Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (β = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350–4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.

Characterization and Degradation of Fatty Acid Methyl Esters and Biodiesel in Artificial Seawater Under UV Exposure Using Raman Spectroscopy

Thesis (Master's)--University of Washington, 2016-06

Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone

Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Peduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthelemy, M., Prigent, Y., Salomon, R. A., Farias, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.

Nitrenes, diradicals, and ylides. Ring expansion and ring opening in 2-quinazolylnitrenes

Tetrazolo[1,5-a] quinazoline (9) is converted to 2-azidoquinazoline (10) on sublimation at 200 degrees C and above, and the azide-tetrazole equilibrium is governed by entropy. 2-Quinazolylnitrenes 11 and 27 and/ or their ring expansion products 14 and 29 can undergo type I (ylidic) and type II (diradicaloid) ring opening. Argon matrix photolysis of 9/10 affords 2-quinazolylnitrene (11), which has been characterized by ESR, UV, and IR spectroscopy. A minor amount of a second nitrene, formed by rearrangement or ring opening, is also observed. A diradical (19) is formed rapidly by type II ring opening and characterized by ESR spectroscopy; it decays thermally at 15 K with a half-life of ca. 47 min, in agreement with its calculated facile intersystem crossing (19T -> 19OSS) followed by facile cyclization/rearrangement to 1-cyanoindazole (21) (calculated activation barrier 1- 2 kcal/mol) and N-cyanoanthranilonitrile (22). 21 and 22 are the isolated end products of photolysis. 21 is also the end product of flash vacuum thermolysis. An excellent linear correlation between the zero-field splitting parameter D (cm(-1)) and the spin density F on the nitrene N calculated at the B3LYP/EPRIII level is reported (R-2 = 0.993 for over 100 nitrenes). Matrix photolysis of 3-phenyltetrazolo[1,5-a] quinazoline (25) affords the benzotriazacycloheptatetraene 29, which can be photochemically interconverted with the type I ring opening product 2-isocyano-alpha-diazo-alpha- phenyltoluene (33) as determined by IR and UV spectroscopy. The corresponding carbene 37, obtained by photolysis of 33, was detected by matrix ESR spectroscopy.

Bandpass switching in a nonlinear optical loop mirror

We demonstrate bandpass nonlinear switching, using a novel device configuration based on a nonlinear-optical loop mirror and an in-fiber Bragg grating. Self-switching is demonstrated in the soliton regime by use of an asymmetrically arranged in-fiber Bragg grating as a wavelength-selective element. In addition, we adapt the configuration to perform efficient two-wavelength switching.

Simultaneous clock recovery and data regeneration using a nonlinear optical loop mirror as an all-optical mixer

High-speed optical clock recovery, demultiplexing and data regeneration will be integral parts of any future photonic network based on high bit-rate OTDM. Much research has been conducted on devices that perform these functions, however to date each process has been demonstrated independently. A very promising method of all-optical switching is that of a semiconductor optical amplifier-based nonlinear optical loop mirror (SOA-NOLM). This has various advantages compared with the standard fiber NOLM, most notably low switching power, compact size and stability. We use the SOA-NOLM as an all-optical mixer in a classical phase-locked loop arrangement to achieve optical clock recovery, while at the same time achieving data regeneration in a single compact device

Single polarisation fibre ring laser by utilising intracavity 45° tilted fibre Bragg grating

Single polarisation operation of fibre ring laser has been realised by employing an intracavity 45deg-tilted fibre Bragg grating (45deg-TFBG). The degree of polarisation up to 99.94% of the laser was demonstrated with good stability.

Refractometer based on fiber Bragg grating Fabry-Pérot cavity embedded with a narrow microchannel

We report on inscription of microchannels of different widths in optical fiber using femtosecond (fs) laser inscription assisted chemical etching and the narrowest channel has been created with a width down to only 1.2µm. Microchannels with 5µm and 35µm widths were fabricated together with Fabry-Pérot (FP) cavities formed by UV laser written fiber Bragg gratings (FBGs), creating high function and linear response refractometers. The device with a 5µm microchannel has exhibited a refractive index (RI) detection range up to 1.7, significantly higher than all fiber grating RI sensors. In addition, the microchannel FBG FP structures have been theoretically simulated showing excellent agreement with experimental measured characteristics.

Evolution of optical pulses in fiber lines with lumped nonlinear devices as a mapping problem

We analyze the steady-state propagation of optical pulses in fiber transmission systems with lumped nonlinear optical devices (NODs) placed periodically in the line. For the first time to our knowledge, a theoretical model is developed to describe the transmission regime with a quasilinear pulse evolution along the transmission line and the point action of NODs. We formulate the mapping problem for pulse propagation in a unit cell of the line and show that in the particular application to nonlinear optical loop mirrors, the steady-state pulse characteristics predicted by the theory accurately reproduce the results of direct numerical simulations.

All-optical passive regeneration of 40 Gbit/s soliton data stream using dispersion-management and in-line nonlinear optical loop mirrors

We numerically demonstrate for the first time that dispersion management and in-line nonlinear optical loop mirrors can achieve all-optical passive regeneration and distance-unlimited transmission of a soliton data stream at 40 Gbit/s over standard fibre.

Numerical modeling of holmium-doped fluoride fiber lasers

We combine all the known experimental demonstrations and spectroscopic parameters into a numerical model of the Ho3+ -doped fluoride glass fiber laser system. Core-pumped and cladding-pumped arrangements were simulated for all the population-bottlenecking mitigation schemes that have been tested, and good agreement between the model and the previously reported experimental results was achieved in most but not in all cases. In a similar way to Er3+ -doped fluoride glass fiber lasers, we found that the best match with measurements required scaled-down rate parameters for the energy transfer processes that operate in moderate to highly concentrated systems. The model isolated the dominant processes affecting the performance of each of the bottlenecking mitigation schemes and pump arrangements. It was established that pump excited-state absorption is the main factor affecting the performance of the core-pumped demonstrations of the laser, while energy transfer between rare earth ions is the main factor controlling the performance in cladding-pumped systems.

Fiber optical parametric amplifier performance in a 1-Tb/s DWDM communication system

We have reduced signal-signal four-wave mixing crosstalk in a fiber optical parametric amplifier (OPA) by using a short nonlinear fiber for the gain medium and a high-power pump. This allowed us to obtain less than 1 dB penalty for amplification of 26 dense wavelength-division multiplexed (WDM) channels modulated at 43.7Gb/s return to zero-differential phase-shift keying, with the OPA placed between transmitter and receiver. We then used the same OPA in several different roles for a long-haul transmission system. We did not insert the OPA within the loop, but investigated this role indirectly by using equivalent results for small numbers of loop recirculations. We found that standard erbium-doped fiber amplifiers currently hold an advantage over this OPA, which becomes negligible for long distances. This paper shows that at this time OPAs can handle amplification of WDM traffic in excess of 1 Tb/s with little degradation. It also indicates that with further improvements, fiber OPAs could be a contender for wideband amplification in future optical communication networks.

Graphene based widely-tunable and singly-polarized pulse generation with random fiber lasers

Pulse generation often requires a stabilized cavity and its corresponding mode structure for initial phase-locking. Contrastingly, modeless cavity-free random lasers provide new possibilities for high quantum efficiency lasing that could potentially be widely tunable spectrally and temporally. Pulse generation in random lasers, however, has remained elusive since the discovery of modeless gain lasing. Here we report coherent pulse generation with modeless random lasers based on the unique polarization selectivity and broadband saturable absorption of monolayer graphene. Simultaneous temporal compression of cavity-free pulses are observed with such a polarization modulation, along with a broadly-tunable pulsewidth across two orders of magnitude down to 900 ps, a broadly-tunable repetition rate across three orders of magnitude up to 3 MHz, and a singly-polarized pulse train at 41 dB extinction ratio, about an order of magnitude larger than conventional pulsed fiber lasers. Moreover, our graphene-based pulse formation also demonstrates robust pulse-to-pulse stability and widewavelength operation due to the cavity-less feature. Such a graphene-based architecture not only provides a tunable pulsed random laser for fiber-optic sensing, speckle-free imaging, and laser-material processing, but also a new way for the non-random CW fiber lasers to generate widely tunable and singly-polarized pulses.

Sub-50 fs Yb-doped laser with anomalous-dispersion photonic crystal fiber

We report on the generation of 42 fs pulses at 1 µm in a completely fiber-integrated format, which are, to the best of our knowledge, the shortest from all-fiber-integrated Yb-doped fiber lasers to date. The ring fiber cavity incorporates anomalous-dispersion, solid-core photonic crystal fiber with low birefringence, which acts as a broadband, in-fiber Lyot filter to facilitate mode locking. The oscillator operates in the stretched-pulse regime under slight normal net cavity dispersion. The cavity generates 4.7 ps long pulses with a spectral bandwidth of 58.2 nm, which are dechirped to 42 fs via a grating pair compressor outside of the cavity. Relative intensity noise (RIN) of the laser is characterized, with the integrated RIN found to be 0.026% in the 3 Hz-250 kHz frequency range.