An apparatus for performing nucleic acid amplification reactions, the apparatus comprising: a thermally-conductive receptacle holder, the receptacle holder comprising a plurality of receptacle wells, each of the receptacle wells being configured to receive a receptacle, and each of the receptacle wells having a through-hole extending from an inner surface of the receptacle well to an outer surface of the receptacle holder; a plurality of optical fibers, each of the optical fibers having a first end and a second end, the first end being in optical communication with an associated one of the receptacle wells, and the second end being in optical communication with at least one of an excitation signal source and an emission signal detector, wherein the first end of each of the optical fibers is disposed outside, within, or extending through, the through-hole of the associated receptacle well, and wherein the first end of each of the optical fibers is moveable within the through-hole relative to the inner surface of the associated receptacle well; a thermally-conductive support; a thermal element positioned between the support and the receptacle holder; and a cover movable between an open position and a closed position relative to the receptacle holder, the cover being configured to seat or secure receptacles within the receptacle wells when the cover moves from the open position to the closed position, wherein the first end of each of the optical fibers is configured to move within the through-hole of the associated receptacle well (i) as the cover moves to the open or closed position or (ii) when the cover moves into or out of contact with any receptacles within the receptacle wells. a thermally-conductive receptacle holder, the receptacle holder comprising a plurality of receptacle wells, each of the receptacle wells being configured to receive a receptacle, and each of the receptacle wells having a through-hole extending from an inner surface of the receptacle well to an outer surface of the receptacle holder; a plurality of optical fibers, each of the optical fibers having a first end and a second end, the first end being in optical communication with an associated one of the receptacle wells, and the second end being in optical communication with at least one of an excitation signal source and an emission signal detector, wherein the first end of each of the optical fibers is disposed outside, within, or extending through, the through-hole of the associated receptacle well, and wherein the first end of each of the optical fibers is moveable within the through-hole relative to the inner surface of the associated receptacle well; a thermally-conductive support; a thermal element positioned between the support and the receptacle holder; and a cover movable between an open position and a closed position relative to the receptacle holder, the cover being configured to seat or secure receptacles within the receptacle wells when the cover moves from the open position to the closed position, wherein the first end of each of the optical fibers is configured to move within the through-hole of the associated receptacle well (i) as the cover moves to the open or closed position or (ii) when the cover moves into or out of contact with any receptacles within the receptacle wells.