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A scalable framework for learning the geometry-dependent solution operators of partial differential equations
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Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots
Abstract For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
A feasible approach for automatically differentiable unitary coupled-cluster on quantum computers
We develop computationally affordable and encoding independent gradient evaluation procedures for unitary coupled-cluster type operators, applicable on quantum computers.
Site specific redox properties in ligand differentiated di-nickel complexes inspired by the acetyl CoA synthase active site
These complexes, comprised of Ni(N 2 S 2 )–Ni(dithiolene) S-bridged units, serve as a platform to interrogate the positions of added electrons. Tuning of the ligand substituents controls electron uptake in S-bridged dinickel complexes.
Modulated spin dynamics of [Co 2 ] coordination helicates via differential strand composition
A family ofbis-pyrazolylpyridine ligands represents a versatile entry into [Co 2 ] triple-stranded helicates encapsulating various anionic guests, enabling to study the effects of different factors on the mechanisms of magnetic relaxation of their individual Co(ii) centers.
Mechanistic implications of excited high-spin states, spin–spin coupling, and differential [2Fe–2S] + cluster temperature relaxations in the electron-bifurcating NfnABC from Thermococcus sibiricus
Electron bifurcation (EB) is a mechanism of biological energy transduction in which multiple oxidation–reduction (redox) reactions are thermodynamically coupled within a single enzyme, enabling the enzyme to harness the excess free energy from an exergonic process to drive an endergonic process. Because of this unprecedented chemistry, there is interest to translate EB principles to artificial and bioengineered systems, but a hurdle is that knowledge pertaining to the fundamental design principles of EB enzymes remains scarce. Here, we investigated the fundamental physical and electronic properties of electron transfer sites in a spectroscopically uncharacterized member of the BfuABC family of EB enzymes, the NADH-dependent reduced-ferredoxin:NADP + oxidoreductase from Thermococcus sibiricus (Tsi NfnABC). Cryo-EM structures of Tsi NfnABC previously demonstrated that it contains twelve redox cofactors: two flavins (one FAD and one FMN), eight [4Fe–4S] clusters, and two [2Fe–2S] clusters. The FMN, one [4Fe–4S] cluster, and one [2Fe–2S] cluster comprise the bifurcating active site termed the electron-bifurcating flavobicluster (BF-FBC), which is found in all BfuABC family members. By using electron paramagnetic resonance spectroscopy, we identified spectral signatures originating from interactions between the FMN radical and [4Fe–4S] + cluster in the BF-FBC and observed temperature dependent behavior of the BF-FBC's [2Fe–2S] + cluster indicative of moderately slow spin–lattice relaxation. Additionally, we uncovered numerous spectral features corresponding to half-integer, S > ½ spin states of [4Fe–4S] + clusters, including one attributable to the consequences of lysine-ligation of a [4Fe–4S] cluster unique to NfnABC. We contextualize these findings to electron transfer theory and NfnABC's structure. Our insights further the understanding of how enzymes are designed to exert control over electron transfer to conduct thermodynamically challenging reactions.
Optimal Operation of Microgrids with Load-Differentiated Demand Response and Renewable Resources
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Differential effect of magnetic alignment on additive manufacturing of magnetocaloric particles
Additive manufacturing of materials using magnetic particles as feedstock has attracted tremendous attention during the past decade owing to its ability to tune both shape and magnetocrystalline anisotropy, which can significantly enhance the magnetic characteristics of materials. We demonstrate that the magnetic response of multilayered thin films of Gd5Si4 can be tailored by controlling the external magnetic field during inkjet printing. The external magnetic field aligns the magnetic particles along their magnetic easy axis, enhancing the magnetic anisotropy of the printed films. Our work demonstrates the ability to print thin magnetic films with a defined anisotropy in any chosen direction with the potential to approaching magnetic properties of corresponding single crystalline materials.
Resonant torque differential magnetometry with high frequency quartz oscillators
Sensitive magnetometry has been a powerful probe for investigating quantum materials. Extreme conditions, such as sub-kelvin cryogenic temperatures and ultrahigh magnetic fields, demand further durability for sensitive magnetometry. However, significant mechanical vibrations and rapid magnetic field changes give enormous challenges to conventional magnetometry. Here, this article presents a possible solution to this problem by developing a new magnetometry technique using high-frequency quartz oscillators. The technique takes advantage of the symmetry and geometry of mechanical vibration configurations of standard commercially available MHz quartz oscillators, and the setup keeps the high quality factor resonance with the sample mounted on the oscillator. We further demonstrate the sensitivity of the technique using bismuth single crystals and a Fe 0.25 TaS 2 ferromagnetic material. Quantum oscillations are observed in the magnetometry response below 1 T, and the detected oscillation frequency is shown to come from the electron pockets of the bismuth.
Photofragment imaging differentiates between one- and two-photon dissociation pathways in MgI+
The bond strength and photodissociation dynamics of MgI+ are determined by a combination of theory, photodissociation spectroscopy, and photofragment velocity map imaging. From 17 000 to 21 500 cm−1, the photodissociation spectrum of MgI+ is broad and unstructured; photofragment images in this region show perpendicular anisotropy, which is consistent with absorption to the repulsive wall of the (1) Ω = 1 or (2) Ω = 1 states followed by direct dissociation to ground state products Mg+ (2S) + I (2P3/2). Analysis of photofragment images taken at photon energies near the threshold gives a bond dissociation energy D0(Mg+-I) = 203.0 ± 1.8 kJ/mol (2.10 ± 0.02 eV; 17 000 ± 150 cm−1). At photon energies of 33 000–41 000 cm−1, exclusively I+ fragments are formed. Over most of this region, the formation of I+ is not energetically allowed via one-photon absorption from the ground state of MgI+. Images show the observed product is due to resonance enhanced two-photon dissociation. The photodissociation spectrum from 33 000 to 38 500 cm−1 shows vibrational structure, giving an average excited state vibrational spacing of 227 cm−1. This is consistent with absorption to the (3) Ω = 0+ state from ν = 0, 1 of the (1) Ω = 0+ ground state; from the (3) Ω = 0+ state, absorption of a second photon results in dissociation to Mg* (3P°J) + I+ (3PJ). From 38 500 to 41 000 cm−1, the spectrum is broad and unstructured. We attribute this region of the spectrum to one-photon dissociation of vibrationally hot MgI+ at low energy and ground state MgI+ at higher energy to form Mg (1S) + I+ (3PJ) products.
Interframe-tunable ultrafast differential-displacement holography
Here we describe the details of a digital holographic microscopy diagnostic capable of quantifying both the topography and velocity of a km/s object with adjustable temporal sensitivity. This technique involves spatially multiplexing a double pulse reflected from a target with reference beams of precisely known temporal separation.
Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies
In 2015, monoclonal antibodies (mAbs) that selectively recognize the 1-pHis or 3-pHis isoforms of phosphohistidine were developed by immunizing rabbits with degenerate Ala/Gly peptides containing the nonhydrolyzable phosphohistidine (pHis) analog- phosphotriazolylalanine (pTza). Here, we report structures of five rabbit mAbs bound to cognate pTza peptides: SC1-1 and SC50-3 that recognize 1-pHis, and their 3-pHis–specific counterparts, SC39-4, SC44-8, and SC56-2. These cocrystal structures provide insights into the binding modes of the pTza phosphate group that are distinct for the 1- and 3-pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl ring. The mode of phosphate recognition in the 3-pHis mAbs recapitulates the Walker A motif, as present in kinases. The complementarity-determining regions (CDRs) of four of the Fabs interact with the peptide backbone rather than peptide side chains, thus conferring sequence independence, whereas SC44-8 shows a proclivity for binding a GpHAGA motif mediated by a sterically complementary CDRL3 loop. Specific hydrogen bonding with the triazolyl ring precludes recognition of pTyr and other phosphoamino acids by these mAbs. Kinetic binding experiments reveal that the affinity of pHis mAbs for pHis and pTza peptides is submicromolar. Bound pHis mAbs also shield the pHis peptides from rapid dephosphorylation. The epitope–paratope interactions illustrate how these anti-pHis antibodies are useful for a wide range of research techniques and this structural information can be utilized to improve the specificity and affinity of these antibodies toward a variety of pHis substrates to understand the role of histidine phosphorylation in healthy and diseased states.
Differentiated roles of Lifshitz transition on thermodynamics and superconductivity in La 2- x Sr x CuO 4
The effect of Lifshitz transition on thermodynamics and superconductivity in hole-doped cuprates has been heavily debated but remains an open question. In particular, an observed peak of electronic specific heat is proposed to originate from fluctuations of a putative quantum critical point p* (e.g., the termination of pseudogap at zero temperature), which is close to but distinguishable from the Lifshitz transition in overdoped La-based cuprates where the Fermi surface transforms from hole-like to electron-like. Here we report an in situ angle-resolved photoemission spectroscopy study of three-dimensional Fermi surfaces in La 2- x Sr x CuO 4 thin films ( x = 0.06 to 0.35). With accurate k z dispersion quantification, the said Lifshitz transition is determined to happen within a finite range around x = 0.21. Normal state electronic specific heat, calculated from spectroscopy-derived band parameters, reveals a doping-dependent profile with a maximum at x = 0.21 that agrees with previous thermodynamic microcalorimetry measurements. The account of the specific heat maximum by underlying band structures excludes the need for additionally dominant contribution from the quantum fluctuations at p* . A d -wave superconducting gap smoothly across the Lifshitz transition demonstrates the insensitivity of superconductivity to the dramatic density of states enhancement.
Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab’-DNA ligand
Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide major histocompatibility complex (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab’-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rates of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells, which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from TCR ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.
Differential methylation pattern in pubertal girls associated with biochemical premature adrenarche
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