Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media
Round 1
Reviewer 1 Report
Dear author,
my report file is attached. you can find my opinion about your paper.
Comments for author File: 
Comments.pdf
Author Response
Dear Reviewer:
Thank you for giving us the opportunity to submit a revised draft of the manuscript “Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media” for publication in the Special Issue: Modeling and Numerical Simulations in Petroleum Engineering in Applied Sciences. We appreciate the time and effort that you dedicated to providing feedback on our manuscript and are grateful for the insightful comments on and valuable improvements to our paper.
We have incorporated most of the suggestions. Those changes are highlighted within the manuscript. Please see below for a point-by-point response to your comments and concerns. All page numbers refer to the revised manuscript file with tracked changes.
1、The authors should show why their manuscript: Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media is relevant to the scope of Special Issue: Modeling and Numerical Simulations in Petroleum Engineering in Applied Sciences Journal.
A: In this manuscript, we focus on the flow of oil-water two-phase in heterogeneous porous media. The physical fields of oil-water two-phase flow and oil-phase solute convection and diffusion in water are successfully coupled together. This achievement facilitates the study on the accumulation of chemotactic bacteria at the oil-water interface, and further helps the understanding and potential applications of chemotactic bacteria in oil contamination remediation and microbial enhanced oil recovery (EOR).
Therefore, we believe that this manuscript is suitable for publication in Special Issue "Modeling and Numerical Simulations in Petroleum Engineering of Applied Sciences, and it fits one of the topics in the journal’s scope - ‘multiphase, multicomponent flow in heterogeneous porous media’.
2、Enrich the abstract with more quantitative results extracted from the paper.
A: We were aware of the lack of quantitative results in the abstract, so we extracted more quantitative results and placed them in the abstract. In lines 31 and 32 of the text.
3、4、5：
A: We have corrected the formatting errors in the Page 1, paper header and paper footer.
6、7：
A： Thank you for pointing it out. Figures 1 and 2 are both geometric model diagrams, which are originally presented in black and white when exported from the COMSOL software.
8、It is better to add Nomenclature section to the papers to define all the parameters in Eq. (1)- Eq. (16).
A: We have added Nomenclature section to the paper to define all the parameters in Eq. (1)- Eq. (16). In line 163.
9、The relevance to Applied Sciences should be enhanced with the considerations of scope and
readership of the Journal by adding some published papers in Applied Sciences to REFERENCES section.
A: We have added some published papers in Applied Sciences to the References section. for increased relevance to Applied Sciences. In lines 63 and 625.
For instance, the article "Single cell chemotactic responses of Helicobacter pylori to urea in a microfluidic chip" published in Applied Sciences observed the single-cell chemotactic responses of Helicobacter pylori to urea through a microfluidic chip, which is relevant to our research. We added this paper to the References section.
Reviewer 2 Report
Please improve the clarity of the text in the scalebars in the Figs. 3~9, and mark the unit of the velocity for all of them.
Author Response
Dear Reviewer:
Thank you for giving us the opportunity to submit a revised draft of the manuscript “Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media” for publication in the Special Issue: Modeling and Numerical Simulations in Petroleum Engineering in Applied Sciences. We appreciate the time and effort that you dedicated to providing feedback on our manuscript and are grateful for the insightful comments on and valuable improvements to our paper.
We have incorporated your suggestions. Those changes are highlighted within the manuscript. Please see below for a point-by-point response to your comments and concerns. All page numbers refer to the revised manuscript file with tracked changes.
1、Please improve the clarity of the text in the scalebars in the Figs. 3~9, and mark the unit of the velocity for all of them.
A: Thank you for pointing out this problem. We have improved the clarity of the text in the scalebars in the Figs.3-9, and mark the unit of the velocity for all of them. In lines 371, 423, 463 and 507.
Reviewer 3 Report
This manuscript studies the spreading of chemotactic bacteria and of a contaminant across an oil-water interface in porous media. The simulations are based on a phase-field model for the oil-water mixture and on the convection-diffusion equation for the contaminant and bacteria, which are solved using Consol. The effects of inlet fluid velocity, porous media porosity and contact angle are studied. The results are interesting and the paper is well written. I list below some questions and suggestions.
Although Consol is used, more details about the model could be provided. For instance, which numerical method is used? Finite volumes? How the wetting boundary condition is implemented?
The advection-diffusion equation is used to simulate the dispersion of bacteria, which assumes that the spreading is diffusive. What are the conditions needed to have the diffusive regime (density, mean free path, etc)?
The preservation of trapped fluid volumes is usually tricky to obtain (see Phys. Fluids 34, 023102 (2022)). Did you observe any change in the fluid volumes with time? Would be possible to maintain this feature with a pressure difference instead of a constant velocity as in the reference above?
It is missing a dot product after the differential operator in Eqs. 2 and 3.
In lines 170 and 211, the same name (surface tension) is given to two different quantities.
In line 199, it is written phi instead of the symbol. The same in other parts of the text. Please check.
In Figs. 3, 4, 6 and 9, the numbers in the colour bar are too small. And some figures are not aligned with the others.
Author Response
Dear Reviewer:
Thank you for giving us the opportunity to submit a revised draft of the manuscript “Numerical Simulation of the Enrichment of Chemotactic Bacte-ria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media” for publication in the Special Issue: Modeling and Numerical Simulations in Petroleum Engineering in Applied Sciences. We appreciate the time and effort that you dedicated to providing feedback on our manuscript and are grateful for the insightful comments on and valuable improvements to our paper.
We have incorporated your suggestions. Those changes are highlighted within the manuscript. Please see below for a point-by-point response to your comments and concerns. All page numbers refer to the revised manuscript file with tracked changes.
1、Although COMSOL is used, more details about the model could be provided. For instance, which numerical method is used? Finite volumes? How the wetting boundary condition is implemented?
A: Thank you for your question. The finite-element solver COMSOL Multiphysics was used to accomplish the numerical modelling and simulation. I added this sentence to Line 122.
The physical model of the phase field method is a diffusion interface method based on density functional theory. The description of the interface uses thermodynamic principles. The origin of the phase field model can be traced back to the density gradient theory proposed by van der Waals and Reynolds. In the phase field model, the interface has a finite thickness, and a diffusive interface of finite thickness separates two immiscible fluids, in contrast to classical hydrodynamics, which describes the interface between the two fluids as a free boundary A key difference. Simulation of multiphase flow in a micropore-scale system with a phase field model achieves the best balance of thermodynamic rigor and computational efficiency. I added the description above to Line 139-147.
Regarding the setting of the wetting boundary condition, the method has been given in Line 304 of the manuscript.
2、The advection-diffusion equation is used to simulate the dispersion of bacteria, which assumes that the spreading is diffusive. What are the conditions needed to have the diffusive regime (density, mean free path, etc)?
A: Thank you for this inspiring question. This manuscript focus on achieving the constant mass transfer of NAPL component from the oil phase to the water phase and the formation of NAPL concentration gradient in water phase near the changing oil/water interface. Chemotactic accumulation is a scenario of application of the achievement above and is not the focus point in this paper, so we the authors simplified bacteria as a soluble solute in water, and also the dispersion coefficient as diffusion coefficient of a solute. Your question is very important and matches our next step plan. Our next step plan is to confirm dispersivity in experiments of chemotactic bacteria, and amend the equation with dispersion coefficient and support the experimental findings.
3、The preservation of trapped fluid volumes is usually tricky to obtain (see Phys. Fluids 34, 023102 (2022)). Did you observe any change in the fluid volumes with time? Would be possible to maintain this feature with a pressure difference instead of a constant velocity as in the reference above?
A: Yes, we observe the volume change with time, but we only did the observation in a relatively short period of time. The reason for that is because we are more concerned with the phenomenon of chemotactic bacteria enrichment at the oil-water two-phase interface, which usually occurs in a relatively short period of time (a few minutes). During this period of time, except the fluid volume change caused by flooding as shown in this study, our previous experimental findings shows no other obvious change in fluid volume. However, we are very interested in your suggestion and reference, when we conduct related research about remediation conducted in a much longer period of time in future, we believe that the further change in fluid volume is a nonnegligible factor and will integrate it into our model according to the question and reference.
To answer the second question, because in reality, the flow of groundwater is usually described as a flow rate rather than a pressure. To ensure compliance with the actual situation, we adopt a constant flow condition for the inlet boundary. But the pressure boundary condition and its effect on the displacement is an interesting topic, and is worth of discussion in the follow-up research.
4、It is missing a dot product after the differential operator in Eqs. 2 and 3.
A: After verification, we believe that the equation is correct. (See Oil & Gas Science and Technology-Rev.IFP Energies nouvelles,2019,74(78):1-15.)
5、In lines 170 and 211, the same name (surface tension) is given to two different quantities.
A: Thank you for pointing this out. We have corrected this error in the manuscript. On line 183, F refers to the surface tension in N, and on line 225, σ refers to the surface tension coefficient in N/m.
6、In line 199, it is written phi instead of the symbol. The same in other parts of the text. Please check.
A: In this manuscript, f is the external free energy and ∂f/∂φ is the derivative of the external free energy with respect to φ, and we have corrected the errors you pointed out in the manuscript. In lines 213, 307 and 315.
7、In Figs. 3, 4, 6 and 9, the numbers in the colour bar are too small. And some figures are not aligned with the others.
A: We have improved the clarity of the text in the scalebars in the Figs.3, 4, 6 and 9, and mark the unit of the velocity for all of them. In lines 371, 423, 463 and 507.
