Virtual mitochondrion: towards an integrated model of oxidative phosphorylation complexes and beyond

2010 ◽  
Vol 38 (5) ◽  
pp. 1215-1219 ◽  
Author(s):  
Jean-Pierre Mazat ◽  
Jonathan Fromentin ◽  
Margit Heiske ◽  
Christine Nazaret ◽  
Stéphane Ransac
Keyword(s):  
Oxidative Phosphorylation ◽  
Integrated Model ◽  
Global Model ◽  
Local Model ◽  
Central Metabolism ◽  
Chemiosmotic Theory ◽  
Respiratory Complexes ◽  
The Individual

The modelling of OXPHOS (oxidative phosphorylation) in order to integrate all kinetic and thermodynamic aspects of chemiosmotic theory has a long history. We briefly review this history and show how new ways of modelling are required to integrate a local model of the individual respiratory complexes into a global model of OXPHOS and, beyond that, into a reliable overall model of central metabolism.

scholarly journals Modeling of the buckstay system of membrane-walls in watertube boiler construction

2014 ◽  
Vol 18 (suppl.1) ◽  
pp. 59-72 ◽  
Author(s):  
Hasan Nagiar ◽  
Tasko Maneski ◽  
Vesna Milosevic-Mitic ◽  
Branka Gacesa ◽  
Nina Andjelic
Keyword(s):  
Finite Element ◽  
Orthotropic Plate ◽  
Global Model ◽  
Local Model ◽  
Thermal Loads ◽  
Water Tube ◽  
Bending Load ◽  
Specific Geometry ◽  
Structural Parts ◽  
Help Model

Membrane walls are very important structural parts of water-tube boiler construction. Based on their specific geometry, one special type of finite element was defined to help model the global boiler construction. That is the element of reduced orthotropic plate with two thicknesses and two elasticity matrixes, for membrane and bending load separately. A global model of the boiler construction showed that the high value of stress is concentrated in plates of the buckstay system in boiler corners. Validation of the new finite element was done on the local model of the part of membrane wall and buckstay. A very precise model of tubes and flanges was compared to the model formed on the element of a reduced orthotropic plate. Pressure and thermal loads were discussed. Obtained results indicated that the defined finite element was quite favorable in the design and reconstruction of the boiler substructures such as a buckstay system.

Local model of a scientific collaboration in physics network compared with the global model

2010 ◽  
Vol 389 (23) ◽  
pp. 5530-5537 ◽  
Author(s):  
A.A. Roohi ◽  
A.H. Shirazi ◽  
A. Kargaran ◽  
G.R. Jafari
Keyword(s):  
Scientific Collaboration ◽  
Global Model ◽  
Local Model

scholarly journals Central metabolism of functionally heterogeneous mesenchymal stromal cells

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mario Barilani ◽  
Roberta Palorini ◽  
Giuseppina Votta ◽  
Roberta Piras ◽  
Giuseppe Buono ◽  
...  
Keyword(s):  
Stem Cells ◽  
Oxidative Phosphorylation ◽  
Cell Fate ◽  
Lactate Production ◽  
Glucose Consumption ◽  
Mitochondrial Activity ◽  
Central Metabolism ◽  
Mt Dna ◽  
Differentiation Potential ◽  
And Function

Abstract Metabolism and mitochondrial biology have gained a prominent role as determinants of stem cell fate and function. In the context of regenerative medicine, innovative parameters predictive of therapeutic efficacy could be drawn from the association of metabolic or mitochondrial parameters to different degrees of stemness and differentiation potentials. Herein, this possibility was addressed in human mesenchymal stromal/stem cells (hMSC) previously shown to differ in lifespan and telomere length. First, these hMSC were shown to possess significantly distinct proliferation rate, senescence status and differentiation capacity. More potential hMSC were associated to higher mitochondrial (mt) DNA copy number and lower mtDNA methylation. In addition, they showed higher expression levels of oxidative phosphorylation subunits. Consistently, they exhibited higher coupled oxygen consumption rate and lower transcription of glycolysis-related genes, glucose consumption and lactate production. All these data pointed at oxidative phosphorylation-based central metabolism as a feature of higher stemness-associated hMSC phenotypes. Consistently, reduction of mitochondrial activity by complex I and III inhibitors in higher stemness-associated hMSC triggered senescence. Finally, functionally higher stemness-associated hMSC showed metabolic plasticity when challenged by glucose or glutamine shortage, which mimic bioenergetics switches that hMSC must undergo after transplantation or during self-renewal and differentiation. Altogether, these results hint at metabolic and mitochondrial parameters that could be implemented to identify stem cells endowed with superior growth and differentiation potential.

Fuel-Sensitive Ignition Delay Models for a Local and Global Description of Direct Injection Internal Combustion Engines

2015 ◽  
Vol 137 (11) ◽  
Author(s):  
Kyoung Hyun Kwak ◽  
Claus Borgnakke ◽  
Dohoy Jung
Keyword(s):  
Ignition Delay ◽  
Alternative Fuels ◽  
Internal Combustion Engines ◽  
Cetane Number ◽  
Global Model ◽  
Local Model ◽  
Delay Model ◽  
Lower Accuracy ◽  
Delay Models ◽  
Single Calibration

Models for ignition delay are investigated and fuel-specific properties are included to predict the effects of different fuels on the ignition delay. These models follow the Arrhenius type expression for the ignition delay modified with the oxygen concentration and Cetane number to extend the range of validity. In this investigation, two fuel-sensitive spray ignition delay models are developed: a global model and a local model. The global model is based on the global combustion chamber charge properties including temperature, pressure, and oxygen/fuel content. The local model is developed to account for temporal and spatial variations in properties of separated spray zones such as local temperature, oxidizer, and fuel concentrations obtained by a quasi-dimensional multizone fuel spray model. These variations are integrated in time to predict the ignition delay. Often ignition delay models are recalibrated for a specific fuel but in this study, the global ignition delay model includes the Cetane number to capture ignition delay of various fuels. The local model uses Cetane number and local stoichiometric oxygen to fuel molar ratio. The model is therefore capable of predicting spray ignition delays for a set of fuels with a single calibration. Experimental dataset of spray ignition delay in a constant volume chamber is used for model development and calibration. The models show a good accuracy for the predicted ignition delay of four different fuels: JP8, DF2, n-heptane, and n-dodecane. The investigation revealed that the most accurate form of the models is from a calibration done for each individual fuel with only a slight decrease in accuracy when a single calibration is done for all fuels. The single calibration case is the more desirable outcome as it leads to general models that cover all the fuels. Of the two proposed models, the local model has a slightly better accuracy compared to the global model. Results for both models demonstrate the improvements that can be obtained for the ignition delay model when additional fuel-specific properties are included in the spray ignition model. Other alternative fuels like synthetic oxygenated fuels were included in the investigation. These fuels behave differently such that the Cetane number does not provide the same explanation for the trend in ignition delay. Though of lower accuracy, the new models do improve the predictive capability when compared with existing types of ignition delay models applied to this kind of fuels.

scholarly journals The E2 Domain of OdhA of Corynebacterium glutamicum Has Succinyltransferase Activity Dependent on Lipoyl Residues of the Acetyltransferase AceF

2010 ◽  
Vol 192 (19) ◽  
pp. 5203-5211 ◽  
Author(s):  
Melanie Hoffelder ◽  
Katharina Raasch ◽  
Jan van Ooyen ◽  
Lothar Eggeling
Keyword(s):  
Corynebacterium Glutamicum ◽  
Pyruvate Dehydrogenase ◽  
The Other ◽  
Central Metabolism ◽  
Mutant Proteins ◽  
Oxoglutarate Dehydrogenase ◽  
The Individual ◽  
Activity Dependent ◽  
Dihydrolipoyl Dehydrogenase ◽  
Mutant Cells

ABSTRACT Oxoglutarate dehydrogenase (ODH) and pyruvate dehydrogenase (PDH) complexes catalyze key reactions in central metabolism, and in Corynebacterium glutamicum there is indication of an unusual supercomplex consisting of AceE (E1), AceF (E2), and Lpd (E3) together with OdhA. OdhA is a fusion protein of additional E1 and E2 domains, and odhA orthologs are present in all Corynebacterineae, including, for instance, Mycobacterium tuberculosis. Here we show that deletion of any of the individual domains of OdhA in C. glutamicum resulted in loss of ODH activity, whereas PDH was still functional. On the other hand, deletion of AceF disabled both PDH activity and ODH activity as well, although isolated AceF protein had solely transacetylase activity and no transsuccinylase activity. Surprisingly, the isolated OdhA protein was inactive with 2-oxoglutarate as the substrate, but it gained transsuccinylase activity upon addition of dihydrolipoamide. Further enzymatic analysis of mutant proteins and mutant cells revealed that OdhA specifically catalyzes the E1 and E2 reaction to convert 2-oxoglutarate to succinyl-coenzyme A (CoA) but fully relies on the lipoyl residues provided by AceF involved in the reactions to convert pyruvate to acetyl-CoA. It therefore appears that in the putative supercomplex in C. glutamicum, in addition to dihydrolipoyl dehydrogenase E3, lipoyl domains are also shared, thus confirming the unique evolutionary position of bacteria such as C. glutamicum and M. tuberculosis.

scholarly journals Study of the combined effects of data assimilation and grid nesting in ocean models – application to the Gulf of Lions

2006 ◽  
Vol 3 (3) ◽  
pp. 291-318
Author(s):  
L. Vandenbulcke ◽  
A. Barth ◽  
M. Rixen ◽  
A. Alvera-Azcárate ◽  
Z. Ben Bouallegue ◽  
...  
Keyword(s):  
Data Assimilation ◽  
Boundary Conditions ◽  
Global Model ◽  
Local Model ◽  
Local Models ◽  
Coastal Zones ◽  
Efficient System ◽  
Nested Models ◽  
Ocean Forecasting ◽  
Grid Nesting

Abstract. Modern operational ocean forecasting systems routinely use data assimilation techniques in order to take observations into account in the hydrodynamic model. Moreover, as end users require higher and higher resolution predictions, especially in coastal zones, it is now common to run nested models, where the coastal model gets its open-sea boundary conditions from a low-resolution global model. This configuration is used in the ''Mediterranean Forecasting System: Towards environmental predictions'' (MFSTEP) project. A global model covering the whole Mediterranean Sea is run weekly, performing 1 week of hindcast and a 10-day forecast. Regional models, using different codes and covering different areas, then use this forecast to implement boundary conditions. Local models in turn use the regional model forecasts for their own boundary conditions. This nested system has proven to be a viable and efficient system to achieve high-resolution weekly forecasts. However, when observations are available in some coastal zone, it remains unclear whether it is better to assimilate them in the global or local model. We perform twin experiments and assimilate observations in the global or in the local model, or in both of them together. We show that, when interested in the local models forecast and provided the global model fields are approximately correct, the best results are obtained when assimilating observations in the local model.

scholarly journals Chemiosmotic coupling in oxidative phosphorylation: The history of a hard experimental effort hampered by the Heisenberg indeterminacy principle

2018 ◽  
Author(s):  
Alessandro Maria Morelli ◽  
Silvia Ravera ◽  
Daniela Calzia ◽  
Isabella Panfoli
Keyword(s):  
Oxidative Phosphorylation ◽  
Proton Translocation ◽  
Structural Data ◽  
Biological Research ◽  
Proton Pumps ◽  
Chemiosmotic Theory ◽  
Respiratory Chain Complexes ◽  
Chain Complexes ◽  
Definition Of ◽  
Chemiosmotic Coupling

Understanding how biological systems convert and store energy is a primary goal of biological research. However, despite the formulation of Mitchell’s chemiosmotic theory, which allowed taking fundamental steps forward, we are still far from the complete decryption of basic processes as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory appears to need updating, as some of its assumptions have proven incorrect in the light of the latest structural data on respiratory chain complexes, bacteriorhodopsin and proton pumps. Moreover, the existence of an OXPHOS on the plasma membrane of cells casts doubt on the possibility to build up a transversal proton gradient across it, while paving the way for important applications in the field of neurochemistry and oncology. Up-to date biotechnologies, such as fluorescence indicators can follow proton displacement and sinks, and a number of reports have elegantly demonstrated that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still unresolved even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. It seems that the concept of diffusion of the proton expressed more than two centuries ago by Theodor von Grotthuss, is decisive for overcoming these issues. All these uncertainties remember us that also in biology it is necessary to take into account the Heisenberg indeterminacy principle, that sets limits to analytical questions.

Glynn and the conceptual development of the chemiosmotic theory: A retrospective and prospective view

1991 ◽  
Vol 11 (6) ◽  
pp. 577-617 ◽  
Author(s):  
Bruce H. Weber
Keyword(s):  
Oxidative Phosphorylation ◽  
Conceptual Development ◽  
Chemiosmotic Theory ◽  
Origin And Evolution ◽  
Independent Laboratory ◽  
Growth Of Knowledge

The origin and evolution of the chemiosmotic theory is described particularly in relation to Peter Mitchell's application of it to model oxidative phosphorylation. Much of the deployment, development and evaluation of the theory occurred at the independent laboratory of the Glynn Research Foundation; the value and future of such an institution is discussed. The role of models mediating between theories and phenomena is analyzed with regard to the growth of knowledge of chemiosmotic systems.

Global-Local Analysis of a Composite Riser

2014 ◽  
Author(s):  
Venkata M. K. Akula
Keyword(s):  
Composite Materials ◽  
Composite Structures ◽  
Coefficient Of Thermal Expansion ◽  
Structural Response ◽  
Global Model ◽  
Local Model ◽  
Cross Sectional ◽  
Beam Elements ◽  
Aspect Ratios ◽  
Hexahedral Elements

Composite materials are often utilized in weight-critical applications, owing to their higher specific strength\stiffness characteristics. In addition, composite materials also possess qualities such as better corrosion resistance, lower coefficient of thermal expansion, etc., which makes them a potential material choice for riser systems in high pressure and high temperature environments. However, design certification of risers using the finite element method requires modeling and analysis techniques, centric to the multi-layered nature of composite structures. Riser systems, owing to their high aspect ratios, have traditionally been modeled with beam elements. The methodology for extracting the stress results and certifying a metallic riser is well established in the Oil and Gas industry. However, for analyzing a composite riser, three-dimensional shell or hexahedral elements are generally required to capture the through-the-thickness (or pipe cross-sectional) variation of structural response, especially in critical regions such as touchdown point, pipe-intersection zones, etc. In this paper, a method for analyzing a detailed local model (discretized with shell\hexahedral elements) driven by results from a global model (meshed with beam elements) is presented. The global model captures the structural response whereas the local model provides cross-sectional stress\strain information for individual layers. Although the method is illustrated for a composite riser, it is also applicable to metallic structures.

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