The invention provides a reaction vessel and temperature control system for performing heat-exchanging chemical reactions, such as nucleic acid amplification. The vessel has a body defining a reaction chamber, and a loading structure extending from the body for loading a sample into the chamber. The loading structure has a loading reservoir, an aspiration port, and respective fluid channels connecting the loading reservoir and aspiration port to the chamber. To load the sample into the vessel, the sample is first dispensed into the loading reservoir and then drawn into the chamber by application of a vacuum to the aspiration port. The vessel also includes a seal aperture extending over the outer ends of the loading reservoir and aspiration port. A plug is inserted into the aperture after loading the sample into the chamber to simultaneously seal the chamber, loading reservoir, and aspiration port from the external environment. The temperature of the sample is controlled by opposing plates positioned to contact opposite sides of the vessel. The system also,includes thermal elements for heating or cooling the plates and optics for detecting one or more analytes in the sample.