Engineering topics

Yoon, Peter H.

Publications and source records attributed to Yoon, Peter H..

At least 19 records

DOE OSTI2024

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation in heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral systems. Here, to address this, we developed an automated structural-search pipeline to identify an ancestral clade of Cas13 (Cas13an) and further trace Cas13 origins to defense-associated ribonucleases. Despite being one-third the size of other Cas13s, Cas13an mediates robust programmable RNA depletion and defense against diverse bacteriophages. However, unlike its larger counterparts, Cas13an uses a single active site for both CRISPR RNA processing and RNA-guided cleavage, revealing that the ancestral nuclease domain has two modes of activity. Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9

Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Long-Term Science Goals with In Situ Observations at the Sun-Earth Lagrange Point L4

The Korean heliospheric community, led by the Korea Astronomy and Space Science Institute (KASI), is currently assessing the viability of deploying a spacecraft at the Sun-Earth Lagrange Point L4 in collaboration with National Aeronautics and Space Administration (NASA). The aim of this mission is to utilize a combination of remote sensing and in situ instruments for comprehensive observations, complementing the capabilities of the L1 and L5 observatories. The paper outlines long-term scientific objectives, underscoring the significance of multi-point in-situ observations to better understand critical heliospheric phenomena. These include coronal mass ejections, magnetic flux ropes, heliospheric current sheets, kinetic waves and instabilities, suprathermal electrons and solar energetic particle events, as well as remote detection of solar radiation phenomena. Furthermore, the mission’s significance in advancing space weather prediction and space radiation exposure assessment models through the integration of L4 observations is discussed. This article is concluded with an emphasis on the potential of L4 observations to propel advancements in heliospheric science.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

Abstract RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and a TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12s. In eukaryotes, TnpB homologs occur as two distinct types, Fanzor1s and Fanzor2s. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, which revealed that both Fanzor1s and Fanzor2s stem from a single lineage of IS607 TnpBs with unusual active site arrangement. The widespread nature of Fanzors implies that the properties of this particular lineage of IS607 TnpBs were particularly suited to adaptation in eukaryotes. Biochemical analysis of an IS607 TnpB and Fanzor1s revealed common strategies employed by TnpBs and Fanzors to co-evolve with their cognate transposases. Collectively, our results provide a new model of sequential evolution from IS607 TnpBs to Fanzor2s, and Fanzor2s to Fanzor1s that details how genes of prokaryotic origin evolve to give rise to new protein families in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Electrostatic upper-hybrid mode instability driven by a ring electron distribution

Quasi electrostatic fluctuations in the upper-hybrid frequency range are commonly detected in the planetary magnetospheric environment. The origin of such phenomena may relate to the instability driven by a loss-cone feature associated with the electrons populating the dipole-like magnetic field. The present paper carries out a one-dimensional electrostatic particle-in-cell simulation accompanied by a reduced quasilinear kinetic theoretical analysis to investigate the dynamics of the upper-hybrid mode instability driven by an initial ring electron distribution function, which is a form of loss-cone distribution. A favorable comparison is found between the two approaches, which shows that the reduced quasilinear theory, which is grounded in the concept of a model of the particle distribution function that is assumed to maintain a fixed mathematical form except that the macroscopic parameters that define the distribution are allowed to evolve in time, can be an effective tool in the study of plasma instabilities, especially if it is guided by and validated against the more rigorous simulation result.

Physics↗

NASA NTRS1994

Theory of 2 omega(sub pe) radiation induced by the bow shock

A new radiation emission mechanism is proposed to explain electomagnetic radiation observed at twice the electron plasma frequency, 2 omega(sub pe), in the upstream region of the Earth's bow shock. This radiation had its origin at the electron foreshock boundary where energetic electron beams and intense narrow-band Langmiur waves are observed. The proposed emission mechanism results from the interaction of the electron beam and Langmuir waves that are backscattered off thermal ions. This interaction is described by a nonlinear dispersion equation which incorporates an effect owing to electron trajectory modulation by the backscattered Langmuir waves. Subsequent analysis of the dispersion equation reveals two important consequences. First, a long-wavelength electrostatic quasi-mode with frequency at 2 omega(sub pe) is excited, and second, the quasi-mode and the electomagnetic mode are nonlinearly coupled. The implication is that, when the excited 2 omega(sub pe) quasi-mode propagates in an inhomgeneous medium with slightly decreasing density, the quasi-mode can be converted directly into an electromagnetic mode. Hense the electomagnetic radiation at twice the plasma frequency is generated. Numerical solutions of the dispersion equation with the choice of parameters that describe physical characteristics of the electron foreshock are presented, which illustrates the viability of the new mechanism.

Yoon, Peter H.↗

NASA NTRS1994

Generation of radiation in solar corona and interplanetary space by energetic electrons

Emissions of electromagnetic waves with frequencies close to the plasma frequency and/or its second harmonic have been frequently observed in the solar corona and interplanetary space. In the past, a number of theories have been put forward to esplain the generation mechanism of the observed radiation. In this paper, a new model is proposed. The essential point of the present theory is that the Langmuir waves amplified as a result of the usual beam instability can lead to two important effects: first, electrostatic waves with frequencies close to twice the plasma frequency can be excited; and second, a significant modification of the dispersion relation can occur, so that these electrostatic waves can naturally change into electomagnetic waves as they propagate in a plasma in which the plasma density decreases spatially. The latter effect is attributed to a mode couplng process. In addition to the second harmonic emission, emission at the fundamental is also briefly discussed. In this case, as in many other theories, the presence of a very low frequency electostatic wave such as the ion-acoustic wave is assumed. The emission process discussed in the present theory stresses the importance of mode coupling and conversion rather than kinetic processes such as a nonlinear wave-wave or wave-particle scattering.

Wu, C. S.↗

NASA NTRS1993

Nonlinear analysis of generalized cross-field current instability

Analysis of the generalized cross-field current instability is carried out in which cross-field drift of both the ions and electrons and their temperatures are permitted to vary in time. The unstable mode under consideration is the electromagnetic generalization of the classical modified-two-stream instability. The generalized instability is made of the modified-two-stream and ion-Weibel modes. The relative importance of the features associated with the ion-Weibel mode and those of the modified-two-stream mode is assessed. Specific applications are made to the Earth's neutral sheet prior to substorm onset and to the Earth's bow shock. The numerical solution indicates that the ion-Weibel mode dominates in the Earth's neutral sheet environment. In contrast, the situation for the bow shock is dominated by the modified-two-stream mode. Notable differences are found between the present calculation and previous results on ion-Weibel mode which restrict the analysis to only parallel propagating waves. However, in the case of Earth's bow shock for which the ion-Weibel mode plays no important role, the inclusion of the electromagnetic ion response is found to differ little from the previous results which treats ions responding only to the electrostatic component of the excited waves.

Yoon, Peter H.↗

NASA NTRS1993

Quasi-linear analysis of ion Weibel instability in the earth's neutral sheet

A quasi-linear analysis of the ion Weibel instability (IWI) for waves with parallel propagation is carried out for parameters appropriate to the earth's neutral sheet during the substorm interval. For ion drift speed reaching sizable fraction of the ion thermal speed, unstable waves grow to a nonlinear regime in a time interval greater than an ion gyroperiod. The saturation level is attained with current density reduced to about 15-28 percent of its preactivity level. The unstable wave amplitude normalized to the initial ambient field is found to be in the range of 0.2-0.8. This is accompanied by ion heating along the magnetic field with the parallel temperature being enhanced by 25-90 percent. Thus, the IWI can provide nonadiabatic heating of ions in current disruptions during substorms. The associated anomalous resistivity is estimated to be about 1 x 10 exp -7 to 1 x 10 exp -6 s, which is about 11 to 12 orders of magnitude above the classical resistivity.

Lui, Anthony T. Y.↗

NASA NTRS1992

Ion heating by kinetic cross-field streaming instability due to reflected ions at a quasiperpendicular shock

The present paper shows that the reflected ion at a supercritical quasi-perpendicular shock wave can excite a purely growing mode propagating parallel to the ambient magnetic field. To discuss the ion heating by such an unstable mode, the self-consistent quasi-linear kinetic equation is solved with the assumption that the present purely growing mode is the dominant unstable mode in the system. In the quasi-linear analysis of the instability, two particular cases are considered: the case of low initial ion beta and that of a high initial ion beta.

Yoon, Peter H.↗

NASA NTRS1991

Kinetic friction attributed to enhanced radiation by cyclotron maser instability

Along the auroral field lines, a fraction of the energetic electrons injected from the magnetotail is reflected by the earth's convergent geomagnetic field. The reflected loss-cone electrons are unstable with respect to the cyclotron maser instability, resulting in the auroral kilometric radiation. This paper investigates the kinetic friction force exerted on the energetic electrons by the enhanced radiation field. It is found that the enhanced radiation results in a deceleration of reflected electrons, thereby providing an effective resistivity. In addition, the rate of decrease (increase) of effective perpendicular (parallel) kinetic temperatures is also evaluated. The analysis is carried out over various physical parameters such as the degree of loss cone, average particle energy, and the ratio of plasma frequency to cyclotron frequency.

Yoon, Peter H.↗

NASA NTRS1991

Kilometric radio waves generated along auroral field lines observed by ground facilities - A theoretical model

A theory of generation of radio waves observed by ground-based facilities in the frequency range 150-700 kHz is discussed. This work is a continuation of an earlier discussion (Wu et al., 1989) in which it was proposed that the trapped electrons along the auroral field lines can lead to a cyclotron instability which amplifies the whistler waves observed at ground level. The objective of the present study is to investigate the propagation effect on the wave amplification and to examine whether the proposed mechanism is indeed viable.

Ziebell, L. F.↗

NASA NTRS1991

Ion pickup by the solar wind via wave-particle interactions

Ion pickup by the solar wind is a topic of current interest. In situ observations and theoretical studies establish a fairly good understanding of the physics of the ion-pickup process. In a weakly turbulent solar wind, hydromagnetic waves that are either intrinsic or excited by the newborn ions can lead to pitch-angle diffusion which can be approximately described by the quasi-linear theory with or without incorporating the resonance-broadening mechanism due to weak turbulence. According to the weak turbulence theory, the pickup ions do not form a complete spherical shell distribution in the time-asymptotic state unless the wave field is sufficiently strong. In some cases the ions only possess a partial or incomplete shell. When the solar wind is highly turbulent, direct interaction between the wave fields and the newborn ions can result in rapid pitch-angle scattering leading to swift formation of a spherical shell distribution on the time scale of an ion gyro-period.

Yoon, Peter H.↗

NASA NTRS1990

Pitch angle and velocity diffusions of newborn ions by turbulence in the solar wind

The temporal evolution of the distribution function of newborn ions under the influence of intrinsic low-frequency solar wind turbulences is studied. In particular, an initial ring-beam distribution of newborn ions under the influence of hydromagnetic waves is considered. A simplified treatment of the resonance broadening effect is given, and its role in the pickup process is discussed. Two different configurations of wave polarization amd direction of propagation are considered. The conditions that lead either to the formation of anisotropic shells as a long-duration transient state or to rapid isotropization of the ion pitch angle distribution are discussed, as are the conditions which lead to significant acceleration of the ions.

Ziebell, L. F.↗

NASA NTRS1990

Pitch angle diffusion of newborn ions due to intrinsic turbulence in the solar wind

The objective of the present study is to understand the interaction of the solar wind with newborn ions in far upstream regions of a comet where the level of intrinsic turbulence is moderately low. Based on the assumption that quasi-linear theory is adequate and applicable, the pitch angle diffusion process and the time evolution of the newborn ion distribution function are investigated. Numerical solutions to the quasi-linear diffusion equation, including the effect of resonance broadening and that of continuous creation of newborn ions due to the ionization process, are obtained under several assumptions and approximations. It is found that theoretical results are consistent with the Giotto observations recently reported by Neugebauer et al. (1989).

Ziebell, L. F.↗

NASA NTRS1990

Development of pitch angle anisotropy and velocity diffusion of pickup ion shell distribution by solar wind turbulence

The evolution of pitch angle anisotropy in initially isotropic spherical shell distribution of pickup ions subjected to a continuous influence of weak or moderate intrinsic solar wind turbulence is investigated using a physical model which assumes that the wave of the solar wind turbulence is propagating mainly in the direction parallel to the ambient magnetic field. It is shown that, because of the pitch angle dependence of the velocity diffusion process, a significant pitch angle anisotropy of pickup ion shell distribution develops in the early stage of the diffusion process. Although it is smeared out later on, the result can be of significant importance, especially if the pickup ion density is large, because the pitch angle anisotropy can excite collective instabilities and increase the wave level, thus accelerating the diffusion process.

Yoon, Peter H.↗

NASA NTRS1990

Gyroharmonic maser instability for weakly relativistic electrons with a loss-cone distribution

The weakly relativisitic dielectric tensor for a system of electrons comprised of cold and energetic populations, embedded in a neutralizing background, is reformulated in terms of an infinite series representation in powers of lamba = alpha ck(perpendicular)/omega (c), where alpha-squared is a parameter proportional to the average thermal energy of the energetic electrons, k(perpendicular) is the perpendicular component of the wave vector k, and omega (c) is the electron gyrofrequency. The energetic electrons are assumed to have a loss-cone feature in the perpendicular momentum space. The present formalism can be used in the problem of cyclotron maser as well as more general gyroharmonic maser (i.e., multiharmonics) emissions resulting from weakly relativistic loss-cone electrons. This is because, unlike the previous theories in which certain approximations such as the single-harmonic approximations are made, the present formalism retains contributions from the entire harmonics.

Yoon, Peter H.↗

NASA NTRS1990

Kinetic instability associated with spherical shell distribution of cometary pickup ions

The stability of ion shell distribution is an interesting and important issue in view of the fact that it is stable under perturbations propagating parallel to the ambient magnetic field, despite large amount of free energy it contains. It was found, however, that if the shell distribution of ions has a sufficient amount of drift speed with respect to the solar wind hydromagnetic waves, it can become unstable. The obliquely propagating hydromagnetic instability associated with the ion shell distribution was recently discovered. This letter presents the unified stability analysis of the ion shell distribution, under what condition the drift-induced instability of the type first discussed by Gary and Sinha (1989), and the oblique hydromagnetic instability discussed by Wu and Yoon (1990) are excited, and how the two types of instabilities are related.

Yoon, Peter H.↗