#################################################################################################### # Vesicle cycle model STEPS script # # # # Gallimore, A. R., Hepburn, I., Georgiev, S. V., Rizzoli, S. O., & De Schutter, E. (2025) # # Dynamic Regulation of Vesicle Pools in a Detailed Spatial Model of the Complete Synaptic Vesicle # # Cycle. Science Advances # # # # Script versions: # # Original author: Andrew Gallimore # # Conversion to new STEPS API: Jules Lallouette # #################################################################################################### import steps.interface from steps.model import * from steps.geom import * from steps.rng import * from steps.sim import * from steps.saving import * import argparse import collections import copy import math import numpy as np import os import pickle import random import sys import time ############################################################################################################ # Example of command line arguments: # python3 {script.py} . ./meshes/pyr_axon_2021 ./logs ./data SimName 1234 1 1 5 10 # With Blender data being recorded: # python3 {script.py} . ./meshes/pyr_axon_2021 ./logs ./data SimName 1234 1 1 5 10 true MODEL_PATH = sys.argv[1] # Path to the folder containing model files (like actin_tets_215nm.txt) MESH_PATH = sys.argv[2] # Path to the xml mesh file that should be used for the simulation LOG_PATH = sys.argv[3] # Path to the folder to which logs should be written DATA_PATH = sys.argv[4] # Path to the folder to which data should be written DATA_ID = sys.argv[5] # Identifier for the simulation group JOB_ID = int(sys.argv[6]) # ID of the SLURM job JOB_INDEX = int(sys.argv[7]) # Index of the SLURM job (start numbering at 1) kcat_can_tomo = float(sys.argv[8]) RATE = float(sys.argv[9]) # Rate of stimulation in Hz INT = float(sys.argv[10]) # The simulation endtime (s) save_blender_data = sys.argv[11].lower() == 'true' if len(sys.argv) > 11 else False checkpoint_mode = sys.argv[12].lower() if len(sys.argv) > 12 else None # 'checkpoint' to checkpoint, 'restore' to restore, 'both' to do both... checkpoint_path = sys.argv[13] if len(sys.argv) > 13 else None # Path to the checkpoint file if checkpoint_mode == 'both': checkpoint_path_2 = sys.argv[14] if len(sys.argv) > 14 else None # Path to the second checkpoint file rng_seed = JOB_ID * JOB_INDEX print('JOB_ID:', JOB_ID) print('seed:', rng_seed) random.seed(1) exportParam = False # Only output on rank 0 if MPI.rank == 0: if LOG_PATH.lower() != 'none': os.makedirs(LOG_PATH, exist_ok=True) LOG_FILE = open(os.path.join(LOG_PATH, f'{DATA_ID}_{JOB_INDEX}_{INT}_{rng_seed}_{JOB_ID}_stdout.txt'), 'w') sys.stdout = LOG_FILE else: LOG_FILE = None else: LOG_FILE = None sys.stdout = None print('FINAL VESICLE MODEL VERSION OCT 28 2021, API_2 version NOV 2023') #Boolean for either static or mobile Ca channels cachan_static = True print('CDK5 kcat = 5') if cachan_static: print('CA CHANNELS ARE STATIC') else: print('CA CHANNELS ARE MOBILE') print('TETHERS ARE ACTIVE') print('TESTING DOCK SITES 3') #number of Ca channels cachan_n = 15 #Choose dock triangle set dock_tris = [42155, 76431, 84872, 61803, 21332, 71084, 79446, 89381] #vesicle membrane protein binding ves_protein_bind_on = True tomo_init = 1500 can_init = 1500 print('TOTAL CALCINEURIN: ', can_init) print('kcat_can_tomo: ', kcat_can_tomo) kcat_can_init = 0.5 print('kcat_can:', kcat_can_init) #################################### CONSTANTS #################################### # Number of iterations NITER = 1 # The data collection time increment (s) DT = 0.001 # The EField dt EF_DT = 1.0e-3 ########## Ca concentrations (M) ######### Ca_oconc = 2e-3 ########## CaP channels density & permiability per channel ########## # CaP_P is permeability per channel (m3/s) # CaP_ro is channel/surface area (/m2) # P in Ca Dynamics model is 0.95e-4 cm/s --> 0.95e-6 m/s CaP_P = 2.5e-20 print('Ca Chan Perm:', CaP_P) CaP_ro = 3.8e13 #membrane SNARE proteins diffusiion scaling factor #######SCALE SNARE MEM DIFF CONSTANTS####### snare_diff_scale = 1 #Boolean for either presence or absence of Calmodulin cam_present = True ########## Initial Membrane Potential ######### init_pot = -60e-3 ########## BULK RESISTIVITY ########## Ra = 235.7*1.0e-2 ########## MEMBRANE CAPACITANCE ########## memb_capac = 1.5e-2 ##########CaP channel parameters #################### def minf_cap(mV): vhalfm = -29.458 cvm = 8.429 return 1 / (1 + math.exp(-(mV - vhalfm) / cvm)) def tau_cap(mV): if mV >= -40: return 0.2702 + 1.1622 * math.exp(-(mV + 26.798) ** 2 / 164.19) else: return 0.6923 * math.exp(mV / 1089.372) alpha_cap = VDepRate.Create( lambda V: (minf_cap(V * 1e3) / tau_cap(V * 1e3)) * 1e3 ) beta_cap = VDepRate.Create( lambda V: (1 - minf_cap(V * 1e3)) / tau_cap(V * 1e3) * 1e3 ) # Initial conditions CaP_pinit = [0.92402, 0.073988, 0.0019748, 1.7569e-05] ###Model Definition### syt_model = Model() r = ReactionManager() with syt_model: vsys, syn_sys, cytERsys = VolumeSystem.Create() memsys, ERsys = SurfaceSystem.Create() #General cytosolic DCST DCST_CYT = 2.0e-12 DCST_CYT_low = 0.028e-12 # Diffusion constant of Calcium DCST_CA = 0.223e-9*1 #CHANGED #General membrane DCST DCST_MEM = 0.25e-12 #0.05 um^2/s DCST_RAFT = 0#0.1e-12#0.01e-12 #0.05 um^2/s DCST_MEM_2 = 0.05e-12 #0.05 um^2/s DCST_MEM_VES = 0.05e-12 #0.05 um^2/s #Ca model k1_pmca = 1.5e8 k2_pmca = 15 k3_pmca = 12 kl_pmca = 4.3 kon_serca_ca = 17147e6 koff_serca_ca = 8426.3 kflux_serca = 250 kleak = 1.8e-06 kon_pv_ca = 107e06 koff_pv_ca = 0.95 kon_pv_mg = 472e06 koff_pv_mg = 25.0 kon_cbs_ca = 5.5e06 koff_cbs_ca = 2.6 kon_cbf_ca = 43.5e06 koff_cbf_ca = 35.8 kinflux = 0.0 ##### Species ##### Ca = Species.Create(valence=2) PMCA_P0, PMCA_P1, SERCA, CaSERCA, Ca2SERCA, PV, PV_Ca, PV_2Ca, MgPV, Mg2PV, Mg, CBs, CaCBs, Ca2CBs, CBf, CaCBf, Ca2CBf = Species.Create() # CALBINDIN 1 (D-28K) (we consider the 2 (hi-aff) : 2 (lo-aff) scenario) # Binding Kinetics of Calbindin-D28k Determined by Flash Photolysis of Caged Ca2 (Nagerl 2000) CBhi, CBhi_Ca, CBhi_2Ca, CBlo, CBlo_Ca, CBlo_2Ca = Species.Create() CRTT, CRTR_Ca, CRRR_2Ca, CRind, CRind_Ca = Species.Create() syt, glu, SNARE_syt, SNARE_syt_CXN, SNARE_syt_CXN_Ca, SNARE_syt_CXN_Ca2, SNARE_syt_CXN_Ca3 = Species.Create() SNARE_syt_CXN_bCa, SNARE_syt_CXN_bCa2, SNARE_syt_CXN_Ca_bCa, SNARE_syt_CXN_Ca_bCa2, SNARE_syt_CXN_Ca2_bCa = Species.Create() SNARE_syt_CXN_Ca2_bCa2, SNARE_syt_CXN_Ca3_bCa, SNARE_syt_CXN_Ca3_bCa2 = Species.Create() # Vesicle docking RIM, M13, RIM_M13, Rab3, RIM_M13_Rab3, SYX, M18, SYX_M18, RIM_M13_Rab3_SYX_M18, RIM_M13_Rab3_SYX_M18_SNP25, SNP25, SYB, SNARE, CXN = Species.Create() aSNAP, SNARE_aSNAP, NSF, cisSNARE, SNARE_aSNAP_NSF, SNARE_aSNAP_NSF_1, SNARE_aSNAP_NSF_2, SNARE_aSNAP_NSF_3, SNARE_aSNAP_NSF_4 = Species.Create() SNARE_aSNAP_NSF_5, SNARE_aSNAP_NSF_6, SNARE_aSNAP_NSF_7, SNARE_aSNAP_NSF_8, SNARE_aSNAP_NSF_9, SNARE_DISS = Species.Create() N0, N1, N2, C0, C1, C2 = SubUnitState.Create() CaM_N_SU = SubUnit.Create([N0, N1, N2]) CaM_C_SU = SubUnit.Create([C0, C1, C2]) CaM = Complex.Create([CaM_N_SU, CaM_C_SU], statesAsSpecies=True) CaN, CaN_CaM, DYNpp, DYNp, DYN, CaN_DYNpp, CaN_DYNp = Species.Create() SYN1, DYN_SYN1, CDK5, DYN_CDK5, DYNp_CDK5, DYN_SYN1_CDK5, AP180, AP2, RabAd, DYN_AD, AC18, AC18_CaM, cAMP, PKA = Species.Create() R2C2, R2C2_cAMP, R2C2_2cAMPbb, R2C2_2cAMPab, R2C2_3cAMP, R2C2_4cAMP, R2C_2cAMPab, R2C_3cAMP, R2C_4cAMP, R2_4cAMP = Species.Create() synapsin, synapsin_p, PKA_synapsin, PP2A, PP2A_synapsin_p, actin, synapsin_actin, synapsin_actin_p, Rab3_TOMO_synapsin_actin = Species.Create() Rab3_TOMO_p_synapsin_actin, Rab3_TOMO_synapsin_actin_p, Rab3_TOMO_p_synapsin_actin_p, ves_syn1_site, Rab3_TOMO_synapsin = Species.Create() Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p, TOMO_p, Rab3_TOMO_p, TOMO, Rab3_TOMO, TOMO_CDK5, Rab3_TOMO_CDK5 = Species.Create() TOMO_p_CaN_CaM, Rab3_TOMO_p_CaN_CaM, Rab3_TOMO_synapsin_PKA, Rab3_TOMO_p_synapsin_PKA, Rab3_TOMO_p_synapsin_p_PP2A, Rab3_TOMO_synapsin_p_PP2A = Species.Create() Rab3_TOMO_synapsin_CDK5, Rab3_TOMO_synapsin_p_CDK5, Rab3_TOMO_p_synapsin_CaN_CaM, Rab3_TOMO_p_synapsin_p_CaN_CaM = Species.Create() RIM_M13_Rab3_SYX_M18_SNP25_TOMO, RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p, RIM_M13_Rab3_SYX_M18_SNP25_TOMOx, RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p = Species.Create() RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P, RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P, RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P, RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P = Species.Create() RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA, RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA, RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P_PP2A, RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P_PP2A = Species.Create() ves_CXN_site, ves_rab3_site, ves_m13_site, ves_m18_site, ves_syndap_site, ves_asnap_site, ves_nsf_site, REL_IND = Species.Create() #Basic states of dimerised synapsins (each "half" of the link between vesicles) #None of the dimers need explicitly defining. synapsin_dimer = LinkSpecies.Create(1e-13) synapsin_dimer_p = LinkSpecies.Create(1e-13) Rab3_TOMO_synapsin_dimer = LinkSpecies.Create(1e-13) #(2 formation routes) Rab3_TOMO_synapsin_dimer_p = LinkSpecies.Create(1e-13) #(2 formation routes) Rab3_TOMO_p_synapsin_dimer = LinkSpecies.Create(1e-13) #(2 formation routes) Rab3_TOMO_p_synapsin_dimer_p = LinkSpecies.Create(1e-13) #(2 formation routes) #Enzyme-complex states of ves-bound dimerised synapsins (assume the complexed enzyme blocks the dimerisation/unbinding reaction) PKA_synapsin_dimer = LinkSpecies.Create(1e-13) Rab3_TOMO_synapsin_dimer_PKA = LinkSpecies.Create(1e-13) Rab3_TOMO_p_synapsin_dimer_PKA = LinkSpecies.Create(1e-13) #PP2A dephos. PP2A_synapsin_dimer_p = LinkSpecies.Create(1e-13) Rab3_TOMO_synapsin_dimer_p_PP2A = LinkSpecies.Create(1e-13) Rab3_TOMO_p_synapsin_dimer_p_PP2A = LinkSpecies.Create(1e-13) #CDK5 phos. Rab3_TOMO_synapsin_dimer_CDK5 = LinkSpecies.Create(1e-13) Rab3_TOMO_synapsin_dimer_p_CDK5 = LinkSpecies.Create(1e-13) #CaN dephos. Rab3_TOMO_p_synapsin_dimer_CaN_CaM = LinkSpecies.Create(1e-13) Rab3_TOMO_p_synapsin_dimer_p_CaN_CaM = LinkSpecies.Create(1e-13) # Channels CaPc, CaPo = SubUnitState.Create() CaP_SU = SubUnit.Create([CaPc, CaPo]) CaPchan = Channel.Create([CaP_SU, CaP_SU, CaP_SU], statesAsSpecies=True) #######VESICLES######### ves_diameter = 40e-9 ves_radius = ves_diameter/2 ves_diff_k = 0.11e-12 #Gaffield 2006 Neuron ves_diff_k_slow = 0.0011e-12 #Rizzoli ves_ssys = VesicleSurfaceSystem.Create() #free vesicles ves = Vesicle.Create(ves_diameter, ves_diff_k, ves_ssys)#0.003e-12 raft_sys = RaftSurfaceSystem.Create() raft = Raft.Create(3e-08, DCST_RAFT, raft_sys) kon_dyn_syn = 1000e06 koff_dyn_syn = 1 kon_cdk_dyn = 3e06 koff_cdk_dyn = 10 kcat_cdk = 0.5 kon_syb_ap180 = 2000e06 kon_syt_ap2 = 2000e06 kon_rab3_rabad = 2000e06 kon_dyn_raft = 2000e06 koff_dyn_raft = 0 #Parameters kon_ac_cam = 500e06 koff_ac_cam = 0.1 kcat_ac18 = 18 kdeg_camp = 1 #Parameters kon_r2c2_camp1 = 2e06 koff_r2c2_camp1 = 0.75 kon_r2c2_camp2bb = 1e06 koff_r2c2_camp2bb = 1.5 kon_r2c2_camp2ab = 10e06 koff_r2c2_camp2ab = 7.5 kon_r2c2_camp3bb = 20e06 koff_r2c2_camp3bb = 7.5 kon_r2c2_camp3ab = 1e06 koff_r2c2_camp3ab = 0.75 kon_r2c2_camp4 = 10e06 koff_r2c2_camp4 = 15 kact_pka_23 = 0.005 kdeact_pka_23 = 5e06 kact_pka_4 = 6 kdeact_pka_4 = 5e06 kon_r2c_camp3 = 1e06 koff_r2c_camp3 = 0.75 kon_r2c_camp4 = 10e06 koff_r2c_camp4 = 7.5 kact_pka_r2c = 3 kdeact_pka_r2c = 10e06 kon_PKA_syn = 10e06 koff_PKA_syn = 1 kcat_PKA_syn = 10 kon_pp2a_synapsin = 3e06 #Gallimore, Cell Reports, 2018 (from PP2A CaMKII dephos parameters) koff_pp2a_synapsin = 10 kcat_pp2a_syn = 0.5 #synapsin bound to vesicle binds to actin kon_synapsin_actin = 1000e06 koff_synapsin_actin = 1 koff_synapsin_actin_p = 1000 kon_cdk_tomo = 3e06 koff_cdk_tomo = 10 kcat_cdk_tomo = 0.5 kon_can_tomo = 1e06 koff_can_tomo = 10 #TOMOSYN binds Rab3 kon_rab3_TOMO_p = 1e06 koff_rab3_TOMO_p = 10 #Rab3-TOMO binds synapsin (non-dimerised) kon_TOMO_p_synapsin = 100e06 koff_TOMO_p_synapsin = 1 kon_TOMO_synapsin = 100e06 koff_TOMO_synapsin = 100 #increase 100x with TOMO_p dephosphorylation kon_synapsin_dimer = 10e06 koff_synapsin_dimer = 10 koff_synapsin_dimer_p = 10000 # #2. Inhibition of vesicle priming (competition with SYB, same rate) kon_tomo_syx = 2.35e06 koff_tomo_syx = 0.0047 kdisp_tomo_syx = 10e06 kflip_tomo_f = 0.01 kflip_tomo_P_f = 10 kflip_tomo_r = 1 kon_tomo_pka = 10e06 koff_tomo_pka = 1 kcat_pka_tomo = 50 kon_tomo_PP2A = 2e06 #Gallimore, Cell Reports, 2018 (from PP2A CaMKII dephos parameters) koff_tomo_PP2A = 8 kcat_PP2A_tomo = 2 if ves_protein_bind_on: kon_cxn_ves = 1.2e06 else: kon_cxn_ves = 0 koff_cxn_ves = 1000 if ves_protein_bind_on: kon_rab3_ves = 10e06 else: kon_rab3_ves = 0 koff_rab3_ves = 1 if ves_protein_bind_on: kon_m13_ves = 1.6e06 else: kon_m13_ves = 0 koff_m13_ves = 1000 if ves_protein_bind_on: kon_m18_ves = 1.6e06 else: kon_m18_ves = 0 koff_m18_ves = 1000 if ves_protein_bind_on: kon_syn1_ves = 2.8e06 else: kon_syn1_ves = 0 koff_syn1_ves = 1000 if ves_protein_bind_on: kon_asnap_ves = 2.8e06 else: kon_asnap_ves = 0 koff_asnap_ves = 1000 if ves_protein_bind_on: kon_nsf_ves = 0.9e06 else: kon_nsf_ves = 0 koff_nsf_ves = 1000 with vsys: #Diffusion rules diff_Ca = Diffusion.Create(Ca, DCST_CA) for spec in [PV, PV_Ca, PV_2Ca, MgPV, Mg2PV, Mg, CBs, CaCBs, Ca2CBs, CBf, CaCBf, Ca2CBf]: Diffusion(spec, DCST_CYT) #Reactions #Ca uncage None >r['Ca_uncage']> Ca r['Ca_uncage'].K = 0.0 (Ca + PV PV_Ca) + Ca PV_2Ca r[1].K = 107000000.0, 0.95 r[2].K = 107000000.0, 0.95 (CBhi + Ca CBhi_Ca) + Ca CBhi_2Ca r[1].K = 11000000.0, 2.607 r[2].K = 11000000.0, 2.607 (CBlo + Ca CBlo_Ca) + Ca CBlo_2Ca r[1].K = 87000000.0, 35.76 r[2].K = 87000000.0, 35.76 kon_T = 1.8e6 koff_T = 53 kon_R = 3.1e8 koff_R = 20 kon_ind = 7.3e6 koff_ind = 252 # pair 1 (you MUST multiply its concentration by 2) because WE'VE GOT TWO PAIRS OF COOPERATIVE CA2+ BINDING SITES (CRTT + Ca CRTR_Ca) + Ca CRRR_2Ca r[1].K = 2*kon_T, koff_T r[2].K = kon_T, 2*koff_R # independent Ca2+ binding site: CRind + Ca CRind_Ca r[1].K = kon_ind, koff_ind diff_M13 = Diffusion.Create(M13, 2.2796e-12) diff_Rab3 = Diffusion.Create(Rab3, 1.7793e-12) diff_M18 = Diffusion.Create(M18, 2.2357e-12) diff_CXN = Diffusion.Create(CXN, 1.7793e-12) diff_aSNAP = Diffusion.Create(aSNAP, 2.1959e-12) diff_NSF = Diffusion.Create(NSF, 2.2788e-12) kon_cam_NT = 7.7e08 kon_cam_NR = 3.2e10 kon_cam_CT = 8.4e07 kon_cam_CR = 2.5e07 koff_cam_NT = 1.6e05 koff_cam_CT = 2.2e04 koff_cam_NR = 2.6e03 koff_cam_CR = 6.5 Diffusion(CaM[...], 1.6496e-12) with CaM[...]: N0 + Ca N1 N1 + Ca N2 r[1].K = 2 * kon_cam_NT, koff_cam_NT r[2].K = kon_cam_NR, 2 * koff_cam_NR C0 + Ca C1 C1 + Ca C2 r[3].K = 2 * kon_cam_CT, koff_cam_CT r[4].K = kon_cam_CR, 2 * koff_cam_CR # NOTE: The following two reactions are added to be identical to the original API_1 script, but they might not be required Ca + CaM[N1, C1] >r[1]> CaM[N2, C1] # Already declared earlier r[1].K = kon_cam_NR Ca + CaM[N1, C1] >r[1]> CaM[N1, C2] # Already declared earlier r[1].K = kon_cam_CR diff_CaN = Diffusion.Create(CaN, DCST_CYT) diff_CaN_CaM = Diffusion.Create(CaN_CaM, DCST_CYT) kon_can_cam = 46e06 koff_can_cam = 1.2 kon_can_dyn = 10e06 koff_can_dyn = 1 kcat_can = 0.5 #Calcineurin binding to CaM CaM[N2, C2] + CaN CaN_CaM r[1].K = kon_can_cam, koff_can_cam diff_DYNpp = Diffusion.Create(DYNpp, 3.2464e-12) diff_DYNp = Diffusion.Create(DYNp, 3.2464e-12) diff_DYN = Diffusion.Create(DYN, 3.2464e-12) #cytosolic dephosphorylation CaN_CaM + DYNpp CaN_DYNpp r[1].K = kon_can_dyn, koff_can_dyn CaN_DYNpp >r[1]> CaN_CaM + DYNp r[1].K = kcat_can CaN_CaM + DYNp CaN_DYNp r[1].K = kon_can_dyn, koff_can_dyn CaN_DYNp >r[1]> CaN_CaM + DYN r[1].K = kcat_can diff_SYN1 = Diffusion.Create(SYN1, 2.1959e-12) diff_DYN_SYN1 = Diffusion.Create(DYN_SYN1, 3.2464e-12) DYN + SYN1 DYN_SYN1 r[1].K = kon_dyn_syn, koff_dyn_syn diff_CDK5 = Diffusion.Create(CDK5, DCST_CYT) diff_DYN_CDK5 = Diffusion.Create(DYN_CDK5, DCST_CYT) diff_DYNp_CDK5 = Diffusion.Create(DYNp_CDK5, DCST_CYT) diff_DYN_SYN1_CDK5 = Diffusion.Create(DYN_SYN1_CDK5, DCST_CYT) #phosphorylation of dynamin in the cytosol CDK5 + DYN DYN_CDK5 r[1].K = kon_cdk_dyn, koff_cdk_dyn DYN_CDK5 >r[1]> CDK5 + DYNp r[1].K = kcat_cdk CDK5 + DYN_SYN1 DYN_SYN1_CDK5 r[1].K = kon_cdk_dyn, koff_cdk_dyn DYN_SYN1_CDK5 >r[1]> CDK5 + DYNp + SYN1 r[1].K = kcat_cdk diff_AC18 = Diffusion.Create(AC18, DCST_CYT) diff_AC18_CaM = Diffusion.Create(AC18_CaM, DCST_CYT) diff_cAMP = Diffusion.Create(cAMP, DCST_CYT) AC18 + CaM[N2, C2] AC18_CaM r[1].K = kon_ac_cam, koff_ac_cam AC18_CaM >r[1]> AC18_CaM + cAMP r[1].K = kcat_ac18 cAMP >r[1]> None r[1].K = kdeg_camp diff_PKA = Diffusion.Create(PKA, DCST_CYT) diff_R2C2 = Diffusion.Create(R2C2, DCST_CYT) diff_R2C2_cAMP = Diffusion.Create(R2C2_cAMP, DCST_CYT) diff_R2C2_2cAMPbb = Diffusion.Create(R2C2_2cAMPbb, DCST_CYT) diff_R2C2_2cAMPab = Diffusion.Create(R2C2_2cAMPab, DCST_CYT) diff_R2C2_3cAMP = Diffusion.Create(R2C2_3cAMP, DCST_CYT) diff_R2C2_4cAMP = Diffusion.Create(R2C2_4cAMP, DCST_CYT) diff_R2C_2cAMPab = Diffusion.Create(R2C_2cAMPab, DCST_CYT) diff_R2C_3cAMP = Diffusion.Create(R2C_3cAMP, DCST_CYT) diff_R2C_4cAMP = Diffusion.Create(R2C_4cAMP, DCST_CYT) diff_R2_4cAMP = Diffusion.Create(R2_4cAMP, DCST_CYT) #Reactions R2C2 + cAMP R2C2_cAMP r[1].K = kon_r2c2_camp1, koff_r2c2_camp1 R2C2_cAMP + cAMP R2C2_2cAMPbb r[1].K = kon_r2c2_camp2bb, koff_r2c2_camp2bb R2C2_cAMP + cAMP R2C2_2cAMPab r[1].K = kon_r2c2_camp2ab, koff_r2c2_camp2ab R2C2_2cAMPbb + cAMP R2C2_3cAMP r[1].K = kon_r2c2_camp3bb, koff_r2c2_camp3bb R2C2_2cAMPab + cAMP >r[1]> R2C2_3cAMP r[1].K = kon_r2c2_camp3ab R2C2_3cAMP >r[1]> R2C2_2cAMPab r[1].K = koff_r2c2_camp3ab R2C2_3cAMP + cAMP R2C2_4cAMP r[1].K = kon_r2c2_camp4, koff_r2c2_camp4 R2C2_2cAMPab PKA + R2C_2cAMPab r[1].K = kact_pka_23, kdeact_pka_23 R2C2_3cAMP PKA + R2C_3cAMP r[1].K = kact_pka_23, kdeact_pka_23 R2C2_4cAMP PKA + R2C_4cAMP r[1].K = kact_pka_4, kdeact_pka_4 R2C_2cAMPab + cAMP R2C_3cAMP r[1].K = kon_r2c_camp3, koff_r2c_camp3 R2C_3cAMP + cAMP R2C_4cAMP r[1].K = kon_r2c_camp4, koff_r2c_camp4 R2C_4cAMP PKA + R2_4cAMP r[1].K = kact_pka_r2c, kdeact_pka_r2c diff_synapsin = Diffusion.Create(synapsin, 2.65e-12) diff_synapsin_p = Diffusion.Create(synapsin_p, 2.65e-12) diff_synapsin_pka = Diffusion.Create(PKA_synapsin, 2.65e-12) diff_synapsin_pp2a = Diffusion.Create(PP2A_synapsin_p, 2.65e-12) #dephos of cytosolic synapsin_p PP2A + synapsin_p PP2A_synapsin_p r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin PP2A_synapsin_p >r[1]> PP2A + synapsin r[1].K = kcat_pp2a_syn diff_actin = Diffusion.Create(actin, 0.0) diff_synapsin_actin = Diffusion.Create(synapsin_actin, 0.0) diff_synapsin_p_actin = Diffusion.Create(synapsin_actin_p, 0.0) diff_Rab3_TOMO_synapsin_actin = Diffusion.Create(Rab3_TOMO_synapsin_actin, 0.0) diff_Rab3_TOMO_p_synapsin_actin = Diffusion.Create(Rab3_TOMO_p_synapsin_actin, 0.0) diff_TOMO_p = Diffusion.Create(TOMO_p, 1.7793e-12) diff_TOMO = Diffusion.Create(TOMO, 1.7793e-12) diff_TOMO_CDK5 = Diffusion.Create(TOMO_CDK5, 1.7793e-12) CDK5 + TOMO TOMO_CDK5 r[1].K = kon_cdk_tomo, koff_cdk_tomo TOMO_CDK5 >r[1]> CDK5 + TOMO_p r[1].K = kcat_cdk_tomo diff_TOMO_p_CaN = Diffusion.Create(TOMO_p_CaN_CaM, 1.7793e-12) CaN_CaM + TOMO_p TOMO_p_CaN_CaM r[1].K = kon_can_tomo, koff_can_tomo TOMO_p_CaN_CaM >r[1]> CaN_CaM + TOMO r[1].K = kcat_can_tomo #initial dimerisation depends on synapsin_actin dimer [5 different forms] (ensures actin is the focus of the clustering) synapsin_dimerise_1a = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_actin.v, None)) synapsin_dimerise_1b = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_actin.v, None)) synapsin_dimerise_1c = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_actin.v, None)) synapsin_dimerise_1d = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_actin_p.v, None)) synapsin_dimerise_1e = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_actin_p.v, None)) #Dimer states (need both VesBind and VesUnbind reactions for each, and ldeps for VesBinds -- 6, one for each state) #synapsin - synapsin -> synapsin_dimer - synapsin_dimer synapsin_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (synapsin, synapsin), (synapsin_dimer, synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_synapsin_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer, synapsin_dimer), (synapsin, synapsin), kcst=koff_synapsin_dimer, immobilization=NO_EFFECT) #synapsin - synapsin_p -> synapsin_dimer - synapsin_dimer_p synapsin_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (synapsin, synapsin_p), (synapsin_dimer, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (synapsin, synapsin_p), (synapsin_dimer, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (synapsin, synapsin_p), (synapsin_dimer, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (synapsin, synapsin_p), (synapsin_dimer, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (synapsin, synapsin_p), (synapsin_dimer, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (synapsin, synapsin_p), (synapsin_dimer, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer, synapsin_dimer_p), (synapsin, synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin - Rab3_TOMO_synapsin -> synapsin_dimer - Rab3_TOMO_synapsin_dimer synapsin_Rab3_TOMO_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_Rab3_TOMO_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_synapsin_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer, Rab3_TOMO_synapsin_dimer), (synapsin, Rab3_TOMO_synapsin), kcst=koff_synapsin_dimer, immobilization=NO_EFFECT) #synapsin - Rab3_TOMO_synapsin_p -> synapsin_dimer - Rab3_TOMO_synapsin_dimer_p synapsin_Rab3_TOMO_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin_p), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_Rab3_TOMO_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin_p), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin_p), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin_p), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin_p), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_synapsin_p), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), (synapsin, Rab3_TOMO_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin - Rab3_TOMO_p_synapsin -> synapsin_dimer - Rab3_TOMO_p_synapsin_dimer synapsin_Rab3_TOMO_p_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_Rab3_TOMO_p_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_p_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_p_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_p_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_p_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_p_synapsin_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), (synapsin, Rab3_TOMO_p_synapsin), kcst=koff_synapsin_dimer, immobilization=NO_EFFECT) #synapsin - Rab3_TOMO_p_synapsin_p -> synapsin_dimer - Rab3_TOMO_p_synapsin_dimer_p synapsin_Rab3_TOMO_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin_p), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_Rab3_TOMO_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin_p), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin_p), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin_p), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin_p), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_Rab3_TOMO_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (synapsin, Rab3_TOMO_p_synapsin_p), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_Rab3_TOMO_p_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), (synapsin, Rab3_TOMO_p_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin_p - synapsin_p -> synapsin_dimer_p - synapsin_dimer_p synapsin_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (synapsin_p, synapsin_p), (synapsin_dimer_p, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (synapsin_p, synapsin_p), (synapsin_dimer_p, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (synapsin_p, synapsin_p), (synapsin_dimer_p, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (synapsin_p, synapsin_p), (synapsin_dimer_p, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (synapsin_p, synapsin_p), (synapsin_dimer_p, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (synapsin_p, synapsin_p), (synapsin_dimer_p, synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_p_synapsin_p_dimerise_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer_p, synapsin_dimer_p), (synapsin_p, synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin_p - Rab3_TOMO_synapsin -> synapsin_dimer_p - Rab3_TOMO_synapsin_dimer synapsin_p_Rab3_TOMO_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_synapsin_dimerise_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer), (synapsin_p, Rab3_TOMO_synapsin), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin_p - Rab3_TOMO_synapsin_p -> synapsin_dimer_p - Rab3_TOMO_synapsin_dimer_p synapsin_p_Rab3_TOMO_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), (synapsin_p, Rab3_TOMO_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin_p - Rab3_TOMO_p_synapsin -> synapsin_dimer_p - Rab3_TOMO_p_synapsin_dimer synapsin_p_Rab3_TOMO_p_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), (synapsin_p, Rab3_TOMO_p_synapsin), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #synapsin_p - Rab3_TOMO_p_synapsin_p -> synapsin_dimer_p - Rab3_TOMO_p_synapsin_dimer_p synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (synapsin_p, Rab3_TOMO_p_synapsin_p), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) synapsin_p_Rab3_TOMO_p_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), (synapsin_p, Rab3_TOMO_p_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin - Rab3_TOMO_synapsin -> Rab3_TOMO_synapsin_dimer - Rab3_TOMO_synapsin_dimer Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin), kcst=koff_synapsin_dimer, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin - Rab3_TOMO_synapsin_p -> Rab3_TOMO_synapsin_dimer - Rab3_TOMO_synapsin_dimer_p Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_synapsin_dimer_p), (Rab3_TOMO_synapsin, Rab3_TOMO_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin - Rab3_TOMO_p_synapsin -> Rab3_TOMO_synapsin_dimer - Rab3_TOMO_p_synapsin_dimer Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin), kcst=koff_synapsin_dimer, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin - Rab3_TOMO_p_synapsin_p -> Rab3_TOMO_synapsin_dimer - Rab3_TOMO_p_synapsin_dimer_p Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_Rab3_TOMO_p_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), (Rab3_TOMO_synapsin, Rab3_TOMO_p_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin_p - Rab3_TOMO_synapsin_p -> Rab3_TOMO_synapsin_dimer_p - Rab3_TOMO_synapsin_dimer_p Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_synapsin_dimer_p), (Rab3_TOMO_synapsin_p, Rab3_TOMO_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin_p - Rab3_TOMO_p_synapsin -> Rab3_TOMO_synapsin_dimer_p - Rab3_TOMO_p_synapsin_dimer Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_synapsin_p - Rab3_TOMO_p_synapsin_p -> Rab3_TOMO_synapsin_dimer_p - Rab3_TOMO_p_synapsin_dimer_p Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_synapsin_p_Rab3_TOMO_p_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), (Rab3_TOMO_synapsin_p, Rab3_TOMO_p_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_p_synapsin - Rab3_TOMO_p_synapsin -> Rab3_TOMO_p_synapsin_dimer - Rab3_TOMO_p_synapsin_dimer Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin), kcst=koff_synapsin_dimer, immobilization=NO_EFFECT) #Rab3_TOMO_p_synapsin - Rab3_TOMO_p_synapsin_p -> Rab3_TOMO_p_synapsin_dimer - Rab3_TOMO_p_synapsin_dimer_p Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_Rab3_TOMO_p_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_p_synapsin_dimer, Rab3_TOMO_p_synapsin_dimer_p), (Rab3_TOMO_p_synapsin, Rab3_TOMO_p_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) #Rab3_TOMO_p_synapsin_p - Rab3_TOMO_p_synapsin_p -> Rab3_TOMO_p_synapsin_dimer_p - Rab3_TOMO_p_synapsin_dimer_p Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_a = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_b = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_c = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_d = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_e = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer.v, None)) Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_dimerise_f = VesicleBind.Create((ves, ves), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), 0, 1e-07, kcst=kon_synapsin_dimer, immobilization=NO_EFFECT, deps=(Rab3_TOMO_p_synapsin_dimer_p.v, None)) Rab3_TOMO_p_synapsin_p_Rab3_TOMO_p_synapsin_p_unbind = VesicleUnbind.Create((ves, ves), (Rab3_TOMO_p_synapsin_dimer_p, Rab3_TOMO_p_synapsin_dimer_p), (Rab3_TOMO_p_synapsin_p, Rab3_TOMO_p_synapsin_p), kcst=koff_synapsin_dimer_p, immobilization=NO_EFFECT) with memsys: diff_PMCA_P0 = Diffusion.Create(PMCA_P0, DCST_MEM) diff_PMCA_P1 = Diffusion.Create(PMCA_P1, DCST_MEM) # Ca + PMCA <-> CaPMCA -> PMCA Ca.i + PMCA_P0.s PMCA_P1.s >r[2]> PMCA_P0.s r[1].K = k1_pmca, k2_pmca r[2].K = k3_pmca # PMCA leak PMCA_P0.s >r[1]> Ca.i + PMCA_P0.s r[1].K = kl_pmca diff_syt = Diffusion.Create(syt, 2.5e-13) sdiff_glu = Diffusion.Create(glu, 0.0) # CaP channel if not cachan_static: Diffusion(CaPchan[...], 0.01e-12) with CaPchan[...]: CaPc.s CaPo.s r[1].K = alpha_cap, beta_cap OC_CaP = GHKCurr.Create( CaPchan[CaPo, CaPo, CaPo], Ca, CaP_P, computeflux=True, virtual_oconc=Ca_oconc, ) # Things will get transported by endocytosis- so even though they will be clamped to 0 in some places need to define them in patches diff_RIM = Diffusion.Create(RIM, 0.0) sdiff_M13 = Diffusion.Create(M13, 0.0) diff_RIM_M13 = Diffusion.Create(RIM_M13, 0.0) sdiff_Rab3 = Diffusion.Create(Rab3, 2.5e-13) diff_RIM_M13_Rab3 = Diffusion.Create(RIM_M13_Rab3, 0.0) diff_SYX = Diffusion.Create(SYX, 2.429e-13) diff_SYX_M18 = Diffusion.Create(SYX_M18, 2.429e-13) sdiff_M18 = Diffusion.Create(M18, 0.0) diff_RIM_M13_Rab3_SYX_M18 = Diffusion.Create(RIM_M13_Rab3_SYX_M18, 0.0) diff_RIM_M13_Rab3_SYX_M18_SNP25 = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25, 0.0) diff_SNP25 = Diffusion.Create(SNP25, 6.51e-13) diff_SYB = Diffusion.Create(SYB, 2.5e-13) diff_SNARE = Diffusion.Create(SNARE, 0.0) sdiff_CXN = Diffusion.Create(CXN, 0.0) #######RIM binds and activates Munc13 homodimer kon_rim_m13 = 10e06 koff_rim_m13 = 0 kon_syx_m18 = 5e06 #Burkhardt 2008 koff_syx_m18 = 0.0011 #Burkhardt 2008 #reactions M13.i + RIM.s RIM_M13.s r[1].K = kon_rim_m13, koff_rim_m13 ##Blocking of Syntaxin-1 by MUNC18a M18.i + SYX.s SYX_M18.s r[1].K = kon_syx_m18, koff_syx_m18 kon_snare_snap = 1.7e05 koff_snare_snap = 0.26 kon_nsf_snap = 20e06 kcat_nsf = 0.116 #Vivona 2013 # #initial loss of CXN, Ca, syt, etc from all SNARE variants k_rim_diss = 1000e12 SNARE.s >r[1]> Rab3.i + RIM_M13.s + cisSNARE.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca3_bCa2.s >r[1]> CXN.i + 5 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca3_bCa.s >r[1]> CXN.i + 4 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca2_bCa2.s >r[1]> CXN.i + 4 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca2_bCa.s >r[1]> CXN.i + 3 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca_bCa2.s >r[1]> CXN.i + 3 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca_bCa.s >r[1]> CXN.i + 2 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_bCa2.s >r[1]> CXN.i + 2 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_bCa.s >r[1]> CXN.i + Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca3.s >r[1]> CXN.i + 3 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca2.s >r[1]> CXN.i + 2 * Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN_Ca.s >r[1]> CXN.i + Ca.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt_CXN.s >r[1]> CXN.i + RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss SNARE_syt.s >r[1]> RIM_M13.s + Rab3.s + cisSNARE.s + syt.s r[1].K = k_rim_diss # # #disassembly of SNARE by NSF/aSNAP aSNAP.i + cisSNARE.s >r[1]> SNARE_aSNAP.s r[1].K = kon_snare_snap SNARE_aSNAP.s >r[1]> aSNAP.i + SNARE.s r[1].K = koff_snare_snap NSF.i + SNARE_aSNAP.s >r[1]> SNARE_aSNAP_NSF.s r[1].K = kon_nsf_snap SNARE_aSNAP_NSF.s >r[1]> M18.i + NSF.i + aSNAP.i + SNARE_DISS.s + SNP25.s + SYB.s + SYX.s r[1].K = kcat_nsf sdiff_DYNpp = Diffusion.Create(DYNpp, 3.2464e-12) sdiff_DYNp = Diffusion.Create(DYNp, 3.2464e-12) sdiff_DYN = Diffusion.Create(DYN, 3.2464e-12) sdiff_CaN_DYNpp = Diffusion.Create(CaN_DYNpp, 3.2464e-12) sdiff_CaN_DYNp = Diffusion.Create(CaN_DYNp, 3.2464e-12) sdiff_DYN_SYN1 = Diffusion.Create(DYN_SYN1, 3.2464e-12) kon_dyn_mem = 0 koff_dyn_mem = 0 DYN_SYN1.i DYN_SYN1.s r[1].K = kon_dyn_mem, koff_dyn_mem DYNp.i DYNp.s r[1].K = kon_dyn_mem, koff_dyn_mem DYN.i DYN.s r[1].K = kon_dyn_mem, koff_dyn_mem sdiff_DYN_SYN1_CDK5 = Diffusion.Create(DYN_SYN1_CDK5, DCST_MEM) #phosphorylation of dynamin in the membrane CDK5.i + DYN_SYN1.s DYN_SYN1_CDK5.s r[1].K = kon_cdk_dyn, koff_cdk_dyn DYN_SYN1_CDK5.s >r[1]> CDK5.i + DYNp.i + SYN1.i r[1].K = kcat_cdk CDK5.s + DYN.s DYN_CDK5.s r[1].K = kon_cdk_dyn, koff_cdk_dyn DYN_CDK5.s >r[1]> CDK5.s + DYNp.s r[1].K = kcat_cdk sdiff_AP2 = Diffusion.Create(AP2, 0.0) sdiff_RabAd = Diffusion.Create(RabAd, 0.0) sdiff_DYN_AD = Diffusion.Create(DYN_AD, 0.0) sdiff_AP180 = Diffusion.Create(AP180, 0.0) sdiff_synapsin = Diffusion.Create(synapsin, 0.0) sdiff_synapsin_p = Diffusion.Create(synapsin_p, 0.0) sdiff_synapsin_pka = Diffusion.Create(PKA_synapsin, 0.0) sdiff_synapsin_pp2a = Diffusion.Create(PP2A_synapsin_p, 0.0) sdiff_Rab3_TOMO_synapsin_actin = Diffusion.Create(Rab3_TOMO_synapsin_actin, 0.0) sdiff_Rab3_TOMO_p_synapsin_actin = Diffusion.Create(Rab3_TOMO_p_synapsin_actin, 0.0) sdiff_Rab3_TOMO_synapsin = Diffusion.Create(Rab3_TOMO_synapsin, 0.0) sdiff_Rab3_TOMO_synapsin_p_ves = Diffusion.Create(Rab3_TOMO_synapsin_p, 0.0) sdiff_Rab3_TOMO_p_synapsin = Diffusion.Create(Rab3_TOMO_p_synapsin, 0.0) sdiff_Rab3_TOMO_p_synapsin_p = Diffusion.Create(Rab3_TOMO_p_synapsin_p, 0.0) sdiff_Rab3_TOMO_p = Diffusion.Create(Rab3_TOMO_p, 0.0) sdiff_Rab3_TOMO = Diffusion.Create(Rab3_TOMO, 0.0) sdiff_Rab3_TOMO_CDK5 = Diffusion.Create(Rab3_TOMO_CDK5, 0.0) sdiff_Rab3_TOMO_p_CaN_CaM = Diffusion.Create(Rab3_TOMO_p_CaN_CaM, 0.0) sdiff_Rab3_TOMO_synapsin_PKA = Diffusion.Create(Rab3_TOMO_synapsin_PKA, 0.0) sdiff_Rab3_TOMO_p_synapsin_PKA = Diffusion.Create(Rab3_TOMO_p_synapsin_PKA, 0.0) sdiff_Rab3_TOMO_synapsin_CDK5 = Diffusion.Create(Rab3_TOMO_synapsin_CDK5, 0.0) sdiff_Rab3_TOMO_synapsin_p_CDK5 = Diffusion.Create(Rab3_TOMO_synapsin_p_CDK5, 0.0) sdiff_Rab3_TOMO_p_synapsin_CaN_CaM = Diffusion.Create(Rab3_TOMO_p_synapsin_CaN_CaM, 0.0) sdiff_Rab3_TOMO_p_synapsin_p_CaN_CaM = Diffusion.Create(Rab3_TOMO_p_synapsin_p_CaN_CaM, 0.0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMOx = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMOx, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P_PP2A = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P_PP2A, 0) sdiff_RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P_PP2A = Diffusion.Create(RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P_PP2A, 0) sdiff_CXN_site = Diffusion.Create(ves_CXN_site, 0) sdiff_rab3_site = Diffusion.Create(ves_rab3_site, 0) sdiff_M13_site = Diffusion.Create(ves_m13_site, 0) sdiff_M18_site = Diffusion.Create(ves_m18_site, 0) sdiff_syndap_site = Diffusion.Create(ves_syndap_site, 0) sdiff_SYN1 = Diffusion.Create(SYN1, 0) sdiff_asnap_site = Diffusion.Create(ves_asnap_site, 0) sdiff_asnap = Diffusion.Create(aSNAP, 0) sdiff_nsf_site = Diffusion.Create(ves_nsf_site, 0) sdiff_NSF = Diffusion.Create(NSF, 0) #####Remove vesicle-protein sites and other proteins from plasma membrane after vesicle fusion ves_syn1_site.s >r[1]> None r[1].K = 1000000.0 ves_CXN_site.s >r[1]> None r[1].K = 1000000.0 ves_m13_site.s >r[1]> None r[1].K = 1000000.0 ves_m18_site.s >r[1]> None r[1].K = 1000000.0 ves_syndap_site.s >r[1]> None r[1].K = 1000000.0 ves_asnap_site.s >r[1]> None r[1].K = 1000000.0 ves_nsf_site.s >r[1]> None r[1].K = 1000000.0 ves_rab3_site.s >r[1]> None r[1].K = 1000000.0 NSF.s >r[1]> NSF.i r[1].K = 1000000.0 synapsin.s >r[1]> synapsin.i r[1].K = 1000000.0 synapsin_p.s >r[1]> synapsin.i r[1].K = 1000000.0 PKA_synapsin.s >r[1]> PKA_synapsin.i r[1].K = 1000000.0 PP2A_synapsin_p.s >r[1]> PP2A_synapsin_p.i r[1].K = 1000000.0 TOMO_p.s >r[1]> TOMO_p.i r[1].K = 1000000.0 Rab3_TOMO_p.s >r[1]> Rab3.i + TOMO_p.i r[1].K = 1000000.0 Rab3_TOMO.s >r[1]> Rab3.i + TOMO.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin.s >r[1]> Rab3.i + TOMO_p.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_synapsin.s >r[1]> Rab3.i + TOMO.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin_p.s >r[1]> Rab3.i + TOMO_p.i + synapsin_p.i r[1].K = 1000000.0 Rab3_TOMO_synapsin_p.s >r[1]> Rab3.i + TOMO.i + synapsin_p.i r[1].K = 1000000.0 actin.s >r[1]> actin.i r[1].K = 1000000.0 synapsin_actin.s >r[1]> actin.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_synapsin_actin.s >r[1]> Rab3.i + TOMO.i + actin.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin_actin.s >r[1]> Rab3.i + TOMO_p.i + actin.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_synapsin_PKA.s >r[1]> PKA.i + Rab3.i + TOMO.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin_PKA.s >r[1]> PKA.i + Rab3.i + TOMO_p.i + synapsin.i r[1].K = 1000000.0 synapsin_actin_p.s >r[1]> actin.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_p_CaN_CaM.s >r[1]> CaN_CaM.i + Rab3.i + TOMO_p.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin_CaN_CaM.s >r[1]> CaN_CaM.i + Rab3.i + TOMO_p.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin_p_CaN_CaM.s >r[1]> CaN_CaM.i + Rab3.i + TOMO_p.i + synapsin_p.i r[1].K = 1000000.0 Rab3_TOMO_CDK5.s >r[1]> CDK5.i + Rab3.i + TOMO.i r[1].K = 1000000.0 Rab3_TOMO_synapsin_CDK5.s >r[1]> CDK5.i + Rab3.i + TOMO.i + synapsin.i r[1].K = 1000000.0 Rab3_TOMO_synapsin_p_CDK5.s >r[1]> CDK5.i + Rab3.i + TOMO.i + synapsin_p.i r[1].K = 1000000.0 Rab3_TOMO_p_synapsin_p_PP2A.s >r[1]> PP2A.i + Rab3.i + TOMO_p.i + synapsin_p.i r[1].K = 1000000.0 Rab3_TOMO_synapsin_p_PP2A.s >r[1]> PP2A.i + Rab3.i + TOMO.i + synapsin_p.i r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO.s >r[1]> M18.i + Rab3.i + TOMO.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p.s >r[1]> M18.i + Rab3.i + TOMO_p.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMOx.s >r[1]> M18.i + Rab3.i + TOMO.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p.s >r[1]> M18.i + Rab3.i + TOMO_p.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P.s >r[1]> M18.i + Rab3.i + TOMO.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P.s >r[1]> M18.i + Rab3.i + TOMO.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P.s >r[1]> M18.i + Rab3.i + TOMO_p.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P.s >r[1]> M18.i + Rab3.i + TOMO_p.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA.s >r[1]> M18.i + PKA.i + Rab3.i + TOMO.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA.s >r[1]> M18.i + PKA.i + Rab3.i + TOMO_p.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P_PP2A.s >r[1]> M18.i + PP2A.i + Rab3.i + TOMO.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P_PP2A.s >r[1]> M18.i + PP2A.i + Rab3.i + TOMO_p.i + RIM_M13.s + SNP25.s + SYX.s r[1].K = 1000000.0 with ERsys: diff_SERCA = Diffusion.Create(SERCA, DCST_MEM) diff_CaSERCA = Diffusion.Create(CaSERCA, DCST_MEM) diff_Ca2SERCA = Diffusion.Create(Ca2SERCA, DCST_MEM) # Ca + SERCA <-> Ca1SERCA +Ca <-> Ca2SERCA -> SERCA SERCA.s + Ca.o CaSERCA.s CaSERCA.s + Ca.o Ca2SERCA.s >r[3]> 2 * Ca.i + SERCA.s r[1].K = 17147000000.0, 8426.3 r[2].K = 17147000000.0, 8426.3 r[3].K = 250.0 with syn_sys: #Diffusion of glutamate in the cleft diff_glu = Diffusion.Create(glu, DCST_CYT) diff_REL_IND = Diffusion.Create(REL_IND, 0) #######Synaptotagmin Model####### #Parameters kon_SNARE_syt_CXN_ca1 = 1000e06 koff_SNARE_syt_CXN_ca1 = 1270 koff_SNARE_syt_CXN_ca1_s = 1000 #Millet 2002 kon_SNARE_syt_CXN_ca2 = 1000e06 koff_SNARE_syt_CXN_ca2 = 227670 koff_SNARE_syt_CXN_ca2_s = 2000 kon_SNARE_syt_CXN_ca3 = 1000e06 koff_SNARE_syt_CXN_ca3 = 12370 koff_SNARE_syt_CXN_ca3_s = 5000 kon_SNARE_syt_CXN_bca1 = 1000e06 koff_SNARE_syt_CXN_bca1 = 50000 kon_SNARE_syt_CXN_bca2 = 1000e06 koff_SNARE_syt_CXN_bca2 = 25780 kon_SNARE_syt_CXN_mem = 2500 koff_SNARE_syt_CXN_mem = 700 with ves_ssys: #vesicle Diffusion of Synaptotagmin vdiff_syt = Diffusion.Create(syt, DCST_MEM_VES) #Reactions Ca.o + SNARE_syt_CXN.v SNARE_syt_CXN_Ca.v r[1].K = kon_SNARE_syt_CXN_ca1, koff_SNARE_syt_CXN_ca1 Ca.o + SNARE_syt_CXN_Ca.v SNARE_syt_CXN_Ca2.v r[1].K = kon_SNARE_syt_CXN_ca2, koff_SNARE_syt_CXN_ca2 Ca.o + SNARE_syt_CXN_Ca2.v SNARE_syt_CXN_Ca3.v r[1].K = kon_SNARE_syt_CXN_ca3, koff_SNARE_syt_CXN_ca3 Ca.o + SNARE_syt_CXN.v SNARE_syt_CXN_bCa.v r[1].K = kon_SNARE_syt_CXN_bca1, koff_SNARE_syt_CXN_bca1 Ca.o + SNARE_syt_CXN_bCa.v SNARE_syt_CXN_bCa2.v r[1].K = kon_SNARE_syt_CXN_bca2, koff_SNARE_syt_CXN_bca2 Ca.o + SNARE_syt_CXN_bCa.v SNARE_syt_CXN_Ca_bCa.v r[1].K = kon_SNARE_syt_CXN_ca1, koff_SNARE_syt_CXN_ca1 Ca.o + SNARE_syt_CXN_Ca_bCa.v SNARE_syt_CXN_Ca2_bCa.v r[1].K = kon_SNARE_syt_CXN_ca2, koff_SNARE_syt_CXN_ca2 Ca.o + SNARE_syt_CXN_Ca2_bCa.v SNARE_syt_CXN_Ca3_bCa.v r[1].K = kon_SNARE_syt_CXN_ca3, koff_SNARE_syt_CXN_ca3 Ca.o + SNARE_syt_CXN_Ca.v SNARE_syt_CXN_Ca_bCa.v r[1].K = kon_SNARE_syt_CXN_bca1, koff_SNARE_syt_CXN_bca1 Ca.o + SNARE_syt_CXN_Ca_bCa.v SNARE_syt_CXN_Ca_bCa2.v r[1].K = kon_SNARE_syt_CXN_bca2, koff_SNARE_syt_CXN_bca2 Ca.o + SNARE_syt_CXN_Ca2.v SNARE_syt_CXN_Ca2_bCa.v r[1].K = kon_SNARE_syt_CXN_bca1, koff_SNARE_syt_CXN_bca1 Ca.o + SNARE_syt_CXN_Ca2_bCa.v SNARE_syt_CXN_Ca2_bCa2.v r[1].K = kon_SNARE_syt_CXN_bca2, koff_SNARE_syt_CXN_bca2 Ca.o + SNARE_syt_CXN_Ca3.v SNARE_syt_CXN_Ca3_bCa.v r[1].K = kon_SNARE_syt_CXN_bca1, koff_SNARE_syt_CXN_bca1 Ca.o + SNARE_syt_CXN_Ca3_bCa.v SNARE_syt_CXN_Ca3_bCa2.v r[1].K = kon_SNARE_syt_CXN_bca2, koff_SNARE_syt_CXN_bca2 Ca.o + SNARE_syt_CXN_bCa2.v SNARE_syt_CXN_Ca_bCa2.v r[1].K = kon_SNARE_syt_CXN_ca1, koff_SNARE_syt_CXN_ca1_s Ca.o + SNARE_syt_CXN_Ca_bCa2.v SNARE_syt_CXN_Ca2_bCa2.v r[1].K = kon_SNARE_syt_CXN_ca2, koff_SNARE_syt_CXN_ca2_s Ca.o + SNARE_syt_CXN_Ca2_bCa2.v SNARE_syt_CXN_Ca3_bCa2.v r[1].K = kon_SNARE_syt_CXN_ca3, koff_SNARE_syt_CXN_ca3_s kon_m13_syx = 20e06 #Mezer 2004 koff_m13_syx = 2.6 #Mezer 2004 kon_syx_snp25 = 10e06 koff_syx_snp25 = 1.26 kon_syb_syx = 2.35e06 koff_syb_syx = 0.0047 #######Vesicle docks by Rab3 via RIM_M13 interaction kon_rim_rab3 = 1000e9 koff_rim_rab3 = 0#15 kon_syt_snare = 57e06 #32e06 #Mezer 2004 koff_syt_snare = 0.24 #9.4 #Mezer 2004 kon_cxn_snare = 30e06 #7e06 #Mezer 2004 koff_cxn_snare = 0.33 #Mezer 2004 vdiff_Rab3 = Diffusion.Create(Rab3, 5e-13) #estimated from similar proteins #vesicle Diffusion of Synaptobrevin vdiff_syb = Diffusion.Create(SYB, 3.245e-13) #reactions mdist=10e-09 RIM_M13.s + Rab3.v RIM_M13_Rab3.v r[1].K = kon_rim_rab3, koff_rim_rab3 r[1].Immobilization = IMMOBILIZING, MOBILIZING r[1].MaxDistance = mdist, None ##Munc13 (active form in complex with RIM) binds and opens syntaxin-1 (which will allow it to bind SNAP25) (Lai 2017) SYX_M18.s + RIM_M13_Rab3.v RIM_M13_Rab3_SYX_M18.v r[1].K = kon_m13_syx, koff_m13_syx #######SNAP25 is incorporated into the SNARE complex (binds to SYX) (Lai 2017) SNP25.s + RIM_M13_Rab3_SYX_M18.v RIM_M13_Rab3_SYX_M18_SNP25.v r[1].K = kon_syx_snp25, koff_syx_snp25 #######Synaptobrevin is incorporated into the SNARE complex (binds to SYX_SNP25 complex) RIM_M13_Rab3_SYX_M18_SNP25.v + SYB.v SNARE.v r[1].K = kon_syb_syx, koff_syb_syx ##Binding of syt to SNARE SNARE.v + syt.v SNARE_syt.v r[1].K = kon_syt_snare, koff_syt_snare ##Binding of CXN to SNARE CXN.o + SNARE_syt.v SNARE_syt_CXN.v r[1].K = kon_cxn_snare, koff_cxn_snare ##VESICLE FUSION EVENT (EXOCYTOSIS) fusion2 = Exocytosis.Create(3000.0, deps=2 * SNARE_syt_CXN_Ca3_bCa2.v) fusion3 = Exocytosis.Create(30000.0, deps=3 * SNARE_syt_CXN_Ca3_bCa2.v) fusion4 = Exocytosis.Create(300000.0, deps=4 * SNARE_syt_CXN_Ca3_bCa2.v) #removal of DYN_SYN1 from newly endocytosed vesicle DYN_SYN1.v >r[1]> DYNp.o + SYN1.o r[1].K = 1000000000.0 diff_synapsin_mem = Diffusion.Create(synapsin, DCST_MEM_VES) diff_synapsin_p_mem = Diffusion.Create(synapsin_p, DCST_MEM_VES) diff_synapsin_pka_mem = Diffusion.Create(PKA_synapsin, DCST_MEM_VES) diff_synapsin_pp2a_ves = Diffusion.Create(PP2A_synapsin_p, DCST_MEM_VES) actin.o + synapsin.v synapsin_actin.v r[1].K = kon_synapsin_actin, koff_synapsin_actin r[1].Immobilization = IMMOBILIZING, MOBILIZING actin.o + synapsin_p.v synapsin_actin_p.v r[1].K = kon_synapsin_actin, koff_synapsin_actin_p r[1].Immobilization = IMMOBILIZING, MOBILIZING diff_Rab3_TOMO_synapsin_ves = Diffusion.Create(Rab3_TOMO_synapsin, DCST_MEM_VES) diff_Rab3_TOMO_synapsin_p_ves = Diffusion.Create(Rab3_TOMO_synapsin_p, DCST_MEM_VES) diff_Rab3_TOMO_p_synapsin_ves = Diffusion.Create(Rab3_TOMO_p_synapsin, DCST_MEM_VES) diff_Rab3_TOMO_p_synapsin_p_ves = Diffusion.Create(Rab3_TOMO_p_synapsin_p, DCST_MEM_VES) diff_Rab3_TOMO_p_ves = Diffusion.Create(Rab3_TOMO_p, DCST_MEM_VES) diff_Rab3_TOMO_ves = Diffusion.Create(Rab3_TOMO, DCST_MEM_VES) diff_Rab3_TOMO_CDK5_ves = Diffusion.Create(Rab3_TOMO_CDK5, 5e-13) diff_Rab3_TOMO_p_CaN_CaM_ves = Diffusion.Create(Rab3_TOMO_p_CaN_CaM, DCST_MEM_VES) diff_Rab3_TOMO_synapsin_PKA_ves = Diffusion.Create(Rab3_TOMO_synapsin_PKA, DCST_MEM_VES) diff_Rab3_TOMO_p_synapsin_PKA_ves = Diffusion.Create(Rab3_TOMO_p_synapsin_PKA, DCST_MEM_VES) diff_Rab3_TOMO_synapsin_CDK5_ves = Diffusion.Create(Rab3_TOMO_synapsin_CDK5, DCST_MEM_VES) diff_Rab3_TOMO_synapsin_p_CDK5_ves = Diffusion.Create(Rab3_TOMO_synapsin_p_CDK5, DCST_MEM_VES) diff_Rab3_TOMO_p_synapsin_CaN_CaM_ves = Diffusion.Create(Rab3_TOMO_p_synapsin_CaN_CaM, DCST_MEM_VES) diff_Rab3_TOMO_p_synapsin_p_CaN_CaM_ves = Diffusion.Create(Rab3_TOMO_p_synapsin_p_CaN_CaM, DCST_MEM_VES) CDK5.o + Rab3_TOMO.v Rab3_TOMO_CDK5.v r[1].K = kon_cdk_tomo, koff_cdk_tomo Rab3_TOMO_CDK5.v >r[1]> CDK5.o + Rab3_TOMO_p.v r[1].K = kcat_cdk_tomo CaN_CaM.o + Rab3_TOMO_p.v Rab3_TOMO_p_CaN_CaM.v r[1].K = kon_can_tomo, koff_can_tomo Rab3_TOMO_p_CaN_CaM.v >r[1]> CaN_CaM.o + Rab3_TOMO.v r[1].K = kcat_can_tomo TOMO_p.o + Rab3.v Rab3_TOMO_p.v r[1].K = kon_rab3_TOMO_p, koff_rab3_TOMO_p Rab3_TOMO.v >r[1]> TOMO.o + Rab3.v r[1].K = koff_rab3_TOMO_p Rab3_TOMO_p.v + synapsin.v Rab3_TOMO_p_synapsin.v r[1].K = kon_TOMO_p_synapsin, koff_TOMO_p_synapsin Rab3_TOMO_p.v + synapsin_p.v Rab3_TOMO_p_synapsin_p.v r[1].K = kon_TOMO_p_synapsin, koff_TOMO_p_synapsin Rab3_TOMO.v + synapsin.v Rab3_TOMO_synapsin.v r[1].K = kon_TOMO_synapsin, koff_TOMO_synapsin Rab3_TOMO.v + synapsin_p.v Rab3_TOMO_synapsin_p.v r[1].K = kon_TOMO_synapsin, koff_TOMO_synapsin #free vesicle synapsin phosphorylation PKA.o + synapsin.v PKA_synapsin.v r[1].K = kon_PKA_syn, koff_PKA_syn PKA_synapsin.v >r[1]> PKA.o + synapsin_p.v r[1].K = kcat_PKA_syn PKA.o + Rab3_TOMO_synapsin.v Rab3_TOMO_synapsin_PKA.v r[1].K = kon_PKA_syn, koff_PKA_syn Rab3_TOMO_synapsin_PKA.v >r[1]> PKA.o + Rab3_TOMO_synapsin_p.v r[1].K = kcat_PKA_syn PKA.o + Rab3_TOMO_p_synapsin.v Rab3_TOMO_p_synapsin_PKA.v r[1].K = kon_PKA_syn, koff_PKA_syn Rab3_TOMO_p_synapsin_PKA.v >r[1]> PKA.o + Rab3_TOMO_p_synapsin_p.v r[1].K = kcat_PKA_syn #dephos of vesicle synapsin_p PP2A.o + synapsin_p.v PP2A_synapsin_p.v r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin PP2A_synapsin_p.v >r[1]> PP2A.o + synapsin.v r[1].K = kcat_pp2a_syn PP2A.o + Rab3_TOMO_p_synapsin_p.v Rab3_TOMO_p_synapsin_p_PP2A.v r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin Rab3_TOMO_p_synapsin_p_PP2A.v >r[1]> PP2A.o + Rab3_TOMO_p_synapsin.v r[1].K = kcat_pp2a_syn PP2A.o + Rab3_TOMO_synapsin_p.v Rab3_TOMO_synapsin_p_PP2A.v r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin Rab3_TOMO_synapsin_p_PP2A.v >r[1]> PP2A.o + Rab3_TOMO_synapsin.v r[1].K = kcat_pp2a_syn CDK5.o + Rab3_TOMO_synapsin.v Rab3_TOMO_synapsin_CDK5.v r[1].K = kon_cdk_tomo, koff_cdk_tomo Rab3_TOMO_synapsin_CDK5.v >r[1]> CDK5.o + Rab3_TOMO_p_synapsin.v r[1].K = kcat_cdk_tomo CDK5.o + Rab3_TOMO_synapsin_p.v Rab3_TOMO_synapsin_p_CDK5.v r[1].K = kon_cdk_tomo, koff_cdk_tomo Rab3_TOMO_synapsin_p_CDK5.v >r[1]> CDK5.o + Rab3_TOMO_p_synapsin_p.v r[1].K = kcat_cdk_tomo CaN_CaM.o + Rab3_TOMO_p_synapsin.v Rab3_TOMO_p_synapsin_CaN_CaM.v r[1].K = kon_can_tomo, koff_can_tomo Rab3_TOMO_p_synapsin_CaN_CaM.v >r[1]> CaN_CaM.o + Rab3_TOMO_synapsin.v r[1].K = kcat_can_tomo CaN_CaM.o + Rab3_TOMO_p_synapsin_p.v Rab3_TOMO_p_synapsin_p_CaN_CaM.v r[1].K = kon_can_tomo, koff_can_tomo Rab3_TOMO_p_synapsin_p_CaN_CaM.v >r[1]> CaN_CaM.o + Rab3_TOMO_synapsin_p.v r[1].K = kcat_can_tomo #####Rab3-TOMO binds to the synapsin dimers##### Rab3_TOMO_p.v + synapsin_dimer.v Rab3_TOMO_p_synapsin_dimer.v r[1].K = kon_TOMO_p_synapsin, koff_TOMO_p_synapsin Rab3_TOMO_p.v + synapsin_dimer_p.v Rab3_TOMO_p_synapsin_dimer_p.v r[1].K = kon_TOMO_p_synapsin, koff_TOMO_p_synapsin Rab3_TOMO.v + synapsin_dimer.v Rab3_TOMO_synapsin_dimer.v r[1].K = kon_TOMO_synapsin, koff_TOMO_synapsin Rab3_TOMO.v + synapsin_dimer_p.v Rab3_TOMO_synapsin_dimer_p.v r[1].K = kon_TOMO_synapsin, koff_TOMO_synapsin #PKA phos. PKA.o + synapsin_dimer.v PKA_synapsin_dimer.v >r[2]> PKA.o + synapsin_dimer_p.v r[1].K = kon_PKA_syn, koff_PKA_syn r[2].K = kcat_PKA_syn PKA.o + Rab3_TOMO_synapsin_dimer.v Rab3_TOMO_synapsin_dimer_PKA.v >r[2]> PKA.o + Rab3_TOMO_synapsin_dimer_p.v r[1].K = kon_PKA_syn, koff_PKA_syn r[2].K = kcat_PKA_syn PKA.o + Rab3_TOMO_p_synapsin_dimer.v Rab3_TOMO_p_synapsin_dimer_PKA.v >r[2]> PKA.o + Rab3_TOMO_p_synapsin_dimer_p.v r[1].K = kon_PKA_syn, koff_PKA_syn r[2].K = kcat_PKA_syn PP2A.o + synapsin_dimer_p.v PP2A_synapsin_dimer_p.v >r[2]> PP2A.o + synapsin_dimer.v r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin r[2].K = kcat_pp2a_syn PP2A.o + Rab3_TOMO_synapsin_dimer_p.v Rab3_TOMO_synapsin_dimer_p_PP2A.v >r[2]> PP2A.o + Rab3_TOMO_synapsin_dimer.v r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin r[2].K = kcat_pp2a_syn PP2A.o + Rab3_TOMO_p_synapsin_dimer_p.v Rab3_TOMO_p_synapsin_dimer_p_PP2A.v >r[2]> PP2A.o + Rab3_TOMO_p_synapsin_dimer.v r[1].K = kon_pp2a_synapsin, koff_pp2a_synapsin r[2].K = kcat_pp2a_syn CDK5.o + Rab3_TOMO_synapsin_dimer.v Rab3_TOMO_synapsin_dimer_CDK5.v >r[2]> CDK5.o + Rab3_TOMO_p_synapsin_dimer.v r[1].K = kon_cdk_tomo, koff_cdk_tomo r[2].K = kcat_cdk_tomo CDK5.o + Rab3_TOMO_synapsin_dimer_p.v Rab3_TOMO_synapsin_dimer_p_CDK5.v >r[2]> CDK5.o + Rab3_TOMO_p_synapsin_dimer_p.v r[1].K = kon_cdk_tomo, koff_cdk_tomo r[2].K = kcat_cdk_tomo CaN_CaM.o + Rab3_TOMO_p_synapsin_dimer.v Rab3_TOMO_p_synapsin_dimer_CaN_CaM.v >r[2]> CaN_CaM.o + Rab3_TOMO_synapsin_dimer.v r[1].K = kon_can_tomo, koff_can_tomo r[2].K = kcat_can_tomo CaN_CaM.o + Rab3_TOMO_p_synapsin_dimer_p.v Rab3_TOMO_p_synapsin_dimer_p_CaN_CaM.v >r[2]> CaN_CaM.o + Rab3_TOMO_synapsin_dimer_p.v r[1].K = kon_can_tomo, koff_can_tomo r[2].K = kcat_can_tomo #binding of TOMO to SNARE (independent of CDK5 phos state, indicated by small p) #######TOMO is incorporated into the SNARE complex (binds to SYX_SNP25 complex) TOMO.o + RIM_M13_Rab3_SYX_M18_SNP25.v RIM_M13_Rab3_SYX_M18_SNP25_TOMO.v r[1].K = kon_tomo_syx, koff_tomo_syx TOMO_p.o + RIM_M13_Rab3_SYX_M18_SNP25.v RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p.v r[1].K = kon_tomo_syx, koff_tomo_syx #switching of TOMO to SYB-displaceable state (unphosphorylated, slow) RIM_M13_Rab3_SYX_M18_SNP25_TOMO.v RIM_M13_Rab3_SYX_M18_SNP25_TOMOx.v r[1].K = kflip_tomo_f, kflip_tomo_r RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p.v RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p.v r[1].K = kflip_tomo_f, kflip_tomo_r #switching of TOMO to SYB-displaceable state (phosphorylated by PKA indicated by big P, fast) RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P.v RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P.v r[1].K = kflip_tomo_P_f, kflip_tomo_r RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p.v >r[1]> RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p.v r[1].K = kflip_tomo_P_f RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P.v >r[1]> RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P.v r[1].K = kflip_tomo_r #displacement of TOMO by SYB RIM_M13_Rab3_SYX_M18_SNP25_TOMOx.v + SYB.v >r[1]> SNARE.v + TOMO.v r[1].K = kdisp_tomo_syx RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p.v + SYB.v >r[1]> SNARE.v + TOMO_p.v r[1].K = kdisp_tomo_syx #displacement of TOMO_P by SYB RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P.v + SYB.v >r[1]> SNARE.v + TOMO.v r[1].K = kdisp_tomo_syx RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P.v + SYB.v >r[1]> SNARE.v + TOMO_p.v r[1].K = kdisp_tomo_syx #phosphorylation of TOMO by PKA PKA.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO.v RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA.v r[1].K = kon_tomo_pka, koff_tomo_pka RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA.v >r[1]> PKA.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P.v r[1].K = kcat_pka_tomo PKA.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p.v RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA.v r[1].K = kon_tomo_pka, koff_tomo_pka RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA.v >r[1]> PKA.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P.v r[1].K = kcat_pka_tomo #dephosphorylation of TOMO by PP2A PP2A.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P.v RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P_PP2A.v r[1].K = kon_tomo_PP2A, koff_tomo_PP2A RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P_PP2A.v >r[1]> PP2A.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO.v r[1].K = kcat_PP2A_tomo PP2A.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P.v RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P_PP2A.v r[1].K = kon_tomo_PP2A, koff_tomo_PP2A RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P_PP2A.v >r[1]> PP2A.o + RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p.v r[1].K = kcat_PP2A_tomo #####BINDING OF PROTEINS TO VESICLES####### ######Binding of synapsin to vesicles kon_synapsin_ves = 10.7e06 koff_synapsin_ves = 0.123 koff_synapsin_p_ves = 123 synapsin.o + ves_syn1_site.v synapsin.v r[1].K = kon_synapsin_ves, koff_synapsin_ves synapsin_p.v >r[1]> synapsin_p.o + ves_syn1_site.v r[1].K = koff_synapsin_p_ves CXN.o + ves_CXN_site.v CXN.v r[1].K = kon_cxn_ves, koff_cxn_ves Rab3.o + ves_rab3_site.v Rab3.v r[1].K = kon_rab3_ves, koff_rab3_ves M13.o + ves_m13_site.v M13.v r[1].K = kon_m13_ves, koff_m13_ves M18.o + ves_m18_site.v M18.v r[1].K = kon_m18_ves, koff_m18_ves SYN1.o + ves_syndap_site.v SYN1.v r[1].K = kon_syn1_ves, koff_syn1_ves aSNAP.o + ves_asnap_site.v aSNAP.v r[1].K = kon_asnap_ves, koff_asnap_ves NSF.o + ves_nsf_site.v NSF.v r[1].K = kon_nsf_ves, koff_nsf_ves with raft_sys: #raft dephosphorylation CaN_CaM.i + DYNpp.r CaN_DYNpp.r r[1].K = kon_can_dyn, koff_can_dyn CaN_DYNpp.r >r[1]> CaN_CaM.i + DYNp.r r[1].K = kcat_can CaN_CaM.i + DYNp.r CaN_DYNp.r r[1].K = kon_can_dyn, koff_can_dyn CaN_DYNp.r >r[1]> CaN_CaM.i + DYN.r r[1].K = kcat_can #Raft binding of dynamin to syndapin 1 (SYN1) SYN1.i + DYN.r DYN_SYN1.r r[1].K = kon_dyn_syn, koff_dyn_syn SYB.s + AP180.r >r[1]> SYB.r r[1].K = kon_syb_ap180 syt.s + AP2.r >r[1]> syt.r r[1].K = kon_syt_ap2 Rab3.s + RabAd.r >r[1]> Rab3.r r[1].K = kon_rab3_rabad DYN_SYN1.s + DYN_AD.r DYN_SYN1.r r[1].K = kon_dyn_raft, koff_dyn_raft DYNp.s + DYN_AD.r DYNp.r r[1].K = kon_dyn_raft, koff_dyn_raft DYN.s + DYN_AD.r DYN.r r[1].K = kon_dyn_raft, koff_dyn_raft ##formation of new vesicle by endocytosis raftendo = RaftEndocytosis.Create(ves, 1000.0, deps=DYN_SYN1.r + 10 * Rab3.r + 26 * syt.r + 68 * SYB.r, inside=True) #################################### #FIND ALL SPECIES WITHOUT MEMBRANE DIFFUSION RULE vsysSpecs = set(spec.getID() for spec in vsys._getStepsObjects()[0].getAllSpecs()) memsysSpecs = set(spec.getID() for spec in memsys._getStepsObjects()[0].getAllSpecs()) ves_ssysSpecs = set(spec.getID() for spec in ves_ssys._getStepsObjects()[0].getAllSpecs()) raft_sysSpecs = set(spec.getID() for spec in raft_sys._getStepsObjects()[0].getAllSpecs()) print(f'TOTAL CYTOSOL SPECIES: {len(vsysSpecs)}') print(f'TOTAL MEMBRANE SPECIES: {len(memsysSpecs)}') print(f'TOTAL VES SPECIES: {len(ves_ssysSpecs)}') #find intersect of vesicle species and surface species ves_surf_spec_diff = ves_ssysSpecs - memsysSpecs print(f'There are {len(ves_surf_spec_diff)} ves species not in the surface system') print('MISSING SURF SPECIES:', ves_surf_spec_diff) print(f'TOTAL RAFT SPECIES: {len(raft_sysSpecs)}') raft_surf_spec_diff = raft_sysSpecs - memsysSpecs print(f'There are {len(raft_surf_spec_diff)} raft species not in the surface system') print('MISSING RAFT SPECIES:', raft_surf_spec_diff) ####Geometry Definition#### scale = 1e-9 scale_100 = 1e-7 mesh = TetMesh.Load(MESH_PATH) print("MESH LOADED") with mesh: #find min and max y-values of outer_tets bounding box cyt_y_min = min(tet.center.y for tet in mesh.outer.tets) cyt_y_max = max(tet.center.y for tet in mesh.outer.tets) print("cyt_y_min", cyt_y_min) print("cyt_y_max", cyt_y_max) print('FOUND OUTER TETS') cyt_tets = TetList(tet for tet in mesh.spine.tets if cyt_y_min < tet.center.y < cyt_y_max) axon_tets = mesh.spine.tets - cyt_tets print('ALL tets in mesh:', len(mesh.tets)) print('Total cytosol tets:', len(mesh.spine.tets)) print('Total axonal tets:', len(axon_tets)) print('Total bouton tets:', len(cyt_tets)) print('Sum bouton + axomal:', len(axon_tets)+len(cyt_tets)) print('Sum bouton, axon, ER, outer:', len(mesh.spine.tets)+len(mesh.er.tets)+len(mesh.outer.tets)) ERmemb_tris = cyt_tets.surface & mesh.er.tets.surface memb_tris = cyt_tets.surface & mesh.outer.tets.surface print('Number of triangles on membrane =', len(memb_tris)) #open actin_tets list print('OPENING ACTIN TETS...') with open(os.path.join(MODEL_PATH, 'actin_tets_215nm.txt'), 'rb') as f: actin_tets = pickle.load(f) print('ACTIN TETS LOADED:', len(actin_tets)) ######FIND AZONE TRIANGLES###### #find membrane triangles within ellipse enclosing coordinates #ellipse foci focus1 = np.array([2036.7e-9, 2982.6e-9]) focus2 = np.array([2185.8e-9, 3280.8e-9]) #find memb triangles closest to foci focus1_tri = min(memb_tris, key=lambda tri: np.linalg.norm(tri.center[:2] - focus1)) focus2_tri = min(memb_tris, key=lambda tri: np.linalg.norm(tri.center[:2] - focus2)) print("Ellipse focus 1 tri:", focus1_tri) print("Ellipse focus 2 tri:", focus2_tri) radius_maj = 380e-9#349.8e-9 azone_tris = TriList(tri for tri in memb_tris if np.linalg.norm(tri.center - focus1_tri.center) + np.linalg.norm(tri.center - focus2_tri.center) < radius_maj) print('Number of triangles in active zone =', len(azone_tris)) print("active zone area =", azone_tris.Area) ######FIND ENDOCYTIC ZONE TRIANGLES###### radius_maj_endo = 550e-9 #550e-9#349.8e-9 endo_tris = TriList(tri for tri in memb_tris if radius_maj <= np.linalg.norm(tri.center - focus1_tri.center) + np.linalg.norm(tri.center - focus2_tri.center) < radius_maj_endo) print('Number of triangles in endo zone:', len(endo_tris)) print("endo zone area =", endo_tris.Area) print("membrane area =", memb_tris.Area) print("ER vol =", mesh.er.tets.Vol) #create compartments #cytosol includes all tets not in the recycling vesicle AZ cluster axon = Compartment.Create(axon_tets) cytosol = Compartment.Create(cyt_tets, vsys) cytER = Compartment.Create(mesh.er.tets, cytERsys) cleft = Compartment.Create(mesh.outer.tets, syn_sys) vac1 = Compartment.Create(mesh.vec1.tets) vac2 = Compartment.Create(mesh.vec2.tets) vac3 = Compartment.Create(mesh.vec3.tets) vac4 = Compartment.Create(mesh.vec4.tets) vac5 = Compartment.Create(mesh.vec5.tets) mito = Compartment.Create(mesh.mit.tets) print("cytosol vol =", cytosol.Vol) print("axon vol =", axon.Vol) ERmemb = Patch.Create(ERmemb_tris, cytER, cytosol, ERsys) memb = Patch.Create(memb_tris, cytosol, cleft, memsys) cyt_tris = mesh.surface & cytosol.surface cyt_verts = VertList(set(vert for tet in cyt_tets for vert in tet.verts)) print("Number of cyt_verts =", len(cyt_verts)) # Create excitable membrane membrane = Membrane.Create([memb]) print("MEMBRANE CREATED") #find tetrahedra in restricted diffusion "tethering" zone around Azone. tether_zone = TetList(tet for tet in cyt_tets if any(np.linalg.norm(tri.center - tet.center) < 100e-09 for tri in azone_tris)) print("Tetrahedra in tether zone:", len(tether_zone)) dock_tris = TriList(dock_tris) #create dictionary of dock tris and surrounding triangles (to capture escaped RIM) all_surr_tris = TriList() azone_and_endo_tris = azone_tris + endo_tris for tri in dock_tris: surr = TriList(t for t in azone_and_endo_tris if np.linalg.norm(t.center - tri.center) < 45e-9) all_surr_tris += surr print(f'Dock tri {tri} has {len(surr)} surrounding tris.') print(f'Dock tri {tri} has {surr.indices} surrounding tris.') all_surr_tris_set = set(all_surr_tris) print('TRI SURROUNDING HAD DUPLICATES:', len(all_surr_tris) != len(all_surr_tris_set)) print(len(all_surr_tris), 'vs', len(all_surr_tris_set)) print('DUPLICATES:', [t for t, v in collections.Counter(all_surr_tris).items() if v > 1]) #add each surrounding triangle to closest dock triangle dock_tri_to_surround_tris = {} for tri in all_surr_tris_set: if tri not in dock_tris: dock_tri = min(dock_tris, key=lambda dt: np.linalg.norm(dt.center - tri.center)) dock_tri_to_surround_tris.setdefault(dock_tri, TriList()).append(tri) surr_tri_count = 0 for d, surr in dock_tri_to_surround_tris.items(): print(f'Dock tris {d} surrond tris: {surr.indices}') surr_tri_count += len(surr) print('TOTAL SURR TRIS:', surr_tri_count) #create dictionary of dock tris and "tether path" ends (tri:[[x0,y0],[x1,y1]]) dock_tri_to_tether_path = {} #find norms for all dock_tris print('FINDING TETHER PATH POINTS') for tri in dock_tris: print('DOCK TRI COORD:', tri.center) outside = tri.center - tri.norm * 100e-9 inside = tri.center + tri.norm * 100e-9 # Make sure it points in cytosol if mesh.tets[inside] not in cyt_tets: print('NORM NOT IN CYTOSOL.... INVERTING') outside, inside = inside, outside dock_tri_to_tether_path[tri] = (outside, inside) print(f'FOUND ALL {dock_tri_to_tether_path} TETHER PATH POINTS') min_dist_dock = min(np.linalg.norm(tri1.center - tri2.center) for i, tri1 in enumerate(dock_tris) for tri2 in dock_tris[i+1:]) print(f'DOCK MIN DIST: {min_dist_dock * 1e09} nm') print("active zone area = ", azone_tris.Area) print("endo zone area = ", endo_tris.Area) mem_area = cyt_tris.Area print("membrane area = ", mem_area) print("ER vol =", cytER.Vol) #################################### SIMULATION DATA FUNCTIONS ETC #################################### def getTOMOcount(rs): TOMO_vesSpecs = [ 'Rab3_TOMO', 'Rab3_TOMO_synapsin', 'Rab3_TOMO_synapsin_actin', 'Rab3_TOMO_synapsin_PKA', 'Rab3_TOMO_synapsin_p', 'Rab3_TOMO_p_CaN_CaM', 'Rab3_TOMO_CDK5', 'Rab3_TOMO_synapsin_CDK5', 'Rab3_TOMO_synapsin_p_PP2A', 'Rab3_TOMO_synapsin_dimer_p_PP2A', 'Rab3_TOMO_synapsin_dimer_PKA', 'Rab3_TOMO_synapsin_dimer', 'Rab3_TOMO_synapsin_dimer_p', 'Rab3_TOMO_synapsin_dimer_CDK5', 'Rab3_TOMO_synapsin_dimer_p_CDK5', ] cyt_TOMO_count = rs.SUM(rs.cytosol.LIST('TOMO', 'TOMO_CDK5').Count) ves_TOMO_count = rs.SUM(rs.cytosol.ves('surf').LIST(*TOMO_vesSpecs).Count) return cyt_TOMO_count + ves_TOMO_count def getVesicleLinkSpecs(vesref): linkspecs = [ 'synapsin_dimer', 'synapsin_dimer_p', 'Rab3_TOMO_synapsin_dimer', 'Rab3_TOMO_synapsin_dimer_p', 'Rab3_TOMO_p_synapsin_dimer', 'Rab3_TOMO_p_synapsin_dimer_p', 'PKA_synapsin_dimer', 'Rab3_TOMO_synapsin_dimer_PKA', 'Rab3_TOMO_p_synapsin_dimer_PKA', 'PP2A_synapsin_dimer_p', 'Rab3_TOMO_synapsin_dimer_p_PP2A', 'Rab3_TOMO_p_synapsin_dimer_p_PP2A', 'Rab3_TOMO_synapsin_dimer_CDK5', 'Rab3_TOMO_synapsin_dimer_p_CDK5', 'Rab3_TOMO_p_synapsin_dimer_CaN_CaM', 'Rab3_TOMO_p_synapsin_dimer_p_CaN_CaM', ] return sum(vesref('surf').LIST(*linkspecs).Count) def getPhosphoSynapsins(rs): syn_phos_ves_specs = [ 'synapsin_p', 'Rab3_TOMO_synapsin_actin_p', 'Rab3_TOMO_p_synapsin_actin_p', 'Rab3_TOMO_p_synapsin_p', 'Rab3_TOMO_synapsin_p', 'Rab3_TOMO_p_synapsin_p_PP2A', 'Rab3_TOMO_synapsin_p_PP2A', 'Rab3_TOMO_synapsin_p_CDK5', 'Rab3_TOMO_p_synapsin_p_CaN_CaM', 'synapsin_dimer_p', 'Rab3_TOMO_synapsin_dimer_p', 'Rab3_TOMO_p_synapsin_dimer_p', 'PP2A_synapsin_dimer_p', 'Rab3_TOMO_synapsin_dimer_p_PP2A', 'Rab3_TOMO_p_synapsin_dimer_p_PP2A', 'Rab3_TOMO_synapsin_dimer_p_CDK5', 'Rab3_TOMO_p_synapsin_dimer_p_CaN_CaM', ] cyt_syn_phos = rs.SUM(rs.cytosol.LIST(synapsin_p, synapsin_actin_p).Count) ves_syn_phos = rs.SUM(rs.cytosol.ves('surf').LIST(*syn_phos_ves_specs).Count) return cyt_syn_phos + ves_syn_phos rng = RNG('mt19937', 512, rng_seed) print ("Creating MPI solver...") use_efield = True sim = Simulation('TetVesicle', syt_model, mesh, rng, MPI.EF_DV_PETSC if use_efield else MPI.EF_NONE) print ("MPI solver created.") def generateDockVesicle(sim, tri, dock_tri_to_tether_path, dock_positions): vesref = sim.cytosol.addVesicle('ves') outside, inside = dock_tri_to_tether_path[tri] pos = tri.center + (inside - tri.center) / np.linalg.norm(inside - tri.center) * (ves.Diameter / 2 + 1e-9) vesref.Pos = pos # test vesicle actually moved if np.linalg.norm(vesref.Pos - pos) < 1e-9: dock_positions.append(pos) print("Added dock vesicle") else: print("VESICLE DOCK ERROR!") return vesref FUSED_VES = [] fusion_count = 0 # Data recording rs = ResultSelector(sim) custom_values = CustomResults(sim, [int] * 9 + [list] * 4) custom_values.labels = [ 'len(nonrec_ves_clust)', 'len(nonrec_ves_free)', 'len(docked_ves)', 'len(init_vesicles_used)', 'len(init_rec_vesicles_used)', 'len(init_nonrec_vesicles_used)', 'len(new_vesicles_used)', 'len(init_rec_vesicles_used) + len(init_nonrec_vesicles_used) + len(new_vesicles_used)', 'total_link_specs', 'VES_RAB3_ALL', 'VES_RAB3_REC', 'VES_RAB3_RES', 'rel_probs', ] recorded_values = ( rs.cytosol.LIST(CaM[N2, C2], AC18_CaM, cAMP, PKA, Ca).Count << rs.cleft.REL_IND.Count \ << rs.SUM(rs.cytosol.LIST(CaN_CaM, CaN_DYNpp, CaN_DYNp).Count) # count active Calcineurin all forms in cytosol << getTOMOcount(rs) # count all dephosphorylated TOMO << rs.SUM(rs.cytosol.LIST(TOMO, TOMO_p).Count) # count all free cytosolic TOMO << rs.SUM(rs.cytosol.ves('surf').LIST( 'RIM_M13_Rab3_SYX_M18_SNP25_TOMO', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMO_P', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_P', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMO_PKA', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMO_p_PKA', ).Count) # Count TOMO bound to Syx in non-displaceable state << rs.SUM(rs.cytosol.ves('surf').LIST( 'RIM_M13_Rab3_SYX_M18_SNP25_TOMOx', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_P', 'RIM_M13_Rab3_SYX_M18_SNP25_TOMOx_p_P', ).Count) # Count TOMO bound to Syx in displaceable state << rs.raftendo.Extent # count recycled vesicles << rs.SUM(rs.memb.raft.LIST(DYNpp, CaN_DYNpp).Count) << rs.SUM(rs.memb.raft.LIST(DYNp, CaN_DYNp).Count) << rs.memb.raft.DYN.Count << rs.SUM(rs.memb.raft.LIST(DYN_SYN1, DYN_SYN1_CDK5).Count) # count dynamin in rafts << rs.memb.raft.SNARE_DISS.Count # count disassembled SNAREs in Rafts << rs.memb.SYB.Count #count SYB in membrane << rs.memb.raft.SYB.Count #count SYB in Rafts << rs.memb.raft.Count #count Rafts << rs.cytosol.ves('surf').Rab3.Count #count free Rab3 on vesicles << getPhosphoSynapsins(rs) #count phosphorylated synapsin ) if save_blender_data: blender_selectors = [ rs.TETS(cytosol.tets).Ca.Count, rs.cytosol.VESICLES().Pos, rs.cytosol.VESICLES()('surf').POINTSPECS([Rab3, SYB, syt]).PosSpherical, rs.cytosol.VESICLES()('in').glu.Count, rs.cytosol.VESICLES()('surf').LINKSPECS().Pos, rs.cytosol.VESICLES()('surf').LINKSPECS().LinkedTo, rs.memb.RAFTS().Pos, rs.memb.RAFTS().LIST(Rab3, SYB, syt, DYNp).Count, rs.ALL(Exocytosis, RaftEndocytosis).Events, ] sim.toSave(recorded_values, *blender_selectors, dt=DT) else: sim.toSave(recorded_values, dt=DT) sim.toSave(custom_values) os.makedirs(DATA_PATH, exist_ok=True) hdfPrefix = os.path.join(DATA_PATH, f'{DATA_ID}_{JOB_ID}_{JOB_INDEX}_results') with XDMFHandler(hdfPrefix) as hdf: sim.toDB(hdf, f'{DATA_ID}_{JOB_ID}_{JOB_INDEX}') for j in range(NITER): sim.newRun() add_tethers_time = 0.7 pka_act_time = 50 camkii_deact_time = 50 rel_prob_test_time = 0.05 print("Running iteration", j + 1) #create list of pulse times pulse_times = np.round(np.arange(5000, INT*1000, 1000 / RATE)) pulse_times_off = pulse_times+1 check_release_times_pre = pulse_times-1 check_release_times = pulse_times+5 if checkpoint_mode in ['restore', 'both']: # First restore the simulation to get the previous time sim.restore(checkpoint_path) tpnts = np.arange(sim.Time, INT, DT) ntpnts = tpnts.shape[0] # If the events already happened, prevent them from happening again if sim.Time > add_tethers_time: add_tethers_time = math.inf if sim.Time > pka_act_time: pka_act_time = math.inf if sim.Time > camkii_deact_time: camkii_deact_time = math.inf if sim.Time > rel_prob_test_time: rel_prob_test_time = math.inf # Restore the state of script variables pkl_path = checkpoint_path + '_script_state.pkl' with open(pkl_path, 'rb') as f: def restore_vesraft_list(f, cls=VesicleReference): return [cls(sim, vesTpe, vesIdx) for vesTpe, vesIdx in pickle.load(f)] dock_positions = pickle.load(f) dock_ves_init_tets = { VesicleReference(sim, vesTpe, vesIdx): mesh.tets[tetIdx] for (vesTpe, vesIdx), tetIdx in pickle.load(f).items() } (nonrec_ves, nonrec_ves_init, rec_ves, recycled_ves_free, recycled_ves_all, init_vesicle_ind, init_vesicles_used, init_rec_vesicles_used, init_nonrec_vesicles_used, new_vesicles_used, fused_ind_all, REC_FUSIONS, RES_FUSIONS, rec_ves_init, all_ves_pre_ap) = [ restore_vesraft_list(f) for i in range(15) ] new_rafts = restore_vesraft_list(f, cls=RaftReference) filled_rafts = restore_vesraft_list(f, cls=RaftReference) r2v_r = restore_vesraft_list(f, cls=RaftReference) r2v_v = restore_vesraft_list(f) raft_to_vesicle = {r:v for r, v in zip(r2v_r, r2v_v)} (fusion_events_tot, rel_ind_count_pre, rel_ind_count_post, total_raft_endo, total_time, action_potentials_fired, ap_n, rel_probs, recycled_vesicles_tot, raft_count_init, synapsin_total, rel_ind_count_pre_ap) = pickle.load(f) rel_probs = np.append(rel_probs, np.zeros(len(pulse_times))) else: # First time setup (no restore from checkpoint) if use_efield: print("E-FIELD IS ACTIVE") sim.EfieldDT = EF_DT sim.membrane.Potential = init_pot sim.membrane.VolRes = Ra sim.membrane.Capac = memb_capac sim.VERTS(cyt_verts).VClamped = True else: print("E-FIELD IS INACTIVE") # #################ADD DOCK VESICLES##################### dock_ves_init = [] dock_positions = [] for tri in dock_tris: vesref = generateDockVesicle(sim, tri, dock_tri_to_tether_path, dock_positions) dock_ves_init.append(vesref) print('Added ves:', vesref.idx) vesref('surf').Rab3.Count = 10 vesref('surf').SYB.Count = 69 vesref('surf').syt.Count = 27 vesref('in').REL_IND.Count = 1 print('Dock vesicles added:', len(dock_positions)) print('Dock triangles:', dock_tris.indices) #find tetrahedron for each dock vesicle dock_ves_init_tets = {vesref: mesh.tets[vesref.Pos] for vesref in dock_ves_init} #set initial diffusion rate for dock vesicles to zero print('SET DOCK TETS DIFF TO ZERO:', list(dock_ves_init_tets.values())) sim.TETS(dock_ves_init_tets.values()).ves.Dcst = 0 #################################################################### # non-recycling vesicles #################################################################### # add non-recycling vesicles to bouton ves_n = 250 nonrec_ves = [] for v in range(ves_n): vesref = sim.cytosol.addVesicle(ves) nonrec_ves.append(vesref) #add synapsin to non-recycling vesicles #Add vesicle membrane species vesref('surf').ves_syn1_site.Count = 10#75 vesref('surf').ves_CXN_site.Count = 1000 vesref('surf').ves_m13_site.Count = 1000 vesref('surf').ves_m18_site.Count = 1000 vesref('surf').ves_syndap_site.Count = 1000 vesref('surf').ves_asnap_site.Count = 1000 vesref('surf').ves_nsf_site.Count = 1000 #adding Rab3 directly for release prob tests vesref('surf').Rab3.Count = 10 vesref('surf').SYB.Count = 69 vesref('surf').syt.Count = 27 vesref('in').REL_IND.Count = 1 print("Added synapsin to non-recycling vesicles") nonrec_ves_init = copy.copy(nonrec_ves) #add recycling vesicles without synapsin rec_ves_n = 50 rec_ves = [] for r in range(rec_ves_n): vesref = sim.cytosol.addVesicle(ves) rec_ves.append(vesref) #Add vesicle membrane species vesref('surf').ves_CXN_site.Count = 1000 vesref('surf').ves_m13_site.Count = 1000 vesref('surf').ves_m18_site.Count = 1000 vesref('surf').ves_syndap_site.Count = 1000 vesref('surf').ves_asnap_site.Count = 1000 vesref('surf').ves_nsf_site.Count = 1000 #adding Rab3 directly for release prob tests vesref('surf').Rab3.Count = 10 #Takamori 2006 vesref('surf').SYB.Count = 69 vesref('surf').syt.Count = 27 #Add glutamate to each vesicle vesref('in').REL_IND.Count = 1 # vesref('in').glu.Count = 400 print('Added recycling vesicles:', len(rec_ves)) #save recycling vesicles at init rec_ves_init = rec_ves + dock_ves_init print('Rec ves ind: ', rec_ves_init) RAFT_N = 40 raft_count = 0 while raft_count < RAFT_N : raftref = sim.TRI(random.choice(endo_tris)).addRaft(raft) if raftref.exists(): raftref.Rab3.Count = 10 # Takamori 2006 raftref.SYB.Count = 69 raftref.syt.Count = 27 raftref.DYNp.Count = 1 raftref.ves_CXN_site.Count = 1000 raftref.ves_m13_site.Count = 1000 raftref.ves_m18_site.Count = 1000 raftref.ves_syndap_site.Count = 1000 raftref.ves_asnap_site.Count = 1000 raftref.ves_nsf_site.Count = 1000 raft_count += 1 raft_count_init = RAFT_N # populate docking sites with RIM sim.TRIS(dock_tris).RIM_M13.Count = 4 if cachan_static: # add 4 Ca channel to each dock triangle sim.TRIS(dock_tris).CaPchan[CaPc, CaPc, CaPc].Count = 4 else: # add 15 Ca channels randomly over active zone indices = random.sample(azone_tris.indices) import mpi4py.MPI indices = mpi4py.MPI.COMM_WORLD.bcast(indices, root=0) sim.TRIS(indices).CaPchan[CaPc, CaPc, CaPc].Count = 1 print(f'Added {sim.memb.RIM_M13.Count} RIM to membrane') print(f'Added {sim.memb.CaPchan[CaPc, CaPc, CaPc].Count} CaP_m0 to membrane') #scale membrane proteins by 1.6 (area of mesh membrane/cylinder membrane) mem_factor = 1.6 sim.cytosol.Ca.Conc = 0.045e-6 # total CB in rat HC: 1.98e-6 sim.cytosol.CBhi.Conc = 0.99e-6 # i.e. 1/2 of total CB molarity (1.98*10e-6) sim.cytosol.CBlo.Conc = 0.99e-6 # i.e. 1/2 of total CB molarity (1.98*10e-6) # total CR in rat HC: 2.47e-6 # WE MODEL TWO IDENTICAL PAIRS OF COOPERATIVE BINDING SITES AS ONE SPECIES. # SO WE SET ITS CONCENTRATION TO 4/5 OF THE TOTAL CONCENTRATION OF CR. THE REMAINING 1/5 IS THE INDEPENDENT SITE/ sim.cytosol.CRTT.Conc = 0.1976e-6 # 4/5 of total CR concentration (2 pairs of cooperative sites) sim.cytosol.CRind.Conc = 0.494e-6 # 1/5 of total CR # total PV in rat HC: 4.55e-6 sim.cytosol.PV.Conc = 4.55e-6 sim.cytosol.PV_Ca.Conc = 8.4e-6 sim.cytosol.MgPV.Conc = 30.45e-6 #Add AC18 and PKAinact sim.cytosol.AC18.Conc = 0.2e-6#0.5e-6 sim.cytosol.R2C2.Conc = 1e-6#0.5e-6 SERCA_ro = 1000*1e12 # Bartol 2015. Computational reconstitution... PMCA_ro = 180*1e12 # Bartol 2015. Computational reconstitution... SERCA_count = ERmemb.Area * SERCA_ro PMCA_count = mem_area * PMCA_ro sim.ERmemb.SERCA.Count = SERCA_count sim.memb.PMCA_P0.Count = PMCA_count print('Added SERCA:', sim.ERmemb.SERCA.Count) print('Added PMCA:', sim.memb.PMCA_P0.Count) sim.cytER.Ca.Conc = 150e-6 sim.cytER.Ca.Clamped = True # clamped means the conc won't change as simulation runs. sim.cytosol.M18.Conc = 28.4e-6 print('Added M18 to cytosol:', sim.cytosol.M18.Count) sim.cytosol.M13.Conc = 10.36e-6 print('Added M13 to cytosol:', sim.cytosol.M13.Count) sim.cytosol.CXN.Conc = 16.59e-6 print('Added complexin to cytosol:', sim.cytosol.CXN.Count) sim.cytosol.Rab3.Conc = 0#125.85e-6 print('Added Rab3 to cytosol:', sim.cytosol.Rab3.Count) sim.cytosol.aSNAP.Conc = 7.68e-6 print('Added aSNAP to cytosol:', sim.cytosol.aSNAP.Count) sim.cytosol.NSF.Conc = 27.14e-6 print('Added NSF to cytosol:', sim.cytosol.NSF.Count) sim.cytosol.synapsin.Conc = 156e-6 synapsin_total = sim.cytosol.synapsin.Count print('Added synapsins to cytosol:', synapsin_total) #add PP2A to cytocol sim.cytosol.PP2A.Conc = 0.5e-6 sim.memb.SYX.Count = 20096*mem_factor sim.memb.SNP25.Count = 26686*mem_factor if cam_present: sim.cytosol.CaM[N0, C0].Conc = 6e-05 #Wilhelm 2014 print("CALMODULIN PRESENT") else: sim.cytosol.CaM[N0, C0].Conc = 0 print("CALMODULIN NOT PRESENT") sim.cytosol.CaN.Conc = 5e-06 sim.cytosol.DYNp.Count = 0 #20 #plus 40 in initial rafts sim.cytosol.CDK5.Conc = 1e-06 sim.cytosol.Rab3.Conc = 0.00012585 sim.cytosol.SYN1.Conc = 2.137e-05 print('Added Syndapin1 to cytosol:', sim.cytosol.SYN1.Count) #add TOMOSYN sim.cytosol.TOMO_p.Count = tomo_init sim.TETS(actin_tets).actin.Count = 1 fusion_events_tot = 0 #check release indicator in cleft pre and post run rel_ind_count_pre = 0 rel_ind_count_post = 0 #create empty list to contain recycled vescicles recycled_ves_free = [] recycled_ves_all = [] #dictionary of Rafts to Vesicle indices (connecting endocytosis) raft_to_vesicle = {} #record total raft endocytosis events total_raft_endo = 0 total_time = 0 rel_ind_count_pre_ap = sim.cleft.REL_IND.Count all_ves_pre_ap = VesicleList(sim.cytosol.ves) #####SCALE DIFFUSION OF SYNTAXIN AND SNAP25##################### sim.TRIS(azone_tris).diff_SYX.D = 0.2429e-12*snare_diff_scale sim.TRIS(azone_tris).diff_SYX_M18.D = 0.2429e-12*snare_diff_scale sim.TRIS(azone_tris).diff_SNP25.D = 0.651e-12*snare_diff_scale action_potentials_fired = 0 #Save release probs ap_n = len(pulse_times) rel_probs = np.zeros(ap_n) #10 APs #Save release dock sites #rel_tris = [] #10 APs #count fusions from "recycling" vs "reserve" pool REC_FUSIONS = [] RES_FUSIONS = [] #get all initial vesicle indices init_vesicle_ind = VesicleList(sim.cytosol.ves) #build list for vesicles (f)used from initial pools init_vesicles_used = [] init_rec_vesicles_used = [] init_nonrec_vesicles_used = [] new_vesicles_used = [] fused_ind_all = [] #record total recycled vesicles recycled_vesicles_tot = 0 #list of new rafts new_rafts = [] filled_rafts = [] #create array of time points tpnts = np.arange(0.0, INT, DT) #find number of time points ntpnts = tpnts.shape[0] print('Number of timepoints =', ntpnts) if MPI.rank == 0 and exportParam: from steps.utils import ExportParameters ExportParameters(sim, 'Vesicle_Cycle', method='pdf', hideColumns=['Defined in', 'valence Units'], unitsToSimplify=[ 'uM', 'uM^-1 s^-1', 'mV', 'um^2 s^-1', 'pS', 'um', 'um^2' ], numPrecision=5, ) for i, t in enumerate(tpnts): if t >= add_tethers_time: #create tether paths for each dock triangle print("CREATING TETHER PATHS...") print('ADDING VESICLES TO TETHER PATHS...') tether_pull_rate_m_s = 200.0 / 60 * 1e-06 # um / min -> m / s print(f'TETHER RATE: {tether_pull_rate_m_s} m/s') tether_paths = [] for tri in dock_tris: path = sim.addVesiclePath(f'actin_{tri.idx}') pos1, pos2 = dock_tri_to_tether_path[tri] p2 = path.addPoint(pos2) p1 = path.addPoint(pos1) print(f'{path.idx} PATH LENGTH: {np.linalg.norm(pos1 - pos2) * 1e9} nm') #connect path points path.addBranch(p2, {p1: 1.0}) path.addVesicle(ves, tether_pull_rate_m_s, dependencies=8 * Rab3.v, stoch_stepsize=2e-9) print('Added vesicle to path:', path.idx) print('VESICLES ADDED TO TETHER PATHS') print("TETHER PATHS CREATED") add_tethers_time = math.inf print(t) if t >= pka_act_time: pka_act_time = math.inf sim.cytosol.PKA.Count = 60 if t >= camkii_deact_time: camkii_deact_time = math.inf #get all vesicles and rafts before the next time step to test for new vesicles by endoctosis all_ves_prerun = VesicleList(sim.cytosol.ves) raft_prerun = RaftList(sim.memb.raft) raft_positions_prerun = {raftref: np.array(raftref.Pos) for raftref in raft_prerun} #get number of exocytosis events pre-run exo_extent_pre = sum(sim.ALL(Exocytosis).Extent) #count release indicators in cleft pre run rel_ind_count_pre = sim.cleft.REL_IND.Count print('Exo_extent_pre =', rel_ind_count_pre) ##########RUN TIME STEP########### start = time.time() sim.run(t) end = time.time() #count release indicators in cleft post run rel_ind_count_post = sim.cleft.REL_IND.Count print("rel_ind_count_post:", rel_ind_count_post) exo_extent_post = sum(sim.ALL(Exocytosis).Extent) print('Exo_extent_post = ', rel_ind_count_post) print("ACTION POTENTIALS FIRED: ", action_potentials_fired) fusion_events = rel_ind_count_post - rel_ind_count_pre print("fusion_events:", fusion_events) fusion_events_tot += fusion_events print('fusion_events_tot =', fusion_events_tot) time_took = end - start print('Took:', time_took) if i != 0: total_time += time_took mean_time = total_time / i print('Mean time:', mean_time) print('Time remaining (hours):', (ntpnts - i) * mean_time / 3600) #move any docked vesicles to their docking site #get list of all vesicles (some may have appeared by endocytosis) #get list of newly formed vesicles all_ves = VesicleList(sim.cytosol.ves) new_ves = [v for v in all_ves if v not in all_ves_prerun] for v in new_ves: #add REL_IND to vesicle v('in').REL_IND.Count = 1 #check that all docked_ves still exist (i.e. haven't fused) for v in all_ves_prerun: if v not in all_ves: FUSED_VES.append(v) if use_efield: if round(t * 1000) in pulse_times: sim.membrane.Potential = 40e-3 print('Action potential ON') if round(t * 1000) in pulse_times_off: sim.membrane.Potential = init_pot print('Action potential OFF') if round(t * 1000) in check_release_times_pre: rel_ind_count_pre_ap = sim.cleft.REL_IND.Count all_ves_pre_ap = VesicleList(sim.cytosol.ves) if round(t * 1000) in check_release_times: all_ves_post_ap = VesicleList(sim.cytosol.ves) rel_ind_count_post_ap = sim.cleft.REL_IND.Count fusions = rel_ind_count_post_ap - rel_ind_count_pre_ap if fusions != 0: rel_probs[action_potentials_fired] = 1 #get all current vesicles to check for fusion fused_ind = [] for v in all_ves_pre_ap: if (v not in all_ves_post_ap): fused_ind.append(v) fused_ind_all.append(v) #add fused vesicle to used vesicle lists print('FUSED VESICLES:', fused_ind) for v in fused_ind: if v in init_vesicle_ind: init_vesicles_used.append(v) print(v, 'is an init vesicle type') if v in rec_ves_init: init_rec_vesicles_used.append(v) print(v, 'is a recycling vesicle type') if v in nonrec_ves_init: init_nonrec_vesicles_used.append(v) print(v, 'is a reserve vesicle type') if v not in init_vesicle_ind: new_vesicles_used.append(v) print(v, 'is a new vesicle type') print(v, 'is not in the list', nonrec_ves_init) print('init_nonrec_vesicles_used', init_nonrec_vesicles_used) #add indices to ves_docktris #create a new Rafts for each fused vesicle count = 0 attempts = 0 print('CREATING NEW RAFT') while count < fusions: rand_tri = random.choice(endo_tris) print('RAND TRI SELECTED:', rand_tri) raftref = sim.TRI(rand_tri).addRaft(raft) print('INDEX: ', raftref) if (raftref.exists()): print('ADDING SPECS TO NEW RAFT') raftref.AP180.Count = 69 raftref.AP2.Count = 27 raftref.Rab3.Count = 10 raftref.DYN_AD.Count = 1 raftref.ves_CXN_site.Count = 1000 raftref.ves_m13_site.Count = 1000 raftref.ves_m18_site.Count = 1000 raftref.ves_syndap_site.Count = 1000 raftref.ves_asnap_site.Count = 1000 raftref.ves_nsf_site.Count = 1000 count += 1 new_rafts.append(raftref) else: attempts+=1 print('RAND TRI SELECTION ATTEMPTS:', attempts) continue else: rel_probs[action_potentials_fired] = 0 action_potentials_fired += 1 # generate list of current docked vesicles docked_ves = [] for v in all_ves: #check immobility if v.Immobility != 0: # ONLY DOCKED VESICLES ARE IMMOBILE IN rec_ves_ind surf_actin_n = sum(v('surf').LIST(synapsin_actin, Rab3_TOMO_p_synapsin_actin, Rab3_TOMO_synapsin_actin).Count) if surf_actin_n == 0: #Check not a non-recycling vesicle bound to actin ves_pos = v.Pos min_dist_ind_2 = np.argmin([np.linalg.norm(tri.center - ves_pos) for tri in dock_tris]) dock_pos = dock_positions[min_dist_ind_2] # only move vesicle if closer enough to dock site (i.e. not actin bound) if np.linalg.norm(ves_pos - dock_pos) < 100e-9: print("Attempted new position:", dock_pos) v.Pos = dock_pos new_pos = v.Pos # test vesicle has actually been moved to dock site (i.e. not blocked by another vesicle) if np.linalg.norm(new_pos - dock_pos) < 1e-09: docked_ves.append(v) print('Ves current pos:', ves_pos) print('Ves new pos:', new_pos) print('Dock ves ind:', docked_ves) #remove dock ves from nonrec_ves (if docked) for d in docked_ves: if d in nonrec_ves: nonrec_ves.remove(d) if d in rec_ves: rec_ves.remove(d) for d in FUSED_VES: if d in nonrec_ves: nonrec_ves.remove(d) if d in nonrec_ves_init: if d not in RES_FUSIONS: RES_FUSIONS.append(d) if d in rec_ves: rec_ves.remove(d) if d in rec_ves_init: if d not in REC_FUSIONS: REC_FUSIONS.append(d) # create dictionary of docked vesicles and their dock sites (ves -> dock_tri) ves_docktris = {v: min(dock_tris, key=lambda t: np.linalg.norm(t.center - v.Pos)) for v in docked_ves} #find Raft each new vesicle came from. rafts = RaftList(sim.memb.raft) rafts_endocytosed = [] for r in raft_prerun: if r not in rafts: rafts_endocytosed.append(r) total_raft_endo += len(rafts_endocytosed) print('Rafts endocytosed:', total_raft_endo) for v in new_ves: if len(rafts_endocytosed) > 0: closest_raft = min(rafts_endocytosed, key=lambda r: np.linalg.norm(raft_positions_prerun[r] - v.Pos)) raft_to_vesicle[closest_raft] = v rafts_endocytosed.remove(closest_raft) print(f'Raft {closest_raft} formed vesicle {v}') #######RELEASE PROBABILITY TEST#################################################### if t >= rel_prob_test_time: rel_prob_test_time = math.inf # add SNARE_SYT_CXN complexes to each docked vesicle for v in docked_ves: print('Priming vesicle:', v) v('surf').SNARE_syt_CXN.Count = 4 # remove RIM and related structures from vesicle dock sites v('surf').RIM_M13_Rab3.Count = 0 v('surf').RIM_M13_Rab3_SYX_M18.Count = 0 v('surf').RIM_M13_Rab3_SYX_M18_SNP25.Count = 0 v('surf').SNARE.Count = 0 v('surf').SNARE_syt.Count = 0 v('surf').SNARE_syt_CXN_Ca.Count = 0 v('surf').SNARE_syt_CXN_Ca2.Count = 0 v('surf').SNARE_syt_CXN_Ca3.Count = 0 v('surf').SNARE_syt_CXN_bCa.Count = 0 v('surf').SNARE_syt_CXN_bCa2.Count = 0 v('surf').SNARE_syt_CXN_Ca_bCa.Count = 0 v('surf').SNARE_syt_CXN_Ca_bCa2.Count = 0 v('surf').SNARE_syt_CXN_Ca2_bCa.Count = 0 v('surf').SNARE_syt_CXN_Ca2_bCa2.Count = 0 v('surf').SNARE_syt_CXN_Ca3_bCa.Count = 0 v('surf').SNARE_syt_CXN_Ca3_bCa2.Count = 0 # set normal diffusion rate for dock vesicles for tet in dock_ves_init_tets.values(): sim.TET(tet).ves.Dcst = ves_diff_k print('SET DOCK TET DIFF TO ZERO:', tet) print('Dock ves ind:', docked_ves) ################################################################################### #shift all SNARE complexes to pole of vesicle (closest to membrane) for v in docked_ves: xd, yd, zd = ves_docktris[v].center - v.Pos theta = np.arctan2(yd, xd) phi = np.arccos(zd / ves_radius) v('surf').SNARE.PosSpherical = [theta, phi] v('surf').SNARE_syt.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca2.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca3.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_bCa.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_bCa2.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca_bCa.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca_bCa2.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca2_bCa.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca3_bCa.PosSpherical = [theta, phi] v('surf').SNARE_syt_CXN_Ca3_bCa2.PosSpherical = [theta, phi] v('surf').RIM_M13_Rab3.PosSpherical = [theta, phi] v('surf').RIM_M13_Rab3_SYX_M18.PosSpherical = [theta, phi] v('surf').RIM_M13_Rab3_SYX_M18_SNP25.PosSpherical = [theta, phi] # find all recycling vesicles not docked rec_ves_free = [v for v in all_ves if (v not in docked_ves) and (v not in nonrec_ves)] #separate non-recycling vesicles into free and clustered nonrec_ves_free = [] nonrec_ves_clust = [] actin_bound_ves = [] total_link_specs = 0 for v in nonrec_ves: dimer_count = getVesicleLinkSpecs(v) total_link_specs += dimer_count if dimer_count < 1: nonrec_ves_free.append(v) else: nonrec_ves_clust.append(v) ves_actin_count = sum(v('surf').LIST(synapsin_actin, Rab3_TOMO_p_synapsin_actin).Count) if ves_actin_count != 0: actin_bound_ves.append(v) #find recycled vesicles recycled_ves_free += [v for v in new_ves if (v not in docked_ves) and (v not in FUSED_VES)] #check no recycled vesicles have docked rec_docked = [v for v in recycled_ves_free if (v in docked_ves) or (v in FUSED_VES)] for v in rec_docked: recycled_ves_free.remove(v) #remove recycled vesicles in rec_ves_free ves_free_to_remove = [v for v in rec_ves_free if v in recycled_ves_free] for v in ves_free_to_remove: rec_ves_free.remove(v) #concatenate rec_ves_free and nonrec_ves_free to get all free vesicles all_ves_free = rec_ves_free + nonrec_ves_free print('Number of docked vesicles =', len(docked_ves)) print('Number of recycled vesicles =', len(recycled_ves_free)) #sanity check print('Total vesicles:', len(all_ves)) ves_sum = docked_ves + all_ves_free + recycled_ves_free print('Summed vesicles:', len(ves_sum) + len(nonrec_ves_clust)) print('rec_ves_free:', len(rec_ves_free)) print('nonrec_ves_free:', len(nonrec_ves_free)) print('all_ves_free:', len(all_ves_free)) rafts_n = len(RaftList(sim.memb.raft)) print("N rafts:", rafts_n) print('Number of SYB in rafts:', sim.memb.raft.SYB.Count) print('SYB in membrane =', sim.memb.SYB.Count) #####calculate SYX and SNAP25 in AZONE#### print('SYX in AZone:', sum(sim.TRIS(azone_tris).LIST(SYX, SYX_M18).Count)) print('SNAP25 in AZone:', sum(sim.TRIS(azone_tris).SNP25.Count)) endo_events = raft_count_init - rafts_n print('Total endo events:', endo_events) print('Ca4CaM count =', sim.cytosol.CaM[N2, C2].Count) print('CaN_CaM count =', sim.cytosol.CaN_CaM.Count) print('DYNpp count =', sim.cytosol.DYNpp.Count) print('DYN count =', sim.cytosol.DYN.Count) print('DYN MEM count =', sum(sim.memb.LIST(DYN_SYN1, DYN_SYN1_CDK5).Count)) synapsin_n = sum(sim.cytosol.LIST(synapsin, synapsin_actin).Count) print('Bound synapsin:', synapsin_total - synapsin_n) synapsin_cluster_perc = (1 - (synapsin_n / synapsin_total)) * 100 print('Percentage SYNAPSIN in cluster:', synapsin_cluster_perc) print('TOTAL CXN in CYTOSOL:', sim.cytosol.CXN.Count) print('TOTAL CXN in AXON:', sim.axon.CXN.Count) print("FUSION COUNT:", fusion_count) print('TOTAL Ca in CYTOSOL:', 1e06 * sim.cytosol.Ca.Conc) print('TOTAL CaM[N2, C2] in CYTOSOL:', sim.cytosol.CaM[N2, C2].Count) print('TOTAL AC18 in CYTOSOL:', sim.cytosol.AC18.Count) print('TOTAL AC18_CaM in CYTOSOL:', sim.cytosol.AC18_CaM.Count) print('TOTAL cAMP in CYTOSOL:', sim.cytosol.cAMP.Count) print('TOTAL R2C2 in CYTOSOL:', sim.cytosol.R2C2.Count) print('TOTAL R2C2_cAMP in CYTOSOL:', sim.cytosol.R2C2_cAMP.Count) print('TOTAL PKA in CYTOSOL:', sim.cytosol.PKA.Count) print('Number of vesicles bound to actin =', len(actin_bound_ves)) syn_dimers_n = sum(sim.cytosol.ves('surf').ALL(LinkSpecies).Count) print('Number of synapsin dimers =', syn_dimers_n) print('NON-CLUSTERED VESICLES:', len(nonrec_ves_free)) print('CLUSTERED VESICLES:', len(nonrec_ves_clust)) print('TOTAL PHOSPHO SYNAPSIN in CYTOSOL:', sim.cytosol.synapsin_p.Count) if MPI.rank == 0: sd_val = recorded_values.data[-1, -1, 16] print('Number of disassembled cis-SNAREs:', sd_val) print('Fused vesicles: ', sorted(fused_ind_all, key=lambda vr: vr.idx)) if MPI.rank == 0: print('Total phosho synapsins: ', recorded_values.data[-1, -1, 21]) print('Total rafts:', sim.memb.raft.Count) total_dynamin_cytosol = sum(sim.cytosol.LIST(DYN, DYNp, DYN_SYN1).Count) print('Total dynamin in cytosol:', total_dynamin_cytosol) total_dynamin_membrane = sum(sim.memb.LIST(DYN, DYNp, DYN_SYN1).Count) print('Total dynamin in membrane:', total_dynamin_membrane) # Dynamin in rafts DYNpp_raft = sum(sim.memb.raft.LIST(DYNpp, CaN_DYNpp).Count) DYNp_raft = sum(sim.memb.raft.LIST(DYNp, CaN_DYNp).Count) DYN_raft = rs.memb.raft.DYN.Count DYN_SYN1_raft = sum(sim.memb.raft.LIST(DYN_SYN1, DYN_SYN1_CDK5).Count) total_dynamin_rafts = DYNpp_raft + DYNp_raft + DYN_raft + DYN_SYN1_raft print('Total dynamin in rafts:', total_dynamin_rafts) print('DYNpp in rafts:', DYNpp_raft) print('DYNp in rafts:', DYNp_raft) print('DYN in rafts:', DYN_raft) print('DYN_SYN1 in rafts:', DYN_SYN1_raft) # check dynamin saturation and add to raft as necessary (only one per time step in chronological order) print('Total new rafts: ', len(new_rafts)) print('Total filled rafts: ', len(filled_rafts)) if total_dynamin_rafts < 60: for raftref in new_rafts: ves_protein_count = raftref.SYB.Count + raftref.syt.Count if ves_protein_count > 93: raftref.DYNp.Count = 1 raftref.DYN_AD.Count = 0 new_rafts.remove(raftref) filled_rafts.append(raftref) break #maintain RIM_M13 in dock tris dock_tris_occupied = list(ves_docktris.values()) for tri in dock_tris: if tri not in dock_tris_occupied: sim.TRI(tri).RIM_M13.Count = 4 for tri in azone_and_endo_tris: if tri not in dock_tris: sim.TRI(tri).RIM_M13.Count = 0 #separate vesicles into RECYCLING and RESERVE POOLS #create lists of Rab3 counts RAB3_dict = sim.VESICLES(sim.cytosol.ves('surf')).Rab3.Count VES_RAB3_ALL = list(RAB3_dict.values()) VES_RAB3_REC = [RAB3_dict[v.idx] for v in rec_ves] VES_RAB3_RES = [RAB3_dict[v.idx] for v in nonrec_ves] custom_values.save([ len(nonrec_ves_clust), len(nonrec_ves_free), len(docked_ves), len(init_vesicles_used), len(init_rec_vesicles_used), len(init_nonrec_vesicles_used), len(new_vesicles_used), len(init_rec_vesicles_used) + len(init_nonrec_vesicles_used) + len(new_vesicles_used), total_link_specs, VES_RAB3_ALL, VES_RAB3_REC, VES_RAB3_RES, list(rel_probs), ]) if LOG_FILE is not None: LOG_FILE.flush() if checkpoint_mode in ['checkpoint', 'both']: if checkpoint_mode == 'both': checkpoint_path = checkpoint_path_2 # Checkpoint the state of the solver sim.checkpoint(checkpoint_path) # Also checkpoint the state of the script variables def checkpoint_vesraft_list(f, lst): pickle.dump([(vesref._type, vesref.idx) for vesref in lst], f) pkl_path = checkpoint_path + '_script_state.pkl' with open(pkl_path, 'wb') as f: pickle.dump(dock_positions, f) pickle.dump({(vesref._type, vesref.idx): tet.idx for vesref, tet in dock_ves_init_tets.items()}, f) veslists = [ nonrec_ves, nonrec_ves_init, rec_ves, recycled_ves_free, recycled_ves_all, init_vesicle_ind, init_vesicles_used, init_rec_vesicles_used, init_nonrec_vesicles_used, new_vesicles_used, fused_ind_all, REC_FUSIONS, RES_FUSIONS, rec_ves_init, all_ves_pre_ap, ] for lst in veslists: checkpoint_vesraft_list(f, lst) checkpoint_vesraft_list(f, new_rafts) checkpoint_vesraft_list(f, filled_rafts) checkpoint_vesraft_list(f, raft_to_vesicle.keys()) checkpoint_vesraft_list(f, raft_to_vesicle.values()) pickle.dump(( fusion_events_tot, rel_ind_count_pre, rel_ind_count_post, total_raft_endo, total_time, action_potentials_fired, ap_n, rel_probs, recycled_vesicles_tot, raft_count_init, synapsin_total, rel_ind_count_pre_ap, ), f) if LOG_FILE is not None: LOG_FILE.close()