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Engineered unique elastic modes at a BaTiO 3 /2x1-Ge(001) interface
Here, the strong interaction at an interface between a substrate and thin film leads to epitaxy and provides a means of inducing structural changes in the epitaxial film. These induced material phases often exhibit technologically relevant electronic, magnetic, and functional properties. The 2×1 surface of a Ge(001) substrate applies a unique type of epitaxial constraint on thin films of the perovskite oxide BaTiO 3 where a change in bonding and symmetry at the interface leads to a non-bulk-like crystal structure of the BaTiO 3 . While the complex crystal structure is predicted using first-principles theory, it is further shown that the details of the structure are a consequence of hidden phases found in the bulk elastic response of the BaTiO 3 induced by the symmetry of forces exerted by the germanium substrate.
Distinguishing Quarks and Gluons in Pion and Kaon PDFs
The leading-twist parton distribution functions of the pion and kwon are calculated for the first time using a rainbow-ladder truncation of QCD's Dyson-Schwinger equations (DSEs) that self-consistently sums all planar diagrams. The nonperturbative gluon dressing of the quarks is thereby correctly accounted for, which in practice means solving the inhomogeneous Bethe-Salpeter equation (BSE) for the quark operator that defines the spin-independent quark distribution functions. An immediate consequence of using this dressed vertex is that gluons carry 35% of the pion's and 30% of the kaon's light-cone momentum, with the remaining momentum carried by the quarks. The scale associated with these DSE results is μ 0 = 0.78 GeV. The gluon effects generated by the inhomogeneous BSE are inherently nonperturbative and cannot be mimicked by the perturbative QCD evolution equations. A key consequence of this gluon dressing is that the valence quarks have reduced support at low-to-intermediate x, where the gluons dominate, and increased support at large x. As a result, our DSE calculation of the pion's valence quark distribution is in excellent agreement with the Conway et al. pion-induced Drell-Yan data, but nevertheless exhibits the q π (x) similar or equal to (1 - x) 2 behavior as x -> 1 predicted by perturbative QCD.
Dark Energy Survey Year 1 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Correlations
We present the first joint analysis of cluster abundances and auto or cross-correlations of three cosmic tracer fields: galaxy density, weak gravitational lensing shear, and cluster density split by optical richness. From a joint analysis (4×2pt+N) of cluster abundances, three cluster cross-correlations, and the auto correlations of the galaxy density measured from the first year data of the Dark Energy Survey, we obtain Ωm=0.305-0.038+0.055 and σ8=0.783-0.054+0.064. This result is consistent with constraints from the DES-Y1 galaxy clustering and weak lensing two-point correlation functions for the flat νΛCDM model. Consequently, we combine cluster abundances and all two-point correlations from across all three cosmic tracer fields (6×2pt+N) and find improved constraints on cosmological parameters as well as on the cluster observable-mass scaling relation. This analysis is an important advance in both optical cluster cosmology and multiprobe analyses of upcoming wide imaging surveys.
Phonon-Driven Femtosecond Dynamics of Excitons in Crystalline Pentacene from First Principles
Nonradiative exciton relaxation processes are critical for energy transduction and transport in optoelectronic materials, but how these processes are connected to the underlying crystal structure and the associated electron, exciton, and phonon band structures, as well as the interactions of all these particles, is challenging to understand. Here, in this work, we present a first-principles study of exciton-phonon relaxation pathways in pentacene, a paradigmatic molecular crystal and optoelectronic semiconductor. We compute the momentum- and band-resolved exciton-phonon interactions, and use them to analyze key scattering channels. We find that both exciton intraband scattering and interband scattering to parity-forbidden dark states occur on the same ~100 fs timescale as a direct consequence of the longitudinal-transverse splitting of the bright exciton band. Consequently, exciton-phonon scattering exists as a dominant nonradiative relaxation channel in pentacene. We further show how the propagation of an exciton wave packet is connected with crystal anisotropy, which gives rise to the longitudinal-transverse exciton splitting and concomitant anisotropic exciton and phonon dispersions. Our results provide a framework for understanding the role of exciton-phonon interactions in exciton nonradiative lifetimes in molecular crystals and beyond.
Microstructure evolution during near- T g annealing and its effect on shear banding in model alloys
By performing extensive molecular dynamics simulations, we investigate herein the deformation behavior in A l 90 S m 10 and C u 64.5 Z r 35.5 alloys after elongated isothermal annealing in the vicinity of the glass-transition temperature ( T g ). Different microstructural response to the annealing process was observed: A l 90 S m 10 maintains the glassy structure with improved energetic stability, enhanced short-range order (SRO), and a more pronounced spatial network that extends beyond the first atomic shell, while C u 64.5 Z r 35.5 forms nanocrystalline Laves C u 2 Zr phases. Shear banding occurs in both annealed systems under shear loading. For A l 90 S m 10 , the spatial network formed by the local clusters characterizing the SRO of the system is significantly weakened but remains appreciable in the shear band. In contrast, the crystalline ordering in the C u 64.5 Z r 35.5 is completely destroyed during shear banding. Consequently, while displaying higher yield strength, the annealed C u 64.5 Z r 35.5 sample appears to be less ductile. By carefully examining the effect of microstructures on the structural ordering in the shear band and the consequent mechanical response, our work contributes to a better understanding of the deformation mechanism of amorphous alloys as compared with that in crystalline materials.
Thermally driven phase transitions in freestanding low-buckled silicene, germanene, and stanene
Low-buckled silicene, germanene, and stanene are group-IV graphene allotropes. They form a honeycomb lattice out of two interpenetrating (A and B) triangular sublattices that are vertically separated by a small distance Δ z . The atomic numbers Z of silicon, germanium, and tin are larger than that of carbon (Z C = 6), making them the first experimentally viable two-dimensional topological insulators. Those materials have a twice-energy-degenerate atomistic structure characterized by the buckling direction of the B sublattice with respect to the A sublattice [whereby the B atom either protrudes above (Δ z > 0) or below (Δ z < 0) the A atoms], and the consequences of that energy degeneracy on their elastic and electronic properties have not been reported thus far. Here, we uncover ferroelastic, bistable behavior on silicene, which turns into an average planar structure at about 600 K. Furthermore, the creation of electron and hole puddles obfuscates the zero-temperature spin-orbit coupling (SOC)-induced band gaps at temperatures as low as 200 K, which may discard silicene as a viable two-dimensional topological insulator for room-temperature applications. Germanene, on the other hand, never undergoes a low-buckled-to-planar two-dimensional transformation, becoming amorphous at around 675 K instead, and preserving its SOC-induced band gap despite band broadening. Stanene undergoes a transition onto a crystalline three-dimensional structure at about 300 K, preserving its SOC-induced electronic band gap up to that temperature. Unlike what is observed in silicene and germanene, stanene readily develops a higher-coordinated structure with a high degree of structural order. Furthermore, the structural phenomena are shown to have far-reaching consequences for the electronic and vibrational properties of those two-dimensional topological insulators.
Spin-orbital correlations from complex orbital order in MgV 2 O 4
MgV 2 O 4 is a spinel based on magnetic V 3+ ions, which host both spin (𝑆 = 1) and orbital (𝑙 eff = 1) moments. Owing to the underlying pyrochlore coordination of the magnetic sites, the spins in MgV 2 O 4 only antiferromagnetically order once the frustrating interactions imposed by the 𝐹𝑑$\overline{3}$𝑚 lattice are broken through an orbitally-driven structural distortion at T 𝑆 ≃ 60 K. Consequently, a Néel transition occurs at T 𝑁 ≃ 40 K. Low-temperature spatial ordering of the electronic orbitals is fundamental to both the structural and magnetic properties; however, considerable discussion on whether it can be described by complex or real orbital ordering is ambiguous. We apply neutron spectroscopy to resolve the nature of the orbital ground state and characterize hysteretic spin-orbital correlations using x-ray and neutron diffraction. Neutron spectroscopy finds multiple excitation bands and we parametrize these in terms of a multilevel (or excitonic) theory based on the orbitally degenerate ground state. Meaningful for the orbital ground state, we report an “optical-like” mode at high energies that we attribute to a crystal-field-like excitation from the spin-orbital 𝑗 eff = 2 ground-state manifold to an excited 𝑗 eff =1 energy level. We parametrize the magnetic excitations in terms of a Hamiltonian with spin-orbit coupling and local crystalline electric field distortions resulting from deviations from perfect octahedra surrounding the V 3+ ions. We suggest that this provides compelling evidence for complex orbital order in MgV 2 O 4 . We then apply the consequences of this model to understand hysteretic effects in the magnetic diffuse scattering where we propose that MgV 2 O 4 displays a high-temperature orbital memory of the low-temperature spin order.
Topological Mixed Valence Model for Twisted Bilayer Graphene
Song and Bernevig (SB) have recently proposed a topological heavy-fermion description of the physics of magic angle twisted bilayer graphene (MATBG), involving the hybridization of flat-band electrons with a relativistic conduction sea. Here, we explore the consequences of this model, seeking a synthesis of understanding drawn from heavy-fermion physics and MATBG experiments. Our work identifies a key discrepancy between measured and calculated on-site Coulomb interactions, implicating renormalization effects that are not contained in the current model. With these considerations in mind, we consider a SB model with a single, renormalized on-site interaction between the f electrons, containing a phenomenological heavy-fermion binding potential on the moiré A A sites. This feature allows the simplified model to capture the periodic reset of the chemical potential with filling and the observed stability of local moment behavior. We argue that a two-stage Kondo effect will develop in MATBG as a consequence of the relativistic conduction band: Kondo I occurs at high temperatures, establishing a coherent hybridization at the Γ points and a non-Fermi liquid of incoherent fermions at the moiré K points; at much lower temperatures, Kondo II leads to a Fermi liquid in the flat band. Utilizing an auxiliary-rotor approach, we formulate a mean-field treatment of MATBG that captures this physics, describing the evolution of the normal state across a full range of filling factors. By contrasting the relative timescales of phonons and valence fluctuations in bulk heavy-fermion materials with that of MATBG, we are led to propose a valley-polaron origin to the Coulomb renormalization and the heavy-fermion binding potential identified from experiment. We also discuss the possibility that the two-fluid, non-Fermi liquid physics of the relativistic Kondo lattice is responsible for the strange-metal physics observed in MATBG. Published by the American Physical Society 2025
Transgenic Perturbation of the Decarboxylation Phase of Crassulacean Acid Metabolism Alters Physiology and Metabolism But Has Only a Small Effect on Growth
Here, mitochondrial NAD-malic enzyme (ME) and/or cytosolic/plastidic NADP-ME combined with the cytosolic/plastidic pyruvate orthophosphate dikinase (PPDK) catalyze two key steps during light-period malate decarboxylation that underpin secondary CO 2 fixation in some Crassulacean acid metabolism (CAM) species. We report the generation and phenotypic characterization of transgenic RNA interference lines of the obligate CAM species Kalanchoë fedtschenkoi with reduced activities of NAD-ME or PPDK. Transgenic line rNAD-ME1 had 8%, and rPPDK1 had 5% of the wild-type level of activity, and showed dramatic changes in the light/dark cycle of CAM CO 2 fixation. In well-watered conditions, these lines fixed all of their CO 2 in the light; they thus performed C 3 photosynthesis. The alternative malate decarboxylase, NADP-ME, did not appear to compensate for the reduction in NAD-ME, suggesting that NAD-ME was the key decarboxylase for CAM. The activity of other CAM enzymes was reduced as a consequence of knocking out either NAD-ME or PPDK activity, particularly phosphoenolpyruvate carboxylase (PPC) and PPDK in rNAD-ME1 . Furthermore, the circadian clock-controlled phosphorylation of PPC in the dark was reduced in both lines, especially in rNAD-ME1 . This had the consequence that circadian rhythms of PPC phosphorylation, PPC kinase transcript levels and activity, and the classic circadian rhythm of CAM CO 2 fixation were lost, or dampened toward arrhythmia, under constant light and temperature conditions. Surprisingly, oscillations in the transcript abundance of core circadian clock genes also became arrhythmic in the rNAD-ME1 line, suggesting that perturbing CAM in K. fedtschenkoi feeds back to perturb the central circadian clock.
Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content
Lignin is a phenolic heteropolymer that is deposited in secondary-thickened cell walls, where it provides mechanical strength. A recent structural characterization of cell walls from monocot species showed that the flavone tricin is part of the native lignin polymer, where it is hypothesized to initiate lignin chains. In this study, we investigated the consequences of altered tricin levels on lignin structure and cell wall recalcitrance by phenolic profiling, nuclear magnetic resonance, and saccharification assays of the naturally silenced maize (Zea mays) C2-Idf (inhibitor diffuse) mutant, defective in the CHALCONE SYNTHASE Colorless2 (C2) gene. We show that the C2-Idf mutant produces highly reduced levels of apigenin- and tricin-related flavonoids, resulting in a strongly reduced incorporation of tricin into the lignin polymer. Moreover, the lignin was enriched in β-β and β-5 units, lending support to the contention that tricin acts to initiate lignin chains and that, in the absence of tricin, more monolignol dimerization reactions occur. In addition, the C2-Idf mutation resulted in strikingly higher Klason lignin levels in the leaves. As a consequence, the leaves of C2-Idf mutants had significantly reduced saccharification efficiencies compared with those of control plants. These findings are instructive for lignin engineering strategies to improve biomass processing and biochemical production.
Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize
Interactions between MADS-box transcription factors are critical in the regulation of floral development, and shifting MADS-box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS-box protein function remains unknown. To assess the impact of changing MADS-box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS-box proteins vary. We tested the functional consequences of this evolutionary variability using maize as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS-box interactions. Our results highlight complexity in the evolution of developmental gene networks - changing protein-protein interactions could affect not only the composition of transcription factor complexes, but also their degradation and persistence in developing flowers. Here, our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.
Model morphing and sequence assignment after molecular replacement
A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.
Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes
A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin. Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.
Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening
An acoustic high-throughput screening method is described for harvesting protein crystals and combining the protein crystals with chemicals such as a fragment library. Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s{sup −1}) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.
A novel digital pulse processing architecture for nuclear instrumentation
The field of nuclear instrumentation covers a wide range of applications, including counting, spectrometry, pulse shape discrimination and multi-channel coincidence. These applications are the topic of many researches, new algorithms and implementations are constantly proposed thanks to advances in digital signal processing. However, these improvements are not yet implemented in instrumentation devices. This is especially true for neutron-gamma discrimination applications which traditionally use charge comparison method while literature proposes other algorithms based on frequency domain or wavelet theory which show better performances. Another example is pileups which are generally rejected while pileup correction algorithms also exist. These processes are traditionally performed offline due to two issues. The first is the Poissonian characteristic of the signal, composed of random arrival pulses which requires to current architectures to work in data flow. The second is the real-time requirement, which implies losing pulses when the pulse rate is too high. Despite the possibility of treating the pulses independently from each other, current architectures paralyze the acquisition of the signal during the processing of a pulse. This loss is called dead-time. These two issues have led current architectures to use dedicated solutions based on re-configurable components like Field Programmable Gate Arrays (FPGAs) to overcome the need of performance necessary to deal with dead-time. However, dedicated hardware algorithm implementations on re-configurable technologies are complex and time-consuming. For all these reasons, a programmable Digital pulse Processing (DPP) architecture in a high level language such as Cor C++ which can reduce dead-time would be worthwhile for nuclear instrumentation. This would reduce prototyping and test duration by reducing the level of hardware expertise to implement new algorithms. However, today's programmable solutions do not meet the need of performance to operate online and not allow scaling with the increase in the number of measurement channel. That is why an innovative DPP architecture is proposed in this paper. This architecture is able to overcome dead-time while being programmable and is flexible with the number of measurement channel. Proposed architecture is based on an innovative execution model for pulse processing applications which can be summarized as follow. The signal is not composed of pulses only, consequently, pulses processing does not have to operate on the entire signal. Therefore, the first step of our proposal is pulse extraction by the use of dedicated components named pulse extractors. The triggering step can be achieved after the analog-to-digital conversion without any signal shaping or filtering stages. Pileup detection and accurate pulse time stamping are done at this stage. Any application downstream this step can work on adaptive variable-sized array of samples simplifying pulse processing methods. Then, once the data flow is broken, it is possible to distribute pulses on Functional Units (FUs) which perform processing. As the date of each pulse is known, they can be processed individually out-of-order to provide the results. To manage the pulses distribution, a scheduler and an interconnection network are used. pulses are distributed on the first FU which is not busy without congesting the interconnection network. For this reason, the process duration does not result anymore in dead-time if there are enough FUs. FUs are designed to be standalone and to comprises at least a programmable general purpose processor (ARM, Microblaze) allowing the implementation of complex algorithms without any modification of the hardware. An acquisition chain is composed of a succession of algorithms which lead to organize our FUs as a software macro-pipeline, A simple approach consists in assigning one algorithm per FU. Consequently, the global latency becomes the worst latency of algorithms execution on FU. Moreover, as algorithms are executed locally - i.e. on a FU - this approach limits shared memory requirement. To handle multichannel, we propose FUs sharing, this approach maximize the chance to find a non-busy FU to process an incoming pulse. This is possible since each channel receive random event independently, the pulse extractors associated to them do not necessarily need to access simultaneously to all Computing resources at the same time to distribute their pulses. The major contribution of this paper is the proposition of an execution model and its associated hardware programmable architecture for digital pulse processing that can handle multiple acquisition channels while maintaining the scalability thanks to the use of shared resources. This execution model and associated architecture are validated by simulation of a cycle accurate architecture SystemC model. Proposed architecture shows promising results in terms of scalability while maintaining zero dead-time. This work also permit the sizing of hardware resources requirement required for a predefined set of applications. Future work will focus on the interconnection network and a scheduling policy that can exploit the variable-length of pulses. Then, the hardware implementation of this architecture will be performed and tested for a representative set of application.
Analytical Expression for DC Link Capacitor Current in a Cascaded H-Bridge Multi-Level Active Front-End Converter
Medium-voltage grid-tied systems often use a cascaded H-bridge multi-level active front-end. In this converter, dc link bus capacitors play an important role in stabilizing the converter and enabling both active and reactive power injections. The present work provides analytical expressions for the capacitor current, which are essential for optimizing system design (especially capacitor size vs. lifetime). Then, the expression is incorporated into the grid connected bidirectional power system model. Consequently, this work contributes to the guiding principles to choose accurate dc link capacitor ratings against grid-side power delivery requirements. The analytical results have been validated with detailed simulations and hardware results.
PRESAGE: Protecting Structured Address Generation against Soft Errors
Modern computer scaling trends in pursuit of larger component counts and power efficiency have, unfortunately, lead to less reliable hardware and consequently soft errors escaping into application data ("silent data corruptions"). Techniques to enhance system resilience hinge on the availability of efficient error detectors that have high detection rates, low false positive rates, and lower computational overhead. Unfortunately, efficient detectors to detect faults during address generation (to index large arrays) have not been widely researched. We present a novel lightweight compiler-driven technique called PRESAGE for detecting bit-flips affecting structured address computations. A key insight underlying PRESAGE is that any address computation scheme that flows an already incurred error is better than a scheme that corrupts one particular array access but otherwise (falsely) appears to compute perfectly. Enabling the flow of errors allows one to situate detectors at loop exit points, and helps turn silent corruptions into easily detectable error situations. Our experiments using PolyBench benchmark suite indicate that PRESAGE-based error detectors have a high error-detection rate while incurring low overheads.