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The choice of a thermodynamic formulation dramatically affects modelled chemical zoning in minerals.

ABSTRACT: Quantifying natural processes that shape our planet is a key to understanding the geological observations. Many phenomena in the Earth are not in thermodynamic equilibrium. Cooling of the Earth, mantle convection, mountain building are examples of dynamic processes that evolve in time and space and are driven by gradients. During those irreversible processes, entropy is produced. In petrology, several thermodynamic approaches have been suggested to quantify systems under chemical and mechanical gradients. Yet, their thermodynamic admissibility has not been investigated in detail. Here, we focus on a fundamental, though not yet unequivocally answered, question: which thermodynamic formulation for petrological systems under gradients is appropriate-mass or molar? We provide a comparison of both thermodynamic formulations for chemical diffusion flux, applying the positive entropy production principle as a necessary admissibility condition. Furthermore, we show that the inappropriate solution has dramatic consequences for understanding the key processes in petrology, such as chemical diffusion in the presence of pressure gradients.

SUBMITTER: Tajcmanova L

PROVIDER: S-EPMC8455693 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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The choice of a thermodynamic formulation dramatically affects modelled chemical zoning in minerals.

Tajčmanová L L Podladchikov Y Y Moulas E E Khakimova L L

Scientific reports 20210921 1

Quantifying natural processes that shape our planet is a key to understanding the geological observations. Many phenomena in the Earth are not in thermodynamic equilibrium. Cooling of the Earth, mantle convection, mountain building are examples of dynamic processes that evolve in time and space and are driven by gradients. During those irreversible processes, entropy is produced. In petrology, several thermodynamic approaches have been suggested to quantify systems under chemical and mechanical ...[more]

PMID: 34548507

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Project description:Introduction: The in vivo tibial loading mouse model has been extensively used to evaluate bone adaptation in the tibia after mechanical loading treatment. However, there is a prevailing assumption that the load is applied axially to the tibia. The aim of this in silico study was to evaluate how much the apparent mechanical properties of the mouse tibia are affected by the loading direction, by using a validated micro-finite element (micro-FE) model of mice which have been ovariectomized and exposed to external mechanical loading over a two-week period. Methods: Longitudinal micro-computed tomography (micro-CT) images were taken of the tibiae of eleven ovariectomized mice at ages 18 and 20 weeks. Six of the mice underwent a mechanical loading treatment at age 19 weeks. Micro-FE models were generated, based on the segmented micro-CT images. Three models using unitary loads were linearly combined to simulate a range of loading directions, generated as a function of the angle from the inferior-superior axis (θ, 0°-30° range, 5° steps) and the angle from the anterior-posterior axis (ϕ, 0°: anterior axis, positive anticlockwise, 0°-355° range, 5° steps). The minimum principal strain was calculated and used to estimate the failure load, by linearly scaling the strain until 10% of the nodes reached the critical strain level of -14,420 με. The apparent bone stiffness was calculated as the ratio between the axial applied force and the average displacement along the longitudinal direction, for the loaded nodes. Results: The results demonstrated a high sensitivity of the mouse tibia to the loading direction across all groups and time points. Higher failure loads were found for several loading directions (θ = 10°, ϕ 205°-210°) than for the nominal axial case (θ = 0°, ϕ = 0°), highlighting adaptation of the bone for loading directions far from the nominal axial one. Conclusion: These results suggest that in studies which use mouse tibia, the loading direction can significantly impact the failure load. Thus, the magnitude and direction of the applied load should be well controlled during the experiments.

Project description:Hypoxia is an adverse prognostic feature of solid cancers that may be overcome with hypoxia-activated prodrugs (HAPs). Tirapazamine (TPZ) is a HAP which has undergone extensive clinical evaluation in this context and stimulated development of optimized analogues. However the subcellular localization of the oxidoreductases responsible for mediating TPZ-dependent DNA damage remains unclear. Some studies conclude only nuclear-localized oxidoreductases can give rise to radical-mediated DNA damage and thus cytotoxicity, whereas others identify a broader role for endoplasmic reticulum and cytosolic oxidoreductases, indicating the subcellular location of TPZ radical formation is not a critical requirement for DNA damage. To explore this question in intact cells we engineered MDA-231 breast cancer cells to express the TPZ reductase human NADPH: cytochrome P450 oxidoreductase (POR) harboring various subcellular localization sequences to guide this flavoenzyme to the nucleus, endoplasmic reticulum, cytosol or inner surface of the plasma membrane. We show that all POR variants are functional, with differences in rates of metabolism reflecting enzyme expression levels rather than intracellular TPZ concentration gradients. Under anoxic conditions, POR expression in all subcellular compartments increased the sensitivity of the cells to TPZ, but with a fall in cytotoxicity per unit of metabolism (termed 'metabolic efficiency') when POR is expressed further from the nucleus. However, under aerobic conditions a much larger increase in cytotoxicity was observed when POR was directed to the nucleus, indicating very high metabolic efficiency. Consequently, nuclear metabolism results in collapse of hypoxic selectivity of TPZ, which was further magnified to the point of reversing O2 dependence (oxic > hypoxic sensitivity) by employing a DNA-affinic TPZ analogue. This aerobic hypersensitivity phenotype was partially rescued by cellular copper depletion, suggesting the possible involvement of Fenton-like chemistry in generating short-range effects mediated by the hydroxyl radical. In addition, the data suggest that under aerobic conditions reoxidation strictly limits the TPZ radical diffusion range resulting in site-specific cytotoxicity. Collectively these novel findings challenge the purported role of intra-nuclear reductases in orchestrating the hypoxia selectivity of TPZ.

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The choice of a thermodynamic formulation dramatically affects modelled chemical zoning in minerals.

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The choice of a thermodynamic formulation dramatically affects modelled chemical zoning in minerals.

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