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At least 1,189 records · Page 66

Bi-cross validation of spectral clustering hyperparameters

One challenge impeding the analysis of terabyte scale X-ray scattering data from the Linac Coherent Light Source (LCLS) is determining the number of clusters required for the execution of traditional clustering algorithms. Here, we demonstrate that the previous work using bi-cross validation to determine the number of singular vectors directly maps to the spectral clustering problem of estimating both the number of clusters and hyperparameter values. Here by applying this method to LCLS X-ray scattering data enables the identification of dropped shots without manually setting boundaries on detector fluence and provides a path toward identifying rare and anomalous events.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Numerical methods for nonlocal and fractional models

Partial differential equations (PDEs) are used with huge success to model phenomena across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDEs fail to adequately model observed phenomena, or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. Here, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis and of specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modelling and algorithmic extensions, which serve to show the wide applicability of nonlocal modelling.

97 MATHEMATICS AND COMPUTING↗

Cluster Analysis of Combined EDS and EBSD Data to Solve Ambiguous Phase Identifications

A common problem in analytical scanning electron microscopy (SEM) using electron backscatter diffraction (EBSD) is the differentiation of phases with distinct chemistry but the same or very similar crystal structure. X-ray energy dispersive spectroscopy (EDS) is useful to help differentiate these phases of similar crystal structures but different elemental makeups. However, open, automated, and unbiased methods of differentiating phases of similar EBSD responses based on their EDS response are lacking. This paper describes a simple data analytics-based method, using a combination of singular value decomposition and cluster analysis, to merge simultaneously acquired EDS + EBSD information and automatically determine phases from both their crystal and elemental data. I use hexagonal TiB 2 ceramic contaminated with multiple crystallographically ambiguous but chemically distinct cubic phases to illustrate the method. Code, in the form of a Python 3 Jupyter Notebook, and the necessary data to replicate the analysis are provided as Supplementary material.

47 OTHER INSTRUMENTATION↗

Chiral Spectroscopy of Nanostructures

Chirality is ubiquitous in the universe and in living creatures over detectable length scales from the subatomic to the galactic, as exemplified in the two extremes by subatomic particles (neutrinos) and spiral galaxies. Between them are living creatures that display multiple levels of chirality emerging from hierarchically assembled asymmetric building blocks. Not too far from the bottom of this pyramid are the foundational building blocks with chiral atomic centers on sp 3 carbon atoms exemplified by L-amino acids and D-sugars that are self-assembled into higher-order structures with increasing dimensions forming highly complex, amazingly functional, and energy-efficient living systems. The organization and materials employed in their construction inspired scientists to replicate complex living systems via the self-assembly of chiral components. Multiple studies pointed to unexpected and unique electromagnetic properties of chiral structures with nanoscale and microscale dimensions, including giant circular dichroism and collective circularly polarized scattering that their constituent units did not possess. To address the wide variety of chiral geometries observed in continuous materials, singular particles, and their complex systems, multiple analytic techniques are needed. Simultaneously, their spectroscopic properties create a pathway to multiple applications. For example, mirror-asymmetric vibrations at chiral centers formed by sp 3 carbon atoms lead to optical activity for the infrared (IR) wavelength regions. At the same time, understanding the optical activity in, for example, the IR region enables biomedical applications because multiple modalities of biomedical imaging and vibrational optical activity (VOA) of biomolecules are known for IR range. In turn, VOA can be realized in both absorption and emission modalities due to large magnetic transition moments, as vibrational circular dichroism (VCD) or Raman optical activity (ROA) spectroscopy. In addition to the VOA, in the range of longer wavelengths, lattice vibrational mode or phononic behavior occurs in chiral crystals and nanoassemblies, which can be readily detected by terahertz circular dichroism (TCD) spectroscopy. Meanwhile, chiral self-assembly can induce circularly polarized light emission (CPLE) regardless of the existence of chirality in coassembled fluorophores. The CPLE from self-assembled chiral materials is particularly interesting because the CPLE can originate from both circularly polarized luminescence and circularly polarized scattering (CPS). Furthermore, because self-assembled nanostructures often exhibit stronger optical activity than their building blocks owing to dimension and resonance effects, the optical activity of single assembled nanostructures can be investigated by using microscopic technology combined with chiral optics. Here, we describe the state of the art for spectroscopic methods for the comprehensive analysis of chiral nanomaterials at various photon wavelengths, addressed with special attention given to new tools emerging both for materials with self-organized hierarchical chirality and single-particle spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Competing Charge/Spin-Stripe and Correlated Metal Phases in Trilayer Nickelates (Pr 1– x La x ) 4 Ni 3 O 8

We report low valent nickelates R n+1 Ni n O 2n+2 (R = rare earth) containing Ni 1+ (d 9 ) with a quasi-two-dimensional (quasi-2D) square-planar coordination geometry possess structural and electronic properties that are similar to those of high T c cuprates, including superconductivity itself in the doped infinite-layer (n = ∞) RNiO 2 system. Within this R n+1 Ni n O 2n+2 nickelate family, the crystallographic isomorphs Pr 4 Ni 3 O 8 and La 4 Ni 3 O 8 exhibit singularly different ground states: Pr 4 Ni 3 O 8 is metallic, and La 4 Ni 3 O 8 is a charge- and spin-stripe-ordered insulator. To explore and understand the ground state evolution from metallic Pr 4 Ni 3 O 8 to stripe-ordered La 4 Ni 3 O 8 in the R 4 Ni 3 O 8 family, we have grown a series of isovalent, substituted single crystals (Pr 1-x La x ) 4 Ni 3 O 8 . Combining thermodynamic, transport, magnetic, and synchrotron X-ray single crystal diffraction measurements, we reveal a T = 0 transition between metallic and stripe-insulator phase regions, with this putative quantum phase transition at x ≈ 0.45. We propose two possible models for (Pr 1-x La x ) 4 Ni 3 O 8 : an electronically inhomogeneous system that could serve as a candidate for exploring quantum Griffiths phase physics or a homogeneous system with a clean quantum critical point at the phase boundary

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparative Life Cycle Evaluation of the Global Warming Potential (GWP) Impacts of Renewable Natural Gas Production Pathways

Renewable Natural Gas (RNG) sources are being considered in future energy strategy discussions as potential replacements for fossil natural gas (FNG). While today’s supply of RNG resources is insufficient to meet U.S. demands, there is significant interest in its viability to supplement and decarbonize the natural gas supply. However, the resources that compare the life cycle global warming potential (GWP) of various RNG production pathways are lacking and focus mostly on a singular pathway. This effort is an attempt to close this gap and provide a comparison between the life cycle GWP of three major RNG pathways and the FNG pathway. The three RNG pathways evaluated are Anaerobic Digestion (AD), Thermal Gasification (TG), and Power-to-Gas (P2G) using various feedstocks. The functional unit is 1MJ of compressed RNG ready for injection into the natural gas transmission network. The results show that RNG production is not always carbon neutral or negative. Depending on the pathway the GWP impact of RNG production can range from -229 to 27 g CO 2 e/MJ compressed RNG, with AD of animal manure and AD of municipal solid waste being the least and the most impactful pathways, respectively, compared to the 10.1 g CO 2 e/MJ impact for compressed FNG.

54 ENVIRONMENTAL SCIENCES↗

Optimization Modeling for Advanced Syngas to Olefin Reactive Systems

Reactor designs with mixed catalysts play an important role in transforming a multiple reactor system to single-shot reactors. In addition to savings in capital and ease of implementation, single-shot reactors are useful to break equilibrium limitations, thereby increasing the yield and selectivity of desired product as shown in previous studies. However, the nonlinear and highly exothermic nature of mixed-catalyst systems makes it difficult for commercial process simulation and optimization tools to optimize these systems. This study describes the development and application of optimization strategies for mixed-catalyst, single-shot reactors for syngas to olefin (STO) processes. Finding the optimal catalyst distribution is challenging and requires advanced solution strategies for singular optimal control problems, which are poorly conditioned and often lead to flat response surfaces. The graded bed and partial-moving finite-element approaches are used to find the optimal catalyst distribution that maximizes the olefins yield. A 1.3% increase in the yield is observed from one zone to three zones. The yield further improves from three zones to the exact infinite dimensional solution by 0.2%. This improvement can be realized in practice by changing only the catalyst distribution, without any extra investment. Lastly, the results suggest that a mixed-catalyst single shot reactor bed can be applied to other reaction mechanisms to increase reactor performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simplified Models of the Bicarbonate Buffer for Scaled Simulations of CO 2 Electrolyzers

Bicarbonate electrolytes are used in a range of chemical processes; however, resolved simulation of these electrolytes is difficult, as disparate reaction time scales lead to numerical stiffness and the formation of fine boundary layers. Based on several physically motivated approximations, we reduce the full set of chemical reactions within a bicarbonate electrolyte to a simpler subset, eliminating the numerical stiffness. We supported this simplification via a two-variable singular perturbation expansion and demonstrated that under neutral conditions (6 < pH < 10) typically found within a fluid-fed CO 2 electrolyzer, the simplifications lead to negligible error. Here, we also discuss two alternative simplifications, one valid at high pH and another valid at arbitrary pH. These simplifications reduce the condition number of the matrices resulting from spatiotemporal discretization by up to 10 orders of magnitude and enable three-dimensional (3D) simulation of CO 2 electrolyzers containing carbonate solutions.

10 SYNTHETIC FUELS↗

Net Present Value Optimization of a Natural Gas Combined Cycle Plant with CO 2 Capture using a Water-Lean Solvent Considering Transient Electricity Price for Multiple Regions

Global CO 2 emissions are increasing at about a 1.5% rate per year. Fossil fuel-based plants are one of the main contributors to this rise. In the power generation industry, fossil fuel plants are dominant, and many plants are under development. In this study, a natural gas combined cycle (NGCC) power plant with postcombustion capture using a leading water-lean solvent is considered. For optimal design and operating schedule, large-scale dynamic optimization is undertaken for net present value (NPV) optimization. The first principle dynamic model of NGCC is developed, including a model of the highly efficient H-class gas turbines. For computational tractability of the dynamic optimization problem, a reduced-order model is developed by using the Hankel singular value decomposition. A waterlean solvent, N-(2-ethoxyethyl)-3-morpholinopropan-1-amine, is used for carbon capture. A model of the capture system is developed in Aspen Plus, which is used to develop a reduced-order model by using ALAMO, a machine learning software. In addition, a reduced model of the CO 2 compression system with a dehydration unit is also considered. The integrated system is used for NPV optimization by using the Python-based PYOMO platform. The PCC process is analyzed for three configurations-conventional packed bed, rotating packed bed (RPB), and a combination of RPB and direct contact cooler. The NPV optimization is performed for 14 regional markets by considering year-long clustered and continuous locational marginal price data with a 1 h interval. Optimization results show that the PCC can achieve 90% CO 2 capture with a positive NPV for six regions. Sensitivity studies conducted by using the PCC configurations indicate that the process is economically feasible for 9 regions out of 14 regional electricity markets with NPV values in the range of 33−540 $MM.

cabon capture↗

Quantum Simulation of Molecular Electronic States with a Transcorrelated Hamiltonian: Higher Accuracy with Fewer Qubits

Simulation of electronic structure is one of the most promising applications on noisy intermediate-scale quantum (NISQ) era devices. However, NISQ devices suffer from a number of challenges like limited qubit connectivity, short coherence times, and sizable gate error rates. Thus, desired quantum algorithms should require shallow circuit depths and low qubit counts to take advantage of these devices. Here, we attempt to reduce quantum resource requirements for molecular simulations on a quantum computer while maintaining the desired accuracy with the help of classical quantum chemical theories of canonical transformation and explicit correlation. In this work, compact ab initio Hamiltonians are generated classically, in the second quantized form, through an approximate similarity transformation of the Hamiltonian with (a) an explicitly correlated two-body unitary operator with generalized pair excitations that remove the Coulombic electron–electron singularities from the Hamiltonian and (b) a unitary one-body operator to efficiently capture the orbital relaxation effects required for accurate description of the excited states. The resulting transcorrelated Hamiltonians are able to describe both the ground and the excited states of molecular systems in a balanced manner. Using the variational quantum eigensolver (VQE) method based on the unitary coupled cluster with singles and doubles (UCCSD) ansatz and only a minimal basis set (ANO-RCC-MB), we demonstrate that the transcorrelated Hamiltonians can produce ground state energies comparable to the reference CCSD energies with the much larger cc-pVTZ basis set. This leads to a reduction in the number of required CNOT gates by more than 3 orders of magnitude for the chemical species studied in this work. Furthermore, using the quantum equation of motion (qEOM) formalism in conjunction with the transcorrelated Hamiltonian, we are able to reduce the deviations in the excitation energies from the reference EOM-CCSD/cc-pVTZ values by an order of magnitude. In conclusion, the transcorrelated Hamiltonians developed here are Hermitian and contain only one- and two-body interaction terms and thus can be easily combined with any quantum algorithm for accurate electronic structure simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimized Auxiliary Functions for Robust Mitigation of Finite-Size Errors in Periodic Hybrid Density Functional Theory

When calculating properties of periodic systems at the thermodynamic limit (TDL), the dominant source of finite size error (FSE) arises from the long-range Coulomb interaction, and can manifest as a slowly converging quadrature error when approximating an integral in the reciprocal space by a finite sum. The singularity subtraction (SS) method offers a systematic approach for reducing this quadrature error and thus the FSE. Here, in this work, we first investigate the performance of the SS method in the simplest setting, aiming at reducing the FSE in exact exchange calculations by subtracting the Coulomb contribution with a single, adjustable Gaussian auxiliary function. We demonstrate that a simple fitting method can robustly estimate the optimal Gaussian width and leads to rapid convergence toward the TDL. Furthermore, we suggest new forms of the auxiliary function, whose optimal parameters could also be determined through least-squares fitting. For a range of semiconductors and insulators, the proposed auxiliary functions achieve robust, millihartree-level accuracy in hybrid density functional theory calculations, including cases with sparse k-meshes and large basis sets.

Quiton, Stephen Jon [University of California, Ber↗

Learning Latent Representations to Bridge Coarse-Grained and Atomistic Resolutions in Polymer Simulations

We present a machine-learning-based framework for learning reduced-order representations of polymer chain conformations across coarse-grained (CG) and united-atom (UA) fidelities. By employing linear singular value decomposition and nonlinear autoencoders, we compress high-dimensional polymer configurations into latent spaces with minimal loss of structural accuracy. Crucially, we demonstrate a near-perfect linear mapping between CG and UA latent spaces, enabling an efficient super-resolution back-mapping procedure that reconstructs high-fidelity UA configurations from CG simulations. While minor structural inaccuracies occur, they are effectively corrected through a brief molecular dynamics relaxation, forming a practical hybrid machine learning−physics scheme. This approach establishes the key structural prerequisites for accelerated polymer dynamics simulations: a compact and accurate latent encoding of polymer chain conformations and a validated multi-fidelity mapping that permits reconstruction of UA structures from CG configurations. The extension of this framework to explicit time evolution within the latent space, enabling dynamics to be propagated at CG fidelity and decoded to UA resolution only when required, represents a natural and well-motivated direction for future work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scaling of Shear Rheology of Concentrated Charged Colloidal Suspensions across Glass Transition

Electrostatic interparticle interactions are a key component in controlling and designing rheological characteristics of concentrated charged colloidal suspensions. Herein, we investigate electroviscous effects on shear rheology using highly charged silica particles. By fixing the volume fraction but varying the salinity, the system undergoes a glass transition as evidenced by the evolution of the yield stress and zero-shear viscosity. We show that the steady shear viscosities obey a critical scaling relation that scales the flow curves into a super- and a sub-critical branch with glass transition salinity serving as the bifurcation point; we also demonstrate an isoviscosity scaling that collapses all isoviscosity lines into a single master curve that exhibits no singularity. Based on each scaling relation, in conjunction with common modeling equations, the quantitative relationships between the shear viscosity, stress, and salinity are established. This study demonstrates a new framework to model the steady shear rheology of concentrated charged colloids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

EPR of Photoexcited Triplet-State Acceptor Porphyrins

The photoexcited triplet states of porphyrin architectures are of significant interest in a wide range of fields including molecular wires, nonlinear optics, and molecular spintronics. Electron paramagnetic resonance (EPR) is a key spectroscopic tool in the characterization of these transient paramagnetic states singularly well suited to quantify spin delocalization. Previous work proposed a means of extracting the absolute signs of the zero-field splitting (ZFS) parameters, D and E, and triplet sublevel populations by transient continuous wave, hyperfine measurements, and magnetophotoselection. Here, we present challenges of this methodology for a series of mesoperfluoroalkyl-substituted zinc porphyrin monomers with orthorhombic symmetries, where interpretation of experimental data must proceed with caution and the validity of the assumptions used in the analysis must be scrutinized. The EPR data are discussed alongside quantum chemical calculations, employing both DFT and CASSCF methodologies. Despite some success of the latter in quantifying the magnitude of the ZFS interaction, the results clearly provide motivation to develop improved methods for ZFS calculations of highly delocalized organic triplet states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Metastable CaSH 3 Phase Composed of HS Honeycomb Sheets that is Superconducting Under Pressure

Evolutionary searches have predicted a number of ternary Ca–S–H phases that could be synthesized at pressures of 100–300 GPa. P6 3 /mmc CaSH 2 , Pnma CaSH 2 , Cmc2 1 CaSH 6 , and I$\bar{4}$CaSH 20 were composed of a Ca–S lattice along with H 2 molecules coordinated in a “side-on” fashion to Ca. The H–H bond lengths in these semiconducting phases were elongated because of H 2 σ → Ca d donation, and Ca d → H 2 σ* back-donation, via a Kubas-like mechanism. P$\bar{6}$m2 CaSH 3 , consisting of two-dimensional HS and CaH 2 sheets, was metastable and metallic above 128 GPa. The presence of van Hove singularities increased its density of states at the Fermi level and concomitantly the superconducting critical temperature, which was estimated to be as high as ~100 K at 128 GPa. Furthermore, this work will inspire the search for superconductivity in materials based upon honeycomb HX (X = S, Se, Te) and MH 2 (M = Mg, Ca, Sr, Ba) layers under pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?

Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein-coding gene by aggregating peptide quantities into protein groups following protein inference or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein-coding gene will demonstrate the same quantitative response. Here, by assuming that all peptides from a protein-coding sequence are representative of the same protein, we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein-coding gene.

59 BASIC BIOLOGICAL SCIENCES↗

A Curated Experimental Compilation Analyzed by Theory Is More than a Review

Macromolecules is an exceptional resource in the field of polymer science and now publishes more than 1000 original articles a year that set the standard for scientific rigor and creative insights. Over the years, these individual contributions have combined to build the foundation of polymer science, broadly and inclusively defined. In addition to the individual articles, many of which are being celebrated in this series of editorials, Macromolecules has published invaluable reviews and perspectives. These scholarly contributions integrate the insights and results from numerous sources into a unified whole and often recommend future directions for the field. Novices and experts alike benefit from these works that capture topics from emerging discoveries to long-pondered topics and everything in between. To explore the importance of Macromolecules’ reviews and perspectives, we considered their influence on the field and found the 1994 review by Fetters et al. entitled “Connection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic Properties”1 to be a singularity. This review expertly curates and compiles a trove of data to build robust correlations between molecular characteristics and macroscopic viscoelastic properties of polymer melts, in the context of the tube model of entanglements.

36 MATERIALS SCIENCE↗

Identifying Topological Defects in Lamellar Phases through Contour Analysis of Complex Wave Fields

Lamellar phases frequently contain structural imperfections that significantly affect their behaviors and properties. Our previous research successfully reconstructed real-space configurations of defective lamellar phases from diffuse scattering patterns, indicating the presence of phase vortices as a potential method for identifying topological defects disrupting the smectic ordering. Here, this report presents a mathematical framework using regularized wave fields to represent defective lamellar structures in real space. Phase singularities, resulting from the interference of random waves and indicating lamellar order disruption, are identified through a contour integral. These wave fields, derived from coherent scattering in reciprocal space, were validated via computational benchmarks analyzing small-angle neutron scattering data from AOT surfactant solutions, facilitating further statistical analysis of the defects. Our study highlights the potential to extract meaningful information about topological defects in lyotropic phases by inversely analyzing experimentally measured two-point static correlations. Our method allows for detailed structural analysis of various lyotropic phases, both particulate and nonparticulate, in their quiescent states and facilitates quantitative investigation of defects’ role in phase transitions. By integrating small-angle scattering, deep learning, and vortex tangle analysis, our comprehensive approach shows promise in addressing complex challenges in the structural analysis of soft matter systems.

36 MATERIALS SCIENCE↗