Yes, SimBiology in MATLAB can simulate one-to-many scenarios, including the reaction you described where two AuNPs can bind to one cDNA at the same time. SimBiology allows for the modeling and simulation of complex reaction networks, including multi-component reactions.
To configure this reaction in SimBiology, you can use the following steps:
1. Define the species: Create species objects for cDNA, AuNP, and the bound complex (e.g., cDNA-AuNP). Specify the initial amounts or concentrations for each species.
2. Define the reactions: Create a reaction object that represents the binding reaction between cDNA and AuNP. Set the reaction rate and stoichiometry appropriately. In this case, the stoichiometry would be 2 AuNP and 1 cDNA, resulting in the formation of 1 cDNA-AuNP complex.
3. Create a model: Create a SimBiology model and add the species and reaction objects to the model.
4. Configure simulation settings: Set the simulation time span, solver options, and any other desired simulation settings.
5. Run the simulation: Use the `simulate` function in SimBiology to run the simulation and obtain the results.
Here's a simplified example to illustrate the configuration of the reaction you described:
% Create species objects
cDNA = sbioselect(m, 'Name', 'cDNA');
AuNP = sbioselect(m, 'Name', 'AuNP');
complex = addspecies(m, 'cDNA-AuNP', 'InitialAmount', 0);
% Create the binding reaction
reaction = addreaction(m, '2 AuNP + cDNA -> cDNA-AuNP');
kineticLaw = addkineticlaw(reaction, 'MassAction');
parameter = addparameter(kineticLaw, 'k', 1); % Set the reaction rate constant
% Set the stoichiometry of the reaction
addstoichiometry(reaction, 'cDNA', -1);
addstoichiometry(reaction, 'AuNP', -2);
addstoichiometry(reaction, 'cDNA-AuNP', 1);
% Configure simulation settings
configset = getconfigset(m);
set(configset, 'StopTime', 10); % Set simulation time span
% Run the simulation
simData = sbiosimulate(m);
% Plot the results
plot(simData.Time, simData.Data(:, [cDNA, AuNP, complex]));
legend('cDNA', 'AuNP', 'cDNA-AuNP');
xlabel('Time');
ylabel('Amount');
This example demonstrates a simple binding reaction between cDNA and AuNP, where two AuNPs bind to one cDNA to form the cDNA-AuNP complex. You can adjust the reaction rate constant and other parameters as needed.
SimBiology provides various analysis and visualization tools to further analyze the simulation results, such as plotting concentrations, calculating reaction rates, and performing parameter estimations.
I hope this helps!
