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101 - 110 / 2000
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101.
Catalytic reactor-utilized ammonia adsorption, absorption, and storage materials: mechanism, nanostructure, and ab initio design
Aleksandra Zamljen, Blaž Likozar, 2024, review article

Published in DiRROS: 17.12.2024; Views: 54; Downloads: 26
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102.
Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost
Filip Buric, Sandra Viknander, Xiaozhi Fu, Oliver Lemke, Oriol Gracia Carmona, Jan Zrimec, Lukasz Szyrwiel, Michael Mülleder, Markus Ralser, Aleksej Zelezniak, 2025, original scientific article

Abstract: Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, an amino acid sequence is tailored to meet the required abundance of a proteome, underscoring the intricate relationship between sequence and functional demand. Yet, the specific role of amino acid sequences in determining proteome abundance remains elusive. Here we show that the amino acid sequence alone encodes over half of protein abundance variation across all domains of life, ranging from bacteria to mouse and human. With an attempt to go beyond predictions, we trained a manageable-size Transformer model to interpret latent factors predictive of protein abundances. Intuitively, the model's attention focused on the protein's structural features linked to stability and metabolic costs related to protein synthesis. To probe these relationships, we introduce MGEM (Mutation Guided by an Embedded Manifold), a methodology for guiding protein abundance through sequence modifications. We find that mutations which increase predicted abundance have significantly altered protein polarity and hydrophobicity, underscoring a connection between protein structural features and abundance. Through molecular dynamics simulations we revealed that abundance-enhancing mutations possibly contribute to protein thermostability by increasing rigidity, which occurs at a lower synthesis cost.
Keywords: molecular biology, biotechnology, bioinformatics, deep learning, gene expression, synthetic biology, protein abundance, amino acid sequence, evolutionary selection, transformer model, MGEM (Mutation guided by an embedded manifold)
Published in DiRROS: 17.12.2024; Views: 40; Downloads: 15
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103.
Numerical analysis of knudsen number of helium flow through gas-focused liquid sheet micro-nozzle
Krištof Kovačič, Saša Bajt, Božidar Šarler, 2024, original scientific article

Abstract: This work aims to verify whether the continuum mechanics assumption holds for the numerical simulation of a typical sample delivery system in serial femtosecond crystallography (SFX). Knudsen numbers were calculated based on the numerical simulation results of helium flow through the gas-focused liquid sheet nozzle into the vacuum chamber, representing the upper limit of Knudsen number for such systems. The analysed flow is considered steady, compressible, and laminar. The numerical results are mesh-independent, with a Grid Convergence Index significantly lower than 1% for global and local analysis. This study is based on an improved definition of the numerical Knudsen number: a combination of the cell Knudsen number and the physical Knudsen number. In the analysis, no-slip boundary and low-pressure boundary slip conditions are compared. No significant differences are observed. This study justifies using computational fluid dynamics (CFD) analysis for SFX sample delivery systems based on the assumption of continuum mechanics.
Keywords: Knudsen number, compressible hypersonic flow, vacuum, liquid sheet nozzle, sample delivery system, CFD
Published in DiRROS: 17.12.2024; Views: 40; Downloads: 17
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104.
Phase-field formulated meshless simulation of axisymmetric Rayleigh-Taylor instability problem
Khush Bakhat Rana, Boštjan Mavrič, Rizwan Zahoor, Božidar Šarler, 2024, original scientific article

Abstract: A formulation of the immiscible Newtonian two-liquid system with different densities and influenced by gravity is based on the Phase-Field Method (PFM) approach. The solution of the related governing coupled Navier-Stokes (NS) and Cahn-Hillard (CH) equations is structured by the meshless Diffuse Approximate Method (DAM) and Pressure Implicit with Splitting of Operators (PISO). The variable density is involved in all the terms. The related moving boundary problem is handled through single-domain, irregular, fixed node arrangement in Cartesian and axisymmetric coordinates. The meshless DAM uses weighted least squares approximation on overlapping subdomains, polynomial shape functions of second-order and Gaussian weights. This solution procedure has improved stability compared to Chorin's pressure-velocity coupling, previously used in meshless solutions of related problems. The Rayleigh-Taylor instability problem simulations are performed for an Atwood number of 0.76. The DAM parameters (shape parameter of the Gaussian weight function and number of nodes in a local subdomain) are the same as in the authors’ previous studies on single-phase flows. The simulations did not need any upwinding in the range of the simulations. The results compare well with the mesh-based finite volume method studies performed with the open-source code Gerris, Open-source Field Operation and Manipulation (OpenFOAM®) code and previously existing results.
Keywords: two-phase flow, phase-field, two-dimensionality, axisymmetry, diffuse approximate method, PISO
Published in DiRROS: 17.12.2024; Views: 41; Downloads: 17
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105.
Fourth-order phase field modelling of brittle fracture with strong form meshless method
Izaz Ali, Gašper Vuga, Boštjan Mavrič, Umut Hanoglu, Božidar Šarler, 2024, original scientific article

Abstract: This study aims to find a solution for crack propagation in 2D brittle elastic material using the local radial basis function collocation method. The staggered solution of the fourth-order phase field and mechanical model is structured with polyharmonic spline shape functions augmented with polynomials. Two benchmark tests are carried out to assess the performance of the method. First, a non-cracked square plate problem is solved under tensile loading to validate the implementation by comparing the numerical and analytical solutions. The analysis shows that the iterative process converges even with a large loading step, whereas the non-iterative process requires smaller steps for convergence to the analytical solution. In the second case, a single-edge cracked square plate subjected to tensile loading is solved, and the results show a good agreement with the reference solution. The effects of the incremental loading, length scale parameter, and mesh convergence for regular and scattered nodes are demonstrated. This study presents a pioneering attempt to solve the phase field crack propagation using a strong-form meshless method. The results underline the essential role of the represented method for an accurate and efficient solution to crack propagation. It also provides valuable insights for future research towards more sophisticated material models.
Keywords: strong form meshless method, fourth-order phase field, crack propagation, staggered approach, polyharmonic splines
Published in DiRROS: 17.12.2024; Views: 32; Downloads: 21
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106.
Direct reconstruction of wet foam from sparse-view, dynamic X-ray CT scans
Jens Renders, Lucia Mancini, Jan De Beenhouwer, Jan Sijbers, 2024, original scientific article

Abstract: X-ray imaging of wet foam dynamics with a high temporal resolution (e.g., 3D videos with a 10 Hz frame rate) requires fast rotation of either the foam sample or the X-ray gantry. This, however, strongly limits the number of X-ray projections per rotation that can be acquired. As a result, conventional computed tomography reconstruction methods generate 3D images with severe undersampling artefacts, complicating subsequent foam analysis. Herein, BubSub, a novel tomographic reconstruction approach that reconstructs a 4D (3D plus time) dynamic image of wet foam bubbles from sparse-view X-ray projections by leveraging prior knowledge about the evolving foam structure, is introduced. BubSub adapts a collection of subdivision surfaces with spherical topology to represent liquid–gas interfaces of foam bubbles. Estimation of bubble positions and shapes at each time point is achieved by minimizing the projection distance in relation to the measured projections. BubSub operates efficiently with minimal memory usage, exhibits robustness against noise, and provides accurate reconstructions, even when the available projections are limited, as evidenced by various experiments using both simulated and real wet foam X-ray data.
Keywords: redki pogledi, dinamika pene, rentgenska mikrotomografija, tomografska rekonstrukcija, sparse views, foam dynamics, X-ray microtomography, tomographic reconstruction
Published in DiRROS: 16.12.2024; Views: 58; Downloads: 31
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107.
108.
Identifying crystal nucleation mechanisms in a synthetic trachybasalt: a multimodal approach
Stefano Peres, Thomas A. Griffiths, Fabio Colle, Stefano Iannini Lelarge, Matteo Masotta, Alessio Pontesilli, Lucia Mancini, Rainer Abart, 2024, original scientific article

Abstract: To develop new criteria to distinguish different crystal nucleation mechanisms in silicate melts, we performed crystallization experiments using a synthetic hydrous (2 wt% H2O) trachybasalt and combined three-dimensional information from synchrotron X-ray computed microtomography with two-dimensional mapping of crystallographic orientation relationships (CORs) using electron backscatter diffraction. Crystallization experiments were performed at 400 MPa by cooling the melt from 1300 °C to resting temperatures of 1150 and 1100 °C and maintaining isothermal conditions for 30 min and 8 h. Three distinct titanomagnetite (Tmt) populations formed: (1) skeletal crystals, isolated or partially embedded in clinopyroxene (Cpx); (2) anhedral crystals, always attached to Cpx; (3) flattened needle-shaped crystals, embedded in Cpx. These morphologically different Tmt populations formed in response to one cooling event, with varying nucleation mechanisms and at different undercooling conditions. The clustered three-dimensional distribution of population 2 and 3 Tmt grains and the high proportion of Tmt-Cpx interfaces sharing CORs indicate that these Tmt grains heterogeneously nucleated on Cpx. The near-random three-dimensional distribution of (often isolated) population 1 Tmt grains, together with the low proportion of Tmt-Cpx interfaces sharing CORs, imply their isolated, possibly homogeneous nucleation, potentially followed by heterogeneous nucleation of Cpx on population 1 Tmt. Heterogeneous nucleation in slightly to moderately undercooled magmas should affect the sequence of crystallization as well as morphology and clustering of crystals, which may actively contribute to the variation of rheological parameters like viscosity. Finally, observed intra- and inter-sample variations in Tmt-Cpx COR frequencies indicate the potential for this parameter to record further petrological information.
Keywords: experimental petrology, nucleation mechanisms, X-ray microtomography, crystal clustering, heterogeneous nucleation
Published in DiRROS: 16.12.2024; Views: 63; Downloads: 48
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109.
Effects of different China and ball clays on traditional ceramic process : a multi-methodological approach
Andreas Bernasconi, Nicoletta Marinoni, Lucia Mancini, Marco Voltolini, Fernando Francescon, R. Sartori, Alessandro Pavese, 2024, original scientific article

Abstract: A combination of technological properties, mineralogical composition and three-dimension (3D) imaging is proposed to get insights into sanitary-ware ceramic bodies of the Vitreous-China technology as a function of the different clay raw materials used in the formulation of slip. Particular attention is paid to the effects induced along the production chain, during casting, after drying (dried body) and after firing (fired body). The different combinations of China and ball clays lead to different casting behaviour, in first instance, and to different mechanical strength, then, due to variations in the particle size distribution rather than in the mineralogical composition. In particular, the finer the particle size, the finer the pore size and, in addition, the better the mechanical properties (with a maximum of 4.7 MPa), due to a better packing. However, fine particle size distribution worsens the slip’s behaviour into moulds, impacting negatively on productivity, with a 17 % reduction of casting thickness. Upon firing process, such differences are mitigated by the body densification and result in more similar pores’ distributions, though the importance of the mineralogical composition is revealed. In fact, differences in mineralogical phases’ contents and in kaolinite HI index guide the comprehension of high temperature phase evolution and technological properties like the fired body thermal expansion, foremost via residual quartz. These results are important for a plastic raw materials’s selection within the ceramic sanitary-ware process.
Keywords: clay raw materials, vitreous-China technology, synchrotron X-ray microtomography, X-ray diffraction, ceramic properties, phase analysis
Published in DiRROS: 16.12.2024; Views: 70; Downloads: 43
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110.
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