Agarose Gel Simulator: Percent, Run Time, Band Positions

The electric field is $F=V/\ell_e$, using the electrode spacing. Band-centre distance is $d=\mu Ft$.

The nominal TBE model uses the empirical reciprocal-exponential interpolation of Van Winkle, Beheshti and Rill (2002), also documented in Beheshti's open dissertation, Eq. 2.56 and Fig. 4.4 (printed pp. 41 and 62): $1/\mu=1/\mu_L-(1/\mu_L-1/\mu_s)\exp(-N/\Gamma)$. For concentration $C$ entered as the numerical percentage, $\mu_s=(3.56-0.58C)10^{-8}$ m²/(V·s), $\mu_L=1.99\exp(-1.59C)10^{-8}$ m²/(V·s), and $\Gamma=1000(2.78C+7.49)$ bp. These coefficients describe 1× TBE near 22°C, 2.78 V/cm, 0.5–1.5% agarose, and 100–10,000 bp. At other fields the tool approximates constant mobility. The thesis prose describes a 24% short-limit decrease; the caption's coefficients imply about 18%. This implementation follows the printed coefficients.

For calibration, measured mobilities are $\mu_i=d_i/(F_c t_c)$. A straight line in $z_i=1-\exp(-N_i/\Gamma)$ fits $1/\mu_i=a+bz_i$; the published crossover size is retained. Positive intercept and slope preserve positive, size-ordered mobilities. TAE uses this measured fit, with no invented buffer multiplier.

Resolution is $R_s=2|d_A-d_B|/(w_A+w_B)$, with full baseline widths supplied by the user. The conventional $R_s=1.5$ threshold is an indicator under the assumed widths. For different migration speeds, its time is $1.5(w_A+w_B)/(2|v_A-v_B|)$. Equal speeds never reach Rs 1.5, and the time calculation states that explicitly. The 80%-length run time leaves a nominal margin before the faster sample exits.

Published size ranges come from Thermo Fisher Tables 2–3. Every published row within 0.5–2.0% is included; size bounds are interpolated logarithmically only between published concentrations. The suggested percentage chooses an eligible row whose geometric midpoint is closest to the sample pair's geometric mean; this selection rule is authored here. Agarose mass is $m=C V_g/100$ g for $V_g$ in mL. To make 1× buffer from $S$× stock, use $V_g/S$ stock and the balance as water.

• Linear, double-stranded DNA with constant effective mobility during a constant-voltage run; nominal data were post-stained.
• Uniform field, matching gel/tank buffer, and negligible heating or buffer exhaustion. Changing voltage scales speed linearly; real DNA mobility can also change with field.
• Calibration entry defaults are illustrative examples, not measurements. Replace them before using calibration.
• Two-band calibration applies only to the recorded percentage and buffer. It retains the empirical crossover shape, so interpolation between measured sizes is more defensible than extrapolation.
• Baseline band widths are user estimates for the observation time and remain fixed during the animation. Gel image thickness depicts those widths; the reference ladder uses a schematic 1 mm width.
• The generic ladder is a set of round-number sizes, not a commercial product or an independent experimental result. In calibration mode the chart and ladder display are limited to the two measured sizes; blank table cells are outside that calibration span.
• Recipe volumes describe casting buffer, excluding tank buffer and stain. Restore water lost during melting according to your laboratory protocol.
• Calibration distances must be measured while bands are on the calibration gel. That gel may have a different length; usable gel length under Run conditions controls only the current run's edge and animation.

Mobility and run time are approximate estimates, not a validated prediction for every apparatus. The published nominal coefficients are for 0.5–1.5% TBE gels near 2.78 V/cm and 22°C. The tool permits 0.5–2.0%, 100–10,000 bp and up to 240 minutes; warnings identify extrapolation. For 2% gels, TAE, stains present during the run, or another apparatus, calibrate with a ladder run under matching conditions.

There is no temperature or Joule-heating model, no diffusion or loading model, and no correction for agarose grade, electroosmosis, salt, sequence-dependent curvature, gel deformation, or buffer depletion. Do not use the sizes for supercoiled/nicked plasmids, RNA, protein gels, or pulsed-field separations. A time longer than the edge time cannot produce an on-gel resolved pair. The 1.5 resolution threshold assumes ordinary band profiles and sensible baseline widths.

Reference checks verify published preparation quantities and gel-range values; they do not independently validate migration accuracy. Property checks verify the mathematical trends and scalings of the implemented approximation.