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Tangentially Active Polymers in Cylindrical Channels

by José Martín-Roca, Emanuele Locatelli, Valentino Bianco, Paolo Malgaretti, Chantal Valeriani

Submission summary

Authors (as registered SciPost users): Emanuele Locatelli · José Martín
Submission information
Preprint Link: https://arxiv.org/abs/2405.02192v1  (pdf)
Date submitted: 2024-05-07 13:04
Submitted by: Martín, José
Submitted to: SciPost Physics
Ontological classification
Academic field: Physics
Specialties:
  • Active Matter
Approaches: Theoretical, Computational

Abstract

We present an analytical and computational study characterizing the structural and dynamical properties of an active filament confined in cylindrical channels. We first outline the effects of the interplay between confinement and polar self-propulsion on the conformation of the chains. We observe that the scaling of the polymer size in the channel, quantified by the end-to-end distance, shows different anomalous behaviours at different confinement and activity conditions. Interestingly, we show that the universal relation, describing the ratio between the end-to-end distance of passive polymer chains in cylindrical channels and in bulk is broken by activity. Finally, we show that the long-time diffusion coefficient under confinement can be rationalised by an analytical model, that takes into account the presence of the channel and the elongated nature of the polymer.

Author indications on fulfilling journal expectations

  • Provide a novel and synergetic link between different research areas.
  • Open a new pathway in an existing or a new research direction, with clear potential for multi-pronged follow-up work
  • Detail a groundbreaking theoretical/experimental/computational discovery
  • Present a breakthrough on a previously-identified and long-standing research stumbling block
Current status:
Awaiting resubmission

Reports on this Submission

Anonymous Report 3 on 2024-6-20 (Invited Report)

Strengths

1) Interesting paper, very thorough in the data analysis and gathering
2) New nontrivial results in the field of active polymers under confinement

Weaknesses

1) Figures can be improved, they are at times hard to read and interpret
2) I have a number of points that need to be addressed

Report

This is an interesting paper. The authors consider the problem of a tangentially driven active polymer under cylindrical confinement.
They study the system under three different degrees of confinement for for two strength of the active forces. They also map their system to that of a single Brownian active particle and study structural and dynamic properties of the system.
They find a couple of intriguing results that are notable and worth of publication, including
1) The way active polymers accumulate on the confining surface, is quite different than how single particles behave near them.

2) This papaer show how the blob scaling used for passive polymers breaks down
for tangential active polymers, and that radius of the channel is not a fundamental length scale of this problem.

Requested changes

1) The conclusions could be written more clearly.

2) What is the interaction between the beads defining the channel and the monomers?

3) In Figure 2 it would be very useful to mark in the horizontal axis at which size N, the passive radius of gyration of the polymer becomes comparable to the degree of confinement, just to have a sense of the degree of confinement the reference passive system would be experiencing.

3) The authors say
“Indeed, here \nu is reminiscent of the passive exponent under confinement (\nu =1); however, as the tangential activity tends to shrink the polymer chains, the final outcome results from their interplay.”
The \nu=1 is only true under very strong confinement. For a passive polymer under weak confinement (small N) that should be ~0.6. I am not sure the authors are in the limit of very strong confinement, as even for the longest polymer discussed in Fig2 (N=200) I would expect a radius of gyration of the order of ~ 15
This is confusing. I get that the activity reduce the power law dependence of Re, I am not sure the reference limit is correct here.

4) 
Put more ticks in the x axis in Figure 3.
The saturation of the red-points in the two figures does not seem to happen at the same value of N as discussed in the paper. Add horizontal lines (or colored dots on the y-axis) to indicate the size of the confinement (R).

4) In discussing Fig. 4 the authors say:
“We observe that, in some regimes of confinement and activity, sufficiently small active polymers behave as their passive counterpart (gray line)”
There is no gray line in the figure (should that be black?).

5) The authors say:
“More importantly, given this rescaling, the reported data do not collapse on a single universal curve.” However the data in Fig.4 (b) seems to suggest that they do in the large Pe limit.
What am I missing? That seems like a pretty good collapse to me, it does not follow the passive prediction, but the data seem to collapse into a master curve nonetheless.

Recommendation

Ask for minor revision

  • validity: high
  • significance: high
  • originality: high
  • clarity: good
  • formatting: excellent
  • grammar: good

Anonymous Report 2 on 2024-6-20 (Invited Report)

Strengths

1 - An interesting problem in the physics of active matter systems
2- Very clean and carefully done numerical simulations
3- Extensive and careful analysis of the results

Weaknesses

1 - Limited relevance to biological systems
2- A bit artificial model of activity

Report

Overall, this is quite interesting and carefully done numerical work with good comparison to theory. The problem is of interest to the community working on active matter systems, in particular those working on problems that go beyond simple active agent models. The model is, however, a bit artificial in terms of the way the activity is introduced - most biological filaments involve some molecular motor that acts to slide pairs of filaments against each other. So, it is not clear how relevant the results would be to biology.

I am also wondering how sensitive are the results on the way the confinement is implemented. At present, the authors use a set of fixed beads which might introduce roughness to the wall. Implementing the actual confinement constraint is conceptually not hard, but might be technically challenging in LAMMPS. Could they please comment?

Requested changes

1 - Please add legends to most figures
2 - Please comment in the caption of Fig. 4 about the solid black line
3- Please make notation consistent between that main text and the SI (e.g. vectors in the main text are shown in bold, and in SI they have overhead arrows).
4 - Full-line equations are part of the text and should include proper punctuation.
5- The last paragraph in Conclusions is highly speculative and vague. Please either remove it or make it more precise.
6 - Please be consistent with the space between a word and the citation that follows it.

Recommendation

Publish (easily meets expectations and criteria for this Journal; among top 50%)

  • validity: high
  • significance: good
  • originality: good
  • clarity: high
  • formatting: good
  • grammar: excellent

Anonymous Report 1 on 2024-6-10 (Invited Report)

Strengths

See my report attached.

Weaknesses

See my report attached.

Report

See my report attached.

Requested changes

See my report attached.

Attachment


Recommendation

Publish (easily meets expectations and criteria for this Journal; among top 50%)

  • validity: high
  • significance: high
  • originality: good
  • clarity: good
  • formatting: excellent
  • grammar: excellent

Login to report


Comments

Anonymous on 2024-05-27  [id 4519]

Category:
objection
validation or rederivation
suggestion for further work

In this interesting manuscript authors consider a numerical simulation of an active polymer. Authors remark "We perform Langevin Dynamics simulations, in the overdamped regime, disregarding hydrodynamics. We employ the open source package LAMMPS, with in-house modifications to implement the tangential activity."

Unfortunately, even though an open source package, with an open license (GPL 2.0) is chosen as a starting point authors do not disclose the code used in their simulations. 1. Such choice makes this numerical-simulation-based manuscript very difficult and perhaps impossible to reproduce / validate. 2. Performing modifications/enhancements of open packages without sharing with wider scientific community goes against principles of open access central to SciPost's mission 3. GPL 2.0 license explicitly requires modified programs to be made available under the same license (or not at all)

I hope this serious oversight is easy to address and high quality, well documented source code repository will accompany this numerics-focussed manuscript. This would also allow for further improvements of simulation method. The authors choose Velocity Verlet algorithm which is not the best choice for simulations where nearest neighbours along the chain are connected using stiff springs. The choice of Velocity Verlet is even stranger given that LAMMPS already implements rRESPA family of algorithms to deal exactly with this type of problem.