This thesis is an investigation of near infrared emissions from Jupiter’s upper atmosphere using observations from high-resolution spectrometers on two ground-based telescopes: the NASA Infrared Telescope Facility (IRTF) and the Keck II. Four studies are presented and discussed in terms of the energetics and dynamics of Jupiter’s upper atmosphere and its connection to the surrounding magnetosphere. The work based on the IRTF data investigates short time scale variability in Jupiter’s near infrared aurora and the effects of that variability on atmospheric heating by examining fluctuations in the velocity of the ion winds in the southern auroral region. These velocities are derived from the Doppler shifting of H3+ emission lines. This thesis presents the highest quality data of Jupiter's near infrared aurora available to date, from the 10-metre Keck II telescope. Many emission features are identified that have not previously been observed outside the laboratory and-emission from the highest reaches of the upper atmosphere are observed for the first time with a ground-based telescope. Three studies based on these data are presented. A mid- to low-latitude study of H3+ emissions is presented, with profiles of intensities and column densities, and a compared with results from a global circulation model. H3+ and CH4 emissions are employed in a study of Jupiter's northern and southern auroral regions; profiles of rotational and vibrational temperatures, column densities, and total emission are presented. Finally, a new method for deriving vertical ion density and temperature profiles in Jupiter's auroral regions is developed. Such profiles have never been recorded and it was previously thought that such vertical profiles in Jupiter’s upper atmosphere could not be made from ground-based observations, but only from spacecraft data. Profiles derived from this new method are presented in the study
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