Publications

Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A significant challenge is re-engineering a partially reductive PKS module to produce a saturated β-carbon through a reductive loop (RL) exchange. In this work, we sought to establish that chemoinformatics, a field traditionally used in drug discovery, offers a viable strategy for RL exchanges. We first introduced a set of donor RLs of diverse genetic origin and chemical substrates into the first extension module of the lipomycin PKS (LipPKS1). Product titers of these engineered unimodular PKSs correlated with chemical structure similarity between the substrate of the donor RLs and recipient LipPKS1, reaching a titer of 165 mg/L of short-chain fatty acids produced by the host <i>Streptomyces albus</i> J1074. Expanding this method to larger intermediates that require bimodular communication, we introduced RLs of divergent chemosimilarity into LipPKS2 and determined triketide lactone production. Collectively, we observed a statistically significant correlation between atom pair chemosimilarity and production, establishing a new chemoinformatic method that may aid in the engineering of PKSs to produce desired, unnatural products.

A small array of various polythiophene derivative OTF' gas sensors with robust operation in air is demonstrated. Air stability is shown not to preclude gas sensor response, and good sensitivity to a range of gas analytes is observed down to 10 ppm. The active materials are all deposited from solution, making these sensors compatible with low-cost gas sensor arrays. Finally, the effect of varying the functional groups and size of a gas analyte on the response it induces in the sensor array is investigated.

Biofilm structural heterogeneity affects a broad range of microbially catalysed processes. Solute transport limitation and autoinhibitor production, two factors that contribute to heterogeneous biofilm development, were investigated using BacMIST, a computer simulation model. BacMIST combines a cellular automaton algorithm for biofilm growth with Brownian diffusion for solute transport. The simulation represented the growth of microbial unit cells in a three-dimensional domain modelled after a repeating section of a constant depth film fermenter. The simulation was implemented to analyse the effects of various levels of transport limitation on a growing single-species biofilm. In a system with rapid solute diffusion, cells throughout the biofilm grew at their maximum rate, and no solute gradient was formed over the biofilm thickness. In increasingly transport-limited systems, the rapidly growing fraction of the biofilm population decreased, and was found exclusively at the biofilm–liquid interface. Trans-biofilm growth substrate gradients also deepened with increasing transport limitation. Autoinhibitory biofilm growth was simulated for various rates of microbially produced inhibitor transport. Inhibitor transport rates affected both the biofilm population dynamics and the resulting biofilm structures. The formation of networks of void spaces in slow-growing regions of the biofilm and the development of columns in the fast-growing regions suggested a possible mechanism for the microscopically observed evolution of channels in biofilms.

Context. We investigate two stripped-envelope supernovae (SNe) discovered in the nearby galaxy NGC 5806 by the (intermediate) Palomar Transient Factory [(i)PTF]. These SNe, designated PTF12os/SN 2012P and iPTF13bvn, exploded within ~520 days of one another at a similar distance from the host-galaxy center. We classify PTF12os as a Type IIb SN based on our spectral sequence; iPTF13bvn has previously been classified as Type Ib having a likely progenitor with zero age main sequence (ZAMS) mass below ~17 M⊙. Because of the shared and nearby host, we are presented with a unique opportunity to compare these two SNe. Aims. Our main objective is to constrain the explosion parameters of iPTF12os and iPTF13bvn, and to put constraints on the SN progenitors. We also aim to spatially map the metallicity in the host galaxy, and to investigate the presence of hydrogen in early-time spectra of both SNe. Methods. We present comprehensive datasets collected on PTF12os and iPTF13bvn, and introduce a new automatic reference-subtraction photometry pipeline (FPipe) currently in use by the iPTF. We perform a detailed study of the light curves (LCs) and spectral evolution of the SNe. The bolometric LCs are modeled using the hydrodynamical code hyde. We analyze early spectra of both SNe to investigate the presence of hydrogen; for iPTF13bvn we also investigate the regions of the Paschen lines in infrared spectra. We perform spectral line analysis of helium and iron lines to map the ejecta structure of both SNe. We use nebular models and late-time spectroscopy to constrain the ZAMS mass of the progenitors. We also perform image registration of ground-based images of PTF12os to archival HST images of NGC 5806 to identify a potential progenitor candidate. Results. We find that our nebular spectroscopy of iPTF13bvn remains consistent with a low-mass progenitor, likely having a ZAMS mass of ~12M⊙. Our late-time spectroscopy of PTF12os is consistent with a ZAMS mass of ~15M⊙. We successfully identify a source in pre-explosion HST images coincident with PTF12os. The colors and absolute magnitude of this object are consistent between pre-explosion and late-time HST images, implying it is a cluster of massive stars. Our hydrodynamical modeling suggests that the progenitor of PTF12os had a compact He core with a mass of 3.25+ 0.77-0.56M⊙ at the time of the explosion, which had a total kinetic energy of 0.54+ 0.41-0.25 × 1051 erg and synthesized 0.063+ 0.020-0.011M⊙ of strongly mixed 56Ni. Spectral comparisons to the Type IIb SN 2011dh indicate that the progenitor of PTF12os was surrounded by a thin hydrogen envelope with a mass lower than 0.02M⊙. We also find tentative evidence that the progenitor of iPTF13bvn could have been surrounded by a small amount of hydrogen prior to the explosion. This result is supported by possible weak signals of hydrogen in both optical and infrared spectra.

In recent photovoltaic research, nanomaterials have offered two new approaches for trapping light within solar cells to increase their absorption: nanostructuring the absorbing semiconductor and using metallic nanostructures to couple light into the absorbing layer. This work combines these two approaches by decorating a single-nanowire silicon solar cell with an octahedral silver nanocrystal. Wavelength-dependent photocurrent measurements and finite-difference time domain simulations show that increases in photocurrent arise at wavelengths corresponding to the nanocrystal's surface plasmon resonances, while decreases occur at wavelengths corresponding to optical resonances of the nanowire. Scanning photocurrent mapping with submicrometer spatial resolution experimentally confirms that changes in the device's photocurrent come from the silver nanocrystal. These results demonstrate that understanding the interactions between nanoscale absorbers and plasmonic nanostructures is essential to optimizing the efficiency of nanostructured solar cells.

We report a hydrogen-bond functionalized N4Py ligand platform (N,N-bis(2-R-6-pyridylmethyl)-N-bis(2-pyridyl)methylamine; R = neopentyl-NH, N4Py(2NpNH), 9; R = phenyl-NH, N4Py(2PhNH), 10) and the ability of its iron(II)-triflate [N4Py(2R)Fe(II)(OTf)][OTf] complexes (R = NpNH, 11; R = PhNH, 12) to activate and reduce dioxygen in a synthetic cycle by coupled proton and electron transfer. A pair of iron(III)-hydroxide [N4Py(2R)Fe(III)(OH)][OTf](2) complexes (R = NpNH, 13; R = PhNH, 14) are isolated and structurally and spectroscopically characterized after exposure of the iron(II)-triflate precursors to 1 atm of O(2) at ambient temperature. The stability of this system to acids and bases allows regeneration of the labile iron(II)-triflate starting materials by sequential electron and proton transfer with cobaltocene and triflic acid, respectively, or through direct proton-coupled reduction with ascorbic acid. In the stepwise process, reduction of the iron(III)-hydroxide complexes with cobaltocene gives structurally homologous iron(II)-hydroxide [N4Py(2R)Fe(II)(OH)][OTf] congeners (R = NpNH, 15; R = PhNH, 16) that can be prepared independently from 11 and 12 with 20% aq. NaOH. Additions of triflic acid to complexes 15 and 16 furnish the starting compounds 11 and 12, respectively, to complete the synthetic cycle. The combined data establish a synthetic cycle for O(2) reduction by an iron platform that manages proton and electron transfer through its first and second coordination spheres.

We present new spectroscopic observations of the LINER (and now Seyfert 1) nucleus of NGC 1097, and discuss the evolution of its broad, double-peaked Balmer lines. When originally discovered in 1991, the red peak of the double-peaked H-alpha line was stronger than the blue, while by 1994 the H-alpha profile had become almost symmetric and the integrated line flux had decreased to half its original value. Our new spectrum, taken in 1996, shows that the broad, double-peaked lines have returned to almost their original strengths, the profiles of H-beta and H-alpha are identical to within errors, and the broad-line emitting region is unreddened. However, the profile of the Balmer lines is now such that the blue peak is stronger than the red, opposite to the asymmetry observed in 1991. Various models are considered for the observed behavior, all assuming that the emission lines originate in an accretion disk. We present a refined version of the precessing, planar, elliptical accretion ring model proposed by Storchi-Bergmann et al. and Eracleous et al. This model provides an acceptable fit to the line profiles. We also consider the possibility that the line profile evolution results from a precessing warp in the disk, induced by irradiation from the center, and show that the range of radii and precession time scales expected in this model are consistent with the observations. The sudden appearance of the "disk-like" broad line profiles in NGC 1097 could have resulted from the formation of a new accretion disk due to, for example, the tidal disruption of a star, or the illumination of a pre-existing disk by a transient ionizing source at the center of the disk.