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In the battle between CRISPR-Cas* prokaryotic immune systems and the elements that they target, a diverse array of “anti-CRISPR” proteins have evolved. These proteins appear to have arisen independently multiple times in evolution and function through diverse mechanisms to inhibit CRISPR-Cas immunity. For comprehensive reviews on anti-CRISPRs, we direct readers to recent publications.
Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.
ABSTRACT The abundance, temperature, and clustering of metals in the intergalactic medium are important parameters for understanding their cosmic evolution and quantifying their impact on cosmological analysis with the Ly α forest. The properties of these systems are typically measured from individual quasar spectra redward of the quasar’s Ly α emission line, yet that approach may provide biased results due to selection effects. We present an alternative approach to measure these properties in an unbiased manner with the two-point statistics commonly employed to quantify large-scale structure. Our model treats the observed flux of a large sample of quasar spectra as a continuous field and describes the one-dimensional, two-point statistics of this field with three parameters per ion: the abundance (column density distribution), temperature (Doppler parameter), and clustering (cloud–cloud correlation function). We demonstrate this approach on multiple ions (e.g. ${\rm C\, \small {\rm IV}}$ , ${\rm Si\, \small {\rm IV}}$ , and ${\rm Mg\, \small {\rm II}}$ ) with early data from the Dark Energy Spectroscopic Instrument (DESI) and high-resolution spectra from the literature. Our initial results show some evidence that the ${\rm C\, \small {\rm IV}}$ abundance is higher than previous measurements and evidence for abundance evolution over time. The first full year of DESI observations will have over an order of magnitude more quasar spectra than this study. In a future paper, we will use those data to measure the growth of clustering and its impact on the Ly α forest, as well as test other DESI analysis infrastructure such as the pipeline noise estimates and the resolution matrix.
Radio transient searches using traditional variability metrics struggle to recover sources whose evolution time-scale is significantly longer than the survey cadence. Motivated by the recent observations of slowly evolving radio afterglows at gigahertz frequency, we present the results of a search for radio variables and transients using an alternative matched-filter approach. We designed our matched-filter to recover sources with radio light curves that have a high-significance fit to power-law and smoothly broken power-law functions; light curves following these functions are characteristic of synchrotron transients, including ‘orphan’ gamma-ray burst afterglows, which were the primary targets of our search. Applying this matched-filter approach to data from Variables and Slow Transients Pilot Survey conducted using the Australian SKA Pathfinder, we produced five candidates in our search. Subsequent Australia Telescope Compact Array observations and analysis revealed that: one is likely a synchrotron transient; one is likely a flaring active galactic nucleus, exhibiting a flat-to-steep spectral transition over 4 months; one is associated with a starburst galaxy, with the radio emission originating from either star formation or an underlying slowly evolving transient; and the remaining two are likely extrinsic variables caused by interstellar scintillation. The synchrotron transient, VAST J175036.1–181454, has a multifrequency light curve, peak spectral luminosity, and volumetric rate that is consistent with both an off-axis afterglow and an off-axis tidal disruption event; interpreted as an off-axis afterglow would imply an average inverse beaming factor $\langle f^{-1}_{\text{b}} \rangle = 860^{+1980}_{-710}$, or equivalently, an average jet opening angle of $\langle \theta _{\textrm {j}} \rangle = 3^{+4}_{-1}\,$ deg.
Recently it was found that scrambled information can be partially recovered by a time-reversed evolution, even after being damaged by an intruder. Here we reconsider the origin of the information recovery, and argue that the presence of classical chaos does not preclude it and only leads to a quantitative reduction of the recovery ratio. We also show how decoherence (i.e., entanglement with the intruder) limits the recovery, by proving an upper bound on the recovery ratio in terms of the entangling power of the intruder's action.
We introduce a technique for recovering noise-free observables in noisy quantum systems by combining the results of many slightly different experiments. Our approach is applicable to a variety of quantum systems, but we illustrate it with applications to quantum information and quantum sensing. The approach corresponds to repeating the same quantum evolution many times with known variations on the underlying systems' error properties, e.g., the spontaneous emission and dephasing times $T_1$ and $T_2$. As opposed to standard quantum error correction methods, which have an overhead in the number of qubits (many physical qubits must be added for each logical qubit), our method has only an overhead in the number of evaluations, allowing the overhead to, in principle, be hidden via parallelization. We show that the effective spontaneous emission $T_1$ and dephasing $T_2$ times can be increased using this method in both simulation and experiments on an actual quantum computer. We also show how to correct more complicated entangled states and how Ramsey fringes relevant to quantum sensing can be significantly extended in time.
This paper compares features, challenges, and puzzles of different models for a unitary black hole S -matrix, focusing on both recent nonisometric models, as well as “nonviolent unitarization,” which is based on new quantum interactions of a black hole. As a foundation for comparison, the description of real-time Hawking evolution is first overviewed, including leading effects of gravitational dressing and backreaction. Connection is then made to qubit models for evolution, and some technology is outlined to facilitate their description. Important features of both nonisometric models and nonviolent unitarization are investigated in qubit models, which illustrate essential differences between the respective approaches. The nonisometric models present puzzles for understanding evolution of internal outgoing excitations, which can be excited by interactions such as particle decay. Qubit models for nonviolent unitarization are further developed, and nicely illustrate aspects of that approach. Some remaining questions in generalizing to more complete models for evolution are discussed. Published by the American Physical Society 2024
In this study, we present a nonintrusive reduced order modeling (ROM) framework for large-scale quasistationary systems. The framework proposed in this work exploits the time series prediction capability of long short-term memory (LSTM) recurrent neural network architecture such that (1) in the training phase, the LSTM model is trained on the modal coefficients extracted from the high-resolution data snapshots using proper orthogonal decomposition (POD) transform, and (2) in the testing phase, the trained model predicts the modal coefficients for the total time recursively based on the initial time history. Hence, no prior information about the underlying governing equations is required to generate the ROM. To illustrate the predictive performance of the proposed framework, the mean flow fields and time series response of the field values are reconstructed from the predicted modal coefficients by using an inverse POD transform. As a representative benchmark test case, we consider a two-dimensional quasigeostrophic ocean circulation model which, in general, displays an enormous range of fluctuating spatial and temporal scales. We first demonstrate that the conventional Galerkin projection-based reduced order modeling of such systems requires a high number of POD modes to obtain a stable flow physics. In addition, ROM-Galerkin projection (ROM-GP) does not seem to capture the intermittent bursts appearing in the dynamics of the first few most energetic modes. However, the proposed nonintrusive ROM framework based on LSTM (ROM-LSTM) yields a stable solution even for a small number of POD modes. We also observe that the ROM-LSTM model is able to capture quasiperiodic intermittent bursts accurately, and yields a stable and accurate mean flow dynamics using the time history of a few previous time states, denoted as the lookback time window in this paper. We show several features of ROM-LSTM framework such as significantly higher accuracy than ROM-GP, and faster performance using larger time step size. Throughout the paper, we demonstrate our findings in terms of time series evolution of the field values and mean flow patterns, which suggest that the proposed fully nonintrusive ROM framework is robust and capable of predicting chaotic nonlinear fluid flows in an extremely efficient way compared to the conventional projection-based ROM framework.
By examining the entropy production in fully kinetic simulations of collisional plasmas, it is shown that the transition from collisional Sweet-Parker reconnection to collisionless Hall reconnection may be viewed as a thermodynamic phase transition. The phase transition occurs when the reconnection electric field satisfies E = $E_{D}\sqrt{m{e}/{m}_i}$ , where ${m{e}/{m}_i}$ is the electron-to-ion mass ratio and E D is the Dreicer electric field. This condition applies for all ${m{e}/{m}_i}$, including ${m{e}/{m}_i}$ = 1 , where the Hall regime vanishes and a direct phase transition from the collisional to the kinetic regime occurs. In the limit ${m{e}/{m}_i}$ → 0, this condition is equivalent to there being a critical electron temperature $Te ≈ m_iΩ^{2}_{i}δ^{2}$, where $Ω_i$ is the ion cyclotron frequency and δ is the current sheet half-thickness. The heat capacity of the current sheet changes discontinuously across the phase transition, and a critical power law is identified in an effective heat capacity. A model for the time-dependent evolution of an isolated current sheet in the collisional regime is derived.
We show that flash experiments with three phase mixed-powders of yttria-stabilized zirconia (8YSZ), MgO, and α-Al 2 O 3 not only produce polycrystals of high density, but also the transformation of magnesia and alumina into single-phase spinel. The presence of zirconia facilitates the onset of the flash. The sintering experiments in the laboratory were extended to live experiments at the National Synchrotron Light Source II at Brookhaven National Laboratory in order to measure the time-dependent evolution of single-phase spinel. The phase transformation occurred in <3 seconds during Stage II. Later, during Stage III the cubic zirconia transformed partly into the monoclinic phase, which reverted back to the cubic phase when the flash was extinguished by turning off the current to the specimen. The results underpin a recent report on the synthesis of single-phase bismuth ferrite from constituent oxides in reactive flash experiments, raising the specter of flash as a method for synthesis as well as sintering of complex oxide ceramics. The role of zirconia in catalyzing the flash in the present study is discussed.
Measuring the field of visible light with high spatial resolution has been challenging, as many established methods only detect a focus-averaged signal. Here, we introduce a near-field method for optical field sampling that overcomes that limitation by employing the localization of the enhanced near-field of a nanometric needle tip. A probe field perturbs the photoemission from the tip, which is induced by a pump pulse, generating a field-dependent current modulation that can easily be captured with our electronic detection scheme. The approach provides reliable characterization of near-petahertz fields. We show that not only the spiral wavefront of visible femtosecond light pulses carrying orbital angular momentum (OAM) can be resolved but also the field evolution with time in the focal plane. Additionally, our method is polarization sensitive, which makes it applicable to vectorial field reconstruction.
Ion migration is one of the prime reasons for the rapid degradation of metal halide perovskite solar cells (PSCs), and we report on a method for quantifying mobile ion concentration (No) using a transient dark current measurement. We perform both ex-situ and in-situ measurements on PSCs and study the evolution of No in films and devices under a range of temperatures. We also study the effect of device architecture, top electrode chemistry, and metal halide perovskite composition and dimensionality on No. Two-dimensional perovskites are shown to reduce the ion concentration along with inert C electrodes that do not react with halides by ~99% while also improving mechanical reliability by ~250%. We believe this work can provide design guidelines for the development of stable PSCs through the lens of minimizing mobile ions and their evolution over time under operational conditions.
The aerosol physics of uranyl particle formation has been addressed in this research using advanced aerosol instrumentation and an aerosol dynamics model. Based on the research works, we conclude that the formation and growth of aerosol particles by gas-phase UF6 hydrolysis strongly depends on the availability of water molecules in our reactor conditions. The total number concentration of the UO 2 F 2 particulate material that could be produced in the hydrolysis reaction is also regulated primarily by the availability of water molecule concentration. The higher the water molecule concentration, the higher the number and the larger the size of UO 2 F 2 aerosol particles that could be produced in a reactor custom-built at ORNL. Although the aerosol reactor was enabling the study of particle formation kinetics, the instrumentation was still insufficient in characterizing the chemical composition of the produced particles as well as the time-dependent evolution of the particulate species. The temporal evolution could impact the eventual fate of the particles upon release to the environment (i.e., the physio-chemical transformation, transport, and removal). On uranyl particle formation kinetics, we found that the growth rates of aerosol particles appeared to approach a single number in the range of 0.05 ± 0.03 - 0.08 ± 0.04 nm/s, statistically, as the ω value becomes smaller than 1. The size of primary particles from the UF6 hydrolysis at water-deprived condition was estimated to be 3.6 ± 0.4 nm; the higher the availability of water molecules, the larger the primary particles. The ability to precisely control the availability of water molecules in the reaction could lead to the production of nearly monodispersed aerosol particles. In other words, the result suggests that one can precisely manipulate the size of UO 2 F 2 aerosol particles by controlling the water vapor availability and interaction of water molecules with U F6 in the reaction. This finding has significant implications in the engineering manufacturing of fuel powder materials and possibly to future development and deployment of an environmental sampling apparatus.
Two-dimensional (2D) materials have extraordinary characteristics that offer promising new approaches for science and technology. Electrons in graphene can move ballistically through a sheet, even though it is only a single atom thick. And transition metal dichalcogenide materials can be cleaved into 2D flakes of all types – metals, semiconductors, insulators, magnetic materials, and superconductors. To benefit from these discoveries, the science needs to be understood to transform 2D materials into useful new devices and systems. The evolution in time of atomic scale graphene structures has been studied in time with a transmission electron microscope (TEM), and ballistic transport of electrons in graphene was been imaged using a cooled scanning probe microscope (SPM), as well as electron motion in MoS 2 . Graphene is only one atom thick but is extremely strong, creating the opportunity to fabricate atomic scale structures in the lateral direction. Using an atomic resolution TEM, a suspended sheet of graphene can be shaped by a Si impurity atom on its surface that acts like a chisel to open up apertures, one atom at a time. The electrons in the TEM provide both the chiseling energy and the ability to image the results. Electrons and holes in graphene form a new type of electronic system with conical conduction and valence bands that meet at the Dirac point, with no energy gap. For moderate densities, the carriers form a Fermi liquid with ballistic transport over micron-scale distances. Using a cooled SPM the cyclotron orbit of electrons in graphene has been imaged. In the magnetic focusing regime, electrons leaving a point contact circle around and leave from a second point contact when the cyclotron diameter is equal to the contact spacing. The paths of electrons are focused - they enter at different angles but converge again at the exiting contact. When the SPM tip knocks an electron out of its orbit, an imaging signal is created. The ballistic motion of carriers in graphene opens the way for ballistic devices that manipulate beams of electrons and holes. Our collaborator Gil-Ho Lee, in Philip Kim's group, created a collimating contact by placing zig-zag absorbers on either side of entering electrons. Our cooled SPM was used to image the electron beam and determine its 9-degree halfwidth. By changing the gate voltage, a collimated beam of holes was also created, opening the way for colliding beam experiments. Coherent beams of carriers are desirable for quantum information processing. Via Andreev reflection, superconducting contacts can covert Cooper pairs in a superconductor to an ingoing and outgoing electrons and holes. Using our cooled SPM, Andreev reflection was imaged from a superconducting contact on a graphene device. Magnetic focusing was used to create an incoming beam of electrons and an outgoing beam of holes, detected by a third point contact. The images show a clear transition from normal reflection above the superconducting transition temperature to Andreev reflection as the device is cooled. Transition metal dichalcogenides offer a wide array of materials that can be exfoliated into ultrathin 2D sheets. A cooled SPM can be used to detect quantum dots as well as to image electron flow. The tip charge capacitively couples to electrons on the dot, acting as a gate to tune the dot conductance. Coulomb blockade peaks appear as a bullseye pattern in an SPM image as the tip is raster scanned above the dot. This approach was used to detect quantum dots in a MoS 2 channel as the carrier density was reduced and electrons pooled in low energy points. Through our DOE supported research, cooled SPM imaging has proven to be a very useful tool to uncover the motion of electrons and holes in the new quantum materials graphene and MoS 2 .
An important part of the simulation technique implemented in the strong motion prediction recipe developed in Japan, originally proposed by Irikura and Miyake (2011) is the earthquake rupture characterization that is based on established empirical scaling relationships between source parameters and seismic moment. These scaling relationships and rupture characterization are derived from recorded data and are tested by simulations. Recent analysis of results obtained with the Recipe for the 2016 M7.1 Kumamoto earthquake performed by several researchers, indicate that in order to reproduce near-fault long-period ground motions with permanent displacements, typical for earthquakes with surface rupturing, the recipe needs modifications. In particular, improvements are required in characterizing the rupture kinematics at shallow depths, above the seismogenic zone (Irikura et al., 2019). Modeling of rupture dynamics for recorded earthquakes, and numerical simulations for different rupture scenarios, provides physical constrains on slip evolution in time and space, which can be used in adjustments of empirical source scaling relationships for large crustal earthquakes. In this study we mainly focused on rupture dynamics modeling of the 2019 M7 Ridgecrest, California earthquake. The characterization of the kinematic rupture model derived from the dynamic rupture models of this earthquake can inform further refinements of rupture modeling proposed by the Recipe. Through different rupture scenarios we investigated potential relationships between characteristics of Long Period Ground Motion Generation Area (LMGA), used in the Recipe, and asperity depth and rupture initiation.
Geophysical imaging techniques are a non-invasive way to image the subsurface and understand both subsurface solid (rock/soil) and fluid property distributions and their evolution in time. Inversions of the geophysical data, such as Electrical Resistance Tomography (ERT) data, are solved to estimate the subsurface property distributions, such as conductivity, and many inversion techniques smooth out sharp gradients in rock or fluid property distributions. Sharp gradients in subsurface properties tend to be present in situations with complex subsurface structures, which are common in many subsurface applications. We have successfully demonstrated that it is possible to inform, or constrain, inversions with neural networks trained on synthetic data with complex subsurface structures. Initial results suggest this process may be optimizable to yield property distributions that better represent the true property distributions than the same inversion process without the neural network constraint. Future work would optimize the neural network performance for this application and then apply the synthetic-data trained neural network to real data to understand the utility and performance of this technique for real data sets.
Experiments were conducted to investigate a passive production mechanism for the world’s most energy intensive commodity, ammonia. A novel method, gamma catalyzed ammonia production at ambient conditions, was investigated. Ammonia is currently produced through the highly energy intensive Haber-Fritz process, which requires an operation pressure of 400 atmosphere and 600 degrees Celsius. Due to the high demand and need for ammonia, the Haber-Bosch process consumes 25% all energy produced globally. Reported herein was an attempt to produce ammonia at ambient temperature (20 C) and ambient pressure (1 atm), through a novel process developed at PNNL, gamma driven catalysis of ammonia. Although the measurements of the ammonia production suggest wild success, reports in the literature by Gao et.al. suggest an experimental positive bias in the results. To rule out the potential positive bias, multiple additional production campaigns would be needed to with an alternate analysis technique such as ion chromatography, as suggested by Gao et.al. Unfortunately, due to this late determination of potential positive bias, the results of this study remain inconclusive to the feasibility of gamma driven catalysis of ammonia and more work is needed to describe the chemical evolution with time. The results are a first step and demonstrate that gamma-catalyst mediated reactions are possible. This represents a key opportunity to explore the fundamental chemistry of high band gap catalysts that can change the paradigm of radiation, transforming it from a waste to a valuable energy source.
This project will create an Engineered Geothermal System (EGS) comprising two or more wells drilled to a depth of 4.25 km into superhot rock (SHR) with a temperature of 425 °C at Newberry Volcano in Central Oregon. An EGS is a manufactured heat exchanger in which water is injected in a deep injection well, or injector, to extract heat from the hot rock at depth and steam is returned to the surface in a production well, or producer, to generate electricity. In this project, the SHR EGS will be made using new methods and technologies to stimulate and connect hydraulic and natural fractures to enable multiple flow pathways between wells, allowing for optimal heat mining from the reservoir rock. The new technologies are designed to operate at rock temperatures much higher than those encountered in traditional geothermal. Following EGS completion, water will be injected into the injector well and steam extracted from the producer well in a long-term connectivity flow test demonstrating SHR reservoir evolution with time and use. Success will be measured by demonstrating the efficacy of new technologies and by producing economic quantities of steam (>40 MWth).