kolmeisky1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000305) Biomodels notes: Reproduction of figure 3 of the original publication. Copasi 4.6 was used to perform a parameter scan over the given range of applied force with 100 intervals. At each point a time course simulation was calculated for 100 sec to retrieve a equilibrated value of the velocity.
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Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 1.0 item | |
| — | 1e-06 mole | |
| — | 1e-06 mole litre^(-1.0) | |
| — | 1.0 litre |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| compartment_ | — | 3.0 | 0.000000000000001 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| ADP | — | 0.0 | compartment_ | ✔ | |
| ATP | — | 20.0 | compartment_ | ✔ | |
| Pi_ | — | 0.0 | compartment_ | ✔ | |
| S0 | — | 10.0 | compartment_ | ✘ | |
| S1 | — | 0.0 | compartment_ | ✘ | |
| back_step1 | — | 0.0 | compartment_ | ✘ | |
| back_step2 | — | 0.0 | compartment_ | ✘ | |
| fwd_step1 | — | 0.0 | compartment_ | ✘ | |
| fwd_step2 | — | 0.0 | compartment_ | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| Bw_1st_step | — | S0 + ATP > S1 + Pi_ + back_step1 k_3 * S0 * ATP * exp(th_3 * Force * d / kT) | |||
| Bw_2nd_step | — | S1 > S0 + ADP + back_step2 k_4 * S1 * exp(th_4 * Force * d / kT) | |||
| Fw_1st_step | — | S0 + ATP > S1 + Pi_ + fwd_step1 k_1 * S0 * ATP * exp(-th_1 * Force * d / kT) | |||
| Fw_2nd_step | — | S1 > S0 + ADP + fwd_step2 k_2 * S1 * exp(-th_2 * Force * d / kT) |
| Id | Value | |
|---|---|---|
| Force | 0.0 | |
| S_tot | 0.0 | |
| V | 0.0 | |
| V_ave | 0.0 | |
| d | 36.0 | |
| kT | 4.1164 | |
| k_1 | 0.7 | |
| k_2 | 12.0 | |
| k_3 | 0.000005 | |
| k_4 | 0.000006 | |
| tau | 0.0 | |
| th_1 | -0.01 | |
| th_2 | 0.045 | |
| th_3 | 0.58 | |
| th_4 | 0.385 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| tau = (k_1 * ATP * exp(-th_1 * Force * d / kT) + k_2 * exp(-th_2 * Force * d / kT) + k_3 * ATP * exp(th_3 * Force * d / kT) + k_4 * exp(th_4 * Force * d / kT)) / (k_1 * ATP * exp(-th_1 * Force * d / kT) * k_2 * exp(-th_2 * Force * d / kT) + k_3 * ATP * exp(th_3 * Force * d / kT) * k_4 * exp(th_4 * Force * d / kT)) | |
| V_ave = d * ((fwd_step1 + fwd_step2) / 2.0 - (back_step1 + back_step2) / 2.0) / (S_tot * time) | |
| V = d * ((Fw_1st_step + Fw_2nd_step) / 2.0 - (Bw_1st_step + Bw_2nd_step) / 2.0) / S_tot | |
| S_tot = S0 + S1 |
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| Definition |
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| Trigger | Assignments |
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