Non-equilibrium Thermodynamics and the Kinetics of Glass Transition and Stabilization

2013 ◽  
pp. 69-125
Author(s):  
Ivan S. Gutzow ◽  
Jürn W. P. Schmelzer
Keyword(s):  
Glass Transition ◽  
Equilibrium Thermodynamics ◽  
Kinetics Of ◽  
Non Equilibrium

scholarly journals The Non-Equilibrium Thermodynamics and Kinetics of Focal Adhesion Dynamics

2010 ◽  
Vol 98 (3) ◽  
pp. 366a
Author(s):  
Krishnakumar Garikipati ◽  
Joseph E. Olberding ◽  
Michael Thouless ◽  
Ellen M. Arruda
Keyword(s):  
Focal Adhesion ◽  
Equilibrium Thermodynamics ◽  
Thermodynamics And Kinetics ◽  
Kinetics Of ◽  
Non Equilibrium

scholarly journals A Non-Equilibrium Thermodynamics-Based View of the Kinetics of Autocatalytic Reactions – a Simple Illustrative Example

2020 ◽  
Author(s):  
Miloslav Pekař
Keyword(s):  
Second Law Of Thermodynamics ◽  
Rate Equations ◽  
Second Law ◽  
Equilibrium Thermodynamics ◽  
Autocatalytic Reactions ◽  
Chemical Potentials ◽  
Entropic Inequality ◽  
Reaction Stoichiometry ◽  
Kinetics Of ◽  
Non Equilibrium

Autocatalytic reactions are in a certain contrast with the linear algebra of reaction stoichiometry, on whose basis rate equations respecting the permanence of atoms are constructed. These mathematical models of chemical reactions are termed conservative.Using a non-equilibrium thermodynamics-based theory of chemical kinetics, this paper demonstrates how to properly introduce an autocatalytic step into a (conservative) rate equation. Further, rate equations based on chemical potentials or affinities are derived, and conditions for the consistency of rate equations with entropic inequality (the second law of thermodynamics) are illustrated.<br><div><br></div>

VARIATIONAL PRINCIPLES OF NON-EQUILIBRIUM THERMODYNAMICS AND KINETICS OF RELAXATION TO THE EQUILIBRIUM OF FLUCTUATING MACROSCOPIC SYSTEMS

1990 ◽  
Vol 04 (10) ◽  
pp. 659-664 ◽  
Author(s):  
YU. M. DEVYATKO ◽  
V. N. TRONIN
Keyword(s):  
Variational Principles ◽  
Equilibrium Thermodynamics ◽  
Perturbative Approach ◽  
Thermodynamics And Kinetics ◽  
Kinetics Of ◽  
Non Equilibrium

On the strength of variational principles of non-equilibrium thermodynamics we have proposed a non-perturbative approach which permits determination of the most probable trajectory of motion of fluctuating macroscopic systems.

scholarly journals A Non-Equilibrium Thermodynamics-Based View of the Kinetics of Autocatalytic Reactions – a Simple Illustrative Example

2020 ◽  
Author(s):  
Miloslav Pekař
Keyword(s):  
Second Law Of Thermodynamics ◽  
Rate Equations ◽  
Second Law ◽  
Equilibrium Thermodynamics ◽  
Autocatalytic Reactions ◽  
Chemical Potentials ◽  
Entropic Inequality ◽  
Reaction Stoichiometry ◽  
Kinetics Of ◽  
Non Equilibrium

Autocatalytic reactions are in a certain contrast with the linear algebra of reaction stoichiometry, on whose basis rate equations respecting the permanence of atoms are constructed. These mathematical models of chemical reactions are termed conservative.Using a non-equilibrium thermodynamics-based theory of chemical kinetics, this paper demonstrates how to properly introduce an autocatalytic step into a (conservative) rate equation. Further, rate equations based on chemical potentials or affinities are derived, and conditions for the consistency of rate equations with entropic inequality (the second law of thermodynamics) are illustrated.<br><div><br></div>

scholarly journals The Non-Equilibrium Thermodynamics and Kinetics of Focal Adhesion Dynamics

PLoS ONE ◽  
2010 ◽  
Vol 5 (8) ◽  
pp. e12043 ◽  
Author(s):  
Joseph E. Olberding ◽  
Michael D. Thouless ◽  
Ellen M. Arruda ◽  
Krishna Garikipati
Keyword(s):  
Focal Adhesion ◽  
Equilibrium Thermodynamics ◽  
Thermodynamics And Kinetics ◽  
Kinetics Of ◽  
Non Equilibrium

Non-equilibrium thermodynamics analysis of transcriptional regulation kinetics

2014 ◽  
Vol 39 (4) ◽  
Author(s):  
Enrique Hernández-Lemus ◽  
Hugo Tovar ◽  
Carmen Mejía
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Networks ◽  
Conformational Changes ◽  
Regulatory Networks ◽  
Kinetic Equations ◽  
Decay Rates ◽  
Equilibrium Thermodynamics ◽  
Gene Regulatory ◽  
Kinetics Of ◽  
Non Equilibrium

AbstractGene expression in eukaryotic cells is an extremely complex and interesting phenomenon whose dynamics are controlled by a large number of subtle physicochemical processes commonly described by means of gene regulatory networks. Such networks consist in a series of coupled chemical reactions, conformational changes, and other biomolecular processes involving the interaction of the DNA molecule itself with a number of proteins usually called transcription factors as well as enzymes and other components. The kinetics behind the functioning of such gene regulatory networks are largely unknown, though its description in terms of non-equilibrium thermodynamics has been discussed recently. In this work we will derive general kinetic equations for a gene regulatory network from a non-equilibrium thermodynamical description and discuss its use in understanding the free energy constrains imposed in the network structure. We also will discuss explicit expressions for the kinetics of a simple model of gene regulation and show that the kinetic role of mRNA decay during the RNA synthesis stage (or transcription) is somehow limited due to the comparatively low values of decay rates. At the level discussed here, this implies a decoupling of the kinetics of mRNA synthesis and degradation a fact that may become quite useful when modeling gene regulatory networks from experimental data on whole genome gene expression.

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