Physical characterization of the rack effect and hydrogen bond networks in blue copper proteins

A summary of previous research is presented that indicates that the purpose of a blue copper protein's fold and hydrogen bond network, aka, the rack effect, enforce a copper(II) geometry around the copper(I) ion in the metal site. In several blue copper proteins, the C-terminal histidine ligand becomes protonated and detaches from the copper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were made to alter the hydrogen bond network and quantify the rack effect by pK_a shifts.

The pK_a's of mutant amicyanins have been measured by pH-dependent electrochemistry. P94F and P94A mutations loosen the Northern loop, allowing the reduced copper to adopt a relaxed conformation: the ability to relax drives the reduction potentials up. The measured potentials are 265 (wild type), 380 (P94A), and 415 (P94F) mV vs. NHE. The measured pK_a's are 7.0 (wild type), 6.3 (P94A), and 5.0 (P94F). The additional hydrogen bond to the thiolate in the mutants is indicated by a red-shift in the blue copper absorption and an increase in the parallel hyperfine splitting in the EPR spectrum. This hydrogen bond is invoked as the cause for the increased stability of the C-terminal imidazole.

Melting curves give a measure of the thermal stability of the protein. A thermodynamic intermediate with pH-dependent reversibility is revealed. Comparisons with the electrochemistry and apoamicyanin suggest that the intermediate involves the region of the protein near the metal site. This region is destabilized in the P94F mutant; coupled with the evidence that the imidazole is stabilized under the same conditions confirms an original concept of the rack effect: a high energy configuration is stabilized at a cost to the rest of the protein.

A fundamental approach to phase noise reduction in hybrid Si/III-V lasers

Spontaneous emission into the lasing mode fundamentally limits laser linewidths. Reducing cavity losses provides two benefits to linewidth: (1) fewer excited carriers are needed to reach threshold, resulting in less phase-corrupting spontaneous emission into the laser mode, and (2) more photons are stored in the laser cavity, such that each individual spontaneous emission event disturbs the phase of the field less. Strong optical absorption in III-V materials causes high losses, preventing currently-available semiconductor lasers from achieving ultra-narrow linewidths. This absorption is a natural consequence of the compromise between efficient electrical and efficient optical performance in a semiconductor laser. Some of the III-V layers must be heavily doped in order to funnel excited carriers into the active region, which has the side effect of making the material strongly absorbing.

This thesis presents a new technique, called modal engineering, to remove modal energy from the lossy region and store it in an adjacent low-loss material, thereby reducing overall optical absorption. A quantum mechanical analysis of modal engineering shows that modal gain and spontaneous emission rate into the laser mode are both proportional to the normalized intensity of that mode at the active region. If optical absorption near the active region dominates the total losses of the laser cavity, shifting modal energy from the lossy region to the low-loss region will reduce modal gain, total loss, and the spontaneous emission rate into the mode by the same factor, so that linewidth decreases while the threshold inversion remains constant. The total spontaneous emission rate into all other modes is unchanged.

Modal engineering is demonstrated using the Si/III-V platform, in which light is generated in the III-V material and stored in the low-loss silicon material. The silicon is patterned as a high-Q resonator to minimize all sources of loss. Fabricated lasers employing modal engineering to concentrate light in silicon demonstrate linewidths at least 5 times smaller than lasers without modal engineering at the same pump level above threshold, while maintaining the same thresholds.