Governing Equations

PCR Amplification:
  Nn = N0 × (1 + E)^n

  Where:
  Nn = DNA copies after n cycles
  N0 = initial template copies
  E = efficiency per cycle (0 < E < 1)
  n = cycle number

Ct (Threshold Cycle):
  Ct = -log10(N0/Nthreshold) / log10(1 + E)

Efficiency Factors:
  E = Emax × f(primer) × f(Mg2+) × f(anneal_temp)
  f(primer) = [primer] / (Kd + [primer])
  f(Mg2+) = 1 - exp(-[Mg2+]/optimal)
  f(anneal_temp) = 1 - |Topt - Tanneal| / 20

Gel Migration:
  log10(MW) = a - b × distance
  Larger fragments migrate slower (lower on gel)