Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds.

Code ↔ Paper

9 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 9 matches · 3 of them tie a paragraph to a whole file without given lines: weak matches, whose lines are not tinted

[1] § Materials and methods › Estimation of elastic moduli ↔ mechanics/analysis/getModulus.m, the whole file · a weak match · score 0.92 · bisquare robust fitting, linear regression, intercept fixed, linear fit, elastic modulus, strain · Report a mismatch
[2] § Results › Rigidity of astral filamentous networks exhibits a maximum at intermediate astral number ↔ mechanics/analysis/getModulus.m, the whole file · a weak match · score 0.68 · steady state, elastic modulus, shear force, strain, stress, behavior · Report a mismatch
[3] § Materials and methods › Geometric analysis: Dangling ends and percolation ↔ geometry/percCurveFitting.m, lines 187 to 283 · score 0.66 · smoothing spline, smoothing parameter, percolation probability, fit, densities, Geometric · Report a mismatch
[4] § Materials and methods › Geometric analysis: Dangling ends and percolation ↔ geometry/percCrit.m, lines 29 to 106 · score 0.65 · smoothing spline, smoothing parameter, percolation probability, fit, densities, Geometric · Report a mismatch
[5] § Materials and methods › Mechanical simulations ↔ mechanics/analysis/rf_tens_aster_actin_physkT.m, lines 174 to 251 · score 0.63 · tensile force, position samples, initial position, displacements, 300 s, spaced · Report a mismatch
[6] § Results › Rigidity of astral filamentous networks exhibits a maximum at intermediate astral number ↔ mechanics/analysis/figures_manu.m, lines 47 to 196 · score 0.61 · filament bending rigidity, angular stiffness, astral centers, moduli, shear, modulus · Report a mismatch
[7] § Materials and methods › Geometric analysis: Dangling ends and percolation ↔ mechanics/analysis/figures_manu.m, lines 47 to 196 · score 0.53 · productive segments, dangling ends, MATLAB, astral networks, percolation, node · Report a mismatch
[8] § Results › Mechanical rigidity is associated with network connectedness ↔ mechanics/analysis/figures_manu_rev1.m, lines 637 to 681 · score 0.53 · connectivity percolation, connected component, percolation probabilities, Heatmaps, density, simulated · Report a mismatch
[9] § Materials and methods › Geometric analysis: Dangling ends and percolation ↔ geometry/percCheck.m, the whole file · a weak match · score 0.51 · connected component, conncomp, graph, intersected, edge, astral networks · Report a mismatch

Paper

Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC

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The paper is loaded by your browser, with JavaScript: read it at doi.org or on Europe PMC.

The authors' code

MATLAB · 83 lines · 3.5 KB · no license · 2 matches

function [modulus,linefit,gof] = getModulus(initCoM,finalCoM,forceVals, ...
type,filtering)
%GETMODULUS estimates a 2D elastic modulus from force-displacement data
% Inputs:
% initCoM (n x 2 double): list of center-of-mass coordinates at
% initial state for each applied force (n = length(forceVals))
% finalCoM (n x 2 double): list of center-of-mass coordinates at
% steady-state for each applied force (n = length(forceVals))
% forceVals (n x 1 double): list of applied shear forces
% corresponding to each row in finalCoM; must start at 0
% type (character vector or string): either "shear" or "extension",
% indicates stress/strain direction
% filtering (1x1 struct): specifies if (and how) to filter networks,
% contains 3 true/false fields:
% -- 'TF' determines if any filtering is done
% -- 'spanCheck' reports if a spanning component was detected
% in the network at the end of the initial crosslinking time window
% -- 'catchDrops' assigns 0 modulus to networks where
% displacement decreases from forceVals(1)=0 to forceVals(2)>0
% (*if unspecified, this field is by default TRUE)
% Outputs:
% modulus (1x1 double): coefficient of linear term from linefit
% linefit (cfit object): result of linear fit to force vs.
% displacement data
% gof (gof structure): goodness-of-fit statistics
if strcmp(type,"shear")
coordIdx = 1;
elseif strcmp(type,"extension")
coordIdx = 2;
else
error("type argument must be one of 'shear' or 'extension'")
end
%%%%% OPTION 1 %%%%%
%%% unconstrained coefficient values, default fit options
% fitopts = fitoptions('poly1');
%%%%% OPTION 2 %%%%%
%%% constrain intercept coeff. p2 to be 0
% fitopts = fitoptions('poly1','Lower',[-Inf,0],'Upper',[Inf,0]);
%%%%% OPTION 3 %%%%% (current selection)
%%% use bisquare robust fitting with intercept fixed at 0
fitopts = fitoptions('poly1','Robust','Bisquare','Lower',[-Inf,0], ...
'Upper',[Inf,0]);
displace = finalCoM(:,coordIdx) - initCoM(:,coordIdx);
% fit with forceVals as the independent variable for better performance
[linefit,gof] = fit(forceVals,displace,'poly1',fitopts);
if filtering.TF
% try to catch networks that may not contain a spanning component, or
% may otherwise result in poor fitting behavior, as identified by
% at least ONE of the following:
% (1) lack of spanning component as determined by checkLinks function
% ^ Do this check in top-level analysis script & pass result in here
% (2) adjacent displacements, except between forceVals(1)=0 and
% forceVals(2)>0, that differ by at least 75% of max. displacement
% ^ Attempt to catch networks with oscillatory displacement data
% (3) displacement decreases from forceVals(1)=0 to forceVals(2)>0
% (condition (3) can be toggled and is by default TRUE)
dispDiffs = diff(displace);
dispFlag = abs(dispDiffs(2:end)) > (0.75 * max(abs(displace)));
if ~filtering.spanCheck % (1) if a spanning component was NOT found
modulus = 0;
elseif any(dispFlag) % (2) large oscillations in displacements
modulus = 0;
elseif dispDiffs(1)<0 % (3) initial decrease in displacements
if ~isfield(filtering,'catchDrops')
filtering.catchDrops = true;
end
if filtering.catchDrops
modulus = 0;
else
modulus = 1/linefit.p1;
end
else
modulus = 1/linefit.p1;
end
else
% report modulus from "blind" linear regression
modulus = 1/linefit.p1;
end
end

getModulus.m at commit ee542ea, no license · at the source

Overview

Authors: Brady Berg¹, Jun Allard^1,2

ORCID iDs: Jun Allard

Mathematical, Computational and Systems Biology, University of California, Irvine, Irvine, California
Department of Mathematics, Department of Physics & Astronomy, Center for Complex Biological Systems, University of California, Irvine, Irvine, California

Institutions: University of California, Irvine (United States)

Journal: Biophysical journal, volume 125, issue 8, pages 1958-1967

Dates: received 2 July 2025; accepted 12 March 2026; published online 31 March 2026; in print 21 April 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1016/j.bpj.2026.03.028 · PMID 41925281 · PMCID PMC13351913 · OpenAlex W7147545617

Open access: hybrid, a free copy (OpenAlex)

Status: code verified (how the code is found and verified)

Categories: computational modeling (no new data) (modality), none (in silico) (organism), computational (subfield)

Methods: Statistics

MeSH: Actin Cytoskeleton*, Cytoskeleton*, Mechanical Phenomena*, Actins, Biomechanical Phenomena, Computer Simulation, Models, Biological (* major topic)

Topic: Cellular Mechanics and Interactions (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex

Funding: National Science Foundation (DMS 2052668); national institutes of health (T32 GM136624)

Citations: cited by 1 paper (Europe PMC); 43 references in the paper

Abstract

A repeated pattern in cytoskeletal architecture is the aster, in which a number of F-actin filaments emerge star shaped from a central node. Aster-based structures occur in cytoplasmic actin, the early stages of the cytokinetic ring in yeast, and in the context of biomimetic materials engineering. In this work, we use computational simulation to show that there is an optimal number of filaments per aster that maximizes rigidity, even at a fixed density of F-actin. This nonlinear dependence holds for both the shear and extensional moduli. At physiological parameters, the maximum corresponds approximately to the same filaments per aster observed in recent super-resolution images of cortical F-actin. Furthermore, we find that increasing filaments per aster leads to dramatic increases in the sample-to-sample variability in network rigidity. We explain both effects using percolation theory, wherein the probability that a given network is productively connected exhibits a sharp dependence on parameters. The dependence of network rigidity on this nanoscale architectural feature may suggest a mechanism by which cells tune the physical properties of their actin networks locally and rapidly (since no new F-actin must be assembled) and may inform efforts to create adaptive synthetic metamaterials inspired by actin networks.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 9 matches between paragraphs and lines of code.

Zenodo 18970832

License: GPL-3.0

State: the link answers, verified on 30 September 2026

Evidence: files inventoried

Size: 1 file

Software Heritage: not checked

Found in: “Data and code availability”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Matplotlib (2 files), NumPy (1 file)

Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)

30 September 2026: the link answers (HTTP 200)

514 files

doc/rendering/import-actin-ico.py, Python, 136 lines
doc/rendering/import-actin-sphere.py, Python, 136 lines
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src/sim/hands/kinesin_prop.cc, C++, 59 lines
src/sim/hands/kinesin_prop.h, C/C++, 72 lines
src/sim/hands/mighty.cc, C++, 110 lines
src/sim/hands/mighty.h, C/C++, 49 lines
src/sim/hands/mighty_prop.cc, C++, 133 lines
src/sim/hands/mighty_prop.h, C/C++, 106 lines
src/sim/hands/motor.cc, C++, 92 lines
src/sim/hands/motor.h, C/C++, 60 lines
src/sim/hands/motor_prop.cc, C++, 126 lines
src/sim/hands/motor_prop.h, C/C++, 96 lines
src/sim/hands/myosin.cc, C++, 89 lines
src/sim/hands/myosin.h, C/C++, 56 lines
src/sim/hands/myosin_prop.cc, C++, 60 lines
src/sim/hands/myosin_prop.h, C/C++, 72 lines
src/sim/hands/nucleator.cc, C++, 185 lines
src/sim/hands/nucleator.h, C/C++, 69 lines
src/sim/hands/nucleator_prop.cc, C++, 115 lines
src/sim/hands/nucleator_prop.h, C/C++, 136 lines
src/sim/hands/regulator.cc, C++, 41 lines
src/sim/hands/regulator.h, C/C++, 48 lines
src/sim/hands/regulator_prop.cc, C++, 50 lines
src/sim/hands/regulator_prop.h, C/C++, 66 lines
src/sim/hands/rescuer.cc, C++, 96 lines
src/sim/hands/rescuer.h, C/C++, 61 lines
src/sim/hands/rescuer_prop.cc, C++, 49 lines
src/sim/hands/rescuer_prop.h, C/C++, 67 lines
src/sim/hands/slider.cc, C++, 61 lines
src/sim/hands/slider.h, C/C++, 51 lines
src/sim/hands/slider_prop.cc, C++, 99 lines
src/sim/hands/slider_prop.h, C/C++, 103 lines
src/sim/hands/tracker.cc, C++, 94 lines
src/sim/hands/tracker.h, C/C++, 53 lines
src/sim/hands/tracker_prop.cc, C++, 54 lines
src/sim/hands/tracker_prop.h, C/C++, 70 lines
src/sim/hands/walker.cc, C++, 118 lines
src/sim/hands/walker.h, C/C++, 75 lines
src/sim/hands/walker_prop.cc, C++, 127 lines
src/sim/hands/walker_prop.h, C/C++, 87 lines
src/sim/interface.cc, C++, 1,078 lines
src/sim/interface.h, C/C++, 103 lines
src/sim/interpolation.cc, C++, 43 lines
src/sim/interpolation.h, C/C++, 138 lines
src/sim/interpolation4.cc, C++, 190 lines
src/sim/interpolation4.h, C/C++, 79 lines
src/sim/lattice.cc, C++, 64 lines
src/sim/lattice.h, C/C++, 553 lines
src/sim/meca.cc, C++, 1,701 lines
src/sim/meca.h, C/C++, 554 lines
src/sim/meca1d.h, C/C++, 218 lines
src/sim/meca_inter.cc, C++, 3,738 lines
src/sim/mecable.cc, C++, 401 lines
src/sim/mecable.h, C/C++, 394 lines
src/sim/mecafil.cc, C++, 323 lines
src/sim/mecafil.h, C/C++, 154 lines
src/sim/mecafil_project.cc, C++, 807 lines
src/sim/mecafil_projectmat.cc, C++, 206 lines
src/sim/mecapoint.cc, C++, 59 lines
src/sim/mecapoint.h, C/C++, 73 lines
src/sim/modulo.cc, C++, 94 lines
src/sim/modulo.h, C/C++, 73 lines
src/sim/movable.cc, C++, 937 lines
src/sim/movable.h, C/C++, 106 lines
src/sim/object.cc, C++, 248 lines
src/sim/object.h, C/C++, 180 lines
src/sim/object_set.cc, C++, 574 lines
src/sim/object_set.h, C/C++, 208 lines
src/sim/organizer.cc, C++, 183 lines
src/sim/organizer.h, C/C++, 124 lines
src/sim/organizer_set.cc, C++, 161 lines
src/sim/organizer_set.h, C/C++, 63 lines
src/sim/organizers/aster.cc, C++, 747 lines
src/sim/organizers/aster.h, C/C++, 264 lines
src/sim/organizers/aster_prop.cc, C++, 69 lines
src/sim/organizers/aster_prop.h, C/C++, 90 lines
src/sim/organizers/bundle.cc, C++, 179 lines
src/sim/organizers/bundle.h, C/C++, 77 lines
src/sim/organizers/bundle_prop.cc, C++, 62 lines
src/sim/organizers/bundle_prop.h, C/C++, 82 lines
src/sim/organizers/fake.cc, C++, 140 lines
src/sim/organizers/fake.h, C/C++, 74 lines
src/sim/organizers/fake_prop.cc, C++, 31 lines
src/sim/organizers/fake_prop.h, C/C++, 60 lines
src/sim/organizers/nucleus.cc, C++, 150 lines
src/sim/organizers/nucleus.h, C/C++, 78 lines
src/sim/organizers/nucleus_prop.cc, C++, 30 lines
src/sim/organizers/nucleus_prop.h, C/C++, 60 lines
src/sim/parser.cc, C++, 1,251 lines
src/sim/parser.h, C/C++, 116 lines
src/sim/point_grid.cc, C++, 650 lines
src/sim/point_grid.h, C/C++, 388 lines
src/sim/sim.cc, C++, 140 lines
src/sim/sim.h, C/C++, 17 lines
src/sim/sim_thread.cc, C++, 528 lines
src/sim/sim_thread.h, C/C++, 224 lines
src/sim/simul.cc, C++, 510 lines
src/sim/simul.h, C/C++, 551 lines
src/sim/simul_custom.cc, C++, 54 lines
src/sim/simul_file.cc, C++, 686 lines
src/sim/simul_prop.cc, C++, 179 lines
src/sim/simul_prop.h, C/C++, 294 lines
src/sim/simul_report.cc, C++, 2,458 lines
src/sim/simul_solve.cc, C++, 450 lines
src/sim/simul_step.cc, C++, 181 lines
src/sim/single.cc, C++, 186 lines
src/sim/single.h, C/C++, 197 lines
src/sim/single_prop.cc, C++, 216 lines
src/sim/single_prop.h, C/C++, 154 lines
src/sim/single_set.cc, C++, 631 lines
src/sim/single_set.h, C/C++, 183 lines
src/sim/singles/picket.cc, C++, 76 lines
src/sim/singles/picket.h, C/C++, 60 lines
src/sim/singles/picket_long.cc, C++, 116 lines
src/sim/singles/picket_long.h, C/C++, 44 lines
src/sim/singles/wrist.cc, C++, 130 lines
src/sim/singles/wrist.h, C/C++, 94 lines
src/sim/singles/wrist_long.cc, C++, 117 lines
src/sim/singles/wrist_long.h, C/C++, 49 lines
src/sim/solid.cc, C++, 1,232 lines
src/sim/solid.h, C/C++, 219 lines
src/sim/solid_prop.cc, C++, 128 lines
src/sim/solid_prop.h, C/C++, 145 lines
src/sim/solid_set.cc, C++, 93 lines
src/sim/solid_set.h, C/C++, 85 lines
src/sim/space.cc, C++, 518 lines
src/sim/space.h, C/C++, 197 lines
src/sim/space_prop.cc, C++, 204 lines
src/sim/space_prop.h, C/C++, 88 lines
src/sim/space_set.cc, C++, 148 lines
src/sim/space_set.h, C/C++, 88 lines
src/sim/spaces/space_banana.cc, C++, 250 lines
src/sim/spaces/space_banana.h, C/C++, 82 lines
src/sim/spaces/space_capsule.cc, C++, 295 lines
src/sim/spaces/space_capsule.h, C/C++, 86 lines
src/sim/spaces/space_cylinder.cc, C++, 282 lines
src/sim/spaces/space_cylinder.h, C/C++, 85 lines
src/sim/spaces/space_cylinderP.cc, C++, 250 lines
src/sim/spaces/space_cylinderP.h, C/C++, 99 lines
src/sim/spaces/space_cylinderZ.cc, C++, 301 lines
src/sim/spaces/space_cylinderZ.h, C/C++, 86 lines
src/sim/spaces/space_dice.cc, C++, 271 lines
src/sim/spaces/space_dice.h, C/C++, 78 lines
src/sim/spaces/space_ellipse.cc, C++, 331 lines
src/sim/spaces/space_ellipse.h, C/C++, 102 lines
src/sim/spaces/space_periodic.cc, C++, 202 lines
src/sim/spaces/space_periodic.h, C/C++, 71 lines
src/sim/spaces/space_polygon.cc, C++, 393 lines
src/sim/spaces/space_polygon.h, C/C++, 92 lines
src/sim/spaces/space_polygonZ.cc, C++, 267 lines
src/sim/spaces/space_polygonZ.h, C/C++, 84 lines
src/sim/spaces/space_ring.cc, C++, 227 lines
src/sim/spaces/space_ring.h, C/C++, 88 lines
src/sim/spaces/space_sphere.cc, C++, 157 lines
src/sim/spaces/space_sphere.h, C/C++, 81 lines
src/sim/spaces/space_square.cc, C++, 381 lines
src/sim/spaces/space_square.h, C/C++, 73 lines
src/sim/spaces/space_strip.cc, C++, 318 lines
src/sim/spaces/space_strip.h, C/C++, 85 lines
src/sim/spaces/space_torus.cc, C++, 157 lines
src/sim/spaces/space_torus.h, C/C++, 72 lines
src/sim/sphere.cc, C++, 652 lines
src/sim/sphere.h, C/C++, 185 lines
src/sim/sphere_prop.cc, C++, 106 lines
src/sim/sphere_prop.h, C/C++, 107 lines
src/sim/sphere_set.cc, C++, 82 lines
src/sim/sphere_set.h, C/C++, 67 lines
src/sim/splash.cc, C++, 2 lines
src/sim/splash.h, C/C++, 41 lines
src/test/test.cc, C++, 61 lines
src/test/test_blas.cc, C++, 97 lines
src/test/test_code.cc, C++, 976 lines
src/test/test_cxx.cc, C++, 30 lines
src/test/test_dispatch.cc, C++, 14 lines
src/test/test_gillespie.cc, C++, 252 lines
src/test/test_glapp.cc, C++, 82 lines
src/test/test_glos.cc, C++, 42 lines
src/test/test_glut.cc, C++, 358 lines
src/test/test_glut3D.cc, C++, 275 lines
src/test/test_grid.cc, C++, 335 lines
src/test/test_math.cc, C++, 126 lines
src/test/test_matrix.cc, C++, 517 lines
src/test/test_omp.cc, C++, 68 lines
src/test/test_opengl.cc, C++, 379 lines
src/test/test_pipe.cc, C++, 184 lines
src/test/test_platonic.cc, C++, 232 lines
src/test/test_quaternion.cc, C++, 182 lines
src/test/test_random.cc, C++, 617 lines
src/test/test_rasterizer.cc, C++, 348 lines
src/test/test_signal.cc, C++, 38 lines
src/test/test_simd.cc, C++, 932 lines
src/test/test_sizeof.cc, C++, 62 lines
src/test/test_solve.cc, C++, 327 lines
src/test/test_space.cc, C++, 567 lines
src/test/test_sphere.cc, C++, 200 lines
src/test/test_string.cc, C++, 20 lines
src/test/test_thread.cc, C++, 57 lines
src/test/test_vbo.cc, C++, 203 lines
src/tools/cymart.cc, C++, 397 lines
src/tools/frametool.cc, C++, 493 lines
src/tools/reader.cc, C++, 164 lines
src/tools/report.cc, C++, 259 lines
src/tools/reportF.cc, C++, 119 lines
src/tools/sieve.cc, C++, 113 lines
LICENSE.txt, License, 674 lines
README.md, Text, 102 lines

At the source: doi.org/10.5281/zenodo.18970832

Zenodo 18970060

License: CC-BY-4.0

State: the link answers, verified on 30 September 2026

Evidence: files inventoried

Size: 1 file

Software Heritage: not checked

Found in: “Data and code availability”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)

30 September 2026: the link answers (HTTP 200)

At the source: doi.org/10.5281/zenodo.18970060

bcberg/berg_astralmikado

License: none: the authors keep all their rights

State: the link answers, verified on 30 September 2026

Evidence: files inventoried

Commit: ee542ea8698ee419fd74bfad3c130fbec5267b60, 22 June 2026

Languages: MATLAB (54), C/C++ (26), C (23), Shell (11)

Size: 78,882 files, 114 scripts

Software Heritage: not archived

Found in: the Zenodo archive record

Holds: README

Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Statistics and Machine Learning Toolbox (16 files), Parallel Computing Toolbox (7 files), Optimization Toolbox (4 files), Curve Fitting Toolbox (2 files)

Availability: 1 check, the latest on 30 September 2026: the link answers

30 September 2026: the link answers

115 files

geometry/astralNetExamples.m, MATLAB, 262 lines
geometry/astralNetExamples_otherTypes.m, MATLAB, 346 lines
geometry/astralNetTestVisuals.m, MATLAB, 112 lines
geometry/astralPercol.m, MATLAB, 107 lines
geometry/astralPercol_eqSpaced.m, MATLAB, 108 lines
geometry/astralPercol_exp.m, MATLAB, 108 lines
geometry/codegen/mex/generateAstralNetwork/assertValidSizeArg.c, C, 95 lines
geometry/codegen/mex/generateAstralNetwork/assertValidSizeArg.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/colon.c, C, 80 lines
geometry/codegen/mex/generateAstralNetwork/colon.h, C/C++, 28 lines
geometry/codegen/mex/generateAstralNetwork/eml_int_forloop_overflow_check.c, C, 33 lines
geometry/codegen/mex/generateAstralNetwork/eml_int_forloop_overflow_check.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/error.c, C, 68 lines
geometry/codegen/mex/generateAstralNetwork/error.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork.c, C, 4,292 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork.h, C/C++, 35 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_data.c, C, 44 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_data.h, C/C++, 32 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_emxutil.c, C, 312 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_emxutil.h, C/C++, 67 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_initialize.c, C, 44 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_initialize.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_internal_types.h, C/C++, 40 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_mex.sh, Shell, 2 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_terminate.c, C, 64 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_terminate.h, C/C++, 28 lines
geometry/codegen/mex/generateAstralNetwork/generateAstralNetwork_types.h, C/C++, 90 lines
geometry/codegen/mex/generateAstralNetwork/indexShapeCheck.c, C, 53 lines
geometry/codegen/mex/generateAstralNetwork/indexShapeCheck.h, C/C++, 27 lines
geometry/codegen/mex/generateAstralNetwork/interface/_coder_generateAstralNetwork_api.c, C, 292 lines
geometry/codegen/mex/generateAstralNetwork/interface/_coder_generateAstralNetwork_api.h, C/C++, 27 lines
geometry/codegen/mex/generateAstralNetwork/interface/_coder_generateAstralNetwork_info.c, C, 80 lines
geometry/codegen/mex/generateAstralNetwork/interface/_coder_generateAstralNetwork_info.h, C/C++, 20 lines
geometry/codegen/mex/generateAstralNetwork/interface/_coder_generateAstralNetwork_mex.c, C, 94 lines
geometry/codegen/mex/generateAstralNetwork/interface/_coder_generateAstralNetwork_mex.h, C/C++, 32 lines
geometry/codegen/mex/generateAstralNetwork/mod.c, C, 34 lines
geometry/codegen/mex/generateAstralNetwork/mod.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/mustBeInteger.c, C, 52 lines
geometry/codegen/mex/generateAstralNetwork/mustBeInteger.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/rand.c, C, 120 lines
geometry/codegen/mex/generateAstralNetwork/rand.h, C/C++, 31 lines
geometry/codegen/mex/generateAstralNetwork/repmat.c, C, 81 lines
geometry/codegen/mex/generateAstralNetwork/repmat.h, C/C++, 28 lines
geometry/codegen/mex/generateAstralNetwork/rt_nonfinite.c, C, 32 lines
geometry/codegen/mex/generateAstralNetwork/rt_nonfinite.h, C/C++, 38 lines
geometry/codegen/mex/generateAstralNetwork/rtwtypes.h, C/C++, 27 lines
geometry/codegen/mex/generateAstralNetwork/sort.c, C, 153 lines
geometry/codegen/mex/generateAstralNetwork/sort.h, C/C++, 27 lines
geometry/codegen/mex/generateAstralNetwork/sortIdx.c, C, 664 lines
geometry/codegen/mex/generateAstralNetwork/sortIdx.h, C/C++, 27 lines
geometry/codegen/mex/generateAstralNetwork/sum.c, C, 170 lines
geometry/codegen/mex/generateAstralNetwork/sum.h, C/C++, 27 lines
geometry/codegen/mex/generateAstralNetwork/sumMatrixIncludeNaN.c, C, 22 lines
geometry/codegen/mex/generateAstralNetwork/sumMatrixIncludeNaN.h, C/C++, 26 lines
geometry/codegen/mex/generateAstralNetwork/warning.c, C, 103 lines
geometry/codegen/mex/generateAstralNetwork/warning.h, C/C++, 26 lines
geometry/collectCurves.m, MATLAB, 40 lines
geometry/connCheck.m, MATLAB, 43 lines
geometry/danglingEnds.m, MATLAB, 170 lines
geometry/estPercProb.m, MATLAB, 39 lines
geometry/estPercProb_eqSpaced.m, MATLAB, 39 lines
geometry/estPercProb_exp.m, MATLAB, 41 lines
geometry/filLengthQuestions.m, MATLAB, 97 lines
geometry/generateAstralNetwork.m, MATLAB, 354 lines
geometry/generateAstralNetwork_eqSpaced.m, MATLAB, 359 lines
geometry/generateAstralNetwork_exp.m, MATLAB, 358 lines
geometry/getAllPercCurves.m, MATLAB, 118 lines
geometry/getAllPercCurves_eqSpaced.m, MATLAB, 118 lines
geometry/getAllPercCurves_exp.m, MATLAB, 120 lines
geometry/getPercCurve.m, MATLAB, 92 lines
geometry/oneVsTwoHalves.m, MATLAB, 74 lines
geometry/percCheck.m, MATLAB, 97 lines, 1 match
geometry/percCrit.m, MATLAB, 183 lines, 1 match
geometry/percCrit_eqSpaced.m, MATLAB, 180 lines
geometry/percCurveFitting.m, MATLAB, 283 lines, 1 match
geometry/percMCRG.m, MATLAB, 95 lines
geometry/percOneSample.m, MATLAB, 29 lines
geometry/springsPerNode.m, MATLAB, 123 lines
mechanics/analysis/checkLinks.m, MATLAB, 99 lines
mechanics/analysis/crosslinker_dens_shear.m, MATLAB, 143 lines
mechanics/analysis/crosslinker_stiff_shear.m, MATLAB, 142 lines
mechanics/analysis/fiberPointLines.m, MATLAB, 20 lines
mechanics/analysis/figures_manu.m, MATLAB, 1,282 lines, 2 matches
mechanics/analysis/figures_manu_rev1.m, MATLAB, 2,231 lines, 1 match
mechanics/analysis/getModulus.m, MATLAB, 83 lines, 2 matches
mechanics/analysis/kbend_shear.m, MATLAB, 157 lines
mechanics/analysis/krot_shear.m, MATLAB, 159 lines
mechanics/analysis/modulus_distr.m, MATLAB, 187 lines
mechanics/analysis/parseForceSweep.m, MATLAB, 39 lines
mechanics/analysis/parseForceSweep_manySamp.m, MATLAB, 62 lines
mechanics/analysis/parseTimeSeries.m, MATLAB, 33 lines
mechanics/analysis/perc_in_cytosim.m, MATLAB, 235 lines
mechanics/analysis/rep_shear_aster_actin.m, MATLAB, 193 lines
mechanics/analysis/rep_shear_aster_otherRhos.m, MATLAB, 189 lines
mechanics/analysis/rep_tens_aster_actin.m, MATLAB, 192 lines
mechanics/analysis/rf_shear_aster_actin_physkT.m, MATLAB, 250 lines
mechanics/analysis/rf_shear_aster_eq_actin.m, MATLAB, 192 lines
mechanics/analysis/rf_shear_aster_eq_otherRhos.m, MATLAB, 189 lines
mechanics/analysis/rf_tens_aster_actin_physkT.m, MATLAB, 251 lines, 1 match
mechanics/analysis/test_end_force.m, MATLAB, 57 lines
mechanics/analysis/timeseries_astralNum.m, MATLAB, 152 lines
mechanics/analysis/timeseries_astralNum_physkT.m, MATLAB, 154 lines
mechanics/analysis/timeseries_sysSize.m, MATLAB, 97 lines
mechanics/analysis/update_fits.m, MATLAB, 277 lines
mechanics/drivers/run_perc_in_cytosim.sh, Shell, 28 lines
mechanics/drivers/run_rf_shear_aster_actin_physkT.sh, Shell, 40 lines
mechanics/drivers/run_rf_tens_aster_actin_physkT.sh, Shell, 40 lines
mechanics/drivers/run_test_end_force.sh, Shell, 27 lines
mechanics/drivers/run_timeseries_astralNum.sh, Shell, 46 lines
mechanics/drivers/run_timeseries_astralNum_physkT.sh, Shell, 46 lines
mechanics/drivers/run_visuals_crslnkdens.sh, Shell, 38 lines
mechanics/drivers/run_visuals_sheargrid.sh, Shell, 40 lines
mechanics/drivers/run_visuals_sheargrid_physkT.sh, Shell, 40 lines
mechanics/drivers/simul_stand.sh, Shell, 51 lines
README.md, Text, 74 lines

At the source: github.com/bcberg/Berg_AstralMikado/tree/v1.0.0

bcberg/cytosim-bcb

License: GPL-3.0

State: the link answers, verified on 30 September 2026

Evidence: files inventoried

Commit: 3192f4845e9c483bd50ecfecaed0da6d7864f3b7, 6 November 2024

Languages: C++ (246), C/C++ (232), Python (28), C (4), Shell (1), MATLAB (1)

Size: 882 files, 512 scripts

Software Heritage: not archived

Found in: the Zenodo archive record

Holds: README, license file, tests, documentation

Not found: CITATION.cff, environment file, continuous integration

Tools: Matplotlib (2 files), NumPy (1 file)

Availability: 1 check, the latest on 30 September 2026: the link answers

30 September 2026: the link answers

514 files

doc/rendering/import-actin-ico.py, Python, 136 lines
doc/rendering/import-actin-sphere.py, Python, 136 lines
doc/rendering/import-actin.py, Python, 136 lines
doc/rendering/import-links.py, Python, 137 lines
doc/rendering/remove-actin.py, Python, 15 lines
doc/tutorials/code/collect.py, Python, 155 lines
doc/tutorials/code/master.sh, Shell, 26 lines
doc/tutorials/code/scan.py, Python, 115 lines
python/look/collect.py, Python, 146 lines
python/look/compare_config.py, Python, 122 lines
python/look/get_data.py, Python, 179 lines
python/look/make_image.py, Python, 171 lines
python/look/make_movie.py, Python, 393 lines
python/look/make_page.py, Python, 263 lines
python/look/make_plots.py, Python, 149 lines
python/look/read_config.py, Python, 492 lines
python/look/scan.py, Python, 163 lines
python/look/tell.py, Python, 163 lines
python/misc/battery_test.py, Python, 103 lines
python/misc/cleanup.py, Python, 135 lines
python/misc/compare.py, Python, 145 lines
python/misc/plot.py, Python, 106 lines
python/misc/pyned.py, Python, 266 lines
python/misc/reduce.py, Python, 116 lines
python/run/go_sim.py, Python, 229 lines
python/run/go_sim_lib.py, Python, 241 lines
python/run/preconfig.py, Python, 676 lines
python/run/submit_one.py, Python, 161 lines
python/run/submit_slurm.py, Python, 276 lines
src/base/array.h, C/C++, 588 lines
src/base/assert_macro.h, C/C++, 90 lines
src/base/backtrace.cc, C++, 48 lines
src/base/backtrace.h, C/C++, 29 lines
src/base/buddy.h, C/C++, 176 lines
src/base/exceptions.cc, C++, 8 lines
src/base/exceptions.h, C/C++, 215 lines
src/base/filepath.cc, C++, 196 lines
src/base/filepath.h, C/C++, 62 lines
src/base/filewrapper.cc, C++, 273 lines
src/base/filewrapper.h, C/C++, 145 lines
src/base/glossary.cc, C++, 820 lines
src/base/glossary.h, C/C++, 543 lines
src/base/inventoried.h, C/C++, 48 lines
src/base/inventory.cc, C++, 265 lines
src/base/inventory.h, C/C++, 118 lines
src/base/iowrapper.cc, C++, 616 lines
src/base/iowrapper.h, C/C++, 213 lines
src/base/messages.cc, C++, 36 lines
src/base/messages.h, C/C++, 121 lines
src/base/node.h, C/C++, 45 lines
src/base/node_list.cc, C++, 429 lines
src/base/node_list.h, C/C++, 131 lines
src/base/operator_new.cc, C++, 54 lines
src/base/print_color.cc, C++, 140 lines
src/base/print_color.h, C/C++, 36 lines
src/base/property.cc, C++, 143 lines
src/base/property.h, C/C++, 192 lines
src/base/property_list.cc, C++, 310 lines
src/base/property_list.h, C/C++, 143 lines
src/base/stream_func.cc, C++, 266 lines
src/base/stream_func.h, C/C++, 48 lines
src/base/tictoc.cc, C++, 138 lines
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LICENSE.txt, License, 674 lines
README.md, Text, 102 lines

At the source: github.com/bcberg/cytosim-bcb/tree/v1.0.0

The paper's code and data availability statement is in the Data section.

Tracing map

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What the map holds:

4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
1,138 scripts, each with its path and the digest of its content;
9 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data and code availability

• All code has been deposited on Github and Zenodo. The fork of Cytosim is at Zenodo: https://doi.org/10.5281/zenodo.18970832. • The configurations, analysis and geometry sampling and analysis are at Zenodo: https://doi.org/10.5281/zenodo.18970060.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 7 MeSH terms, 2 funders, 38 references.

Cite

This paper

Berg, B., & Allard, J. (2026). Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds. Biophysical journal, 125(8), 1958-1967. https://doi.org/10.1016/j.bpj.2026.03.028

BibTeX

@article{berg2026astral, author = {Berg, Brady and Allard, Jun}, title = {{Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds}}, journal = {Biophysical journal}, year = {2026}, month = mar, volume = {125}, number = {8}, pages = {1958--1967}, publisher = {The Biophysical Society}, issn = {0006-3495}, doi = {10.1016/j.bpj.2026.03.028}, url = {https://doi.org/10.1016/j.bpj.2026.03.028}, pmid = {41925281}, pmcid = {PMC13351913} }

RIS

TY - JOUR AU - Berg, Brady AU - Allard, Jun TI - Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds T2 - Biophysical journal J2 - Biophys J PY - 2026 DA - 2026/03/31 VL - 125 IS - 8 SP - 1958 EP - 1967 SN - 0006-3495 PB - The Biophysical Society DO - 10.1016/j.bpj.2026.03.028 UR - https://doi.org/10.1016/j.bpj.2026.03.028 LA - en ER -

CSL-JSON

{ "id": "10.1016/j.bpj.2026.03.028", "type": "article-journal", "title": "Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds", "container-title": "Biophysical journal", "author": [ { "family": "Berg", "given": "Brady" }, { "family": "Allard", "given": "Jun" } ], "container-title-short": "Biophys J", "volume": "125", "issue": "8", "page": "1958-1967", "DOI": "10.1016/j.bpj.2026.03.028", "PMID": "41925281", "PMCID": "PMC13351913", "ISSN": "0006-3495", "publisher": "The Biophysical Society", "URL": "https://doi.org/10.1016/j.bpj.2026.03.028", "language": "en", "issued": { "date-parts": [ [ 2026, 3, 31 ] ] } }

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Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds.

Code ↔ Paper

Paper

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Overview

Abstract

Repositories

Zenodo 18970832

Zenodo 18970060

bcberg/berg_astralmikado

bcberg/cytosim-bcb

Tracing map

Data

Data and code availability

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Version 1, 30 September 2026: the first record

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