SimulateEquilibrium -- Performs simulation of the equilibrium state from the chemical reactions with given initial conditions.

SimulateKinetics -- Performs simulation of the chemical reactions with given initial conditions and duration and returns the trajectory of concentrations of reaction components against time.

SimulateFreeEnergy -- Computes the Gibbs free energy from the chemical reactions, and from the hybridization or melting reactions of oligonucleotides.

SimulateEquilibriumConstant -- Computes the equilibrium constant from the chemical reactions.

SimulateEnthalpy -- Computes the change in enthalpy of the given reaction between two oligonucleotides with traditional Nearest Neighbor thermodynamic analysis.

SimulateEntropy -- Computes the change in entropy of the given reaction between two oligonucleotides with traditional Nearest Neighbor thermodynamic analysis.

SimulateFreeEnergy -- Computes the free energy of the given reaction between two oligonucleotides at the specified concentration with traditional Nearest Neighbor thermodynamic analysis.

SimulateEquilibriumConstant -- Computes the equilibrium constant of the given reaction between two oligonucleotides at the specified concentration with traditional Nearest Neighbor thermodynamic analysis.

SimulateFolding -- Predicts potential secondary structures of the given oligonucleotides.

SimulateHybridization -- Predicts potential hybridized structures from multiple given oligonucleotides.

SimulateReactivity -- Generates a putative reaction mechanism that describes the hybridization behavior of the system of nucleic acids or adds reaction rates to known reaction types from the given nucleic acid reaction.

SimulateEquilibrium -- Performs simulation of the equilibrium state from the oligonucleotides reactions with given initial conditions.

SimulateKinetics -- Performs simulation of the oligonucleotides reactions with given initial conditions and duration and returns the trajectory of concentrations of reaction components against time.

SimulateMeltingCurve -- Performs simulation of the melting reactions from given oligonucleotides and returns the trajectory of concentrations of oligonucleotide species against temperature.

SimulateMeltingTemperature -- Computes the melting temperature of the given reaction between two oligonucleotides at the specified concentration with traditional Nearest Neighbor thermodynamic analysis.

SimulateProbeSelection -- Simulates which probe sequence would most faithfully bind to the target sequence, with any folding or self-pairing of the probe or target sequence taken into account.