scholarly journals Reactive Transport: A Review of Basic Concepts with Emphasis on Biochemical Processes

2021 ◽  
Author(s):  
Jesus Carrera ◽  
Maarten W. Saaltink ◽  
Joaquim Soler-Sagarra ◽  
Jingjing Wang ◽  
Cristina Valhondo
Keyword(s):  
Reactive Transport ◽  
Biochemical Processes ◽  
Chemical Systems ◽  
Flow And Transport ◽  
Advection Dispersion ◽  
Body Of Knowledge ◽  
Equilibrium Reactions ◽  
Engineering Problems ◽  
Basic Equations ◽  
Scientific Questions

Reactive transport (RT) couples bio-geo-chemical reactions and transport. RT is important to understand numerous scientific questions and solve some engineering problems. RT is highly multidisciplinary, which hinders the development of a body of knowledge shared by RT modelers and developers. The goal of this paper is to review the basic conceptual issues shared by all RT problems, so as to facilitate advance along the current frontier: biochemical reactions. To this end, we review the basic equations to point that chemical systems are controlled by the set of equilibrium reactions, which are easy to model, but whose rate is controlled by mixing. Since mixing is not properly represented by the standard advection-dispersion equation (ADE), we conclude that this equation is poor for RT. This leads us to review alternative transport formulations, and the methods to solve RT problems using both the ADE and alternative equations. Since equilibrium is easy, difficulties arise for kinetic reactions, which is especially true for biochemistry, where numerous frontiers are open (how to represent microbial communities, impact of genomics, effect of biofilms on flow and transport, etc.). We conclude with the basic 10 issues that we consider fundamental for any conceptually sound RT effort.

Assessment of groundwater contamination by chlorpyrifos using the PWC model in Valencia Region (Spain)

2021 ◽  
Author(s):  
Ricardo Pérez Indoval ◽  
Javier Rodrigo-Ilarri ◽  
Eduardo Cassiraga
Keyword(s):  
Reactive Transport ◽  
Management Practices ◽  
Fate And Transport ◽  
Environmental Modeling ◽  
Transport Processes ◽  
Negative Effects ◽  
Advection Dispersion ◽  
Agricultural Applications ◽  
Transformation Processes ◽  
Mass Transport Equation

<p>Chlorpyrifos is commoly used as an pesticide to control weeds and prevent nondesirable grow of algae, fungi and bacteria in many agricultural applications. Despite its highly negative effects on human health, environmental modeling of this kind of pesticide in the groundwater is not commonly done in real situations. Predicting the fate of pesticides released into the natural environment is necessary to anticipate and minimize adverse effects both at close and long distances from the contamination source. A number of models have been developed to predict the behavior, mobility, and persistence of pesticides. These models should account for key hydrological and agricultural processes, such as crop growth, pesticide application patterns, transformation processes and field management practices.</p><p>This work shows results obtained by the Pesticide Water Calculator (PWC) model to simulate the behavior of chlorpyrifos. PWC model is used as a standard pesticide simulation model in USA and in this work it has been used to  simulate the fate and transport of chlorpyrifos in the unsaturated zone of the aquifer. The model uses a whole set of parameters to solve a modified version of the mass transport equation considering the combined effect of advection, dispersion and reactive transport processes. PWC is used to estimate the daily concentrations of chlorpyrifos in the Buñol-Cheste aquifer in Valencia Region(Spain).</p><p>A whole set of simulation scenarios have been designed to perform a parameter sensitivity analysis. Results of the PWC model obtained in this study represents a crucial first step towards the development of a pesticide risk assessment in Valencia Region. Results show that numerical simulation is a valid tool for the analysis and prediction of the fate  and transport of pesticides in the groundwater.</p>

Reactive transport in porous media with local mixing limitation: A Lagrangian modeling approach

2020 ◽  
Author(s):  
Guillem Sole-Mari ◽  
Daniel Fernàndez-Garcia ◽  
Xavier Sanchez-Vila ◽  
Diogo Bolster
Keyword(s):  
Porous Media ◽  
Reactive Transport ◽  
Mathematical Formulation ◽  
Random Motion ◽  
Concentration Fluctuations ◽  
Local Concentration ◽  
Flow And Transport ◽  
Transport In Porous Media ◽  
Lagrangian Modeling ◽  
Rate Interaction

<p>Hydrological models are unable to fully resolve subsurface flow and transport down to the microscale. Instead, modelers usually work with upscaled flow and transport properties that represent the behavior of the system at a given coarse scale. While this approach is justified from a practical standpoint, it disregards the local heterogeneity of porous media flows, which tend to produce mixing-limited reactive transport behaviors that cannot be captured by classical modeling approaches. While some innovative methods have been suggested in the past in order to address this problem, none of them has proposed a mathematical formulation which can potentially reproduce the generation, transport and decay of local concentration fluctuations and their impact on chemical reactions, for general initial and boundary conditions. Here, we propose a Lagrangian approach based on the random motion of fluid particles that locally mix following a Multi-Rate Interaction by Exchange with the Mean (MRIEM) formulation. Concentration fluctuations in the proposed model display the typical behavior associated to transport in porous media with mixing-limited conditions. Experimental results of reactive transport are successfully reproduced by the model.</p>

scholarly journals NUMERICAL SIMULATING THE CHEMICAL INTERACTION OF FLUID WITH ROCK AT THE PORE SCALE

2021 ◽  
Vol 2 (3) ◽  
pp. 46-54
Author(s):  
Tatyana S. Khachkova ◽  
Vadim V. Lisitsa
Keyword(s):  
Porous Medium ◽  
Fluid Flow ◽  
Reactive Transport ◽  
Chemical Interaction ◽  
Pore Space ◽  
Heterogeneous Reactions ◽  
Pore Scale ◽  
Active Components ◽  
Flow And Transport ◽  
The Finite Difference Method

The article presents a numerical algorithm for modeling the chemically reactive transport in a porous medium at a pore scale. The aim of the study is to research the change in the geometry of the pore space during the chemical interaction of the fluid with the rock. First, fluid flow and transport of chemically active components are simulated in the pore space. Heterogeneous reactions are then used to calculate their interactions with the rock. After that, the change in the interface between the liquid and the solid is determined using the level-set method, which allows to handle changes in the topology of the pore space. The algorithm is based on the finite-difference method and is implemented on the GP-GPU.

scholarly journals A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems

2021 ◽  
Author(s):  
Zhen Peng ◽  
Jeff Linderoth ◽  
David Baum
Keyword(s):  
Reaction Networks ◽  
Food Utilization ◽  
Complex Reaction ◽  
Chemical Systems ◽  
Promising Strategy ◽  
Underlying Basis ◽  
Scientific Questions ◽  
Emergence Of Life

The complexity gap between the biotic and abiotic worlds has made explaining abiogenesis one of the hardest scientific questions. A promising strategy for addressing this problem is to identify features shared by abiotic and biotic chemical systems that permit the stepwise accretion of complexity. Therefore, we compared abiotic and biotic reaction networks in order to evaluate the presence of autocatalysis, the underlying basis of biological self-propagation, and to see if the organization of autocatalytic motifs permits stepwise complexification. We provide an algorithm to detect seed-dependent autocatalytic systems (SDASs), namely subnetworks that can use food chemicals to self-propagate but must be seeded by some non-food chemicals to become activated. We show that serial activation of SDASs can cause incremental complexification. Furthermore, we identify life-like features that emerge during the accretion of SDASs, including the emergence of new ecological opportunities and improvements in the efficiency of food utilization. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify without the need for genetic polymers. This framework also suggests experiments that have the potential to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems.

scholarly journals A higher-order finite element reactive transport model for unstructured and fractured grids

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joachim Moortgat ◽  
Mengnan Li ◽  
Mohammad Amin Amooie ◽  
Di Zhu
Keyword(s):  
Finite Element ◽  
Reactive Transport ◽  
Transport Model ◽  
Numerical Dispersion ◽  
Benchmark Problems ◽  
Fe Method ◽  
Multicomponent Transport ◽  
Advection Dispersion ◽  
Mixed Hybrid Finite Element ◽  
Second Order Convergence

Abstract This work presents a new reactive transport framework that combines a powerful geochemistry engine with advanced numerical methods for flow and transport in subsurface fractured porous media. Specifically, the PhreeqcRM interface (developed by the USGS) is used to take advantage of a large library of equilibrium and kinetic aqueous and fluid-rock reactions, which has been validated by numerous experiments and benchmark studies. Fluid flow is modeled by the Mixed Hybrid Finite Element (FE) method, which provides smooth velocity fields even in highly heterogenous formations with discrete fractures. A multilinear Discontinuous Galerkin FE method is used to solve the multicomponent transport problem. This method is locally mass conserving and its second order convergence significantly reduces numerical dispersion. In terms of thermodynamics, the aqueous phase is considered as a compressible fluid and its properties are derived from a Cubic Plus Association (CPA) equation of state. The new simulator is validated against several benchmark problems (involving, e.g., Fickian and Nernst-Planck diffusion, isotope fractionation, advection-dispersion transport, and rock-fluid reactions) before demonstrating the expanded capabilities offered by the underlying FE foundation, such as high computational efficiency, parallelizability, low numerical dispersion, unstructured 3D gridding, and discrete fraction modeling.

scholarly journals A general real-time formulation for multi-rate mass transfer problems

2009 ◽  
Vol 13 (8) ◽  
pp. 1399-1411 ◽  
Author(s):  
O. Silva ◽  
J. Carrera ◽  
M. Dentz ◽  
S. Kumar ◽  
A. Alcolea ◽  
...  
Keyword(s):  
Mass Transfer ◽  
Reactive Transport ◽  
River Flow ◽  
Breakthrough Curves ◽  
Published Data ◽  
Flow And Transport ◽  
Slow Kinetics ◽  
Multiple Processes ◽  
Transfer Problems ◽  
Non Equilibrium

Abstract. Many flow and transport phenomena, ranging from delayed storage in pumping tests to tailing in river or aquifer tracer breakthrough curves or slow kinetics in reactive transport, display non-equilibrium (NE) behavior. These phenomena are usually modeled by non-local in time formulations, such as multi-porosity, multiple processes non equilibrium, continuous time random walk, memory functions, integro-differential equations, fractional derivatives or multi-rate mass transfer (MRMT), among others. We present a MRMT formulation that can be used to represent all these models of non equilibrium. The formulation can be extended to non-linear phenomena. Here, we develop an algorithm for linear mass transfer, which is accurate, computationally inexpensive and easy to implement in existing groundwater or river flow and transport codes. We illustrate this approach by application to published data involving NE groundwater flow and solute transport in rivers and aquifers.

Simulating reactive transport in time dependent multiphase flow problems

2004 ◽  
Vol 92 (9-11) ◽  
Author(s):  
Maarten Saaltink ◽  
Francisco Batlle ◽  
Carlos Ayora ◽  
Jesús Carrera
Keyword(s):  
Multiphase Flow ◽  
Reactive Transport ◽  
Pyrite Oxidation ◽  
Time Dependent ◽  
Time Varying ◽  
Mass Balances ◽  
Flow Properties ◽  
Flow And Transport ◽  
Flow Problems ◽  
Time Stepping

SummaryThis paper discusses issues on time stepping and time weighing when simulating reactive transport in time dependent multiphase flow problems. It proposes to solve the flow and transport equation with different time increments. We analyze how the time varying flow properties should be evaluated in order to obtain correct solute mass balances. The proposed algorithm is illustrated by an example that models pyrite oxidation in an unsaturated soil. The example shows that flow and transport may require completely different time steps for numerical reasons and illustrates well the utility of using different time steps.

scholarly journals Modeling of Flow and Transport in Saturated and Unsaturated Porous Media

Water ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1088
Author(s):  
Anis Younes ◽  
Marwan Fahs ◽  
Philippe Ackerer
Keyword(s):  
Porous Media ◽  
Fluid Flow ◽  
Reactive Transport ◽  
Transport Processes ◽  
Flow And Transport ◽  
Current Trends ◽  
Process Understanding ◽  
Wide Range ◽  
Hyporheic Zones ◽  
Relevant Topic

Modeling fluid flow and transport processes in porous media is a relevant topic for a wide range of applications. In water resources problems, this topic presents specific challenges related to the multiphysical processes, large time and space scales, heterogeneity and anisotropy of natural porous media, and complex mathematical models characterized by coupled nonlinear equations. This Special Issue aims at collecting papers presenting new developments in the field of flow and transport in porous media. The 25 published papers deal with different aspects of physical processes and applications such as unsaturated and saturated flow, flow in fractured porous media, landslide, reactive transport, seawater intrusion, and transport within hyporheic zones. Based on their objectives, we classified these papers into four categories: (i) improved numerical methods for flow and mass transport simulation, (ii) looking for reliable models and parameters, (iii) laboratory scale experiments and simulations, and (iv) modeling and simulations for improved process understanding. Current trends on modeling fluid flow and transport processes in porous media are discussed in the conclusion.

scholarly journals Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 308
Author(s):  
Sandeep Ameta ◽  
Yoshiya J. Matsubara ◽  
Nayan Chakraborty ◽  
Sandeep Krishna ◽  
Shashi Thutupalli
Keyword(s):  
Experimental Evolution ◽  
Experimental Studies ◽  
Theoretical Work ◽  
Living System ◽  
Darwinian Evolution ◽  
Chemical System ◽  
Chemical Systems ◽  
Open Questions ◽  
Scientific Questions ◽  
Emergence Of Life

Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as “a self-sustaining chemical system capable of Darwinian evolution”. It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.

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