Appendix B: Free Energy and Thermodynamic Feasibility of Chemical and Biochemical Reactions

2005 ◽  
pp. 535-542
Keyword(s):  
Free Energy ◽  
Biochemical Reactions ◽  
Thermodynamic Feasibility

The Formulation of Chemical Potentials and Free Energy Changes in Biochemical Reactions

2021 ◽  
Author(s):  
William Cannon ◽  
Lionel Raff
Keyword(s):  
Free Energy ◽  
Free Energies ◽  
Biochemical Reactions ◽  
Chemical Potentials

In 1994, an IUBMB-IUPAC joint committee recommended a revised formulation for standard chemical potentials and reaction free energies motivated by the fact that, in biochemistry, the reactants and products often...

Definitions of free energy levels in biochemical reactions

Nature ◽  
1976 ◽  
Vol 263 (5578) ◽  
pp. 615-618 ◽  
Author(s):  
R. M. SIMMONS ◽  
TERRELL L. HILL
Keyword(s):  
Free Energy ◽  
Energy Levels ◽  
Biochemical Reactions

scholarly journals Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions

2018 ◽  
Vol 35 (15) ◽  
pp. 2634-2643 ◽  
Author(s):  
Meshari Alazmi ◽  
Hiroyuki Kuwahara ◽  
Othman Soufan ◽  
Lizhong Ding ◽  
Xin Gao
Keyword(s):  
Free Energy ◽  
Feature Selection ◽  
Gibbs Free Energy ◽  
Supplementary Information ◽  
Biochemical Reactions ◽  
Chemical Fingerprint ◽  
Energy Prediction ◽  
Systematic Feature ◽  
Metabolic Systems ◽  
Selection Of

Abstract Motivation Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. Results Here, we introduce a machine learning method with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. Since a manual selection of 2D structure-based features can be a tedious and time-consuming task, requiring expert knowledge about the structure-activity relationship of chemical compounds, the systematic feature selection step in our method offers a convenient means to identify relevant 2D fingerprint-based features. By comparing our method with state-of-the-art linear regression-based methods for the standard Gibbs free energy prediction, we demonstrated that its prediction accuracy and prediction coverage are most favorable. Our results show direct evidence that a number of 2D fingerprints collectively provide useful information about the Gibbs free energy of biochemical reactions and that our systematic feature selection procedure provides a convenient way to identify them. Availability and implementation Our software is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Thermodynamic Assessment of Possible Substrates for Sulphate-reducing Bacteria

1977 ◽  
Vol 30 (2) ◽  
pp. 155 ◽  
Author(s):  
LV Wake ◽  
RK Christopher ◽  
Pamela AD Rickard ◽  
JE Andersen ◽  
BJ Ralph
Keyword(s):  
Free Energy ◽  
Thermodynamic Assessment ◽  
Electron Pair ◽  
Energy Requirement ◽  
Atp Synthesis ◽  
Wide Range ◽  
Thermodynamic Feasibility ◽  
Reducing Bacteria ◽  
Thermodynamic Basis ◽  
Do So

A thermodynamic feasibility study was applied as a means of predicting suitable energy-yielding substrates for growth of sulphate-reducing microorganisms. The average free energy release per electron pair for a substrate-sulphate oxidoreduction may be more or less than the energy requirement for ATP synthesis from ADP and Pi. Substrates were divided into two groups on this thermodynamic basis and the division was shown to accord with previous experimental reports; those substrates which released an average of at least 8� 4 kcal per electron pair (35�2 kJ per electron pair) were able to support growth whilst those releasing less than 8� 4 kcal were unable to do so. It is proposed that the thermodynamic assessment could be applied to a wide range of possible substrates to predict the likelihood of their serving as sole substrates for growth of these organisms.

Encultured minds, not error reduction minds

2020 ◽  
Vol 43 ◽  
Author(s):  
Robert Mirski ◽  
Mark H. Bickhard ◽  
David Eck ◽  
Arkadiusz Gut
Keyword(s):  
Free Energy ◽  
Error Reduction ◽  
Energy Principle ◽  
Free Energy Principle ◽  
Current Article

Abstract There are serious theoretical problems with the free-energy principle model, which are shown in the current article. We discuss the proposed model's inability to account for culturally emergent normativities, and point out the foundational issues that we claim this inability stems from.

On the free energy of a ferromagnet : anisotropy and rotation

1987 ◽  
Vol 48 (2) ◽  
pp. 169-171 ◽  
Author(s):  
G. Aubert ◽  
E. du Tremolet de Lacheisserie
Keyword(s):  
Free Energy
Sign in / Sign up

Export Citation Format

Share Document