scholarly journals A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

2017 ◽  
Vol 4 (6) ◽  
pp. 170429 ◽  
Author(s):  
Brian Chapman
Keyword(s):  
Kinetic Modelling ◽  
Reaction Rates ◽  
Mass Action ◽  
Model Parameters ◽  
Facilitated Diffusion ◽  
Equilibrium Thermodynamics ◽  
New Approach ◽  
Rate Limiting ◽  
Substrate Concentrations ◽  
Non Equilibrium

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

Non Equilibrium Thermodynamics and the City: A New Approach to Urban Studies

2006 ◽  
Vol 96 (9-10) ◽  
pp. 543-552 ◽  
Author(s):  
Riccardo Maria Pulselli ◽  
Francesca Ciampalini ◽  
Alessandro Galli ◽  
Federico Maria Pulselli
Keyword(s):  
Urban Studies ◽  
Equilibrium Thermodynamics ◽  
New Approach ◽  
The City ◽  
Non Equilibrium

Thermodynamics and foundations of mass-action kinetics

2005 ◽  
Vol 30 (1-2) ◽  
pp. 3-113 ◽  
Author(s):  
Miloslav Pekař
Keyword(s):  
Chemical Kinetics ◽  
Reaction Rate ◽  
Chemical Potential ◽  
Kinetic Equations ◽  
Reaction Rates ◽  
Equilibrium States ◽  
Mass Action ◽  
Rate Equations ◽  
Mass Action Kinetics ◽  
Non Equilibrium

A critical overview is given of phenomenological thermodynamic approaches to reaction rate equations of the type based on the law of mass-action. The review covers treatments based on classical equilibrium and irreversible (linear) thermodynamics, extended irreversible, rational and continuum thermodynamics. Special attention is devoted to affinity, the applications of activities in chemical kinetics and the importance of chemical potential. The review shows that chemical kinetics survives as the touchstone of these various thermody-namic theories. The traditional mass-action law is neither demonstrated nor proved and very often is only introduced post hoc into the framework of a particular thermodynamic theory, except for the case of rational thermodynamics. Most published “thermodynamic'’ kinetic equations are too complicated to find application in practical kinetics and have merely theoretical value. Solely rational thermodynamics can provide, in the specific case of a fluid reacting mixture, tractable rate equations which directly propose a possible reaction mechanism consistent with mass conservation and thermodynamics. It further shows that affinity alone cannot determine the reaction rate and should be supplemented by a quantity provisionally called constitutive affinity. Future research should focus on reaction rates in non-isotropic or non-homogeneous mixtures, the applicability of traditional (equilibrium) expressions relating chemical potential to activity in non-equilibrium states, and on using activities and activity coefficients determined under equilibrium in non-equilibrium states.

scholarly journals Non-equilibrium thermodynamics as a tool to compute temperature at the catalyst surface

2019 ◽  
Vol 21 (27) ◽  
pp. 15195-15205
Author(s):  
Carolina Cruz ◽  
Daniel Barragán ◽  
Elisa Magnanelli ◽  
Anders Lervik ◽  
Signe Kjelstrup
Keyword(s):  
Driving Forces ◽  
Catalyst Surface ◽  
Reaction Rates ◽  
Equilibrium Thermodynamics ◽  
Arrhenius Plots ◽  
Non Linear ◽  
Non Equilibrium

The NET theory predicts the coupling between reaction rates and thermal driving forces and gives new insights into why Arrhenius plots may turn out to be non-linear.

scholarly journals Non-Equilibrium Thermodynamics View on Kinetics of Autocatalytic Reactions—Two Illustrative Examples

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 585
Author(s):  
Miloslav Pekař
Keyword(s):  
Second Law Of Thermodynamics ◽  
Mass Action ◽  
Rate Equations ◽  
Equilibrium Thermodynamics ◽  
Mass Action Kinetics ◽  
Autocatalytic Reactions ◽  
Chemical Potentials ◽  
Entropic Inequality ◽  
Reaction Stoichiometry ◽  
Non Equilibrium

Autocatalytic reactions are in certain contrast with the linear algebra of reaction stoichiometry, on which rate equations respecting the permanence of atoms are constructed. These mathematical models of chemical reactions are called conservative. Using a non-equilibrium thermodynamics-based theory of chemical kinetics, it is shown how to introduce autocatalytic step into such (conservative) rate equation properly. Further, rate equations based on chemical potentials or affinities are derived, and conditions for the consistency of rate equations with the entropic inequality (the second law of thermodynamics) are illustrated. The theory illustrated here can be viewed as a tool for verifying and generalizing traditional mass-action kinetics by means of modern non-equilibrium thermodynamics, which is able to deal also with such rather problematic cases.

scholarly journals A New Approach to Group Multi-Objective Optimization under Imperfect Information and Its Application to Project Portfolio Optimization

2021 ◽  
Vol 11 (10) ◽  
pp. 4575
Author(s):  
Eduardo Fernández ◽  
Nelson Rangel-Valdez ◽  
Laura Cruz-Reyes ◽  
Claudia Gomez-Santillan
Keyword(s):  
Portfolio Optimization ◽  
Imperfect Information ◽  
Model Parameters ◽  
Final Decision ◽  
Project Portfolio ◽  
Objective Functions ◽  
Multi Objective Optimization ◽  
New Approach ◽  
Multi Objective ◽  
Group Member

This paper addresses group multi-objective optimization under a new perspective. For each point in the feasible decision set, satisfaction or dissatisfaction from each group member is determined by a multi-criteria ordinal classification approach, based on comparing solutions with a limiting boundary between classes “unsatisfactory” and “satisfactory”. The whole group satisfaction can be maximized, finding solutions as close as possible to the ideal consensus. The group moderator is in charge of making the final decision, finding the best compromise between the collective satisfaction and dissatisfaction. Imperfect information on values of objective functions, required and available resources, and decision model parameters are handled by using interval numbers. Two different kinds of multi-criteria decision models are considered: (i) an interval outranking approach and (ii) an interval weighted-sum value function. The proposal is more general than other approaches to group multi-objective optimization since (a) some (even all) objective values may be not the same for different DMs; (b) each group member may consider their own set of objective functions and constraints; (c) objective values may be imprecise or uncertain; (d) imperfect information on resources availability and requirements may be handled; (e) each group member may have their own perception about the availability of resources and the requirement of resources per activity. An important application of the new approach is collective multi-objective project portfolio optimization. This is illustrated by solving a real size group many-objective project portfolio optimization problem using evolutionary computation tools.

scholarly journals Contraction of polymer gels created by the activity of molecular motors

Soft Matter ◽  
2019 ◽  
Vol 15 (22) ◽  
pp. 4467-4475 ◽  
Author(s):  
Mattia Bacca ◽  
Omar A. Saleh ◽  
Robert M. McMeeking
Keyword(s):  
Mechanical Behavior ◽  
Molecular Motors ◽  
Polymer Gels ◽  
Polymer Gel ◽  
Equilibrium Thermodynamics ◽  
Non Equilibrium

We propose a theory based on non-equilibrium thermodynamics to describe the mechanical behavior of an active polymer gel created by the inclusion of molecular motors in its solvent.

Non-equilibrium thermodynamics and dissipative fluid theories

1993 ◽  
Vol 15 (8) ◽  
pp. 1063-1086 ◽  
Author(s):  
Z. Banach ◽  
S. Piekarski
Keyword(s):  
Equilibrium Thermodynamics ◽  
Dissipative Fluid ◽  
Non Equilibrium
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