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DOE OSTI2015

Fragmentation of fast Josephson vortices and breakdown of ordered states by moving topological defects

Topological defects such as vortices, dislocations or domain walls define many important effects in superconductivity, superfluidity, magnetism, liquid crystals, and plasticity of solids. Here we address the breakdown of the topologically-protected stability of such defects driven by strong external forces. We focus on Josephson vortices that appear at planar weak links of suppressed superconductivity which have attracted much attention for electronic applications, new sources of THz radiation, and low-dissipative computing. Our numerical simulations show that a rapidly moving vortex driven by a constant current becomes unstable with respect to generation of vortex-antivortex pairs caused by Cherenkov radiation. As a result, vortices and antivortices become spatially separated and accumulate continuously on the opposite sides of an expanding dissipative domain. This effect is most pronounced in thin film edge Josephson junctions at low temperatures where a single vortex can switch the whole junction into a resistive state at currents well below the Josephson critical current. In conclusion, our work gives a new insight into instability of a moving topological defect which destroys global long-range order in a way that is remarkably similar to the crack propagation in solids.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Anomalous transport in the H-mode pedestal of Alcator C-Mod discharges

Anomalous transport in the H-mode pedestal region of five Alcator C-Mod discharges, representing a collisionality scan is analyzed. The understanding of anomalous transport in the pedestal region is important for the development of a comprehensive model for the H-mode pedestal slope. In this research, a possible role of the drift resistive inertial ballooning modes (Rafiq et al 2010 Phys. Plasmas 17 082511) in the edge of Alcator C-Mod discharges is analyzed. The stability analysis, carried out using the TRANSP code, indicates that the DRIBM modes are strongly unstable in Alcator C-Mod discharges with large electron collisionality. An improved interpretive analysis of H-mode pedestal experimental data is carried out utilizing the additive flux minimization technique (Pankin et al 2013 Phys. Plasmas 20 102501) together with the guiding-center neoclassical kinetic XGC0 code. The neoclassical and neutral physics are simulated in the XGC0 code and the anomalous fluxes are computed using the additive flux minimization technique. The anomalous fluxes are reconstructed and compared with each other for the collisionality scan Alcator C-Mod discharges. It is found that the electron thermal anomalous diffusivities at the pedestal top increase with the electron collisionality. This dependence can also point to the drift resistive inertial ballooning modes as the modes that drive the anomalous transport in the plasma edge of highly collisional discharges.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Anomalous transport in the H-mode pedestal of Alcator C-Mod discharges

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Non-linear MHD modelling of edge localized modes suppression by resonant magnetic perturbations in ITER

Edge localized modes (ELMs) suppression by resonant magnetic perturbations (RMPs) was studied with the non-linear magneto-hydro-dynamic (MHD) code JOREK for the ITER H-mode scenarios at 15 MA, 12.5 MA, 10 MA/5.3 T. In this study, the main aim was to demonstrate that ELMs can be suppressed by RMPs while the divertor 3D footprints of heat and particle fluxes remain within divertor material limits. The unstable peeling–ballooning modes responsible for ELMs without RMPs were modelled first for each scenario using numerically accessible parameters for ITER. Then the stabilization of ELMs by RMPs was modelled with the same parameters. RMP spectra, optimized by the linear MHD MARS-F code, with main toroidal harmonics N = 2, N = 3, N = 4 have been used as boundary conditions of the computational domain of JOREK, including realistic RMP coils, main plasma, scrape off layer (SOL) divertor and realistic first wall. The model includes all relevant plasma flows: toroidal rotation, two fluid diamagnetic effects and neoclassical poloidal friction. With RMPs, the main toroidal harmonic and the non-linearly coupled harmonics remain dominant at the plasma edge, producing saturated modes and a continuous MHD turbulent transport thereby avoiding ELM crashes in all scenarios considered here. The threshold for ELM suppression was found at a maximum RMP coils current of 45 kAt–60 kAt compared to the coils maximum capability of 90 kAt. In the high beta poloidal steady-state 10 MA/5.3 T scenario, a rotating QH-mode without ELMs was observed even without RMPs. In this scenario with RMPs N = 3, N = 4 at 20 kAt maximum current in RMP coils, similar QH-mode behaviour was observed however with dominant edge harmonic corresponding to the main toroidal number of RMPs. The present MHD modelling was limited in time by few tens of ms after RMPs were switched on until the magnetic energy of the modes saturates. As a consequence the thermal energy was still evolving on this time scale, far from the ITER confinement time scale and hence only the form of 3D footprints on the divertor targets can be indicated within this set-up. Also note, that the divertor physics was missing in this model, so realistic values of fluxes are out of reach in this modelling. However the stationary 3D divertor and particle fluxes could be simply extrapolated from these results to the stationary situation considering that a large power fraction should be radiated in the core and SOL and only about 50 MW power is going to the divertor, which is an arbitrary, but reasonable number used here. The 3D footprints with RMPs show the characteristic splitting with the main RMP toroidal symmetry. The maximum radial extension of the footprints typically was ~20 cm in inner divertor and ~40 cm in outer divertor with stationary heat fluxes decreasing further out from the initial strike point from ~5 MW m ₋2 to ~1 MW m ₋2 assuming a total power in the divertor and walls is 50 MW. The heat fluxes remain within the divertor target and baffle areas, however with rather small margin in the outer divertor which could be an issue for the first wall especially in transient regimes when part of the plasma thermal energy is released due to switching on the RMP coils. This fact should be considered when RMPs are applied with a more favorable application before or soon after the L–H transition, although optimization is required to avoid increasing the L–H power threshold with RMPs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Spectrally accelerated edge and scrape-off layer gyrokinetic turbulence simulations

This paper presents the first gyrokinetic (GK) simulations of edge and scrape-off layer (SOL) turbulence accelerated by a velocity-space spectral approach in the full-f GK code GENE-X. Building upon the original grid velocity-space discretization, we derive and implement a new spectral formulation and verify the numerical implementation using the method of manufactured solution. We conduct a series of spectral turbulence simulations focusing on the TCV-X21 reference case (Oliveira et al., 2022 [26]) and compare these results with previously validated grid simulations (Ulbl et al., 2023 [25]). The spectral approach reproduces the outboard midplane (OMP) profiles (density, temperature, and radial electric field), dominated by trapped electron mode (TEM) turbulence, with excellent agreement and significantly lower velocity-space resolution. As a consequence, the spectral approach reduces the computational cost (CPUh) by at least an order of magnitude, of approximately 50 for the TCV-X21 case. This enables high-fidelity GK simulations to be performed within a few days on modern CPU-based supercomputers for medium-sized devices and establishes GENE-X as a powerful tool for studying edge and SOL turbulence, moving towards reactor-relevant devices like ITER.

Gyrokinetic↗

DOE OSTI2023

Non-bonding interaction of dual atom catalysts for enhanced oxygen reduction reaction

Here, we demonstrate the design of graphene-supported dual atom catalysts (DACs) for the four-electron oxygen reduction reaction (ORR), by utilizing the non-bonding interaction of counterpart metals (M) that synergistically tune the electronic properties and catalytic activity of the Fe active site in FeMN 6 -DAC and FeMN 8 -DAC systems, where M stands for Fe, Co, Ni, Cu, and Zn. More specifically, for Fe-M distances below 15Å, the non-bonding interaction is significant, making the system act as the DAC. We predicted that FeNiN 6 -DAC and FeNiN 8 -DAC exhibit a low ORR overpotential (η ORR ) of 0.28 V and 0.47 V, respectively, which are at the summits of volcano plots. This low η ORR originates from the high Bader charge transfer coupled with high spin density at the Fe site in both the FeNiN 6 -DAC and FeNiN 8 -DAC systems, which weakens the adsorption of OH* intermediate while enhancing its desorption to H 2 O. Guided by these density functional theory (DFT) computational results, we synthesized FeCoN 8 -DAC and FeNiN 8 -DAC along with N-doped graphene and confirmed their structures with scanning transmission electron microscopy (STEM), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and electron spin resonance (ESR). We verify experimentally the catalytic activities and find that FeNiN 8 -DAC has the low experimental overpotential of 0.39 V with a Tafel slope of 47 mVdec -1 . Based on these results, we propose a DFT-guided strategy to tune the charge transfer and spin population of the active site toward designing DACs for electrochemical ORR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Accelerating Quantum Materials Development with Advances in Transmission Electron Microscopy

Quantum materials are driving a technology revolution in sensing, communication, and computing, while simultaneously testing many core theories of the past century. Materials such as topological insulators, complex oxides, superconductors, quantum dots, color center-hosting semiconductors, and other types of strongly correlated materials can exhibit exotic properties such as edge conductivity, multiferroicity, magnetoresistance, superconductivity, single photon emission, and optical-spin locking. These emergent properties arise and depend strongly on the material’s detailed atomic-scale structure, including atomic defects, dopants, and lattice stacking. In this review, we describe how progress in the field of electron microscopy (EM), including in situ and in operando EM, can accelerate advances in quantum materials and quantum excitations. We begin by describing fundamental EM principles and operation modes. We then discuss various EM methods such as (i) EM spectroscopies, including electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and electron energy gain spectroscopy (EEGS); (ii) four-dimensional scanning transmission electron microscopy (4D-STEM); (iii) dynamic and ultrafast EM (UEM); (iv) complementary ultrafast spectroscopies (UED, XFEL); and (v) atomic electron tomography (AET). We describe how these methods could inform structure–function relations in quantum materials down to the picometer scale and femtosecond time resolution, and how they enable precision positioning of atomic defects and high-resolution manipulation of quantum materials. For each method, we also describe existing limitations to solve open quantum mechanical questions, and how they might be addressed to accelerate progress. Among numerous notable results, our review highlights how EM is enabling identification of the 3D structure of quantum defects; measuring reversible and metastable dynamics of quantum excitations; mapping exciton states and single photon emission; measuring nanoscale thermal transport and coupled excitation dynamics; and measuring the internal electric field and charge density distribution of quantum heterointerfaces- all at the quantum materials’ intrinsic atomic and near atomic-length scale. Finally, we conclude by describing open challenges for the future, including achieving stable sample holders for ultralow temperature (below 10K) atomic-scale spatial resolution, stable spectrometers that enable meV energy resolution, and high-resolution, dynamic mapping of magnetic and spin fields. With atomic manipulation and ultrafast characterization enabled by EM, quantum materials will be poised to integrate into many of the sustainable and energy-efficient technologies needed for the 21st century.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Optical N-plasmon: topological hydrodynamic excitations in graphene from repulsive Hall viscosity

Abstract Edge states occurring in Chern and quantum spin-Hall phases are signatures of the topological electronic band structure in two-dimensional (2D) materials. Recently, a new topological electromagnetic phase of graphene characterized by the optical N-invariant was proposed. Optical N-invariant arises from repulsive Hall viscosity in hydrodynamic many-body electron systems, distinct from the Chern and Z 2 invariants. In this paper, we introduce the topologically protected edge excitation—optical N-plasmon of interacting many-body electron systems in the topological optical N-phase. These optical N-plasmons are signatures of the topological plasmonic band structure in 2D materials. We demonstrate that optical N-plasmons exhibit unique dispersion relations, stability against various boundary conditions, and edge profiles when compared with the topologically trivial edge magneto plasmons. Based on the optical N-plasmon, we design an ultra sub-wavelength broadband topological hydrodynamic circulator, which is a chiral quantum radio-frequency circuit component crucial for information routing and interfacing quantum–classical computing systems. Furthermore, we reveal that optical N-plasmons can be effectively tuned by the neighboring dielectric environment without breaking the topological properties. Our work provides a smoking gun signature of topological electromagnetic phases occurring in 2D materials arising from repulsive Hall viscosity.

Physics↗

DOE OSTI2016

MO-DE-207A-11: Sparse-View CT Reconstruction Via a Novel Non-Local Means Method

Purpose: Sparse-view computed tomography (CT) reconstruction is an effective strategy to reduce the radiation dose delivered to patients. Due to its insufficiency of measurements, traditional non-local means (NLM) based reconstruction methods often lead to over-smoothness in image edges. To address this problem, an adaptive NLM reconstruction method based on rotational invariance (RIANLM) is proposed. Methods: The method consists of four steps: 1) Initializing parameters; 2) Algebraic reconstruction technique (ART) reconstruction using raw projection data; 3) Positivity constraint of the image reconstructed by ART; 4) Update reconstructed image by using RIANLM filtering. In RIANLM, a novel similarity metric that is rotational invariance is proposed and used to calculate the distance between two patches. In this way, any patch with similar structure but different orientation to the reference patch would win a relatively large weight to avoid over-smoothed image. Moreover, the parameter h in RIANLM which controls the decay of the weights is adaptive to avoid over-smoothness, while it in NLM is not adaptive during the whole reconstruction process. The proposed method is named as ART-RIANLM and validated on Shepp-Logan phantom and clinical projection data. Results: In our experiments, the searching neighborhood size is set to 15 by 15 and the similarity window is set to 3 by 3. For the simulated case with a resolution of 256 by 256 Shepp-Logan phantom, the ART-RIANLM produces higher SNR (35.38dB<24.00dB) and lower MAE (0.0006<0.0023) reconstructed image than ART-NLM. The visual inspection demonstrated that the proposed method could suppress artifacts or noises more effectively and preserve image edges better. Similar results were found for clinical data case. Conclusion: A novel ART-RIANLM method for sparse-view CT reconstruction is presented with superior image. Compared to the conventional ART-NLM method, the SNR and MAE from ART-RIANLM increases 47% and decreases 74%, respectively.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

GDB: A global 3D two-fluid model of plasma turbulence and transport in the tokamak edge

Here, the global drift-ballooning (GDB) code is developed to study tokamak edge low frequency turbulence and transport, and their relationship to global profile evolution. The code employs a 3D electromagnetic fluid model that does not discriminate between equilibrium and perturbative contributions, capturing arbitrary amplitude fluctuations. Primitive plasma variables, including the flow profiles, are evolved self-consistently in both closed-flux surfaces and the scrape-off-layer (SOL). A suite of numerical techniques described here handle the linear and non-linear components of the model efficiently so as to support realistic discharge parameters (such as realistic deuterium mass ratio √m i /m e ≈ 60) and yield good scaling on high performance computing (HPC) systems. GDB resolves turbulence slower than the ion gyrofrequency in simulations that capture the millisecond-scale evolution of global plasma profiles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

A Walking Method for Non-Decomposition Intersection and Union of Arbitrary Polygons and Polyhedrons

We present a method for computing the intersection and union of non- convex polyhedrons without decomposition in O(n log n) time, where n is the total number of faces of both polyhedrons. We include an accompanying Python package which addresses many of the practical issues associated with implementation and serves as a proof of concept. The key to the method is that by considering the edges of the original ob- jects and the intersections between faces as walking routes, we can e ciently nd the boundary of the intersection of arbitrary objects using directional walks, thus handling the concave case in a natural manner. The method also easily extends to plane slicing and non-convex polyhedron unions, and both the polyhedron and its constituent faces may be non-convex.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction

TRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with a Transcription Factor (TF)-gene regulatory network (TRN), which is modeled via a Bayesian network (BN). In this paper, we focus on sensitivity analysis of metabolic flux prediction for uncertainty quantification of BN structures for TRN modeling in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty given transcriptomic expression data. With that, we analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yields of interest. The obtained sensitivity analyses can guide Optimal Experimental Design (OED) to help acquire new data that can enhance TRN modeling and achieve specific metabolic engineering objectives, including metabolite yield alterations. Here we have performed small- and large-scale simulated experiments, demonstrating the effectiveness of our developed sensitivity analysis strategy for BN structure learning to quantify the edge importance in terms of metabolic flux prediction uncertainty reduction and its potential to effectively guide OED.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Comprehensive Phase Diagrams of MoS 2 Edge Sites Using Dispersion-Corrected DFT Free Energy Calculations

A comprehensive set of surface phase diagrams addressing the catalytically relevant edges of the (100) surface of MoS 2 catalysts is developed using dispersion-corrected density functional theory and ab initio thermodynamic modeling. The results of the temperature-dependent, free energy-based thermodynamic model are presented over the full range of catalytically relevant temperatures and pressures, in addition to S- and H-coverages ranging from 0 to 100%. The results of this work allow for a full thermodynamic analysis to be performed at the conditions relevant to any promising reaction involving MoS 2 , ranging from hydrodesulfurization to dehydrogenation to electrocatalysis. Several methodological recommendations are discussed and implemented with the goal of improving the accuracy of the surface phase diagrams at minimal computational expense. A library of the most stable S- and H-adsorption modes is also developed so that linear scaling relationships can be used to correlate thermodynamic stability with kinetic activity. Applying the results to C–H bond activation of methane with a S 2 oxidant, here we predict S-coverages near 100% on the Mo- and S-edges to be thermodynamically favored and S monomers on edge sites with high S-coverages to be kinetically favorable. For H-abstraction on surface S atoms, the Mo-edge is also predicted to be more active than the S-edge.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Uncovering the Atomistic Mechanism for Calcite Step Growth

Determining a complete atomic-level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO 3 ) in water, computer simulations have been used in this paper to map the complex thermodynamic landscape leading to growth of the two distinct steps, acute and obtuse, on the basal surface. The carbonate ion is found to preferentially adsorb at the upper edge of acute steps while Ca 2+ only adsorbs after CO 3 2- . In contrast to the conventional picture, ion pairs prefer to bind at the upper edge of the step with only one ion, at most, coordinated to the step and lower terrace. Finally, migration of the first carbonate ion to a growth site is found to be rate-limiting for kink nucleation, with this process having a lower activation energy on the obtuse step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Realization of fermionic Laughlin state on a quantum processor

Strongly correlated topological phases of matter are central to modern condensed matter physics and quantum information technology but often challenging to probe and control in material systems. The experimental difficulty of accessing these phases has motivated the use of engineered quantum platforms for simulation and manipulation of exotic topological states. Among these, the Laughlin state stands as a cornerstone for topological matter, embodying fractionalization, anyonic excitations, and incompressibility. Although its bosonic analogs have been realized on programmable quantum simulators, a genuine fermionic Laughlin state has yet to be demonstrated on a quantum processor. Here, we realize the ν = 1/3 fermionic Laughlin state on IonQ’s trapped-ion quantum computer using an efficient and scalable Hamiltonian variational ansatz with 369 two-qubit gates on a 16-qubit circuit. Employing symmetry-verification error mitigation, we extract key observables that characterize the Laughlin state, including correlation hole, bulk-edge correspondence, and topological entanglement entropy, with strong agreement to exact diagonalization benchmarks. This work demonstrates an end-to-end workflow to simulate material-intrinsic topological orders and provides a starting point to explore its dynamics and excitations on digital quantum processors.

Shen, Lingnan [Univ. of Washington, Seattle, WA (U↗

DOE OSTI2026

Drift-kinetic effects of tungsten on plasma response to RMP in ITER

Here, effects of high- Z ( Z is the particle charge number) tungsten impurity ions on the plasma response to the resonant magnetic perturbation (RMP) field are numerically investigated for the ITER 15 MA baseline scenario, where the tungsten contribution to the plasma response is computed with a drift-kinetic model while the bulk thermal particle contributions follow the fluid approximation. The study yields three highlights: (i) the drift-kinetic contribution of the tungsten impurity exerts minor influence on the plasma response compared to that computed by the pure fluid model without tungsten; (ii) a new figure of merit, based on the resonant spectrum perturbation at the plasma boundary surface, results in different optimal coil phasing compared to that previously obtained by maximizing the edge-peeling plasma response; (iii) the optimal $n = 3$ RMP (for edge localized mode (ELM) control, $n$ is the toroidal mode number) is found to induce a large tungsten particle influx near the plasma edge associated with the neoclassical toroidal viscosity. The study thus provides useful data on the compatibility of the full tungsten wall with RMP ELM control in ITER.

ITER↗

DOE OSTI2026

Community detection robustness of graph neural networks

Graph neural networks (GNNs) are increasingly widely used for community detection in attributed networks. They combine structural topology with node attributes through message passing and pooling. However, their robustness or lack thereof with respect to different perturbations and targeted attacks in conjunction with community detection tasks is not well understood. To shed light on latent mechanisms behind GNN sensitivity on community detection tasks, we conduct a systematic computational evaluation of six widely adopted GNN architectures graph convolutional network, graph attention network, graph sample and aggregate (GraphSAGE), differentiable pooling (DiffPool), minimum cut pooling (MinCUT), and deep modularity networks (DMoN). The analysis covers three perturbation categories: node attribute manipulations, edge topology distortions, and adversarial attacks. We use element-centric similarity as the evaluation metric on synthetic benchmarks and real-world citation networks. Our findings indicate that supervised GNNs tend to achieve higher baseline accuracy, while unsupervised methods, particularly DMoN, maintain stronger resilience under targeted and adversarial perturbations. Furthermore, robustness appears to be strongly influenced by community strength, with well-defined communities reducing performance loss. Across all models, node attribute perturbations associated with targeted edge deletions and shifts in attribute distributions tend to cause the largest degradation in community recovery. These findings highlight important trade-offs between accuracy and robustness in GNN-based community detection and offer insights into selecting architectures resilient to noise and adversarial attacks.

Goel, Jaidev [Virginia Polytechnic Inst. and State↗

DOE OSTI2022

Geometric remapping of particle distributions in the Discrete Element Model for Sea Ice (DEMSI v0.0)

Abstract. A new sea ice dynamical core, the Discrete Element Model for Sea Ice (DEMSI), is under development for use in coupled Earth system models. DEMSI is based on the discrete element method, which models collections of ice floes as interacting Lagrangian particles. In basin-scale sea ice simulations the Lagrangian motion results in significant convergence and ridging, which requires periodic remapping of sea ice variables from a deformed particle configuration back to an undeformed initial distribution. At the resolution required for Earth system models we cannot resolve individual sea ice floes, so we adopt the sub-grid-scale thickness distribution used in continuum sea ice models. This choice leads to a series of hierarchical tracers depending on ice fractional area or concentration that must be remapped consistently. The circular discrete elements employed in DEMSI help improve the computational efficiency at the cost of increased complexity in the effective element area definitions for sea ice cover that are required for the accurate enforcement of conservation. An additional challenge is the accurate remapping of element values along the ice edge, the location of which varies due to the Lagrangian motion of the particles. In this paper we describe a particle-to-particle remapping approach based on well-established geometric remapping ideas that enforces conservation, bounds preservation, and compatibility between associated tracer quantities, while also robustly managing remapping at the ice edge. One element of the remapping algorithm is a novel optimization-based flux correction that enforces concentration bounds in the case of nonuniform motion. We demonstrate the accuracy and utility of the algorithm in a series of numerical test cases.

58 GEOSCIENCES↗