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Data from: Extremely persistent dense active fluids

Cite this dataset

Flenner, Elijah; Szamel, Grzegorz (2024). Data from: Extremely persistent dense active fluids [Dataset]. Dryad. https://doi.org/10.5061/dryad.xsj3tx9q4

Abstract

We study the dynamics of dense three-dimensional systems of active particles for large persistence times τp at constant average self-propulsion force f. These systems are fluid counterparts of previously investigated extremely persistent systems, which in the large persistence time limit relax only on the time scale of τp. We find that many dynamic properties of the systems we study, such as the mean-squared velocity, the self-intermediate scattering function, and the shear-stress correlation function, become τp-independent in the large persistence time limit. In addition, the large τp limits of many dynamic properties, such as the mean-square velocity and the relaxation times of the scattering function, and the shear-stress correlation function, depend on f as power laws with non-trivial exponents. We conjecture that these systems constitute a new class of extremely persistent active systems.

README: Data from: Extremely persistent dense active fluids

https://doi.org/10.5061/dryad.xsj3tx9q4

We have submitted the data derived from molecular dynamics simulations of active fluids appearing in the figures of the Soft Matter paper titled "Extremely persistent dense active fluids" by Grzegorz Szamel and Elijah Flenner. 

Description of the data and file structure

The data is sorted and named by the figure that they appear in the paper. If there are a different number of points along the x-axis we divided the data into separate files. All the files are text files with the data appearing in the files ending in .dat. All the files are text files and can be read with any text editor. 

figure1.dat:  This file is divided into five blocks. The first line of each block is "f=#" where # is the average self propulsion force. There are two columns in each block. The first column is the persistence time and the second column is the average-square-velocity.

figure2n1.dat: The mean-square-displacement for an average self propulsion force of f=5.48. There are 12 columns with 2-column pairs of time and mean-square displacement. The first two columns correspond to a persistence time of 0.001, columns 3 and 4 correspond to a persistence time of 0.005, columns 5 and 6 correspond to a persistence time of 0.01, columns 7 and 8 correspond to a persistence time of 0.05, columns 9 and 10 correspond to a persistence time of 1, and columns 11 and 12 correspond to a persistence time of 10. 

figure2n2.dat: The mean-square-displacement for an average self propulsion force of f=5.48 and a persistence time of 100. The first column is time and the second column is the mean-square-displacement. 

figure2n3.dat: The mean-square-displacement for an average self propulsion force of f=5.48 and a persistence time of 1000. The first column is time and the second column is the mean-square-displacement. 

figure2n4.dat: The mean-square-displacement for an average self propulsion force of f=5.48 and a persistence time of 10000. The first column is time and the second column is the mean-square-displacement.  

figure3.dat: This five is divided into five blocks. The first line of each block is "f=#" where # is the average self propulsion force. There are two columns in each block. The first column is the persistence time and the second column is the self diffusion coefficient.

figure4an1.dat: The mean-square-displacement divided by the average-square-velocity and the square of the time for the average self propulsion force f=5.48. The first column is time and the second column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of 0.1. The third column is time and the fourth column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of 10.

figure4an2.dat: The mean-square-displacement divided by the average-square-velocity and the square of the time for the average self propulsion force f=5.48. The first column is time and the second column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of 100.

figure4an3.dat: The mean-square-displacement divided by the average-square-velocity and the square of the time for the average self propulsion force f=5.48. The first column is time and the second column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of 1000 at long times. The third column is time and the fourth column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of 1000 at short times.

figure4an4.dat: The mean-square-displacement divided by the average-square-velocity and the square of the time for the average self propulsion force f=5.48. The first column is time and the second column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of 10000.

figure4an5.dat: The mean-square-displacement divided by the average-square-velocity and the square of the time for the average self propulsion force f=5.48. The first column is time and the second column is the mean-square-displacement divided by the average-square-velocity and the square of the time for a persistence time of infinity.

figure4bn1.dat: The velocity correlation function divided by its value at t=0 for the average self propulsion force f=5.48. The first column is time and the second column is the velocity correlation function divided by its value at t=0 for a persistence time of 0.1. The third column is time and the fourth column is the velocity correlation function divided by its value at t=0 for a persistence time of 10.

figure4bn2.dat: The velocity correlation function divided by its value at t=0 for the average self propulsion force f=5.48. The first column is time and the second column is the velocity correlation function divided by its value at t=0 for a persistence time of 100.

figure4bn3.dat: The velocity correlation function divided by its value at t=0 for the average self propulsion force f=5.48. The first column is time and the second column is the velocity correlation function divided by its value at t=0 for a persistence time of 1000 at long times. The third column is time and the fourth column is velocity correlation function divided by its value at t=0 for a persistence time of 1000 at short times.

figure4bn4.dat: The velocity correlation function divided by its value at t=0 for the average self propulsion force f=5.48. The first column is time and the second column is velocity correlation function divided by its value at t=0 for a persistence time of 10000.

figure4bn5.dat: The velocity correlation function divided by its value at t=0 for the average self propulsion force f = 5.48. The first column is time and the second column velocity correlation function divided by its value at t=0 for a persistence time of infinity.

figure5.dat: The probability of the velocity for an average self propulsion force of 0.0548. Column 1 is the velocity and column 2 is the probability of the velocity for a persistence time of 1. Column 3 is the velocity and column 4 is the probability of the velocity for a persistence time of 3. Column 5 is the velocity and column 6 is the probability of the velocity for a persistence time of 5. Column 7 is the velocity and column 8 is the probability of the velocity for a persistence time of 10. Column 9 is the velocity and column 10 is the probability of the velocity for a persistence time of 100. Column 11 is the velocity and column 12 is the probability of the velocity for a persistence time of 1000. Column 13 is the velocity and column 14 is the probability of the velocity for a persistence time of 10000.

figure6n1.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 1. The first column is time and the second column is the self-intermediate scattering function. 

figure6n2.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 3. The first column is time and the second column is the self-intermediate scattering function. 

figure6n3.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 5. The first column is time and the second column is the self-intermediate scattering function. 

figure6n4.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 10. The first column is time and the second column is the self-intermediate scattering function. 

figure6n5.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 100. The first column is time and the second column is the self-intermediate scattering function. 

figure6n6.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 1000. The first column is time and the second column is the self-intermediate scattering function. 

figure6n7.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 10000. The first column is time and the second column is the self-intermediate scattering function. 

figure6n8.dat: The self-intermediate scattering function versus time for an average self propulsion force of 0.0548 for a persistence time of 100000. The first column is time and the second column is the self-intermediate scattering function. 

figure6inset.dat: The stretching exponent found by fitting the self intermediate scattering function to a stretched exponential for an average self propulsion force f = 0.0548. The first column is the persistence time and the second column is the stretching exponent. 

figure7.dat: The first column is the average self propulsion force, the second column is the diffusion coefficient divided by the square of the persistence time, the third column is the average velocity squared, and the fourth column is the inverse of the relaxation time of the self-intermediate scattering function. 

figure7inset.dat: The first column is the average self propulsion force and the second column is the diffusion coefficient divided by the average square velocity and the square of the persistence time. 

figure8n1.dat The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 1.

figure8n1short.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 1 at short times.

figure8n2.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 3.

figure8n2short.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 3 at short times.

figure8n3.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 5.

figure8n4.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 10.

figure8n5.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 100.

figure8n6.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 1000.

figure8n7.dat: The shear-stress autocorrelation function divided by its value at t=0 for an average self propulsion force of 0.0548. The first column is the time and the second column is the shear-stress autocorrelation function divided by its value at t=0 for a persistence time of 10000.

figure8inset.dat: The value of the shear-stress autocorrelation function at t=0 for an average self propulsion force of 0.0548. The first column is the persistence time and the second column is the shear-stress autocorrelation function at t=0.

figure9n1.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 0.1.

figure9n2.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 0.3.

figure9n3.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 0.5.

figure9n4.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 1.0.

figure9n5.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 10.

figure9n6.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 1000.

figure9n7.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 5000.

figure9n8.dat: The average shear stress divided by the shear rate for an average self propulsion force of 0.548. The first column is the shear rate and the second column is the average shear stress divided by the shear rate for a persistence time of 10000.

figure10.dat: This file is divided into five blocks. The first line of each block is "f=#" where # is the average self propulsion force. There are two columns in each block. The first column is the persistence time and the second column is the viscosity.

figure11.dat: The first column is the average self propulsion force, the second column is the relaxation time of the shear-stress autocorrelation function for large persistence times, and the third column is the viscosity for large persistence times.

figure12.dat: The structure factor for an average self propulsion force of 0.548. The first column is the wave vector. Column 2 is the structure factor for a persistence time of 0.3.  Column 3 is the structure factor for a persistence time of 0.5. Column 4 is the structure factor for a persistence time of 1.0. Column 5 is the structure factor for a persistence time of 10. Column 6 is the structure factor for a persistence time of 100. Column 7 is the structure factor for a persistence time of 1000. Column 8 is the structure factor for a persistence time of 10000.

figure13.dat: The pair correlation function for representative average self propulsion force and persistence times.  The first column is the distance divided by the diameter of the larger particles. Column 2 is the pair correlation function for a persistence time of 1 and an average self propulsion force of 0.548.  Column 3 is the pair correlation function for a persistence time of 10000 and an average self propulsion force of 0.548. Column 4 is the pair correlation function for a persistence time of 1 and an average self propulsion force of 5.48.  Column 5 is the pair correlation function for a persistence time of 10000 and an average self propulsion force of 5.48. 

figure14.dat: The first peak of the pair correlation function for representative average self propulsion force and persistence times.  The first column is the distance divided by the diameter of the larger particles. Column 2 is the pair correlation function for a persistence time of 1 and an average self propulsion force of 0.548.  Column 3 is the pair correlation function for a persistence time of 10000 and an average self propulsion force of 0.548. Column 4 is the pair correlation function for a persistence time of 1 and an average self propulsion force of 5.48.  Column 5 is the pair correlation function for a persistence time of 10000 and an average self propulsion force of 5.48. 

figure15a.dat: The structure factor for the average self propulsion force of 54.8. The first column is the wavevector. Column 2 is the structure factor for a persistence time of 1. Column 3 is the structure factor for a persistence time of 100. Column 4 is the structure factor for a persistence time of 1000.

figure15b.dat: The probability of the local density for some representative average self propulsion forces and persistence times. The first column is the density. Column 2 is the probability of the density for a persistence time of 1 and an average self propulsion force of 54.8.   Column 3 is the probability of the density for a persistence time of 100 and an average self propulsion force of 54.8. Column 4 is the probability of the density for a persistence time of 1000 and an average self propulsion force of 54.8. Column 5 is the probability of the density for a persistence time of 0.3 and an average self propulsion force of 0.548. Column 6 is the probability of the density for a persistence time of 10000 and an average self propulsion force of 0.548.      

Methods

The data was obtained from running molecular dynamics simulations of active matter systems. The trajectories were stored and then post processed to obtain the needed information. 

Funding

National Science Foundation, Award: CHE 2154241, Chemistry