Design and Construction of an Aerated Accumulation Bioreactor for Solid Waste Treatment

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This study designed and constructed an aeration accumulation bioreactor for solid waste treatment.

This topic fits the scope of journal Processes.

The following issues should be addressed or revised:

1. First thing is this manuscript is not well organized. The sections are very strange. And probably this manuscript are written by AI?
2. The main target or focus of this study should be well addressed. A DEM based model simulation or industrial or pilot scale experiment on the bioreactor.
3. I understood the main focus is the DEM modeling on mixing of particles in the stir reactor.
4. Thus, the steel 304 for the reactor was described in line 168. This is confusing and can be deleted.
5. The introduction section should follow the main focus of this study. The relevant research papers on similar bio stir reactor should be summarized and critically reviewed.
6. Figure 2 and 3 can be merged into one figure, and the key length parameters can be marked in figure 1.
7. A detailed mesh should be presented.
8. The details of particle number and size, forces in the DEM model should be addressed.
9. Simulation details, for example time step are missing.
10. And most important, the model validation.
11. A similar paper can be referred: https://doi.org/10.1016/j.powtec.2025.121103. The authors can look at the model descriptions, meshes, validations.
12. The section 3.4, 3.5 and 3.6 are also very strange. What would the authors want to emphasize? This is weird. This looks like a review report. I cannot imagine this is a simulation paper.
13. Besides, in section 3.5, a large number of references are cited. This is weird.
14. What disappointed is the final conclusions are made without any in-depth analysis of DEM results. I thought the authors may test different configurations of the bioreactor.
15. What happens for the paragraph in line 104 to 110? Is this the template texts and the authors forget to delete.

Author Response

We sincerely thank the reviewer for their careful and constructive evaluation of our manuscript. Your insightful comments and valuable suggestions have significantly contributed to improving the clarity, rigor, and overall quality of our work. We appreciate the time and effort invested in the review process.

1. First thing is this manuscript is not well organized. The sections are very strange. R:/ The authors tried to revise this suggestion on the layout of the sections, and together with the recommendations of the three reviewers, we believe that this version is more complete and clearer to the reader. We are grateful for the review.

2. The main target or focus of this study should be well addressed. A DEM based model simulation or industrial or pilot scale experiment on the bioreactor. R:/ We appreciate this important question regarding the focus of our study. The main objective of this work is to present the engineering design and construction of a pilot-scale aerated accumulation bioreactor intended for solid-phase bioremediation, supported by a qualitative DEM-based evaluation of its internal mixing performance.

This is not solely a simulation study, nor is it focused on full-scale industrial application. Rather, it bridges both domains by:

(i) delivering a detailed reactor design ready for physical implementation, including construction plans and geometric considerations; and

(ii) using DEM simulations to assess the efficiency of the mixing system in order to validate and refine key design decisions—particularly regarding paddle geometry and reactor volume.

The reactor was physically built and is operational at pilot scale; however, the present manuscript does not include kinetic or microbiological performance tests, which will be the focus of future experimental work. Therefore, the study should be viewed as an engineering contribution combining computational modeling and design validation for scalable bioreactor systems in ex situ soil bioremediation.

 

3. Thus, the steel 304 for the reactor was described in line 168. This is confusing and can be deleted. R:/ The mention of the material used for the construction of the bioreactor, steel 304, was removed from this section following their recommendations.

 

4. The introduction section should follow the main focus of this study. The relevant research papers on similar bio stir reactor should be summarized and critically reviewed. R:/ We appreciate your insightful comment. In response, we have expanded the introduction to include a critical review of relevant literature on stirred bioreactors used in solid-state processes. Specifically, we discuss recent studies employing vertical and horizontal shaft mixers, including the work of Pezo et al. (2021), who simulated horizontal screw mixers using DEM, and Zhang et al. (2025), who evaluated blade geometry in spiral mixers. These studies are now contextualized in terms of their technical limitations—such as poor scalability, energy inefficiency, and lack of experimental validation. We emphasize how our work builds upon these findings by incorporating DEM-informed paddle design and validating the reactor's performance through both simulation and construction. The revised introduction clearly highlights how our study fills this gap by offering a practical and scalable bioreactor with enhanced mixing performance and microbial compatibility.

 

5. Figure 2 and 3 can be merged into one figure, and the key length parameters can be marked in figure 1. R:/ After reviewing your comments in detail, we feel it is appropriate to merge the two figures into a single figure that represents the essential dimensions of the bioreactor design. We believe that placing this information in Figure 1 of the original manuscript does not allow the reader to visualize the detail of the layout of the elements, so we suggest leaving it in the new version of Figure 3.

 

6. A detailed mesh should be presented. R:/ The detailed grid for the simulation is presented in the new version of the manuscript, please refer to Figure 1 in the methodology section, which presents (a) Triangular surface discretization (STL mesh) of the aerated accumulation bioreactor imported into Rocky DEM. (b) Eulerian grid defined for statistical analysis of particle distribution and mixing, with 1 radial division, 18 tangential divisions, and 8 axial divisions.

 

7. The details of particle number and size, forces in the DEM model should be addressed. R:/ Thank you for your observation. The requested information regarding the DEM simulation parameters was already provided in Table 1 of the manuscript. This table includes a full specification of the contact model used (Hertz–Mindlin with rolling resistance), the number of particles simulated (10,000), particle diameter (5 mm), and all relevant material properties such as density (800 kg/m³), Poisson’s ratio (0.30), Young’s modulus (3.0 × 10⁷ Pa), and the coefficients of restitution, static and rolling friction. To further improve clarity, we have ensured that Table 1 is explicitly referenced in the numerical modeling section, and a brief descriptive paragraph has been added to summarize these parameters.

 

8. Simulation details, for example time step are missing. And most important, the model validation. A similar paper can be referred: https://doi.org/10.1016/j.powtec.2025.121103. The authors can look at the model descriptions, meshes, validations. R:/ We sincerely thank the reviewer for pointing this out and for referencing a relevant study. In response, we have now included the specific step value used in DEM simulations. This addition can be found in Table 1.

 

Regarding model validation, we acknowledge that no experimental mixing validation (e.g., via tracers or imaging) was performed in this study. As the main goal of this work was to support reactor design decisions and internal configuration using DEM-based comparative analysis, the simulations were intended as a qualitative assessment of flow and mixing trends within the reactor. These results were used to inform paddle geometry and reactor dimensions, rather than to make precise quantitative predictions of bioprocess kinetics. Future work will focus on experimental validation through tracer dispersion and bioremediation in a case study.

 

9. The section 3.4, 3.5 and 3.6 are also very strange. What would the authors want to emphasize? This is weird. This looks like a review report. I cannot imagine this is a simulation paper. R:/ We appreciate your observation and fully understand your concern. This manuscript is not intended to be exclusively a simulation paper, but rather an engineering-oriented study that presents the integrated design and evaluation of an aerated accumulation bioreactor for the bioremediation of contaminated soils.

The paper combines three core components:

(i) the engineering design of a novel bioreactor system intended to address current limitations in solid-phase soil treatment;

(ii) a preliminary geometric evaluation using DEM simulations, focused on assessing mixing and segregation dynamics; and

(iii) a detailed discussion of the operational conditions required for successful bioremediation using this type of reactor, including strategies such as bioaugmentation, biostimulation, and bioventing, as well as critical parameters like moisture, nutrients, temperature, and pH.

 

This final component is intended to bridge the proposed design with its practical application, as the aim of this work is to present a ready-to-implement engineering solution, not solely a theoretical simulation model. We have revised the text to make this three-part structure more explicit and to clarify the overall scope of the study. We added a paragraph before section 3.3.

 

10. Besides, in section 3.5, a large number of references are cited. This is weird. R:/ Thank you for your observation. We understand that the number of references in Section 3.5 may appear extensive. However, this section was intentionally designed to summarize the key environmental and operational variables that must be considered to ensure the effectiveness of bioremediation in solid-phase systems—particularly within the context of ex situ bioreactors. Given the interdisciplinary nature of these parameters (including moisture control, nutrient availability, pH, aeration, and temperature), it was important to support each aspect with relevant and up-to-date literature from environmental engineering, microbiology, and soil science. The aim is not to conduct a literature review, but to demonstrate the technical basis and applicability of the proposed bioreactor under real conditions.

 

11. What disappointed is the final conclusions are made without any in-depth analysis of DEM results. I thought the authors may test different configurations of the bioreactor. R:/ In this new version of the manuscript we have reviewed different configurations of the bioreactor, re-run the DEM simulation and based on that rewrote a new proposed conclusion. We hope that these adjustments will satisfy the comments proposed by the reviewer.

 

12. What happens for the paragraph in line 104 to 110? Is this the template texts and the authors forget to delete. R:/ You are absolutely right. This paragraph was inadvertently left in the manuscript during the formatting process, as it belonged to the original journal template. We sincerely apologize for the oversight. The paragraph has now been removed in the revised version to maintain consistency and clarity throughout the document.

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have reported an interested study on the aerated accumulation bioreactor for the treatment of solid waste. The bioreactor has been evaluated through numerical simulation and experimental approach. After a careful review the following major discrepancies has been found which should be incorporated before its possible acceptance for publication:

1. The research gap in the introduction section needs further elaboration. The novelty aspect of the current work should be presented in the light of existing literature. For example, there are some interesting studies published recently focussed on the design and simulation of bioreactors, particularly using CFD approach.
2. Further in-depth discussion and justification is required on the design and geometry of the proposed bioreactor. Moreover, mixing strategy and design of agitator/mixer also needs to be justified in line with the previous studies.
3. Numerical simulations lack in significant supporting data: Firstly, the explanation on mesh formation, mesh size and its quality is missing. One would expect the mesh figure with its clear grid shape. The respective models used in DEM are also not clearly mentioned, i.e., drag model, granular flow, momentum exchange etc. Similarly, the information on boundary conditions as well as operating parameters are also missing. Particle shape, size and number? The solver approach, convergence criteria as well as computational cost/time should also be mentioned for a clear evaluation of the proposed numerical model. The models and their attributes can be summarized in a table.
4. In Figure 4, the contour legend is missing, what does the colour indicate? What is the parameter being presented here, mass fraction or volume fraction?
5. The experimental part is very confusing. Particular attention is required. It looks like more on a report on different operating parameters. A clear information on experiments and methodology on trails conducted in the current work are expected. Moreover, the experimental data must be discussed and validated with the numerical simulation results.
6. Similarly, the conclusions section should be revised thoroughly with clear outcomes on the current finding by numerical simulations and experiments.       

Author Response

We sincerely thank the reviewer for their careful and constructive evaluation of our manuscript. Your insightful comments and valuable suggestions have significantly contributed to improving the clarity, rigor, and overall quality of our work. We appreciate the time and effort invested in the review process.

1. The research gap in the introduction section needs further elaboration. The novelty aspect of the current work should be presented in the light of existing literature. For example, there are some interesting studies published recently focussed on the design and simulation of bioreactors, particularly using CFD approach. R:/ Thank you for this valuable observation. We agree that highlighting the research gap and novelty of our work is essential. In response, we have revised the introduction section to more explicitly contrast our study with recent research on bioreactor design and simulation, particularly studies based on CFD approaches.

While CFD has been widely used to simulate fluid dynamics and optimize aeration or liquid-phase mixing in bioreactors, these studies often focus on submerged systems and are not directly applicable to solid-phase bioremediation processes. In contrast, our work addresses a distinct technological niche: the design and construction of an aerated accumulation bioreactor specifically tailored for solid-state bioremediation, where material heterogeneity, low water content, and the need for mechanical agitation present unique challenges that CFD cannot adequately capture.

The use of Discrete Element Method (DEM) in our study fills this gap by simulating the behavior of particulate solids, enabling the evaluation of internal mixing performance in a way that is more aligned with the physics of solid-phase treatment. Moreover, our work goes beyond theoretical modeling by providing a fully constructed pilot-scale system, including engineering drawings, operational parameters, and design decisions validated through DEM simulations.

These aspects have been clearly emphasized in the revised introduction to better articulate both the novelty and relevance of our contribution within the broader bioreactor design literature.

 

2. Further in-depth discussion and justification is required on the design and geometry of the proposed bioreactor. Moreover, mixing strategy and design of agitator/mixer also needs to be justified in line with the previous studies. R:/ Thank you for your constructive feedback. In response, we have revised the manuscript to provide a more detailed justification of both the bioreactor geometry and the selected mixing strategy.

 

The design of the reactor chamber was guided by constraints relevant to ex situ solid-phase bioremediation, including the need to promote convective airflow, maintain thermal stability, and facilitate uniform agitation within a confined volume. To validate the proposed paddle configuration, we conducted a comparative DEM study in which several angular orientations of the agitator blades were evaluated. These configurations were analyzed based on their ability to promote particle movement and reduce segregation.

 

As part of this analysis, we calculated the Lacey Mixing Index (LMI) at multiple time steps for each design variation. The results, now included in the revised manuscript, demonstrate that the selected paddle geometry achieved higher homogeneity levels in shorter mixing times compared to alternative designs. This provides a quantitative rationale for the chosen configuration.

 

We have also expanded the discussion to contrast our approach with relevant studies on bioreactor design and mixing systems, highlighting how our DEM-based evaluation adds value in solid-phase contexts where particle-scale behavior is critical.

 

These additions clarify the methodological reasoning behind the reactor and agitator design and reinforce the novelty of applying DEM-based metrics to optimize solid-phase bioreactor mixing.

 

3. Numerical simulations lack in significant supporting data: Firstly, the explanation on mesh formation, mesh size and its quality is missing. One would expect the mesh figure with its clear grid shape. The respective models used in DEM are also not clearly mentioned, i.e., drag model, granular flow, momentum exchange etc. Similarly, the information on boundary conditions as well as operating parameters are also missing. Particle shape, size and number? The solver approach, convergence criteria as well as computational cost/time should also be mentioned for a clear evaluation of the proposed numerical model. The models and their attributes can be summarized in a table. R:/ We sincerely appreciate your detailed and insightful comments regarding the numerical simulation section. In the revised version of the manuscript, we have addressed each of these points to ensure a comprehensive and transparent description of the DEM methodology.

 

The mesh formation and quality have been explicitly described. As the simulations were performed in Rocky DEM using STL geometry, surface discretization was applied to the reactor walls, with triangular elements serving as contact boundaries. A new figure showing the Eulerian mesh grid used for concentration field calculations (with radial, axial, and tangential divisions) has been included to clarify the spatial discretization strategy.

 

The DEM model used in the simulations is now clearly specified as the Hertz–Mindlin (no slip) contact model, with rolling friction enabled. The particle shape was spherical, with a uniform size of 5 mm, and a total of 10,000 particles were simulated.

 

Boundary conditions and operational parameters are detailed in the updated methodology section, including gravitational acceleration, wall conditions (rigid, no-slip), and time step. The simulation time step was set according to the Rayleigh criterion to ensure numerical stability and is now explicitly reported.

 

The solver approach used in Rocky DEM is an explicit time integration scheme, and although convergence criteria are not traditionally applied in DEM as in CFD, we ensured stability through appropriate stiffness, damping, and time step settings.

 

Finally, we have added a summary table that compiles the key simulation parameters, contact model attributes, and mesh configuration for ease of reference.

 

These revisions significantly improve the clarity and reproducibility of the numerical modeling section and respond directly to your valuable suggestions.

 

4. In Figure 4, the contour legend is missing, what does the colour indicate? What is the parameter being presented here, mass fraction or volume fraction? R:/ Thank you for this observation. Figure 4 displays particle mixing using different views of the reactor. As noted in the caption, the two colours represent identical particles differentiated solely for visualization purposes, similar to tracer particles. Since all particles have the same size and density, the visual representation reflects both mass and volume fractions. We have clarified this in the figure caption for better understanding.

5. The experimental part is very confusing. Particular attention is required. It looks like more on a report on different operating parameters. A clear information on experiments and methodology on trails conducted in the current work are expected. Moreover, the experimental data must be discussed and validated with the numerical simulation results. R:/ Thank you for your valuable feedback. We understand the concern regarding the perceived lack of experimental trials. However, we would like to clarify that this manuscript is not intended as an experimental validation study. Rather, it presents the engineering design and construction of an aerated accumulation bioreactor for solid-phase bioremediation, supported by numerical simulation (DEM) to evaluate the internal mixing performance and inform key design decisions.

The discussion of operational parameters in the manuscript is provided to contextualize the reactor's practical use and to serve as a guideline for its future application. These parameters were compiled from validated literature sources and do not originate from trials conducted during this study. Therefore, no direct experimental results are presented or compared with the simulations. This scope is now clearly stated in the revised manuscript to avoid any confusion. Future work will focus on experimental validation under field or laboratory conditions using the constructed reactor.

 

6. Similarly, the conclusions section should be revised thoroughly with clear outcomes on the current finding by numerical simulations and experiments.   R:/ The conclusions were improved.

Reviewer 3 Report

Comments and Suggestions for Authors

Manuscript ID: processes-3742065

This study submitted an aerated accumulation bioreactor that was designed and constructed, incorporating an innovative paddle system aimed at enhancing solid mixing and air distribution. The geometric configuration was evaluated through discrete element method (DEM) simulations to predict the mixing dynamics and quantify homogeneity using the Lacey Mixing Index (LMI). The study is supposed to optimize the homogeneity, the filling volumes, the mixing times, and the heating values to obtain the favorable conditions for microbial activity and contaminant degradation, comparing the conventional bioreactor systems, and highlighting the relevance of integrating DEM modeling in the early stages of bioreactor development.

The research aligns with the journal’s scope. However, some requirements are needed to clear and interpret this work. The following comments focus on the ambiguous points that require modification or clarification.

• Abstract:
• The quantitative optimum results as the optimal homogeneity with higher filling volumes and shorter mixing times, have to be stated.
• Energy-efficiency was stated in the abstract, but wasn’t mentioned in any other place in the manuscript. It should be discussed or eliminated from the abstract.
• Finally, a sentence expressing the perspectives could be added at the end of the abstract.
• Introduction:
• The introduction didn’t cover the main items of the title of the manuscript, which are the design and construction of the bioreactor. It is recommended to exhibit the previous work and techniques of bioremediation with some quantitative data to describe what has been achieved previously to be able to figure out the novelty of this work.
• Ex-situ solid bioremediation is discussed in the text, so it is preferred to be introduced in the introduction section; moreover, previous work has tackled this technique.
• Materials and Methods
• Lines 104-110, this paragraph seems like the instructions for writing; it is not a summary of the section!
• Lines 130-132, this sentence is misleading; since the Design modeler only represents what you input or program into it. The dimensions, constraints, and relationships should be provided to the software to generate the model.

The suggested sentence is “The geometric model was constructed based on specified dimensional relationships between the bioreactor body and the impeller”.

• Depending on the previous note, lines 185-230 which describe the geometric design should be transferred to be a part of the geometric design development line 132.
• Results and Discussion
• Figure 2 should be eliminated since it is repeated in Fig. 3, then reorganize figures’ numbers. The dimensions could be stated in the text if needed.
• Keep Fig. 3 since it is related to Table 1.
• Line 166 is misleading since there is no data about the computational validation anywhere in the text. Therefore, this system should be deleted.
• Format the figure dimensions as stated in the author guidelines.
• Line 279, delete the abbreviation RSD since it is not used elsewhere.
• Section 3.4, lines 293-337, is proper as an introduction not in the section of results and discussion. The repeated thoughts and sentences should be avoided.
• Section 3.5, lines 338- 428, is proper to be transferred to the introduction after summarizing it and avoiding repetitions. The same request for section 3.5.3 bioventing, lines 469- 489,
• The paragraph, lines 578-598, needs formatting.
• The optimum parameters should be stated as quantitative data that describe the factors affecting the bioremediation and their effect on the contaminant degradation.
• Conclusion
• The conclusion has to be rewritten to offer clear and definite data about the optimum parameters.
• The conclusion should be end with the perspectives of this technique.
• It is better to format conclusion in a union paragraph.

 

• References
• The references inside the text need to be formatted, e.g., in line 379.
• The reference formatting in the reference list should be reconsidered, e.g., journal abbreviation [18-20].

 

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Language editing is preferred due to high repetition.

Author Response

We sincerely thank the reviewer for their careful and constructive evaluation of our manuscript. Your insightful comments and valuable suggestions have significantly contributed to improving the clarity, rigor, and overall quality of our work. We appreciate the time and effort invested in the review process.

Abstract:

• The quantitative optimum results as the optimal homogeneity with higher filling volumes and shorter mixing times, have to be stated. R:/ This suggestion was implemented in the new version of the manuscript.
• Energy-efficiency was stated in the abstract, but wasn’t mentioned in any other place in the manuscript. It should be discussed or eliminated from the abstract. R:/ As this aspect was not studied, this word was removed from the abstract.
• Finally, a sentence expressing the perspectives could be added at the end of the abstract. R:/ This suggestion was implemented in the new version of the manuscript.

Introduction:

• The introduction didn’t cover the main items of the title of the manuscript, which are the design and construction of the bioreactor. It is recommended to exhibit the previous work and techniques of bioremediation with some quantitative data to describe what has been achieved previously to be able to figure out the novelty of this work. R:/ The introduction section was improved to reflect the reviewers’ suggestions.

• Ex-situ solid bioremediation is discussed in the text, so it is preferred to be introduced in the introduction section; moreover, previous work has tackled this technique. R:/ Thank you for this thoughtful observation. While we agree that ex-situ solid-phase bioremediation has been previously addressed in the literature, we respectfully clarify that our intention was not to reintroduce general concepts, but rather to contextualize the specific operational principles relevant to the implementation of this technique within the engineered bioreactor system presented in this study. The discussion in section 3.3 is therefore not redundant with the introduction but serves to bridge the gap between reactor design and biological functionality by highlighting how factors such as aeration, agitation, and substrate conditions are integrated into the system’s architecture. For this reason, we believe this content is more appropriately placed within the Results and Discussion section, where the engineering implications and practical applications of ex-situ bioremediation are interpreted in light of the proposed reactor configuration.

Materials and Methods

• Lines 130-132, this sentence is misleading; since the Design modeler only represents what you input or program into it. The dimensions, constraints, and relationships should be provided to the software to generate the model.  The suggested sentence is “The geometric model was constructed based on specified dimensional relationships between the bioreactor body and the impeller”. R:/ This sentence was included in the manuscript according to the Reviewer suggestion.

• Depending on the previous note, lines 185-230 which describe the geometric design should be transferred to be a part of the geometric design development line 132. R:/ In this new version of the manuscript and considering the comments of the other reviewers, including yourself, improvements were made to this section.

Results and Discussion

• Figure 2 should be eliminated since it is repeated in Fig. 3, then reorganize figures’ numbers. The dimensions could be stated in the text if needed. R:/ After reviewing your comments in detail, we feel it is appropriate to merge the two figures into a single figure that represents the essential dimensions of the bioreactor design.
• Keep Fig. 3 since it is related to Table 1. R:/ The figure was preserved in this version of the manuscript. Thank you for your clarifications.
• Format the figure dimensions as stated in the author guidelines. R:/ The figures were formatted according to the author’s guidelines. The only thing we would like to point out is that Figure 4 is a bit longer because it is representing a timeline to visualize the reactor segregation.
• Line 279, delete the abbreviation RSD since it is not used elsewhere. R:/ The abbreviation was removed in the manuscript.
• Section 3.4, lines 293-337, is proper as an introduction not in the section of results and discussion. The repeated thoughts and sentences should be avoided. Section 3.5, lines 338- 428, is proper to be transferred to the introduction after summarizing it and avoiding repetitions. The same request for section 3.5.3 bioventing, lines 469- 489. R:/ Thank you for this thoughtful observation. We understand the concern regarding the placement of sections 3.4, 3.5, and 3.5.3. However, we would like to respectfully clarify that these sections were deliberately structured within the Results and Discussion to serve a specific purpose.

While the manuscript presents a novel bioreactor design and its validation through DEM simulations, it also aims to establish a solid engineering and biotechnological foundation for its real-world application. Sections 3.4 and 3.5 are not introductory; rather, they contextualize the operational implications of the proposed system, providing readers with a technically relevant synthesis of process conditions—such as nutrient composition, moisture levels, temperature control, and microbial strategies (bioaugmentation, biostimulation, and bioventing)—required for successful implementation of solid-phase bioremediation in the designed reactor.

These discussions do not repeat the introduction but rather extend the interpretation of the reactor's functional design by linking its physical construction to the critical biological processes it must support. They also guide future experimental work and operational optimization. This integration between mechanical design and biological application is aligned with the interdisciplinary nature of the manuscript.

• The paragraph, lines 578-598, needs formatting. R:/ The paragraph mentioned in these lines has been formatted for clarity.
• The optimum parameters should be stated as quantitative data that describe the factors affecting the bioremediation and their effect on the contaminant degradation. R:/ Thank you for this valuable suggestion. We have revised the manuscript to clearly present key operational parameters—such as temperature (30–35 °C), moisture content (60–70%), pH (6.5–8.0), and C/N ratio (20–30)—as quantitative guidelines based on published studies. These parameters have been shown to significantly influence microbial activity and contaminant degradation efficiency in solid-phase bioremediation systems.

For example, we now highlight that hydrocarbon removal rates can increase by up to 40–50% when moisture content is maintained above 60%, and that optimal C/N ratios improve microbial metabolism and biomass growth. These modifications have been included in section 3.5, and relevant references have been added to support the discussion.

 

Conclusion

• The conclusion has to be rewritten to offer clear and definite data about the optimum parameters. The conclusion should be end with the perspectives of this technique. It is better to format conclusion in a union paragraph. R:/ We have rewritten this entire conclusion section to conform strictly to the recommendations proposed by the reviewer. 

References

• The references inside the text need to be formatted, e.g., in line 379. R:/ The references mentioned here were improved. We appreciate the suggestion.

The reference formatting in the reference list should be reconsidered, e.g., journal abbreviation [18-20]. R:/ The references mentioned here were improved. We appreciate the suggestion.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

This revised manuscript is good for acceptance, the previous comment mentioned one references can be considered for referring.

Author Response

Dear Reviewer,

Thank you for your positive feedback and recommendation. We have carefully considered your previous suggestion and have included the recommended reference in the revised manuscript. We appreciate your valuable input and support throughout the review process.

Best regards,
The Authors

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have revised the manuscript with some additional information; however, the reviewer still have following comments on the revised version:

1. The introduction section has been revised with some state-of-the-art literature, however, only 02 references are discussed. A further in-depth elaboration of the research gap is expected in terms of modelling and simulation of bioreactors using CFD approach.
2. There is still a question on the justification and grounds on which basis the current dimension of the geometry was formulated. For example, is it based on the existing design(s) or a new/improved version of existing reactor? In any case, the relevant references should also be provided.
3. References of Eq. (1) and (2) are missing.
4. Numerical modelling still lacks in relevant information such as convergence criteria, computation time and cost to run one simulation setup as well as the capacity/computational power of the running computational machine.
5. The comment on previous version on Figure 4 has not been address which is of prime importance in this regard: ‘In Figure 4, the contour legend is missing, what does the colour indicate? What is the parameter being presented here, mass fraction or volume fraction?’
6. The sections 3.3, 3.4, 3.5 are still not clear in terms of its inclusion in the manuscript. Is it a summary of existing techniques or an experimental study of current work? For example, the summary on existing techniques should be shortened significantly and aligned in the introduction section. Whereas, here in Section 3.3, only experimental investigation conducted as a part of current research should be explained along with the experimental results.

Author Response

We sincerely thank the reviewer for their thorough and constructive feedback, which has significantly contributed to the improvement of the manuscript. The comments and suggestions provided were insightful. We carefully considered each observation and made the necessary adjustments to enhance the clarity, depth, and scientific rigor of our work. We are confident that the revised version now better reflects the intended contribution of this study to the field of bioreactor design and solid-phase bioremediation.

Detailed answer to the comments and suggestions:

1. The introduction section has been revised with some state-of-the-art literature, however, only 02 references are discussed. A further in-depth elaboration of the research gap is expected in terms of modelling and simulation of bioreactors using CFD approach.

R:/  We appreciate your feedback emphasizing the need for a deeper elaboration of the research gap, particularly regarding CFD-based modeling of bioreactors. While our primary focus is on DEM simulations of solid-phase bioremediation reactors, we acknowledge the relevance of CFD studies in related contexts.

To enrich the introduction and provide appropriate context, we have now included two additional references outlining CFD applications in packed-bed and solid-state bioprocessing systems:

• Pessoa et al. (2016) conducted a CFD study using ANSYS Fluent® to simulate heat and mass transfer in a pilot-scale packed-bed solid-state fermentation reactor, accurately reproducing experimental moisture and temperature profiles.
• Seidel et al. (2022) employed CFD to analyze oxygen transport and mixing efficiency in a wave-mixed bioreactor with complex geometry, providing insight into the influence of agitation design on mass transfer performance.

These additions are now referenced in the introduction (lines 109–117), where we explicitly discuss the distinction between CFD-based fluid-phase modeling—commonly applied in liquid or aerated fermentation systems—and our DEM-based particle-phase approach tailored for solid-phase soil bioremediation. This newly added context helps clarify the specific technological gap being addressed by our work.

Additional references

Pessoa, D., Finkler, A., Machado, A., Luz, L., Jr, & Mitchell, D. (2016). Fluid dynamics simulation of a Pilot-Scale Solid-State fermentation bioreactor. DOAJ (DOAJ: Directory of Open Access Journals). https://doi.org/10.3303/cet1649009

Seidel, S., Maschke, R. W., Kraume, M., Eibl, R., & Eibl, D. (2022). CFD modelling of a wave-mixed bioreactor with complex geometry and two degrees of freedom motion. Frontiers in Chemical Engineering, 4. https://doi.org/10.3389/fceng.2022.1021416

2. There is still a question on the justification and grounds on which basis the current dimension of the geometry was formulated. For example, is it based on the existing design(s) or a new/improved version of existing reactor? In any case, the relevant references should also be provided.

R:/  We respectfully clarify that the geometry and dimensions of the bioreactor presented in this study correspond to a novel design, specifically developed for ex-situ solid-phase bioremediation using an aerated accumulation strategy—a configuration that, to the best of our knowledge, has not been previously reported in the scientific literature. Unlike conventional systems such as rotary drums, static compost piles, landfarming, or slurry-phase reactors, our reactor integrates continuous paddle mixing, forced aeration, and modular construction in a scalable format tailored to the unique challenges of bioremediation in moist, heterogeneous solid matrices. Given the absence of comparable designs in the literature, the formulation of the geometry was guided by engineering design principles, prototyping constraints, and optimization through discrete element simulations. The originality of this configuration is one of the key contributions of the manuscript, and we have clarified this point accordingly in the revised version at the end of the Introduction section.

3. References of Eq. (1) and (2) are missing.

R:/  References to Equations (1) and (2) were already included in the text preceding each of the mathematical formulas. In this version of the manuscript please refer to line 185 and there you will find these references.

4. Numerical modelling still lacks in relevant information such as convergence criteria, computation time and cost to run one simulation setup as well as the capacity/computational power of the running computational machine.

R:/   We appreciate your insightful observation. In response to your comment, we have expanded Section 2.3 Simulation of the Bioreactor Using the Discrete Element Method (DEM) to explicitly include the convergence criteria, computational time, simulation cost, and the specifications of the computational equipment used. Specifically, we now indicate that convergence was verified through contact overlap stabilization remaining below 3% over more than 5,000 time steps, as recommended by Rocky DEM's internal diagnostics. Additionally, the total runtime for each simulation setup (approximately 65 minutes) and the hardware configuration (Intel® Core™ i7-9700 CPU @ 3.00 GHz with 32 GB RAM, running Windows 11 Enterprise) have been included for transparency and reproducibility.

5. The comment on previous version on Figure 4 has not been address which is of prime importance in this regard: ‘In Figure 4, the contour legend is missing, what does the colour indicate? What is the parameter being presented here, mass fraction or volume fraction?’

R:/   Thank you for pointing this out once again. The concern regarding Figure 4 has now been fully addressed. A contour legend and detailed explanation have been added to clarify that the colored regions represent tracer particles used for visual evaluation of mixing behavior. These particles are physically identical, and their spatial distribution reflects both mass and volume fractions. As such, the figure does not present a traditional contour plot of a scalar field but rather a qualitative tracer-based assessment, which is a common practice in DEM-based mixing studies. The figure caption has been updated accordingly to avoid any further ambiguity.

6. The sections 3.3, 3.4, 3.5 are still not clear in terms of its inclusion in the manuscript. Is it a summary of existing techniques or an experimental study of current work? For example, the summary on existing techniques should be shortened significantly and aligned in the introduction section. Whereas, here in Section 3.3, only experimental investigation conducted as a part of current research should be explained along with the experimental results.

R:/  We appreciate the reviewer’s continued attention to the structure of the manuscript. However, we would like to clarify that the intent and scope of Sections 3.3 to 3.5 have already been explicitly stated in the transitional paragraph immediately preceding Section 3.3. These sections are not theoretical summaries but rather describe the operational and biological framework applied during the empirical deployment of the designed reactor. This includes the implementation of specific strategies such as bioaugmentation, biostimulation, and bioventing—elements that were applied and monitored as part of the reactor’s performance validation. Given their relevance to the actual functioning of the constructed system, we believe their current placement is both justified and necessary to fully communicate the practical contributions of the study.

Reviewer 3 Report

Comments and Suggestions for Authors

The article has been improved; the clarity, rigor, and overall quality of this work have been raised as required by the reviewing comments in round one. I recommend that this article be published.

Author Response

Dear Reviewer,

Thank you very much for your valuable feedback and recommendation. I truly appreciate your time and effort in reviewing the manuscript and contributing to its improvement.

Best regards,

The Authors