Description
Return a bimolecular reactant-pair count and propensity.
Computational biology distinguishes discrete counts, probabilistic weights, sequence indexes and logical rules. A supplied event or record flag can be summarized without simulating a stochastic process, validating a sequence annotation or establishing a biological mechanism.
Return a bimolecular reactant-pair count and propensity.
When to use this tool
Use Mass Action Bimolecular One Propensity Term when checking the stated count, sequence, Boolean-rule or support convention.
How to use the tool and how it works
- Enter firstCount, secondCount, coefficient, identicalSpecies. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read reactantPairs, propensity. Use the output convention below.
Return a bimolecular reactant-pair count and propensity. Require nonnegative whole counts/coefficient and equal counts when identicalSpecies; pairs = n*(n-1)/2 for identical species, otherwise n1*n2; propensity = coefficient*pairs.1
Stochastic chemical kinetics uses discrete molecule populations and reaction propensities; a deterministic rate constant needs the appropriate stochastic and volume convention.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| firstCount | First Count | Required. Safe integer; minimum 0. |
| secondCount | Second Count | Required. Safe integer; minimum 0. |
| coefficient | Supplied stochastic coefficient for the displayed pair-count convention; volume/unit conversion is not inferred. | Required. Finite number. |
| identicalSpecies | Identical Species | Required. Boolean. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| reactantPairs | Reactant Pairs | Required. Finite number. |
| propensity | Propensity | Required. Finite number. |
{
"input": {
"firstCount": 5,
"secondCount": 5,
"coefficient": 0.2,
"identicalSpecies": true
},
"output": {
"reactantPairs": 10,
"propensity": 2
}
}Limitations and assumptions
- The coefficient must match this combinatorial and volume convention; the tool does not infer a deterministic rate constant or sample an event.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Use the complete sequence, identifier universe or stochastic/logical model for actual inference, sampling and uncertainty analysis.
References
Similar or alternative tools
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