Molecular Dynamics Simulations of Shockwave Affected STMV Virus to Measure the Frequencies of the Oscillatory Response

Round 1

Reviewer 1 Report

The manuscript submitted by Burkhartsmeyer et al, titled " Molecular Dynamics Simulations of Shockwave Affected STMV Virus to Measure the Frequencies of the Oscillatory Response” tried to explore the molecular dynamics simulations of shockwaves interacting with a Satellite Tobacco Mosaic Virus structure. Overall, the manuscript is well written. The method section is written in detail and easy to follow except in a few instances. I have a few comments that will improve the readability of this paper.

Comments

• Use the full name for any abbreviation used at its first appearance. For example, VMD in the third line of the result section.
• In both figures 1 and 2 captions, add period at the end of the caption sentence.
• Need to put reason behind why water velocities of 99.999 Å/ps were used in figure 2.
• Figure 2- need to put all three panels together. Panel B and C mention what those colors represent.

Author Response

Comment:

    Use the full name for any abbreviation used at its first appearance. For example, VMD in the third line of the result section.

Response:
        We agree with the reviewer.  Full names for abbreviations have been added on Lines 61, 80, 82, 83, 143

Comment:

    In both figures 1 and 2 captions, add period at the end of the caption sentence.

Response:

        We agree with the reviewer.
        A period has been added to all caption sentences.

Comment:

    Need to put reason behind why water velocities of 99.999 Å/ps were used in figure 2.

Response:
        We agree with the reviewer.  The reson for using 99.999 Å/ps has been added on Line 152-153

Comment:

    Figure 2- need to put all three panels together. 
        Agreed. The images in Figure 2 have been combined into one.

Response:

    Panel B and C mention what those colors represent.
        Agreed - description of the color scheme has been added on Line 171-172.

Reviewer 2 Report

it is necessary to improve the quality of the drawings and briefly describe the algorithm of the program used 

Author Response

Reviewer comment:
    it is necessary to improve the quality of the drawings and briefly describe the algorithm of the program used

Response:
        We agree - the images have been improved and the algorithm of the program has been described in Lines 90-100

Reviewer 3 Report

the problem is well defined and contestualized in the introduction but unfortunately the reported results are not enough to build up a convincing and interesting story deserving publication in Acoustic - the two figures should be merged in one figure to represent the starting point of the story... but then where is the rest of the story? 

the approach is intriguing but the conclusions are not convinging on the base of the reported results

Author Response

Comment:    

the problem is well defined and contestualized in the introduction but unfortunately the reported results are not enough to build up a convincing and interesting story deserving publication in Acoustic - 
    the two figures should be merged in one figure to represent the starting point of the story... but then where is the rest of the story? the approach is intriguing but the conclusions are not convinging on the base of the reported results

Response:
        We agree with the reviewer - additional content has been added, describing another experiment in which the virus was driven by repeated shockwaves of varying repetition rate, to show the plausibility of driving a resonant response by driving the system with acoustic energy at the appropriate frequency. 
        This is described on: Lines 26-28; 162-164; & 222-227, as well as shown with a new Figure 1(b), added to show the effect.
        A video showing the oscillatory motion of the virus structure after perturbation by simulated shockwave will also be provided.

Round 2

Reviewer 3 Report

the referee does not consider that the manuscript has been significantly improved - same figures, and is still missing the building up of a full and convincing story

Author Response

Reviewer comment:
    "the referee does not consider that the manuscript has been significantly improved - same figures, and is still missing the building up of a full and convincing story"

Response:
    In the previous response we highlighted the changes made to the manuscript: we improved the existing figures, added a video, and added a new figure (Figure 1(b)) and significant text discussing the new figure. There were changes to the abstract, main text, and conclusions - all related to the new figure. So please note, it is not the case that the figures are the same, as any careful reading of the revised manuscript would reveal.

    These changes also added to the story, by showing the choice of frequency of repeated shockwaves can significantly alter the combined effect. For more details as to the changes, we again include our comments from the last round of revision below.

Response, round 1:

    "additional content has been added, describing another experiment in which the virus was driven by repeated shockwaves of varying repetition rate, to show the     plausibility of driving a resonant response by driving the system with acoustic energy at the appropriate frequency. 
    
    This is described on: Lines 26-28; 162-164; & 222-227, as well as shown with a new Figure 1(b), added to show the effect.
    
    A video showing the oscillatory motion of the virus structure after perturbation by simulated shockwave will also be provided."