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"Applications" - Sims / Solver Name
Scott_Fraley_Rangamani_YAP_TAZ_model_2021(... prangamani

None

02/13/21
SA 314 2xD Fig 5,...
Fully-Implicit Finite Volum...
"SA 314 2xD Fig 5,6" - R 20 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 415 2xD Fig 5,6" - R 23 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 490 2xD Fig 5,6" - R 25 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 250 2xD Fig 5,6" - R 18 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 200 2xD Fig 5,6" - R 16 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Compartmental model" - Parameter scan over stiffness
Combined Stiff Solver (IDA/CVODE)
Scott_Fraley_Rangamani_YAP_TAZ_model_2021 ... prangamani

None

02/13/21
SA 314 2xD figure...
Fully-Implicit Finite Volum...
"SA 314 2xD figure 5,6" - R 20 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" R10 2D figure 4" - R 10 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 490 2xD figure 5,6" - R 25 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 415 2xD figure 5,6" - R 23 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 250 2xD figure 5,6" - R 18 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R13 2D figure 4" - R 13 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 314 3D figure 5,6" - New SA 314 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 415 3D figure 5,6" - New SA 415 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 490 3D figure 5,6" - New SA 490 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 250 3D figure 5,6" - New SA 250All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 200 3D figure 5,6" - New SA 200 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"SA 200 2xD figure 5,6" - R 16 Bot 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R15 LD 0.5 Figure 7" - Copy of Simulation88
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Compartmental model" - Parameter scan over stiffness
Combined Stiff Solver (IDA/CVODE)
"Compartmental model" - Parameter scan over cytosolic stiffness varying exponent
Combined Stiff Solver (IDA/CVODE)
"Compartmental model" - Parameter scan over cytosolic stiffness varying p
Combined Stiff Solver (IDA/CVODE)
"R15LD 1.5Figure 7" - Simulation113
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R13 LD 1.5 Figure 7" - Simulation114
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R13 LD 0.5 Figure 7" - Simulation117
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R16 LD 1.5Figure 7" - Simulation126
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R16 LD 1.5Figure 7" - Copy of Simulation126
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R16 LD 0.5 Figure 7" - Simulation131
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R10 Bottom wide Figure 7" - Simulation135
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R10 LD 0.5 Figure 7" - Simulation138
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R15 3D Figure 3, 4, and S7" - R 15 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R15 3D Figure 3, 4, and S7" - R 15 All 0.1,5.7,70E6 with different FAK diffusion
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R13 3D figure 4" - R 13 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R10 3D figure 4" - R 10 All 0.1,5.7,70E6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R15 2D Fig 3, 4, and S7" - R15 2D 0.1, 5.7, 7e6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R15 2D Fig 3, 4, and S7" - R15 2D 7e6 with different FAK diffusion
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R16 LD 1Figure 7" - Simulation22
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R-25 FAK diffusion variation 3D substrate stiffness Figure S7" - R 25 3D 70E6 FAK diffusion 0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R-25 FAK diffusion variation 3D substrate stiffness Figure S7" - R 25 3D 70E6 FAK diffusion 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R-25 FAK diffusion variation 3D substrate stiffness Figure S7" - R 25 3D 70E6 FAK diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R-25 FAK diffusion variation 2D substrate stiffness Fig S7" - R 25 2D varying FAK diffusion 0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R-25 FAK diffusion variation 2D substrate stiffness Fig S7" - R 25 2D varying FAK diffusion 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R-25 FAK diffusion variation 2D substrate stiffness Fig S7" - R 25 2D varying FAK diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Energy-production-pathway-reduced-model-01... nasrin 34396153 02/24/21
Tubular...
Fully-Implicit Finite Volum...
"Tubular" - Simulation24
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"No Cristae" - Simulation86
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"No Cristae" - Simulation87
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Lamellar" - Simulation166
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Lamellar" - Copy of Simulation166
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"2D_15_Cristae" - Simulation233
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"2D_15_Cristae" - Simulation234
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"2D_5_Cristae" - Simulation233_1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"2D_5_Cristae" - Simulation234_1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
NucleationMechanism AaronRosenbloom 34509503 10/14/21
Simulations of Se...
Combined Stiff Solver (IDA/...
"Simulations of Sept and McCammon and this paper" - Sept and McCammon 2.5 uM
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - Sept and McCammon 10 uM
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - This paper 1 uM
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - This paper 2.5 uM
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - This paper 10 uM
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - 7.5% pyrenyl-actin
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - 15% pyrenyl-actin
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - Sept and McCammon 1 uM
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - 25% pyrenyl-actin
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - 50% pyrenyl-actin
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - 75% pyrenyl-actin
Combined Stiff Solver (IDA/CVODE)
"Simulations of Sept and McCammon and this paper" - 100% pyrenyl-actin
Combined Stiff Solver (IDA/CVODE)
SpermCalcium Juliajessica 34360784 07/24/21
Application0...
Fully-Implicit Finite Volum...
"Application0" - Calcium diffusionvariationosc
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Kerbai_PLoSone_2021_teardrop_polarization_... KerbaicBITE 33735291 04/02/21
real cell...
Fully-Implicit Finite Volum...
"real cell" - simulation3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"real cell" - simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"real cell" - simulation2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Kerbai_PLoSone_2021_teardrop_polarization_... KerbaicBITE 33735291 03/25/21
real cell...
Fully-Implicit Finite Volum...
"real cell" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"real cell" - Simulation2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
5HT7_Jang_2020 wojang 33199589 09/16/20
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Histamine-RhoA Model_Final3 jzz002 32881857 03/06/20
Application1...
Combined Stiff Solver (IDA/...
"Application1" - Simulation 1
Combined Stiff Solver (IDA/CVODE)
Histamine-RhoA Model_FInal jzz002 32881857 04/03/20
Application1...
Combined Stiff Solver (IDA/...
"Application1" - Simulation 1
Combined Stiff Solver (IDA/CVODE)
Nosbisch chemotaxis 2020 jnosbis 32255775 01/30/20
Symmetric Geometr...
Fully-Implicit Finite Volum...
"Symmetric Geometry" - Fig 2A: PFL 1 scan 0% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2A: PFL 1 scan 3% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2A: PFL 1 scan 10% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2A: PFL 1 scan 30% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2A: PFL 1 scan 67% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2B: PFL 1 scan without MARCKS 0% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2B: PFL 1 scan without MARCKS 3% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2B: PFL 1 scan without MARCKS 10% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2B: PFL 1 scan without MARCKS 30% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 2B: PFL 1 scan without MARCKS 67% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3A: M and Mp diffusivity scan x 0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3A: M and Mp diffusivity scan x 0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3A: M and Mp diffusivity scan x 0.5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3A: M and Mp diffusivity scan x 2.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3A: M and Mp diffusivity scan x 5.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3A: M and Mp diffusivity scan x 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3B: pT and mT diffusivity scan x 0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3B: pT and mT diffusivity scan x 0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3B: pT and mT diffusivity scan x 0.5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3B: pT and mT diffusivity scan x 2.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3B: pT and mT diffusivity scan x 5.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 3B: pT and mT diffusivity scan x 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 5B: 0.3 x kDAGK scan 10% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 5B: 3.0 x kDAGK scan 10% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 5D: 3.0 x kDAGK scan 3% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 5E: Variation of DAG and PA scan x 0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 5E: Variation of DAG and PA scan x 0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 5E: Variation of DAG and PA scan x 0.5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 6A: PFL 2 + MARCKS
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 6B: PFL 1+ PFL 2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig 6C: PFL 1+ PFL 2 + MARCKS
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kon,e
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans koff,e
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans epsilon
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans KPA
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans khyd,PLC
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kpm
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kdpm
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kbasal,dp
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kDAGK
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kPAP
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kon,c
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans koff,c
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kdpc
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans kpc
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S4: Parameter scans Vsynth,dp
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 2 + MARCKS, kDAGK
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 2 + MARCKS, KPLD
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 1 + PFL 2, kDAGK
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 1 + PFL 2, KPA
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 1 + PFL 2, KPLD
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 1 + PFL 2 + MARCKS, kDAGK
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 1 + PFL 2 + MARCKS, KPA
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Symmetric Geometry" - Fig S5: PFL 1 + PFL 2 + MARCKS, KPLD
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4B: PFL 1 scan
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4C: M and Mp diffusivity scan x 0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4C: M and Mp diffusivity scan x 0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4C: M and Mp diffusivity scan x 0.5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4C: M and Mp diffusivity scan x 2.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4C: M and Mp diffusivity scan x 5.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4C: M and Mp diffusivity scan x 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Back end blunted scan 3% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Back end blunted scan 10% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Back end blunted scan 30% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Back end blunted scan 67% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Front end blunted scan 3% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Front end blunted scan 10% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Front end blunted scan 30% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Asymmetric Geometry" - Fig 4D: Front end blunted scan 67% gradient
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
PI cycle Figure 4 & S4 Myeong 33186442 09/18/20
modeling PI cycle...
Combined Stiff Solver (IDA/...
"modeling PI cycle" - 4K acceleration backbone
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 4K acceleration InsP3_LIBRA
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 5K acceleration backbone
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 4K acceleration DAG_C1A
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 5K acceleration InsP3_LIBRA
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 5K acceleration DAG_C1A
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - PLC decrease DAG_C1A
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - PLC decrease backbone
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - PLC decrease InsP3_LIBRA
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 4P and 5P decrease backbone
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 4P and 5P decrease InsP3_LIBRA
Combined Stiff Solver (IDA/CVODE)
"modeling PI cycle" - 4P and 5P decrease DAG_C1A
Combined Stiff Solver (IDA/CVODE)
PI cycle Figure 6, 7 & S9 Myeong 33186442 09/18/20
Modeling PI cycle...
Combined Stiff Solver (IDA/...
"Modeling PI cycle" - S Figure 9D. InsP3_LIBRA
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - S Figure 9A. PtdIns4P_M_P4M
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - Backbone Figure 7
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - S Figure 9E. DAG_C1A
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - S Figure 9C. PH domain
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - S Figure 9B. FAPP1
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - Figure 6G. PtdIns4P_M_P4M Sac1
Combined Stiff Solver (IDA/CVODE)
"Modeling PI cycle" - Figure 6F. PH domain Sac1
Combined Stiff Solver (IDA/CVODE)
Minimum Stochastic Model BetaCell mgetz 33201801 07/30/20
Copy of Applicati...
Gibson (Next Reaction Stoch...
"Copy of Application0 1" - done 1 2 1
Gibson (Next Reaction Stochastic Method)
"Copy of Application0 1" - double done 1 2 1
Gibson (Next Reaction Stochastic Method)
Monkeyflower_pigmentation_v2 colreeze 32155414 11/13/19
Pattern_formation...
Fully-Implicit Finite Volum...
"Pattern_formation" - WT
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.09
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.06
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.15
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.18
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.185
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.19
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.21
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_RNAi_0.24
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.06
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.09
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.15
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - NEGAN_RNAi_0.18
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.01
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.05
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.06
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.07
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.08
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.09
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Pattern_formation" - RTO_OE_0.1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
A predictive computational model reveals t... mgetz 31017840 04/30/19
unnamed...
Combined Stiff Solver (IDA/...
"unnamed" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"unnamed" - GIV+EGFR variation
Combined Stiff Solver (IDA/CVODE)
SH2 biosensor jmhaugh 31164479 05/19/15
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Complex internalizes at turnover rate; vary koff and [SH2] 1
Combined Stiff Solver (IDA/CVODE)
"Application0" - Vary EGF, no SH2
Combined Stiff Solver (IDA/CVODE)
Surve_et_al_RAF1 pmyers1995 30586319 01/03/19
+sorafenib...
Combined Stiff Solver (IDA/...
"+sorafenib" - Fitted binding
Combined Stiff Solver (IDA/CVODE)
"-sorafenib" - 60 min
Combined Stiff Solver (IDA/CVODE)
"-sorafenib" - Fitted binding rates
Combined Stiff Solver (IDA/CVODE)
"+sorafenib after 60 min EGF pretreatment" - 60 min EGF pretreat
Combined Stiff Solver (IDA/CVODE)
"+sorafenib after 15 min EGF pretreatment" - 15 min EGF pretreat
Combined Stiff Solver (IDA/CVODE)
"+sorafenib after 30 min EGF pretreatment" - 30 min EGF pretreat
Combined Stiff Solver (IDA/CVODE)
"+sorafenib after 5 min EGF pretreatment" - 5 min EGF pretreat
Combined Stiff Solver (IDA/CVODE)
"const. active Ras-GTP, -sorafenib" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"const. active Ras-GTP, -sorafenib" - 10x Ras
Combined Stiff Solver (IDA/CVODE)
Kruse_Kohout_Hille_CiVSP mkruse 30622132 12/04/18
modelinOct2010...
Combined Stiff Solver (IDA/...
"modelinOct2010" - DFH Figures 4D and 5B "Oxo" and 6F
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figures 4C and 5A "Oxo"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 5A "UTP"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 5B "UTP"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 6B "Oxo"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 6B pipette dialysis
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 6E
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 7B
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - VSP
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 8C
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 8D "4K at resting rate"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 8D "4K turned off"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 1E
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 1F
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figures 4G and 4H
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 6B
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figures 6C and 6D
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8A except Fura, Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8A Fura
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8A Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8B except Fura, Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8C except Fura, Libra, C1
Combined Stiff Solver (IDA/CVODE)
Macrophage Cargo Capacity awillmer

None

05/30/19
Matching w/ Matla...
Combined Stiff Solver (IDA/...
"Matching w/ Matlab data" - Amiodarone
Combined Stiff Solver (IDA/CVODE)
"Matching w/ Matlab data" - Clofazimine
Combined Stiff Solver (IDA/CVODE)
"Matching w/ Matlab data" - Bupivacaine
Combined Stiff Solver (IDA/CVODE)
"Matching w/ Matlab data" - Chlorprothixene
Combined Stiff Solver (IDA/CVODE)
"Matching w/ Matlab data" - Lidocaine
Combined Stiff Solver (IDA/CVODE)
"Matching w/ Matlab data" - Celiprolol
Combined Stiff Solver (IDA/CVODE)
Mohan chemotaxis 2017 jnosbis 28700916 06/12/17
Relative_gradient...
Fully-Implicit Finite Volum...
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, DM=scan, DMp=scan
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1, konm=0, koffm=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 4
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 7
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 14
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 15
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 16
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 17
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 18
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 19
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 20
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 21
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 22
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 23
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 24
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_p67" - rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 25
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Relative_gradient_0" - rel_grad=0, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p1" - rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p1" - rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p1" - rel_grad=0.1, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p1" - rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p1" - rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1, konm=0, koffm=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p1" - rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" Relative_gradient_p3" - rel_grad=0.3, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Yeast 3D_FRAP Wasim 29205883 01/31/18
01_06_2017...
Fully-Implicit Finite Volum...
"01_06_2017" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"01_06_2017" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Falkenberg_PodocyteStability falkenbe 28301477 08/16/16
non-spatial...
Combined Stiff Solver (IDA/...
"non-spatial" - high alpha2, followed by high alpha
Combined Stiff Solver (IDA/CVODE)
"non-spatial" - high alpha2 followed by higher alpha
Combined Stiff Solver (IDA/CVODE)
"non-spatial" - low beta2 followed by highr alpha
Combined Stiff Solver (IDA/CVODE)
"extra: simple test geometry. "few fingers"" - stable - test localization
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. "few fingers"" - Copy of stable - test localization
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. "few fingers"" - Copy of Copy of stable - test localization
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - good mesh (GM0): check loc
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - GM0: try single stable point
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - short, to check details
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - My19, increase alpha z>3.5; tmax=200
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - Copy of My19, increase alpha z>3.5;
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: generate initial condition; full geometry,no LocCorr" - Copy of My19, increase alpha z>3.5; change ic
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: smaller pert region" - My19, increase alpha (7>z>13)&&(x>15);
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: smaller pert region" - Copy of My19, increase alpha (7>z>13)&&(x>15);
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: smaller pert region" - Copy of My19, increase alpha (7>z>13)&&(x>15); 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: smaller pert region" - Copy of My19, increase alpha (7>z>13)&&(x>15); 1, change ic
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: smaller pert region" - Copy of Copy of My19, increase alpha (7>z>13)&&(x>15); - later trigger
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: smaller pert region" - Copy of Copy of Copy of My19, increase alpha (7>z>13)&&(x>15); - later trigger
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: uniform" - testloc
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: uniform" - peak in alpha
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: uniform" - change ic
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: uniform" - triggger at 800
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: tests, full geometry, no LocCorr: uniform" - change ic, tr 800
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - delay 200
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - delay 40
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - delay 500 - recovered
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - low beta2 - delay 200
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - low beta2 - delay 40
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - low beta2 - delay 500 - recovered
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (a) delay3000 (st)-(p5)-(p6): still OK
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (b) low beta2 - delay 2500 (st)-(p0)-(p4): too late
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (b) low beta2 - delay 1500 (st)-(p0)-(p4): dt2=2500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (b) low beta2 - delay 2000 (st)-(p0)-(p4): dt2=3000
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (a) delay 4000 (st)-(p5)-(p6):
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (a) delay 6000 (st)-(p5)-(p6):
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - damage: p5 (IIA) ; recover delay3000
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - damage: p5 (IIA) ; recover delay4500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - damage: p0 (IIB) ; recover delay 500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - damage: p0 (IIB) ; recover delay 1500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (Ia) delay3000 (st)-(p5)-(p7)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (Ia) delay4500 (st)-(p5)-(p7)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (Ib) delay 500 (st)-(p0)-(p3)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: simple test geometry. few fingers: uniform, pert n fix" - (Ib) delay 1500 (st)-(p0)-(p3)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"non-spatial" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"extra: test, import ic: of few fingers: uniform, pert n fix" - try to copy ic
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - keep extending to SS
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (a) delay3000 - Figure 3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (a) delay4500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (Ia) delay3000
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (Ia) delay4500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (IIa) delay3000
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (IIa) delay4500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (b) delay500 - Figure6 ( i, j)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (b) delay1500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (Ib) delay500 - Figure 6 (f,g)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (Ib) delay1500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (IIb) delay500 - Figure 6 (d, e)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (IIb) delay1500
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figures 3 and 6; with SS ic: full geometry,no LocCorr" - (a) delay3000 -fast diffusion G
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z)" - keep alpha=0.32+(1+0.1*(Sin(x/2...))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z)" - keep alpha=0.32+(1+0.5*(Sin(x/2...)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z)" - keep alpha=0.32+(1 - 0.5*(Sin(x/2...))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)" - -13<z<-7, 7>x>10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)" - amplitude (1+0.1exp(-r/30))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)" - amplitude (1+0.5 exp(-r/30))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)" - amplitude (1+0.75 exp(-r/30))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)" - amplitude (1+1 exp(-r/30))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)" - amplitude (1-0.5 exp(-r/30))
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1" - -13<z < - 6.6, 7.0<x < 10.0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1" - -13<z < - 6.6, 7.0<x < 10.0 (weaker stim)
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2" - -12.8<z<-8, 1.5>x>3.5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3" - Simulation3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3" - slower diff Ga: 5um2/s, as in BJ 2008, 95:1627-1638; Biophys. J. 75:2070¿2078
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3" - faster diff Ga: 20um2/s
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4" - Simulation6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4" - weaker pert
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Jung_PNAS_2017_BiasedM1R_Figure4 jsr007 28652372 01/08/18
Deterministic...
Combined Stiff Solver (IDA/...
"Deterministic" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Jung_PNAS_2017_wildtypeM1R_figure5 jsr007 28652372 01/08/18
Deterministic...
Combined Stiff Solver (IDA/...
"Deterministic" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Dreyer_2017_AIMS Biophysics idreyer

None

08/29/17
Channel_test...
Combined Stiff Solver (IDA/...
"Channel_test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
spatial protection test- two way competiti... jjadwin 29162725 01/04/18
Application2...
Combined Stiff Solver (IDA/...
"Application2" - Simulation1
Combined Stiff Solver (IDA/CVODE)
"Application2" - Copy of Simulation1
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation2
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation3
Combined Stiff Solver (IDA/CVODE)
"Application2" - Copy of Simulation3
Combined Stiff Solver (IDA/CVODE)
spatial protection test- no flux two way c... jjadwin 29162725 01/04/18
Application2...
Combined Stiff Solver (IDA/...
"Application2" - Copy of Simulation1
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation1
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation2
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation3
Combined Stiff Solver (IDA/CVODE)
"Application2" - Simulation4
Combined Stiff Solver (IDA/CVODE)
"Application2" - Copy of Simulation4
Combined Stiff Solver (IDA/CVODE)
"Application2" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"Application2" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Wittek_et_al_JIntegrPlantBiol_2017_Phloem ... idreyer 28296205 08/29/17
Application0...
Combined Stiff Solver (IDA/...
"Application0" - A, slope_ZmSUT1
Combined Stiff Solver (IDA/CVODE)
"Application0" - standard condition
Combined Stiff Solver (IDA/CVODE)
"Application0" - D, slope_UmSRT1
Combined Stiff Solver (IDA/CVODE)
"Application0" - G, slope_BG_p
Combined Stiff Solver (IDA/CVODE)
"Application0" - K, slope_BG_f
Combined Stiff Solver (IDA/CVODE)
"Application0" - V0_p, Vrev_BG_p
Combined Stiff Solver (IDA/CVODE)
"Application0" - V0_f, Vrev_BG_f
Combined Stiff Solver (IDA/CVODE)
"Application0" - H_apo
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-250xPDEtest4 bboras 27409243 08/06/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-1000xPDEtest4 bboras 27409243 08/06/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Boras-Diffusional Study No geometry1x larg... bboras 27409243 08/04/15
Application0...
Fully-Implicit Finite Volum...
"Application0" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Application0" - Copy of Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Boras-Diffusional Study No geometry10x lar... bboras 27409243 08/04/15
Application0...
Fully-Implicit Finite Volum...
"Application0" - Copy of Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Application0" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Boras-Diffusional Study-25xPDEtest4 bboras 27409243 08/03/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-100xPDEtest7 bboras 27409243 08/03/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-10xPDEtest5 bboras 27409243 07/31/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-100xPDEtest5 bboras 27409243 07/31/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-100xPDEtest6 for i... bboras 27409243 07/31/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras-Diffusional Study-1xPDEtest5 bboras 27409243 07/31/15
Correct PDE conc....
Fully-Implicit Finite Volum...
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 75
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 300
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation6
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation7
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Simulation13
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Copy of Simulation12
Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)
"Copy of Correct PDE conc. with new geo with crop correct size" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ode" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 360000 elements
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Correct PDE conc. with new geo with crop correct size" - Simulation0 137826 elements diffusion 9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
hillelab: JungSR_PAR2_desensitization2015 jsr007 26927499 06/13/16
modelinOct2010...
Combined Stiff Solver (IDA/...
"modelinOct2010" - Figure 7
Combined Stiff Solver (IDA/CVODE)
Schott_et_al_2016 AMF Symbiosis with SWEET idreyer 27446142 08/29/17
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Simulation0
Combined Stiff Solver (IDA/CVODE)
RS_JBC2016 rsong 27605670 09/29/16
Application0...
Combined Stiff Solver (IDA/...
"Application0" - DA1.0
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1 + MMPX
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1 + BAY607550
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1 + SNAP
Combined Stiff Solver (IDA/CVODE)
hillelab: KruseVivasTraynorKaplanHille_PI-... mkruse 26818524 02/18/16
simulations...
Combined Stiff Solver (IDA/...
"simulations" - Oxo-M
Combined Stiff Solver (IDA/CVODE)
"simulations" - Oxo-M with TubbyR332
Combined Stiff Solver (IDA/CVODE)
"simulations" - VSP
Combined Stiff Solver (IDA/CVODE)
"simulations" - Oxo-M with fura-2
Combined Stiff Solver (IDA/CVODE)
"simulations" - Oxo-M with PH-PLCd1
Combined Stiff Solver (IDA/CVODE)
"simulations" - Oxo-M with LIBRAVIII
Combined Stiff Solver (IDA/CVODE)
"simulations" - Oxo-M with C1-domain
Combined Stiff Solver (IDA/CVODE)
fX_platelet_binding agolomy 26874201 01/20/16
Application0...
Fully-Implicit Finite Volum...
"Application0" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
fX_thrombus_binding agolomy 26874201 01/20/16
Application1...
Fully-Implicit Finite Volum...
"Application1" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
BEN sayak66 27271916 01/12/15
Needle...
Fully-Implicit Finite Volum...
"Needle" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Smoldyn sayak66 27271916 11/26/14
Det...
Fully-Implicit Finite Volum...
"Det" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"stoch" - Simulation0
Smoldyn (Spatial Stochastic Simulator)
Pin1_2Domains(diffKds)_monovalentligand mjr323 28652372 08/29/17
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Pin1-FLw/p131_first titration point
Combined Stiff Solver (IDA/CVODE)
Pin1_2domain(diffKds)_w_Bivalentligand(dif... mjr323 28652372 08/29/17
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Pin1_p131/p144_titrationsample1_no bivalent species
Combined Stiff Solver (IDA/CVODE)
"Application0" - Pin1_p131/p144_titrationsample1
Combined Stiff Solver (IDA/CVODE)
Pin1_2domain(diffKds)_w_Bivalentligand(dif... mjr323 28652372 08/24/17
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Pin1=196uM,IKpS163173=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - Pin1=212uM,IKpS163173=2640uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=196uM,IKpS163173=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=206uM,IKpS163173=82uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=224uM,IKpS163173=165uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=237uM,IKpS163173=330uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=250uM,IKpS163173=660uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=244uM,IKpS163173=1320uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2BR_prot_Pin1=212uM,IKpS163173=2640uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - from2brprot Pin1=196uM,IKpS131144=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=37uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=73uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=147uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=293uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=587uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=1174uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_Pin1=250uM,IKpS163173=2347uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=37uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=73uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=147uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=293uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=587uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=1174uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 131144_2br_nitrogen_Pin1=250uM,IKpS163173=2347uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - testw1branch#_2BR_prot_Pin1=196uM,IKpS163173=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - testw1branch#_2BR_prot(lessbr2)_Pin1=196uM,IKpS163173=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=13uM,IKpS163173=519uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=27uM,IKpS163173=519uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=53uM,IKpS163173=518uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=106uM,IKpS163173=516uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=213uM,IKpS163173=511uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=425uM,IKpS163173=503uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - IRAK1B_2BR_prot_Pin1=850uM,IKpS163173=485uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=37uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=73uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=147uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=293uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=587uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=1174uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=2347uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=37uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=73uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=147uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=293uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=587uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=1174uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=2347uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=196uM,IKpS163173=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=206uM,IKpS163173=82uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=224uM,IKpS163173=165uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=237uM,IKpS163173=330uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=250uM,IKpS163173=660uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=244uM,IKpS163173=1320uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel6373_refitOct_prot_Pin1=212uM,IKpS163173=2640uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=196uM,IKpS163173=44uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=206uM,IKpS163173=82uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=224uM,IKpS163173=165uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=237uM,IKpS163173=330uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=250uM,IKpS163173=660uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=244uM,IKpS163173=1320uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitOct_Ni_Pin1=212uM,IKpS163173=2640uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=206uM,IKpS163173=82uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=224uM,IKpS163173=165uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=237uM,IKpS163173=330uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=250uM,IKpS163173=660uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=244uM,IKpS163173=1320uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_refitNov_Ni_Pin1=212uM,IKpS163173=2640uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=37uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=147uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=293uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=587uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=1170uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=2347uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_testpopgrab_Ni_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_testpopcalc_Ni_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_testscalekeq_Ni_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
"Application0" - 2brmodel_testnewscalekeq_Ni_Pin1=201uM,IKpS163173=55uM
Combined Stiff Solver (IDA/CVODE)
Spine Model Final Rangamani et al PNAS 201... prangamani 27551076 08/24/16
Application0...
Combined Stiff Solver (IDA/...
"Application0" - basic simulation
Combined Stiff Solver (IDA/CVODE)
"Application0" - Arp23 variation
Combined Stiff Solver (IDA/CVODE)
"Application0" - Nuc-Sev phase
Combined Stiff Solver (IDA/CVODE)
"Application0" - cofilin variation
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaM variation
Combined Stiff Solver (IDA/CVODE)
"Application0" - Ng variation
Combined Stiff Solver (IDA/CVODE)
"Application0" - PP1 variation
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaN variation
Combined Stiff Solver (IDA/CVODE)
"Application0" - Rho GTP level
Combined Stiff Solver (IDA/CVODE)
"Application0" - sensitivity kage
Combined Stiff Solver (IDA/CVODE)
"Application0" - sensitivity with cofilin
Combined Stiff Solver (IDA/CVODE)
"Application0" - sensitivity with Arp2/3
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaN sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaMKII-f-actin
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaMKII-G-actin sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - cdc42GTP sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - Cdc42 GEF sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - I1 sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - LIMK sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - MLC sensitivity
Combined Stiff Solver (IDA/CVODE)
"Application0" - Myoppase active sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - Myoppase sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - Ng sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - phi sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - PP1 sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - Rho GAP sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - Rho GEF sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - Rho GDP sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - ROCK sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - SSH1 sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - VO sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - w sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - WASP sens
Combined Stiff Solver (IDA/CVODE)
"Application0" - k-arp23 inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - k-calcineurin-activation-by-cam
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcap
Combined Stiff Solver (IDA/CVODE)
"Application0" - kdeg
Combined Stiff Solver (IDA/CVODE)
"Application0" - knuc
Combined Stiff Solver (IDA/CVODE)
"Application0" - ksev
Combined Stiff Solver (IDA/CVODE)
"Application0" - kshrink
Combined Stiff Solver (IDA/CVODE)
"Application0" - KAPPA
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat1
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat2
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat 3
Combined Stiff Solver (IDA/CVODE)
"Application0" - Kcat CaMKII activation by CAM
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat camkii inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat cd42 acticaion
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat cdc42 gef activation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat cdc42 gef inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat cdc42 hydrolysis
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat cofilin activation through ssh1
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat cofilin inactivation through LIMK
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat i1 inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat limk rock
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat mlc rock
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat myoppase dephos
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat myoppase rock1
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat myoppase rock
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat pp1 by camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat rhogap camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat rho gef camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - kcat Rho gtp by Rho gef
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf arp23 activation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf CaM NG
Combined Stiff Solver (IDA/CVODE)
"Application0" - camkii f-actin
Combined Stiff Solver (IDA/CVODE)
"Application0" - camkii g-actin
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf cdc42 wasp
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf MLC phosphorylation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf myoppase basal
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf rock act by rho
Combined Stiff Solver (IDA/CVODE)
"Application0" - kf rock inact
Combined Stiff Solver (IDA/CVODE)
"Application0" - Km
Combined Stiff Solver (IDA/CVODE)
"Application0" - km1 camkii activation by cam
Combined Stiff Solver (IDA/CVODE)
"Application0" - km1 PP1 activation by i1
Combined Stiff Solver (IDA/CVODE)
"Application0" - km2
Combined Stiff Solver (IDA/CVODE)
"Application0" - km can cam
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaN inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - CaMKii activation by CaM
Combined Stiff Solver (IDA/CVODE)
"Application0" - Km CaMKII inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - km cdc42 activation
Combined Stiff Solver (IDA/CVODE)
"Application0" - km cdc42 gef activation
Combined Stiff Solver (IDA/CVODE)
"Application0" - km cdc42 gef
Combined Stiff Solver (IDA/CVODE)
"Application0" - km cdc42 hydrolysis
Combined Stiff Solver (IDA/CVODE)
"Application0" - km cofilin actiation ssh1
Combined Stiff Solver (IDA/CVODE)
"Application0" - km i1 activation by CaN
Combined Stiff Solver (IDA/CVODE)
"Application0" - Km i1 inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - km limk activation by rock
Combined Stiff Solver (IDA/CVODE)
"Application0" - km limk inactivation by rock
Combined Stiff Solver (IDA/CVODE)
"Application0" - km mlc dephosphorylation
Combined Stiff Solver (IDA/CVODE)
"Application0" - km myoppase activation dephos
Combined Stiff Solver (IDA/CVODE)
"Application0" - km myoppase inactivation rock
Combined Stiff Solver (IDA/CVODE)
"Application0" - km pp1 inct by camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - km rho gef inactivation
Combined Stiff Solver (IDA/CVODE)
"Application0" - km rhogap camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - km rho gap pp1
Combined Stiff Solver (IDA/CVODE)
"Application0" - km rhogef camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - km rhogtp by rhogef
Combined Stiff Solver (IDA/CVODE)
"Application0" - km rhogtp hhydrolysis
Combined Stiff Solver (IDA/CVODE)
"Application0" - km ssh1 dephos
Combined Stiff Solver (IDA/CVODE)
"Application0" - km ssh1 phos camkii
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr arp activation
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr CaM binding NG
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr caMkii binding f-actin
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr camkii g-actin
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr cdc42 wasp
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr MLCp basal
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr myosin ppase basal
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr rock by rho
Combined Stiff Solver (IDA/CVODE)
"Application0" - kr rock inacivation
Combined Stiff Solver (IDA/CVODE)
KeumKruseKimHilleSuh_2016 hillelab 27222577 01/28/16
modelinOct2010...
Combined Stiff Solver (IDA/...
"modelinOct2010" - DFH Figure 5A "UTP"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 5B "UTP"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 6B "Oxo"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 6B pipette dialysis
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 6E
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 7B
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - VSP
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 8C
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 8D "4K at resting rate"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figure 8D "4K turned off"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 1E
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 1F
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figures 4G and 4H
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 6B
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figures 6C and 6D
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8A except Fura, Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8A Fura
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8A Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8B except Fura, Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - FDH Figure 8C except Fura, Libra, C1
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figures 4C and 5A "Oxo"
Combined Stiff Solver (IDA/CVODE)
"modelinOct2010" - DFH Figures 4D and 5B "Oxo" and 6F
Combined Stiff Solver (IDA/CVODE)
minepsp gregl 27783155 06/01/16
compartment...
Combined Stiff Solver (IDA/...
"compartment" - Simulation1
Combined Stiff Solver (IDA/CVODE)
Axon_FDAP marynka 27831495 11/29/16
wt uniform...
Fully-Implicit Finite Volum...
"wt uniform" - F/G=10/190, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=40-50, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=20-30 , Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=60-70, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=80-90, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=100-110, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=120-130, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=140-150, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=160-170, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=180-190, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt uniform" - Factin=40-190, Kd=0.005,0.0075
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
GF-actin FDAP marynka 27831495 08/18/16
wt D=3...
Fully-Implicit Finite Volum...
"wt D=3" - F/G=10/190, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=20-30 , Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=40-50, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=60-70, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=80-90, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=100-110, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=120-130, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=140-150, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=160-170, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=3" - Factin=180-190, Kd=0.01-0.2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation4
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation7
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"smaller+tall" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation20
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation21
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation22
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation23
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation24
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation25
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation26
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation27
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation28
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - Simulation29
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"wt D=5" - F=100 D=10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Boras_PKA-Dual bboras 25202018 06/18/15
test...
Combined Stiff Solver (IDA/...
"test" - C_kr=.23
Combined Stiff Solver (IDA/CVODE)
"test" - C_kr=23
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.0038
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.000038
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.8
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.008
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.12
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.0012
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.82
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.0082
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.00221
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=31.75
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=.3175
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=50
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=.5
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.13
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.0013
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.3
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.003
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=3
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=.03
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=230
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=2.3
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_CBD-A_mutant_B-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - free R more points
Combined Stiff Solver (IDA/CVODE)
"test" - Holo more points
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_CBD-B_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_Dual_mutant_B-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - More points free R
Combined Stiff Solver (IDA/CVODE)
"test" - More points Holo
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_Dual_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - R-C
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Free R
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_CBD-A_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - More points free R
Combined Stiff Solver (IDA/CVODE)
"test" - More points Holo
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_Dimer_mutant_B-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Holo more points
Combined Stiff Solver (IDA/CVODE)
"test" - free R more points
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Dimer_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - More points Holo
Combined Stiff Solver (IDA/CVODE)
"test" - More points free R
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Unconstrained bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-CBD-B bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-CBD-A bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Dimer bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - C_kr=.23
Combined Stiff Solver (IDA/CVODE)
"test" - C_kr=23
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.0038
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.000038
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.8
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.008
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.12
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.0012
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.82
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.0082
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.00221
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=31.75
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=.3175
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=50
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=.5
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.13
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.0013
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.3
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.003
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=3
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=.03
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=230
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=2.3
Combined Stiff Solver (IDA/CVODE)
Li2015_geometryCreatesNonlinearNuclearPKA luli 25692798 12/23/14
cAMPinput_tertiar...
Fully-Implicit Finite Volum...
"cAMPinput_tertiary3" - cAMPtertiaryEnd
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_secondary3" - cAMPsecondaryEnd
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_primary3" - cAMPprimaryEnd
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_primary1" - cAMPprimaryBegin
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_primary2" - primaryMiddle
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_secondary1" - cAMPsecondaryMiddle1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_secondary2" - cAMPsecondaryMiddle2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_tertiary1" - cAMPtertiaryMiddle1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"cAMPinput_tertiary2" - cAMPtertiaryMiddle2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
AKAP7_PLB_Binding_2PKA Marc.Rigatti 26027516 06/10/15
PLB 0.2uM...
Combined Stiff Solver (IDA/...
"PLB 0.2uM" - Simulation7
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - Simulation13
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - PDE_0.2
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - PDE_0.3
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - PDE_0.4
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - AC_0.15_PDE_0.3
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - Copy of PDE_0.4
Combined Stiff Solver (IDA/CVODE)
"PLB 5.0uM" - Copy of AC_0.15_PDE_0.3
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - Simulation2
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - AC_0.2
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - Copy of Copy of Simulation2
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - AC_0.15
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - Copy of AC_0.15
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - AC_0.15 PDE_0.2
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - Baseline AC PDE_0.2
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - Copy of AC_0.15 PDE_0.2
Combined Stiff Solver (IDA/CVODE)
"cAMP_PDE_Gs_param" - Copy of Copy of AC_0.15 PDE_0.2
Combined Stiff Solver (IDA/CVODE)
"Copy of PLB 0.2uM" - Simulation3
Combined Stiff Solver (IDA/CVODE)
"Copy of PLB 2.0uM" - Simulation4
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP low
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP ~1uM
Combined Stiff Solver (IDA/CVODE)
"PLB 2.0uM" - Simulation1
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP ~0.62uM
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP ~0.62uM increased PP
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP ~0.62uM Km PP 10 vs 2.7
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP ~0.62uM Km PP 5
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Baseline cAMP low PLB 50
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Baseline cAMP low
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Copy of Baseline cAMP low PLB 50
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Copy of Copy of Baseline cAMP low PLB 50
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Copy of Copy of Copy of Baseline cAMP low PLB 50
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Copy of Copy of Copy of Baseline cAMP low PLB 50 1
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Copy of Baseline cAMP ~0.62uM
Combined Stiff Solver (IDA/CVODE)
"PLB 38uM" - Baseline cAMP ~0.62uM Increased PP
Combined Stiff Solver (IDA/CVODE)
fXii_activation agolomy 25688860 08/31/13
Application0...
Fully-Implicit Finite Volum...
"Application0" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
CPX Binding jdittman 25809246 10/28/14
Bouton R200...
Fully-Implicit Finite Volum...
"Bouton R200" - Long Sim
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"R200 Steady" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Buffer in cylinder" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Bouton R200" - Short Sim
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
FDAP diffusion marynka 25865895 08/16/16
Application half-...
Fully-Implicit Finite Volum...
"Application half-cell" - short D= from 2 to 10 Gactin=1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Application half-cell" - Copy of D=2 - 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" half-cell-smaller+tall" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" half-cell-smaller+tall" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" half-cell-smaller+tall" - Simulation2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" half-cell-smaller+tall" - Simulation3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Application half-cell" - short D between 2 and 10 Gactin=100
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"Application half-cell" - D=2 - 10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Greenwald MIMB 2012 - Fit 1 ecg5pc 24052393 09/12/12
Application0...
Combined Stiff Solver (IDA/...
"Application0" - Simulation0
Combined Stiff Solver (IDA/CVODE)
Greenwald MIMB 2012 - Perturb ecg5pc 24052393 04/27/12
Combined Stiff Solver (IDA/...
"" - Baseline
Combined Stiff Solver (IDA/CVODE)
"" - Saturation - 25 uM FSK
Combined Stiff Solver (IDA/CVODE)
"" - Saturation - 100 uM FSK
Combined Stiff Solver (IDA/CVODE)
"" - Buffering - 1.5 uM ICUE
Combined Stiff Solver (IDA/CVODE)
"" - Buffering - 3 uM ICUE
Combined Stiff Solver (IDA/CVODE)
"" - Kinetics - 10%
Combined Stiff Solver (IDA/CVODE)
"" - Kinetics - 1%
Combined Stiff Solver (IDA/CVODE)
"" - Kinetics - 0.1%
Combined Stiff Solver (IDA/CVODE)
"" - Original Simulation
Combined Stiff Solver (IDA/CVODE)
Greenwald MIMB 2012 - Fit 1 ecg5pc 24052393 04/27/12
Combined Stiff Solver (IDA/...
"" - Fit2_results
Combined Stiff Solver (IDA/CVODE)
"" - Fit_PreTest
Combined Stiff Solver (IDA/CVODE)
Greenwald MIMB 2012 - Fit 2 ecg5pc 24052393 04/27/12
Combined Stiff Solver (IDA/...
"" - Fit_PreTest
Combined Stiff Solver (IDA/CVODE)
Greenwald MIMB 2012 - Base Model ecg5pc 24052393 04/27/12
Combined Stiff Solver (IDA/...
"" - Fit_PreTest
Combined Stiff Solver (IDA/CVODE)
"" - Fit1_results
Combined Stiff Solver (IDA/CVODE)
Podocyte Nested FFM model (copy sensitivit... sihar 24497609 07/03/13
Compart...
CVODE (Variable Order, Vari...
"Compart" - 31) PTP dephospho by PP1 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 32) MEK* dephospho by PP2A Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 32) MEK* dephospho by PP2A kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 33) MEK_ser dephospho by PP2A Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 33) MEK_ser dephospho by PP2A kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 34) MAPK* dephospho by MKP1 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 34) MAPK* dephospho by MKP1 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 35) MAPK_tyr dephospho by MKP1 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 35) MAPK_tyr dephospho by MKP1 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 36) MAPK* dephospho by MKP1* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 36) MAPK* dephospho by MKP1* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 37) MAPK_tyr dephospho by MKP1* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 37) MAPK_tyr dephospho by MKP1* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 38) MAPK* dephospho by MKP2 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 38) MAPK* dephospho by MKP2 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 39) MAPK_tyr dephospho by MKP2 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 39) MAPK_tyr dephospho by MKP2 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 40) MAPK* dephospho by PTP Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 40) MAPK* dephospho by PTP kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 41) MKP1 phospho by MAPK* cyto Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 41) MKP1 phospho by MAPK* cyto kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 42) MKP1* dephospho cyto kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 43) MKP1 degradation kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 44) MKP1* degradation kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 45) PDE phospho by PKA Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 45) PDE phospho by PKA kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 46) PDE* dephospho Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 46) PDE* dephospho kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 47) R2C2 1 kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 47) R2C2 1 kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 48) R2C2 2 kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 48) R2C2 2 kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 49) R2C2 3 kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 49) R2C2 3 kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 50) R2C2 4 kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 50) R2C2 4 kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 51) PKA release 1 kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 51) PKA release 1 kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 52) PKA release 2 kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 52) PKA release 2 kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 53) PKA release by PKI kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 54) EPAC activated by cAMP kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 54) EPAC activated by cAMP kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 55) MEK phospho by RapRaf Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 55) MEK phospho by RapRaf kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 56) MEK_ser phospho by RapRaf Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 56) MEK_ser phospho by RapRaf kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 57) Braf activation by Rap kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 57) Braf activation by Rap kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 58) RapGDP - RapGTP kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 58) RapGDP - RapGTP kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 59) Rap1 activation by EPAC step 1
CVODE (Variable Order, Variable Time Step)
"Compart" - 59) Rap1 activation by EPAC step 2
CVODE (Variable Order, Variable Time Step)
"Compart" - 60) Rap1 activation by EPAC step 3
CVODE (Variable Order, Variable Time Step)
"Compart" - 61) Rap1 deactivation step 1
CVODE (Variable Order, Variable Time Step)
"Compart" - 61) Rap1 deactivation step 2
CVODE (Variable Order, Variable Time Step)
"Compart" - 62) Rap1 deactivation step 3
CVODE (Variable Order, Variable Time Step)
"Compart" - 63) cAMP production Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 63) cAMP production kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 64) BAR phosphorylation Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 64) BAR phosphorylation kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 65) BAR activation by ISO kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 65) BAR activation by ISO kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 66) Gtrimer binds to BAR kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 66) Gtrimer binds to BAR kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 67) Gprotein activation kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 67) Gprotein activation kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 68) GRK recruitment by Gbg kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 68) GRK recruitment by Gbg kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 69) GRK on membrane kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 69) GRK on membrane kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 70) GRK to cytosol kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 71) AC activation kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 71) AC activation kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 72) Gs deactivation kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 73) G trimerization kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 74) BAR recycling kf
CVODE (Variable Order, Variable Time Step)
"Compart" - MAPK* import
CVODE (Variable Order, Variable Time Step)
"Compart" - MAPK* export
CVODE (Variable Order, Variable Time Step)
"Compart" - MAPK import
CVODE (Variable Order, Variable Time Step)
"Compart" - MAPK export
CVODE (Variable Order, Variable Time Step)
"Compart" - PKA import
CVODE (Variable Order, Variable Time Step)
"Compart" - PKA export
CVODE (Variable Order, Variable Time Step)
"Compart" - PKI.PKA export
CVODE (Variable Order, Variable Time Step)
"Compart" - PKI import
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1 mRNA export
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1 import
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1 export
CVODE (Variable Order, Variable Time Step)
"Compart" - 15) MKP1 phospho by MAPK kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 16) MKP1* dephospho kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 15) MKP1 phospho by MAPK Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 17) MKP1 turnover kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 18) MKP1* turnover kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 19) PKI + PKA kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 19) PKI + PKA kr
CVODE (Variable Order, Variable Time Step)
"Compart" - 20) MKP1 translation kf
CVODE (Variable Order, Variable Time Step)
"Compart" - 21) MEK phospho by Braf* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 21) MEK phospho by Braf* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 22) MEK_ser phospho by Braf* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 22) MEK_ser phospho by Braf* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 23) MAPK phospho by MEK* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 23) MAPK phospho by MEK* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 24) MAPK_tyr phospho by MEK* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 24) MAPK_tyr phospho by MEK* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 25) cAMP degradation by PDE Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 25) cAMP degradation by PDE kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 26) cAMP degradation by PDE* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 26) cAMP degradation by PDE* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 27) cAMP degradation by PDE_high Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 27) cAMP degradation by PDE_high kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 28) Braf phospho by PKA Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 28) Braf phospho by PKA kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 29) Braf dephospho by PP2A Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 29) Braf dephospho by PP2A kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 30) PTP phospho by PKA Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 30) PTP phospho by PKA kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 31) PTP dephospho by PP1 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - Iso
CVODE (Variable Order, Variable Time Step)
"Compart" - BAR
CVODE (Variable Order, Variable Time Step)
"Compart" - Gs trimer
CVODE (Variable Order, Variable Time Step)
"Compart" - AC
CVODE (Variable Order, Variable Time Step)
"Compart" - MAPK
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1* import
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1* export
CVODE (Variable Order, Variable Time Step)
"Compart" - R2C2
CVODE (Variable Order, Variable Time Step)
"Compart" - ATP
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1
CVODE (Variable Order, Variable Time Step)
"Compart" - bRaf
CVODE (Variable Order, Variable Time Step)
"Compart" - Rap1GAP
CVODE (Variable Order, Variable Time Step)
"Compart" - MEK
CVODE (Variable Order, Variable Time Step)
"Compart" - EPAC
CVODE (Variable Order, Variable Time Step)
"Compart" - PTP
CVODE (Variable Order, Variable Time Step)
"Compart" - PP2A
CVODE (Variable Order, Variable Time Step)
"Compart" - GRK
CVODE (Variable Order, Variable Time Step)
"Compart" - PDE
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP2
CVODE (Variable Order, Variable Time Step)
"Compart" - Rap1GDP
CVODE (Variable Order, Variable Time Step)
"Compart" - MSK
CVODE (Variable Order, Variable Time Step)
"Compart" - PP1A
CVODE (Variable Order, Variable Time Step)
"Compart" - MKP1 DNA
CVODE (Variable Order, Variable Time Step)
"Compart" - PP2A nucleus
CVODE (Variable Order, Variable Time Step)
"Compart" - CREB
CVODE (Variable Order, Variable Time Step)
"Compart" - 1) MAPK phospho MSK Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 1) MAPK phospho MSK kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 2) MSK dephospho
CVODE (Variable Order, Variable Time Step)
"Compart" - 3) PKA phospho CREB Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 3) PKA phospho CREB kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 4) MSK phospho CREB Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 4) MSK phospho CREB kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 5) PP2A dephosho CREB Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 5) PP2A dephosho CREB kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 6) PP1A dephospho CREB Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 6) PP1A dephospho CREB kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 7) MKP1 gene activation Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 7) MKP1 gene activation kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 8) MKP1 basal transcription
CVODE (Variable Order, Variable Time Step)
"Compart" - 9) MAPK_act dephospho by MKP2 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 9) MAPK_act dephospho by MKP2 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 10) MAPK_act dephospho by MKP1 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 10) MAPK_act dephospho by MKP1 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 11) MAPK_act dephospho by MKP1* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 11) MAPK_act dephospho by MKP1* kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 12) MAPK_tyr dephospho by MKP2 Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 12) MAPK_tyr dephospho by MKP2 kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 13) MAPK_tyr dephospho by MKP Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 13) MAPK_tyr dephospho by MKP kcat
CVODE (Variable Order, Variable Time Step)
"Compart" - 14) MAPK_tyr dephospho by MKP1* Km
CVODE (Variable Order, Variable Time Step)
"Compart" - 14) MAPK_tyr dephospho by MKP1* kcat
CVODE (Variable Order, Variable Time Step)
Podocyte Nested FFM model sihar 24497609 05/14/13
Compart...
CVODE (Variable Order, Vari...
"Compart" - U0126
CVODE (Variable Order, Variable Time Step)
"Compart" - baseline
CVODE (Variable Order, Variable Time Step)
"Compart" - Rolipram + U0216
CVODE (Variable Order, Variable Time Step)
"Compart" - Rolipram2
CVODE (Variable Order, Variable Time Step)
"Compart" - Copy of iso
CVODE (Variable Order, Variable Time Step)
"Compart" - Copy of Copy of iso
CVODE (Variable Order, Variable Time Step)
"Compart" - Copy of iso 1
CVODE (Variable Order, Variable Time Step)
"Compart" - Copy of iso 2
CVODE (Variable Order, Variable Time Step)
"Compart" - Copy of iso 3
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of EPAC
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of bRaf activation by PKA
CVODE (Variable Order, Variable Time Step)
"Compart" - Iso 2
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of PKA
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of PKA deact PTP
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of MSK
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of PKI inhibition
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of PKA act CREB
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of bRaf->MEK
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal MEK->MAPK
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of PTP-|MAPK
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of PKA import
CVODE (Variable Order, Variable Time Step)
"Compart" - Removal of MAPK import
CVODE (Variable Order, Variable Time Step)
"Compart" - iso
CVODE (Variable Order, Variable Time Step)
"Compart" - rpcamp
CVODE (Variable Order, Variable Time Step)
epsp_gcs gregl 24671529 05/22/13
compartment...
Combined Stiff Solver (IDA/...
"compartment" - Simulation1
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Dual bboras 25202018 06/18/15
test...
Combined Stiff Solver (IDA/...
"test" - C_kr=.23
Combined Stiff Solver (IDA/CVODE)
"test" - C_kr=23
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.0038
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.000038
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.8
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.008
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.12
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.0012
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.82
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.0082
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.00221
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=31.75
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=.3175
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=50
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=.5
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.13
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.0013
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.3
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.003
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=3
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=.03
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=230
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=2.3
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_CBD-A_mutant_B-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - free R more points
Combined Stiff Solver (IDA/CVODE)
"test" - Holo more points
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_CBD-B_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_Dual_mutant_B-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - More points free R
Combined Stiff Solver (IDA/CVODE)
"test" - More points Holo
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_Dual_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - R-C
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Free R
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_CBD-A_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - More points free R
Combined Stiff Solver (IDA/CVODE)
"test" - More points Holo
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA_Dimer_mutant_B-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Holo more points
Combined Stiff Solver (IDA/CVODE)
"test" - free R more points
Combined Stiff Solver (IDA/CVODE)
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Dimer_mutant_A-inhibited bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - More points Holo
Combined Stiff Solver (IDA/CVODE)
"test" - More points free R
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Unconstrained bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-CBD-B bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-CBD-A bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-CBD-A bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
Boras_PKA-Dimer bboras 25202018 09/17/14
test...
Combined Stiff Solver (IDA/...
"test" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Simulation0
Combined Stiff Solver (IDA/CVODE)
"test" - C_kr=.23
Combined Stiff Solver (IDA/CVODE)
"test" - C_kr=23
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.0038
Combined Stiff Solver (IDA/CVODE)
"test" - C_kd=.000038
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.8
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_A=.008
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.12
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_A=.0012
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.82
Combined Stiff Solver (IDA/CVODE)
"test" - Kf_B=.0082
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.00221
Combined Stiff Solver (IDA/CVODE)
"test" - Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - Copy of Kr_B=.0000221
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=31.75
Combined Stiff Solver (IDA/CVODE)
"test" - F_B_binding=.3175
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=50
Combined Stiff Solver (IDA/CVODE)
"test" - B_factor=.5
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.13
Combined Stiff Solver (IDA/CVODE)
"test" - B_kd=.0013
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.3
Combined Stiff Solver (IDA/CVODE)
"test" - A_kd=.003
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=3
Combined Stiff Solver (IDA/CVODE)
"test" - F_A_binding=.03
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=230
Combined Stiff Solver (IDA/CVODE)
"test" - A_Factor=2.3
Combined Stiff Solver (IDA/CVODE)
Falkenberg_GTPases_Rac_betaCell falkenbe 23326220 09/06/11
Combined Stiff Solver (IDA/...
"" - find SS
Combined Stiff Solver (IDA/CVODE)
"" - effect of ps-gdi only
Combined Stiff Solver (IDA/CVODE)
"" - effect of increase konM over t; coef on Gr=0; coef pld0=1.5
Combined Stiff Solver (IDA/CVODE)
"" - effect of increase konM and konGr: coef on Gr=1.5; coef pld0=[1,1.5,2]
Combined Stiff Solver (IDA/CVODE)
"" - effect of increase konM and konGr: coef on Gr=2; coef pld0=[1,1.5,2]
Combined Stiff Solver (IDA/CVODE)
Rangamani Cell 2013 B2R signaling prangamani 24034255 09/13/13
ellipse_099_nucl...
Fully-Implicit Finite Volum...
" ellipse_099_nucleus5_1" - Simulation4
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" ellipse_099_nucleus5_1" - Copy of Simulation4
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying receptor" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying receptor" - Copy of Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
EGF ras Sep 2012 prangamani 24034255 07/18/13
compartmental...
IDA (Variable Order, Variab...
"compartmental" - Simulation0
IDA (Variable Order, Variable Time Step, ODE/DAE)
"compartmental" - Simulation13
Combined Stiff Solver (IDA/CVODE)
"ellipse_0999 receptor activation only" - Simulation12
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse_0999 receptor activation only" - Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse_0999 receptor activation only" - Copy of Copy of Simulation12 1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse_0999 receptor activation only" - varying diffusion of EGFR
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse_0999 receptor activation only" - varying receptor density
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle" - Simulation2
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle" - Copy of Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse_099_nucleus1_1" - Simulation5
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse_099_nucleus3_1" - Simulation3
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" ellipse_099_nucleus5_1" - Simulation4
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
" ellipse_099_nucleus5_1" - Copy of Simulation4
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying diffusion and receptor number" - Simulation6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying diffusion and receptor number" - Simulation7
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying diffusion and receptor number" - Simulation8
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying diffusion and receptor number" - Simulation9
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying diffusion and receptor number" - Simulation10
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"spatially varying diffusion and receptor number" - Copy of Simulation6
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle fine mesh" - Simulation11
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle fine mesh" - Simulation14
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"ellipse fine mesh" - Simulation15
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
PDGF Src March 2012 prangamani 24034255 05/18/13
compartmental...
Combined Stiff Solver (IDA/...
"compartmental" - compartmental
Combined Stiff Solver (IDA/CVODE)
"ellipse 0999" - Simulation0
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle" - Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
"circle" - Copy of Simulation1
Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)
Song_PNAS_2013 rsong 23986500 09/23/13
Application0...
Combined Stiff Solver (IDA/...
"Application0" - DA0.1
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1+U0126
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1+Rolipram
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA0.1+BDNF
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA1.0
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA1.0+U0126
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA1.0+Rolipram
Combined Stiff Solver (IDA/CVODE)
"Application0" - DA1.0+BDNF
Combined Stiff Solver (IDA/CVODE)
Baik & Rosania 2013 JPP - 03 Transcellular... jsbaik 24364041 04/25/15
Imported Zhang et...
Combined Stiff Solver (IDA/...
"Imported Zhang et al 2006 Mol Pharm" - logKow2 impact on acid, neutral, base
Combined Stiff Solver (IDA/CVODE)
"Imported Zhang et al 2006 Mol Pharm" - Emm -160 vs -220 pKa 7,9,11
Combined Stiff Solver (IDA/CVODE)
"test pH outside" - Simulation0
Combined Stiff Solver (IDA/CVODE)
"test pH outside" - Simulation1
Combined Stiff Solver (IDA/CVODE)
Baik & Rosania 2013 JPP - 02 Transcellular... jsbaik 24364041 08/20/13
Matching w/ Matla...
Combined Stiff Solver (IDA/...
"Matching w/ Matlab data" - logKow impact on c=1,0,-1
Combined Stiff Solver (IDA/CVODE)
"Matching w/ Matlab data" - Fig 6A influx pKa 9.6, logKow=1.88, c=1
CVODE (Variable Order, Variable Time Step)
"Matching w/ Matlab data" - Fig 6B efflux pKa 9.6, logKow=1.88, c=1
CVODE (Variable Order, Variable Time Step)
"10x10x10 numbered geometry" - acid, base, neutral scan for logKow -2, 0, 2
Combined Stiff Solver (IDA/CVODE)
"10x10x10 numbered geometry" - Fig6A Influx, pKa 9.6, logKow=1.88, c=1
CVODE (Variable Order, Variable Time Step)
"10x10x10 numbered geometry" - Fig6B Efflux, pKa 9.6, logKow=1.88, c=1
CVODE (Variable Order, Variable Time Step)
"10x10x10 numbered geometry" - Fig6C Efflux pHa=6.5 vs 7.4, pKa 9.6, logKow=1.88, c=1
CVODE (Variable Order, Variable Time Step)