A Probabilistic Formulation of the Diffusion Coefficient in Porous Media as Function of Porosity

We investigate the upscaling of diffusive transport parameters using a stochastic framework. At sub-REV (representative elementary volume) scale, the complexity of the pore space geometry leads to a significant scatter of the observed diffusive transport. We study a large set of volumes reconstructed from focused ion beam-scanning electron microscopy data. Each individual volume provides us sub-REV measurements on porosity and the so-called transport-ability, being a dimensionless parameter representing the ratio of diffusive flux through the porous volume to that through an empty volume. The detected scatter of the transport-ability is mathematically characterized through a probability distribution function (PDF) with a mean and variance as function of porosity, which includes implicitly the effect of pore structure differences among sub-REV volumes. We then investigate domain size effects and predict when REV scale is reached. While the scatter in porosity observations decreases linearly with increasing sample size as expected, the observed scatter in transport-ability does not converge to zero. Our results confirm that differences in pore structure impact transport parameters at all scales. Consequently, the use of PDFs to describe the relationship of effective transport coefficients to porosity is advantageous to deterministic semiempirical functions. We discuss the consequences and advocate the use of PDFs for effective parameters in both continuum equations and data interpretation of experimental or computational work. The presented statistics-based upscaling technique of sub-REV microscopy data provides a new tool in understanding, describing and predicting macroscopic transport behavior of microporous media.

Структурный переход в пленках триацетата целлюлозы

Electron microscopy data are used to comparative analysis of the topological structure of the surface of two samples of cellulose triacetate (СTA) films. The samples were obtained from CTA solutions without use (sample №1) and with the use of a small sodium fluoride additive that lowers the viscosity of the solution (sample №2). It is shown that in sample №1, the nodes of the physical network of macromolecules are periodically alternating regions of local orientation order - microdomains of average size d~18 nm. In sample №2, due to repackaging of microdomains on the scale R >d, a uniformly disordered fractal cluster of the mesophase CTA is formed. The fractalization of the surface and the growth of structural anisotropy are consistent with the decrease in the viscosity of the solution and explain the change in the deformation properties of sample №2 compared to №1.

Laser synthesis of nanocomposite hydrocarbon fuel and CARS diagnostics of its combustion flame

We report an analysis of diffusive combustion in oxygen of a composite fuel formed by the addition of aluminium nanoparticles (NPs) to isopropanol. The process of obtaining Al NPs consisted in laser fragmentation of initially large industrial NPs using radiation of a pulsed nanosecond neodymium laser. The size distribution of Al NPs was determined using a measuring disk centrifuge. The average nanoparticle size was 20 nm, which is confirmed by transmission electron microscopy data. A diagnostic system based on coherent anti-Stokes Raman scattering (CARS) was used to experimentally study the diffusive combustion of composite fuel. The temperature distributions were measured in two mutually orthogonal directions (along the flame and in the transverse direction) in pure isopropanol and in isopropanol with the addition of 0.15 wt % of Al nanoparticles.

TXM-Sandbox: an open-source software for transmission X-ray microscopy data analysis

A transmission X-ray microscope (TXM) can investigate morphological and chemical information of a tens to hundred micrometre-thick specimen on a length scale of tens to hundreds of nanometres. It has broad applications in material sciences and battery research. TXM data processing is composed of multiple steps. A workflow software has been developed that integrates all the tools required for general TXM data processing and visualization. The software is written in Python and has a graphic user interface in Jupyter Notebook. Users have access to the intermediate analysis results within Jupyter Notebook and have options to insert extra data processing steps in addition to those that are integrated in the software. The software seamlessly integrates ImageJ as its primary image viewer, providing rich image visualization and processing routines. As a guide for users, several TXM specific data analysis issues and examples are also presented.

FRACTAL ANALYSIS OF THE NANOSTRUCTURE OF A HETEROGENEOUS HIGH COERCITY ALLOY

Методом атомно-силовой микроскопии получены изображения наноструктры составляющих гетерогенного интерметаллида SmCoCuFeZr в высококоэрцитивном состоянии. На микроуровне в сплавах выделили два типа областей (фазовых составляющих) отличающихся по интегральному элементному составу и интервалам коэрцитивности. На основе данных атомно-силового микроскопа проводится анализ фрактальных характеристик поверхности этих областей. Показано, что фрактальная размерность наноструктуры коррелирует с локальной коэрцитивностью фазовых составляющих. Фазовая составляющая с относительно низкой коэрцитивностью демонстрирует возможность существования структур с фрактальной размерностью в диапазоне 2,396 - 2,475, что соответствует умеренно развитому фрактальному рельефу. При этом высококоэрцитивная составляющая с регулярной наноструктурой характеризуется более высокой фрактальной размерностью 2,452 - 2,508, а на отдельных участках образца встречались области с фрактальной размерностью до 2,577 . The atomic force microscopy was used to obtain images of the nanostructure of components of a heterogeneous intermetallic SmCoCuFeZr compound in a highly coercive state. At the microlevel, two types of regions were distinguished in the alloys, differing in integral elemental composition and coercivity intervals. Based on the atomic force microscopy data, an analysis of the fractal characteristics of the surface is carried out on both of the above types of areas. It is shown that the fractal dimension of the nanostructure correlates with the local coercivity of the phase components. The phase component with a relatively low coercivity demonstrates the possibility of the existence of structures with fractal dimensions in the 2,396 - 2,475 range corresponding to a moderately developed fractal relief. In this case, the high-coercive component with a regular nanostructure is characterized by a higher fractal dimension of 2,452 - 2,508, and in some areas of the sample there were regions with a fractal dimension up to the value of 2,577.

The BioImage Archive - home of life-sciences microscopy data

Despite the importance of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. It accepts bioimaging data associated with publication in any format, from any imaging modality at any scale, as well as reference datasets. The BioImage Archive will improve reproducibility of published studies that derive results from image data. In addition, providing reference datasets to the scientific community reduces duplication of effort and allows downstream analysis to focus on a consistent set of data. The BioImage Archive will also help to generate new insights through reuse of existing data to answer new biological questions, or provision of training, testing and benchmarking data for image analysis tool development. The Archive is available at https://www.ebi.ac.uk/bioimage-archive/.

3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

Recent technological advances in electron cryo-microscopy (cryo-EM) have led to significant improvements in the resolution of many single-particle reconstructions and a sharp increase in the number of entries released in the Electron Microscopy Data Bank (EMDB) every year, which in turn has opened new possibilities for data mining. Here we present a resolution-dependent library of rotamer-specific amino-acid map motifs mined from entries in the EMDB archive with reported resolution between 2.0 and 4.0A. We further describe 3D-Strudel, a method for map/model validation based on these libraries. 3D-Strudel calculates linear correlation coefficients between the map values of a map-motif from the library and the experimental map values around a target residue. We also present "Strudel Score", a plug-in for ChimeraX, as a user-friendly tool for visualisation of 3D-Strudel validation results.