medecstaMethods and sources
What each calculator computes, where its constants come from, what it assumes, and how the calculators are checked. The formula list below is generated from the same code the calculators run, so it cannot drift from them.
How the calculators are checked
- Worked cases. Every calculator has ten hand-worked cases: typical values, the same values in other units, extreme magnitudes, invalid inputs that must be refused, and one reference case tied to a known answer. Each case is run through the arithmetic and again through the real page in Chrome, typed into the actual fields.
- A second implementation. A separate implementation of every calculator was written without access to this code (it was generated by a separate AI model, so it is a cross-check, not a peer review). The two are compared on thousands of random inputs per calculator. The only differences accepted are the documented conventions listed below.
- Published anchors. Some checks need no hand-worked answer at all: A260 = 1.0 for dsDNA must give 50 µg/mL, [S] = Km must give half of Vmax, and equal acid and base must give pH = pKa.
- Hostile input. Every field is fed blanks, text, commas, huge and tiny numbers. The page must show either a number or a plain error message, never “NaN”, “undefined” or a blank box.
- Limitation. The hand-worked answers were written by the same process that wrote the formulas. That is why the second implementation and the published anchors exist: passing tests alone would not prove the science is right. If you find a result you disagree with, please report it.
Conventions you should know about
| Quantity | Used here | The other common choice |
|---|---|---|
| dsDNA mass per base pair | 617.96 g/mol + 36.04 for the ends (free acid) | 660 g/mol (sodium salt), about 6.8 % heavier. Moles and copy numbers under 660 come out about 6.4 % lower; every dsDNA result shows both. |
| Oligo (ssDNA) mass | 303.7 g/mol per nt − 61.96 (free 5′-OH, as synthesised) | +79 instead of −61.96 models a 5′-phosphorylated oligo; about 2.3 % heavier for a 20-mer. |
| Primer Tm | Wallace rule below 14 nt, GC formula above | Nearest-neighbour thermodynamics (NEB, IDT, Primer3): usually a few °C different. Use those for final annealing temperatures. |
| ppm / ppb | mg/L and µg/L | Strictly mass/mass; equal to mg/L only where the solution density is 1 g/mL. |
| Percent (w/v) | g per 100 mL of final solution | Dissolving into 100 mL of solvent gives a weaker solution. |
Corrections made after checking against published sources
- Oligo end correction. Originally +79.0 g/mol (a 5′-phosphorylated oligo); changed to −61.96 g/mol for a standard oligo with a free 5′-OH. A 20-mer had read about 2.3 % heavy.
- A280 coefficient label. The protein calculator was titled “E 1%” while its arithmetic used E 0.1 % (per 1 mg/mL). A user entering an E 1 % datasheet value would have got a concentration ten times too low. It is now labelled E 0.1 % and says to divide E 1 % values by 10.
- dsDNA convention figure. Help text said the 660 g/mol convention is “6.5 %” heavier; the correct figure is 6.8 % (660 ÷ 617.96).
Every calculator
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Animal Dose Converter
The species conversions (FDA Km factors and allometric scaling) have their own method notes, citations and disclaimer under Details in the Animal Dose Converter.