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At least 523 records · Page 29

Sampling two-dimensional isometric tensor network states

Sampling a quantum system’s underlying probability distributions is an important computational task, e.g., for quantum advantage experiments and quantum Monte Carlo algorithms. Tensor networks are an invaluable tool for efficiently representing states of large quantum systems with limited entanglement. Algorithms for sampling one-dimensional (1D) tensor networks are well-established and utilized in several 1D tensor network methods. In this paper we introduce two novel sampling algorithms for two-dimensional (2D) isometric tensor network states (isoTNS) that generalize existing 1D tensor network sampling algorithms. Our first proposed algorithm performs independent sampling and yields a single configuration together with its associated probability. The second algorithm employs a greedy search strategy to identify high-probability configurations and their corresponding probabilities. Numerical results demonstrate the effectiveness of these algorithms across quantum states with varying entanglement and system size.

Dumitrescu, Eugene [ORNL] (ORCID:0000000158519567)↗

Mechanistic Pathways for N 2 O Elimination from trans -R 3 Sn-O-N=N-O-SnR 3 and for Reversible Binding of CO 2 to R 3 Sn-O-SnR 3 (R = Ph, Cy)

The rate and mechanism of the elimination of N 2 O from trans-R 3 Sn-O-N=N-O-SnR 3 (R = Ph ( 1 Ph ) and R = Cy ( 1 Cy )) to form R 3 Sn-O-SnR 3 (R = Ph ( 2 Ph ) and R = Cy ( 2 Cy )) have been studied using both NMR and IR techniques to monitor the reactions in the temperature range of 39–79 °C in C 6 D 6 . Activation parameters for this reaction are ΔH ‡ = 15.8 ± 2.0 kcal·mol –1 and ΔS ‡ = –28.5 ± 5 cal·mol –1 ·K –1 for 1 Ph and ΔH ‡ = 22.7 ± 2.5 kcal·mol –1 and ΔS ‡ = –12.4 ± 6 cal·mol –1 ·K –1 for 1 Cy . Addition of O 2 , CO 2 , N 2 O, or PPh 3 to sealed tube NMR experiments did not alter in a detectable way the rate or product distribution of the reactions. Computational DFT studies of elimination of hyponitrite from trans-Me 3 Sn-O-N=N-O-SnMe 3 ( 1 Me ) yield a mechanism involving initial migration of the R 3 Sn group from O to N passing through a marginally stable intermediate product and subsequent N 2 O elimination. Reactions of 1 Ph with protic acids HX are rapid and lead to formation of R 3 SnX and trans-H 2 N 2 O 2 . Reaction of 1 Ph with the metal radical •Cr(CO) 3 C 5 Me 5 at low concentrations results in rapid evolution of N 2 O. At higher •Cr(CO) 3 C 5 Me 5 concentrations, evolution of CO 2 rather than N 2 O is observed. Addition of 1 atm or less CO 2 to benzene or toluene solutions of 2 Ph and 2 Cy resulted in very rapid reaction to form the corresponding carbonates R 3 Sn-O-C(=O)-O-SnR 3 (R = Ph ( 3 Ph ) and R = Cy ( 3 Cy )) at room temperature. Evacuation results in fast loss of bound CO 2 and regeneration of 2 Ph and 2 Cy . Variable temperature data for formation of 3 Cy yield ΔH o = –8.7 ± 0.6 kcal·mol –1 , ΔS o = –17.1 ± 2.0 cal·mol –1 ·K –1 , and ΔG o 298K = –3.6 ± 1.2 kcal·mol –1 . Furthermore, DFT studies were performed and provide additional insight into the energetics and mechanisms for the reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Capacitance of Carbon Nanotube/Graphene Composite Electrodes with [BMIM + ][BF$_4^–$]/Acetonitrile: Fixed Voltage Molecular Dynamics Simulations

The capacitance of nanoporous carbon electrode materials is dictated by the physical interactions with electrolyte ions and molecules at the accessible interior electrode surface. While significant progress has been made in designing and synthesizing carbon materials with well-defined and relatively homogeneous nanoporosity, the majority of materials remain heterogeneous, and the resulting properties reflect an average over this distribution. In this regard, computer simulations can be a valuable tool to predict or validate structure/property relationships by systematically investigating well-defined, model electrode morphologies. In this work, we utilize fixed-voltage molecular dynamics simulations to predict structure/capacitance relationships for five different model morphologies of carbon nanotube/graphene (CNT/G) composite electrodes with 1-butyl-3-methylimidazolium tetrafluoroborate/acetonitrile electrolyte. The CNT/G electrode models are inspired by experimental “layer-by-layer” syntheses and strike a balance between realism and computational tractability. Comparison between different model electrode architectures elucidates important structure/property relationships. We find that CNT/graphene contact points serve as “hot spots” with significantly enhanced charge separation relative to the rest of the electrode. Furthermore, we demonstrate a specific nanoconfinement motif that provides substantial 3–4$\times$ enhancement of local capacitance, resulting in a ~40% increase of the total electrode differential capacitance. Because the accessible surface area of the model CNT/G electrodes is precisely determined, a comparison of per-area capacitance across systems is unambiguous. Our results thus complement a prior computational demonstration of capacitance enhancement in nanoconfinement while elucidating additional interaction motifs at CNT/G electrochemical interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Light-Promoted C(sp 3 )–C(sp 3 ) Reductive Elimination from Dialkyl NiII Complexes

Ni-catalyzed cross-coupling is a powerful strategy to forge C(sp 3 )–C(sp 3 ) bonds. Typically, to do so requires overcoming a challenging C–C bond-forming reductive elimination, often enabled by the intermediacy of highly oxidized Ni species or outer-sphere processes. While direct C(sp 3 )–C(sp 3 ) reductive elimination from the Ni II base oxidation state is normally thermally inaccessible, light-activation provides an avenue to affect such transformations. Here, we investigate the mechanism of light-induced C(sp 3 )–C(sp 3 ) bond formation from dialkyl bipyridine Ni II complexes through a variety of organometallic, spectroscopic, and computational studies. Wavelength-dependent quantum yields, ligand electronics–reactivity relationships, excited-state lifetimes, computed barriers, and product distributions from crossover studies support a photolysis/radical rebound mechanism. Furthermore, this reactivity paradigm complements existing strategies in the literature to promote reductive elimination from Ni II , such as the use of destabilizing, sterically hindered ligands and reduction of electron density at Ni through the binding of electron-deficient olefins. Hence, we envision that light-induced reductive elimination may enable the development of challenging C(sp 3 )–C(sp 3 ) couplings.

Alkyls↗

Down-selection of biomolecules to assemble “reverse micelle” with perovskites

Abstract Biological molecule-semiconductor interfacing has triggered numerous opportunities in applied physics such as bio-assisted data storage and computation, brain-computer interface, and advanced distributed bio-sensing. The introduction of electronics into biological embodiment is being quickly developed as it has great potential in providing adaptivity and improving functionality. Reciprocally, introducing biomaterials into semiconductors to manifest bio-mimetic functionality is impactful in triggering new enhanced mechanisms. In this study, we utilize the vulnerable perovskite semiconductors as a platform to understand if certain types of biomolecules can regulate the lattice and endow a unique mechanism for stabilizing the metastable perovskite lattice. Three tiers of biomolecules have been systematically tested and the results reveal a fundamental mechanism for the formation of a “reverse-micelle” structure. Systematic exploration of a large set of biomolecules led to the discovery of guiding principle for down-selection of biomolecules which extends the classic emulsion theory to this hybrid systems. Results demonstrate that by introducing biomaterials into semiconductors, natural phenomena typically observed in biological systems can also be incorporated into semiconducting crystals, providing a new perspective to engineer existing synthetic materials.

59 BASIC BIOLOGICAL SCIENCES↗

Stochastic evaluation of four-component relativistic second-order many-body perturbation energies: A potentially quadratic-scaling correlation method

A second-order many-body perturbation correction to the relativistic Dirac-Hartree-Fock energy is evaluated stochastically by integrating 13-dimensional products of four-component spinors and Coulomb potentials. The integration in the real space of electron coordinates is carried out by the Monte Carlo (MC) method with the Metropolis sampling, whereas the MC integration in the imaginary-time domain is performed by the inverse-CDF (cumulative distribution function) method. The computational cost to reach a given relative statistical error for spatially compact but heavy molecules is observed to be no worse than cubic and possibly quadratic with the number of electrons or basis functions. This is a vast improvement over the quintic scaling of the conventional, deterministic second-order many-body perturbation method. The algorithm is also easily and efficiently parallelized with demonstrated 92% strong scalability going from 64 to 4096 processors for a fixed job size.

74 ATOMIC AND MOLECULAR PHYSICS↗

Equity and modeling in sustainability science: Examples and opportunities throughout the process

Equity is core to sustainability, but current interventions to enhance sustainability often fall short in adequately addressing this linkage. Models are important tools for informing action, and their development and use present opportunities to center equity in process and outcomes. This Perspective highlights progress in integrating equity into systems modeling in sustainability science, as well as key challenges, tensions, and future directions. We present a conceptual framework for equity in systems modeling, focused on its distributional, procedural, and recognitional dimensions. We discuss examples of how modelers engage with these different dimensions throughout the modeling process and from across a range of modeling approaches and topics, including water resources, energy systems, air quality, and conservation. Synthesizing across these examples, we identify significant advances in enhancing procedural and recognitional equity by reframing models as tools to explore pluralism in worldviews and knowledge systems; enabling models to better represent distributional inequity through new computational techniques and data sources; investigating the dynamics that can drive inequities by linking different modeling approaches; and developing more nuanced metrics for assessing equity outcomes. We also identify important future directions, such as an increased focus on using models to identify pathways to transform underlying conditions that lead to inequities and move toward desired futures. By looking at examples across the diverse fields within sustainability science, we argue that there are valuable opportunities for mutual learning on how to use models more effectively as tools to support sustainable and equitable futures.

54 ENVIRONMENTAL SCIENCES↗

ML-Based Pebble Power Reconstruction for Pebble Bed Reactor Analysis

Pebble power reconstruction has been explored to complement the conventional homogenized modeling approach in pebble bed reactor (PBR) analysis, as detailed heterogeneous geometry calculations are computationally expensive. The random distribution of pebble fuels within the core challenges the application of conventional pin power reconstruction methods. To address this, we introduce a machine learning approach based on the transformer model, composed of encoder and decoder layers, to estimate the flux and power form functions for reconstructing individual pebble neutron fluxes and powers. The homogeneous neutron flux distribution within each spectral zone (SZ) is obtained from finite element solutions of global diffusion or transport calculations. Verification tests demonstrate that the trained transformer model accurately predicts power form functions over a range of conditions, including variations in pebble enrichment, location, type, SZ size, and burnup. In particular, verification using a three-dimensional PBR benchmark with burned pebbles shows good agreement in heterogeneous pebble power distributions between Griffin and Serpent. These results highlight the potential of applying conventional pin power reconstruction approaches to PBR cores with randomly distributed pebbles.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)

Abstract Motivation Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation. Results Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore. This is then extended to provide the probability distribution for the number of localizations in a direct stochastic optical reconstruction microscopy experiment involving an arbitrary number of molecules. We demonstrate that when training data are available to estimate photoswitching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localizations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein linker for activation of T cells on the cell surface of the T-cell immunological synapse. Availability and implementation Software and data available at https://github.com/lp1611/mol_count_dstorm. Supplementary information Supplementary data are available at Bioinformatics online.

Patel, Lekha↗

Fast calculation of diffraction patterns from an ensemble of aligned molecules

We report an algorithm to calculate electron diffraction patterns for molecules with anisotropic angular distribution, which is significantly faster than existing methods. The algorithm uses a transform to convert the molecular orientation distribution, which is a function of three Euler angles, to the atom-pair distribution functions which depend on the polar and azimuthal angles. The diffraction signal can then be calculated from the atom-pair distributions. We demonstrate the computation method numerically by calculating electron diffraction patterns for a symmetric top molecule (trifluoroiodomethane) and an asymmetric top molecule (formaldehyde) and show that it reduces the calculation time by approximately two orders of magnitude compared to the standard brute-force method. Here, the method can also be applied to the calculation of x-ray diffraction patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗

From Reproducible Edge–Cloud Experimentation to Real-World Practice: The E2Clab Experience

Reproducibility is already difficult in distributed systems; on the computing continuum, it becomes substantially harder. Applications that span sensing devices, edge and fog resources, and cloud platforms must be evaluated across heterogeneous hardware, variable network conditions, cross-layer orchestration decisions, and long-running workflow lifecycles. We use E2Clab as a case study to examine these challenges and their implications for experimental methodology. We explain why reproducible experimentation is harder on the continuum, then revisit E2Clab as an initial response based on explicit modeling of infrastructure, workflow lifecycle, and artifacts. Lastly, we discuss how its evolution toward more realistic application settings can be understood through the lens of Translational Computer Science. We argue that reproducible continuum experimentation requires methods that are rigorous enough for research while remaining adaptable to real-world practice.

42 ENGINEERING↗

Deep Reinforcement Learning for Distribution System Restoration Using Distributed Energy Resources and Tie-Switches

Distributed energy resources (DERs), such as solar PVs and energy storage, can be used to restore distribution system critical loads after the extreme weather events to increase grid resilience. However, coordinating multiple DERs together with tie-switches for multi-step restoration process under renewable uncertainty is challenging. This paper proposes a deep reinforcement learning to control discrete actions of switching on/off tie switches and DERs for critical load restoration. The restoration problem is first cast into the Markov decision process suitable for DRL. Then, the original soft actor critic (SAC) method for continuous actions has been extended to handle discrete and continuous actions. Numerical comparison results with other stochastic optimization-based approaches on the modified IEEE 33-bus system show that the proposed method can achieve fast critical load restoration in the presence of substation power outage while maintaining system voltage limit throughout the restoration process.

active distribution systems↗

Cybersecurity Value-at-Risk Framework

As more variable renewable energy sources are added to the grid, the role of hydropower as a reliable baseline and firming resource is growing more critical. However, the U.S hydropower fleet is not fully prepared to face modern issues such as cybersecurity threats. Hydropower accounts for 37% of U.S. utility-scale renewable electricity but is challenged by diverse infrastructure and legacy devices that predate modern security practices. While new cybersecurity solutions cannot simply be added to current hydropower generation and operation technologies, custom cybersecurity assessments can reveal system-specific threats and risk probabilities and identify mitigating enhancements.

cybersecurity valuation methodology↗