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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: 42; Downloads: 16
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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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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: 59; Downloads: 32
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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: 64; Downloads: 49
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Published in DiRROS: 16.12.2024; Views: 67; Downloads: 30
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