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Salek MM, Carrara F, Zhou J, Stocker R, Jimenez‐Martinez J. Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310121. [PMID: 38445967 PMCID: PMC11132056 DOI: 10.1002/advs.202310121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Indexed: 03/07/2024]
Abstract
Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.
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Affiliation(s)
- M. Mehdi Salek
- Department of Biological Engineering, School of EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Francesco Carrara
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Jiande Zhou
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Microsystems LaboratoryInstitute of MicroengineeringSchool of EngineeringEPFLLausanneSwitzerland
| | - Roman Stocker
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Joaquin Jimenez‐Martinez
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Department of Water Resources and Drinking WaterEawagDubendorfSwitzerland
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Markale I, Cimmarusti GM, Britton MM, Jiménez-Martínez J. Phase Saturation Control on Mixing-Driven Reactions in 3D Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8742-8752. [PMID: 34106702 DOI: 10.1021/acs.est.1c01288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transported chemical reactions in unsaturated porous media are relevant to environmental and industrial applications. Continuum scale models are based on equivalent parameters derived from analogy with saturated conditions and cannot appropriately account for incomplete mixing. It is also unclear how the third dimension controls mixing and reactions. We obtain three-dimensional (3D) images by magnetic resonance imaging using an immiscible nonwetting liquid as a second phase and a fast irreversible bimolecular reaction. We study the impact of phase saturation on the dynamics of mixing and the reaction front. We quantify the temporally resolved effective reaction rate and describe it using the lamellar theory of mixing, which explains faster than Fickian (t0.5) rate of product formation by accounting for the deformation of the mixing interface between the two reacting fluids. For a given Péclet, although stretching and folding of the reactive front enhance as saturation decreases, enhancing the product formation, the product formation is larger as saturation increases. After breakthrough, the extinction of the reaction takes longer as saturation decreases because of the larger nonmixed volume behind the front. These results are the basis for a general model to better predict reactive transport in unsaturated porous media not achievable by the current continuum paradigm.
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Affiliation(s)
- Ishaan Markale
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland
| | | | - Melanie M Britton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Joaquín Jiménez-Martínez
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland
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Portela R, Perez-Ferreras S, Serrano-Lotina A, Bañares MA. Engineering operando methodology: Understanding catalysis in time and space. Front Chem Sci Eng 2018. [DOI: 10.1007/s11705-018-1740-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Britton MM. MRI of chemical reactions and processes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 101:51-70. [PMID: 28844221 DOI: 10.1016/j.pnmrs.2017.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
As magnetic resonance imaging (MRI) can spatially resolve a wealth of molecular information available from nuclear magnetic resonance (NMR), it is able to non-invasively visualise the composition, properties and reactions of a broad range of spatially-heterogeneous molecular systems. Hence, MRI is increasingly finding applications in the study of chemical reactions and processes in a diverse range of environments and technologies. This article will explain the basic principles of MRI and how it can be used to visualise chemical composition and molecular properties, providing an overview of the variety of information available. Examples are drawn from the disciplines of chemistry, chemical engineering, environmental science, physics, electrochemistry and materials science. The review introduces a range of techniques used to produce image contrast, along with the chemical and molecular insight accessible through them. Methods for mapping the distribution of chemical species, using chemical shift imaging or spatially-resolved spectroscopy, are reviewed, as well as methods for visualising physical state, temperature, current density, flow velocities and molecular diffusion. Strategies for imaging materials with low signal intensity, such as those containing gases or low sensitivity nuclei, using compressed sensing, para-hydrogen or polarisation transfer, are discussed. Systems are presented which encapsulate the diversity of chemical and physical parameters observable by MRI, including one- and two-phase flow in porous media, chemical pattern formation, phase transformations and hydrodynamic (fingering) instabilities. Lastly, the emerging area of electrochemical MRI is discussed, with studies presented on the visualisation of electrochemical deposition and dissolution processes during corrosion and the operation of batteries, supercapacitors and fuel cells.
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Affiliation(s)
- Melanie M Britton
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
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Jimenez-Martinez J, Negre CFA. Eigenvector centrality for geometric and topological characterization of porous media. Phys Rev E 2017; 96:013310. [PMID: 29347210 DOI: 10.1103/physreve.96.013310] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 11/07/2022]
Abstract
Solving flow and transport through complex geometries such as porous media is computationally difficult. Such calculations usually involve the solution of a system of discretized differential equations, which could lead to extreme computational cost depending on the size of the domain and the accuracy of the model. Geometric simplifications like pore networks, where the pores are represented by nodes and the pore throats by edges connecting pores, have been proposed. These models, despite their ability to preserve the connectivity of the medium, have difficulties capturing preferential paths (high velocity) and stagnation zones (low velocity), as they do not consider the specific relations between nodes. Nonetheless, network theory approaches, where a complex network is a graph, can help to simplify and better understand fluid dynamics and transport in porous media. Here we present an alternative method to address these issues based on eigenvector centrality, which has been corrected to overcome the centralization problem and modified to introduce a bias in the centrality distribution along a particular direction to address the flow and transport anisotropy in porous media. We compare the model predictions with millifluidic transport experiments, which shows that, albeit simple, this technique is computationally efficient and has potential for predicting preferential paths and stagnation zones for flow and transport in porous media. We propose to use the eigenvector centrality probability distribution to compute the entropy as an indicator of the "mixing capacity" of the system.
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Affiliation(s)
- Joaquin Jimenez-Martinez
- Department of Water Resources and Drinking Water, EAWAG, 8600 Dubendorf, Switzerland; Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland; and Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Christian F A Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Bánsági T, Taylor AF. Helical Turing patterns in the Lengyel-Epstein model in thin cylindrical layers. CHAOS (WOODBURY, N.Y.) 2015; 25:064308. [PMID: 26117119 DOI: 10.1063/1.4921767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The formation of Turing patterns was investigated in thin cylindrical layers using the Lengyel-Epstein model of the chlorine dioxide-iodine-malonic acid reaction. The influence of the width of the layer W and the diameter D of the inner cylinder on the pattern with intrinsic wavelength l were determined in simulations with initial random noise perturbations to the uniform state for W < l/2 and D ∼ l or lower. We show that the geometric constraints of the reaction domain may result in the formation of helical Turing patterns with parameters that give stripes (b = 0.2) or spots (b = 0.37) in two dimensions. For b = 0.2, the helices were composed of lamellae and defects were likely as the diameter of the cylinder increased. With b = 0.37, the helices consisted of semi-cylinders and the orientation of stripes on the outer surface (and hence winding number) increased with increasing diameter until a new stripe appeared.
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Affiliation(s)
- T Bánsági
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - A F Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
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Kiss IZ, Pojman JA. Introduction to Focus Issue: Oscillations and Dynamic Instabilities in Chemical Systems: Dedicated to Irving R. Epstein on occasion of his 70th birthday. CHAOS (WOODBURY, N.Y.) 2015; 25:064201. [PMID: 26117111 DOI: 10.1063/1.4922594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- István Z Kiss
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, USA
| | - John A Pojman
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Vallatos A, Evans R, Thompson BW, Taylor AF, Britton MM. Chemical patterns in translating vortices: inter- and intra-cellular mixing effects. CHAOS (WOODBURY, N.Y.) 2013; 23:023115. [PMID: 23822480 DOI: 10.1063/1.4807619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Stationary chemical patterns-flow distributed oscillations (FDOs)-are obtained when the Belousov-Zhabotinsky reaction is coupled with translating vortex flow in a Vortex Flow Reactor. For certain conditions, the FDOs are unstable with the observation of disappearing bands or complex patterns. The transitions between modes of pattern formation are reproduced in a modified Oregonator model consisting of two-zone cells connected in series. We show that increasing inter-cellular mixing of the outer zones results in a transition from FDO to absolute instabilities (AI) and increasing intra-cellular mixing between the core and outer zones can drive the reverse transition between modes (AI to FDO).
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Affiliation(s)
- Antoine Vallatos
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom
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Berenstein I. Distinguishing similar patterns with different underlying instabilities: effect of advection on systems with Hopf, Turing-Hopf, and wave instabilities. CHAOS (WOODBURY, N.Y.) 2012; 22:043109. [PMID: 23278044 DOI: 10.1063/1.4766591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Systems with the same local dynamics but different types of diffusive instabilities may show the same type of patterns. In this paper, we show that under the influence of advective flow the scenario of patterns that is formed at different velocities change; therefore, we propose the use of advective flow as a tool to uncover the underlying instabilities of a reaction-diffusion system.
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Affiliation(s)
- Igal Berenstein
- Institute of Physics and Astronomy, University of Potsdam, Karl- Liebknecht-Str. 24/25, 14476 Potsdam, Germany
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Novak J, Thompson BW, Wilson MCT, Taylor AF, Britton MM. Low frequency temperature forcing of chemical oscillations. Phys Chem Chem Phys 2011; 13:12321-7. [DOI: 10.1039/c1cp21096c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
Magnetic resonance imaging (MRI) has long been recognized as one of the most important tools in medical diagnosis and research. However, MRI is also well placed to image chemical reactions and processes, determine the concentration of chemical species, and look at how chemistry couples with environmental factors, such as flow and heterogeneous media. This tutorial review will explain how magnetic resonance imaging works, reviewing its application in chemistry and its ability to directly visualise chemical processes. It will give information on what resolution and contrast are possible, and what chemical and physical parameters can be measured. It will provide examples of the use of MRI to study chemical systems, its application in chemical engineering and the identification of contrast agents for non-clinical applications. A number of studies are presented including investigation of chemical conversion and selectivity in fixed-bed reactors, temperature probes for catalyst pellets, ion mobility during tablet dissolution, solvent dynamics and ion transport in Nafion polymers and the formation of chemical waves and patterns.
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Affiliation(s)
- Melanie M Britton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Thompson BW, Novak J, Wilson MCT, Britton MM, Taylor AF. Inward propagating chemical waves in Taylor vortices. Phys Rev E 2010; 81:047101. [PMID: 20481860 DOI: 10.1103/physreve.81.047101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Indexed: 11/07/2022]
Abstract
Advection-reaction-diffusion (ARD) waves in the Belousov-Zhabotinsky reaction in steady Taylor-Couette vortices have been visualized using magnetic-resonance imaging and simulated using an adapted Oregonator model. We show how propagating wave behavior depends on the ratio of advective, chemical and diffusive time scales. In simulations, inward propagating spiral flamelets are observed at high Damköhler number (Da). At low Da, the reaction distributes itself over several vortices and then propagates inwards as contracting ring pulses--also observed experimentally.
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13
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Koptyug IV, Zhivonitko VV, Sagdeev RZ. Advection of Chemical Reaction Fronts in a Porous Medium. J Phys Chem B 2008; 112:1170-6. [DOI: 10.1021/jp077612r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Igor V. Koptyug
- International Tomography Center SB RAS, 3A Institutskaya St., Novosibirsk 630090, Russia
| | - Vladimir V. Zhivonitko
- International Tomography Center SB RAS, 3A Institutskaya St., Novosibirsk 630090, Russia
| | - Renad Z. Sagdeev
- International Tomography Center SB RAS, 3A Institutskaya St., Novosibirsk 630090, Russia
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Zhivonitko VV, Koptyug IV, Sagdeev RZ. Temperature Changes Visualization during Chemical Wave Propagation. J Phys Chem A 2007; 111:4122-4. [PMID: 17451231 DOI: 10.1021/jp071435c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magnetic resonance imaging was used for two-dimensional temperature visualization of chemical waves propagation in the autocatalytic exothermal reaction of thiosulfate oxidation by chlorite. The technique presented is based on the temperature dependence of the water chemical shift. Temperature maps were acquired by employing the TurboFLASH imaging method. The results obtained allow one to judge about directions of buoyancy flows. Two types of convection critical modes in a vertical tube during the wave propagation were detected.
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Affiliation(s)
- Vladimir V Zhivonitko
- International Tomography Center, 3A Institutskaya Street, Novosibirsk 630090, Russia
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Taylor AF, Britton MM. Magnetic resonance imaging of chemical waves in porous media. CHAOS (WOODBURY, N.Y.) 2006; 16:037103. [PMID: 17014237 DOI: 10.1063/1.2228129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Magnetic resonance imaging (MRI) provides a powerful tool for the investigation of chemical structures in optically opaque porous media, in which chemical concentration gradients can be visualized, and diffusion and flow properties are simultaneously determined. In this paper we give an overview of the MRI technique and review theory and experiments on the formation of chemical waves in a tubular packed bed reactor upon the addition of a nonlinear chemical reaction. MR images are presented of reaction-diffusion waves propagating in the three-dimensional (3D) network of channels in the reactor, and the 3D structure of stationary concentration patterns formed via the flow-distributed oscillation mechanism is demonstrated to reflect the local hydrodynamics in the packed bed. Possible future directions regarding the influence of heterogeneities on transport and reaction are discussed.
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Affiliation(s)
- Annette F Taylor
- Department of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom.
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Gladden L, Mantle M, Sederman A. Magnetic Resonance Imaging of Catalysts and Catalytic Processes. ADVANCES IN CATALYSIS 2006. [DOI: 10.1016/s0360-0564(06)50001-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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