Individual Pores Research Articles

FEM heat transfer modelling with tomography-based SiCf/SiC unit cell

Modern industry has become increasingly reliant on composite materials for a variety of applications, and the nuclear industry is no exception to this. Among the materials being researched as Enhanced Accident Tolerant Fuels, ceramic matrix composites such as SiC-fiber-reinforced SiC (SiCf/SiC) figure as some prime candidates due to their excellent high temperature performances. SiCf/SiC so far shows adequate nuclear, mechanical and chemical properties; still, the thermal properties need further investigation. The thermal behavior of a material is an important factor for its performance as a nuclear fuel cladding, i.e. the first barrier encapsulating the fuel pellets. Many features determine the resulting properties of composite materials, such as matrix and fiber reinforcement properties and orientation, void fraction, and pore morphology. This study establishes a methodology to study the physical properties of composite materials and applies it to SiCf/SiC. A FEM model is used to characterize the thermal properties of a fundamental SiCf/SiC element, referred to as a �unit cell�, with the objective of accurately predicting the thermal properties of this complex class of materials where experimental data is often difficult to obtain. The unit cell is built based on data acquired with high-resolution tomographic microscopy performed at the TOMCAT beamline of the Swiss Light Source. By using phase-retrieval prior to tomographic reconstruction, the pores, fibers and matrix that compose the material can be distinguished in the data analysis. The separated information is processed to obtain geometrical information about the individual pores and fibers, which is then used to parametrize them as cylindrical objects. This allows constructing a FEM model of a cubic unit cell that is used to extract the effective thermal properties of SiCf/SiC. The analysis scheme includes steady-state and dynamic thermal transport simulations, which yield directional effective thermal conductivity and diffusivity values, respectively. Both modes of analysis show isotropic thermal conductivity values in the range of 71 W/m/K at room temperature, more than three times that of currently employed nuclear cladding materials. Combining these results with the data on the larger structural features of the material will lead to realistic results on the macroscopic thermal properties.

Зависимость плотности, твердости, прочности и размеров образцов твердого сплава WC – 15 Co от содержания пластификатора в заготовках, полученных при использовании пластиковой пресс-формы, изготовленной методом 3D-печати

The paper studies influence of the content of the plasticizer (rubber) on the density, microstructure and properties of the WC – 15 Co samples got using a plastic which was made using additive technologies. We have experimentally established that in polylactide molds with strength of 70 MPa, workpieces up to 120 MPa can be pressed. Studies have shown that an increase in the concentration of the plasticizer from 1 % to 4 % leads to an increase in the density of samples from 61 % to 90 % after pressing and a decrease in the density of samples from 99.5 % to 99.3 % after sintering. This is 0.3 – 0.6 % less than the density of samples obtained after pressing in a steel mold at a pressure of 210 MPa. Deviations in density do not affect the microstructure and hardness of the obtained samples, which is 1140 – 1170 HV. Due to the lower density and the presence of individual large pores up to 100 μm in length, the strength of the samples obtained using a plastic mold (1550 – 1980 MPa) turned out to be lower than the strength of the samples obtained using a steel mold (2230 – 2430 MPa). Nevertheless, the density of workpieces and obtained cemented carbide samples turned out to be significantly higher than the density and hardness of samples obtained using existing additive technologies.

Molecular Dynamics Study of the Development of the Dislocation Structure of an FCC Crystal Containing an Ensemble of Spherical Pores under an External Force Action

Radiation swelling is one of the most urgent problems in radiation materials science. Its successful solution requires an understanding of the features of the mechanisms of pore healing. In this regard, there are various experimental and theoretical works devoted to this topic. At present, due to the increase in the power of computing tools, computer simulation allows for more and more complex studies and is used, among other things, in the field of materials science. In this paper, we present the results of molecular dynamics simulations devoted to the study of the processes of healing of a group of spherical pores in an fcc crystal subjected to shear deformation. As the study showed, for pores located in close proximity to each other, the formation of a common dislocation loop is characteristic, which is formed as a result of the attraction of individual loops having sections with opposite signs of helical orientation. The formation and subsequent development of such a loop contributes to a decrease in the free volume localized in the crystal in the form of pores. In addition, structural transformations that occur when a shock wave is generated in the computational cell, which creates additional stresses, are considered separately. In this case, the formation of the loop described above and the subsequent collapse of individual pores are also observed. Taking into account that the simulation was carried out at temperatures insufficient to activate diffusion processes, and the temperature control procedure was used in model experiments with wave generation, we can conclude that the shock wave is the cause of pore collapse even in the absence of high temperatures, and one of the main mechanisms of this process is the development of the dislocation structure of the ensemble of pores. Keywords: crystal, model, deformation, pore, dislocation.

Молекулярно-динамическое исследование развития дислокационной структуры ГЦК-кристалла, содержащего ансамбль сферических пор, при внешнем силовом воздействии

Radiation swelling is one of the most urgent problems in radiation materials science. Its successful solution requires an understanding of the features of the mechanisms of pore healing. In this regard, there are various experimental and theoretical works devoted to this topic. At present, due to the increase in the power of computing tools, computer simulation allows for more and more complex studies and is used, among other things, in the field of materials science. In this paper, we present the results of molecular dynamics simulations devoted to the study of the processes of healing of a group of spherical pores in an fcc crystal subjected to shear deformation. As the study showed, for pores located in close proximity to each other, the formation of a common dislocation loop is characteristic, which is formed as a result of the attraction of individual loops having sections with opposite signs of helical orientation. The formation and subsequent development of such a loop contributes to a decrease in the free volume localized in the crystal in the form of pores. In addition, structural transformations that occur when a shock wave is generated in the computational cell, which creates additional stresses, are considered separately. In this case, the formation of the loop described above and the subsequent collapse of individual pores are also observed. Taking into account that the simulation was carried out at temperatures insufficient to activate diffusion processes, and the temperature control procedure was used in model experiments with wave generation, we can conclude that the shock wave is the cause of pore collapse even in the absence of high temperatures, and one of the main mechanisms of this process is the development of the dislocation structure of the ensemble of pores.

Hierarchical Porous Structure Fabrication Via Hybrid Stereolithography and Inkjet Printing With Sacrificial Liquid

Abstract Inspired by porous morphology in nature, such as bone and lung tissues, synthetic porous materials are widely adopted in engineering applications that require lightweight, thermal resistance, energy absorption, and structural flexibility. One of the main challenges in the current porous material manufacturing techniques is their limited control over individual pore size, connectivity, and distribution. This paper presents a novel additive manufacturing process to fabricate porosity-embedded structures by integrating stereolithography and inkjet printing using a sacrificial liquid–water. A solenoid-based inkjet nozzle dispenses water droplets onto a layer of liquid photopolymer resin. Then the resin layer is photocured by a mask image projection device using a digital light processing device. The photocuring process defines the layer profile and captures the deposited water droplets in the solidified layer. The refilled fresh resin will further embed water droplets and form a new layer for the subsequent water droplet deposition. Three-dimensional (3D) structures with embedded water droplets can be printed layer-by-layer. The captured water will evaporate when heated, leaving an air-filled porous 3D structure. By selectively depositing water droplets and varying inkjet printing parameters, including pressure, nozzle opening time, and jetting frequency, the micropores whose sizes from 100 µm to 500 µm and distributions within the 3D-printed part can be modulated. This hybrid process can fabricate 3D structures with homogenously distributed pores and graded polymer structures with varying porosities. The elastic modulus of 3D-printed foam structures in different pore distributions has been tested and compared.

Deep-learned generators of porosity distributions produced during metal Additive Manufacturing

Laser Powder Bed Fusion has become a widely adopted method for metal Additive Manufacturing (AM) due to its ability to mass produce complex parts with increased local control. However, AM produced parts can be subject to undesirable porosity, negatively influencing the properties of printed components. Thus, controlling porosity is integral for creating effective parts. A precise understanding of the porosity distribution is crucial for accurately simulating potential fatigue and failure zones. Previous research on generating synthetic porous microstructures have succeeded in generating parts with high density, isotropic porosity distributions but are often inapplicable to cases with sparser, boundary-dependent pore distributions. Our work bridges this gap by providing a method that considers these constraints by deconstructing the generation problem into its constitutive parts. A framework is introduced that combines Generative Adversarial Networks with Mallat Scattering Transform-based autocorrelation methods to construct novel realizations of the individual pore geometries and surface roughness, then stochastically reconstruct them to form realizations of a porous printed part. The generated parts are compared to the existing experimental porosity distributions based on statistical and dimensional metrics, such as nearest neighbor distances, pore volumes, pore anisotropies and scattering transform based auto-correlations.

Tracking changes of individual cortical pores over 1 year via HR-pQCT in a small cohort of 60-year-old females

IntroductionHigh-resolution peripheral quantitative computed tomography (HR-pQCT) is a powerful tool that has revolutionized 3D longitudinal assessment of bone microarchitecture. However, cortical porosity, a common characteristic of cortical bone loss, is still often determined by static evaluation of overall porosity at one timepoint. Therefore, we sought to 1) describe a technique to evaluate individual cortical pore dynamics in aging females over one year using HR-pQCT imaging and 2) determine whether formation and expansion of pores would exceed contraction and infilling of pores. MethodsHR-pQCT (60.7 μm resolution) images were acquired one year apart at the distal tibia and distal radius in seven female volunteers (60–72 years of age). Baseline and one-year images were registered at each bone site and a custom software was used to quantify dynamic activity of individual cortical pores using the following categories: developed, infilled, expanded, contracted, and static. ResultsOver the one-year period, cortical pores actively developed, contracted, expanded, and infilled. More pores expanded and developed vs. infilled or contracted leading to increased pore area in both tibial and radial sites (p = 0.0034 and p = 0.0474, respectively). Closed pores in the tibia, those that were not connected to the endosteal or periosteal surfaces, were the most dynamic of any pores type (open/closed) at either bone site. ConclusionThis study demonstrates an approach to longitudinally track individual cortical pore activity in tibial and radial sites. These data expand conventional parameters for assessing cortical porosity and show increased porosity in one year of aging is caused by newly developed pores and expansion of existing pores.

A Unified Pore Network Model for Evaluation of Permeability, Relative Permeability, and Sealing Capacity From Mercury Intrusion Measurement

SummaryThis paper presents a new 3D mathematical pore network model for evaluating some important, but hard-to-measure physical properties, including permeability, relative permeability, recovery factor, and sealing capacity from easy-to-measure mercury intrusion data. A 3D pore network is constructed by mimicking the penetration process of mercury based on an idealized pore shape. The pore shape is two frustra of cones connected at their base. A pore orientates in 3D space with an alignment angle to the bedding, which is a function of deformation of the sedimentary rock. Since mercury intrusion measures a 3D pore network and intrudes pores from largest to smallest, a pore size distribution measured by mercury intrusion is itemized into individual pores; a 3D pore network model is then formed by adding pores, one by one from the largest to the smallest, to the pore network. In the process, pores are connected into pore strings along the three orthogonal directions. The properties are derived by modeling fluid flow in the pore strings in a particular direction. Sealing capacity is simply the capillary pressure of the smallest pore of the first three largest orthogonal pore strings of the 3D pore network. Permeability is modeled by applying the modified Hagen-Poiseuille equation, Darcy’s law, energy and mass conservation, and the effect of eddy formation and flow direction change in the pores to the constructed 3D pore network model. Relative permeability is modeled for the imbibition process for two-phase flow based on the below imbibition theory proposed in this paper. Initially, the nonwetting phase exists in large pore strings, and the wetting phase occupies small pore strings. There are always some pores in a large pore string connected with pores of the small pore strings. In the imbibition process, under the differential pressure and capillary pressure, the wetting phase in some small pores invades some large pores filled with the nonwetting phase at the contact to form interfaces. As a result, in these pore strings, the effective pressure drop, which drives the movement of the fluids, is reduced by the capillary pressure of the interfaces. The constructed relative permeability model is a function of viscosity, interfacial tension (IFT), and contact angle of the fluids, and also pressure gradient, which is often overlooked. The developed model has been applied to some mudstone and limestone samples. The modeled sealing capacities of 29 mudstone samples show that a mudstone with a clay content greater than 40% and porosity less than 0.2 would be an effective caprock to oil. The modeled permeabilities of 29 limestone samples show that the model is able to predict limestone permeability within a factor of two in nearly four orders of magnitude range. The modeled relative permeabilities of two limestone samples demonstrate the effect of IFT, contact angle, and pressure gradient on the relative permeability and recovery factor and the capability of the model to simulate a special phenomenon—permeability jail.

Investigating the Influence of Humidity on Liquid Water Transport Mechanisms in Fuel Cell Gas Diffusion Layers Using Operando X-Ray Computed Tomography

The intermittent nature of many renewable energy sources, such as solar and wind, presents the need to acquire on-demand renewable energy either through energy storage or energy production methods. The polymer electrolyte membrane (PEM) fuel cell is quickly becoming an attractive solution as it can produce high power densities under a rapid change in load while producing zero local carbon emissions [1] and is ideal for large-scale applications, such as automotive [2]. However, barriers to their widespread implementation are attributed to the high costs associated with mass transport losses at high current density operation due to inefficiencies in liquid water management in the gas diffusion layer (GDL) [3][4]. Understanding the relationship between liquid water distributions in the cathode GDL and transport properties of PEM fuel cells under varying operating conditions can lead to improved GDL configurations for improved performance. Previously, studies have been conducted to characterize the effect of operating temperature on liquid water pathways in GDLs by using 3D imaging techniques on operando PEM fuel cells [5]. High-speed, high-resolution 3D imaging techniques, such as computed tomography (CT), enable the visualization of dynamic pore-scale effects and are advantageous in elucidating transport mechanisms in the GDL.In this work, the effect of operating relative humidity on the formation of liquid water pathways in the GDL will be explored by imaging an operando PEM fuel cell with synchrotron X-ray CT. To date, a custom PEM fuel cell has been developed in-house which features a novel design with two rotary unions on either side of the cell. The rotary unions enable continuous rotation of the cell during imaging, and thus are central to achieving high temporal resolution for visualizing the development of preferential water pathways. High spatial resolution (pixel resolution of 1.44 microns per pixel [6]) is also obtained with the synchrotron beam, which allows for the visualization of liquid water in individual pores at the microscale in the GDL. Visualizing water in the micropores of the GDL can help us further understand water transport mechanisms within the complex structure of the GDL to ultimately develop methods to expel excess water efficiently. In the next steps of this research, we will use the results from electrochemical testing and the reconstructed images of the fuel cell to draw important conclusions about the relationship between liquid water distributions in the GDL and fuel cell performance. As well, the effect that operating relative humidity has on this relationship will be determined. The aim of this work is to inform optimal design for GDL materials for improved PEM fuel cell performance, which will ultimately accelerate their utilization on a global scale as a reliable and sustainable energy source.[1] P. Shrestha, CH. Lee, K. F. Fahy, M. Balakrishnan, N. Ge, and A. Bazylak, “Formation of Liquid Water Pathways in PEM Fuel Cells: A 3-D Pore-Scale Perspective,” Journal of The Electrochemical Society, vol. 167, no. 5, p. 054516, Jan. 2020, doi: 10.1149/1945-7111/ab7a0b.[2] S. Park, J. W. Lee, and B. N. Popov, “A review of gas diffusion layer in PEM fuel cells: Materials and designs,” International Journal of Hydrogen Energy, vol. 37, no. 7, pp. 5850– 5865, Apr. 2012, doi: 10.1016/J.IJHYDENE.2011.12.148.[3] Y. Nagai et al., “Improving water management in fuel cells through microporous layer modifications: Fast operando tomographic imaging of liquid water,” Journal of Power Sources, vol. 435, p. 226809, Sep. 2019, doi: 10.1016/J.JPOWSOUR.2019.226809.[4] U. U. Ince et al., “3D classification of polymer electrolyte membrane fuel cell materials from in situ X-ray tomographic datasets,” International Journal of Hydrogen Energy, vol. 45, no. 21, pp. 12161–12169, Apr. 2020, doi: 10.1016/J.IJHYDENE.2020.02.136.[5] Hong Xu, Shinya Nagashima, Hai P. Nguyen, Keisuke Kishita, Federica Marone, Felix N. Büchi, Jens Eller, Temperature dependent water transport mechanism in gas diffusion layers revealed by subsecond operando X-ray tomographic microscopy, Journal of Power Sources, Volume 490, 2021, 229492, ISSN 0378-7753, https://doi.org/10.1016/j.jpowsour.2021.229492.[6] Canadian Light Source, “Detectors,” BMIT. [Online]. Available: https://bmit.lightsource.ca/tech-info/detectors/. [Accessed: 05-Apr-2022].

Investigation of membrane wetting for CO2 capture by gas–liquid contactor based on ceramic membrane

In recent years, global climate change caused by excessive CO2 emissions has attracted wide attention. Within this context, CO2 capture by gas–liquid contactor based on membranes is one of the most promising technologies for post-combustion CO2 capture. However, mass transfer deterioration due to membrane wetting becomes one of barriers for its development. In this paper, based on Laplace-Young equation, reliable individual membrane pore wetting model is constructed to demonstrate detailed wetting process inside membrane pores, which is verified by molecular dynamic (MD) numerical simulation. The wetting conditions of ceramic membrane with 1.26 µm average pore size and 51.4° contact angle are investigated in experiments. The results show that neither average nor maximum pore diameters can accurately predict liquid and bubble breakthrough pressures of ceramic membrane. The actual liquid and bubble breakthrough pressures of ceramic membrane are slightly lower than critical liquid and bubble breakthrough pressures corresponding to the maximum pore size. The wetting state of ceramic membrane can be determined by combining individual pore wetting model and actual membrane pore distribution. In addition, for practical application process of CO2 capture by gas–liquid contactor with ceramic membrane, some suggestions to avoid membrane wetting are proposed for selection of ceramic membrane and system operation perspective. The membrane wetting analysis method proposed in this paper not only contributes to future applications of ceramic membrane in CO2 capture, but is also widely applicable to other gas–liquid contactors in membrane separation process.

The Propagation of Coherent Waves Across Multiple Solar Magnetic Pores

Solar pores are efficient magnetic conduits for propagating magnetohydrodynamic wave energy into the outer regions of the solar atmosphere. Pore observations often contain isolated and/or unconnected structures, preventing the statistical examination of wave activity as a function of the atmospheric height. Here, using high-resolution observations acquired by the Dunn Solar Telescope, we examine photospheric and chromospheric wave signatures from a unique collection of magnetic pores originating from the same decaying sunspot. Wavelet analysis of high-cadence photospheric imaging reveals the ubiquitous presence of slow sausage-mode oscillations, coherent across all photospheric pores through comparisons of intensity and area fluctuations, producing statistically significant in-phase relationships. The universal nature of these waves allowed an investigation of whether the wave activity remained coherent as they propagate. Utilizing bisector Doppler velocity analysis of the Ca ii 8542 Å line, alongside comparisons of the modeled spectral response function, we find fine-scale 5 mHz power amplification as the waves propagate into the chromosphere. Phase angles approaching zero degrees between co-spatial line depths spanning different line depths indicate standing sausage modes following reflection against the transition region boundary. Fourier analysis of chromospheric velocities between neighboring pores reveals the annihilation of the wave coherency observed in the photosphere, with examination of the intensity and velocity signals from individual pores indicating they behave as fractured waveguides, rather than monolithic structures. Importantly, this work highlights that wave morphology with atmospheric height is highly complex, with vast differences observed at chromospheric layers, despite equivalent wave modes being introduced into similar pores in the photosphere.

Quantitative Comparison of 3D Pore Space Properties With Magnetic Pore Fabrics—Testing the Ability of Magnetic Methods to Predict Pore Fabrics in Rocks

AbstractPore fabrics characterize the anisotropy of pore space in rocks and influence the direction of fluid flow. This is important in reservoir characterization, and petroleum and geothermal energy exploitation. X‐ray computed micro‐tomography (XRCT) is commonly used to analyze pore fabrics, but limited by the micron‐scale resolution for representative 1‐inch rock cores. The magnetic pore fabric (MPF) method has been proposed to capture pores down to 10 nm. Although empirical relationships between MPF and pore space properties or permeability anisotropy are available, their application is compromised by large variability. This study integrates He pycnometry and XRCT‐derived pore space models with MPFs, and provides a quantitative comparison for calcarenite (∼50 vol% porosity and complex pore structure), and molasse sandstone (10%–30% porosity and relatively homogeneous pore fabrics). The preferred orientation of pores obtained from XRCT is described by a total shape ellipsoid, calculated by summing the second‐order tensors reflecting the best‐fit ellipsoids of individual pores. This ellipsoid is then compared to the MPF magnitude ellipsoid in terms of fabric orientation, degree and shape of anisotropy. The MPF and total shape ellipsoids are generally coaxial. The MPF has a smaller anisotropy degree than the total shape ellipsoid, and their relationship depends on the ferrofluid properties. The anisotropy shapes show large variability. Nevertheless, the good agreement of principal directions in most samples makes MPFs a valuable and efficient complementary tool to analyze a large number of samples, in combination with XRCT on selected samples, for a field‐scale pore space characterization.

High-Throughput Nanopore Fabrication and Classification Using Xe-Ion Irradiation and Automated Pore-Edge Analysis.

Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding membrane-wide permeation properties. In this work, we investigate Xe-ion focused ion beam as a tool for scalable, large-area nanopore fabrication on atomically thin, free-standing molybdenum disulfide. The presented irradiation protocol enables designing ultrathin membranes with tunable porosity and pore dimensions, along with spatial uniformity across large-area substrates. Fabricated nanoporous membranes are then characterized using scanning transmission electron microscopy imaging, and the observed nanopore geometries are analyzed through a pore-edge detection and analysis script. We further demonstrate that the obtained structural and statistical data can be readily passed on to computational and analytical tools to predict the permeation properties at both individual pore and membrane-wide scales. As an example, membranes featuring angstrom-scale pores are investigated in terms of their emerging water and ion flow properties through extensive all-atom molecular dynamics simulations. We believe that the combination of experimental and analytical approaches presented here will yield accurate physics-based property estimates and thus potentially enable a true function-by-design approach to fabrication for applications such as osmotic power generation and desalination/filtration.

New tools for dead roots: Radioisotope labelling and compound‐specific analysis reveal how subsoil hotspots work

AbstractSubsoils are increasingly studied as they, first, store a great deal of terrestrial carbon (C) and possibly even more, and second, offer resources like water and nutrients to plants, potentially mitigating negative consequences of global change. As subsoil access is often hampered by compacted soil layers, the key to accessing subsoil resources and storing more C below ground might be in biopores. Appropriately nicknamed ‘highways of root growth’, biopores are macropores left behind by dying roots and earthworm activities, often enriched with organic matter (OM) and nutrients. They are thought to be the most abundant microbial hotspots in the subsoil, thus possibly accounting for a large part of C turnover, as well as offering pore wall nutrients to subsequent crops. Understanding the multifunctionality and complexities of biopores remains challenging. This contribution aims to showcase analytical ways to deepen our understanding of origin and functioning of biopores and hotspots. Regarding their biogeochemistry, biopore OM quality and its turnover can be better unravelled through compound‐specific analysis to deduct biopore‐specific OM turnover. Biopores can be reliably differentiated by their OM quality. A more profound understanding of subsoil C turnover in very contrasting hotspots is crucially important for managing subsoil functions. Biopores are often assumed to be beneficial in crop sequences. Roots making use of specific biopores can be, for the first time, quantified after radiotracer application, two‐step phosphor imaging, and image processing. Combining radioactive with stable isotopes as well as plant and microbial biomarkers allows to investigate the relevance of individual pore wall nutrients in plant growth in consideration of physical biopore properties. Biopore‐friendly management practices (e.g., reduced tillage, perennial cover cropping) could be part of smart subsoil management. Faster access to subsoil water and concentrated biopore nutrients may safeguard agricultural production—especially in times of rising fertiliser costs (both monetary and environmental) and more frequent droughts.

DNA Origami in the Quest for Membrane Piercing

The tool kit for label-free single-molecule sensing, nucleic acid sequencing (DNA, RNA and protein) and other biotechnological applications has been significantly broadened due to the wide range of available nanopore-based technologies. Currently, various sources of nanopores, including biological, fabricated solid-state, hybrid and recently de novo chemically synthesized ion-like channels have put in use for rapid single-molecule sensing of biomolecules and other diagnostic applications. At length scales of hundreds of nanometers, DNA nanotechnology, particularly DNA origami-based devices, enables the assembly of complex and dynamic 3-dimensional nanostructures, including nanopores with precise control over the size/shape. DNA origami technology has enabled to construct nanopores by DNA alone or hybrid architects with solid-state nanopore devices or nanocapillaries. In this review, we briefly discuss the nanopore technique that uses DNA nanotechnology to construct such individual pores in lipid-based systems or coupled with other solid-state devices, nanocapillaries for enhanced biosensing function. We summarize various DNA-based design nanopores and explore the sensing properties of such DNA channels. Apart from DNA origami channels we also pointed the design principles of RNA nanopores for peptide sensing applications.

Analysis of ultrastructure and microstructure of blackbird (Turdus merula) and song thrush (Turdus philomelos) eggshell by scanning electron microscopy and X-ray computed microtomography

The unique structure of the egg allows for efficient reproduction on land. Although the functions of the egg are ensured by the concomitant cooperation of all its structures, the eggshell also plays a significant role. Apart from maintaining an aqueous environment within the egg along with controlled gas exchange, the color and pigmentation pattern of eggshell contributes to identification and protection. As a result of all these functions, the structure, shape, and pigmentation of eggshell greatly vary across the class of birds, and understanding these three variability-determining factors may aid in better interpretation of evolutionary mechanisms. In this study, we analyzed for the first time the structure, mineral composition, and characteristics of the pigmentation of blackbird (Turdus merula) and song thrush (Turdus philomelos) eggshells. The shell of blackbird eggs is much thicker compared to the shell of song thrush eggs which is due to a much thicker crystalline and palisade layers. In both species, strongly elongated mammillary knobs are observed, which create a large space between the mineralized shell and the egg membranes. The blackbird egg shell has a higher water vapor conductivity which is due to the larger diameter of the circle and the surface area of individual pores. The primary compound entering the mineral composition of the shell in both species is CaCO3 however, the thrush egg shells contained more Mg in all layers except the crystalline layer, and S in the crystalline and palisade layers. The two species clearly differ in the size and distribution of pigment spots on the eggshell. We suppose that the differences in shell structure and pigmentation presented in this study may in the future provide a basis for explaining the reasons for the much lower reproductive efficiency of song thrush compared to blackbird.

Large-scale osteocyte lacunar morphological analysis of transiliac bone in normal and osteoporotic premenopausal women.

Bone's ability to adapt is governed by the network of embedded osteocytes, which inhabit individual pores called lacunae. The morphology of these lacunae and their resident osteocytes are known to change with age and diseases such as postmenopausal osteoporosis. However, it is unclear whether alterations in lacunar morphology are present in younger populations with osteoporosis. To investigate this, we implemented a previously validated methodology to image and quantify the three-dimensional morphometries of lacunae on a large scale with ultra-high-resolution micro-computed tomography (microCT) in transiliac bone biopsies from three groups of premenopausal women: control n=39; idiopathic osteoporosis (IOP) n=45; idiopathic low BMD (ILBMD) n=19. Lacunar morphometric parameters were measured in both trabecular and cortical bone such as lacunar density (Lc.N/BV), lacunar volume (Lc.V), and lacunar sphericity (Lc.Sr). These were then compared against each other and also with previously measured tissue morphometries such as bone volume density (BV/TV), trabecular separation (Tb.Sp), trabecular number (Tb.N), and others. We detected no differences in lacunar morphology between the IOP, ILBMD and healthy premenopausal women. In contrast, we did find significant differences between lacunar morphologies including Lc.N/BV, Lc. V, and Lc. Sr in cortical and trabecular regions within all three groups (p<0.001), which was consistent with our previous findings on a subgroup of the healthy group. Furthermore, we discovered strong correlations between Lc. Sr from trabecular regions with the measured BV/TV (R=-0.90, p<0.05). The findings and comprehensive lacunar dataset we present here will be a crucial foundation for future investigations of the relationship between osteocyte lacunar morphology and disease.

ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing.

MotivationNanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.ResultsHere, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background.Availability and implementationThe C++ source code is available at https://gitlab.com/dacs-hpi/readbouncer.Supplementary information Supplementary data are available at Bioinformatics online.

High-resolution micro-CT with 3D image analysis for porosity characterization of historic bricks

The study of pores in historic bricks is important for characterizing and comparing brick materials, evaluating the degree of deterioration, predicting behavior in future weathering conditions, studying the effectiveness of protective measures, and analyzing the potential effects of cleaning treatments. High-resolution micro-CT coupled with 3D image analysis is a promising new approach for studying porosity and pore systems in bricks. In this technique, hundreds or even thousands of X-ray projection images are acquired at 360 degrees around a sample. The X-radiation passing through the sample is absorbed, with radiation attenuated to varying degrees depending on the varying densities of phases within the object. The 3D volume is reconstructed by a computer algorithm, producing images where each voxel has a grayscale intensity value associated with the component it represents. Recent new instrument designs allow fast scanning with good spatial resolution. In this research, we present a set of protocols for creating optimal images of brick pores in micro-CT scans and for conducting 3D image analysis to extract both qualitative and quantitative data from those scans. Small samples give better spatial resolution for imaging of pores, so given the typical heterogeneity of bricks, scanning multiple samples from each brick ensures that the results are more likely to be representative. Machine learning and deep learning with convolutional neural networks were found to be important tools for better distinguishing pores from the surrounding matrix in the segmentation process, especially at the very limits of spatial resolution. Statistical analyses revealed which of the many parameters that can be measured are potentially most significant for characterizing the pore systems of bricks. These significant pore variables came from a multi-staged image analysis approach and include the total volume percent occupied by pores, the percentage of those pores accessible to the surface versus isolated interior ones, a variety of statistical properties of individual pores related to their size and shape, the average number of connections that pores have to other pores, and the length, diameter, and directness of those connections.Graphical

Pore closure in thick aluminum plate: From industrial hot rolling to individual pore observation

Pores are often present in large aluminum ingots after casting. To ensure the mechanical reliability of the final thick plates, these pores must be closed during the forming process, hot rolling in the present case. This study aims at understanding the effects of rolling parameters on the volume evolution of pores. To do so, X-ray microtomography is used to track real casting pores during deformation. Nevertheless, thick plates are too large to enable a fine characterization of the evolution of pores during the process. The size and shape of the samples as well as the mechanical boundary conditions must be optimized to meet imaging constraints. This paper focuses on the reproduction of complex loading paths. Multi-scale FE simulations are used to reproduce the loading conditions of thick plate rolling with uniaxial tests on samples of a few millimeters. Uniaxial tests are then characterized with tomography on a synchrotron X-ray beamline. In each sample, tens of pores are individually tracked, giving access to their volume evolution. The local loading path experienced by each pore is determined with FE simulation. It is shown that the volume evolution of a real pore correlates with the hydrostatic integration which is the integral of stress triaxiality along cumulated strain. This confirms that the closure of complex casting pores is enhanced by a high relative reduction and high values of L/H ratio during rolling similarly to what was observed numerically on simpler shapes.