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At least 469 records · Page 26

Model and Standard Operating Procedures Supporting Signal Variation Flow Graph Analysis

This document will describe the principles of the Signal Variation Flow Technique, and the uncertainty models generated using it. We focus on the capture of the variation between the ideal signal and the measured signal. The ideal signal is defined to represent the signal output of a system whose full state behavior is known, with no variation in environment or during operation, and whose photons trajectories are not modified by the object. A CT uncertainty analysis is the result of two main steps. First, the radiography regime extends from the source to the collected image, which is 2D in the case of standard CT. This maps all upstream uncertainties into the variation observed on the radiograph and captures all variation in the physical domain. Second, the reconstruction regime extends from the captured images to the reconstructed 3D image. This regime is purely in the mathematical domain and corrects reconstruction algorithm artifacts/anomalies. The present work focuses on building the model through the radiography regime. The reconstruction regime is expected to be largely a study of algorithmic sensitivity, requiring the definition of a range of standardized tests through which the algorithms would be run. Radiographic variation would then be mapped through reconstruction sensitivities to predict the signal variation in the final image. An incomplete list for the reconstructed image variation output basis includes voxel density, edge blur and length variation, in analogous fashion to the basis functions presented in this work. The signal variation occurs in several forms at the radiograph. These forms are gathered into a complete basis set of functions describing all variation on the radiograph. The scale of each basis function is calculated independently via a specific SVFG. This includes 0D pixel noise (0DI), 0D energy noise (0DE), 1D blur (1DB), 1D length (1DL) or 2D position (2DP). These models are orthogonal in that they each explore a space in the signal variation domain that cannot be reached by the other basis functions. The variation basis functions, and associated SVFG models are split by output dimensionality, a term loosely used for categorization, and explained further below.

42 ENGINEERING↗

Mechanism of tethered agonist-mediated signaling by polycystin-1

Mutations of polycystin-1 (PC1) are the major cause (85% of cases) of autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. PC1 is thought to function as an atypical G protein-coupled receptor, yet the mechanism by which PC1 regulates G-protein signaling remains poorly understood. A significant portion of ADPKD mutations of PC1 encode a protein with defects in maturation or reduced function that may be amenable to functional rescue. In this work, we have combined complementary biochemical and cellular assay experiments and accelerated molecular simulations, which revealed an allosteric transduction pathway in activation of the PC1 C-terminal fragment. Our findings will facilitate future rational drug design efforts targeting the PC1 signaling function. Polycystin-1 (PC1) is an important unusual G protein-coupled receptor (GPCR) with 11 transmembrane domains, and its mutations account for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 shares multiple characteristics with Adhesion GPCRs. These include a GPCR proteolysis site that autocatalytically divides these proteins into extracellular, N-terminal, and membrane-embedded, C-terminal fragments (CTF), and a tethered agonist (TA) within the N-terminal stalk of the CTF that is suggested to activate signaling. However, the mechanism by which a TA can activate PC1 is not known. Here, we have combined functional cellular signaling experiments of PC1 CTF expression constructs encoding wild type, stalkless, and three different ADPKD stalk variants with all-atom Gaussian accelerated molecular dynamics (GaMD) simulations to investigate TA-mediated signaling activation. Correlations of residue motions and free-energy profiles calculated from the GaMD simulations correlated with the differential signaling abilities of wild type and stalk variants of PC1 CTF. They suggested an allosteric mechanism involving residue interactions connecting the stalk, Tetragonal Opening for Polycystins (TOP) domain, and putative pore loop in TA-mediated activation of PC1 CTF. Key interacting residues such as N3074–S3585 and R3848–E4078 predicted from the GaMD simulations were validated by mutagenesis experiments. Together, these complementary analyses have provided insights into a TA-mediated activation mechanism of PC1 CTF signaling, which will be important for future rational drug design targeting PC1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modification at the C2'-O-Position with 2-Methylbenzothiophene Induces Unique Structural Changes and Thermal Transitions on Duplexes of RNA and DNA

Oligonucleotides can be chemically modified for a variety of applications that include their use as biomaterials, in therapeutics, or as tools to understand biochemical processes, among others. This work focuses on the functionalization of oligonucleotides of RNA and DNA (12- or 14-nucleotides long) with methylbenzothiophene (BT), at the C2'-O-position, which led to unique structural features. Circular dichroism (CD) analyses showed that positioning the BT units on one strand led to significant thermal destabilization, while duplexes where each strand contained 4-BT rings formed a distinct arrangement with cooperativity/interactions among the modifications (evidenced from the appearance of a band with positive ellipticity at 235 nm). Interestingly, the structural arrays displayed increased duplex stabilization (>10 °C higher than the canonical analogue) as a function of [Na + ] with an unexpected structural rearrangement at temperatures above 50 °C. Density functional theory–polarizable continuum model (DFT-PCM) calculations were carried out, and the analyses were in agreement with induced structural changes as a function of salt content. A model was proposed where the hydrophobic surface allows for an internal nucleobase rearrangement into a more thermodynamically stable structure, before undergoing full denaturation, with increased heat. While this behavior is not common, B- to Z-form duplex transitions can occur and are dependent on parameters that were probed in this work, i.e., temperature, nature of modification, or ionic content. To take advantage of this phenomenon, we probed the ability of the modified duplexes to be recognized by Zα (an RNA binding protein that targets Z-form RNA) via electrophoretic analysis and CD. Interestingly, the protein did not bind to canonical duplexes of DNA or RNA; however, it recognized the modified duplexes, in a [monovalent/divalent salt] dependent manner. Overall, the findings describe methodology to attain unique structural motifs of modified duplexes of DNA or RNA, and control their behavior as a function of salt concentration. While their affinity to RNA binding proteins, and the corresponding mechanism of action, requires further exploration, the tunable properties can be of potential use to study this, and other, types of modifications. The novel arrays that formed, under the conditions described herein, provide a useful way to explore the structure and behavior of modified oligonucleotides, in general.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First-Principles Dissociation Pathways of BCl 3 on the Si(100)-2 × 1 Surface

BCl 3 is a promising acceptor precursor for atomic-precision δ-doping of silicon, as it has been observed to rapidly dissociate into boron doped into the silicon surface and surface chlorine, which can be removed upon annealing. The chemical pathway and the resulting kinetics, through which BCl 3 adsorbs and dissociates on silicon, however, have only been partially explained. Here, in this work, we use density functional theory to expand the dissociation reactions of BCl 3 to include reactions that take place across multiple silicon dimer rows and reactions which end in a bare B atom either at the surface, substituted for a surface silicon, or in a subsurface position. We further simulate the resulting scanning tunneling microscopy images for each of these BCl x dissociation fragments, demonstrating that they often display distinct features that may allow for relatively confident experimental identification. Finally, we input the full dissociation pathway for BCl 3 into a kinetic Monte Carlo model, which simulates realistic reaction pathways as a function of environmental conditions, such as the pressure and temperature of dosing. We find that BCl 2 is broadly dominant at low temperatures, while high temperatures and ample space on the silicon surface for dissociation encourage the formation of bridging BCl fragments and B substitutions on the surface. This work provides the chemical mechanisms for understanding atomic-precision doping of Si with B, enabling a number of relevant quantum applications, such as bipolar nanoelectronics, acceptor-based qubits, and superconducting Si.

Campbell, Quinn T. [Sandia National Laboratories (↗

Monitoring Local Electric Fields using Stark Shifts on Napthyl Nitrile-Functionalized Silicon Photoelectrodes

in this paper, we report spectroscopic measurements of the local electric field using vibrational Stark shifts of napthyl nitrile-functionalized silicon under electrochemical working conditions. The C$\equiv$N bond is particularly sensitive to applied electric fields and serves as a good probe for the local electric fields at the silicon–aqueous interface. Here, surface-enhanced Raman spectra (SERS) are collected at a silicon surface using a water immersion lens as a function of the reference potential in a three-terminal potentiostat. In deionized (DI) water and KCl solutions, the nitrile (i.e., C$\equiv$N) stretch downshifts by 4.7 and 8.6 cm –1 , respectively, under an applied potential of –1 V vs Ag/AgCl. Density functional theory (DFT) calculations of the napthyl nitrile complex carried out under various electric fields establish the Stark tuning rate to be 0.5622 cm–1/(MV cm –1 ). Based on this relation, electric fields of –8.4 and –15.2 MV/cm were obtained under negative applied potentials. These measurements report the electric field strength within the double (i.e., Helmholtz) layer, which is responsible for pulling positively charged ions (e.g., H + ) toward the surface in reduction reaction processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Addressing Issues with Working Memory in Video Object Segmentation

Contemporary state-of-the-art video object segmentation (VOS) models compare incoming unannotated images to a history of image-mask relations via affinity or cross-attention to predict object masks. We refer to the internal memory state of the initial image-mask pair and past image-masks as a working memory buffer. While the current state of the art models perform very well on clean video data, their reliance on a working memory of previous frames leaves room for error. Affinity-based algorithms include the inductive bias that there is temporal continuity between consecutive frames. To account for inconsistent camera views of the desired object, working memory models need an algorithmic modification that regulates the memory updates and avoid writing irrelevant frames into working memory. A simple algorithmic change is proposed that can be applied to any existing working memory-based VOS model to improve performance on inconsistent views, such as sudden camera cuts, frame interjections, and extreme context changes. The resulting model performances show significant improvement on video data with these frame interjections over the same model without the algorithmic addition. Our contribution is a simple decision function that determines whether working memory should be updated based on the detection of sudden, extreme changes and the assumption that the object is no longer in frame. By implementing algorithmic changes, such as this, we can increase the real-world applicability of current VOS models.

97 MATHEMATICS AND COMPUTING↗

Gibbs mixing of partially distinguishable photons with a polarising beamsplitter membrane

For a thought experiment concerning the mixing of two classical gases, Gibbs concluded that the work that can be extracted from mixing is determined by whether or not the gases can be distinguished by a semi-permeable membrane; that is, the mixing work is a discontinuous function of how similar the gases are. Here we describe an optomechanical setup that generalises Gibbs’ thought experiment to partially distinguishable quantum gases. Specifically, we model the interaction between a polarisation dependent beamsplitter, that plays the role of a semi-permeable membrane, and two photon gases of non-orthogonal polarisation. We find that the work arising from the mixing of the gases is related to the potential energy associated with the displacement of the microscopic membrane, and we derive a general quantum mixing work expression, valid for any two photon gases with the same number distribution. The quantum mixing work is found to change continuously with the distinguishability of the two polarised gases. In addition, fluctuations of the work on the microscopic membrane become important, which we calculate for Fock and thermal states of the photon gases. Our findings generalise Gibbs’ mixing to the quantum regime and open the door for new quantum thermodynamic (thought) experiments with quantum gases with non-orthogonal polarisations and microscopic pistons that can distinguish orthogonal polarisations.

distinguishability↗

Electrochemical reduction of europium(iii) using tetra- n -octyl diglycolamide functionalized ordered mesoporous carbon microelectrodes

This work investigates the one-electron reduction of Eu(III) to Eu(II) with ordered mesoporous carbon (OMC) in cavity microelectrode (CME) systems. OMC materials with and without tetra-n-octyl diglycolamide (TODGA) functionalization were subjected to voltammetric measurements and compared with commercial carbon black Vulcan® XC-72. The electrochemical reduction of solution Eu(III) with unfunctionalized OMC, XC-72, and TODGA-functionalized OMC—both within the electrode matrix and on the electrode surface—is reported. The complexation of Eu(III) by TODGA-functionalized OMC prior to electrode preparation incorporates Eu(III) as part of the bulk electrode matrix. Under these conditions, the high capacitance obscures the Eu(III)/Eu(II) redox couple. A signal emerges above the background (capacitive) currents when 2-octanol is added to the TODGA-functionalized OMC as a wetting agent. In contrast, surface Eu(III)–TODGA complexation, when Eu(III) contacts the electrode surface exclusively after electrode preparation, provides a strong response. The addition of 2-octanol to TODGA reduces the capacitance of the electrode and narrows the Eu(III)/Eu(II) redox peak widths. In conclusion, the desorption by reductive stripping of Eu(II) was demonstrated using a 2-octanol modified TODGA OMC CME, opening the possibility for selective separation of Eu from adjacent trivalent lanthanides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Representing plant diversity in land models: An evolutionary approach to make “Functional Types” more functional

Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. Here we review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.

59 BASIC BIOLOGICAL SCIENCES↗

A novel technique for minimizing energy functional using neural networks

An energy functional describes the equilibrium state of a system. In this work, we present a novel technique, Functional Optimization using Neural Networks (FONN), for minimizing the system’s energy. FONN utilizes neural networks to process information at discrete grid points, considering their interactions with neighboring grid points, to update the state of the system. The training process involves formulating a loss function based on the system’s energy, and with the help of multiple fine-tuning steps, the method employs a progressive energy reduction technique that decreases the energy in multiple steps. FONN’s effectiveness is demonstrated across various problems, including the minimization of the heat and Lyapunov energy. Furthermore, the paper explores the minimization of the elastic bending energy with an area constraint.

97 MATHEMATICS AND COMPUTING↗

How Accurate Are Approximate Density Functionals for Noncovalent Interaction of Very Large Molecular Systems?

Noncovalent intermolecular interactions are very important in many research areas. Therefore, it is vital to understand the extent to which approximate density functionals give a proper description of noncovalent interactions. Previous research has demonstrated that some approximate density functionals can predict usefully accurate interaction energies for many noncovalent systems; however, most of that work is limited to small and moderate-sized molecules. Very recently though, accurate benchmarks have become available for some very large molecules. Here, the present work applies 21 approximate density functionals to compute the binding energies of seven large molecular systems that have a number of atoms ranging from 200 to 910. The results are judged by comparison to the recently published CIM-DLPNO-CCSD(T) results, which are assumed to provide a reliable benchmark. The five most accurate methods among those tested are found to be PW6B95-D4, PW6B95-D3(BJ), revM11, M06-L, and MN15.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Workhorse minimally empirical dispersion-corrected density functional with tests for weakly bound systems: r 2 SCAN + rVV 10

SCAN+rVV10 has been demonstrated to be a versatile van der Waals (vdW) density functional that delivers good predictions of both energetic and structural properties for many types of bonding. Recently, the r 2 SCAN functional was devised as a revised form of SCAN with improved numerical stability. In this work, we refit the rVV10 functional to optimize the r 2 SCAN+rVV10 vdW density functional and test its performance for molecular interactions and layered materials. Our molecular tests demonstrate that r 2 SCAN+rVV10 outperforms its predecessor SCAN+rVV10 in both efficiency (numerical stability) and accuracy. This good performance is also found in lattice-constant predictions. In comparison with benchmark results from higher-level theories or experiments, r 2 SCAN+rVV10 yields excellent interlayer binding energies and phonon dispersions for layered materials.

36 MATERIALS SCIENCE↗

Growth functions of periodic space tessellations

This work analyzes the rules governing the growth of the numbers of vertices, edges and faces in all possible periodic tessellations of the 2D Euclidean space, and encodes those rules in several types of polynomial growth functions. These encodings map the geometric, combinatorial and topological properties of the tessellations into sets of integer coefficients. Several general statements about these encodings are given with rigorous mathematical proof. The variation of the growth functions is represented graphically and analyzed in orphic diagrams, so named because of their similarity to orphic art. Several examples of 3D space groups are included, to emphasize the complexity of the growth functions in higher dimensions. A freely available Python library is presented to facilitate the discovery of the growth functions and the generation of orphic diagrams.

Chemistry↗

Machine learning defect properties in Cd-based chalcogenides

Impurity energy levels in the band gap can have serious consequences for a semiconductor's performance as a photovoltaic absorber. Data-driven approaches can help accelerate the prediction of point defect properties in common semiconductors, and thus lead to the identification of potential deep lying impurity states. In this work, we use density functional theory (DFT) to compute defect formation energies and charge transition levels of hundreds of impurities in CdX chalcogenide compounds, where X = Te, Se or S. We apply machine learning techniques on the DFT data and develop on-demand predictive models for the formation energy and relevant transition levels of any impurity atom in any site. The trained ML models are general and accurate enough to predict the properties of any possible point defects in any Cd-based chalcogenide, as we prove by testing on a few selected defects in mixed chalcogen compounds CdTe 0.5 Se 0.5 and CdSe 0.5 S 0.5 . The ML framework used in this work can be extended to any class of semiconductors.

density functional theory↗

CrI 3 revisited with a many-body ab initio theoretical approach

CrI 3 has recently been shown to exhibit low-dimensional, long-range magnetic ordering from few layers to single layers of CrI 3 . The properties of CrI 3 bulk and few layered systems are uniquely defined by a combination of short-range intralayer and long-range interlayer interactions; including strong correlations, exchange and spin orbit coupling. Unfortunately, both the long-range van der Waals interactions, which are driven by dynamic, many-body electronic correlations and the competing strong intralayer correlations, present a formidable challenging for the local or semi local mean-field approximations employed in workhorse electronic structure approaches like density functional theory. In this work, we employ a sophisticated many-body approach that can simultaneously describe long- and short-range correlations. Herein, we establish that the fixed-node diffusion Monte Carlo (FNDMC) method reproduces the experimental interlayer separation distance of bulk CrI 3 for the high-temperature, monoclinic phase, with a reliable prediction of the interlayer binding energy. We subsequently employed, the FNDMC results to benchmark the accuracy of several density functional theory exchange-correlation approximations.

36 MATERIALS SCIENCE↗

The role of coverage effects on the structure–sensitivity of formic acid electrooxidation on Pd surfaces

Direct formic acid (FA) fuel cells (DFAFCs) with Pd anode catalysts are promising for small portable applications. During the electrooxidation of formic acid (FAO), CO accumulates on the Pd electrocatalyst, thereby decreasing its performance. In this work, we use density functional theory (DFT; RPBE) to elucidate the significance of coverage effects on the structure–sensitivity of FAO over four low–index Pd surfaces: Pd(1 1 1), Pd(1 0 0), Pd(1 1 0), and Pd(2 1 1). We construct coverage–dependent Gibbs free energy diagrams and in agreement with experiment, predict that Pd(1 0 0) and Pd(2 1 1) are the most active surfaces. Additionally, we find that the presence of CO spectator species can alter the preferred electrooxidation pathway under different applied potentials. Furthermore, such pathway transitions appear to be critical for rationalizing experimental trends regarding electrocatalytic activity and are only captured when coverage effects are accounted for. Insights derived from this work may facilitate the design of improved FAO electrocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Raman-based sorting of microbial cells to link functions to their genes

In our recent work, we developed an optofluidic platform that allows a direct link to be made between the phenotypes (functions) and the genotypes (genes) of microbial cells within natural communities. By combining stable isotope probing, optical tweezers, Raman microspectroscopy, and microfluidics, the platform performs automated Raman-based sorting of taxa from within a complex community in terms of their functional properties. In comparison with manual sorting approaches, our method provides high throughput (up to 500 cells per hour) and very high sorting accuracy (98.3 ± 1.7%), and significantly reduces the human labour required. The system provides an efficient manner to untangle the contributions of individual members within environmental and host-associated microbiomes. In this News and Thoughts, we provide an overview of our platform, describe potential applications, suggest ways in which the system could be improved, and discuss future directions in which Raman-based analysis of microbial populations might be developed.

59 BASIC BIOLOGICAL SCIENCES↗

Custom-trained Machine-learning Interatomic Potentials: ZnCl2 Aqueous Solution

This dataset was generated using an iterative active-learning strategy implemented in the ArcaNN software package (https://github.com/arcann-chem/arcann_training) to train machine-learning interatomic potentials for aqueous ZnCl2 solutions. Each active-learning cycle consisted of three stages: training, exploration, and labeling. The initial training set combined configurations generated in this work from enhanced-sampling ab initio molecular dynamics simulations with configurations from a previously reported neural-network-potential study of aqueous ZnCl2. The enhanced-sampling ab initio molecular dynamics simulations involved Zn–Cl separation and the chloride coordination number around Zn²? as collective variables. These configurations served as the seed dataset. Subsequent active-learning cycles expanded the training set by identifying and labeling configurations that were poorly represented by the current models, thereby improving coverage of ion-association states and changes in local coordination and charge-state environments relevant to the solution free-energy landscape. For all selected configurations, single-point calculations of the total energies and atomic forces were performed within density functional theory using the CP2K Quickstep module. Reference calculations employed the revPBE-D3 and r2SCAN exchange-correlation functionals. Motivated by recent work on aqueous Zn²?, the main revPBE calculations omitted D3 dispersion contributions involving Zn²?, while retaining the D3 correction for water and chloride. For comparison, fully dispersion-corrected revPBE-D3 reference calculations were also performed, with D3 applied to all species, including Zn²?. Valence electrons were treated explicitly, while core electrons were represented using norm-conserving Goedecker–Teter–Hutter pseudopotentials. The wave functions were expanded using the mixed Gaussian-and-plane-wave scheme with TZV2P-MOLOPT basis sets for all elements and a 600 Ry auxiliary plane-wave cutoff for the electron density. Self-consistent-field convergence was accelerated using the orbital-transformation and Direct Inversion in the Iterative Subspace algorithms, with a convergence threshold of 10?6. All single-point calculations were performed in periodic orthorhombic cells. The CELL_REF keyword in CP2K was used to define a fixed reference cell with a box length of 25 Å. This treatment ensured a consistent reference for configurations extracted from NpT trajectories with fluctuating cell dimensions. The resulting DFT energies and atomic forces constitute the ground-truth labels used to train the MLIPs. The resulting MLIP was trained for aqueous ZnCl2 solutions spanning concentrations from 0 to 30 molal and a broad pH range, from strongly acidic to strongly basic conditions. Representative examples of configurations included in the MLIP training dataset are provided below. These include 1) Representative configurations from the dataset labeled at the revPBE-D3 level, with D3 dispersion interactions involving Zn2+ excluded (revPBE-wo-D3). 2) Representative configurations from the dataset labeled at the fully dispersion-corrected revPBE-D3 level, with D3 interactions applied to all species, including Zn2+ (revPBE-D3). 3) Representative configurations from the dataset labeled at the r2SCAN level of theory (r2SCAN).

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗