Thermal adapter for automated thermal cycling

Systems and methods for processing samples in a multi-well reaction vessel can include inserting a multi-well reaction vessel into a heating chamber of a thermal cycler, enclosing the multi-well reaction vessel in the heating chamber, and compressing a bottom surface of the multi-well reaction vessel into a compliant thermally conductive insert to increase a thermal contact area between the bottom surface and the compliant thermally conductive insert. The compliant thermally conductive insert can be placed between the multi-well reaction vessel and a heating element of the thermal cycler, where heat flux from the heating element passes through the compliant thermally conductive insert to the reaction vessel. The compliant thermally conductive insert can include an elastically deformable creped graphite sheet that can reversibly deform according to different compression profiles depending on the topography or flexure of the reaction vessel and/or heating element.