The Thermodynamic Driving Force for Kinetics in General and Enzyme Kinetics in Particular

Pekař, Miloslav

doi:10.1002/cphc.201402778

Cited by 13 publications

(8 citation statements)

References 4 publications

(6 reference statements)

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“…Note that Equation (35) still contains the kinetic factor (k o ). Very similar conclusions were reported for a simple enzymatic reaction [12]. Efforts to formulate the thermodynamic driving force in terms of energy are probably motivated by the general use of energy in the descriptions of the causes and directions of natural processes.…”

Section: Chemical Potential In the Role Of The Driving Forcesupporting

confidence: 68%

Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State

Pekař

2020

Molecules

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Molar balances of continuous and batch reacting systems with a simple reaction are analyzed from the point of view of finding relationships between the thermodynamic driving force and the chemical reaction rate. Special attention is focused on the steady state, which has been the core subject of previous similar work. It is argued that such relationships should also contain, besides the thermodynamic driving force, a kinetic factor, and are of a specific form for a specific reacting system. More general analysis is provided by means of the non-equilibrium thermodynamics of linear fluid mixtures. Then, the driving force can be expressed either in the Gibbs energy (affinity) form or on the basis of chemical potentials. The relationships can be generally interpreted in terms of force, resistance and flux.

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Section: Chemical Potential In the Role Of The Driving Forcesupporting

confidence: 68%

Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State

Pekař

2020

Molecules

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“…Note that (35) still contains the kinetic factor (U b ). Very similar conclusions were reported for a simple enzymatic reaction (Pekař, 2015). Efforts to formulate the thermodynamic driving force in terms of energy are probably motivated by the general use of energy in the descriptions of the causes and directions of natural process -natural processes are usually described as being "propelled" by a high energy, running in the direction of decreasing energy and settling at the point of minimum energy.…”

Section: Chemical Potential In the Role Of The Driving Forcesupporting

confidence: 55%

Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State

Pekař¹

2020

Preprint

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Molar balances of continuous and batch reacting systems with a simple reaction are analyzed from the point of view of finding relationships between the thermodynamic driving force and the chemical reaction rate. Special attention is focused on steady state, which has been the core subject of previous similar work. It is argued that such relationships should contain, besides the thermodynamic driving force, also a kinetic factor, and are of a specific form for a specific reacting system. More general analysis is provided by means of the non-equilibrium thermodynamics of linear fluid mixtures. Then, the driving force can be expressed either in Gibbs energy (affinity) form or on the basis of chemical potentials. The relationships can be generally interpreted in terms of forceresistance-flux.

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“…The equilibrium constant of a reaction, K eqm , can be expressed both in terms of the reaction free energy under standard conditions,

, and in terms of the reaction’s product concentrations (index k ) and those of its reactants (index j ) where a k and a j represent coefficients of stoichiometry for the reaction (Beard and Qian, 2007 ; Pekar, 2015 ):

…”

Section: Methodsmentioning

confidence: 99%

Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine

Pietak

Levin

2016

Front. Bioeng. Biotechnol.

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Bioelectric cell properties have been revealed as powerful targets for modulating stem cell function, regenerative response, developmental patterning, and tumor reprograming. Spatio-temporal distributions of endogenous resting potential, ion flows, and electric fields are influenced not only by the genome and external signals but also by their own intrinsic dynamics. Ion channels and electrical synapses (gap junctions) both determine, and are themselves gated by, cellular resting potential. Thus, the origin and progression of bioelectric patterns in multicellular tissues is complex, which hampers the rational control of voltage distributions for biomedical interventions. To improve understanding of these dynamics and facilitate the development of bioelectric pattern control strategies, we developed the BioElectric Tissue Simulation Engine (BETSE), a finite volume method multiphysics simulator, which predicts bioelectric patterns and their spatio-temporal dynamics by modeling ion channel and gap junction activity and tracking changes to the fundamental property of ion concentration. We validate performance of the simulator by matching experimentally obtained data on membrane permeability, ion concentration and resting potential to simulated values, and by demonstrating the expected outcomes for a range of well-known cases, such as predicting the correct transmembrane voltage changes for perturbation of single cell membrane states and environmental ion concentrations, in addition to the development of realistic transepithelial potentials and bioelectric wounding signals. In silico experiments reveal factors influencing transmembrane potential are significantly different in gap junction-networked cell clusters with tight junctions, and identify non-linear feedback mechanisms capable of generating strong, emergent, cluster-wide resting potential gradients. The BETSE platform will enable a deep understanding of local and long-range bioelectrical dynamics in tissues, and assist the development of specific interventions to achieve greater control of pattern during morphogenesis and remodeling.

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The Thermodynamic Driving Force for Kinetics in General and Enzyme Kinetics in Particular

Cited by 13 publications

References 4 publications

Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State

Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State

Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State

Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine

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