Rewards-based image analysis in microscopy
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Barakati, Kamyar↗
Engineering topics
Liu, Yu
Publications and source records attributed to Liu, Yu.
Mechanism-Resolved PFM of Ferroionic and Ferroelectric Responses in Thickness-Gradient Hf 0.5 Zr 0.5 O 2 Libraries
Resolving growth mechanisms and thickness evolution of functional properties is one of the key tasks in materials discovery and optimization involving thin-film materials, traditionally requiring significant experimental budgets. Here we introduce the combination of thickness-gradient libraries and automated scanning probe microscopy as a systematic pathway to elucidate growth modes and disentangle ferroelectric and electrochemical contributions in ferroelectric thin films. As a model system, we explore the Hf 0.5 Zr 0.5 O 2 (HZO) gradient thin films grown on La x Sr 1-x MnO 3 (LSMO) bottom electrode thin films. Automated piezoresponse force microscopy, spectroscopy, and lithography reveals that irreversible topographic deformation arises from electrochemical activity at the LSMO surface, whereas reversible phase inversion in HZO reflects ferroelectric switching. Automated topography height-map scans are used to further quantify nucleation density, particle-size evolution, and roughness correlations across the thickness-gradient, demonstrating that improved plume stabilization during growth suppresses interfacial reactions and promotes dense, fine-grained HZO conducive to ferroelectric phase formation. This combined materials-engineering and automated-SPM framework establishes a platform for high-throughput, mechanism-resolved characterization of ferroionic and ferroelectric responses in complex oxide films.
FOS: Physical sciences↗
Mechanistic studies of small molecule ligands selective to RNA single G bulges
Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.
Biochemistry & Molecular Biology↗
Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems
Not provided.
Science & Technology - Other Topics↗
Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers
The sugar-binding receptors dectin-2 and blood dendritic cell antigen 2 (BDCA-2) bind oligosaccharide ligands through extracellular carbohydrate-recognition domains (CRDs) and initiate intracellular signaling through Fc receptor γ adapters (FcRγ). Dectin-2 stimulates macrophages in response to pathogen binding while BDCA-2 modulates cytokine production in plasmacytoid dendritic cells. The oligomeric states of these receptors and the orientations of their CRDs have been investigated by analysis of a naturally occurring disulfide-bonded variant of BDCA-2 and by replacement of transmembrane domains with N-terminal dimerization domains to create extracellular domain dimers of both dectin-2 and BDCA-2. Analysis of these constructs, as well as previously described crystal structures of the CRDs from these proteins and a novel structure of an extended version of the extracellular domain of dectin-2, showed that there is only limited interaction of the CRDs in the dimers, but interactions can be stabilized by the presence of the neck region. The resulting orientation of sugar-binding sites in the dimers would favor crosslinking of multiple dimers by oligosaccharide ligands, causing clustering of FcRγ to initiate signaling.
carbohydrate-binding protein↗
Integration of scanning probe microscope with high-performance computing: Fixed-policy and reward-driven workflows implementation
The rapid development of computation power and machine learning algorithms has paved the way for automating scientific discovery with a scanning probe microscope (SPM). The key elements toward operationalization of the automated SPM are the interface to enable SPM control from Python codes, availability of high computing power, and development of workflows for scientific discovery. Here, we build a Python interface library that enables controlling an SPM from either a local computer or a remote high-performance computer, which satisfies the high computation power need of machine learning algorithms in autonomous workflows. We further introduce a general platform to abstract the operations of SPM in scientific discovery into fixed-policy or reward-driven workflows. Furthermore, our work provides a full infrastructure to build automated SPM workflows for both routine operations and autonomous scientific discovery with machine learning.
47 OTHER INSTRUMENTATION↗
Anisotropic hybridization in CeRhSn
The optical conductivity σ(ω, T) of CeRhSn was studied by broadband infrared spectroscopy. Temperature-dependent spectral weight transfer occurs over high energy (0.8 eV) and temperature (~500 K) scales, classifying CeRhSn as a mixed-valent compound. The optical conductivity reveals a substantial anisotropy in the electronic structure. Renormalization of σ(ω, T) occurs as a function of temperature to a coherent Kondo state with concomitant effective mass generation. Associated spectroscopic signatures were reproduced remarkably well by the combination of density functional theory and dynamical mean-field theory using a momentum-independent self-energy. The theory shows that the anisotropy for energies > 10 meV is mainly driven by the bare three-dimensional electronic structure that is renormalized by local electronic correlations. The possible influence of magnetic frustration and quantum criticality is restricted to lower energies.
36 MATERIALS SCIENCE↗
Excess heat capacity in magnetically ordered Ce heavy-fermion metals
Herein we study the magnetic heat capacity of a series of magnetically ordered Ce-based heavy-fermion materials, which show an anomalous T 3 heat capacity in excess of the phonon contribution in many materials. For compounds for which magnon models have been worked out, we show that the local-moment magnon heat capacity derived from the measured magnon spectra underestimates the experimental specific heat. The excess heat capacity reveals increasing density of states with increasing energy, akin to a pseudogap. We show that this anomalous temperature-dependent term is not associated with proximity to a quantum critical point, but is strongly correlated with T N , indicating the anomalous excitations are governed by the magnetic exchange interaction. This insight may hold key information for understanding magnetically ordered heavy fermions.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Final Scientific/Technical Report Wood Honeycombs for Lightweight, Energy Efficient Structural Applications
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Ramakrishnan, Kishore↗
Effect of Surface Oxidation and Crystal Thickness on the Magnetic Properties and Magnetic Domain Structures of Cr 2 Ge 2 Te 6
van der Waals (vdW) magnetic materials, such as Cr 2 Ge 2 Te 6 (CGT), show promise for memory and logic applications. This is due to their broadly tunable magnetic properties and the presence of topological magnetic features such as skyrmionic bubbles. A systematic study of thickness and oxidation effects on magnetic domain structures is important for designing devices and vdW heterostructures for practical applications. Here, we investigate thickness effects on magnetic properties, magnetic domains, and bubbles in oxidation-controlled CGT crystals. We find that CGT exposed to ambient conditions for 5 days forms an oxide layer approximately 5 nm thick. This oxidation leads to a significant increase in the oxidation state of the Cr ions, indicating a change in local magnetic properties. This is supported by real-space magnetic texture imaging through Lorentz transmission electron microscopy. By comparing the thickness-dependent saturation field of oxidized and pristine crystals, we find that oxidation leads to a nonmagnetic surface layer that is thicker than the oxide layer alone. We also find that the stripe domain width and skyrmionic bubble size are strongly affected by the crystal thickness in pristine crystals. Finally, these findings underscore the impact of thickness and surface oxidation on the properties of CGT, such as saturation field and domain/skyrmionic bubble size, and suggest a pathway for manipulating magnetic properties through a controlled oxidation process.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
State-to-State Molecular Reactions in the Ultracold Regime (Final Scientific Report)
We have achieved the proposed goal to experimentally probe the AB + CD and AB + C types of reactions with state-to-state resolution, which we also compared to advanced theoretical calculations to help elucidate the role of quantum mechanics in the processes of bond breakage and formation. Our approach uses reactants that are prepared at ultracold temperatures (< 1µK) such that the quantum effects of translational motion are an important factor. Specific example reactions, including the potassium-rubidium metathesis reaction KRb + KRb → K 2 + Rb 2 as well as the atom exchange reaction Rb + KRb → Rb2 + K, are chosen because the technology of quantum internal and motional state control of these types of molecules is particularly advanced. The results for the entire funding period are fruitful. For the majority of this grant, we have constructed a one-of-the-kind quantum degenerate gas apparatus that integrates ion detection and velocity map imaging capabilities, allowing us to explore the KRb + KRb → K 2 + Rb 2 bimolecular reaction in detail. Specifically, we first verified such a reaction indeed proceed at ultracold temperatures by direct detection of reaction products. We then mapped out the complete product state distribution, which was compared to a state-counting model based on statistical theory. Our results show an overall agreement with the statistical state counting model, but also reveal several deviating state-pairs. An exact quantum calculation for molecule-molecule collisions, that is needed to understand these deviations, is however beyond the current state-of-the-art. Beside scrutinizing the reaction products, we also directly observe the reaction intermediate complex, which was quite a surprise to us. The intermediate complexes are long-lived and can interact with the inferred light that we use to trap the ultracold gas. After molecule-molecule collisions, we then explored the more theoretically tractable Rb + KRb reaction, which is endothermic. Surprisingly, we observed an exceedingly long-lived KRb$^*_2$ collisional complexes, with our experimentally measured complex lifetime deviating from conventional theoretical calculations by five orders of magnitude. This discrepancy has motivated many explorations of possible underlying causes, though no model yet captures this phenomenon completely. In the final year and the work that continues today, we extend upon these atom-molecule collision experiments to explore the origin of the long-lived KRb$^*_2$ complex lifetime and develop means to control the outcome of the reaction complex. The 5-year funded work advanced our understanding of chemical reactions at the lowest possible temperatures and at the same time opened up many new questions that are beyond our initial imaginations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Endotaxial stabilization of 2D charge density waves with long-range order
Charge density waves are emergent quantum states that spontaneously reduce crystal symmetry, drive metal-insulator transitions, and precede superconductivity. In low-dimensions, distinct quantum states arise, however, thermal fluctuations and external disorder destroy long-range order. Here we stabilize ordered two-dimensional (2D) charge density waves through endotaxial synthesis of confined monolayers of 1T-TaS 2 . Specifically, an ordered incommensurate charge density wave (oIC-CDW) is realized in 2D with dramatically enhanced amplitude and resistivity. By enhancing CDW order, the hexatic nature of charge density waves becomes observable. Upon heating via in-situ TEM, the CDW continuously melts in a reversible hexatic process wherein topological defects form in the charge density wave. From these results, new regimes of the CDW phase diagram for 1T-TaS 2 are derived and consistent with the predicted emergence of vestigial quantum order.
36 MATERIALS SCIENCE↗
Dissimilar material joining of densified superwood to aluminum by adhesive bonding
Abstract Superwood is a densified wood product that shows promise as a lightweight and renewable alternative for metallic materials. In order for this high-performance new material to be used in multi-material products, it must be able to be joined with other major materials. For example, joining superwood to aluminum would provide a key enabling technology for its use in automotive components since aluminum is presently a major lightweight material for such applications. In this paper, a methacrylate-based adhesive has been identified to provide high lap shear strength (7.5 MPa) for aluminum-to-superwood joints. The aluminum-to-superwood samples were prepared with different amounts of pre-polishing to create openings to the pores in the superwood so adhesive could penetrate into them and create a mechanical interlock, in addition to the hydrogen/chemical bonding at the surface between the methyl methacrylate (MMA) in methacrylate-based adhesive and the cellulose in superwood. For aluminum samples, a thin layer (typically a few nanometers) of oxide film on the surfaces provides hydrogen/chemical bond to MMA structure in the adhesive layer. The failure strength of the superwood-to-aluminum joint sample is about 50% higher than that of natural wood to natural wood joint sample and comparable to that of aluminum-to-aluminum joint sample.
Automation & Control Systems↗
Coexistence of Dirac fermion and charge density wave in the square-net-based semimetal LaAuSb 2
Here, we report a comprehensive study of magnetotransport properties, angle-resolved photoemission spectroscopy (ARPES), and density functional theory (DFT) calculations on self-flux grown LaAuSb 2 single crystals. Resistivity and Hall measurements reveal a charge density wave (CDW) transition at 77 K. MR and de Haas-Van Alphen (dHvA) measurements indicate that the transport properties of LaAuSb 2 are dominated by Dirac fermions that arise from Sb square nets. ARPES measurements and DFT calculations reveal an electronic structure with a common feature of the square-net-based topological semimetals, which is in good agreement with the magnetotransport properties. Our results indicate the coexistence of CDW and Dirac fermion in LaAuSb 2 , both of which are linked to the bands arising from the Sb-square net, suggesting that the square net could serve as a structural motif to explore various electronic orders.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nanoscale inhomogeneity and the evolution of correlation strength in FeSe$$_{1-x}$$S$$_x$$
Abstract We report a comprehensive study of the nanoscale inhomogeneity and disorder on the thermoelectric properties of FeSe $$_{1-x}$$ 1 - x S $$_x$$ x ( $$0 \le x \le 1$$ 0 ≤ x ≤ 1 ) single crystals and the evolution of correlation strength with S substitution. A hump-like feature in temperature-dependent thermpower is enhanced for x = 0.12 and 0.14 in the nematic region with increasing in orbital-selective electronic correlations, which is strongly suppressed across the nematic critical point and for higher S content. Nanoscale Se/S atom disorder in the tetrahedral surroundings of Fe atoms is confirmed by scanning transmission electron microscopy measurements, providing an insight into the nanostructural details and the evolution of correlation strength in FeSe $$_{1-x}$$ 1 - x S $$_x$$ x .
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Interplay of broken symmetry and delocalized excitations in the insulating state of 1 T –TaS 2
Coexistence of localized and extended excitations is central to the macroscopic properties of correlated materials. For 5d transition-metal compounds, electron correlations alone generally do not lead to a metal-insulator (Mott) transition, with insulating behavior usually resulting from their coupling with magnetic ordering and/or structural distortions. 1T–TaS 2 is a prototypical example of such correlated insulating behavior, with a high-symmetry metallic phase transforming into a distorted, charge-density wave (CDW) insulating state at low temperatures. The nature of the insulating phase as well as the existence and relevance of the localized electron physics remains debated. We resolve this standing controversy in 1T–TaS 2 combining resonant inelastic x-ray spectroscopy and first-principles calculations. We observe five electronic excitations arising from the interband transitions of the Ta 5d orbitals and the S 3p ligand state, with none of the excitations on the order of the Mott gap. These excitations cannot be explained within the framework of standard multiplet calculations that assume a localized wave function, but instead, are captured by a band-theory framework accounting for the low symmetry of the crystal field in the CDW state. Our findings suggest that the electronic properties of 1T–TaS 2 are dominated in the visible by both plasmonic quasiparticles and interband transitions, with no resonance associated with a putative Mott transition observed in the 0–3 eV energy range. Finally, our discovery provides insights into the electron localization and the Mott vs band-insulator debate in 1T–TaS 2 and other transition-metal materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
A novel integrated time-resolved array avalanche photodiode detection system for nuclear resonant scattering measurements
Here, the nuclear resonant scattering (NRS) experiment requires photon-counting detectors with high time resolution, short dead time, large dynamic range, low noise, and large detection area. An 8-channel avalanche photodiode (APD) array detector system with high integrity, flexibility, and reliability has been developed to adapt to the demands of NRS experiments. The detector system mainly consists of four key parts: (i) an array-APD sensor, (ii) 8-channel integrated fast preamplifiers, (iii) the time-to-digital converter readout electronics, and (iv) a data acquisition system and EPICS support software. Remarkably, the system exhibits a time resolution of better than 500 ps and has a sufficiently low noise level, allowing for the lowest detection energy threshold of 4 keV. The performance of the new array-APD system as well as its real application in nuclear forward scattering (NFS) and nuclear resonant inelastic x-ray scattering (NRIXS) experiments was tested in two synchrotron facilities. With the new system, the NFS signal very close to the prompt electronic scattering signal can be extracted. Thanks to the customized EPICS-areaDetector-based control software, NRIXS spectra can be readily measured with time and energy information of the NRIXS signal stored in the raw data, which is promising for developing NRIXS data analysis in the time domain. The array-APD detector can be deployed for nuclear resonant scattering experiments at various synchrotron radiation facilities.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗