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Shi, Yi

Publications and source records attributed to Shi, Yi.

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗
DOE OSTI2022

High-throughput, in situ imaging of multi-layer powder-blown directed energy deposition with angled nozzle

Laser metal additive manufacturing (AM) has become an increasingly popular technology due to its flexibility in geometry and materials. As one of the commercialized additive processes, powder-blown directed energy deposition (DED) has been used in multiple industries such as aerospace, automotive, medical device, etc. However, a lack of fundamental understanding remains for this process, and many opportunities for alloy development and implementation can be identified. A high-throughput, in situ DED system capable of multi-layer builds that can address these issues is presented here. In this work, implications of layer heights and energy density are investigated through an extensive process parameter sweep, showcasing the power of a high-throughput setup while also discussing multi-layer interactions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Intramolecular structure and dynamics in computationally designed peptide-based polymers displaying tunable chain stiffness

Here, polymers assembled using computationally designed coiled coil bundlemers display tunable stiffness via control of interbundlemer covalent connectivity as confirmed using small-angle neutron scattering. Neutron spin echo spectroscopy reveals that rigid rod polymers show a decay rate Γ~Q 2 (Q is the scattering vector) expected of straight cylinders. Semirigid polymers assembled using bundlemers linked via 4-armed organic linker show flexible segmental dynamics at mid-Q and Γ~Q 2 behavior at high Q. The results give insight into linker flexibility-dependent interbundlemer dynamics in the hybrid polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Nonequilibrium phonon tuning and mapping in few-layer graphene with infrared nanoscopy

Electron-phonon interactions are fundamentally important physical processes responsible for many key discoveries in condensed matter physics and material sciences. Herein, by exploiting the scattering-type scanning near-field optical microscope (s-SNOM) excited with a femtosecond infrared (IR) laser, we explored the strong coupling between IR phonons in few-layer graphene (FLG) with ultrahot electrons, which are heated up by the intense laser field enhanced by the s-SNOM tip. More specifically, we found that the intensity of the phonon resonance can be tuned systematically by varying the laser power that controls the electron temperature. Furthermore, the high spatial resolution of s-SNOM allows us to map the local phonon characteristics at sharp boundaries and nanostructures. Our results offer insights into the intriguing physics behind the electron-phonon interactions in nonequilibrium conditions and open a pathway for manipulating phonons with optical means.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗