README.md

Active Polymer Simulation

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LAMMPS Simulation

• Tangentially-driven active polymer

Tangentially-driven by active force, active polymers are prone to collapse (E. Locatelli et al.2021 PRL) in closed topology (unknotted ring).

The code is modified from the fix_propel_self.cpp in LAMMPS.

• Achiral active Brownian polymer

Active Brownian particles can be chained together as a polymer. See image below.

We can then run the simulation using fix self/propel in LAMMPS. I will post HOOMD-Blue code later.

• Chiral active Brownian polymer

Chirality can be introduced into active Brownian particles. See this comprehensive paper by Sevilla. Chiral ABPs can also be chained to form a polymer.

As stated in the paper by Sevilla, the chirality is introduced by making the mean of rotational Gaussian noise some non-zero constant.

Usage

To compile the source codes, simply put the .cpp file and its .h header file into your lammps/src directory, and compile as detailed here.

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• Tangentially-driven active polymer

Use

fix         tang all tangential/propel ${mag} ${angle_tyle}
fix         brownian all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}

OR for Langevin simulation:

fix         tang all tangential/propel ${mag} ${angle_tyle}
fix         langevin all langevin ${temp} ${temp} ${damp} ${seed}

(Active force is defined with atom->anglelist in LAMMPS).

To run tutorial code: go to tangential/run_scripts.

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• Achiral active Brownian polymer

Use

fix         brownian all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix         actforce all propel/self dipole ${f_mag}

To run tutorial code: go to 'achiral/'

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• Chiral active Brownian polymer

Use

fix         chiral all chiral/brownian/sphere ${temp} ${seed} chiral ${tau_x} ${tau_y} ${tau_z} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix         actforce all propel/self dipole ${f_mag}

${tau_x,y,z} is the torque magnitude along x,y,z axis. It also is the mean value for rotational Gaussian noise. You can use plannar_rotation flag to introduce chirality only in x-y plane.

To run tutorial code: go to 'chiral/run_scripts'

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NOTE: fix tangential/propel does not require dipole. Fix with dipole should be used in parallel with fix brownian/sphere. Check LAMMPS for more details.

HOOMD scripts

Citation

You can cite this repository as Zhiyu Z., Active polymer simulation, GitHub repository 2025, https://github.com/kizzhang/ActivePolymer

@misc{Zhiyu2025,
  author = {Zhiyu, Z.},
  title = {Active Polymer Simulation},
  year = {2025},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/kizzhang/ActivePolymer}},
  commit = {main}
}