTK and provides direct evidence for the presence of an ALK-ALKAL2 complex with 2:1 stoichiometry next to the reported 2:2 stoichiometric assembly in the EMPIAR-10930 dataset. Finally, our analysis emphasizes the importance of public deposition of raw cryo-EM data to allow reanalysis and interpretation.

Theoretical grounds are given in this paper for two methods of determining preferred orientation of crystal particles in a cloud. The methods proposed in the paper enable one to do this in a much simpler way than it could be done when measuring full backscattering phase matrix. One of the methods proposed assumes that a polarization lidar can be rotated as a whole, while the second technique uses rotation of the polariztion plane of a linearly polarized sounding beam. Feasibility of the former technique is illustrated in the paper with the results of field experiments on sounding of a snowfall. Recent experimental studies of crystal clouds conducted with a polarization lidar capable of measuring backscattering phase matrices (BPM) have revealed the fact that preferred orientation of symmetry axes of particles in crystal clouds is very often observed to be in horizontal plane. This conclusion is drawn from the fact that off-diagonal elements of BPMs measured differ from zero. Using a model ensemble of crystal particles of axially symmetric plates and columns one can determine the direction of preferred orientation and the degree of particles orientation about this direction. For many practical reasons it is quite desirable to try to construct a technique for detecting situations in clouds under study when a preferred orientation of crystal particles occurs, which is more simple than that based on measurements of BPMs of clouds. Below we describe two possible versions of lidar measurements using a polarization lidar with a linearly polarized sounding radiation. Such a lidar can record two cross polarized components of lidar returns from scattering medium, i.e. two first Stokes parameters. One of the versions assumes that a lidar facility can be turned around the sounding beam axis as a whole, white in the second version we need to use a (lambda) /2 phase plate in the lidar transmitter to enable changes of sounding beam polarization. In order to make understanding of the techniques proposed easier, let us remind basic relationships for a polarization lidar sensing scheme.

Anisotropy in particle orientation controls water diffusion in clay materials

(111) preferentially oriented Pt nanoparticles supported on expanded graphite were prepared by impregnation of the support with an aqueous solution of H2PtCl6. The catalyst was characterized by a number of techniques and tested in the liquid-phase hydrogenation of cinnamaldehyde. The preferential surface orientation of the metal particles favours a very high selectivity towards the hydrogenation of the carbonyl bond of cinnamaldehyde to yield cinnamyl alcohol. The performance of this catalytic system is comparable to that obtained with similar catalysts prepared by more complex methods. Furthermore, expanded graphite provides a good alternative as support to other graphitic materials such as carbon nanotubes and carbon nanofibres.

One of the major aspects of mudrocks which influences their engineering behaviour is anisotropy, especially that of strength and stiffness. Anisotropy is caused by an underlying preferential alignment in particle orientations. Many factors contribute to the production of enhanced preferred particle orientations including: sedimentation process; particle shapes; bioturbation; burial depth; tectonism; weathering; and aging; in short the material’s entire geological history. Initial structure is formed by sedimentation processes during deposition. These are then modified by post-depositional events. With burial, the particles of sediments tend to rearrange to allow for a decrease in void ratio which is combined with an expulsion of water from the soil. Much of the southern UK is underlain by mudrocks of Mesozoic and Cenozoic age displaying some degree of preferred particle orientation and hence anisotropy in their engineering behaviour. The degree of particle orientation is quantified by analysis using environmental scanning electron microscope imagery. Anisotropy in engineering behaviour has been quantified by a range of laboratory and field, static and dynamic, methods that allow the anisotropic elastic behaviour of the mudrocks to be investigated at very small strains. Generally good agreement is observed between four fully independent methods for evaluating the elastic GVH stiffness mode. The results of both the image analysis and the laboratory testing build up a picture of microstructure anisotropy that results from the total geological history of each of the mudrocks investigated.

Single particle cryo-electron microscopy (cryoEM) is a powerful tool for elucidating the structures of biological macromolecules without requiring crystallisation or fixation. However, certain barriers to obtaining high-resolution structures persist, particularly during grid preparation when samples are in a thin liquid film. At this stage, extensive exposure to the air-water interface (AWI) can lead to subunit dissociation, denaturation, and preferred orientation of particles. Another obstacle to high-resolution cryoEM is molecular flexibility, which introduces heterogeneity in the dataset, weakening the signal during image processing. This study explores the effects of AWI interactions and molecular flexibility on the cryoEM density maps of KtrA, the soluble regulatory subunit of the potassium transporter KtrAB from Bacillus subtilis. From grids prepared using a standard blotting technique, we observed a lack of density in the C-lobe domains and preferred orientation. Modifications such as reducing AWI exposure through faster vitrification times (6s vs≤100ms) notably improved C-lobe density. Moreover, the addition of cyclic di-AMP, which binds to the C-lobes, combined with a 100ms plunge time, further enhanced C-lobe density and eliminated preferred orientation. These findings demonstrate that both AWI interactions and flexibility had to be addressed to obtain density for the C-lobe domains of KtrA. This study underscores the ongoing complexities in achieving high-resolution cryoEM for many samples.

Quantification of preferred orientation in graphite electrodes for Li-ion batteries with a novel X-ray-diffraction-based method

Shale units can be important barriers to fluid flow in sedimentary basins and commonly serve as seals to petroleum reservoirs. Little is known, however, about the controls on shale permeability. Consequently, variation in seal competency is one of the greatest risk factors associated with petroleum exploration.Here, we examine possible controls on sealing capacity in two Cretaceous marine shale units in the Denver basin, Colorado. Sealing capacity, as determined by mercury injection–capillary pressure analysis, is compared to several textural and compositional parameters and to sequence-stratigraphic setting. These two shale units display highly variable sealing capacity, even between some adjacent samples. This suggests that variability in some small-scale shale characteristics may strongly influence sealing capacity. The best seals are generally in transgressive systems tracts, especially within or immediately below condensed sections.Textural characteristics of shale appear to be especially important in determining sealing capacity. In particular, well-sorted pore-throat sizes and well-developed bedding-parallel preferred orientation of flattened organic matter particles strongly favor high sealing capacity. High degrees of bioturbation degrade sealing capacity, possibly by disrupting preferred orientation and by increasing variability in grain size and hence in pore-throat sorting. Preferred orientation of matrix clays parallel to bedding also appears to increase with increasing sealing capacity, but is probably less important than the preferred orientation of organic matter.Compositional characteristics are generally less important than textural characteristics in determining sealing capacity in these shale units. Neither silt content nor cement content appears to be important to sealing capacity in these shale units. Total organic carbon is generally high in samples with good sealing capacity, but can be either high or low where sealing capacity is poor.Overall, the variables that most strongly favor high sealing capacity, pore-throat sorting, organic matter bedding-parallel preferred orientation, and low bioturbation, are most likely in anoxic, deep-water settings, hence, the association between good seals and condensed sections.

Particles are a key component of aquatic light climate due to their attenuation of light. Near the water surface, waves and sheared currents can induce a preferential orientation of nonspherical particles that alters their inherent optical properties and the associated light attenuation. This modeling study focuses on how particle shape, and the corresponding preferential orientation, impacts the light climate in an aquatic environment. We assume aquatic particles, such as bacteria, algae, and microplastic pollutants, are optically homogeneous spheroids that move with the flow. The model computes their preferential orientations within the upper water column in flow driven by linear water waves and sheared currents. This is combined with the anomalous diffraction optical approximation to examine the effect of particle orientation on the beam attenuation coefficient. We find that the preferential orientation by waves and shear tends to increase the projected area of the spheroid compared to random (isotropic) orientation. This has particle size‐dependent effects on light attenuation: for particles comparable in size and shape to algae or microplastics, the preferential orientation corresponds to an increase of 10–25% in the beam attenuation coefficient, whereas there is a decrease of 10–20% in the beam attenuation coefficient for smaller particles comparable in size to bacteria. Overall, our results reveal how preferential orientation of nonspherical particles by waves and currents can impact light climate in the upper water column.

Soil structure changes during compaction of a cohesive soil