All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
The paper is accepted. Please do the final minor edit as noted by Reviewer 4.
The author introduced open-source Python application for modeling plasmonic systems of bulk and nanoparticle-embedded metallic films, and also present the PAME’s theory and design. The paper was well organized and the examples are suitable.
After building the model, the author gave two examples for the application, one is Refractometer and another on e is Multiplexed Ag-Au Sensor. Those two examples are sufficiently support the author's ideas.
The examples in this paper are simulations of a fiberoptic refractometer,and protein binding to a multiplexed sensor composed of a mixed layer of gold and silver colloids.
The examples, data and citation can support the author's view points in modeling the plasmonic system.
The author introduced a method to model the plasmonic systems based on open-source Python, and also provide some examples and data to support the view points. This modeling method is meaningful in analyze the plasmonic systems.
.
This article meet all standards of PeerJ with a very high quality.
Experimental design are carefully described and results are well discussed.
No additional comments.
Again, this article is of very high quality in terms of basic structure, scientific reporting, theory and experiment design. The authors had fixed previous issues and now is fully ready for publication.
No comments
No comments
No comments
The authors reported a python-based software platform that could model and simulate the behavior of plasmonic assays assuming certain experimental conditions. PAGE also provides an user friendly interface for modeling and simulation.
The authors reported three examples of how PAGE could be utilized. In the first example, PAGE was used to simulate the sensor response to increasing concentrations of glycerine for an axial fiber. It was shown that there was a strong agreement of between measured and PAGE simulated response. In the second example, PAGE was used to model a multiplexed dip sensor containing gold and silver nanoparticle species. Despite several approximations, PAGE was able to provide several insights into the multiplexed sensor.
In the first example, PAGE’s simulated results aligned well with the experimental results. In the second example, PAGE’s simulated results were supported by several lines of evidence from previous publications.
Page 2, change “PAME if a fully graphical application that …” to “PAME is a fully graphical application that …”
Overall the paper is well organized and presented since a big portion of it has been posted online. Authors should revise the paper according to the comments of the reviewers.
In the abstract, the author stated that the plasmonic assays own the advantages such as labeling free and measurement in real time. The combination of nanoparticles and fiberoptics show promise in in-situ probing and implantable devices. But the author did not provide information to support those advantages in the article. It will be better if the advantages of plasmonic assays and combination of nanoparticles and fiberoptics can be moved to the "Introduction" Chapter.
The abstract should focus on building, verify the model with PAME platform.
In Figure 4, the horizontal coordinate seems represent the wave length. What is the meaning of “counts” in vertical coordinate? How the normalized counts in Figure 6c and 6d were obtained? Provide detail information will make those clearer.
No Comments.
This article meet all standards of PeerJ with a very high quality.
For example, the structure of the article are well organized, content are self-sustained with appropriate introduction and background information. Data and source are openly shared online.
Several experimental examples are given in this article to show how to use the open-sourced tool PAME.
Experiments are clear described and results are well discussed. A very high technical standard are maintained in the experiment design.
Meanwhile, supplemental examples are also abundant and very helpful for new users.
The software introduced in this article shows a very convenient interface, comprehensive functionalities for modeling plasmonic systems, as well as many previous modeling examples in literature.
With the authors open-sourcing the software, it will be easily accessible to researchers in the area, and bring a great contribution to the community.
The submitted paper discuss the plasmonic assay modeling and simulation, and introduced an open-sourcePython application for modeling plasmic systems of bulk and nanoparticle-embedded metallic films.
The article is of very high quality in terms of basic structure, scientific reporting, theory and experiment design, and final validation.
Very minor issues are: 1. a few ? marks in Page 1( in Introduction), and Page 11 (2 paragraph before section 4 IMPLEMENTATION AND PERFORMANCE).
2. Format issue, Page 2, COMSOL Multiphysics is extending to margin area.
Please give more introduction and analysis for the section 4 implementation and performance
The experimental design is well organized and reasonable
The data can support authors’ ideas and conclusions
This paper has innovated idea and good simulation; it is also well organized. If the authors can provide more introduction and analysis for section 4 implementation and performance, it is much better.
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.