scholarly journals A Drive towards Thermodynamic Efficiency for Dissipative Structures in Chemical Reaction Networks

Entropy ◽  
2021 ◽  
Vol 23 (9) ◽  
pp. 1115
Author(s):  
Kai Ueltzhöffer ◽  
Lancelot Da Costa ◽  
Daniela Cialfi ◽  
Karl Friston
Keyword(s):  
Chemical Reaction ◽  
Metastable State ◽  
Chemical Potential ◽  
Biological Systems ◽  
Reaction Network ◽  
Dissipative Structures ◽  
Dissipative Systems ◽  
Thermodynamic Efficiency ◽  
Chemical Potential Difference ◽  
Selection Of

Dissipative accounts of structure formation show that the self-organisation of complex structures is thermodynamically favoured, whenever these structures dissipate free energy that could not be accessed otherwise. These structures therefore open transition channels for the state of the universe to move from a frustrated, metastable state to another metastable state of higher entropy. However, these accounts apply as well to relatively simple, dissipative systems, such as convection cells, hurricanes, candle flames, lightning strikes, or mechanical cracks, as they do to complex biological systems. Conversely, interesting computational properties—that characterize complex biological systems, such as efficient, predictive representations of environmental dynamics—can be linked to the thermodynamic efficiency of underlying physical processes. However, the potential mechanisms that underwrite the selection of dissipative structures with thermodynamically efficient subprocesses is not completely understood. We address these mechanisms by explaining how bifurcation-based, work-harvesting processes—required to sustain complex dissipative structures—might be driven towards thermodynamic efficiency. We first demonstrate a simple mechanism that leads to self-selection of efficient dissipative structures in a stochastic chemical reaction network, when the dissipated driving chemical potential difference is decreased. We then discuss how such a drive can emerge naturally in a hierarchy of self-similar dissipative structures, each feeding on the dissipative structures of a previous level, when moving away from the initial, driving disequilibrium.

The Equilibrium Constant

1993 ◽  
Author(s):  
Greg M. Anderson ◽  
David A. Crerar
Keyword(s):  
Equilibrium State ◽  
Equilibrium Constant ◽  
Chemical Reaction ◽  
Metastable State ◽  
Chemical Potential ◽  
Energy Potential ◽  
General Terms ◽  
Chemical Potentials ◽  
Equilibrium Relationship ◽  
The Difference

Consider a chemical reaction, involving any number of reactants and products and any number of phases, which may be written where Mi represents the chemical formulae of the reaction constituents and Vi represents the stoichiometric coefficients, negative for reactants and positive for products. An example would be where, if MI is SiO2(s), M2 is H2O, and M3 is H4SiO4(ag), and v1 = —I, i/2 = —2, and V3 = 1 , the reaction is Now let's recall (from Chapter 3) what we mean by an equation such as (13.3). If there are no constraints placed on the system containing M1, M2, and M3 other than T and P (or T and V; U and V; S and P; etc.) then M1, M2, and M3 react until they reach an equilibrium state characterized by a minimum in the appropriate energy potential as indicated by expressions like dGT,p = 0. A corollary of this equilibrium relationship, to be fully developed in the next chapter, is that the sums of the chemical potentials of the reactants and products must be equal. In the example, this would be or or in general terms, No notation is necessary for the phases involved because μ must be the same in every phase in the system. However, if more than the minimum two constraints apply to the system, then any equilibrium state achieved will be in our terms a metastable state, (14.25) does not apply, and the difference in chemical potential between products and reactants is not zero. In our example, a solution might be supersaturated with H4SIO4 but prevented from precipitating quartz by a nucleation constraint, so that μ H4SiO4 — μ SiO2 ~ 2 μ H2o > 0.

General Thermodynamic Efficiency Loss and Scaling Behavior of Eukaryotic Organisms

2020 ◽  
Vol 15 (03) ◽  
pp. 143-169
Author(s):  
Jorge A. Montemayor-Aldrete ◽  
Rafael F. Márquez-Caballé ◽  
Marcelo del Castillo-Mussot ◽  
Fidel Cruz-Peregrino
Keyword(s):  
New York ◽  
Homo Sapiens ◽  
Continuous Process ◽  
Dissipative Structures ◽  
Dissipative Systems ◽  
Thermodynamic Efficiency ◽  
Efficiency Loss ◽  
Functional Efficiency ◽  
Biological Structures ◽  
Cyclic Processes

A simple and general thermodynamic theory is applied to describe the irreversible aspects of the continuous process of functional efficiency loss, which occurs in dissipative biological structures after they reach maturity. Following Prigogine [G. Nicolis and I. Prigogine, Self-organization in Nonequilibrium Systems (Wiley, New York, 1997), pp. 2–3], this theory considers that these dissipative structures perform their functions carrying out cyclic processes per se since they are self-organized far from equilibrium. Starting from the theoretical fact that after biological dissipative systems reach adulthood, the functionality of their organs decreases linearly over time. We show that cumulative damage leads to the exponential law of increasing mortality rate with age for population groups, known as Gompertz’s law. The theory was applied to the determination of functional efficiency loss parameter, [Formula: see text], for 71 living beings as a function of mass covering 18 orders of magnitude. The mathematical adjustment allowed us to conclude that there is a minimum in the value of the [Formula: see text] parameter for a 23.3 kg mass which is close enough to the Homo sapiens one. We obtained useful expressions to describe the [Formula: see text] parameter for smaller masses than those of saccharomyces cerevisiae, so perhaps this theory may contribute to the study of the evolution of some dissipative pre-biological structures.

Multistage Pressure-Retarded Osmosis

2016 ◽  
Vol 41 (4) ◽  
Author(s):  
Devesh Bharadwaj ◽  
Thomas M. Fyles ◽  
Henning Struchtrup
Keyword(s):  
Energy Source ◽  
Energy Recovery ◽  
Chemical Potential ◽  
Salinity Gradient ◽  
Thermodynamic Efficiency ◽  
Membrane Process ◽  
Chemical Potential Difference ◽  
Pressure Retarded Osmosis ◽  
Gradient Energy ◽  
Unified Description

AbstractOne promising sustainable energy source is the chemical potential difference between salt and freshwater. The membrane process of pressure-retarded osmosis (PRO) has been the most widely investigated means to harvest salinity gradient energy. In this report, we analyse the thermodynamic efficiency of multistage PRO systems to optimize energy recovery from a salinity gradient. We establish a unified description of the efficiencies of the component pumps (

Synthesis and Breakdown of the Universal Precursors to Biological Metabolism Promoted by Ferrous Iron

2018 ◽  
Author(s):  
Kamila B. Muchowska ◽  
Sreejith Jayasree VARMA ◽  
Joseph Moran
Keyword(s):  
Amino Acids ◽  
Chemical Reaction ◽  
Metabolic Pathways ◽  
Ferrous Iron ◽  
Reaction Network ◽  
Tca Cycle ◽  
Chemical Reaction Network ◽  
Metabolic Precursors ◽  
Tca Cycle Intermediates

How core biological metabolism initiated and why it uses the intermediates, reactions and pathways that it does remains unclear. Life builds its molecules from CO<sub>2 </sub>and breaks them down to CO<sub>2 </sub>again through the intermediacy of just five metabolites that act as the hubs of biochemistry. Here, we describe a purely chemical reaction network promoted by Fe<sup>2+ </sup>in which aqueous pyruvate and glyoxylate, two products of abiotic CO<sub>2 </sub>reduction, build up nine of the eleven TCA cycle intermediates, including all five universal metabolic precursors. The intermediates simultaneously break down to CO<sub>2 </sub>in a life-like regime resembling biological anabolism and catabolism. Introduction of hydroxylamine and Fe<sup>0 </sup>produces four biological amino acids. The network significantly overlaps the TCA/rTCA and glyoxylate cycles and may represent a prebiotic precursor to these core metabolic pathways.

Combining computational and experimental approaches to select chromophores to enable the detection of fatty acids via HPLC

2019 ◽  
Vol 11 (23) ◽  
pp. 2952-2959 ◽  
Author(s):  
Jessica Pandohee ◽  
Robert J. Rees ◽  
Michelle J. S. Spencer ◽  
Aaron Raynor ◽  
Oliver A. H. Jones
Keyword(s):  
Fatty Acids ◽  
Quantum Mechanics ◽  
Chemical Reaction ◽  
Experimental Approaches ◽  
Systematic Selection ◽  
Selection Of

This paper outlines a protocol, which combines quantum mechanics calculations and experimental synthesis, to enable systematic selection of suitable chromophores based on their stability of fluorescence and efficiency of the chemical reaction.

Axisymmetric Finite-Element Analysis for Interface Migration-Controlled Shape Instabilities of Plate-Like Double-Crystal Grains

2012 ◽  
Vol 460 ◽  
pp. 230-235
Author(s):  
Pei Zhen Huang ◽  
Zhou Zhou Zhang ◽  
Jian Wei Guo ◽  
Jun Sun
Keyword(s):  
Finite Element ◽  
Grain Boundary ◽  
Chemical Potential ◽  
Boundary Energy ◽  
Element Analysis ◽  
Interface Motion ◽  
Double Crystal ◽  
Energy Principle ◽  
Chemical Potential Difference ◽  
Interface Migration

An axisymmetric finite-element method is developed to predict the evolution behavior of microstructures by interface migration. The formulation of the method is conducted on the basis of the energy principle during the interface motion. The computations extend earlier models by accounting in detail for the effects of grain-boundary energy, surface energy and chemical potential difference. The eventual shape of the plate-like double-crystal grain depends on both the initial β and the thermal grooving angle Ψ. For a given β, a critical Ψcexists. When Ψ>Ψc, the eventual shape is one made of two sphere segments with a thermal groove. When Ψ≤Ψc, grain splitting along the grain boundary occurs, and the splitting segments evolve into two spheres, respectively. Both the spheroidization time and the splitting time increase with Ψ and β increasing. The volume shrinkage rate decreases with increasing Ψ.

Reliability Implications of Defects in High Temperature Annealed Si/SiO2/Si Structures

1994 ◽  
Vol 338 ◽  
Author(s):  
W. L. Warren ◽  
D. M. Fleetwood ◽  
M. R. Shaneyfelt ◽  
P. S. Winokur ◽  
R. A. B. Devine ◽  
...  
Keyword(s):  
High Temperature ◽  
Chemical Potential ◽  
Field Effect Transistors ◽  
Radiation Sensitivity ◽  
Oxide Semiconductor ◽  
Interfacial Region ◽  
Si Substrate ◽  
Paramagnetic Defect ◽  
Chemical Potential Difference ◽  
Hole Trapping

ABSTRACTHigh-temperature post-oxidation annealing of poly-Si/SiO2/Si structures such as metal-oxidesemiconductor capacitors and metal-oxide-semiconductor field effect transistors is known to result in enhanced radiation sensitivity, increased 1/f noise, and low field breakdown. We have studied the origins of these effects from a spectroscopic standpoint using electron paramagnetic resonance (EPR) and atomic force microscopy. One result of high temperature annealing is the generation of three types of paramagnetic defect centers, two of which are associated with the oxide close to the Si/SiO2 interface (oxygen-vacancy centers) and the third with the bulk Si substrate (oxygen-related donors). In all three cases the origin of the defects may be attributed to out-diffusion of O from the SiO2 network into the Si substrate with associated reduction of the oxide. We present a straightforward model for the interfacial region which assumes the driving force for O out-diffusion is the chemical potential difference of the O in the two phases (SiO2 and the Si substrate). Experimental evidence is provided to show that enhanced hole trapping and interface-trap and border-trap generation in irradiated high-temperature annealed Si/SiO2/Si systems are all related either directly, or indirectly, to the presence of oxygen vacancies.

scholarly journals Antibody selection using clonal cocultivation of Escherichia coli and eukaryotic cells in miniecosystems

2018 ◽  
Vol 115 (27) ◽  
pp. E6145-E6151 ◽  
Author(s):  
Tianqing Zheng ◽  
Jia Xie ◽  
Zhuo Yang ◽  
Pingdong Tao ◽  
Bingbing Shi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phage Genome ◽  
Biological Systems ◽  
Gene Sequencing ◽  
Eukaryotic Cells ◽  
Target Cells ◽  
Antibody Repertoire ◽  
Functional Antibodies ◽  
Selection Of

We describe a method for the rapid selection of functional antibodies. The method depends on the cocultivation of Escherichia coli that produce phage with target eukaryotic cells in very small volumes. The antibodies on phage induce selectable phenotypes in the target cells, and the nature of the antibody is determined by gene sequencing of the phage genome. To select functional antibodies from the diverse antibody repertoire, we devised a selection platform that contains millions of picoliter-sized droplet ecosystems. In each miniecosystem, the bacteria produce phage displaying unique members of the antibody repertoire. These phage interact only with eukaryotic cells in the same miniecosystem, making phage available directly for activity-based antibody selection in biological systems.

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