Publications

GRB 170519A was discovered by \emph{Swift}/BAT, and then observed by \emph{Swift}/XRT, \emph{Swift}/UVOT, and ground-based telescopes. We report Lick/KAIT observations of GRB 170519A, and make temporal analysis and spectral joint fits of its multiwavelength light curves. The observations present a relatively complete afterglow structure, including two X-ray flares (Flares I and II), optical onset (Slice 1), normal decay (Slices 2 and 3), and a possible jet break. The spectrum of the bright X-ray flare (Flare II) indicates that a thermal component exists at $t = 190$--240~s. \textbf{The blackbody emits in the photospheric radius $R_{\rm ph}\sim 10^{11}$ cm,} and its temperature ($kT$) decreases with time from \textbf{1.08 to 0.37 keV, its Lorentz factor of blackbody ($Γ_{\rm BB}$) decreases with time from 67.71 to 46.70. The luminosity of the blackbody ($L_{\rm BB}$), $kT$ and $Γ_{\rm BB}$ follow the relations $\bf L_{\rm BB} \propto kT^{2.49\pm 0.03}$ and $Γ_{\rm BB}\propto L_{\rm BB}^{0.27}$ (estimated from \cite{fan2012}).} In the optical light curves, there is an onset bump in the early-time afterglow, rising with an index $α_{O,1} \approx -0.43$ and peaking $\sim1174.9$ s since the BAT trigger. The bump then decays with $\bf α_{O,2} \approx 0.88$ in the normal decay phase, and the X-ray flux decays with a similar index of $\bf α_{X,1} \approx 0.95$. There is no obvious spectral evolution in the normal decay phases, with photon index $\hatΓ = 1.86$ and 1.92 in Slices 2 and 3, respectively. We find that the multiwavelength light curves of the GRB 170519A afterglow can be well fitted by an external shock with time-dependent $ε_B$. In the early afterglow, the value of $ε_B$ decays rapidly from $\bf 4.29\times10^{-2}$ to $\bf 8.23\times10^{-3}$.

Terminal alkenes are easily derivatized, making them desirable functional group targets for polyketide synthase (PKS) engineering. However, they are rarely encountered in natural PKS systems. One mechanism for terminal alkene formation in PKSs is through the activity of an acyl-CoA dehydrogenase (ACAD). Herein, we use biochemical and structural analysis to understand the mechanism of terminal alkene formation catalyzed by an γ,δ-ACAD from the biosynthesis of the polyketide natural product FK506, TcsD. While TcsD is homologous to canonical α,β-ACADs, it acts regioselectively at the γ,δ-position and only on α,β-unsaturated substrates. Furthermore, this regioselectivity is controlled by a combination of bulky residues in the active site and a lateral shift in the positioning of the FAD cofactor within the enzyme. Substrate modeling suggests that TcsD utilizes a novel set of hydrogen bond donors for substrate activation and positioning, preventing dehydrogenation at the α,β position of substrates. From the structural and biochemical characterization of TcsD, key residues that contribute to regioselectivity and are unique to the protein family were determined and used to identify other putative γ,δ-ACADs that belong to diverse natural product biosynthetic gene clusters. These predictions are supported by the demonstration that a phylogenetically distant homologue of TcsD also regioselectively oxidizes α,β-unsaturated substrates. This work exemplifies a powerful approach to understand unique enzymatic reactions and will facilitate future enzyme discovery, inform enzyme engineering, and aid natural product characterization efforts.

Graph neural networks are powerful architectures for structured datasets. However, current methods struggle to represent long-range dependencies. Scaling the depth or width of GNNs is insufficient to broaden receptive fields as larger GNNs encounter optimization instabilities such as vanishing gradients and representation oversmoothing, while pooling-based approaches have yet to become as universally useful as in computer vision. In this work, we propose the use of Transformer-based self-attention to learn long-range pairwise relationships, with a novel "readout" mechanism to obtain a global graph embedding. Inspired by recent computer vision results that find position-invariant attention performant in learning long-range relationships, our method, which we call GraphTrans, applies a permutation-invariant Transformer module after a standard GNN module. This simple architecture leads to state-of-the-art results on several graph classification tasks, outperforming methods that explicitly encode graph structure. Our results suggest that purely-learning-based approaches without graph structure may be suitable for learning high-level, long-range relationships on graphs. Code for GraphTrans is available at https://github.com/ucbrise/graphtrans.

We present the spectroscopic and photometric evolution of the nearby (z = 0.059) spectroscopically confirmed type Ic supernova, SN 2010bh, associated with the soft, long-duration gamma-ray burst (X-ray flash) GRB 100316D. Intensive follow-up observations of SN 2010bh were performed at the ESO Very Large Telescope (VLT) using the X-shooter and FORS2 instruments. Owing to the detailed temporal coverage and the extended wavelength range (3000--24800 A), we obtained an unprecedentedly rich spectral sequence among the hypernovae, making SN 2010bh one of the best studied representatives of this SN class. We find that SN 2010bh has a more rapid rise to maximum brightness (8.0 +/- 1.0 rest-frame days) and a fainter absolute peak luminosity (L_bol~3e42 erg/s) than previously observed SN events associated with GRBs. Our estimate of the ejected (56)Ni mass is 0.12 +/- 0.02 Msun. From the broad spectral features we measure expansion velocities up to 47,000 km/s, higher than those of SNe 1998bw (GRB 980425) and 2006aj (GRB 060218). Helium absorption lines He I lambda5876 and He I 1.083 microm, blueshifted by ~20,000--30,000 km/s and ~28,000--38,000 km/s, respectively, may be present in the optical spectra. However, the lack of coverage of the He I 2.058 microm line prevents us from confirming such identifications. The nebular spectrum, taken at ~186 days after the explosion, shows a broad but faint [O I] emission at 6340 A. The light-curve shape and photospheric expansion velocities of SN 2010bh suggest that we witnessed a highly energetic explosion with a small ejected mass (E_k ~ 1e52 erg and M_ej ~ 3 Msun). The observed properties of SN 2010bh further extend the heterogeneity of the class of GRB supernovae.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

A catalytic system combining the high activity of homogeneous catalysts and the ease of use of heterogeneous catalysts for methane activation is reported. The vanadium-containing metal-organic frameworks (MOFs) MIL-47 and MOF-48 are found to have high catalytic activity and chemical stability. They convert methane selectively to acetic acid with 70% yield (490 TON) based on K(2)S(2)O(8) as an oxidant. Isotopic labeling experiments showed that two methane molecules are converted to the produced acetic acid. The MOF catalysts are reusable and remain catalytically active for several recycling steps without losing their crystalline structures.