Search

Advent of pre-exascale and exascale computers opens possibility for much higher resolution simulations of porous media flows. During the launch phase of the LUMI supercomputer, a number of simulations of wormhole growth commenced with an aim to use as much spatial information as possible with up to 1e9 DOFs. The goal was to investigate if properties of growing wormholes could be recovered if sufficient resolution is assured. Samples used in this study underwent experimental studies. They were scanned before and after the experiment, as well as during the dissolution. This 4D tomographic data provided necessary input for high-res simulations as well as validation framework. Fig: Wormhole groth patter with branching and rapid direction change observed in evperiment As the LUMI computer, as well as most of the newly built HPC machines, is based on GPUs we decided to use the Lattice Boltzmann code as main flow and transport solver. LBM has significant number-crunching performance thanks to its intrinsic parallelization properties which was paramount for this study. Based on an open-source, highly parallel multi-GPU TCLB solver, we design the model capable of handling Darcy - scale simulations with the initial porosity fields constructed based on X-ray microtomography images. In particular, we analyze the reactive-infiltration instabilities, which lead to the formation of dissolution fingers (wormholes), in which both the flow and reactant transport become spontaneously localized. Since dissolution fingers dramatically increase permeability of the rock, wormholing is important both for industrial applications and in hydrogeological studies. The main problem in modeling of wormholing is a multi-scale character of this process, with flow and transport near a wormhole tip strongly coupled to the macroscopic geometry of the emerging structures. The ability to perform large scale parametric and sensitivity studies of wormholing constitutes thus an important addition to experimental studies, hence the need for a high throughput simulator. We test our numerical predictions against the data from time-lapse dissolution experiments in an aim of constructing a predictive model capable of recovering time evolution of 3D wormhole shape based on the initial X-ray tomography data.

Mineral dendrites are an example of a pattern which forms in rocks when they are infiltrated by the hydrothermal, manganese-rich fluids. As these fluids mix with other oxygenated fluids within the fractured rock, manganese oxide is formed. The oxide then precipitates, forming intricate, branched patterns. Several models of this process have been proposed, which vary in complexity. One model assumes crystallization of manganese oxides directly on the surface of the growing dendrite, causing it to elongate. Another model involves an initial growth of small nanoparticles of manganese oxide, which then aggregate into larger structures. The evolution of the system in both models is described by the system of reaction-diffusion equations. We study this process using lattice-Boltzmann method to track the evolving concentrations of the species involved in reaction. Next, we analyze the dependence of the morphology of the resulting patterns on the physical parameters characterizing the reaction and growth, such as initial concentrations of manganese ions and oxygen molecules, reaction rates, nucleation thresholds or surface energy of the dendrites. Our study has been focused on planar structures, growing along fractures or bedding planes. We have investigated the impact of multiple infiltrations of manganese-bearing fluid on the morphology of the dendrites. We compare the numerical results to the morphologies of the real systems with the aim of reconstructing the hydrochemical conditions prevailing during their growth

Manganese (Mn) dendrites are a common type of mineral dendrite that typically forms two-dimensional structures on rock surfaces. Three-dimensional (3-D) Mn dendrites in rocks have rarely been reported, and so their growth implications have largely escaped attention. Here, we combined high-resolution X-ray and electron-based data with numerical modeling to give the first detailed description of natural 3-D Mn dendrites (in clinoptilolite tuffs) and elucidate their growth dynamics. Our data show that 3-D dendrite growth occurred by accretion of Mn-oxide nanoparticles formed when Mn-bearing fluids mixed with oxygenated pore water. The geometry of the resulting structures is sensitive to ion concentrations, the volume of infiltrating fluid, and the number of fluid pulses; thus, 3-D dendrites record the hydrogeochemical rock history.

The main topic of the presented work is the evaluation of the in-line viscometer (VIS) operation installed on the industrial line for polyethylene terephthalate (PET) foil production. The tests were performed during the regular operation of the machine, which results from the need to maintain production continuity. Polymer viscosity control is of particular importance in the production of degradable materials and recycled polymers. The processing of PET film is, therefore, a particularly difficult issue due to the presence of both of these problems at the same time. The conducted research had a two-pronged character: assessment of the correct operation of the viscosity measurement system and testing of the effectiveness of reactive additives during the extrusion process. Measurements were carried out with the use of several types of input materials, including recycled blends. The key tests were carried out with the addition of viscosity modifiers. Measurements conducted during the extrusion process confirmed the effectiveness and high sensitivity of the in-line system (VIS), while clear changes in the polymer flow characteristics were observed only after the addition of chain extenders. The in-line measurements revealed that the addition of 1% of the reactive compound increased the viscosity from the initial 150 Pa∙s to over 350 Pa∙s. The most significant increase in viscosity for the additive based on pyromellitic dianhydride (PMDA) confirms the effectiveness of the reactive extrusion method and the suitability of the used measuring. During further analysis, the obtained films were also tested. The results showed no negative effects of the reactive extrusion on the mechanical performance of the foil; however, for recycled materials, the average values of tensile strength and elongation at break have deteriorated. A positive aspect of the use of reactive additives was the greater uniformity of mechanical properties. For some materials, there was a significant increase in the haze factor (transparency), which should be considered a disadvantage.

Dissolution of carbonate rocks is a complex process in which the interplay of flow, transport, reaction, and geometric evolution plays an important role. The nonlinear couplings between these processes may lead to the formation of intricate patterns, including spontaneously formed channels (wormholes) [1]. It has been long established that the shapes of the dissolution patterns depend on fluid flow and mineral dissolution rates [2]. Recently, it also has become increasingly clear that pore-scale processes can impact large-scale morphologies [3,4]. However, the effects of pore-scale mixing on large-scale patterns remain unclear.In this work, we investigate the effect of pore-scale mixing processes on the evolution of dissolution channels. Pore space is represented by a network of cylindrical tubes with the diameter of each segment increasing in proportion to the local reactant consumption. The inlet concentration of each pore is controlled by local mixing rules. Two different mixing protocols are considered: full mixing, in which the incoming reactant fluxes are assumed to be completely mixed at the intersection, and streamline routing, where the tracer follows the streamlines into the outgoing pores. We found that streamline routing enhances the flow focusing particularly strongly in moderate Damköhler number regimes where relatively wide dissolution channels appear spontaneously in the system. With the same initial conditions as the full mixing case, the winning channels obtained with streamline routing not only propagate faster but also could grow at a different location in the system. The enhanced flow focusing caused by streamline routing produces thinner wormholes and leads to shorter breakthrough times. Lastly, the evolution of velocity distribution is also found to be distinctive depending on the mixing rule.[1] Hoefner, M. L. and Fogler, H. S. AIChE J. 34: 45–54, 1988[2] Golfier, F., et al. J. Fluid. Mech. 457: 213-254, 2002[3] Li, L., Peters, C. A., & Celia, M. A. Adv. Water Res., 29: 1351–1370, 2006[4] R. Roded, P. Szymczak, R. Holtzman, Geophys. Res. Lett. 48:e2021GL093659, 202

DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.

Many ramified, network-like patterns in nature, such as river networks or blood vessels, form as a result of unstable growth of moving boundaries in an external diffusive field. Here, we pose the inverse problem for the network growth—can the growth dynamics be inferred from the analysis of the final pattern? We show that by evolving the network backward in time one can not only reconstruct the growth rules but also get an insight into the conditions under which branch splitting occurs. Determining the growth rules from a single snapshot in time is particularly important for growth processes so slow that they cannot be directly observed, such as growth of river networks and deltas or cave passages. We apply this approach to analyze the growth of a real river network in Vermont, USA. We determine its growth rule and argue that branch splitting events are triggered by an increase in the tip growth velocity., Scientific Reports, 12 (1), ISSN:2045-2322

Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model of this process with a time-periodic potential that mimics the action of a molecular motor. We calculate the translocation time as a function of the period of the pulling force, discuss the asymptotic limits and biological relevance of the results.

In this brief report, we examined (N = 449; 50.1% men) the role of the Dark Tetrad traits (i.e., psychopathy, sadism, narcissism, and Machiavellianism) and Fundamental Social Motives (i.e., social bonds, status, safety, mate-seeking, mate-retention, pathogen avoidance, family, and autonomy) in relation to self-reported perpetration of cyberstalking short-term and long-term intimate partners. Women were more likely to cyberstalk long-term partners, those with higher levels of Dark Tetrad traits were more likely to cyberstalk their partners regardless of relationship context, and Fundamental Social Motives only played a minor role. Results highlight the importance of exploring intimate partner cyberstalking across different relationship contexts.

We developed a computationally efficient approach to approximate near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. The proposed method relies on extremum principles for Stokes flows produced by the motion of rigid bodies. In the presence of the wall, the rate of energy dissipation is decreased relative to the unbounded fluid. In our approach, the position- and orientation-dependent mobility matrix of a body suspended near a no-slip plane is calculated numerically using a coarse-grained molecular model and the Rotne-Prager-Yamakawa description of hydrodynamics. Effects of the boundary are accounted for via Blake's image construction. The matrix components are scaled using ratios of the corresponding bulk values evaluated for the detailed representation of the molecule and its coarse-grained model, leading to accurate values of the near-wall diffusion coefficients. We assess the performance of the approach for two biomolecules at different levels of coarse-graining.

Per- and polyfluoroalkyl substances (PFASs) have become emerging contaminants of critical concern. Comprehensive understanding of the transport and fate of PFAS in the vadose-zone, a type of water-unsaturated porous media, is key to determination of the risks of the PFAS contamination in the subsurface and to the development of the effective remediation strategies. Accurate modeling of the PFAS transport in the unsaturated porous media is still a challenge due to the variable surface tension induced by the adsorption of PFAS to the air-water interfaces. In an effort to address this challenge, we propose a multidimensional modeling framework for the transient PFAS transport in the unsaturated porous media based on the second order accuracy finite volume method. In the modeling, the adsorption of PFAS to the solid surfaces and to the air-water interfaces is described by the two-domain sorption kinetics model, i.e., both the instantaneous and the rate limited PFAS adsorptions are taken into account. The diffusive and convective terms in the governing equations for the PFAS transport and the water flow are discretized by the central difference and the quadratic upstream interpolation for convective kinetics schemes, respectively. Both of these two schemes have the second order accuracy. We investigate the effects of the convergent criteria, coupling method, and variation of the surface tension on the average and the local PFAS concentration and water content in the computational domain. We find that the convergent criteria should be chosen carefully so as to get the accurate results. The differences between the different coupling methods are affected by the boundary conditions. The variation in the surface tension due to the variation of the PFAS concentration cannot be neglected. These studies not only guide the numerical schemes used in the modeling but also provide the insights into the transport of PFAS in unsaturated porous media. The multidimensional modeling framework presented in this work can be further extended to explore in detail the transport of PFAS in the vadose-zone.

We develop methods for qualitative and quantitative assessment of the transformation of pore geometry of a rock as a result of karstification. We then apply these tools to characterize dissolution-induced changes in Miocene limestone samples collected from a quarry located near Smerdyna (Poland), where intense epikarst development is observed, with the formation of hundreds of solution pipes. Partially dissolved samples collected in the immediate vicinity of the pipes are compared with undissolved samples collected several meters away.For both types of samples 26 micron resolution grayscale X-ray scans has been performed, and cubical regions of interest of size 506^3 voxels, which corresponds to (13,156 mm)^3, have been studied. Images have been segmented by tuning the grayscale threshold to match the experimentally measured porosity values of respective samples. Additionally, based on the segmented tomograph of undissolved sample another geometry was numerically created in order to mimic a uniform dissolution of the rock up to a porosity value equal to that of the dissolved sample.The irregular geometry of the pore space, vast majority of which forms a single connected component, can be conveniently characterized by a local thickness function, which corresponds to a diameter of the largest sphere that fits within the pore space and contains a given point. A similar measure can be introduced for the solid component (grains). We have compared thickness distributions of undissolved and dissolved sample as well as numerically generated uniformly dissolved sample. Such a comparison allowed us to quantify the extent of homogeneity of the natural karstification process.To further characterize pore geometry, we have calculated the ellipsoid factor, which – based on the axis lengths of the fitted ellipsoids – can be used to characterize how prolate or oblate the pore space locally is. Next, we have used (modified) Flinn diagram to quantify differences between undissolved, numerically eroded and naturally dissolved samples, especially those indicating pore merging and inhomogeneous dissolution.The above analysis is complemented by calculation of connectivity density – a topological measure of the degree to which a structure is multiply connected. Values obtained for undissolved, numerically dissolved and naturally dissolved samples indicate on ‘excessive’ reduction of interconnections during natural dissolution, which may be understood on the basis of high degree of pore merging due to inhomogeneous dissolution.Both methods: (generalized) thickness analysis and connectivity calculation emphasise the role of merging of pores and inhomogeneous dissolution in the process of natural dissolution for the analyzed samples.

The aim of the current study (N = 238) was to examine the relationship between narcissistic personality, depicted by the Trifurcated Model of Narcissism (namely, agentic extraversion, antagonism, and narcissistic neuroticism) and beliefs about human nature: interpersonal trust (the belief that human nature is good) and cynicism (the belief that human nature is evil and egoistic). Former studies on cynicism and trust in relation to vulnerable and grandiose narcissism bring inconsistent findings. We found that agentic extraversion was positively related to trust and unrelated to cynicism, antagonism was negatively related to trust and positively related to cynicism, and narcissistic neuroticism was not related to trust nor cynicism. Therefore, our findings indicate that the positive relationship between narcissism and cynical beliefs is limited to its antagonistic aspect so that antagonism is crucial in explaining beliefs held by narcissists towards others. Furthermore, narcissism indicates a positive relationship to trust as it is related to the agentic extraversion aspect, which might be considered as an adaptive aspect of narcissism. Therefore, the current study sheds a light on the relationship between narcissistic personality and beliefs about human nature.

Theoretical approaches to earthquake instabilities propose shear-dominated source mechanisms. Here we take a fresh look at the role of possible volumetric instabilities preceding a shear instability. We investigate the phenomena that may prepare earthquake instabilities using the coupling of thermo-hydro-mechano-chemical reaction–diffusion equations in a THMC diffusion matrix. We show that the off-diagonal cross-diffusivities can give rise to a new class of waves known as cross-diffusion or quasi-soliton waves. Their unique property is that for critical conditions cross-diffusion waves can funnel wave energy into a stationary wave focus from large to small scale. We show that the rich solution space of the reaction–cross-diffusion approach to earthquake instabilities can recover classical Turing instabilities (periodic in space instabilities), Hopf bifurcations (spring-slider-like earthquake models), and a new class of quasi-soliton waves. Only the quasi-soliton waves can lead to extreme focussing of the wave energy into short-wavelength instabilities of short duration. The equivalent extreme event in ocean waves and optical fibres leads to the appearance of “rogue waves” and high energy pulses of light in photonics. In the context of hydromechanical coupling, a rogue wave would appear as a sudden fluid pressure spike. This spike is likely to cause unstable slip on a pre-existing (near-critically stressed) fault acting as a trigger for the ultimate (shear) seismic moment release.

We perform Brownian dynamics simulations of shear-induced unfolding of bovine serum albumin. This protein was reported to unfold irreversibly in the shear flow. Using a coarse-grained model of a protein, we track the conformational changes induced by the flow and observe that after an extended exposure to shear albumin loses its ability to refold even when the flow has been turned off. Instead, it is trapped in a metastable state characterized by a large degree of self-entanglement which prevents the molecule from folding into the native conformation. This state becomes more populated with time, which can explain the cumulative effect of the shear observed in the experiments.

SummaryA relatively large number of calcite-cemented fractures are present in gas-bearing shale formations. During hydraulic fracturing, some of these fractures will be reactivated and may become important flow paths in the resulting stimulated fracture network. On the other hand, the presence of carbonate lamina on fracture surfaces will have a hindering effect on the transport of shale gas from the matrix toward the wellbore. We investigate numerically the effect of low-pH reactive fluids on such fractures, and show that dissolution of the cement proceeds in a highly nonuniform manner. The morphology of the emerging flow paths (“wormholes”) strongly depends on the thickness of the calcite layer. For thick carbonate layers, a hierarchical, fractal pattern appears, with highly branched wormhole-like channels competing for an available flow. For thin layers, the pattern is much more diffuse, with less-pronounced wormholes that merge easily with each other. Finally, for intermediate thicknesses, we observe a strong attraction between shorter and longer wormholes, which leads to the formation of islands of carbonate lamina surrounded by the dissolved regions. We argue that the wormhole-formation processes are not only important for the increase of shale-gas recovery, but also can be used for retaining the fracture permeability, even in the absence of proppant.

We consider elastic microfilaments which form closed loops. We investigate how the loops change shape and orientation while settling under gravity in a viscous fluid. Loops are circular at the equilibrium. Their dynamics are investigated numerically based on the Stokes equations for the fluid motion and the bead-spring model of the microfilament. The Rotne-Prager approximation for the bead mobility is used. We demonstrate that the relevant dimensionless parameter is the ratio of the bending resistance of the filament to the gravitation force corrected for buoyancy. The inverse of this ratio, called the elasto-gravitation number B, is widely used in the literature for sedimenting elastic linear filaments. We assume that B is of the order of 104-106, which corresponds to easily deformable loops. We find out that initially tilted circles evolve towards different sedimentation modes, depending on B. Very stiff or stiff rings attain almost planar, oval shapes, which are vertical or tilted, respectively. More flexible loops deform significantly and converge towards one of several characteristic periodic motions. These sedimentation modes are also detected when starting from various shapes, and for different loop lengths. In general, multi-stability is observed: an elastic ring converges to one of several sedimentation modes, depending on the initial conditions. This effect is pronounced for very elastic loops. The surprising diversity of long-lasting periodic motions and shapes of elastic rings found in this work gives a new perspective for the dynamics of more complex deformable objects at micrometer and nanometer scales, sedimenting under gravity or rotating in a centrifuge, such as red blood cells, ring polymers or circular DNA.

We review theoretical and computational research, primarily from the past 10 years, addressing the flow of reactive fluids in porous media. The focus is on systems where chemical reactions at the solid–fluid interface cause dissolution of the surrounding porous matrix, creating nonlinear feedback mechanisms that can often lead to greatly enhanced permeability. We discuss insights into the evolution of geological forms that can be inferred from these feedback mechanisms, as well as some geotechnical applications such as enhanced oil recovery, hydraulic fracturing, and carbon sequestration. Until recently, most practical applications of reactive transport have been based on Darcy-scale modeling, where averaged equations for the flow and reactant transport are solved. We summarize the successes and limitations of volume averaging, which leads to Darcy-scale equations, as an introduction to pore-scale modeling. Pore-scale modeling is computationally intensive but offers new insights as well as tests of averaging theories and pore-network models. We include recent research devoted to validation of pore-scale simulations, particularly the use of visual observations from microfluidic experiments.

Inclusion of hydrodynamic interactions is essential for a quantitatively accurate Brownian dynamics simulation of colloidal suspensions or polymer solutions. We use the generalized Rotne–Prager–Yamakawa (GRPY) approximation, which takes into account all long-ranged terms in the hydrodynamic interactions, to derive the complete set of hydrodynamic matrices in different geometries: unbounded space, periodic boundary conditions of Lees–Edwards type, and vicinity of a free surface. The construction is carried out both for non-overlapping as well as for overlapping particles. We include the dipolar degrees of freedom, which allows one to use this formalism to simulate the dynamics of suspensions in a shear flow and to study the evolution of their rheological properties. Finally, we provide an open-source numerical package, which implements the GRPY algorithm in Lees–Edwards periodic boundary conditions.

Dissolution of porous rocks by reactive fluids is a highly nonlinear process resulting in a variety of dissolution patterns, the character of which depends on physical conditions such as flow rate and reactivity of the fluid. Long, finger-like dissolution channels, “wormholes”, are the main subject of interest in the literature, however, the underlying dynamics of their growth remains unclear. While analyzing the tomography data on wormhole growth. one open question is to define the exact position of the tip of the wormhole. Near the tip the wormhole gradually thins out and the proper resolution of its features is hindered by the finite spatial resolution of the tomographs. In particular, we often observe in the near-tip region several disconnected regions of porosity growth, which - as we hypothesized - are connected by the dissolution channels at subpixel scale. In this study, we show how these features can be better resolved by using numerically calculated flow fields in the reconstructed pore-space. We used 70 micrometers, 16-bit grayscale X-ray computed microtomography (XCMT) time series scans of limestone cores, 14mm in diameter and 25mm in length. Scans were performed during the entire dissolution experiment with an interval of 8 minutes. These scans were further processed using a 3-phase segmentation proposed by Luquot et al.[1], in which grayscale voxels are converted to macro-porosity, micro-porosity and grain phases from their grayscale values. The macro-porous phase is assigned a porosity of 1, while the grain phase is assigned 0. Micro-porous regions are assigned an intermediate value determined by linear interpolation between pore and grain threshold using grayscale values. An OpenFOAM based, Darcy-Brinkman solver, porousFoam, is then used to calculate the flow field in this extracted porosity field. Porosity contours reconstructed from the tomographs show some disconnected porosity growth near the tip region which later become part of the wormhole in subsequent scans. We have used a novel approach by including the micro-porosity phase in pore-space to calculate the flow-fields in the near-tip region. The calculated flow fields clearly show an extended region of focused flow in front of the wormhole tip, which is a manifestation of the presence of a wormhole at the subpixel scale. These results show that micro-porosity plays an important role in dissolution and 3-phase segmentation combined with the flow field calculations is able to capture the sub-resolved dissolution channels. [1] Luquot, L., Rodriguez, O., and Gouze, P.: Experimental characterization of porosity structure and transport property changes in limestone undergoing different dissolution regimes, Transport Porous Med., 101, 507–532, 2014

Dissolution of porous media introduces a positive feedback between fluid transport and chemical reactions at mineral surfaces leading to the formation of pronounced wormhole-like channels. While the impact of flow rate and reaction rate on the shapes of the wormholes is now well understood, much less is known about the dynamics of their propagation. In this study we capture the evolution of wormholes and their effects on flow patterns by in-situ X-ray microCT imaging of dissolving limestone cores. 4D tomography allows us in particular to correlate the permeability changes in a dissolving core with the advancement of the tip position of the wormhole. Surprisingly, we find that the relation between the two is highly nonlinear, with extensive periods of relatively fast growth of the wormhole which is nevertheless not reflected in any significant change in the overall permeability. We hypothesize that this is caused by the presence of highly cemented regions in the core which act as permeability barriers for the flow. The presence of such regions is confirmed by a detailed analysis of the pore geometry based on the tomographic data. The results demonstrate that the analysis of the wormhole dynamics in 4d tomography can be used to probe the internal structure of the rock.

Optimization of industrial processes requires further research on the integration of machine-centric systems with human-centric cloud-based services in the context of new emerging disciplines, namely the fourth industrial revolution coined as Industry 4.0 and Industrial Internet of Things. The following research aims at working out a new generic architecture and deployment scenario applicable to that integration. A reactive interoperability relationship of the communication parties is proposed to deal with the network traffic propagation asymmetry or assets’ mobility. Described solution based on the OPC Unified Architecture international standard relaxes issues related to the real-time multi-vendor environment. The discussion concludes that the embedded gateway software component best suits all requirements and thus has been implemented as a composable part of the selected reactive OPC UA framework which promotes separation of concerns and reusability.

We study the behaviour of circular flexible loops sedimenting in a viscous fluid by numerical simulations and linear stability analysis. The numerical model involves a local slender-body theory approximation for the flow coupled to the Euler–Bernoulli elastic forces for an inextensible fibre. Starting from an inclined circle, we simulate the dynamics using truncated Fourier modes to observe three distinct regimes of motion: absolute stability, two- and three-dimensional dynamics, depending on the relative importance of the elastic and gravitational forces. We identify the governing parameter and develop a simple semi-analytic stability criterion, which we verify numerically. In all cases, sedimenting loops converge to stable, planar shape equilibria with one free parameter related to the initial conditions and material properties of the fibre.

Focused flow forms distinctive features termed solution pipes (vertical cylindrical voids) in the epikarst zone of porous calcareous rocks with medium to high matrix porosity. Solution pipes vary in size, but are generally less than 1 m in diameter with variable depths, the deepest reaching 100 m. Most occur in eogenetic rocks, particularly in Quaternary calcareous sandstones (calcarenites), but some pipes are also reported in Miocene-Pliocene and Cretaceous chalk and calcarenites. Most of the published research favours their dissolutional origin, but offers different theories regarding the initial trigger that focused the water flow in the host rock matrix, including vegetation patterns and rock heterogeneities. Here we review the current state of knowledge regarding geomorphology of solution pipes and discuss in greater detail the potential role of dynamic instabilities and self-organisation in the emergence of focusing patterns. We review theoretical and numerical studies which allow estimation of interpipe distances, distribution of pipe lengths, extent of pipe merging and the influence of rock porosity on their shapes. In theory, linking the numerical predictions with field measurements might allow the use of pipe characteristics as potential paleoclimatic indicators, provided the problems of dating can be overcome.

Dissolution by reactive fluid flow is a fundamental process in geological systems. It controls diagenesis and karst evolution and has broad implications for groundwater hydrology. Specifically, reactive flow controls the evolution of the void-space structure via the feedback between the reaction and transport. In some instances, advective transport rate is high compared to that of geochemical reactions (low Damkӧhler number, Da), such that the reactive fluid penetrates the system before its reactivity is exhausted, resulting in a relatively spatially-uniform dissolution. Despite the importance of low Da conditions, the emerging transformations in the medium structure, flow field, and its bulk properties are not well understood. Likewise, our ability to decipher diagenetic history and preexisting structure is lacking.Here, using a network model, we investigate the evolution of heterogeneous and anisotropic medium during dissolution at low Da conditions. The numerical simulations show that the medium progressively becomes more homogeneous as well as isotropic, which consequently makes the flow field more uniform. Homogenization is particularly notable for anisotropic media, in which the transverse channels are wide relative to the channels parallel to the main flow direction. In this case, flow is initially focused within a few highly tortuous pathways, hence emphasizing the effect of dissolution on flow heterogeneity and tortuosity. The homogenization process is further enhanced when the surface reaction is transport-controlled—that is, when diffusion of dissolved ions away from the mineral surface to the bulk fluid is slow, reducing the reactivity adjacent to the surface: At first, since diffusive transport is more effective in narrow channels, they undergo faster dissolution, which selectively enlarges them leading to an initial steep rise in permeability. Later, however, as dissolution proceeds and the channels broaden, the overall dissolution rate drops, diminishing the growth rate of permeability. Our findings provide fundamental insights into reactive transport and hydrogeological processes in fractured and porous media.

We apply conformal mapping to find the evolving shapes of a dissolving cylinder in a potential flow. Similar equations can be used to describe melting in a flowing liquid phase. Results are compared with microfluidic experiments and numerical simulations. Shapes predicted by conformal mapping agree almost perfectly with experimental observations, after a modest (20 %) rescaling of the time. Finite-volume simulations show that the differences with experiment are connected to the underlying assumptions of the analytical model: potential flow and diffusion-limited dissolution. Approximate solutions of the equations describing the evolution of the shape of the undissolved solid can be derived from a Laurent expansion of the mapping function from the unit circle. Asymptotic expressions for the evolution of the area of the disk and the shift in its centre of mass have been derived at low and high Peclet number. Analytic approximations to the leading-order Laurent coefficients provide additional insight into the mechanisms underlying pore-scale dissolution.

Theoretical approaches to earthquake instabilities propose shear-dominated instabilities as a source mechanism. Here we take a fresh look at the role of possible volumetric instabilities preceding a shear instability. We investigate the phenomena that may prepare earthquake instabilities using the coupling of Thermo-Hydro-Mechano-Chemical reaction-diffusion equations in a THMC diffusion matrix. We show that the off-diagonal cross-diffusivities can give rise to a new class of waves known as cross-diffusion waves. Their unique property is that for critical conditions cross-diffusion waves can funnel wave energy into a quasi-stationary wave focus from large to small-scale. The equivalent extreme event in ocean waves and optical fibres leads to the appearance of rogue waves and high energy pulses of light in lasers. In the context of hydromechanical coupling, a rogue wave would appear as a sudden fluid pressure spike on the future fault plane. This is here interpreted as a trigger for the ultimate (shear) seismic moment release.

International audience; Experimental observations of the dissolution of calcium sulfate by flowing water have been used to investigate the assumptions underlying pore-scale models of reactive transport. Microfluidic experiments were designed to observe changes in size and shape as cylindrical disks (radius 10 mm) of gypsum dissolved for periods of up to 40 days. The dissolution flux over the whole surface of the sample can be determined by observing the motion of the interface. However, in order to extract surface reaction rates, numerical simulations are required to account for diffusional hindrance across the concentration boundary layer; the geometry is too complex for analytic solutions.We have found that a first-principles simulation of pore-scale flow and transport, with a single value of the surface reaction rate, was able to reproduce the time sequence of sample shapes without any fitting parameters. The value of the rate constant is close to recent experimental measurements but much smaller than some earlier values. The shape evolution is a more stringent test of the validity of the method than average measurements such as effluent concentration, because it requires the correct flux at each point on the sample surface.

In this work we have investigated numerically the formation of channelised dissolution patterns, termed “wormholes”, using initial pore geometries generated from tomographic images of limestone cores. We have employed an OpenFOAM-based Darcy-scale numerical solver, porousFoam, which combines a Darcy/Darcy-Brinkman flow solver and a reactive transport solver in an evolving pore space. Simulated geometries, of both final and intermediate steps, are compared to dissolution experiments on samples the initial pore geometry is generated from, with the same acid concentration and flow rate applied. The initial condition of porosity distribution is set from X-Ray Computed Microtomography (XCMT) images via three phase segmentation into macroporosity, microporosity, and grain regions. Porosity values for microporous regions are set using linear interpolation between pore and grain grayscale values [1]. The inlet boundary conditions of flow rate and acid concentration are set as in the dissolution experiment. To test the effect of the permeability-porosity constitutive relationship we have investigated several options including power laws of varying exponent, and the Carman-Kozeny relation. We have also analyzed the impact of using Darcy versus Darcy-Brinkman flow solvers. Despite a qualitatively similar appearance to experimental results, the simulated wormholes are usually significantly thicker than their experimental counterparts, a fact noted by other researchers as well [2]. We comment on possible reasons for this discrepancy and on the limitations of Darcy-scale solvers in general. Additionally, we find that higher exponents in the power law makes the numerical dissolution very sensitive to grayscale threshold values as a small variation in this value changes the path of the wormhole. [1] Luquot, L., Rodriguez, O., and Gouze, P.: Experimental characterization of porosity structure and transport property changes in limestone undergoing different dissolution regimes, Transport Porous Med., 101, 507–532, 2014.[2] Yue Hao, Megan Smith, Yelena Sholokhova, Susan Carroll, CO2-induced dissolution of low permeability carbonates. Part II: Numerical modeling of experiments, Advances in Water Resources, 62, 388-408, 2013

Dissolution by a reactive flow is a complex phenomenon influenced by a number of different parameters, including flow rate, diffusion rate of the reactant, reaction rate and the pore space characteristics of the host rock. Depending on the values of these parameters, the dissolution patterns will have different morphological features. In particular, there is range of parameters where the dissolution front becomes unstable, which is accompanied by a formation of pronounced dissolution channels, which are called solution pipes in geological literature and wormholes in the petroleum industry, where they are produced to stimulate the flow from oil reservoirs. In the natural settings, these features are formed in rocks with a very high porosity and then with a rather large flow rate. Their shapes are strongly related to their characteristic sizes. At the macroscale (1-10metres) they are usually almost cylindrical with a diameter from a few cm up to a meter, while at microscale they show a highly ramified, fractal-like shape. To investigate this variability and to understand their formation and evolution, we are conducting microfluidic experiments using a self-constructed microfluidic cell. We are using a system consisting of two polycarbonate chips in which it is possible to have a control on flow rate and on the aperture. The lower plate has an indentation that can be filled with gypsum, while on the upper chip there is a reservoir that allows water to be supplied to the system in a controlled way. We are using powder gypsum during these experiments because it has a very simple chemistry, high solubility in water and therefore allows a greater speed of dissolution The two chips are joined together with an ultrathin, double coated tape of variable thickness that allows us to control the aperture of the system, which can thus be regarded as an analog fracture. As the gypsum chip is dissolved, we observe the appearance of fingers of different shapes, depending on the flow rate and the aperture. We report the results of these experiments and relate the observed features with the natural shapes found in the karst systems. We also investigate how the shapes of the pipes change as we vary the flow rate periodically, which reflects annual variations in the flow in the natural karst systems.Key words: dissolution, solution pipes, microfluidics

Dissolution of porous media is a complex process involving nonlinear couplings between flow, transport, the evolving geometry of the media, and the process of dissolution itself. In some cases these couplings lead to the formation of intricate patterns, the characteristics of which depend strongly on flow, mineral dissolution rate, and initial pore space geometry. In particular, finger-like channels, termed "wormholes", are spontaneously formed where the majority of flow is focused. Capturing the dynamics of wormhole growth has so far been largely limited to numerical models, with few studies observing their time evolution in real rocks. In this study we capture the dynamics of both wormhole growth and their alteration of flow in the rock by placing the experiment within neutron and X-Ray tomographs and scanning while actively dissolving limestone cores. To observe the evolution of wormhole geometry limestone samples are dissolved in a cell translucent to X-Rays and neutrons. For each experiment a high (30-35 micrometer) resolution scan was taken of the initial sample geometry, as well as the geometry after dissolution. During acidization tomography was performed at 60-70 micrometer resolution with acquisition times ranging from three to six minutes. For several experiments dissolution was paused and and a contrasting agent injected to visualize the flow field within the sample. Flow field experiments were performed with neutron tomography by first injecting heavy water, followed by light water as the contrast agent, and with X-Ray tomography by injection a solution of potassium iodide into light water. Results of dissolution experiments show that wormhole growth can be tracked at sufficiently high spatial and temporal resolution to measure changes to the pore space.These experiments highlight the importance of the near-tip region on the dynamics of wormhole propagation. In particular, focusing of the flow is shown to take place not only within the wormhole but also significantly (>5mm) into the porous region past the wormhole tip. These "virtual channels" link the tip with the neighboring regions of high porosity. Several such virtual channels can exist, indicating potential paths of further growth, and demonstrate the strong coupling of flow and geometry evolution. Additionally, we observe a dramatic dependence of the dissolution patterns on the initial pore structure, in particular the total initial porosity, distribution of pore sizes and connectivity of the pore space. In pore spaces with poor connectivity and low porosity the wormholes tend to be very tortuous and thin. Such wormholes advance through rapid, almost discontinuous jumps, guided by the above-described pre-focusing mechanism. On the other hand, the advancement of a wormhole in a well-connected rock is much more diffuse, controlled by merging between neighboring pore spaces.

We investigate the dissolution of a single grain of soluble mineral by microfluidic experiments and numerical simulations. The experiments use gypsum cylinders (10 mm radius, 0.5 mm thick) cast from rehydrated CaSO4 hemihydrate. The numerical simulations used a finite-volume discretization of the reactive-transport equations with a mesh that conforms to the evolving shape of the mineral. Using the coefficients for dilute aqueous ions, we overpredict the dissolution rate by about 25%. However, including the Debye-Huckel correction for the ion activity gives a substantial reduction in diffusion across the boundary layer at the dissolving solid surface and brings the simulation time scale into quantitative agreement with experiment.The asymmetry introduced by the flow causes the initially cylindrical sample to take on a shape resembling one half of a figure eight, with the tip pointing in the downstream direction. The simulations give a near perfect match to the experimental size and shape. We quantify the evolution of the volume of the grain and its surface area, as well as its overall shape as the function of the Peclet number. Next we discuss the differences between the geometric surface area and the reactive surface area of a dissolving grain and explore a potential use of these results to upscale the reactive transport problem and obtain the effective reaction rates in a multi-grain system.

The dissolution of fractured or porous media by reactive flow is often occurring preferentially, forming highly conductive channels, so-called “wormholes”. Wormhole formation prevails in subsurface karst where it can form extensive speleological systems, and is also significant for a large range of applications, e.g. well acidizing or CO2 geo-sequestration. The underlying mechanism involves positive feedback between reaction and transport— the flow pathways that focus the reactive flow dissolve preferentially and increase their conductivity, and in turn their flow. An increased pressure ahead of the longer wormholes screens off the shorter ones, which ultimately cease to grow. Over time, the characteristic spacing between active (growing) wormholes increases, while their number declines, which results in a hierarchical scale-invariant distribution of wormhole lengths. Interestingly, a variety of other pattern-forming processes in nature show a similar competitive dynamics and emergent of hierarchical structures, with examples ranging from viscous fingering to crack propagation in brittle solids and side-branches growth in crystallization [1].The importance of wormholing and its intriguing dynamics motivated intensive research, including on the emergence of reactive-infiltration instabilities [2], as well as on the effects of medium heterogeneity on the wormhole growth. Here, we study wormholing in anisotropic media using a network model of regular geometry— longitudinal channels (aligned along the main flow direction) and transverse ones, of a different average cross-section. Our simulations show that anisotropy substantially affects wormholing, controlling the characteristic spacing between the wormholes and the overall permeability evolution. In the case of wider transverse channels, wormhole interaction via the pressure field is enhanced, resulting in stronger wormhole competition and hence larger spacing. Conversely, in the extreme case of very narrow transverse channels, spacing becomes minimal and neighboring wormholes tend to merge. Simulations further reveal that narrow transverse channels promote the emergence of thinner and more conical wormholes with several side-branches.Additionally, we discuss the relation between the wormhole development in an anisotropic medium and viscous fingering phenomena in a network of microfluidic channels [3]. Despite many similarities between these systems we also find important differences— while the spacing between viscous fingers increases linearly with anisotropy, the corresponding relation for wormholes turns out to be nonlinear. This nonlinearity could be attributed to the effect of anisotropy on wormhole shape and advancement velocity and is of interest for future investigation. Our findings contribute to the understanding of wormholing in geological systems and demonstrate how the small-scale features can fundamentally affect the resulting large-scale morphologies.[1] Krug, J., Adv. Phys., 46, 139, 1997[2] Ortoleva, P. et al, Amer. J. Sci., 287, 1008, 1987[3] Budek, A. et al, Phys. Fluids, 27, 112109, 2015

International audience; Fractures play an important role as flow paths in porous media. When an undersaturated reactive fluid is flowing in a fracture, the dissolution process will alter the flow paths locally. Dissolution patterns grow slowly, but they may lead to a dramatic reorganization of the flow. Here, we study dissolution in a radial geometry, which is relevant for a number of practical applications, e.g., the acidization of oil reservoirs. Different dissolution patterns are presented in a phase diagram with the Péclet and Damköhler numbers as parameters. We also analyze quantitatively the density of wormholes and the relation between the aperture roughness and the ramified patterns.

International audience; Two oppositely charged surfaces separated by a dielectric medium attract each other. In contrast we observe a strong repulsion between two plates of a capacitor that is filled with an aqueous electrolyte upon application of an alternating potential difference between the plates. This longrange force increases with the ratio of diffusion coefficients of the ions in the medium and reaches steady state after a few minutes, which is much larger than the millisecond time scale of diffusion across the narrow gap. The repulsive force, an order of magnitude stronger than the electrostatic attraction observed in the same setup in air, results from the increase in osmotic pressure as a consequence of the field-induced excess of cations and anions due to lateral transport from adjacent reservoirs.

Correction for ‘Stokesian dynamics of sedimenting elastic rings’ by Magdalena Gruziel-Słomka et al., Soft Matter, 2019, 15, 7262–7274, https://doi.org/10.1039/C9SM00598F.

Passengers, who travel by public transport, including urban transport, are in need of fast and reliable passenger information. Replacement of simple and scant passenger information based on rigid assumptions, transmitted mainly using tables and printed time-sheets, with modern, dynamic and adaptive, but also complicated systems, which use audio-visual devices has become a common trend. The article presents the characteristics of the Dynamic Passenger Information System in Radom public transport, commissioned for use in 2014. The main needs of introducing the DPIS are discussed followed by the analysis of the complexity and functionality of the system and the assessment of its validity.

Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.

Analyzing the dissolution of rocks and other porous materials is simplified by the large disparity between mineral and reactant concentrations. In essence, the porosity remains frozen on the time scale of the reactant transport, which can then be treated as a quasi-stationary process. This conceptual idea can be derived mathematically using asymptotic methods, which show that the length scales in the system are, to a first approximation, independent of the ratio of reactant and mineral concentrations. Nevertheless, in a growing number of papers on dissolutional instabilities, the reactant-mineral concentration ratio has been incorrectly linked to the thickness of the dissolution front. In this paper we critically review the application of asymptotic methods to the reaction-infiltration instability. In particular we discuss the limited validity of the thin-front or “Stefan” limit, where the interface between dissolved and undissolved mineral is sharp. This article is protected by copyright. All rights reserved.

In elastic macromolecules, the value of the short-time diffusion coefficient depends on the choice of the point the displacement of which is tracked. On the other hand, the experimentally more relevant long-time diffusion coefficient is independent of the reference point, but its estimation usually requires computationally expensive Brownian dynamics simulations. Here we show how to obtain a precise estimate of the long-time diffusion coefficient of elastic macromolecules in a fast and robust manner, without invoking Brownian dynamics.

We consider the process of chemical erosion of a porous medium infiltrated by a reactive fluid in a thin-front limit, in which the width of the reactive front is negligible with respect to the diffusive length. We show that in the radial geometry the advancing front becomes unstable only if the flow rate in the system is sufficiently high. The existence of such a stable region in parameter space is in contrast to the Saffman-Taylor instability in radial geometry, where for a given flow rate the front always eventually becomes unstable, after reaching a certain critical radius. We also examine the similarities between the reactive-infiltration instability and the similar instability in the heat transfer, which is driving the formation of star-like patterns on frozen lakes.