- high-resolution terminology - matching measurements at high-resolution
System
Description
The term system has a variety of meanings and dictionary definitions in different contexts, e.g., the International System of Units (SI), MKSA system, data management system, biological or mechanical system, redox system, Electron transfer system, loosely or completely coupled system, instrumental system. In thermodynamics and ergodynamics, the system is considered as an experimental system (experimental chamber), separated from the environment as an isolated, adiabatic, closed, or open system. {quote Gnaiger 1993 Pure Appl Chem}: The internal domain of any system is separated from the external domain (the surroundings) by a boundary. In theory, energy transformations outside the system can be ignored when describing the system. The surroundings are merely considered as a source or sink for quantities transferred across the system boundary. According to the transfer properties of the boundary, three types of thermodynamic systems are distinguished. (1) The boundaries of isolated systems are impermeable for all forms of energy and matter. Isolated systems do not interact with the surroundings. Strictly, therefore, internal changes of isolated systems cannot be observed from outside since any observation requires interaction. (2) The boundaries of closed systems are permeable for heat and work, but impermeable for matter. A limiting case is electrons which cross the system boundary when work is exchanged in the form of electric energy [added: and light]. The volume of a closed system may be variable. (3) The boundaries of open systems allow for the transfer of heat, work and matter. Changes of isolated systems have exclusively internal origins, whereas changes of closed and open systems can be partitioned according to internal and external sources. Production and destruction of a quantity within the system are internal changes, whereas changes of heat, work and matter due to transfer across the system boundaries are labelled extenal. (External) transfer is thus contrasted with (internal) production or destruction. {end of quote}
A system may be treated as a black box. In the analysis of continuous or discontinuous systems, however, information is implied on the internal structure of the system.
Reference: BEC 2020.1, Gnaiger 1993 Pure Appl Chem
Communicated by Gnaiger E (2019-01-01) last update 2020-06-04
Instrumental chamber and experimental chamber
- The O2k-chamber of the Oroboros O2k is taken as an example, but the concept is entirely general.
The volume of the experimental chamber
- The instrumental chambers of the O2k consist of Duran glass with an inner diameter of either 16 mm of the '2 mL chamber', or a smaller diameter for the '0.5 mL chamber' of the O2k-sV-Module. 2 mL and 0.5 mL are the 'operation volumes', which do not include the volume of the glass wall. The operation volumes, therefore, are not the instrumental volumes but the experimental volumes, including the liquid volume and sample enclosed in the chamber with a volume-calibrated stopper inserted, to obtain a closed system. It is useful, therefore, to distinguish the experimental chamber as the closed or open system operated under experimental conditions of temperature and pressure, with a particular stirrer inserted, but without including the volume of the stirrer in the volume V of the experimental system. For the experimental chamber it may be entirely irrelevant, if the wall is composed of Duran or quartz glass. But an instrumental chamber of Duran glass is a different product than an instrumental chamber of quartz glass. You may have a number of instrumental spare chambers, which are stored in the accessory box. An experimental chamber, however, is by definition inserted into the O2k, containing a defined medium (usually aqueous, but it might be gaseous) and operated under experimental conditions of temperature, pressure, stirring speed and optionally containing a sample. Thus the experimental chamber is defined as the thermodynamic system including the sample if a sample is inserted, whereas the instrumental chamber is a particular product described in the catalogue. The 2 mL and 0.5 mL volumes V refer to the experimental chamber volumes of the instrumental chambers.
- The O2k-Chamber is the instrumental chamber of the O2k with product ID 23100-01. The instrumental chamber may be a physical object inserted in the O2k or placed in the accessory box or storage room, or it may even be a non-physical concept displayed on the website. The instrumental chamber is effectively the chamber wall (product ID 23100-01 does not include the stirrer bar).
- The O2k-chamber is the experimental chamber in the O2k operated under experimental conditions. The experimental chamber does not include the chamber wall, but the system boundary is the area separating the wall from the contents — an area of zero thickness and hence the boundary has zero volume. Yet the experimental chamber is a physical object, characterized by the experimental contents of the chamber. The stirrer bar is inserted into the instrumental chamber, but the volume of the stirrer bar is excluded from the experimental chamber volume.
- Whereas the instrumental chamber lasts over time until it breaks (the O2k does not have disposable chambers), the experimental chamber exists for the duration of an experiment. The instrumental chamber is the container (made of glass), the experimental chamber is defined by the experimental contents and experimental conditions.
The volume of the study object, the sample, the medium, and the experimental chamber
- In a sample consisting of a pure substance S, the sample volume VS equals the experimental chamber volume V — the sample is the system:
Sample S for a pure substance B: VB = V
- Take a sample s of freeze-dried yeast cells as countable objects or entities X. The pure sample of yeast cells is added into the experimental chamber containing mitochondrial respiration medium — the sample is not the system, the sample is not the object.
- Take a sample s of a tissue homogenate of volume Vthom and inject this volume into the experimental chamber containing mitochondrial respiration medium. In this mixture the sample does not contain countable objects but units of sample volume, occupying a volume Vthom that is smaller than V — the sample is not the system, the sample is the object:
Sample s for a mixture: Vs < V
- For cells suspended at high dilution, the volume Vce is small to the extent that it can be ignored relative to the volume VMiR of the mitochondrial respiration medium — the medium is the system:
Cells at high dilution: VMiR ~ V
The O2k-chamber is not an ideally closed system
- The polarographic oxygen sensor is neither part of the instrumental O2k-Chamber nor experimental O2k-chamber. Oxygen diffuses across the system boundary from the experimental medium to the cathode of the sensor, where 4 electrons reduce O2 to H2O, and the corresponding electron flow is measured as a current Iel which is the primary signal of the polarographic oxygen sensor (polarized at 800 mV to push the reduction of oxygen). In an ideally closed system (= experimental chamber), oxygen would be prevented from escaping to the oxygen sensor. Therefore, this external flow of oxygen (a negative flow has the direction out of the system) is accounted for as a component of the instrumental background oxygen flux J°O2. The experimental background oxygen flux includes additionally the chemical background oxygen flux due to processes of autooxidation, if any unstable components are added to the incubation medium (correction for chemical O2 background).
References
| Bioblast link | Reference | Year |
|---|---|---|
| Gnaiger 1993 Pure Appl Chem | Gnaiger E (1993) Nonequilibrium thermodynamics of energy transformations. Pure Appl Chem 65:1983-2002. http://dx.doi.org/10.1351/pac199365091983 | 1993 |
| Gnaiger 2020 BEC MitoPathways | Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2. https://doi.org/10.26124/bec:2020-0002 | 2020 |
| BEC 2020.1 doi10.26124bec2020-0001.v1 | Gnaiger E et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1 | 2020 |
| MiPNet14.06 Instrumental O2 background |  | 2023-10-19 |
- Bioblast links: System - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
MitoPedia concepts:
Ergodynamics
