Scott_Fraley_Rangamani_YAP_TAZ_model_2021(...

prangamani

None

02/13/21 
SA 314 2xD Fig 5,...

FullyImplicit Finite Volum...

"SA 314 2xD Fig 5,6"
 R 20 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 415 2xD Fig 5,6"
 R 23 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 490 2xD Fig 5,6"
 R 25 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 250 2xD Fig 5,6"
 R 18 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 200 2xD Fig 5,6"
 R 16 Bot 0.1,5.7,70E6

FullyImplicit 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...

FullyImplicit Finite Volum...

"SA 314 2xD figure 5,6"
 R 20 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" R10 2D figure 4"
 R 10 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 490 2xD figure 5,6"
 R 25 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 415 2xD figure 5,6"
 R 23 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 250 2xD figure 5,6"
 R 18 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R13 2D figure 4"
 R 13 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 314 3D figure 5,6"
 New SA 314 All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 415 3D figure 5,6"
 New SA 415 All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 490 3D figure 5,6"
 New SA 490 All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 250 3D figure 5,6"
 New SA 250All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 200 3D figure 5,6"
 New SA 200 All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"SA 200 2xD figure 5,6"
 R 16 Bot 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R15 LD 0.5 Figure 7"
 Copy of Simulation88

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R13 LD 1.5 Figure 7"
 Simulation114

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R13 LD 0.5 Figure 7"
 Simulation117

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R16 LD 1.5Figure 7"
 Simulation126

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R16 LD 1.5Figure 7"
 Copy of Simulation126

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R16 LD 0.5 Figure 7"
 Simulation131

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R10 Bottom wide Figure 7"
 Simulation135

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R10 LD 0.5 Figure 7"
 Simulation138

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R15 3D Figure 3, 4, and S7"
 R 15 All 0.1,5.7,70E6

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R13 3D figure 4"
 R 13 All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R10 3D figure 4"
 R 10 All 0.1,5.7,70E6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R15 2D Fig 3, 4, and S7"
 R15 2D 0.1, 5.7, 7e6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R15 2D Fig 3, 4, and S7"
 R15 2D 7e6 with different FAK diffusion

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R16 LD 1Figure 7"
 Simulation22

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R25 FAK diffusion variation 3D substrate stiffness Figure S7"
 R 25 3D 70E6 FAK diffusion 0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R25 FAK diffusion variation 3D substrate stiffness Figure S7"
 R 25 3D 70E6 FAK diffusion 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R25 FAK diffusion variation 3D substrate stiffness Figure S7"
 R 25 3D 70E6 FAK diffusion 10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R25 FAK diffusion variation 2D substrate stiffness Fig S7"
 R 25 2D varying FAK diffusion 0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R25 FAK diffusion variation 2D substrate stiffness Fig S7"
 R 25 2D varying FAK diffusion 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R25 FAK diffusion variation 2D substrate stiffness Fig S7"
 R 25 2D varying FAK diffusion 10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Energyproductionpathwayreducedmodel01...

nasrin

34396153

02/24/21 
Tubular...

FullyImplicit Finite Volum...

"Tubular"
 Simulation24

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"No Cristae"
 Simulation86

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"No Cristae"
 Simulation87

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Lamellar"
 Simulation166

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Lamellar"
 Copy of Simulation166

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"2D_15_Cristae"
 Simulation233

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"2D_15_Cristae"
 Simulation234

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"2D_5_Cristae"
 Simulation233_1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"2D_5_Cristae"
 Simulation234_1

FullyImplicit 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% pyrenylactin

Combined Stiff Solver (IDA/CVODE)

"Simulations of Sept and McCammon and this paper"
 15% pyrenylactin

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% pyrenylactin

Combined Stiff Solver (IDA/CVODE)

"Simulations of Sept and McCammon and this paper"
 50% pyrenylactin

Combined Stiff Solver (IDA/CVODE)

"Simulations of Sept and McCammon and this paper"
 75% pyrenylactin

Combined Stiff Solver (IDA/CVODE)

"Simulations of Sept and McCammon and this paper"
 100% pyrenylactin

Combined Stiff Solver (IDA/CVODE)


SpermCalcium

Juliajessica

34360784

07/24/21 
Application0...

FullyImplicit Finite Volum...

"Application0"
 Calcium diffusionvariationosc

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Kerbai_PLoSone_2021_teardrop_polarization_...

KerbaicBITE

33735291

04/02/21 
real cell...

FullyImplicit Finite Volum...

"real cell"
 simulation3

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"real cell"
 simulation1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"real cell"
 simulation2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Kerbai_PLoSone_2021_teardrop_polarization_...

KerbaicBITE

33735291

03/25/21 
real cell...

FullyImplicit Finite Volum...

"real cell"
 Simulation1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"real cell"
 Simulation2

FullyImplicit 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)


HistamineRhoA Model_Final3

jzz002

32881857

03/06/20 
Application1...

Combined Stiff Solver (IDA/...

"Application1"
 Simulation 1

Combined Stiff Solver (IDA/CVODE)


HistamineRhoA 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...

FullyImplicit Finite Volum...

"Symmetric Geometry"
 Fig 2A: PFL 1 scan 0% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2A: PFL 1 scan 3% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2A: PFL 1 scan 10% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2A: PFL 1 scan 30% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2A: PFL 1 scan 67% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2B: PFL 1 scan without MARCKS 0% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2B: PFL 1 scan without MARCKS 3% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2B: PFL 1 scan without MARCKS 10% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2B: PFL 1 scan without MARCKS 30% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 2B: PFL 1 scan without MARCKS 67% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3A: M and Mp diffusivity scan x 0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3A: M and Mp diffusivity scan x 0.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3A: M and Mp diffusivity scan x 0.5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3A: M and Mp diffusivity scan x 2.0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3A: M and Mp diffusivity scan x 5.0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3A: M and Mp diffusivity scan x 10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3B: pT and mT diffusivity scan x 0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3B: pT and mT diffusivity scan x 0.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3B: pT and mT diffusivity scan x 0.5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3B: pT and mT diffusivity scan x 2.0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3B: pT and mT diffusivity scan x 5.0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 3B: pT and mT diffusivity scan x 10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 5B: 0.3 x kDAGK scan 10% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 5B: 3.0 x kDAGK scan 10% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 5D: 3.0 x kDAGK scan 3% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 5E: Variation of DAG and PA scan x 0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 5E: Variation of DAG and PA scan x 0.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 5E: Variation of DAG and PA scan x 0.5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 6A: PFL 2 + MARCKS

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 6B: PFL 1+ PFL 2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig 6C: PFL 1+ PFL 2 + MARCKS

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kon,e

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans koff,e

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans epsilon

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans KPA

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans khyd,PLC

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kpm

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kdpm

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kbasal,dp

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kDAGK

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kPAP

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kon,c

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans koff,c

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kdpc

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans kpc

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S4: Parameter scans Vsynth,dp

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 2 + MARCKS, kDAGK

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 2 + MARCKS, KPLD

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 1 + PFL 2, kDAGK

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 1 + PFL 2, KPA

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 1 + PFL 2, KPLD

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 1 + PFL 2 + MARCKS, kDAGK

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 1 + PFL 2 + MARCKS, KPA

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Symmetric Geometry"
 Fig S5: PFL 1 + PFL 2 + MARCKS, KPLD

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4B: PFL 1 scan

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4C: M and Mp diffusivity scan x 0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4C: M and Mp diffusivity scan x 0.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4C: M and Mp diffusivity scan x 0.5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4C: M and Mp diffusivity scan x 2.0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4C: M and Mp diffusivity scan x 5.0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4C: M and Mp diffusivity scan x 10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Back end blunted scan 3% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Back end blunted scan 10% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Back end blunted scan 30% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Back end blunted scan 67% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Front end blunted scan 3% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Front end blunted scan 10% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Front end blunted scan 30% gradient

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Asymmetric Geometry"
 Fig 4D: Front end blunted scan 67% gradient

FullyImplicit 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...

FullyImplicit Finite Volum...

"Pattern_formation"
 WT

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.09

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.06

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.15

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.18

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.185

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.19

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.21

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_RNAi_0.24

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.06

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.09

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.15

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 NEGAN_RNAi_0.18

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.01

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.05

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.06

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.07

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.08

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.09

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Pattern_formation"
 RTO_OE_0.1

FullyImplicit 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 RasGTP, sorafenib"
 Simulation0

Combined Stiff Solver (IDA/CVODE)

"const. active RasGTP, 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...

FullyImplicit Finite Volum...

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=1, kpc2=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=1, kpc2=0, DM=scan, DMp=scan

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1, konm=0, koffm=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 3

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 4

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 7

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 14

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 15

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 16

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 17

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 18

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 19

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 20

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 21

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 22

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 23

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 24

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_p67"
 rel_grad=0.67, Lmid=3e5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 25

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Relative_gradient_0"
 rel_grad=0, Lmid=3e5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p1"
 rel_grad=0.1, Lmid=3e5, kpm=1, kdpm=1, kpc1=1, kpc2=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p1"
 rel_grad=0.1, Lmid=3e5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p1"
 rel_grad=0.1, Lmid=3e5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p1"
 rel_grad=0.1, Lmid=3e5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p1"
 rel_grad=0.1, Lmid=3e5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1, konm=0, koffm=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p1"
 rel_grad=0.1, Lmid=3e5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" Relative_gradient_p3"
 rel_grad=0.3, Lmid=3e5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Yeast 3D_FRAP

Wasim

29205883

01/31/18 
01_06_2017...

FullyImplicit Finite Volum...

"01_06_2017"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"01_06_2017"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Falkenberg_PodocyteStability

falkenbe

28301477

08/16/16 
nonspatial...

Combined Stiff Solver (IDA/...

"nonspatial"
 high alpha2, followed by high alpha

Combined Stiff Solver (IDA/CVODE)

"nonspatial"
 high alpha2 followed by higher alpha

Combined Stiff Solver (IDA/CVODE)

"nonspatial"
 low beta2 followed by highr alpha

Combined Stiff Solver (IDA/CVODE)

"extra: simple test geometry. "few fingers""
 stable  test localization

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. "few fingers""
 Copy of stable  test localization

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. "few fingers""
 Copy of Copy of stable  test localization

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: generate initial condition; full geometry,no LocCorr"
 good mesh (GM0): check loc

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: generate initial condition; full geometry,no LocCorr"
 GM0: try single stable point

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: generate initial condition; full geometry,no LocCorr"
 short, to check details

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: generate initial condition; full geometry,no LocCorr"
 My19, increase alpha z>3.5; tmax=200

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: generate initial condition; full geometry,no LocCorr"
 Copy of My19, increase alpha z>3.5;

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: tests, full geometry, no LocCorr: smaller pert region"
 My19, increase alpha (7>z>13)&&(x>15);

FullyImplicit 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);

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: tests, full geometry, no LocCorr: uniform"
 testloc

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: tests, full geometry, no LocCorr: uniform"
 peak in alpha

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: tests, full geometry, no LocCorr: uniform"
 change ic

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: tests, full geometry, no LocCorr: uniform"
 triggger at 800

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: tests, full geometry, no LocCorr: uniform"
 change ic, tr 800

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 delay 200

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 delay 40

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 delay 500  recovered

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 low beta2  delay 200

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 low beta2  delay 40

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 low beta2  delay 500  recovered

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (a) delay3000 (st)(p5)(p6): still OK

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (a) delay 4000 (st)(p5)(p6):

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (a) delay 6000 (st)(p5)(p6):

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 damage: p5 (IIA) ; recover delay3000

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 damage: p5 (IIA) ; recover delay4500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 damage: p0 (IIB) ; recover delay 500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 damage: p0 (IIB) ; recover delay 1500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (Ia) delay3000 (st)(p5)(p7)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (Ia) delay4500 (st)(p5)(p7)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (Ib) delay 500 (st)(p0)(p3)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: simple test geometry. few fingers: uniform, pert n fix"
 (Ib) delay 1500 (st)(p0)(p3)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"nonspatial"
 Simulation0

Combined Stiff Solver (IDA/CVODE)

"extra: test, import ic: of few fingers: uniform, pert n fix"
 try to copy ic

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 keep extending to SS

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (a) delay3000  Figure 3

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (a) delay4500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (Ia) delay3000

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (Ia) delay4500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (IIa) delay3000

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (IIa) delay4500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (b) delay500  Figure6 ( i, j)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (b) delay1500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (Ib) delay500  Figure 6 (f,g)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (Ib) delay1500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (IIb) delay500  Figure 6 (d, e)

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (IIb) delay1500

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Figures 3 and 6; with SS ic: full geometry,no LocCorr"
 (a) delay3000 fast diffusion G

FullyImplicit 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...))

FullyImplicit 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...)

FullyImplicit 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...))

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)"
 amplitude (1+0.1exp(r/30))

FullyImplicit 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))

FullyImplicit 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))

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)"
 amplitude (1+1 exp(r/30))

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)"
 amplitude (10.5 exp(r/30))

FullyImplicit 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

FullyImplicit 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)

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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, 95:16271638; Biophys. J. 75:2070Â¿2078

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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)


BorasDiffusional Study250xPDEtest4

bboras

27409243

08/06/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 360000 elements

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"ode"
 Simulation0

Combined Stiff Solver (IDA/CVODE)


BorasDiffusional Study1000xPDEtest4

bboras

27409243

08/06/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


BorasDiffusional Study No geometry1x larg...

bboras

27409243

08/04/15 
Application0...

FullyImplicit Finite Volum...

"Application0"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Application0"
 Copy of Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


BorasDiffusional Study No geometry10x lar...

bboras

27409243

08/04/15 
Application0...

FullyImplicit Finite Volum...

"Application0"
 Copy of Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Application0"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


BorasDiffusional Study25xPDEtest4

bboras

27409243

08/03/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 360000 elements

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"ode"
 Simulation0

Combined Stiff Solver (IDA/CVODE)


BorasDiffusional Study100xPDEtest7

bboras

27409243

08/03/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 360000 elements

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"ode"
 Simulation0

Combined Stiff Solver (IDA/CVODE)


BorasDiffusional Study10xPDEtest5

bboras

27409243

07/31/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 360000 elements

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"ode"
 Simulation0

Combined Stiff Solver (IDA/CVODE)


BorasDiffusional Study100xPDEtest5

bboras

27409243

07/31/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 360000 elements

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"ode"
 Simulation0

Combined Stiff Solver (IDA/CVODE)


BorasDiffusional Study100xPDEtest6 for i...

bboras

27409243

07/31/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 360000 elements

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"ode"
 Simulation0

Combined Stiff Solver (IDA/CVODE)


BorasDiffusional Study1xPDEtest5

bboras

27409243

07/31/15 
Correct PDE conc....

FullyImplicit Finite Volum...

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 75

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 300

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation0 137826 elements diffusion 9

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation6

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation7

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation11

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Simulation13

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Copy of Simulation12

SemiImplicit Finite VolumeParticle Hybrid, Regular Grid (Fixed Time Step)

"Copy of Correct PDE conc. with new geo with crop correct size"
 Copy of Simulation12 1

FullyImplicit 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

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Correct PDE conc. with new geo with crop correct size"
 Simulation0 137826 elements diffusion 9

FullyImplicit 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"
 OxoM

Combined Stiff Solver (IDA/CVODE)

"simulations"
 OxoM with TubbyR332

Combined Stiff Solver (IDA/CVODE)

"simulations"
 VSP

Combined Stiff Solver (IDA/CVODE)

"simulations"
 OxoM with fura2

Combined Stiff Solver (IDA/CVODE)

"simulations"
 OxoM with PHPLCd1

Combined Stiff Solver (IDA/CVODE)

"simulations"
 OxoM with LIBRAVIII

Combined Stiff Solver (IDA/CVODE)

"simulations"
 OxoM with C1domain

Combined Stiff Solver (IDA/CVODE)


fX_platelet_binding

agolomy

26874201

01/20/16 
Application0...

FullyImplicit Finite Volum...

"Application0"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


fX_thrombus_binding

agolomy

26874201

01/20/16 
Application1...

FullyImplicit Finite Volum...

"Application1"
 Simulation1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


BEN

sayak66

27271916

01/12/15 
Needle...

FullyImplicit Finite Volum...

"Needle"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Smoldyn

sayak66

27271916

11/26/14 
Det...

FullyImplicit Finite Volum...

"Det"
 Simulation1

FullyImplicit 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"
 Pin1FLw/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"
 NucSev 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"
 CaMKIIfactin

Combined Stiff Solver (IDA/CVODE)

"Application0"
 CaMKIIGactin 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"
 karp23 inactivation

Combined Stiff Solver (IDA/CVODE)

"Application0"
 kcalcineurinactivationbycam

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 factin

Combined Stiff Solver (IDA/CVODE)

"Application0"
 camkii gactin

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 factin

Combined Stiff Solver (IDA/CVODE)

"Application0"
 kr camkii gactin

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...

FullyImplicit Finite Volum...

"wt uniform"
 F/G=10/190, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=4050, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=2030 , Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=6070, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=8090, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=100110, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=120130, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=140150, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=160170, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=180190, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt uniform"
 Factin=40190, Kd=0.005,0.0075

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


GFactin FDAP

marynka

27831495

08/18/16 
wt D=3...

FullyImplicit Finite Volum...

"wt D=3"
 F/G=10/190, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=2030 , Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=4050, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=6070, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=8090, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=100110, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=120130, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=140150, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=160170, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=3"
 Factin=180190, Kd=0.010.2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation3

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation4

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation5

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation6

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation7

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation8

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"smaller+tall"
 Simulation9

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation20

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation21

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation22

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation23

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation24

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation25

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation26

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation27

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation28

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 Simulation29

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"wt D=5"
 F=100 D=10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


Boras_PKADual

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_CBDA_mutant_Binhibited

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_CBDB_mutant_Ainhibited

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_Binhibited

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_Ainhibited

bboras

25202018

09/17/14 
test...

Combined Stiff Solver (IDA/...

"test"
 RC

Combined Stiff Solver (IDA/CVODE)

"test"
 Simulation0

Combined Stiff Solver (IDA/CVODE)

"test"
 Free R

Combined Stiff Solver (IDA/CVODE)


Boras_PKA_CBDA_mutant_Ainhibited

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_Binhibited

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_PKADimer_mutant_Ainhibited

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_PKAUnconstrained

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_PKACBDB

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_PKACBDA

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_PKADimer

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...

FullyImplicit Finite Volum...

"cAMPinput_tertiary3"
 cAMPtertiaryEnd

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_secondary3"
 cAMPsecondaryEnd

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_primary3"
 cAMPprimaryEnd

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_primary1"
 cAMPprimaryBegin

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_primary2"
 primaryMiddle

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_secondary1"
 cAMPsecondaryMiddle1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_secondary2"
 cAMPsecondaryMiddle2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_tertiary1"
 cAMPtertiaryMiddle1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"cAMPinput_tertiary2"
 cAMPtertiaryMiddle2

FullyImplicit 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...

FullyImplicit Finite Volum...

"Application0"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


CPX Binding

jdittman

25809246

10/28/14 
Bouton R200...

FullyImplicit Finite Volum...

"Bouton R200"
 Long Sim

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"R200 Steady"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Buffer in cylinder"
 Simulation1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Bouton R200"
 Short Sim

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)


FDAP diffusion

marynka

25865895

08/16/16 
Application half...

FullyImplicit Finite Volum...

"Application halfcell"
 short D= from 2 to 10 Gactin=1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Application halfcell"
 Copy of D=2  10

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" halfcellsmaller+tall"
 Simulation0

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" halfcellsmaller+tall"
 Simulation1

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" halfcellsmaller+tall"
 Simulation2

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

" halfcellsmaller+tall"
 Simulation3

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Application halfcell"
 short D between 2 and 10 Gactin=100

FullyImplicit Finite Volume, Regular Grid (Variable Time Step)

"Application halfcell"
 D=2  10

FullyImplicit 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 PTPMAPK

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_PKADual

bboras

25202018
