Clustering of fast gyrotactic particles in low-Reynolds-number flow

Jenny Lynn Ongue Almerol; Marissa Pastor Liponhay

doi:10.1371/journal.pone.0266611

Peer Review History

Original SubmissionNovember 30, 2021
10 Jan 2022 Decision Letter - Fang-Bao Tian, Editor PONE-D-21-37882Clustering of fast gyrotactic particles in low-Reynolds-number flowPLOS ONE Dear Dr. Almerol, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Feb 24 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Fang-Bao Tian Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf. 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: [We would like to thank the Department of Science and Technology (DOST)-SEI 252 Accelerated Science and Technology Human Resource Development Program (ASTHRDP) and University of San Carlos for supporting this research. M. Liponhay would also like to acknowledge the funding from DOST-CRADLE Program, Project No. 8419. Finally, we thank Professors Danilo M. Yanga, Christopher P. Monterola, and Christian M. Alis for the fruitful discussions about this work.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [The author(s) received no specific funding for this work.] Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This manuscript is on the clustering of fast gyro-tactic particles in low-Reynolds-number flow, which is beneficial to understand various ecological phenomena, for example, harmful algal blooms in lakes. The authors' efforts are appreciated, and the authors should consider the following points to improve further the quality of this manuscript. (1) The primary method used in this paper was reported in previous work by Durham et al. (Durham WM, Climent E, Barry M, De Lillo F, Boffetta G, Cencini M, et al. Turbulence drives microscale patches of motile phytoplankton. Nature communications. 2013). This work presents swimming particles' velocity and acceleration characteristics for different parameters. However, the numerical analysis in this work has not been verified by some experiments and relevant literature. At least, more cases of numerical simulation should be performed and analyzed for flows of various Reynolds numbers to make the conclusion powerful. (2) The conclusion is given for fast gyrotactic particles in low-Reynolds-number flow. More limitations are required to specify the scope of the conclusion, for example, the range of low-Reynolds-number flow. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0266611.r001
Revision 1
27 Jan 2022 Author Response RESPONSE TO THE EDITOR COMMENT 1: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf. RESPONSE 1: Thank you for the resources. We have Added corresponding author’s initials beside email address. Removed funding information from the Acknowledgements section. Improved the citations of equations and figures in Methods and Results and discussions sections. COMMENT 2: Thank you for stating the following in the Acknowledgments Section of your manuscript: [We would like to thank the Department of Science and Technology (DOST)-SEI 252 Accelerated Science and Technology Human Resource Development Program (ASTHRDP) and University of San Carlos for supporting this research. M. Liponhay would also like to acknowledge the funding from DOST-CRADLE Program, Project No. 8419. Finally, we thank Professors Danilo M. Yanga, Christopher P. Monterola, and Christian M. Alis for the fruitful discussions about this work.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [The author(s) received no specific funding for this work.] Please include your amended statements within your cover letter; we will change the online submission form on your behalf. RESPONSE 2: Concerning the Acknowledgments Section of the manuscript, we have removed the funding-related statement and incorporated this correction in the revised manuscript. We propose the following amendment to the funding statement: “JA and ML acknowledge the Department of Science and Technology (DOST)-SEI Accelerated Science and Technology Human Resource Development Program (ASTHRDP) and the University of San Carlos for supporting this research. ML acknowledges the Department of Science and Technology (DOST) of the Philippines with Project No. 8419, 2020 under the Collaborative R&D to Leverage the Economy (CRADLE) Program (https://s4cp.dost.gov.ph/programs/cradle/). The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.” COMMENT 3: We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. RESPONSE 3: Thank you for the information. We are changing our Data Availability statement to “All preprocessed data files are available from 10.5281/zenodo.5904617, 10.5281/zenodo.5905360, and 10.5281/zenodo.5904923.” We have also mentioned this in our cover letter. RESPONSE TO THE REVIEWER Reviewer #1: This manuscript is on the clustering of fast gyro-tactic particles in low-Reynolds-number flow, which is beneficial to understand various ecological phenomena, for example, harmful algal blooms in lakes. The authors' efforts are appreciated, and the authors should consider the following points to improve further the quality of this manuscript. COMMENT 1: The primary method used in this paper was reported in previous work by Durham et al. (Durham WM, Climent E, Barry M, De Lillo F, Boffetta G, Cencini M, et al. Turbulence drives microscale patches of motile phytoplankton. Nature communications. 2013). This work presents swimming particles' velocity and acceleration characteristics for different parameters. However, the numerical analysis in this work has not been verified by some experiments and relevant literature. At least, more cases of numerical simulation should be performed and analyzed for flows of various Reynolds numbers to make the conclusion powerful. RESPONSE 1: We thank the reviewer for this comment. We have performed additional numerical simulations using different Reynolds numbers, where clustering of gyrotatic cells is observed inside the vortices in the previous studies. We use similar values to confirm whether the mechanism of particle clustering discussed in our study can be observed in such flows. We found the same behavior for Re_λ=[21,36] – the presence of clustering with the same characteristics with respect to velocity and acceleration distribution as when Re_λ=59, which supports our conclusions. Shown below are the corresponding snapshots of the distribution of particles for Re_λ=[21,36] for different swimming numbers. We have also provided additional discussions in the Results and discussions section (in the third paragraph of the Cluster formation subsection and in the last paragraph of the Velocity and acceleration characteristics of swimming particles subsection) to support our conclusions and have incorporated the results in the manuscript as supporting information. COMMENT 2: The conclusion is given for fast gyrotactic particles in low-Reynolds-number flow. More limitations are required to specify the scope of the conclusion, for example, the range of low-Reynolds-number flow. RESPONSE 2: We thank the reviewer for the suggestion. We agree with the reviewer, and we have included the range of low-Reynolds-number flow and the basis of selection of these values in Paragraph 2 of the Numerical procedure subsection of Methods. Our findings that motile particles cluster outside vortices when also happen for low Re numbers, i.e., when the particle speed is high enough. Given these observations, our data and findings now better support the conclusions with its scope for fluid flow at low Reynolds number and high particle speed. The results of the numerical experiments using these values have been discussed in the Results and Discussions and are presented in the Supporting information section. In addition to the revisions made to the manuscript above, we have also made corrections in the values used to de-dimensionalize the swimming parameters, changing the values of the swimming parameters. These changes only affect the swimming parameter values reported in the figures (axis values in Figs 3 and 4 and legends of Figs 2-7) and do not affect the trend in our plots or the analyses of the data. We have incorporated these corrections in the Methodology and Results and Discussions sections of the manuscript. We also added a new paragraph at the beginning of the Results and discussion section to add clarity in the organization of the presentation of results. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0266611.r002
8 Mar 2022 Decision Letter - Fang-Bao Tian, Editor PONE-D-21-37882R1Clustering of fast gyrotactic particles in low-Reynolds-number flowPLOS ONE Dear Dr. Almerol, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Apr 22 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Fang-Bao Tian Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: (No Response) ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: (1) Please check Eq.2; it is not written correctly. p->dp/dt (2) The references for Eqs. 1 and 2 should be given. (3) Figures are unclear, and authors should make sure all figures are clear enough for reading. (4) Texts and languages should be improved further. For example, Navier-Stokes NS equation -> Navier-Stokes equation. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0266611.r003
Revision 2
16 Mar 2022 Author Response RESPONSE TO THE EDITOR Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Response: We thank the editor for this comment. We have checked our reference list and found no articles that have been retracted. We made no major changes in the reference list except for a few additional information added in reference numbers 8, 21, 24, and 25. RESPONSE TO THE REVIEWER Reviewer #1: (1) Please check Eq.2; it is not written correctly. p->dp/dt Thank you for spotting this error. We have made corrections to the expression of Eq. 2 and have incorporated it in the revised manuscript. (2) The references for Eqs. 1 and 2 should be given. We thank the reviewer for this comment. We have now cited the reference for Eqs. 1 and 2 in line number 66. We have also checked if there are parts in the manuscript where we may have failed to properly cite the references and made the necessary corrections in the revised manuscript. We cited the references in line numbers 29-30 and line numbers 120-122. (3) Figures are unclear, and authors should make sure all figures are clear enough for reading. Thank you for pointing out this concern. We have improved our figures and increased their resolutions making sure that they are all clear enough for reading. We have also revised Fig 7, S3 Fig and S4 Fig so that the axis titles are shown. (4) Texts and languages should be improved further. For example, Navier-Stokes NS equation -> Navier-Stokes equation. Regarding this concern, we have now improved the texts and languages used in the manuscript. We have changed the Navier-Stokes NS equation to Navier-Stokes (NS) equation, as NS equation is repeatedly used in the manuscript. Similar necessary changes have also been made throughout the manuscript to remove inconsistencies in the usage of other terms and abbreviations. We have also significantly improved the clarity of the discussions in our manuscript by revisiting our choices of words and by polishing our use of the English language. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0266611.r004
24 Mar 2022 Decision Letter - Fang-Bao Tian, Editor Clustering of fast gyrotactic particles in low-Reynolds-number flow PONE-D-21-37882R2 Dear Dr. Almerol, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Fang-Bao Tian Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0266611.r005
Formally Accepted
30 Mar 2022 Acceptance Letter - Fang-Bao Tian, Editor PONE-D-21-37882R2 Clustering of fast gyrotactic particles in low-Reynolds-number flow Dear Dr. Almerol: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Prof. Fang-Bao Tian Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0266611.r006

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