Using a novel wide-slit, multi-object approach with the GMOS spectrograph on the 8-meter Gemini South telescope, we have obtained precise time-series spectrophotometry of the binary brown dwarf Luhman 16 at optical wavelengths over two full nights. The B component of this binary system is known to be variable in the red optical and near-infrared with a period of 5 hr and an amplitude of 5--20%. Our observations probe its spectrally-resolved variability in the 6000--10000 Angstrom range. At wavelengths affected by the extremely strong, broadened spectral lines of the neutral alkali metals (the potassium doublet centered near 7682 Angstroms and the sodium doublet at 5893 Angstroms), we see photometric variations that differ strikingly from the those of the 8000--10000 Angstrom `red continuum that dominates our detected flux. On UT 2014 February 24, these variations are anticorrelated with the red continuum, while on Feb 25 they have a large relative phase shift. The extent to which the wavelength-dependent photometric behavior diverges from that of the red continuum appears to correlate with the strength of the alkali absorption. We consider but ultimately reject models in which our observations are explained by lightning or auroral activity. A more likely cause is cloud-correlated, altitude-dependent variations in the gas-phase abundances of sodium and potassium, which are in chemical equilibrium with their chlorides in brown dwarf atmospheres. Clouds could influence these chemical equilibria by changing the atmospheric temperature profile and/or through cloud particles acting as chemical catalysts.
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