Nanoparticle Assembly in High Polymer Concentration Solutions Increases Superlattice Stability
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Lee, Margaret S.↗
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Engineering Supramolecular Hybrid Architectures with Directional Organofluorine Bonds
Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while “piggybacking” on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis.
Kotei, Patience A.↗
No-Core Shell Model Analysis of Light Nuclei
The fundamental description of both structural properties and reactions of light nuclei in terms of constituent protons and neutrons interacting through nucleon-nucleon and three-nucleon forces is a long-sought goal of nuclear theory. I will briefly present a promising technique, built upon the ab initio no-core shell model, which emerged recently as a candidate to reach such a goal: the no-core shell model/resonating-group method. This approach, capable of describing simultaneously both bound and scattering states in light nuclei, complements a microscopic cluster technique with the use of two-nucleon realistic interactions, and a microscopic and consistent description of the nucleon clusters. I will discuss applications to light nuclei binary scattering processes and fusion reactions that power stars and Earth based fusion facilities, such as the deuterium–3He fusion, and outline the progress toward the inclusion of the three-nucleon force into the formalism and the treatment of three-body clusters.
Physics↗
Spectral emission characteristics near 646 nm and plasma properties of laser-induced plasma of gaseous uranium hexafluoride
We present a detailed investigation of the temporal evolution of line and continuum emissions in laser-induced breakdown spectroscopy (LIBS) of gaseous uranium hexafluoride (UF 6 ), focusing on the spectral region near 646 nm. Spectral emission features, signal-to-background ratios (SBRs) of selected uranium lines, and spectral linewidths were examined under varying UF 6 pressures (15–60 Torr) and laser pulse energies (10–60 mJ). Higher pressures and pulse energies enhanced continuum emission and reduced SBRs but did not cause significant spectral congestion. Additional studies with the use of different laser systems, including nanosecond-pulsed Nd:YAG lasers (at fundamental and various harmonics) and a femtosecond-pulsed Ti:sapphire laser, revealed long-lived plasma continua in all cases. This persistent continuum is attributed to a pseudo-continuum from overlapping molecular emissions, as its intensity scales linearly with electron number density, deviating from the expected quadratic dependence of classical ion–electron interactions for free-free and free-bound continuum emission. Based on plasma persistence time, SBR, U II/U I intensity ratios, and electronic excitation temperature, no fundamental advantage was found for femtosecond-pulsed lasers over conventional nanosecond-pulsed ones for UF 6 enrichment assay with direct LIBS measurement.
Laser-induced breakdown spectroscopy↗
Heterogenized Molecular Catalysts: Vibrational Sum-Frequency Spectroscopic, Electrochemical, and Theoretical Investigations
Rhenium and manganese bipyridyl tricarbonyl complexes have attracted intense interest for their promising applications in photocatalytic and electrocatalytic CO 2 reduction in both homogeneous and heterogenized systems. To date, there have been extensive studies on immobilizing Re catalysts on solid surfaces for higher catalytic efficiency, reduced catalyst loading, and convenient product separation. However, in order for the heterogenized molecular catalysts to achieve the combination of the best aspects of homogeneous and heterogeneous catalysts, it is essential to understand the fundamental physicochemical properties of such heterogeneous systems, such as surface-bound structures of Re/Mn catalysts, substrate–adsorbate interactions, and photoinduced or electric-field-induced effects on Re/Mn catalysts. For example, the surface may act to (un)block substrates, (un)trap charges, (de)stabilize particular intermediates (and thus affect scaling relations), and shift potentials in different directions, just as protein environments do. The close collaboration between the Lian, Batista, and Kubiak groups has resulted in an integrated approach to investigate how the semiconductor or metal surface affects the properties of the attached catalyst. Synthetic strategies to achieve stable and controlled attachment of Re/Mn molecular catalysts have been developed. Steady-state, time-resolved, and electrochemical vibrational sum-frequency generation (SFG) spectroscopic studies have provided insight into the effects of interfacial structures, ultrafast vibrational energy relaxation, and electric field on the Re/Mn catalysts, respectively. Various computational methods utilizing density functional theory (DFT) have been developed and applied to determine the molecular orientation by direct comparison to spectroscopy, unravel vibrational energy relaxation mechanisms, and quantify the interfacial electric field strength of the Re/Mn catalyst systems. This Account starts with a discussion of the recent progress in determining the surface-bound structures of Re catalysts on semiconductor and Au surfaces by a combined vibrational SFG and DFT study. The effects of crystal facet, length of anchoring ligands, and doping of the semiconductor on the bound structures of Re catalysts and of the substrate itself are discussed. This is followed by a summary of the progress in understanding the vibrational relaxation (VR) dynamics of Re catalysts covalently adsorbed on semiconductor and metal surfaces. The VR processes of Re catalysts on TiO 2 films and TiO 2 single crystals and a Re catalyst tethered on Au, particularly the role of electron–hole pair (EHP)-induced coupling on the VR of the Re catalyst bound on Au, are discussed. The Account also summarizes recent studies in quantifying the electric field strength experienced by the catalytically active site of the Re/Mn catalyst bound on a Au electrode based on a combined electrochemical SFG and DFT study of the Stark tuning of the CO stretching modes of these catalysts. Finally, future research directions on surface-immobilized molecular catalyst systems are discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water
Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a simple physical picture, elucidating the roles of different interactions in nucleation processes. In this study, we make use of three complementary techniques to disentangle the role played by short- and long-range interactions in solvent-mediated nucleation. Specifically, the first approach we utilize is the local molecular field (LMF) theory to renormalize long-range Coulomb electrostatics. Second, we use well-tempered metadynamics to speed up rare events governed by short-range interactions. Third, the deep learning-based State Predictive Information Bottleneck approach is employed in analyzing the reaction coordinate of the nucleation processes obtained from the LMF treatment coupled with well-tempered metadynamics. We find that the two-step nucleation mechanism can largely be captured by the short-range interactions, while the long-range interactions further contribute to the stability of the primary crystal state under ambient conditions. Furthermore, by analyzing the reaction coordinate obtained from the combined LMF-metadynamics treatment, we discern the fluctuations on different time scales, highlighting the need for long-range interactions when accounting for metastability.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Atomically Resolved Electrically Active Intragrain Interfaces in Perovskite Semiconductors
Deciphering the atomic and electronic structures of interfaces is key to developing state-of-the-art perovskite semiconductors. However, conventional characterization techniques have limited previous studies mainly to grain-boundary interfaces, whereas the intragrain-interface microstructures and their electronic properties have been much less revealed. Herein using scanning transmission electron microscopy, we resolved the atomic-scale structural information on three prototypical intragrain interfaces, unraveling intriguing features clearly different from those from previous observations based on standalone films or nanomaterial samples. These intragrain interfaces include composition boundaries formed by heterogeneous ion distribution, stacking faults resulted from wrongly stacked crystal planes, and symmetrical twinning boundaries. The atomic-scale imaging of these intragrain interfaces enables us to build unequivocal models for the ab initio calculation of electronic properties. Our results suggest that these structure interfaces are generally electronically benign, whereas their dynamic interaction with point defects can still evoke detrimental effects. This work paves the way toward a more complete fundamental understanding of the microscopic structure-property-performance relationship in metal halide perovskites.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Modulated phases of graphene quantum Hall polariton fluids
There is a growing experimental interest in coupling cavity photons to the cyclotron resonance excitations of electron liquids in high-mobility semiconductor quantum wells or graphene sheets. These media offer unique platforms to carry out fundamental studies of exciton-polariton condensation and cavity quantum electrodynamics in a regime, in which electron–electron interactions are expected to play a pivotal role. Here, focusing on graphene, we present a theoretical study of the impact of electron–electron interactions on a quantum Hall polariton fluid, that is a fluid of magneto-excitons resonantly coupled to cavity photons. We show that electron–electron interactions are responsible for an instability of graphene integer quantum Hall polariton fluids towards a modulated phase. We demonstrate that this phase can be detected by measuring the collective excitation spectra, which is often at a characteristic wave vector of the order of the inverse magnetic length.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Towards complete assignment of the infrared spectrum of the protonated water cluster H + (H 2 O) 21
The spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior of the proton in water with gas-phase water clusters H + (H 2 O) n extensively studied as bottom-up model systems. We present a new protocol for the calculation of the infrared (IR) spectra of complex systems, which combines the fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, and demonstrate its accuracy towards the complete and accurate assignment of the IR spectrum of the H + (H 2 O) 21 cluster. The site-specific IR spectral signatures reveal two distinct structures for the internal and surface four-coordinated water molecules, which are ice-like and liquid-like, respectively. The effect of inter-molecular interaction between water molecules is addressed, and the vibrational resonance is found between the O-H stretching fundamental and the bending overtone of the nearest neighboring water molecule. The revelation of the spectral signature of the excess proton offers deeper insight into the nature of charge accommodation in the extended hydrogen-bonding network underpinning this aqueous cluster.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Self-oscillating synchronematic colloids
Self-oscillators that sustain periodic dynamics under constant input are ubiquitous in natural and engineered systems, where their interactions enable spatiotemporal coordination among many individual units. New forms of organization can emerge when these self-oscillating units are free to move and rotate, coupling their spatial arrangement and alignment with their oscillation frequencies and phases. Here, we report experiments and simulations on populations of Quincke colloids that behave as self-oscillating units with position, orientation, frequency, and phase. Depending on the initial distribution, these active oscillators spontaneously organize into distinct collective states characterized by temporal synchronization and directional alignment, which we term synchronematic order. In fluid-like clusters, this order is short-ranged and decays over a length scale set by the competition between hydrodynamic interactions and athermal noise. In crystalline clusters, these interactions drive flobal synchronization and circular alignment-synchronematic crystals-whose collective frequency increases with cluster size due to non-reciprocal interactions. Our results establish self-oscillating colloids as a model system for active oscillatory matter and reveal fundamental principles by which synchronization, alignment, and structure co-emerge, offering new pathways for designing adaptive, frequency-tunable materials.
colloids↗
Visualization of clustered protocadherin neuronal self-recognition complexes
Neurite self-recognition and avoidance are fundamental properties of all nervous systems. These processes facilitate dendritic arborization, prevent formation of autapses and allow free interaction among non-self neurons. Avoidance among self neurites is mediated by stochastic cell-surface expression of combinations of about 60 isoforms of α-, β- and γ-clustered protocadherin that provide mammalian neurons with single-cell identities. Avoidance is observed between neurons that express identical protocadherin repertoires, and single-isoform differences are sufficient to prevent self-recognition. Protocadherins form isoform-promiscuous cis dimers and isoform-specific homophilic trans dimers. Although these interactions have previously been characterized in isolation, structures of full-length protocadherin ectodomains have not been determined, and how these two interfaces engage in self-recognition between neuronal surfaces remains unknown. Here we determine the molecular arrangement of full-length clustered protocadherin ectodomains in single-isoform self-recognition complexes, using X-ray crystallography and cryo-electron tomography. We determine the crystal structure of the clustered protocadherin γB4 ectodomain, which reveals a zipper-like lattice that is formed by alternating cis and trans interactions. Using cryo-electron tomography, we show that clustered protocadherin γB6 ectodomains tethered to liposomes spontaneously assemble into linear arrays at membrane contact sites, in a configuration that is consistent with the assembly observed in the crystal structure. These linear assemblies pack against each other as parallel arrays to form larger two-dimensional structures between membranes. Furthermore, our results suggest that the formation of ordered linear assemblies by clustered protocadherins represents the initial self-recognition step in neuronal avoidance, and thus provide support for the isoform-mismatch chain-termination model of protocadherin-mediated self-recognition, which depends on these linear chains.
59 BASIC BIOLOGICAL SCIENCES↗
In-situ weak-beam and polarization control of multidimensional laser sidebands for ultrafast optical switching
All-optical switching has myriad applications in optoelectronics, optical communications, and quantum information technology. To achieve ultrafast optical switching in a compact yet versatile setup, we demonstrate distinct sets of two-dimensional (2D) broadband up-converted multicolor arrays (BUMAs) in a thin type-I β-barium-borate crystal with two noncollinear near-IR femtosecond pulses at various phase-matching conditions. The unique interaction mechanism is revealed as quadratic spatial solitons (QSSs)-coupled cascaded four-wave mixing (CFWM), corroborated by numerical calculations of the governing phase-matching conditions. Broad and continuous spectral-spatial tunability of the 2D BUMAs are achieved by varying the time delay between the two incident pulses that undergo CFWM interaction, rooted in the chirped nature of the weak white light and the QSSs generation of the intense fundamental beam. The control of 2D BUMAs is accomplished via seeding a weak second-harmonic pulse in situ to suppress the 2D arrays with polarization dependence on the femtosecond timescale that matches the control pulse duration of ∼35 fs. A potential application is proposed on femtosecond all-optical switching in an integrated wavelength-time division multiplexing device.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis
Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely, normal mode analysis and Gaussian network model (GNM). The accuracy of the FRI method is tested using four sets of proteins, three sets of relatively small-, medium-, and large-sized structures and an extended set of 365 proteins. A fifth set of proteins is used to compare the efficiency of the FRI, fFRI, aFRI, and GNM methods. Intensive validation and comparison indicate that the FRI, particularly the fFRI, is orders of magnitude more efficient and about 10% more accurate overall than some of the most popular methods in the field. The proposed fFRI is able to predict B-factors for α-carbons of the HIV virus capsid (313 236 residues) in less than 30 seconds on a single processor using only one core. Finally, we demonstrate the application of FRI and aFRI to protein domain analysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Guided ink and process design for aerosol jet printing based on annular drying effects
Aerosol jet printing is a promising microscale additive manufacturing technology for emerging applications in printed and flexible electronics. However, the more widespread adoption of this emerging technique is hindered by a limited fundamental understanding of the process. This work focuses on a critical and underappreciated aspect of the process, the interaction between drying induced by the sheath gas and impaction. Combining focused experiments with support from numerical modeling, it is shown that these effects have a dramatic impact on key outputs of the process, including deposition rate, resolution, and morphology. These effects can amplify minor changes in ink composition or atomization yield, increasing process sensitivity and drift. Moreover, these effects can confound strategies for in-line process monitoring and control based on empirical observables. Strategies to directly manipulate this annular drying phenomenon are presented, providing a viable tool to tailor and study the process. This work clarifies coupled effects of printer design, ink formulation, and print parameters, establishing a more robust theoretical framework for understanding the aerosol jet printing process and advancing the maturity of this promising technology.
42 ENGINEERING↗
Simulating the weak death of the neutron in a femtoscale universe with near-Exascale computing
The fundamental particle theory called Quantum Chromodynamics (QCD) dictates everything about protons and neutrons, from their intrinsic properties to interactions that bind them into atomic nuclei. Quantities that cannot be fully resolved through experiment, such as the neutron lifetime (whose precise value is important for the existence of light-atomic elements that make the sun shine and life possible), may be understood through numerical solutions to QCD. We directly solve QCD using Lattice Gauge Theory and calculate nuclear observables such as neutron lifetime. We have developed an improved algorithm that exponentially decreases the time-tosolution and applied it on the new CORAL supercomputers, Sierra and Summit. We use run-time autotuning to distribute GPU resources, achieving 20% performance at low node count. We also developed optimal application mapping through a job manager, which allows CPU and GPU jobs to be interleaved, yielding 15% of peak performance when deployed across large fractions of CORAL.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Designing Metabolic Division of Labor in Microbial Communities
ABSTRACT Microbes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A “gedanken” (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. We implemented this idealized experiment using in silico genome-scale models. In particular, we used mixed-integer linear programming to identify trade-off solutions in communities of Escherichia coli strains. The strategies that we found revealed a large space of opportunities in nuanced and nonintuitive metabolic division of labor, including, for example, splitting the tricarboxylic acid (TCA) cycle into two separate halves. The systematic computation of possible solutions in division of labor for 1-, 2-, and 3-strain consortia resulted in a rich and complex landscape. This landscape displayed a nonlinear boundary, indicating that the loss of an intracellular reaction was not necessarily compensated for by a single imported metabolite. Different regions in this landscape were associated with specific solutions and patterns of exchanged metabolites. Our approach also predicts the existence of regions in this landscape where independent bacteria are viable but are outcompeted by cross-feeding pairs, providing a possible incentive for the rise of division of labor. IMPORTANCE Understanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the space of possible strategies for division of labor, we applied advanced optimization algorithms to computational models of cellular metabolism. Specifically, we searched for communities able to survive under constraints (such as a limited number of reactions) that would not be sustainable by individual species. We found that predicted consortia partition metabolic pathways in ways that would be difficult to identify manually, possibly providing a competitive advantage over individual organisms. In addition to helping understand diversity in natural microbial communities, our approach could assist in the design of synthetic consortia.
59 BASIC BIOLOGICAL SCIENCES↗
The UPR Branch IRE1- bZIP60 in Plants Plays an Essential Role in Viral Infection and Is Complementary to the Only UPR Pathway in Yeast
The unfolded protein response (UPR) signaling network encompasses two pathways in plants, one mediated by inositol-requiring protein-1 (IRE1)-bZIP60 mRNA and the other by site-1/site-2 proteases (S1P/S2P)-bZIP17/bZIP28. As the major sensor of UPR in eukaryotes, IRE1, in response to endoplasmic reticulum (ER) stress, catalyzes the unconventional splicing of HAC1 in yeast, bZIP60 in plants and XBP1 in metazoans. Recent studies suggest that IRE1p and HAC1 mRNA, the only UPR pathway found in yeast, evolves as a cognate system responsible for the robust UPR induction. However, the functional connectivity of IRE1 and its splicing target in multicellular eukaryotes as well as the degree of conservation of IRE1 downstream signaling effectors across eukaryotes remains to be established. Here, we report that IRE1 and its substrate bZIP60 function as a strictly cognate enzymesubstrate pair to control viral pathogenesis in plants. Moreover, we show that the S1P/ S2P-bZIP17/bZIP28 pathway, the other known branch of UPR in plants, does not play a detectable role in virus infection, demonstrating the distinct function of the IRE1-bZIP60 pathway in plants. Furthermore, we provide evidence that bZIP60 and HAC1, products of the enzyme-substrate duet, rather than IRE1, are functionally replaceable to cope with ER stress in yeast. Taken together, we conclude that the downstream signaling of the IRE1- mediated splicing is evolutionarily conserved in yeast and plants, and that the IRE1-bZIP60 UPR pathway not only confers overlapping functions with the other UPR branch in fundamental biology but also may exert a unique role in certain biological processes such as virus-plant interactions.
59 BASIC BIOLOGICAL SCIENCES↗
An Overview of RF Systems for the EIC
The Electron Ion Collider (EIC) to be constructed at Brookhaven National Laboratory in the USA will be a complex system of accelerators providing high luminosity, high polarization, variable center of mass energy collisions between electrons and protons or ions. To achieve this a variety of RF systems are required. They must provide for capture, formation and storage of Ampere-class beams in the electron and hadron storage rings (ESR and HSR), fast acceleration of high-charge polarized electron bunches in the rapid cycling synchrotron (RCS), provision of cold high current electron bunches in the high-energy cooler ERL and precise high-gradient crabbing of electrons and hadrons either side of the interaction point. The challenges include strong HOM damping in the storage ring cavities and cooler ERL, very high fundamental mode power in the ESR and cooler injector, extremely stable low-noise operation of the crab cavities, mitigation of transient beam loading from gaps, and operating over a wide range of energies and beam currents. We describe the high-level system parameters and principal design choices made and progress on the R&D plan to develop these state of the art systems.
Rimmer, R. A.↗