├── .gitignore ├── AUTHORS.txt ├── MATmodel ├── MatlabMeshDiffusion │ ├── DendriteMeshDiffusion.m │ ├── TriMeshBuilder.m │ ├── TriMeshFunctions.m │ ├── alphaShape.png │ ├── meshdata │ │ ├── getfulltets.m │ │ └── getfullverts.m │ └── pathdata │ │ └── getpaths.m ├── mainfigures │ ├── ActinMultiplexGUI.fig │ ├── BradsModelGUI.fig │ ├── BradsModelGUI2.fig │ └── DENDRITE.png ├── mainfunctions │ ├── ATdata.mat │ ├── ATdata │ │ ├── .gitignore │ │ ├── ATdata.mat │ │ ├── ATdataP1a.mat │ │ ├── ATdataP1b.mat │ │ ├── ATdataP1c.mat │ │ ├── ATdataP1d.mat │ │ ├── ATdataP1e.mat │ │ ├── ATdataP1f.mat │ │ ├── ATdataP2a.mat │ │ ├── ATdataP2b.mat │ │ ├── ATdataP2c.mat │ │ ├── RobustData.mat │ │ └── savetipdir.m │ ├── ActinMultiplex.m │ ├── ActinMultiplexGUI.m │ ├── ActinMultiplex_Orig.m │ ├── STARShiP.m │ ├── STARShiPGUI.m │ └── advance │ │ ├── Makefile │ │ ├── PlotActin.m │ │ ├── S3D.m │ │ ├── SAPkernel.m │ │ ├── _cython_interface.c │ │ ├── _cython_interface.h │ │ ├── _cython_interface.pyx │ │ ├── advance_one_step.c │ │ ├── dendritic_mesh_serialized.mat │ │ ├── dendritic_meshs_serialized.mat │ │ ├── dolfin_mesh_utils.py │ │ ├── libadvanceonestep.so │ │ ├── particle_diffusion_on_mesh.py │ │ ├── particle_diffusion_plot_utils.py │ │ └── test_mex.m ├── matpydiffusion │ ├── MatDiffusion.m │ ├── TriMeshBuilder.m │ ├── TriMeshFunctions.m │ ├── TriMeshImporter.m │ ├── dolfinXML.m │ ├── dolfinXMLalpha.m │ └── wavefront │ │ ├── dendrite.obj │ │ ├── read_wobj.m │ │ └── write_wobj.m ├── miscfunctions │ ├── EXITBOX.m │ ├── EXITSPINE.m │ ├── ORM │ │ ├── 100YearCluster │ │ │ ├── Math.m │ │ │ ├── ORM3e9.m │ │ │ └── ORM3e9sc.m │ │ ├── ACTIN │ │ │ ├── ActMx.png │ │ │ ├── ActinMainStageGood.m │ │ │ ├── ActinMath.m │ │ │ ├── Archive │ │ │ │ ├── ActinBranchMath.m │ │ │ │ ├── ActinBranchMath2.m │ │ │ │ ├── ActinBranchMath2.m~ │ │ │ │ ├── ActinBranchMaths.m │ │ │ │ ├── ActinBranchMaths.m~ │ │ │ │ ├── ActinHelix.m │ │ │ │ ├── ActinMainStage2.m │ │ │ │ ├── ActinMath2.m │ │ │ │ ├── ActinMath3.m │ │ │ │ ├── ActinMath4.m │ │ │ │ ├── ActinModel.m │ │ │ │ ├── ActinModeling.m │ │ │ │ ├── ActinNetwork.m │ │ │ │ ├── ActinNetwork2.m │ │ │ │ ├── ActinRateModel.m │ │ │ │ ├── ActinRateModel2.m │ │ │ │ ├── ActinRotation.m │ │ │ │ ├── ActinRotation2.m │ │ │ │ ├── ActinRotation2.m~ │ │ │ │ ├── ActinRotation3.m │ │ │ │ ├── ActinSimulation.m │ │ │ │ ├── MathActin.m~ │ │ │ │ ├── MathActinGood.m │ │ │ │ ├── MathActinGood2.m │ │ │ │ ├── RotMx.m │ │ │ │ ├── actinangles.m │ │ │ │ ├── actinangles2.m │ │ │ │ ├── actinangles3.m │ │ │ │ ├── actinfun.m │ │ │ │ ├── actinfun2.m │ │ │ │ ├── actinfun3.m │ │ │ │ ├── rot.m~ │ │ │ │ ├── rota.m │ │ │ │ ├── rota.m~ │ │ │ │ ├── rota2.m │ │ │ │ ├── rota2.m~ │ │ │ │ ├── rota3.m │ │ │ │ ├── rota4.m │ │ │ │ ├── rota4.m~ │ │ │ │ ├── rota5.m │ │ │ │ ├── rota6.m │ │ │ │ ├── rota6.m~ │ │ │ │ ├── rota7.m │ │ │ │ ├── rota7.m~ │ │ │ │ ├── rotat.m │ │ │ │ ├── rotat2.m │ │ │ │ ├── rotat3.m │ │ │ │ └── rotat4.m │ │ │ ├── MathActin.m │ │ │ └── actin_good │ │ │ │ ├── ActinGrowth.m │ │ │ │ ├── ActinHelix.m │ │ │ │ ├── ActinMainStageGood1.m │ │ │ │ ├── MathActin.m │ │ │ │ └── scrap.m │ │ ├── ActinMultiplex2.m │ │ ├── MASK │ │ │ ├── SAPMASKS.m │ │ │ ├── SAPMASKSGUI.fig │ │ │ ├── SAPMASKSGUI.m │ │ │ └── SAPMASKSsc.m │ │ ├── ORMATHFUN.m │ │ ├── ORMarchive │ │ │ ├── ACTIN.m │ │ │ ├── ACTINFUN.m │ │ │ ├── ActinMultiplex.m │ │ │ ├── Curves.m │ │ │ ├── Math.m │ │ │ ├── RobustData.mat │ │ │ ├── RobustSAP │ │ │ │ ├── OTHERSAP │ │ │ │ │ ├── BRUTESAP │ │ │ │ │ │ ├── DualSAP.m │ │ │ │ │ │ ├── SAPbrute.m │ │ │ │ │ │ ├── SAPbruteGUI.fig │ │ │ │ │ │ ├── SAPbruteGUI.m │ │ │ │ │ │ └── brutesapscript.m │ │ │ │ │ ├── OFFDEPSAP │ │ │ │ │ │ ├── OffRM │ │ │ │ │ │ │ ├── GUID │ │ │ │ │ │ │ │ ├── SAPGUID.fig │ │ │ │ │ │ │ │ ├── SAPGUID.m │ │ │ │ │ │ │ │ └── SAPGUIDFUN.m │ │ │ │ │ │ │ ├── OFFDEPSAP.m │ │ │ │ │ │ │ ├── SAPOffRMGUI.fig │ │ │ │ │ │ │ └── SAPOffRMGUI.m │ │ │ │ │ │ ├── OnRM │ │ │ │ │ │ │ ├── SAPFUN.m │ │ │ │ │ │ │ ├── SAPGUI.fig │ │ │ │ │ │ │ ├── SAPGUI.m │ │ │ │ │ │ │ ├── ShouvalORM.m │ │ │ │ │ │ │ └── ShouvalORMFUN.m │ │ │ │ │ │ ├── RobustTEST │ │ │ │ │ │ │ ├── DualSAP.m │ │ │ │ │ │ │ ├── RobustSAP.m │ │ │ │ │ │ │ ├── RobustSAPscr.m │ │ │ │ │ │ │ └── RobustSAPscr2.m │ │ │ │ │ │ └── surf_from_scatter │ │ │ │ │ │ │ ├── RobustData.mat │ │ │ │ │ │ │ ├── license.txt │ │ │ │ │ │ │ ├── surf_from_scatter.html │ │ │ │ │ │ │ ├── surf_from_scatter.m │ │ │ │ │ │ │ ├── surf_from_scatter.png │ │ │ │ │ │ │ ├── surf_from_scatter_01.png │ │ │ │ │ │ │ ├── surf_from_scatter_02.png │ │ │ │ │ │ │ ├── surf_from_scatter_03.png │ │ │ │ │ │ │ └── surf_from_scatter_04.png │ │ │ │ │ └── SAPSPACE │ │ │ │ │ │ ├── DualSAP.m │ │ │ │ │ │ ├── DualSAP2.m │ │ │ │ │ │ ├── DualSAPbrute.m │ │ │ │ │ │ ├── JUNKSCRIPT.m │ │ │ │ │ │ ├── ReverseSAP.m │ │ │ │ │ │ ├── ReverseSAP2.m │ │ │ │ │ │ └── ReverseSAP3.m │ │ │ │ ├── ROBUSTSAP │ │ │ │ │ ├── DualSAP.m │ │ │ │ │ ├── RobustData.mat │ │ │ │ │ ├── RobustSAP.m │ │ │ │ │ ├── RobustSAPscr.m │ │ │ │ │ ├── RobustSAPscr2.m │ │ │ │ │ ├── SAPFUN.m │ │ │ │ │ ├── SAPGUI.fig │ │ │ │ │ ├── SAPGUI.m │ │ │ │ │ └── surf_from_scatter │ │ │ │ │ │ ├── RobustData.mat │ │ │ │ │ │ ├── license.txt │ │ │ │ │ │ ├── surf_from_scatter.html │ │ │ │ │ │ ├── surf_from_scatter.m │ │ │ │ │ │ ├── surf_from_scatter.png │ │ │ │ │ │ ├── surf_from_scatter_01.png │ │ │ │ │ │ ├── surf_from_scatter_02.png │ │ │ │ │ │ ├── surf_from_scatter_03.png │ │ │ │ │ │ └── surf_from_scatter_04.png │ │ │ │ ├── RobustData.mat │ │ │ │ ├── RobustSAP.m │ │ │ │ ├── RobustSAP2.m │ │ │ │ ├── RobustSAPsc.m │ │ │ │ ├── RobustSAPsc2.m │ │ │ │ ├── RobustSAPsc3.m │ │ │ │ └── ShouvalRobust │ │ │ │ │ ├── RobustData.mat │ │ │ │ │ ├── SRobustSAP.m │ │ │ │ │ └── SRobustSAPsc.m │ │ │ ├── RobustSAP4.m │ │ │ ├── RobustSAPsc4.m │ │ │ └── SAPSHOVAL.m │ │ ├── RobustGR.m │ │ ├── RobustGRsc.m │ │ ├── SAPORM.m │ │ ├── SAPORMGUI.fig │ │ └── SAPORMGUI.m │ ├── PRIMARY │ │ ├── BMSurfD.m │ │ ├── Bounce.m │ │ ├── BrownianMotion.m │ │ ├── CalciumFunction.m │ │ ├── CircleDiffusion.m │ │ ├── DiffData.csv │ │ ├── ExitNeck.m │ │ ├── JMPDIFFUSION.m │ │ ├── MatLabNotes.m │ │ ├── SClusters.m │ │ ├── SimpleCircleDiffusion.m │ │ ├── SimpleDiffusion.m │ │ ├── SimpleDiffusionSc.m │ │ ├── SimpleMultiplex.m │ │ ├── SimpleSAP.m │ │ ├── TrackMSD.m │ │ ├── annulus.m │ │ ├── bradftp.m │ │ ├── fixPSlinestyle.m │ │ ├── inbox.m │ │ ├── izhikevich.jpg │ │ ├── izhikevich.m │ │ ├── mapdendrite.m │ │ ├── normdist.m │ │ ├── spinesurf.m │ │ └── spinesurf2.m │ ├── Shouval │ │ └── Shouval1.m │ ├── TRACKDOT.m │ ├── bonusItems │ │ ├── TrackMSD.m │ │ ├── clustersim.m │ │ ├── postspike.jpg │ │ ├── postspike.m │ │ ├── trimesh_3D_data_96.mat │ │ ├── trimesh_data_96.mat │ │ ├── view_3d_near_top.m │ │ └── view_top_component.m │ ├── graphics │ │ ├── CIenvFun.m │ │ ├── CIplot.m │ │ ├── ClrMap1.m │ │ ├── ClrMap2.m │ │ ├── FIGROT.m │ │ ├── FigSetup.m │ │ ├── PlotSugar.m │ │ ├── addaxis.m │ │ ├── anotext.m │ │ ├── boundedline │ │ │ ├── boundedline.m │ │ │ ├── boundedline2.m │ │ │ ├── license.txt │ │ │ ├── outlinebounds.m │ │ │ └── outlinebounds2.m │ │ ├── circus.m │ │ ├── colors │ │ │ └── Choose_Color.fig │ │ ├── confplot │ │ │ ├── ciplot.m │ │ │ ├── confidence_plot_test.m │ │ │ ├── confplot.m │ │ │ └── testpic.jpg │ │ ├── figures │ │ │ └── ResBarsFun.m │ │ ├── goodfont.m │ │ ├── plot3prep.m │ │ ├── scatter3prep.m │ │ └── simlegend.m │ ├── inpoly │ │ ├── inpoly.m │ │ ├── lake.m │ │ └── polydemo.m │ ├── misc │ │ ├── Diffusion.m │ │ ├── DiffusionMem.m │ │ ├── DiffusionMemPos.m │ │ ├── MoleDiffusion.m │ │ ├── MoleDiffusionMemPos.m │ │ ├── MoleDiffusionMembrane.m │ │ ├── Mye.m │ │ ├── NernstCal.m │ │ ├── Unmye.m │ │ ├── bounce │ │ │ ├── diffusionT.m │ │ │ ├── diffusionTKurs.m │ │ │ └── diffusionTgleich.m │ │ ├── moveParticlesChargePot.m │ │ ├── numberMoleculesIn.m │ │ └── scrollwheel_view.m │ ├── msdanalyzer.m │ └── trig │ │ ├── RotVertDemo.m │ │ ├── RotateVertex.m │ │ ├── euler.png │ │ └── misctrig │ │ ├── ExampleMainFunction.m │ │ ├── RotMx.m │ │ ├── RotMx1.m │ │ ├── Trig.m │ │ └── VertexRotateFun.m └── outputfigs │ ├── STARShiP0.png │ ├── STARShiP1.png │ ├── STARShiP2.png │ ├── STARShiP3.png │ └── saveoutputfigs.m ├── PyDiffusion ├── README.md ├── advance_one_step_mex │ ├── Makefile │ ├── _cython_interface.c │ ├── _cython_interface.h │ ├── _cython_interface.pyx │ ├── advance_one_step.c │ ├── advance_one_step_global_k_clean │ │ ├── Makefile │ │ ├── _cython_interface.pyx │ │ ├── advance_one_step.c │ │ ├── dendritic_mesh_serialized.mat │ │ ├── dolfin_mesh_utils.py │ │ ├── generate_diffusion_paths.py │ │ ├── particle_diffusion_on_mesh.py │ │ ├── particle_diffusion_plot_utils.py │ │ └── test_mex.m │ ├── advance_one_step_particle_k_clean │ │ ├── Makefile │ │ ├── _cython_interface.pyx │ │ ├── advance_one_step.c │ │ ├── dendritic_mesh_serialized.mat │ │ ├── dolfin_mesh_utils.py │ │ ├── particle_diffusion_on_mesh.py │ │ ├── particle_diffusion_plot_utils.py │ │ └── test_mex.m │ ├── dendritic_mesh_serialized.mat │ ├── dolfin_mesh_utils.py │ ├── libadvanceonestep.so │ ├── particle_diffusion_on_mesh.py │ ├── particle_diffusion_plot_utils.py │ ├── run_core.m │ └── test_mex.m └── build_mesh │ ├── data │ ├── data_archive │ │ ├── exterior_faces_res_96_full.npz │ │ ├── faces_top_indices_res_96_full.npz │ │ ├── faces_top_res_96_full.npz │ │ ├── mesh_res_96_boundary.xml │ │ ├── mesh_res_96_full.xml │ │ ├── serialized_mesh_res_34.mat │ │ ├── serialized_mesh_res_96.mat │ │ └── serialized_mesh_res_96.npz │ ├── dendritic_mesh.xml │ ├── dendritic_mesh_serialized.mat │ ├── dendritic_mesh_serialized.npz │ └── vcell.mat │ ├── dendrite_components │ ├── dendritic_shaft_mesh.py │ ├── face_neighbors_and_top_components.py │ ├── find_near_top_faces.py │ ├── find_synapse_top_and_exterior_faces.py │ ├── full_dendrite_mesh.py │ ├── full_dendrite_mesh_redux.py │ ├── generate_2D_diffusion.py │ ├── plot_trisurf_mesh.py │ ├── refine_boundary_mesh.py │ ├── sample_code.py │ └── surfmesh.py │ ├── generate_mesh.py │ └── serialize_mesh.py └── README.md /.gitignore: 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