Yang Et Al 2018

RESEARCH ARTICLE
Patterns of entropy production in dissolving

natural porous media with flowing fluid
Y. Yang ID*, S. Bruns ID, S. L. S. Stipp, H. O. Sørensen ID
Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
* yiyang@nano.ku.dk
a1111111111 Abstract
a1111111111
a1111111111 The tendency for irreversible processes to generate entropy is the ultimate driving force for
a1111111111 structure evolution in nature. In engineering, entropy production is often used as an indicator
a1111111111 for loss of usable energy. In this study, we show that the analysis of entropy production pat-
terns can provide insight into the diverse observations from experiments that investigate
porous medium dissolution in imposed flow field. We first present a numerical scheme for
the analysis of entropy production in dissolving porous media. Our scheme uses a greyscale
OPEN ACCESS digital model for chalk (an extremely fine grained rock), that was obtained using X-ray nano-
Citation: Yang Y, Bruns S, Stipp SLS, Sørensen HO tomography. Greyscale models preserve structural heterogeneities with very high fidelity.
(2018) Patterns of entropy production in dissolving We focussed on the coupling between two types of entropy production: the percolative
natural porous media with flowing fluid. PLoS ONE
entropy, generated by dissipating the kinetic energy of fluid flow, and the reactive entropy,
13(9): e0204165. https://doi.org/10.1371/journal.
pone.0204165 originating from the consumption of chemical free energy. Their temporal patterns pinpoint
three stages of microstructural evolution. We then showed that local mixing deteriorates
Editor: Amitava Mukherjee, VIT University, INDIA
fluid channelisation by reducing local variations of reactant concentration. We also showed
Received: May 4, 2018
that microstructural evolution can be sensitive to the initial transport heterogeneities, when
Accepted: September 3, 2018 the macroscopic flowrate is low. This dependence on flowrate indicates the need to resolve
Published: September 20, 2018 the structural features of a porous system when fluid residence time is long.
Copyright: © 2018 Yang et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited.
Introduction
Data Availability Statement: All data needed to
The production of entropy in irreversible processes drives the emergence and transformation
evaluate the conclusions are presented in the of many structures in nature [1, 2]. Spatial and temporal patterns of entropy production can
paper. help us understand the diversity and the self-organisation inherent to many complex systems
Funding: Funding for this project was provided by
[3, 4]. In engineering, all loss of usable work can be monitored in units of entropy generation
the European Union Horizon 2020 Research and as a currency [5]. Reactive infiltration instability stems from positive feedback between the
Innovation Programme under the Marie coupling of chemical reaction and mass transfer and induces the development of a wide variety
Sklodowska-Curie grant no. 653241, https://cordis. of biotic and abiotic flow systems [6–10]. Predicting the development of flow systems in
europa.eu/project/rcn/194840_en.html; the porous media is essential for many energy and environmental applications, such as geologic
Innovation Fund Denmark through the CINEMA
carbon storage [11], oil reservoir simulation [12], bioremediation [13] and in situ contaminant
project, http://www.cinema-dsf.dk/; the Innovation
Fund Denmark and Maersk Oil and Gas A/S
remediation [14]. Characterising the inherent heterogeneities of a porous material is impor-
through the p3 project, https://innovationsfonden. tant because infiltration instability can amplify transport heterogeneities indefinitely [15, 16].
dk/en/node/660. The funders had no role in study It is thus desirable to use nondestructive, three dimensional imaging techniques, such as high
PLOS ONE | https://doi.org/10.1371/journal.pone.0204165 September 20, 2018 1 / 20

Patterns of entropy production in dissolving natural porous media with flowing fluid
design, data collection and analysis, decision to resolution X-ray tomography [17–20], to obtain greyscale microstructure models of porous
publish, or preparation of the manuscript. media [21, 22]. Because of the information preserved in these models, analysis of entropy pro-
Competing interests: During the course of the duction can be carried out with very high fidelity [17].
research, our team has received funding from In this study, we treated a porous medium as a thermodynamic device that constantly dissi-
Maersk Oil and Gas A/S. Funding received from pates the energy it receives from the environment. The evolution of the device’s internal struc-
commercial affiliations does not alter our
ture is affected by its initial morphology and the energy input. The initial morphology dictates
adherence to PLOS ONE policies on sharing data
and materials. the pre-existing heterogeneities in the transport properties of the medium, while the energy
input describes the different forms of energy that are dissipated by the device. Here we focus
on the kinetic energy of fluid flow and the chemical energy of reactive solutes.
Fig 1 shows four examples of a simulated, developing flow system, where a reactive fluid is
injected at the centre of a dissolving 2D porous medium. With different properties of fluid
flow, very different morphologies and patterns of entropy production can develop from pre-
cisely the same initial geometry. Experimentally, such a study can be almost impossible to per-
form because the initial geometry is inevitably destroyed after each experiment. Currently
available manufacturing technology has not yet made it possible to reliably replicate natural
geologic materials with identical geometry and local chemical homogeneity at the submicro-
metre level. In this study, we analysed numerically the effects of global fluid input on energy
dissipation in a natural porous material with a fixed initial geometry. The geometric profile
was obtained from a nanometre resolution tomogram of a chalk sample [23].
Chalk is a frequent host rock for drinking water aquifers, oil and gas reservoirs and because
of its calcium carbonate composition, it serves as a useful model for a fast reacting rock. Chalk
is dominated by the shields of coccolithophorids. These shields, called coccoliths, consist of
nanometre to submicrometre sized single calcite crystals, that are irregular in size, shape and
orientation [24]. Characterising the microstructure in chalk at the pore scale is difficult
because of its extremely small grain size and its geometric complexity so chalk also serves as an
excellent model for testing the resolution limits in our work. The complexities are encoded in
the greyscale intensities in tomography reconstructions. They were preserved in the 3D images
by avoiding simplification, which would usually arise from segmenting the reconstruction. We
transferred the greyscale intensities to a material density representation, which maintains com-
parability between samples. Our aim was to present a mathematical scheme that uses the
derived voxel level porosity in simulations of entropy production and to show: (i) that three
stages of microstructural evolution during dissolution result in distinct temporal patterns in
entropy generation, (ii) that local mixing deteriorates reaction front instability and (iii) that
transport heterogeneities become more important when the macroscopic flowrate is low.
Reactive infiltration instability has been formulated mathematically by pioneers of geo-
chemical transport modelling [6–9, 15, 16, 25–29]. This work aims to incorporate a high reso-
lution greyscale nanotomography reconstruction of a natural porous material into an
irreversibility analysis. This inclusion of realistic geometries is useful because of the sensitivity
of the reaction front propagation to spatial heterogeneities [28]. Therefore, by fixing the initial
geometry, our results allow us to unambiguously define the influence of global energy con-
straints on morphology evolution. It is also possible to put the much diversified and sometimes
inconsistent experimental observations from real reactive percolation systems into a coherent
big picture [30].
Material and methods

We used a previously published static tomogram of Hod chalk (HC16) from the North Sea
Basin, collected with the X-ray holotomography setup at the ID22 beamline at the European
Synchrotron Research Facility (ESRF), in Grenoble, France [31]. This data set offers high

Fig 1. Example morphologies of simulated, developing flow systems dominated by infiltration instability. A dissolutive fluid is
injected from the centre of the 2D domain, which consists of 4 million, i.e. 2000 by 2000, reacting units. The colours correspond to the
apparent solid dissolution rate (yellow means greater rates). (a) a system where development is limited by fluid reactivity, i.e. fluid
reaches equilibrium before it leaves each simulation domain; (b): a system where development is limited by solid availability, i.e. the solid
depletes locally before the fluid reaches chemical equilibrium; (c) a system with a low injection rate compared with (d) a high injection
rate.
https://doi.org/10.1371/journal.pone.0204165.g001
spatial resolution and has been shown to be most amenable to the image processing algorithms
developed by our team in a few related studies [32–37]. The data were reconstructed from
1999 radiographs (360˚ rotation, 0.5 s exposure) at 100 nm voxel resolution using the holoto-
mography reconstruction method [23, 31] and processed as described in Bruns et al. [35, 36].
The goal of the processing routine was to generate a greyscale volume image where variations
in voxel intensity could be related to local material density, i.e. greyscale variations resulted
from partial volume effects and not from signal blur, noise or artefacts. The average intensities
of these phases are initially unknown so we used a seven phase Gaussian mixture model to

identify the most likely intensities for the chalk and void phases, resulting in a macroscopic
porosity of 0.22 for the 1350×1350×1514 voxel reconstruction. From this reconstruction, a
subvolume sample of 60×60×300 voxels (6×6×30 μm3) were chosen and subjected to a general
dissolution reaction, which we can write for Material A as: A (solid) , A (aqueous).
We adopted the model framework of Yang et al. [32–34, 37]. The mathematical scheme is
designed to treat the assemblage of greyscale voxels as a network of ideal chemical reactors.
Any structural feature that is smaller than a voxel size is homogenized in a greyscale tomo-
graphic data set. Nevertheless, greyscale data contain more microstructure information than
binarised (segmented) data. This is because the voxel intensity that translates to porosity
through the Gaussian mixture model is a function of X-ray absorbance. A porosity value
between 0 and 1 indicates that a real structure exists inside that voxel and the magnitude of the
intensity reflects the density of the material. In a 32-bit greyscale data set, 232 different sub-
voxel possibilities can be registered. In comparison, voxels in a segmented tomogram can only
take two values.
The advantage of preserving information of structure smaller than a voxel in numerical
simulation is meaningful for two reasons. First, chalk is a rock with very fine grains, whose fea-
tures are difficult to be fully resolved. Yet small heterogeneities can be important in distorting
the morphology of migrating reaction front and as a result, shaping the porous structure devel-
opment. Having an alternative mathematical scheme, which offers the possibility to import
these features into numerical simulation, can be very useful. Second, governing equations that
are derived from first principles, e.g. the NS equations, can only be applied to void space with
explicit surface boundaries. These equations are better grounded on physics than the phenom-
enological equations that describe chemical reactor behaviours. However, in pursue of the
overall physical realism, one needs to consider both the governing equations and the geometry
to start with. It remains to be seen whether the gain in the physical soundness can compensate
for the significant loss of microstructural information when a segmented initial geometry is
used.
The following equations quantify voxel behaviour–each voxel is considered phenomenolog-
ically as a set of ideal chemical reactors. These reactors are the elementary units in the numeri-
cal simulation that follows. I.e. the scheme is inherently discrete. The equations used in the
simulation are summarised below. In the model, all physical quantities were first normalised
to reduce the total number of parameters:
Q l P CA;eq CA
q¼ ; ln ¼ ; p¼ and C ¼ ; ð1Þ
Q0 Lref Pref CA;eq CA;inj
where Q represents the voxel level volumetric flowrate (m3/s), l, the voxel size (nm) and P, the
pressure (Pa). Q0, Lref and Pref represent the reference values, which can be chosen arbitrarily.
In this study, they were given the following values:
" #1:5
ðm0A þ RT ÞðCA;eq CA;inj Þ
Q0 ¼ ; ð2Þ
kA0 1=3 mðφexp =kexp Þ
sffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
ðm0A þ RT ÞðCA;eq CA;inj Þ
Lref ¼ ; and ð3Þ
kA0 mðφexp =kexp Þ
Pref ¼ ðm0A þ RT ÞðCA;eq CA;inj Þ; ð4Þ
where m0A represents the reference chemical potential of A (kJ/mol), R, the universal gas

constant (kJ/molK), T, the temperature (K), μ, viscosity of the fluid (Pas), φexp and kexp, the
experimentally measured porosity and permeability (m2) of the sample [23], and kA0, the
apparent first order rate constant of the dissolution reaction (s-1), defined as:
rA0 =ssa
kA0 ¼ ; ð5Þ
C0 ðCA;eq CA;inj Þ
where ssa represents the voxel level specific surface area (m2/m3) and CA, the concentration of
A at the exit of a voxel (mol/m3). CA,eq and CA,inj represent the equilibrium concentration and
the concentration of A in the injection fluid (mol/m3). C0 represents the dimensionless con-
centration at the inlet of a voxel (i.e., corresponding to CA0) and rA0 represents the dissolution
rate (mol/m2s) where C = C0.
The pressure drop across a voxel is simplified to follow Darcy’s law:
" !#
Pref Lref kexp
q¼ ðln φ2 Þ Dp; ð6Þ
m Q0 φexp
in which φ represents the voxel level porosity. The voxel level tortuosity and permeability are
expanded around zero with respect to the empty volume in each voxel. The truncation error is
expected to decrease with the voxel size, ln.
For each voxel, the continuity equation for an incompressible fluid applies at the center:
P6
i¼1 qi þ qs ¼ 0: ð7Þ
where qi is the volumetric flow from the six neighbouring voxels and qs, from the
environment.
The macroscopic fluid distribution was determined, based on the permeability tensor:
Κ ¼ NxKxNxT þ NyKyNy T þ NzKzNzT ; ð8Þ
where Nx, Ny and Nz are nodal matrices along the three Cartesian axes and Kx, Ky and Kz are
diagonal matrices containing voxel level permeability values. The pressure field can be calcu-
lated using
QS ¼ Κp; ð9Þ
where Qs and p represent vectors that describe the global constraints on the system and its
pressure field.
In each voxel, the chemical conversion in the subvolume with complete mixing was calcu-
lated to be:
P
i qi C0i þ ð1 þ DaÞ qC ¼ 0; ð10Þ
in which i indicates the summation over all inlets of reactive fluid and the Damköhler number,
Da, is defined as:
!
rA0 L3ref 3 ssa
Da ¼ Z ln ; ð11Þ
C0 ðCA;eq CA;inj Þ Q0 q
where η represents the portion of a voxel within which reactants and products are completely
mixed. The conversion in the nonmixing subvolume was calculated from
C0 þ eDa C ¼ 0; ð12Þ

where the reactor volume in Da takes a different value:

!
rA0 L3ref 1 Z 3 ssa
Da ¼ ln : ð13Þ
C0 ðCA;eq CA;inj Þ Q0 3 q
The dissolution reaction is assumed to be much slower than establishing the velocity profile
and the voxel level porosities was updated according to:

CA;eq CA;inj dt
ðZ dφÞi ¼ qðC0 CÞ ðQ0 =L3ref Þ 3 : ð14Þ
r=M ln
It is worth emphasising that the aforementioned modules–the governing equations for fluid
flow and for solute transport (e.g., Eqs 6–9), the fidelity of the initial geometry (the tomo-
graphic dataset) as well as the kinetics of mineral dissolution (the linear rate law used in this
study to derive Eqs 10–13)–can be replaced by their counterparts. And more accurate physical
representations of these modules will produce more realistic simulation results. We chose to
use these equations because they allowed us to put into the context of a physically realistic rock
microstructure the following general system behaviours. First, given a constant macroscopic
flowrate, fluid tends to be distributed according to local permeability differences, and more
porous materials are more permeable. Second, the rate of mineral dissolution relies on the
chemical affinity of the dissolution reaction, which in turn relies on the residence time of the
stream. Third, the presence of inherent transport heterogeneities distorts the morphology of
migrating dissolution front. To give a qualitative description of the consequences stemming
from these behaviours, we define the following entropy production terms. Percolative entropy
generation (Sgen, per) is the rate of entropy production in flow with friction [5]. It is propor-
tional to the volumetric flowrate and the pressure drop in each voxel and is calculated using:
! ," !#
T S_ gen;per q2 Pref Lref kexp
¼ 2 : ð15Þ
Q0 Pref ln φ m Q0 φexp
The reactive and mixing entropies were not distinguished because the chemical conversion
in each reactor is inherently determined by its extent of mixing. The reactive entropy term is
therefore calculated as the change in Gibbs free energy on the voxel scale:
S_ gen;rxn ¼ ðm0A =T þ RÞðCA;eq CA;inj ÞQ0 q ðC0 CÞ: ð16Þ
Results
Three stages of microstructural evolution that show distinct patterns of
entropy generation
Fig 2 shows the initial geometry for the porous medium used in this study and the temporal
patterns of entropy generation by the various mechanisms. The geometry is modelled using a
greyscale tomography reconstruction that realistically represents the microstructure of a 6 x 6
x 30 μm3 sample of North Sea Basin chalk, with a macroscopic, i.e. volume averaged, porosity
of 0.20. The volume consists of 1.08×106 voxels (1003 nm3 each) and the porosity of each voxel
is represented by a 32 bit real number. We simulated an injection of reactive fluid from the
inlet (yellow plane in Fig 2A) to the outlet (blue plane). The normalized percolative entropy,
SP, is an integral of entropy generated over the simulation domain for overcoming fluid fric-
tion and serves as a measure of kinetic energy dissipation. The reactive entropy, SR, is


Fig 2. Temporal pattern of percolative and reactive entropy production based on a 32 bit greyscale tomography
reconstruction of chalk. (a) Perspective view of the simulation domain where the initial porosity is 0.20; (b) temporal
patterns of entropy generation divide the microstructural evolution into three stages: induction, breakthrough and
stabilisation. The volume averaged, i.e. macroscopic, porosity is used as a measure for the overall reaction progress.
The blue curve shows the evolution of SP, the percolative entropy production, and corresponds to the left axis; the red
curve shows SR and corresponds to the right axis (indicated by arrows). The dimensionless quantities are normalised
with respect to combinations of reference temperature (T), flowrate (Q0), pressure (P0) and Gibbs free energy (-ΔGref).
The equations are marked next to the plots. The two curves are rescaled using their initial and final values.
calculated based on changes of Gibbs free energy in each and every voxel and is a measure of
chemical energy dissipation.
The temporal patterns of percolative entropy, SP, and reactive entropy, SR, showed three
stages during the microstructure evolution: induction, breakthrough and stabilisation (Fig
2B). During the induction phase, SR remained on a plateau because the residence time was suf-
ficiently long that the fluid reactivity was depleted, i.e. it reached chemical equilibrium before
arriving at the outlet. By monitoring the effluent composition, one might naïvely conclude that
the system had reached steady state. However, tracking SP revealed the system dynamics. Per-
colative entropy generation decreased nonlinearly because mineral dissolution led to the devel-
opment of a dominant flow path within the complex geometry. This development started from
the inlet and the dissolution front in that pathway advanced gradually downstream, preferen-
tially removing solid material in the more porous voxels (Fig 3, porosity). This biased removal
is characteristic of reactive infiltration instability, which amplifies local differences in
permeability.
The arrival of the reaction front at the outlet (Fig 3, reactive entropy at dimensionless time,
τ = 50) marked the start of the breakthrough stage. During breakthrough, a significant increase
in macroscopic permeability was accompanied by a shift in the spatial pattern of percolative
entropy generation. The newly developed major flow path connected the fluid inlet and outlet,
thereby channelling the fluid. This minimizes the energy dissipation for overcoming flow resis-
tance. Before this change took place, regions with lower porosity generated more percolative
entropy (Fig 3, porosity and percolative entropy, τ = 50). After breakthrough, this pattern
reversed as a result of fluid channelling (Fig 3, τ = 108 and onward). It is noted that the macro-
scopic flowrate was kept constant throughout the microstructure development. When a differ-
ent boundary condition applies, e.g. if a constant pressure difference is imposed, the overall
flux should increase with the rising permeability, and more viscous entropy would have been
produced. And this difference would have been reflected in the slope of the SP curve near the
inflection point. Meanwhile, SR began to decrease as a result of shortened residence time. The
last inflection point in SP marked the end of breakthrough and the beginning of a stabilisation
phase. During stabilisation, SP was dominated by the expansion of the major flow path and
decreased gradually until all solid was depleted. Reactive entropy generation was limited to
regions where sharp gradients of porosity were observed (Fig 3, τ = 300). These regions can be
physically interpreted as solid-fluid interfaces and this change in the spatial pattern marked a
transition from advection driven reaction pattern to one that is dominated by interfacial
interactions.
Local mixing deteriorates fluid channelisation

Mixing can be considered the net effect of solute transport. Different transport mechanisms
produce different mixing patterns. For example, convection preserves the composition of the
bulk flow while diffusion is driven by concentration gradients and tends to smear out spatial
variations in the solute distribution. Hence, diffusion enhances mixing whereas convection

Fig 3. Patterns of entropy production during microstructural evolution. (a) Temporal pattern. The black, blue and
red curves show the evolution of macroscopic porosity, percolative entropy and reactive entropy production rate. The
three stages of structure development are colour-shaded: yellow–induction; green–breakthrough; blue–stabilisation.
Five representative instants are chosen from the timeline (marked by yellow vertical lines in a) and visualised in (b). (b)
Spatial patterns–porosity distribution (grey, first row), percolative entropy (yellow-blue, second row) and reactive
entropy (red-black, third row). The 3D perspective views are isosurface drawn at a handpicked value of the
corresponding quantity. The rectangular and square images (sheets above and below each three-dimensional figure)
are cross sections of the corresponding quantities at the middle of the radial and the axial directions (indicated by
semi-transparent boxes imposed on the perspective views). The colour bars indicate the dimensionless, numerical
values of the corresponding quantity. The pattern of percolative entropy generation inverses after breakthrough
because of fluid channelling. The spatial patterns of reactive entropy visualise the dissolving regions in the pore
structure.
does not. In this study, we did not distinguish among transport mechanisms. Instead, we ana-
lysed the net effect of mixing on the chemical conversion of reactants. This analysis was done
by adjusting the contact pattern between reactant and product at the voxel level. A dimension-
less parameter, η, was used for this purpose. η represents a continuous function that varies
between 0 and 1. When η = 0, there is no mixing between reactant and product as a reaction
takes place; when η = 1, reaction happens only when the reactant and the product are
completely mixed. A simplistic analogy can be drawn between η and the Péclet number (Pe)
on the voxel level. η close to 1 corresponds to a small Pe, i.e., a transport mechanism that
enhances mixing (e.g. molecular diffusion) dominates. Similarly, η close to 0 corresponds to a
large Pe. The caveat of adopting η is that one cannot predict precisely the system behaviour.
Instead, η allows bracketing the possible outcomes of a real system by two extreme cases (η = 0
and 1). Assigning a single value of η to all voxels in a dataset also ignores local heterogeneity in
the strength of molecular transport, which might not be appropriate when the scale of the sys-
tem is large. Nevertheless, we consider η to be a general descriptor of mixing phenomena in
this study because it is not limited to any specific combination of transport mechanisms and
because of the moderate scale of the simulation domain.
Mixing protracts the development of the major flow path and delays the occurrence of
breakthrough (Fig 4A). This delay is because mixing counteracts the instability that drives the
morphing of the system. The evolution of the microstructure, especially the development of
the major flow path, is induced by infiltration instability. This instability provides a positive
feedback between mass transfer and mineral dissolution. The net observable effect is autocata-
lytic, i.e. flow and reaction enhance each other locally. Mixing introduces a negative feedback
to this chain of coupling by reducing the reactant concentration and therefore the rate of the
dissolution. This negative feedback can only be observed when the reaction rate increases


Fig 4. Impact of voxel level mixing on entropy production. η = 1 corresponds to complete mixing and η = 0, to no
mixing between reactant and product. (a) Mixing effect on the temporal patterns of entropy generation. Percolative
entropy was affected monotonically by mixing while reactive entropy was affected by two counteracting effects. (b)
Cross sections of porosity distribution. The solid-liquid interface is sharpened near the fluid inlet, showing a rapid
spatial transition from pure solid to pure fluid within a few voxels. (c) Distribution of reactive entropy production
shows highly localised dissolving regions. Brighter means more dissolution. Mixing leads to a longer residence time
and higher surface smoothness. Macroscopic porosity = 0.5 in (b) and (c).
monotonically with chemical affinity. This prerequisite is met by a wide range of geochemical
reactions that follow a transition state theory (TST) rate law.
The effect of mixing on SP escalates as the main flow path develops toward the outlet, reach-
ing a maximum during the breakthrough stage. It then diminishes rapidly during stabilisation.
This variation can be attributed to the sensitivity of the percolation entropy generation to the
geometric complexity of a porous medium before the development of a main flow path. This
flow path advanced faster without mixing, hence SP was low when η was small. For example,
for a volume with average porosity of 0.53, a 43% difference between η = 0 and 1 was observed
for the mechanical energy dissipation, suggesting that more energy was needed to drive the
same amount of fluid through an evolving microstructure. After breakthrough, the pressure
drop was determined by the permeability of the major flow path and SP became insensitive to
mixing in the solid residual.
Fig 4B and 4C show cross sections (x = 30 μm) of the microstructure and the corresponding
spatial patterns of reactive entropy generation in two limiting cases of micromixing. Because
the impact of η is monotonic on SP (Fig 4A), one could expect that the porosity distribution
resembles an interpolation of the two images at an intermediate micromixing (η = 0.5).
Regions of interest (ROIs) are highlighted with rectangular boxes. The temporal patterns of SR
suggest that, with decreased mixing, the reactive fluid becomes more penetrating and the reac-
tion front reaches the outlet with less solid dissolved (upper right inset in Fig 4A). This effect is
manifested in Fig 4B, given the same overall porosity, stronger mixing (η = 1) results in more
thorough dissolution of the upstream materials (ROI1) but with a less developed pore struc-
tures downstream (ROIs 2–4). As a consequence, mixing led to increased residence time, leav-
ing fewer voxels partially filled with solid.
These two aspects exerted opposite influences on reactive entropy generation. Long resi-
dence time enhances the chemical conversion and thus increases SR. Meanwhile, a decrease in
the number of intermediate grey voxels can be physically interpreted as generation of a
smoother surface on the material, which leads to a drop in reactive surface area and hence, SR.
These counteracting factors result in a complex temporal pattern of entropy generation. Before
breakthrough, residence time dominated the chemical conversion. A system with better mix-
ing dissipates more chemical energy. After breakthrough, the residence time quickly con-
verged to a single value that was determined by the major flow path. Therefore, a system with
less mixing produces more reactive entropy than a well-mixed system. Fig 4A shows this tran-
sition between these cases: the apparent insensitivity of SR to mixing during the breakthrough
stage is actually a superposition of two contradicting effects. During the stabilisation stage, SR
was greater for systems with a “rougher” surface (in a porosity distribution image, a sharp
interface is manifested by a rapid transition from black to white pixels, in the absence of transi-
tional, grey features; in a reactive entropy production map, a sharp interface is indicated by
bright, thin lines).
Fig 4C shows that while the overall SR was similar for both systems at φ = 0.5, less mixing
led to weaker but more dispersed entropy hotspots (ROIs 5–7). In contrast, when η = 1 the sys-
tem showed sharp and bright entropy hotspots along the interfaces upstream but far less so

downstream. In general, more mechanical energy is needed to drive the evolution of a porous
medium toward complete dissolution when mixing is strong. We would like to emphasize that
the overall entropy production is not conservative–because the two types of entropy are not
produced from the same type of energy input. However, their patterns do correlate and can be
interpreted from the mass transfer perspective. Both the porosity distribution and the spatial
distribution of reactive entropy production are ultimately affected by the morphology of solid-
fluid interface, where the rock erodes. But this effect is not instantaneous and will only become
clear as time elapses. The impact of local mixing is to “blur” the solid-liquid interface. This
blurring stems from the tendency of mixing that reduces the gradient of solute concentration
(and this effect is instantaneous and observable within the same time step).
Greater flow rate reduces the impact of initial heterogeneities

In this study, porous media are considered thermodynamic devices that dissipate the energy
they receive from the environment. It is thus of interest to investigate the effects of a global con-
straint, i.e. the total amount of energy that a medium receives, on the microstructural evolution.
We used the macroscopic flow rate as a measure of this global constraint because it reflects both
the energy requirement for overcoming the resistance to the fluid flow and the amount of chem-
ical reactant input given the same solvent composition. Given the size of a simulation domain, a
greater flow rate indicates a shorter residence time for the medium to digest fluid reactivity. Fig
5 shows the impact of the macroscopic dimensionless flowrate, Q, on the temporal and spatial
patterns of entropy generation. Both percolative and reactive entropies scale with the flow rate
because with greater throughput, the medium received more mechanical and chemical energy.
SP increases with Q because more energy is required to drive a larger volume of flow through
the same microstructure. The temporal pattern of SP is most sensitive to the geometric complex-
ity when Q is low, while with greater Q, the system resembles a homogeneous medium, for
which the various stages of structural evolution are not distinct. For example, in Fig 5A, the last
inflection point of SP can be easily identified for Q = 0.1 (at φ = 0.53) but not for Q = 10 (at a φ
less than 0.4). Close examination of the geometric cross sections (Fig 5B) shows that high fluid
throughput results in greater surface roughness (manifested by a higher number of partially
filled voxels). In contrast, the cross section of Q = 0.1 shows that the original heterogeneities
have been amplified, leaving sharp interfaces and a more thoroughly dissolved upstream geome-
try. Fig 5C shows that the channelling effect is insignificant for Q = 10 and many less porous
locations are percolative entropy hotspots (ROI 1).
The impact of the global flow rate is also evident in the patterns of reactive entropy produc-
tion. Fig 5D shows that the temporal pattern of SR can also be divided into three stages. In the
first stage, SR is limited by the fluid reactivity. Given reactant concentration at the inlet, the
available chemical energy scales with flow rate. The second stage shows a gradual decrease of
SR as the major flow path expands and the fluid residence time shortens. The last stage features
a quick drop of SR, which stems from the depletion of solid reactivity as the macroscopic
porosity approaches unity, i.e. complete dissolution. When less reactant is available, solid reac-
tivity depletion is delayed and vice versa. When Q = 10, the third stage of SR begins before the
macroscopic porosity reaches 0.8, while for Q = 2.0 this change takes place at approximately φ
= 0.9. A visualisation of local Damköhler number (Fig 5E, Eqs 11 & 13) shows that greater
fluid throughput drives the reactants into less permeable regions and thus enlarges the sample
subvolume that is available for chemical reactions (ROI 2). However, chemical conversion in
these voxels is low because of the short residence time, leaving many partially dissolved voxels
behind. The spatial pattern of SR (Fig 5F) clearly shows that the reaction is more convection
driven and dispersive when Q = 10 and is more interface dominant when Q = 0.1.

Fig 5. Effects of macroscopic flow rate, Q, on microstructural evolution. (a) Temporal patterns of percolative entropy generation. (b) Cross sections of porosity
distribution at different Q. (c) Spatial patterns of percolative entropy generation with regions of interest (ROI) showing entropy hotspots in a low porosity subvolume at
high fluid throughput. (d) Temporal patterns of reactive entropy generation. (e) Local Damköhler number with ROI 2 showing distinct spatial patterns of Da in a low
porosity subvolume. (f) Spatial patterns of reactive entropy generation. In (a) and (d), the dimensionless quantities (SP and SR) are normalised with respect to the same
combination of reference quantities, i.e. reference temperature, flowrate, pressure and Gibbs free energy (see also Fig 2B). In (b), (c), (e) and (f), all cross sections were
made when macroscopic porosity = 0.5, with the upper image showing Q = 10 and the lower one, Q = 0.1.

The effects of the global constraint on microstructural evolution have two important impli-
cations. First, the amplification of transport heterogeneity during structural morphing is Q
dependent. The distinguishability of different stages in the temporal entropy generation is a
measure of system sensitivity to the initial geometry. Fig 5 shows that this distinguishability
depends heavily on the global constraint, which implies that the reactive infiltration instability
is important in big systems where the fluid input can be considered small and local. In con-
trast, the prediction of system evolution with a large Q requires lower resolving ability of the
initial geometry. Second, percolative entropy generation is closely related to the macroscopic
permeability of a porous medium. When the evolution of a system needs to be accounted for, a
representative elementary volume might have to be defined accordingly, not only regarding
the nature of the porous material but also the specific petrophysical parameter and the envi-
ronment that controls the global constraint, e.g. flow rate.
Discussion
Irreversibility analysis based on greyscale tomography images provides unprecedented insights
into the structural development in a natural, microfluidic system. Assuming chemical homo-
geneity, the evolution of a system is controlled by only four dimensionless parameters: voxel
level porosity (φ), dimensionless voxel size (ln), extent of regional mixing (η) and the global
constraint (measured by Q). φ and ln are determined by the tomographic data but η and Q can
vary, depending on the nature of the porous material and the operational conditions of core
flooding. This variability can help us decouple the effects of geometric complexity from those
of other factors by conducting numerical experiments with a fixed initial geometry. This
method allows us to revisit many experimental observations and put the results into a more
coherent and big picture.
A defining moment during the instability induced microstructural evolution is the fluid
breakthrough. This is the moment when the location where most percolative entropy is gener-
ated changes from the porous portion of the medium (partially occupied by solid) to the chan-
nels (fully occupied by fluid), e.g. Fig 3, SP pattern at τ = 50 vs τ = 108. This transition leads to
distinct system behaviours, which in the past have been interpreted differently and given vari-
ous names. Before breakthrough, the major flow path develops from the reactive fluid inlet
and slowly advances downstream. Because of the system’s tendency to amplify transport het-
erogeneity, this path development is usually accompanied by the preferential removal of the
more permeable or more reactive materials. For example, microcrystalline and concomitant
particles have been observed to dissolve preferentially during the early stage of acidic fluid per-
colation in limestone [38, 39]. The sharpening of solid-liquid interfaces after breakthrough,
most clearly shown in the spatial patterns of reactive entropy generation (e.g. Fig 3, τ = 300
and Fig 5F), has also been observed by registering boundary geometry [30, 40]. This interface
focussed reaction pattern that accompanies the expansion of the major flow path has been
referred to as sparitic dissolution [38], interface smoothing [39], surface/transport control [41]
and heterogeneous dissolution [42]. In contrast, the convective and dispersive pattern before
breakthrough has been referred to as reaction control or uniform/homogeneous dissolution
[30]. The homogeneous/heterogeneous categorisation is particularly informative because it
describes the spatial patterns of structural evolution and also implies that as Q approaches
infinity, the effect of inherent geometric heterogeneity on morphology development would
vanish (Fig 5A), i.e. a porous medium would evolve as if perfectly homogeneous. It is worth
emphasising that homogeneous and heterogeneous dissolution patterns can coexist and are
separated spatially by the advancing front of the developing major flow path (e.g. Fig 3., SR pat-
tern at τ = 108 and Fig 5F, Q = 10). The breakthrough event, marked by the last inflection

point in the temporal SP pattern, has been documented experimentally as a transition regime
[42]. Physically, breakthrough means connection between the percolation inlet and outlet by
the newly developed major flow pathway (Fig 3). As a result, the macroscopic permeability
increases sharply with a minor change in porosity [42]; the pore connectivity increases [38, 39]
as small pores are interconnected through the major flow path; the volume averaged tortuosity
decreases [42] because of the shortened residence time and both the effective porosity [43], i.e.
the porosity in the convective subvolume of a sample, and the effective hydraulic radius
increase [42] because the fluid is channelled into the major flow path.
The temporal pattern of SR helps reconcile inconsistencies between experimental observa-
tions based on solution chemistry analysis. The value of SR reflects the overall dissipation of
chemical free energy entering the system and can thus be related to the outlet concentrations
of reactants (e.g., pH) or products (e.g., metal cations). Percolation experiments might cover
different stages of the SR evolution and observe inconsistent trends in outlet concentration
and, as a derivative, reactive surface area. This apparent contradiction can be best interpreted
by the relative reactivity between the fluid and the solid. Fig 6 shows the effects of ln, used as a
measure of system size, on entropy generation patterns. Small ln corresponds to a medium
with the same geometric complexity but smaller in scale (and thus containing less solid mate-
rial given the same porosity). If percolation is initially limited by fluid reactivity (Fig 6B, ln =
0.5, 1.0, 5.0 and 10.0) the effluent would be saturated with dissolving minerals [44]. This quasi
steady state corresponds to the initial plateau in reactive entropy generation. As the pore structure
develops, the outlet concentration of dissolution products decreases exponentially as a result of
shortened residence time [38, 41, 42]. The concentration can eventually drop to zero as the reac-
tion becomes limited by solid availability (e.g. as φ approaches 1, when the microstructure dis-
solve completely). However, if the percolation is initially limited by solid reactivity, as is very
often seen in aluminosilicate dissolution [45, 46], it is possible for the reactive surface area to
increase over time, as more pores open, enabling interfacial contact (Fig 6B, initial SR increase for
ln = 0.1). If percolation starts from the stabilisation stage with pre-existing major flow paths (e.g.
fractures in rocks), mineralogical heterogeneity can result in preferential removal of the more
reactive materials and lead to surface roughening. This roughening increases the contact between
the fluid and the slower dissolving minerals [47]. Natural porous media usually consist of multi-
ple mineral phases that differ in reactivity. It is thus expected that a single dissolutive percolation
could display different trends representing the concentrations of dissolution products from the
various minerals. For example, Noiriel et al. observed a decrease in the dissolution rate of micrite
(fast) and an increase in sparite (slow) over time in the same percolation experiment [40].
Fig 6 also suggests that the effects of the global constraint, represented by Q, and of the sys-
tem size, represented by ln, can be equivalent. Greater ln corresponds to smaller Q given the
same chemical free energy input, because it provides a longer residence time for the reactive
fluid. A small system (ln = 0.1, Fig 6C and 6D) dissolves homogeneously while a large system
(ln = 10) demonstrates both homogeneous and heterogeneous regimes separated by the disso-
lution front. Experimentally the effect of Q can be measured by a macroscopic Damköhler
number. This number can be changed through tuning the reaction rate e.g. by manipulating
the partial pressure of CO2 [41] or by varying residence time (by adjusting the flow rate) [39].
However, this number reflects the relative amount of the two forms of energy a system can dis-
sipate (mechanical vs chemical) and should not be considered identical to the local Damköhler
number (Fig 5E) that controls local reactant conversion.
Last but not least, we would like to point out that this study does not include a systematic
investigation of φ’s impact. The spatial distribution of φ defines the initial geometry. This dis-
tribution is determined by the imaging technology and is sample specific. Our reactor network
model has three conceptual components i) the reactant conveyer network, which distributes fluid


Fig 6. Effect of system size on entropy generation. System size is varied by changing the dimensionless voxel size (ln)
while keeping the geometry constant. A smaller ln corresponds to a system with less solid material and, given the same
fluid throughput, greater fluid residence time. (a) and (b) temporal patterns of entropy production. (c) and (d) cross
sections of porosity and entropy generation when macroscopic porosity reaches 0.5. A smaller system dissolves more
homogeneously, consistent with experimental observations.
influx among all possible pathways; ii) the kinetic module, which determines how fast solid
depletes spatially and iii) the voxel level mass balancing, which defines how the results of chemical
reaction are reflected in the temporal evolution of voxel porosity. The initial geometry affects the
first component, i.e. the flow field. An improved imaging technology provides a more realistic
field, while a different microstructure sample yields a different flow field. We have previously ana-
lysed the effect of imaging resolution in two numerical contexts. We used a conventional CFD
approach (finite volume method to solve the Stokes equation on binarised tomogram [48]) to
show that the influence is rock type specific and is predominately reflected in the interconnectiv-
ity of pore spaces that require discretisation. We have also applied the reactor network model on
tomographic data at three different resolutions [34]. The results suggested that both the effect of
the voxel size and that of the initial microstructure are secondary compared to the apparent solu-
bility of the solid in the flowing fluid. It is thus important to ask if any variation in the initial flow
field, caused by the different geometries, changes the qualitative behaviour of entropy production.
I.e. is the three-stage pattern in localised rock dissolution conditioned on a very specific flow
field? We argue that this is not the case. The pattern discussed above stems from the positive cou-
pling between mineral dissolution and fluid advection, which is a result of three facts. First,
within the same flow field fluid tends to flow through more porous materials because they are
more permeable. Second, the rate of mineral dissolution is affected by the residence time of the
fluid. Third, the presence of inherent transport heterogeneities breaks the symmetry of the geom-
etry. A variation in the initial flow field does not negate any of these.
Conclusions
We present an analysis of the patterns of entropy production in a dissolving natural porous
medium, using a fixed initial microstructure. This approach uses a greyscale digital model of chalk
obtained using X-ray nanotomography. Greyscale models allow the preservation of structural het-
erogeneities with very high fidelity. This is important for simulating systems in which local differ-
ences in material density can be amplified. We studied two types of entropy production: the
percolative entropy generated by dissipating the kinetic energy of fluid flow and the reactive
entropy that originates from the consumption of chemical free energy. By analysing these temporal
patterns, we identified three distinct stages of microstructural evolution in a dissolving porous
medium: induction, breakthrough and stabilisation. We found that local mixing dampens fluid
channelling by reducing variations in reactant concentration. In addition, we show that the micro-
structural evolution can be particularly sensitive to initial transport heterogeneities when the global
flow rate is small. This dependence on flow rate indicates that, to make accurate predictions, resolv-
ing microstructure is essential when the residence time of the fluid is long. We conclude the discus-
sion by presenting a few examples of how patterns of entropy production can explain the
diversified experimental observations and interpretations of water-rock interaction in Nature.
Acknowledgments
We thank the three anonymous reviewers for the very helpful comments and suggestions,
which have significantly improved the quality of the paper. We are grateful to Dr. A. Mukher-
jee for prompt processing of the manuscript.

Author Contributions
Conceptualization: Y. Yang.
Data curation: Y. Yang, S. Bruns, H. O. Sørensen.
Formal analysis: Y. Yang.
Funding acquisition: S. L. S. Stipp.
Investigation: Y. Yang.
Methodology: Y. Yang, H. O. Sørensen.
Project administration: S. L. S. Stipp, H. O. Sørensen.
Resources: S. L. S. Stipp, H. O. Sørensen.
Supervision: S. L. S. Stipp, H. O. Sørensen.
Validation: Y. Yang.
Visualization: Y. Yang.
Writing – original draft: Y. Yang.
Writing – review & editing: S. Bruns, S. L. S. Stipp, H. O. Sørensen.
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RESEARCH ARTICLE

Patterns of entropy production in dissolving

PLOS ONE | https://doi.org/10.1371/journal.pone.0204165 September 20, 2018 1 / 20

Material and methods

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Pref ¼ ðm0A þ RT ÞðCA;eq CA;inj Þ; ð4Þ

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Κ ¼ NxKxNxT þ NyKyNy T þ NzKzNzT ; ð8Þ

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where the reactor volume in Da takes a different value:

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Local mixing deteriorates fluid channelisation

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Greater flow rate reduces the impact of initial heterogeneities

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