scholarly journals Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates

2011 ◽  
Vol 100 (10) ◽  
pp. 2475-2485 ◽  
Author(s):  
Benzhuo Lu ◽  
Y.C. Zhou
Keyword(s):  
Size Effects ◽  
Reaction Rates ◽  
Diffusion Reaction ◽  
Reaction Processes ◽  
And Diffusion

scholarly journals A biochemo-mechano coupled, computational model combining membrane transport and pericellular proteolysis in tissue mechanics

2017 ◽  
Vol 473 (2199) ◽  
pp. 20160812 ◽  
Author(s):  
A.-T. Vuong ◽  
A. D. Rauch ◽  
W. A. Wall
Keyword(s):  
Porous Medium ◽  
Computational Model ◽  
Solid Phase ◽  
Chemical Species ◽  
Reaction Rates ◽  
Tissue Mechanics ◽  
Diffusion Reaction ◽  
Advection Diffusion ◽  
Reaction Processes ◽  
Pericellular Proteolysis

We present a computational model for the interaction of surface- and volume-bound scalar transport and reaction processes with a deformable porous medium. The application in mind is pericellular proteolysis, i.e. the dissolution of the solid phase of the extracellular matrix (ECM) as a response to the activation of certain chemical species at the cell membrane and in the vicinity of the cell. A poroelastic medium model represents the extra cellular scaffold and the interstitial fluid flow, while a surface-bound transport model accounts for the diffusion and reaction of membrane-bound chemical species. By further modelling the volume-bound transport, we consider the advection, diffusion and reaction of sequestered chemical species within the extracellular scaffold. The chemo-mechanical coupling is established by introducing a continuum formulation for the interplay of reaction rates and the mechanical state of the ECM. It is based on known experimental insights and theoretical work on the thermodynamics of porous media and degradation kinetics of collagen fibres on the one hand and a damage-like effect of the fibre dissolution on the mechanical integrity of the ECM on the other hand. The resulting system of partial differential equations is solved via the finite-element method. To the best of our knowledge, it is the first computational model including contemporaneously the coupling between (i) advection–diffusion–reaction processes, (ii) interstitial flow and deformation of a porous medium, and (iii) the chemo-mechanical interaction impelled by the dissolution of the ECM. Our numerical examples show good agreement with experimental data. Furthermore, we outline the capability of the methodology to extend existing numerical approaches towards a more comprehensive model for cellular biochemo-mechanics.

scholarly journals Time-Space Characterization of Wellbore-Cement Alteration by CO2-Rich Brine

Geosciences ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 490
Author(s):  
Maria Garcia-Rios ◽  
Philippe Gouze
Keyword(s):  
Numerical Models ◽  
Reaction Rates ◽  
Diffusion Reaction ◽  
Cement Matrix ◽  
Relative Distribution ◽  
Reaction Fronts ◽  
Time Space ◽  
Mass Transfers ◽  
Dissolution And Precipitation ◽  
Diffusion Properties

The risk of CO2 leakage from damaged wellbore is identified as a critical issue for the feasibility and environmental acceptance of CO2 underground storage. For instance, Portland cement can be altered if flow of CO2-rich water occurs in hydraulic discontinuities such as cement-tubing or cement-caprock interfaces. In this case, the raw cement matrix is altered by diffusion of the solutes. This fact leads to the formation of distinctive alteration fronts indicating the dissolution of portlandite, the formation of a carbonate-rich layer and the decalcification of the calcium silicate hydrate, controlled by the interplay between the reaction kinetics, the diffusion-controlled renewing of the reactants and products, and the changes in the diffusion properties caused by the changes in porosity induced by the dissolution and precipitation mechanisms. In principle, these mass transfers can be easily simulated using diffusion-reaction numerical models. However, the large uncertainties of the parameters characterizing the reaction rates (mainly the kinetic and thermodynamic coefficients and the evolving reactive surface area) and of the porosity-dependent diffusion properties prevent making reliable predictions required for risk assessment. In this paper, we present the results of a set of experiments consisting in the alteration of a holed disk of class-G cement in contact with a CO2-rich brine at reservoir conditions (P = 12 MPa and T = 60 °C) for various durations. This new experimental protocol allows producing time-resolved data for both the spatially distributed mass transfers inside the cement body and the total mass transfers inferred from the boundary conditions mass balance. The experimental results are used to study the effect of the fluid salinity and the pCO2 on the overall reaction efficiency. Experiments at high salinity triggers more portlandite dissolution, thinner carbonate layers, and larger alteration areas than those at low salinity. These features are accompanied with different spatial distribution of the alteration layers resulting from a complex interplay between salinity-controlled dissolution and precipitation mechanisms. Conversely, the effect of the pCO2 is more intuitive: Increasing pCO2 results in increasing the overall alteration rate without modifying the relative distribution of the reaction fronts.

scholarly journals Viscoadaptation controls intracellular reaction rates in response to heat and energy availability

2019 ◽  
Author(s):  
Laura Persson ◽  
Vardhaan S. Ambati ◽  
Onn Brandman
Keyword(s):  
Cellular Response ◽  
Reaction Rates ◽  
Acute Response ◽  
Cellular Environment ◽  
Diffusion Controlled ◽  
Intracellular Diffusion ◽  
Response To Temperature ◽  
And Diffusion ◽  
Tunable Property ◽  
Multiple Conditions

Summary/AbstractCells must precisely orchestrate thousands of reactions in both time and space. Yet reaction kinetics are highly dependent on uncontrollable environmental conditions such as temperature. Here, we report a novel mechanism by which budding yeast influence reaction rates through adjustment of intracellular viscosity. This “viscoadaptation” is achieved by production of two carbohydrates, trehalose and glycogen, which combine to create a more viscous cellular environment in which biomolecules retain solubility. We demonstrate that viscoadaptation functions as both an acute response to temperature increase as well as a homeostatic mechanism, allowing cells grown at temperatures spanning from 22°C to 40°C to maintain equivalent rates of intracellular diffusion and diffusion-controlled chemical reactions. Multiple conditions that lower ATP trigger viscoadaptation, suggesting that viscoadaptation may be a general cellular response to low energy. Viscoadaptation reveals viscosity to be a tunable property of cells through which they can regulate diffusion-controlled processes dynamically in response to a changing environment.

CHEMICAL TESSELLATIONS — RESULTS OF BINARY AND TERTIARY REACTIONS BETWEEN METAL IONS AND FERRICYANIDE OR FERROCYANIDE LOADED GELS

2010 ◽  
Vol 20 (07) ◽  
pp. 2241-2252 ◽  
Author(s):  
B. P. J. DE LACY COSTELLO ◽  
I. JAHAN ◽  
P. HAMBIDGE ◽  
K. LOCKING ◽  
D. PATEL ◽  
...  
Keyword(s):  
Metal Ions ◽  
Voronoi Diagram ◽  
Metal Salt ◽  
Voronoi Diagrams ◽  
Reaction Rates ◽  
Cross Reactivity ◽  
Diffusion Reaction ◽  
Reactive Metal ◽  
Simple Chemical ◽  
Pattern Forming

In our recent letter [de Lacy Costello et al., 2009] we described the formation of spontaneous complex tessellations of the plane constructed in simple chemical reactions between drops of metal salts and ferricyanide or ferrocyanide loaded gels. In this paper, we provide more examples of binary tessellations and extend our analysis to tessellations constructed via tertiary mixtures of reactants. We also provide a classification system which describes the tessellation based on the reactivity of the metal salt with the substrate and also the cross-reactivity of the primary products. This results in balanced tessellations where both reactants have equal reactivity or unbalanced tessellations where one reactant has a lower reactivity with the gel. The products can also be partially or fully cross reactive which gives a highly complex tessellation. The tessellations are made up of colored cells (corresponding to different metal ferricyanides or ferrocyanides) separated by bisectors of low precipitate concentration. The tessellations constructed by these reactions constitute generalized Voronoi diagrams. In the case of certain binary or tertiary combinations of reactants where the diffusion/reaction rates differ, then multiplicatively weighted crystal growth Voronoi diagrams are constructed. Where one reactant has limited or no reactivity with the gel (or the products are cross reactive) then the fronts originating from the reactive metal ions cross the fronts originating from the partially reactive metal ions. The fronts can annihilate in the formation of a second Voronoi diagram relating to the relative positions of the reactive drops. Therefore, two or more generalised or weighted Voronoi diagrams can be calculated in parallel by these simple chemical systems. However when these reactions were used to calculate an additively weighted Voronoi diagram (the reaction was initiated at different time intervals) the diagram constructed did not correspond to the theoretical calculation. We use the failure of these reactions to construct an additively weighted Voronoi diagram to prove a mechanism of substrate competition for bisector formation. These tessellations are an important class of pattern forming reactions and are useful in modeling natural pattern forming phenomena in addition to being a great resource for scientific demonstrations.

A computational model for diffusion-reaction-deformation coupled problems and its finite element implementation

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Bao Qin ◽  
Yexin Zhou ◽  
Zheng Zhong
Keyword(s):  
Finite Element ◽  
Chemical Reaction ◽  
Reaction Rate ◽  
Diffusion Processes ◽  
Diffusion Reaction ◽  
Governing Equations ◽  
Content Type ◽  
Finite Element Software ◽  
And Diffusion ◽  
Reaction And Diffusion

PurposeA diffusion-reaction-deformation coupled model is employed and implemented as a user-defined element (UEL) subroutine in the commercial finite element software package ABAQUS.Design/methodology/approachChemical reaction and diffusion are treated as two distinct processes by introducing the extent of reaction and the diffusion concentration as two kinds of independent variables, for which the independent governing equations for chemical reaction and diffusion processes are obtained. Furthermore, an exponential form of chemical kinetics, instead of the linearly phenomenological relation, between the reaction rate and the chemical affinity is used to describe reaction process. As a result, complex chemical reaction can be simulated, no matter it is around or away from equilibrium.FindingsTwo numerical examples are presented, one for validation of the model and another for the modeling of the deflection of a plane caused by a chemical reaction.Originality/value1. Independent governing equations for diffusion and reaction processes are given. 2. An exponential relation between the reaction rate and its driving force is employed. 3. The UEL subroutine is used to implement the finite element procedure.

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