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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex

Prokaryotic cells possess CRISPR-mediated adaptive immune systems that protect them from foreign genetic elements, such as invading viruses. Here, a central element of this immune system is an RNA-guided surveillance complex capable of targeting non-self DNA or RNA for degradation in a sequence- and site-specific manner analogous to RNA interference. Although the complexes display considerable diversity in their composition and architecture, many basic mechanisms underlying target recognition and cleavage are highly conserved. Using cryoelectron microscopy (cryo-EM), we show that the binding of target double-stranded DNA (dsDNA) to a type I-F CRISPR system yersinia (Csy) surveillance complex leads to large quaternary and tertiary structural changes in the complex that are likely necessary in the pathway leading to target dsDNA degradation by a trans-acting helicase-nuclease. Comparison of the structure of the surveillance complex before and after dsDNA binding, or in complex with three virally encoded anti-CRISPR suppressors that inhibit dsDNA binding, reveals mechanistic details underlying target recognition and inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

ERM-CAS Integration

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ERM = Enterprise Risk Management CAS = Contractor ↗
DOE OSTI2021

CAS without SCF—Why to use CASCI and where to get the orbitals

The complete active space self-consistent field (CASSCF) method has seen broad adoption due to its ability to describe the electronic structure of both the ground and excited states of molecules over a broader swath of the potential energy surface than is possible with the simpler Hartree–Fock approximation. However, it also has a reputation for being unwieldy, computationally costly, and un-black-box. Here, we discuss a class of alternatives, complete active space configuration interaction (CASCI) methods, paying particular attention to their application to electronic excited states. The goal of this Perspective is fourfold. First, we argue that CASCI is not merely an approximation to CASSCF, in that it can be designed to have important qualitative advantages over CASSCF. Second, we present several insights drawn from our experience experimenting with different schemes for computing orbitals to be employed in CASCI. Third, we argue that CASCI is well suited for application to nanomaterials. Lastly, we reason that, with the rise in new low-scaling approaches for describing multireference systems, there is a greater need than ever to develop new methods for defining orbitals that provide an efficient and accurate description of both static correlation and electronic excitations in a limited active space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Dust survival rates in clumps passing through the Cas A reverse shock – I. Results for a range of clump densities

ABSTRACT The reverse shock in the ejecta of core-collapse supernovae is potentially able to destroy newly formed dust material. In order to determine dust survival rates, we have performed a set of hydrodynamic simulations using the grid-based code astrobear in order to model a shock wave interacting with clumpy supernova ejecta. Dust motions and destruction rates were computed using our newly developed external, post-processing code paperboats, which includes gas drag, grain charging, sputtering, and grain–grain collisions. We have determined dust destruction rates for the oxygen-rich supernova remnant Cassiopeia A as a function of initial grain sizes and clump gas density. We found that up to $30\,\mathrm{{{\ \rm per\ cent}}}$ of the carbon dust mass is able to survive the passage of the reverse shock if the initial grain size distribution is narrow with radii around ∼10–50 nm for high gas densities, or with radii around $\sim 0.5\!-\!1.5\,\mathrm{\mu m}$ for low and medium gas densities. Silicate grains with initial radii around 10–30 nm show survival rates of up to $40\,\mathrm{{{\ \rm per\ cent}}}$ for medium- and high-density contrasts, while silicate material with micron-sized distributions is mostly destroyed. For both materials, the surviving dust mass is rearranged into a new size distribution that can be approximated by two components: a power-law distribution of small grains and a lognormal distribution of grains having the same size range as the initial distribution. Our results show that grain–grain collisions and sputtering are synergistic and that grain–grain collisions can play a crucial role in determining the surviving dust budget in supernova remnants.

79 ASTRONOMY AND ASTROPHYSICS↗