Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines
, Chi Zhang 1,2,*, Ali Shomali 1,2, Benoit Coasne 3, Jan Carmeliet 1 and Dominique Derome 2
Round 1
Reviewer 1 Report
Comments to Authors and Editor:
The paper “Wood-Moisture Relationships Studied With Molecular Simulations - Methdological Guidelines" by Mingyang Chen, Chi Zhang, Ali Shomali, Benoit Coasne, Jan Carmeliet, and Dominique Derome discusses the application of molecular dynamics (MD) techniques to gain further insight into the hygroscopic and mechanical behavior of wood. The manuscript does not focus on the simulation of a specific material but reviews the different aspects and challenges of MD methodologies for moisture predictions. Overall, the paper is well organized and very well written. The figures are clear, and the corresponding captions are appropriate. The guidelines, references, and examples in the manuscript provide a great source of information for beginners in the field of MD simulations for wood-like systems. In this context, I do recommend this paper for publication in Forests after MAJOR revisions that must be addressed in its final version. Below are my specific comments.
Major comments
1. Page 16: For the data presented in Fig.7, include snapshots (as in Fig3a) of the representative simulation box at different instants of the equilibration process and well as at different moisture contents.
Minor Comments:
1. Page 1, line 37: The reader should also be referred to Fig 1 after mentioning the structure of the cell wall layers for the first time.
2. Page 2, line 45: Add a brief paragraph at the end of this section summarizing the goal of each section and how they connect to each other.
3. Page 6, line 247: Add a reference to GCMC simulations.
4. Page 6, line 263: The equations should be numbered and there should be no indentation after them (…where…). Apply these changes to all other instances the manuscript.
5. Page 6, line 269: Add a reference for the derivation of the probability equations.
6. Page 11, line 461: I believe the “equal” sign in the Boltzmann distribution relation should be replaced by a “proportional” sign . Please confirm if there is a pre-exponential term and, if needed, correct the expression accordingly.
7. Page 13, line 546: What is the difference between “E_swelling” and “E_V”? Correct the nomenclature for consistency between the text and Fig. 4.
8. Page 14, line 567: What does p=0 bar mean? Is it a gauge or absolute value?
9. Page 14, line 579: What is the difference between “X” and “x”, which was introduced in Page 13? Correct the nomenclature accordingly for consistency.
10. Page 14, line 589: Replace “Bulk” by “bulk”.
11. Page 15, line 600: Is Fig. 5 based on present calculations? If yes, provide the simulations details (e.g., # of particles, potential energy, equilibration process, etc) and compare these results to available experimental data so that the reader can ascertain the accuracy of simulations. Otherwise, provide a reference.
12. Page 17, line 669: Black or blue circles? What is the meaning of the error bars? Does it represent the standard deviation on the averaging process? Update captions accordingly.
13. Page 18, line 729: Provide a reference for the finite element method cited in the text.
Author Response
Response to Reviewer 1 Comments
The paper “Wood-Moisture Relationships Studied With Molecular Simulations - Methdological Guidelines" by Mingyang Chen, Chi Zhang, Ali Shomali, Benoit Coasne, Jan Carmeliet, and Dominique Derome discusses the application of molecular dynamics (MD) techniques to gain further insight into the hygroscopic and mechanical behavior of wood. The manuscript does not focus on the simulation of a specific material but reviews the different aspects and challenges of MD methodologies for moisture predictions. Overall, the paper is well organized and very well written. The figures are clear, and the corresponding captions are appropriate. The guidelines, references, and examples in the manuscript provide a great source of information for beginners in the field of MD simulations for wood-like systems. In this context, I do recommend this paper for publication in Forests after MAJOR revisions that must be addressed in its final version. Below are my specific comments,
Major comments
Point 1:Page 16: For the data presented in Fig.7, include snapshots (as in Fig3a) of the representative simulation box at different instants of the equilibration process and well as at different moisture contents.
Response 1: We add in Figure 7 b) several snapshot of configurations, and referred to them on the graph of Figure 7 a). A sentence is added in the text to refer to the new Figure 7b.
Minor Comments:
Point 1: Page 1, line 37: The reader should also be referred to Fig 1 after mentioning the structure of the cell wall layers for the first time.
Response 1: We add the reference to Figure 1
Point 2: Page 2, line 45: Add a brief paragraph at the end of this section summarizing the goal of each section and how they connect to each other.
Response 2: We have added the paragraph:
This paper is organized in the following order. In the introduction (Section 1), wood component, structure and behavior are summarized with the related molecular modeling literature upon wood-moisture relation briefly reviewed. In Section 2, for the experimental researchers who may not be familiar with modeling studies, basic concepts of molecular simulation are introduced, including notions, principles of Monte Carlo and molecular dynamics, the relevant force fields and solvers. Then the numerical framework of molecular simulation of wood polymer-moisture sorption behavior is described. Section 3 is about the modeling procedure of atomistic system, where simulation techniques are combined with the experimental knowledge of wood. In section 4, various sorption-related phenomena, such as swelling, mechanical weakening and hysteresis probed by molecular simulation are discussed. The harvested hygromechanical information can then be upscaled and incorporated into continuum modeling for the investigation at a larger scale (Section 5). The final part, Section 6, involves the highlights of the molecular modeling work carried out in our group and, based on these advances, future directions are discussed.
Point 3: Page 6, line 247: Add a reference to GCMC simulations.
Response 3: We add a reference to GCMC
Point 4: Page 6, line 263: The equations should be numbered and there should be no indentation after them (…where…). Apply these changes to all other instances the manuscript.
Response 4: All the equations are numbered, and indentation is deleted.
Point 5: Page 6, line 269: Add a reference for the derivation of the probability equations.
Response 5: A reference is given.
Point 6: Page 11, line 461: I believe the “equal” sign in the Boltzmann distribution relation should be replaced by a “proportional” sign . Please confirm if there is a pre-exponential term and, if needed, correct the expression accordingly.
Response 6: Indeed, the “equal” sign in the Boltzmann distribution relation is replaced by a “proportional” sign. There is no pre-exponential term.
Point 7: Page 13, line 546: What is the difference between “E_swelling” and “E_V”? Correct the nomenclature for consistency between the text and Fig. 4.
Response 7: “E_swelling” is corrected and changed to “E_V” for the consistency.
Point 8: Page 14, line 567: What does p=0 bar mean? Is it a gauge or absolute value?
Response 8: We actually mean bar, an absolute pressure, a metric unit referring to atmospheric pressure, i.e. 1 bar =100 000 Pa.. To avoid misunderstanding, we change bar to Pa, the accepted SI unit.
Point 9: Page 14, line 579: What is the difference between “X” and “x”, which was introduced in Page 13? Correct the nomenclature accordingly for consistency.
Response 9: We change X into x for the consistency.
Point 10: Page 14, line 589: Replace “Bulk” by “bulk”.
Response 10: We replace “Bulk” by “bulk”.
Point 11: Page 15, line 600: Is Fig. 5 based on present calculations? If yes, provide the simulations details (e.g., # of particles, potential energy, equilibration process, etc) and compare these results to available experimental data so that the reader can ascertain the accuracy of simulations. Otherwise, provide a reference.
Response 11: We provide the reference that presents this work in full detail.
Point 12: Page 17, line 669: Black or blue circles? What is the meaning of the error bars? Does it represent the standard deviation on the averaging process? Update captions accordingly.
Response 12: We correct ‘black’ to ‘blue’. We add the meaning of the error bar in the caption; ‘the error bar represents the standard deviation on the averaging process’.
Point 13: Page 18, line 729: Provide a reference for the finite element method cited in the text.
Response 13: We add a reference.
Reviewer 2 Report
A very good review and platform for future researchers joining this field.
Some spelling or grammar queries are listed below. I would also like to question the topics in section 6.1, as the first two examples are clearly supported by a publication within the field, whereas the second two are more speculative. Although I can see a potential for application for archaeological timbers such as the Vasa, the MD simulations i understand could be suited to understanding the distribution of PEG within the wood, but not to predict the chemical reactions (i.e. breakage of bonds due to acidic reactions (elsehwere in the text you state that MD is limitted to simulations which do not form or break bonds). I suggest that you clarify this, and possibly point to a reference in which the project aims are set out, or preliminary findings reported (or adjust the paragraph so that it is clearly early stage investigation). SImilarly with the continuum model based on DDM, there is no supporting reference, so I cannot be sure whether this is preliminary work, work in progress or initial proposal. Also, DDM is not previously mentioned in the text, so full name should be given.
In Section 1.2, introducing the modelling of atomistic systems, a basic refrence could be used to support your comments on quantum mechanics and computing costs involved.
In Section 4.2, on page 16, you give an example using SPC/E water model to look at adsorption and desorption. Earlier in the text you have commented that SPC/E is not as good as other systems for sorption studies, yet here it is not mentioned. Why?
Spellings and grammar:
page 4, line 171, 'simulations to analyse'
page 5, line187, unsure of meaning' carried for real' do you mean carried out for real?,
page 5, line 89-90, 'allow considering' could be allow consideration of an
page 5 line 199, media should be medium
page 6, line 256, 'from a dry polymer'
page 9, line 357, seems to be a word missing, a Hamiltonian what?
page 9, line 393, the researches presented above show ... or the research presented above shows
page 10, line 406, better phrase for 'crystal water different interfaces', is there a word missing?
page 12, line 513, i think you mean 'hysteretic'
page 13, line 557, academia not academy
page 14, line 574, unsure of sentence structure, 'remain the system', could be to ensure the system remains in the'
Page 14, line 592, for the units E-5 nm/ps, should the -5 be superscript, or what does it stand for?
Page 14, line 593, 'respectively' not 'separately'
Page 14, line 595, 'the system intermittently relaxes' or '... is relaxed'?
Page 15, line 619, unsure what you mean 'life'
Page 16, line 644, should be Figure 6 (not 2)
Page 17, line 680, word order, 'silulation still impose limitations'
Page 17, line 696, 'surface covered by a film'
Page 19, line 741, 'investigating the moisture...'
Page 19, line 742, 'activities in our group combine'
Page 20, line 819, 'wood-moisture relations'
Author Response
Response to Reviewer 2 Comments
A very good review and platform for future researchers joining this field.
Point 1: Some spelling or grammar queries are listed below. I would also like to question the topics in section 6.1, as the first two examples are clearly supported by a publication within the field, whereas the second two are more speculative. Although I can see a potential for application for archaeological timbers such as the Vasa, the MD simulations i understand could be suited to understanding the distribution of PEG within the wood, but not to predict the chemical reactions (i.e. breakage of bonds due to acidic reactions (elsewhere in the text you state that MD is limitted to simulations which do not form or break bonds). I suggest that you clarify this, and possibly point to a reference in which the project aims are set out, or preliminary findings reported (or adjust the paragraph so that it is clearly early stage investigation). SImilarly with the continuum model based on DDM, there is no supporting reference, so I cannot be sure whether this is preliminary work, work in progress or initial proposal. Also, DDM is not previously mentioned in the text, so full name should be given.
Response 1: We agree with the reviewer that the organization in section 6.1 is not very clear.
On the use of atomistic investigation on archeological wood, we add that no chemical reaction are included:
The cell walls of treated archeological wood are polymeric systems of slightly higher complexity that new wood cell walls. However, molecular dynamics simulation can be used to elucidate the interaction between PEG molecules and both new and degraded wood biopolymers, assuming the system is stable chemically.
We add a mention that the work is in progress.
On the DDM work, we add a more detailed description to DDM including the motivation and the brief idea in Section 5. Upscaling as follows:
‘Independent Domain Model which neglects the mechanical interaction between neighboring pores is not adequate, although it has been used for wood or another nanoporous materials. Alternatively, the Dependent Domain Model (DDM) includes the mechanical influence between neighboring pores when becoming filled and swollen and is able to give a quantitative description of the coupling of sorption and deformation and related hysteresis. Briefly, DDM decomposes the porous media into a collection of porous elements following a certain pore size distribution. Deformation and sorption are connected under the framework of poromechanics. The breakage and reformation of polymer-to-polymer hydrogen bonds in the wood-related polymers can be represented by open and closed states of the pores in the continuum model. Based on the coupling between sorption and deformation, the element can switch its own states upon the influence of its neighbors, which finally leads to hysteresis in both sorption and deformation.’
Point 2: In Section 1.2, introducing the modelling of atomistic systems, a basic reference could be used to support your comments on quantum mechanics and computing costs involved.
Response 2: Two references are added to give the reader a basic idea about the system sizes of quantum mechanics calculation.
Point 3: In Section 4.2, on page 16, you give an example using SPC/E water model to look at adsorption and desorption. Earlier in the text you have commented that SPC/E is not as good as other systems for sorption studies, yet here it is not mentioned. Why?
Response 3: We admit that the comments made on the SPC/E lack balance.. SPC/E deviates from the absolute value of saturation pressure from the experiments. However, this disadvantage is compressed as we discuss all the results in the context of relative humidity. In fact, there is currently still no consensus on which water model is the best. For instance, SPC reproduces a saturation pressure closer to the experiments compared to SPC/E but gives a poor prediction on the density. Currently both SPC and SPC/E are popular in the adsorption community. We add this explanation in section 3.3 as follows
‘However, SPC/E outperforms SPC model in terms of density and diffusion constant [104]. There is no consensus on the best water model regarding sorption. Currently both water modules are popular in the sorption community.’
Point 4: Spellings and grammar:
page 4, line 171, 'simulations to analyse'
page 5, line187, unsure of meaning' carried for real' do you mean carried out for real?,
page 5, line 89-90, 'allow considering' could be allow consideration of an
page 5 line 199, media should be medium
page 6, line 256, 'from a dry polymer'
page 9, line 357, seems to be a word missing, a Hamiltonian what? Response: OK as it.
page 9, line 393, the researches presented above show ... or the research presented above shows
page 10, line 406, better phrase for 'crystal water different interfaces', is there a word missing?
page 12, line 513, i think you mean 'hysteretic'
page 13, line 557, academia not academy
page 14, line 574, unsure of sentence structure, 'remain the system', could be to ensure the system remains in the'
Page 14, line 592, for the units E-5 nm/ps, should the -5 be superscript, or what does it stand for?
Page 14, line 593, 'respectively' not 'separately'
Page 14, line 595, 'the system intermittently relaxes' or '... is relaxed'?
Page 15, line 619, unsure what you mean 'life'
Page 16, line 644, should be Figure 6 (not 2)
Page 17, line 680, word order, 'silulation still impose limitations'
Page 17, line 696, 'surface covered by a film'
Page 19, line 741, 'investigating the moisture...'
Page 19, line 742, 'activities in our group combine'
Page 20, line 819, 'wood-moisture relations'
Response 3: We are very grateful for the reviewer’s careful reading and kind suggestions on spellings and grammar. All the raised points have been addressed accordingly.
Reviewer 3 Report
Dear Sir,
Thank you for your confidence of reviewing the article: Wood-Moisture Relationships Studied with Molecular Simulations - Methodological Guidelines
This article presents a complex and comprehensive possibilities of studying the relation water-wood, but one main general comment on this.
Despite the extensive introductory part, it is difficult to assess whether the article could be interpreted as a review article. In terms of scientific article, I miss the exact presentation of materials and methods as well as concrete results. From this point of view, the review of the article may not be quite correct.
Anyway, a more precise explanation of all of used equations is needed.
Author Response
Response to Reviewer 3 Comments
Point 1. Thank you for your confidence of reviewing the article: Wood-Moisture Relationships Studied with Molecular Simulations - Methodological Guidelines
This article presents a complex and comprehensive possibilities of studying the relation water-wood, but one main general comment on this.
Despite the extensive introductory part, it is difficult to assess whether the article could be interpreted as a review article. In terms of scientific article, I miss the exact presentation of materials and methods as well as concrete results. From this point of view, the review of the article may not be quite correct.
Anyway, a more precise explanation of all of used equations is needed.
Response 1:
We see the point of view of the reviewer. From our side, we see that, in studying wood-moisture relations with the help of molecular simulation techniques, our group can not only reproduce macroscopic phenomenon such as sorption isotherms and sorption-induced swelling and weakening of wood issues, but also find the molecular mechanism of sorption hysteresis of wood, which has remains as a perplexing and unexplained feature for decades. Thus, we find that molecular simulations can greatly enrich our knowledge on the wood-moisture relations. We firmly believe that the multi-scale modelling based on the molecular simulations is becoming one of the cutting-edge directions in the wood community and attracting more and more attentions. However, molecular simulations require a background of physical chemistry and statistical mechanics, which is unacquainted to the majority in the wood community.
Thus, we have written this paper as compiling all the methodological developments made by our group and included more regular atomistic practices with the purpose of introducing this method to the wood and polymeric community and helping the beginners dealing with the steep learning curve.
We classify this article as a review with the emphasis laid on methodology and, given our strong investment of the last years, this review captures mainly our work. However one may consider this paper to be a research article, not of the classical type, but in terms of an endeavor to develop and present a research methodology. This intention is clearly disclosed in the introduction of the paper.
All equations have their terms fully determined and their aim described. We admit that the theoretical background required to understand molecular simulation is different from most of the experimental work. This paper strives to provide the most essential ingredients of molecular simulation, achieving a balance between brevity and comprehensiveness. We believe that the reader can readily find information in the given references.
Round 2
Reviewer 1 Report
The authors need to make sure that higher quality images are uploaded in the final submission. The resolution of the images in the current revised version (v2) of the manuscript are not satisfactory.
Eq.6: The symbol "~" must be replaced by "∝" (directly proportional).
