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Lu, Yi

Publications and source records attributed to Lu, Yi.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Nuclear states projected from a pair condensate

Atomic nuclei exhibit deformation, pairing correlations, and rotational symmetries. To meet these competing demands in a computationally tractable formalism, we revisit the use of general pair condensates with good particle number as a trial wave function for even-even nuclei. After minimizing the energy of the condensate, allowing for general triaxial deformations, we project out states with good angular momentum with a fast projection technique. To show applicability, we present example calculations from pair condensates in several model spaces and compare against angular-momentum projected Hartree-Fock and full configuration-interaction shell-model calculations. This approach successfully generates spherical, vibrational, and rotational spectra, demonstrating potential for modeling medium- to heavy-mass nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic 5 engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas 6 genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, in this paper we report 7 peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand 8 DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on 9 target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much 10 smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, 11 demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data from PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, we herein report peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

Conversion↗
DOE OSTI2021

An Extended Halo-based Group/Cluster Finder: Application to the DESI Legacy Imaging Surveys DR8

We extend the halo-based group finder developed by Yang et al. (2005c) to use data simultaneously with either photometric or spectroscopic redshifts. A mock galaxy redshift survey constructed from a high-resolution N-body simulation is used to evaluate the performance of this extended group finder. For galaxies with magnitude z ≤ 21 and redshift 0 < z ≤ 1.0 in the DESI legacy imaging surveys (the Legacy Surveys), our group finder successfully identifies more than 60% of the members in about 90% of halos with mass ≳10 12.5 h –1 M ⊙ . Detected groups with mass ≳10 12.0 h –1 M ⊙ have a purity (the fraction of true groups) greater than 90%. The halo mass assigned to each group has an uncertainty of about 0.2 dex at the high-mass end ≳10 13.5 h –1 M ⊙ and 0.45 dex at the low-mass end. Groups with more than 10 members have a redshift accuracy of ~0.008. We apply this group finder to the Legacy Surveys DR8 and find 6.4 million groups with at least three members. About 500,000 of these groups have at least 10 members. Furthermore, the resulting catalog containing 3D coordinates, richness, halo masses, and total group luminosities is made publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Molecular understanding of heteronuclear active sites in heme–copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O 2 , NO, and SO 3 2- , respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. Here, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations and areas of ongoing study.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Exact sum rules with approximate ground states

Electromagnetic and weak transitions tell us a great deal about the structure of atomic nuclei. Yet modeling transitions can be difficult: it is often easier to compute the ground state, if only as an approximation, than excited states. One alternative is through transition sum rules, in particular the non-energy-weighted and energy-weighted sum rules, which can be computed as expectation values of operators. We investigate by computing sum rules for a variety of nuclei, comparing the numerically exact full configuration-interaction shell model, as a reference, to Hartree-Fock, projected Hartree-Fock, and the nucleon pair approximation. Furthermore, these approximations yield reasonable agreement, which we explain by prior work on the systematics of transition moments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Photocaged functional nucleic acids for spatiotemporal imaging in biology

Imaging of species in living organisms with high spatiotemporal resolution is essential for understanding biological processes. While functional nucleic acids (FNAs), such as catalytic nucleic acids and aptamers, have emerged as effective sensors for a wide range of molecules, photocaged control of these FNAs has played a key role in translating them into bioimaging agents with high spatiotemporal control. In this paper, we summarize methods and results of photocaged FNAs based on photolabile modifications, photoisomerization, and photothermal activation. Future directions, including strategies to improve the performance of these photocaged FNAs, are also described.

59 BASIC BIOLOGICAL SCIENCES↗