A high-quality genome assembly of the tetraploid Teucrium chamaedrys unveils a recent whole-genome duplication and a large biosynthetic gene cluster for diterpenoid metabolism
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The parallel development of ultramicroelectrodes (UMEs) and groundbreaking scanning probe microscopy techniques in the late 1980s led to the development of the scanning electrochemical microscope. Scanning electrochemical microscopy (SECM) was born from the idea of using a tiny electrode to measure the local electrochemical behavior at operating electrodes. From its foundations, the technique displayed an inherent versatility in measuring sample properties beyond topography. It allowed experimenters to measure and map chemical reactions occurring at diverse interfaces, from inspecting the reversibility of redox mediators at metal electrodes, to detecting the hallmarks of cellular respiration on living plant leaves. Related but distinct electrochemical scanning probe techniques, such as electrochemical atomic force microscopy (EC-AFM), scanning ion conductance microscopy (SICM), and scanning electrochemical cell microscopy (SECCM) have developed in parallel. These techniques have demonstrated exquisite spatial resolution down to the nanoscale regime. However, it is the proposition of this review that SECM remains unmatched at revealing the chemical aspects of electrochemistry. Furthermore, it is our intention to review and demonstrate that the versatile architecture of SECM continues to evolve and address fundamental and emerging challenges in the fields of energy storage and conversion, chemical biology, materials science, and environmental chemistry, among others.
Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations. Here, we show that semiempirical methods can be used as alternatives to density functional theory (DFT) to assess convergence in sequences of models generated by various automated protocols. The cost of these convergence tests is reduced even further by means of a many-body expansion. We use this approach to examine convergence (with respect to model size) of protein–ligand binding energies. Fragment-based semiempirical calculations afford well-converged interaction energies in a tiny fraction of the cost required for DFT calculations. Two-body interactions between the ligand and single-residue amino acid fragments afford a low-cost way to construct a “QM-informed” enzyme model of reduced size, furnishing an automatable active-site model-building procedure. This provides a streamlined, user-friendly approach for constructing ligand binding-site models that needs neither a priori information nor manual adjustments. Extension to model-building for thermochemical calculations should be straightforward.
An accurate determination of singlet−triplet gaps in biradicals, including cyclobutadiene in the automerization barrier region where one has to balance the substantial nondynamical many-electron correlation effects characterizing the singlet ground state with the predominantly dynamical correlations of the lowest-energy triplet, remains a challenge for many quantum chemistry methods. High-level coupled-cluster (CC) approaches, such as the CC method with a full treatment of singly, doubly, and triply excited clusters (CCSDT), are often capable of providing reliable results, but routine application of such methods is hindered by their high computational costs. We have recently proposed a practical alternative to converging the CCSDT energetics at small fractions of the computational effort, even when electron correlations become stronger and connected triply excited clusters are larger and nonperturbative, by merging the CC(P;Q) moment expansions with the selected configuration interaction methodology abbreviated as CIPSI. We demonstrate that one can accurately approximate the highly accurate CCSDT potential surfaces characterizing the lowest singlet and triplet states of cyclobutadiene along the automerization coordinate and the gap between them using tiny fractions of triply excited cluster amplitudes identified with the help of relatively inexpensive CIPSI Hamiltonian diagonalizations.
A systematically converging series of ab initio, post-density-functional, size-consistent, electron-correlated approximations is desired for predictive computing of felectronic band structures of insulating, semiconducting, and metallic solids. A series that meets all of these desiderata (except the applicability to metals) is ab initio many-body Green's function theory based on Gaussian-type-orbital (GTO) basis sets. Here, its leading-order approximation, the second-order Green's function (GF2) method in the diagonal and frequency-independent approximations with the aug-cc-pVDZ basis set, is applied to the fundamental band gaps of three semiconductors (diamond, silicon, and silicon carbide in the zincblende structure) using cluster models. Corrections are made to the basis-set-incompleteness errors by the explicit-correlation (F12) ansatz (GF2-F12) for the valence band edges. The crystals are modeled as surface-passivated clusters of increasing sizes, whose wave functions are expanded by up to 2709 GTO basis functions. Immense computational costs of these calculations are overcome by the highly scalable stochastic algorithm of the Monte Carlo GF2-F12 method, whose operation cost per state increases only as a cubic power of system size, which has a tiny memory footprint and easily achieves near-perfect parallel efficiency on thousands of CPUs or on hundreds of GPUs. The correlated, F12-corrected highest-occupied and lowest-unoccupied molecular-orbital energy (HOMO-LUMO) gap is 5.78 ± 0.07 eV for C 87 H 76 as compared with the experimental value of the fundamental (indirect) band gap of bulk diamond at 5.48 eV. The correlated, F12-corrected HOMO-LUMO gaps for Si 75 H 76 and Si 32 C 43 H 76 are 2.56 ± 0.15 eV and 3.50 ± 0.12 eV, respectively, which are expected to decrease further with increasing cluster sizes. As a result, the experimental fundamental (indirect) band gaps of bulk silicon and silicon carbide are 1.17 eV and 2.42 eV, respectively.
Abstract The carbon capture, utilization, and storage (CCUS) framework is an essential component in reducing greenhouse gas emissions, with its success hinging on the comprehensive knowledge of subsurface geology and geomechanics. Passive seismic event relocation and fault detection offer vital insights into subsurface structures and the ability to monitor fluid migration pathways. Accurate identification and localization of seismic events, however, face significant challenges, including the necessity for high‐quality seismic data and advanced computational methods. To address these challenges, we introduce a novel deep learning method, , specifically designed for passive seismic source relocation and fault delineating for passive seismic monitoring projects. By leveraging data domain‐adaptation, allows us to train a neural network with labeled synthetic data and apply it directly to field data. Using , the passive seismic sources are automatically clustered based on their recording time and spatial locations, and subsequently, faults and fractures are delineated accordingly. We demonstrate the efficacy of on a field case study involving injection related microseismic data from Decatur, Illinois area. Our approach accurately and efficiently relocated passive seismic events, identified faults and could aid in potential damage induced by seismicity. Our results highlight the potential of as a valuable tool for passive seismic monitoring, emphasizing its role in ensuring CCUS project safety. This research bolsters the understanding of subsurface characterization in CCUS, illustrating machine learning’s capacity to refine these methods. Ultimately, our work has significant implications for CCUS technology deployment, an essential strategy in combating climate change. Plain Language Summary In our quest to tackle climate change, we use a strategy known as carbon capture, utilization, and storage (CCUS) to keep greenhouse gases out of the atmosphere. This strategy relies heavily on our ability to understand what's happening deep under the earth's surface. To make sure we store super critical safely, we need to accurately map out the geological structure, especially faults, but this is tough without high‐quality data and complex computer programs. We've developed a new tool called “DeFault,” which uses advanced machine learning to improve how we find and map these underground features. “DeFault” is smart enough to learn from numerically simulated data and then apply what it’s learned to real‐world situations. It groups together seismic activity—tiny tremors and shifts in the earth—based on when and where they happen, which helps us spot where there might be cracks or faults. We tested “DeFault” in Illinois, where CO 2 is injected underground, and it successfully pinpointed where these tremors occurred and mapped out the faults, helping to prevent accidents accurately in the future. Our study shows that “DeFault” will be a powerful ally in making CCUS safer and more effective, especially for the Illinois Basin Decatur Project. Key Points Faults and fractures introduced by carbon storage can be monitored by passive seismicity DeFault algorithm enables an automatic process for accurate and efficient passive seismic event locating and clustering
Water has extraordinary electrical properties when trapped in tiny channels — Here, a finding that calls for a re-think about key processes in biology, climate and nanotechnology.
The sol-gel synthesis represents a versatile platform to fabricate ceramic inorganic membranes. However, it is still a grand challenge to push the boundary of sol-gel chemistry towards high-quality organic membrane construction. Herein, a facile and controlled nanocrystal suturing strategy in sol-gel solutions is developed to afford highly crystalline and free-standing covalent organic framework membranes. The key chemistry design lies in deploying tiny threads (1 mol% dual-NH 2 -tail linear polymer) to efficiently suture the highly charged covalent organic framework nanocrystals stabilized and confined in sol-gel solutions, creating a continuous and intact membrane surface. A subsequent treatment heals the sutured covalent organic framework nanocrystals, yielding a free-standing membrane with high crystallinity and ordered pores. The structure evolution and role of the thread linker are elucidated via operando spectroscopy and microscopy. The as-afforded covalent organic framework membranes demonstrate attractive proton transport performance in high temperature and anhydrous fuel cell applications.
Endowing functional properties with mechanical responses in traditional metals has been a frontier topic, akin to transforming base metal into gold. Chromium and its alloys, with their functional deficiencies and limited ductility, serve as typical examples. Herein, we report a Cr96Fe4Ge1.3B1 alloy that unifies low thermal expansion (LTE, αl = 1.79 × 10-6 K-1, 200 − 315 K) with exceptional toughness (240.2 J·cm-3). The enhancement in mechanical responses is primarily attributed to layered Cr2B intermetallic precipitates, which ameliorate interfacial cohesion and simultaneously refine the grain structure. The weakened interlayer interactions within the Cr-B layers facilitate the nucleation and movement of numerous tiny stacking faults in precipitates, efficiently alleviating strain energy and resulting in marked work-hardening ability. Additionally, antiferromagnetic fluctuations in the BCC matrix contribute to the unique LTE behavior. This paves the way for the design of high-performance alloys featuring layered-symmetry precipitates.
A simple similarity has been proposed for kinetic (e.g., particle-in-cell) simulations of plasma transport that can effectively address the long-standing challenge of reconciling the tiny Debye length with the vast system size. This applies to both transport in unmagnetized plasma and parallel transport in magnetized plasmas, where the characteristics length scales are given by the Debye length, collisional mean free paths, and the system or gradient lengths. The controlled scaled variables are the configuration space, x/L, and an artificial Coulomb Logarithm, L ln Λ, for collisions, while the scaled time, t/L, and electric field, LE, are automatic outcomes. The similarity properties are examined, demonstrating that the macroscopic transport physics is preserved through a similarity transformation while keeping the microscopic physics at its original scale of Debye length. To showcase the utility of this approach, two examples of 1D plasma transport problems were simulated using the VPIC code: the plasma thermal quench in tokamaks [Li et al., Nuclear Fusion 63, 066030 (2023)] and the plasma sheath in the high-recycling regime [Li et al., Physics of Plasmas 30, 063505 (2023)].
Here, we develop a Fermi–Bose bootstrap embedding framework for the ground state of interacting electrons coupled to a phonon mean field. The method combines bootstrap embedding for correlated electrons with a self-consistent coherent-state mean-field treatment for phonons. This method models the interacting electron–phonon problem as a system of correlated electrons traveling in a self-consistently specified potential landscape, allowing for efficient treatment of large lattice systems. Convergence of the methods for fragment size and total system size is demonstrated for the one-dimensional Hubbard–Holstein model for up to 350 sites. Finite-size scaling is performed to extrapolate to the infinite system size. Benchmarking against the density matrix renormalization group for a small 8-site system at half- and quarter-filling shows an orders-of-magnitude runtime advantage. The comparison further reveals that the method performs best in regimes dominated by localization, such as the Mott insulating phase and the strong-coupling tiny polaron regime, where the local embedding ansatz is still valid. However, due to the mean-field treatment for phonons, we find limitations of our methods in the weakly coupled delocalized region and at the Peierls transition, where quantum phonon fluctuations and long-range kinetic correlations become substantial.
Abstract In this work, we report a method that enables a standard electrostatic MEMS device to perform complex sensing functionalities, such as detecting the presence of helium without a sensing material or a conditioning circuit. Helium is a noble, odorless, non-reactive gas that is very challenging to detect. It is used in critical applications such as storing nuclear fuel waste inside a dry cask. In these applications, its leakage from the dry cask may indicate the cask's safe operation's degradation. A departure from the common practice of exciting the MEMS around its mechanical resonance, the method is based on exciting the MEMS around its electrical resonance circuit. This method shows that the tiny difference between the air dielectric constant (1.00059) and helium (1.000067) corresponding to only a few Femtofarad level capacitances produces a 25 mV difference without a conditioning circuit. Simulation results confirmed those findings and explored the sensor response at different operation conditions. This method eliminates the need for a heated microstructure and the need for absorption material. This method is not limited to gas sensing. It can be applied to other sensing mechanisms, such as acceleration and pressure measurements, and eliminate the complex circuit to read small capacitance in these applications.
Abstract Spike-timing-dependent plasticity (STDP) is an unsupervised learning mechanism for spiking neural networks that has received significant attention from the neuromorphic hardware community. However, scaling such local learning techniques to deeper networks and large-scale tasks has remained elusive. In this work, we investigate a Deep-STDP framework where a rate-based convolutional network, that can be deployed in a neuromorphic setting, is trained in tandem with pseudo-labels generated by the STDP clustering process on the network outputs. We achieve 24.56% higher accuracy and 3.5 × faster convergence speed at iso-accuracy on a 10-class subset of the Tiny ImageNet dataset in contrast to a k -means clustering approach.
We perform the first measurement of the thermal and ionization state of the intergalactic medium (IGM) across 0.9 < z < 1.5 using 301 Ly α absorption lines fitted from 12 archival Hubble Space Telescope Space Telescope Imaging Spectrograph quasar spectra. We employ the machine-learning-based inference method that uses joint Doppler parameter–column density (b-N HI ) distributions obtained from Ly α forest decomposition. Our results show that the Γ HI photoionization rates, , agree with recent ultraviolet background synthesis models, with log(Γ HI /s -1 ) = $-11.79^{+0.18}_{-0.15}$, $-11.98^{+0.09}_{-0.09}$, and $-12.32^{+0.10}_{-0.12}$, at z = 1.4, 1.2, and 1, respectively. We obtain the IGM temperature at the mean density, T 0 , and the adiabatic index, γ, as [log(T 0 /K), γ] = $[4.13^{+0.12}_{-0.10}, 1.34^{+0.10}_{-0.15}]$, $[3.79^{+0.11}_{-0.11}, 1.70^{+0.09}_{-0.09}]$, and $[4.12^{+0.15}_{-0.25}, 1.34^{+0.21}_{-0.26}]$ at z = 1.4, 1.2, and 1. Our measurements of T 0 at z = 1.4 and 1.2 are consistent with the trend predicted from previous z < 3 temperature measurements and theoretical expectations, where the IGM cools down after $He\tiny{II}$ reionization in the absence of any non-standard heating. However, our T 0 measurement at z = 1 unexpectedly high IGM temperature. Given the relatively large uncertainty in these measurements, where σ T$_0$ ~ 5000 K, mostly emanating from the limited size of our data set, we cannot conclude whether the IGM cools down as expected. Lastly, we generate mock data sets to test the constraining power of future measurement with larger data sets. The results demonstrate that, with redshift path-length Δz ~ 2 for each redshift bin, three times the current data set, we can constrain the T 0 of IGM within 1500 K, which would be sufficient to constrain the IGM thermal history at z < 1.5 conclusively.
Unveiling the interplay between spin density wave (SDW) and charge density wave (CDW) orders in correlated electron materials is important in obtaining a comprehensive understanding of their electronic, structural, and magnetic properties. Kagome lattice materials are interesting because their flat electronic bands, Dirac points, and Van Hove singularities can enable a variety of exotic electronic and magnetic phenomena. The kagome metal FeGe (the B35 phase), which exhibits a CDW order deep within an A-type antiferromagnetic (AFM) phase, was found to respond dramatically to postgrowth annealing—with the ability to tune the CDW repeatedly from long-range order to negligible order. Additionally, neutron scattering studies suggest that incommensurate magnetic peaks that onset at 𝑇 Canting = 𝑇 SDW ≈ 60 K in the system arise from a SDW order instead of the AFM double-cone structure. Here, in this study, we use inelastic neutron scattering to show that two distinct spin excitations exist below 𝑇 Canting corresponding to two coexisting magnetic orders in the system in both sets of annealed samples with and without CDW. While CDW order or negligible order can dramatically affect the onset temperature of 𝑇 Canting and elastic incommensurate magnetic scattering, its impact on low-energy spin fluctuations is more limited. In both samples, a pair of gapless incommensurate spin excitations arising from the SDW order wave vector coexist with gapped commensurate spin waves from the A-type AFM order across 𝑇 Canting . The low-energy spin excitations for both samples couple dynamically to the lattice through enhanced magnetic scattering intensity on cooling below 𝑇 CDW , regardless of the status of the static long-range CDW order. The incommensurate SDW order in the long-range CDW ordered sample also induces a tiny in-plane lattice distortion of the kagome lattice that is absent in the negligible CDW ordered sample, in a way that is different from the previously known SDW and CDW ordering materials.
Antiferromagnets that break both space-time reversal and translation-spin-rotation symmetries were recently predicted [L.-D. Yuan, Z. Wang, J.-W. Luo, E. I. Rashba, and A. Zunger, Phys. Rev. B 102, 014422 (2020)] to possess splitting between the otherwise spin-degenerate energy bands even without the relativistic spin-orbit coupling (SOC). Here, we point out that such nonrelativistic spin splitting (NRSS)—in particular, “spin splitting type 4” (SST-4) symmetry-broken antiferromagnets—can be divided into subgroups having distinct patterns of spin splitting and spin textures, depending on additional auxiliary symmetries of spin interconversion and polarity. These SST-4 subgroups include the 𝛼-type (no spin-interconverting symmetry) having spin splitting at the Brillouin zone center, as well as the 𝛽 subgroup in which a rotation symmetry is applied and determines the alternating spin texture and the 𝛾 subgroup having exclusively reflection spin-interconverting symmetry. Unlike ferrimagnets, the 𝛼-type compounds are shown to have tiny net magnetization at finite temperature and thus avoid the adverse effect of the stray field. The 𝛼 and 𝛽 subgroups can be either polar or nonpolar, whereas the 𝛾 subgroup is polar only, providing a basis for possible switching by external fields. The combination of NRSS-enabling and auxiliary symmetries is used here as a filter for identifying previously synthesized compounds as specific prototypes. Their characteristic splitting and spin polarization are calculated by density functional theory to the benefit of potential future experimental testing. Interesting results are as follows: (i) SOC-independent NRSS can exceed the magnitude of the SOC-induced Rashba and Dresselhaus spin splitting in semiconductors. (ii) Examples of predicted 𝛼-type insulating compounds include BiCrO 3 (nonpolar) and Mn 2 ScSbO 6 (polar), the latter having spin splitting of 158 meV and 160 meV in the valence and conduction bands, respectively. (iii) The 𝛽-type (Cu 2 Y 2 O 5 and FeF 2 ) and 𝛾-type compounds (Mn 4 Nb 2 O 9 and FeScO 3 ) are distinguished both by their auxiliary symmetries and polarity. The spin textures of 𝛾-type compounds are mirror reflected with spin degeneracy of the wave vectors on that mirror. These observations will likely broaden the experimental playing field of NRSS physics significantly.
In this paper, we report the temperature-field phase diagram as well as present a comprehensive study of the electronic structure and three-dimensional fermiology of the triangular-lattice magnet EuAg 4 Sb 2 , utilizing quantum oscillation measurements, angle-resolved photoemission spectroscopy, and first-principles calculations. The complex magnetic phase diagram of EuAg 4 Sb 2 highlights many transitions through nontrivial AFM states. Shubnikov-de Haas and de Haas-van Alphen oscillations were observed in the polarized ferromagnetic state of EuAg 4 Sb 2 , revealing three pairs of distinct spin-split frequency branches with small effective masses. A comparison of the angle-dependent oscillation data with first-principles calculations in the ferromagnetic state and angle-resolved photoemission spectra shows good agreement, identifying tubular hole pockets and hourglass-shaped hole pockets at the Brillouin zone center, as well as diamond-shaped electron pockets at the zone boundary. As the temperature increases, the frequency branches of the tiny hourglass pockets evolve into a more cylindrical shape, while the larger pockets remain unchanged. This highlights that variations in exchange splitting, driven by changes in the magnetic moment, primarily impact the small Fermi pockets without significantly altering the overall band structure. As a result, this is consistent with first-principles calculations, which show minimal changes near the Fermi level across ferromagnetic and simple antiferromagnetic states or under varying on-site Coulomb repulsion.
We study the QCD equation of state and the chiral condensate using the hadron resonance gas model with repulsive mean-field interactions. We find that the repulsive interactions improve the agreement with the lattice results on the derivatives of the pressure with respect to the baryon chemical potential up to eighth order. From the temperature dependence of the chiral condensate we estimate the crossover temperature as a function of baryon chemical potential, T p c ( μ B ) . We find that the chiral crossover line starts to deviate significantly from the chemical freeze-out line already for μ B > 400 MeV . Furthermore, we find that the chiral pseudocritical line can be parametrized as T p c ( μ B ) / T p c ( 0 ) = 1 − κ 2 [ μ B / T p c ( 0 ) ] 2 − κ 4 [ μ B / T p c ( 0 ) ] 4 with κ 2 = 0.0150 ( 2 ) and κ 4 = 3.1 ( 6 ) × 10 − 5 , which are in agreement with lattice QCD results for small values of μ B . For the first time we find a tiny but nonzero value of κ 4 in our study. Published by the American Physical Society 2024