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DOE OSTI2021

De novo design of transmembrane β barrels

Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a “hypothesis, design, and test” approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.

Vorobieva, Anastassia A.↗

DOE OSTI2026

Schiff Moment of 129 Xe and 199 Hg [Slides]

Using Chicoma in 2025, we advanced DFT-based calculations needed to connect fundamental T violating interactions to measurable Schiff moments in heavy nuclei. We implemented DFT for polarized odd nuclear systems, a first step toward treating the time-reversal-breaking mean fields required for Schiff moment calculations. As a validation test, we computed polarizabilities using a perturbation with the dipole operator (see figure to the right) for the odd systems shown in Table 1; while no odd-system effect is expected for polarizabilities, this capability is essential for Schiff moments. Initial mean-field solutions for 129 Xe Schiff moment calculations were also generated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Numerical Analysis of Regular Material Point Method and its Application to Multiphase Flows

The material point method (MPM) is gaining wide popularity in engineering research to model and simulate complex multiphase flow dynamics. The method relies on solving the governing equations of motion and transport in a Lagrangian framework using particles also known as material points. The fluid and kinematic properties are stored on the material points while the spatial gradient calculation and temporal integration are performed on a background grid. This Lagrangian framework allows for large deformations, easy integration of constitutive models, and direct import of complex geometries as particles. However, despite their increasing popularity, very few studies have addressed the issues of numerical resolution and stability of MPM techniques. The presence of additional factors such as the number of material points-per-cell, the location of the material points, the CFL-like condition used in time update, and the grid shape functions also increase the complexity of the error analysis when compared to other finite element methods. In this presentation, we analyze the various forms of error incurred in the application of MPM to continuum mechanics and multiphase flows. The effect of the previously mentioned factors on the error dynamics is studied. The application of these principles to canonical and industrial problems is also presented.

high pressure reverse osmosis↗

DOE OSTI2020

Computationally Predicted High-Throughput Free-Energy Phase Diagrams for the Discovery of Solid-State Hydrogen Storage Reactions

The design of multinary solid-state material systems that undergo reversible phase changes via changes in temperature and pressure provides a potential means of safely storing hydrogen. However, fully mapping the stabilities of known or newly targeted compounds relative to competing phases at reaction conditions has previously required many stringent experiments or computationally demanding calculations of each compound’s change in Gibbs energy with respect to temperature, G(T). Here, we have extended the approach of constructing chemical potential phase diagrams based on ΔG f (T) to enable the analysis of phase stability at non-zero temperatures. We first performed density functional theory calculations to compute the formation enthalpies of binary, ternary, and quaternary compounds within several compositional spaces of current interest for solid-state hydrogen storage. Temperature effects on solid compound stability were then accounted for using our recently introduced machine learned descriptor for the temperature-dependent contribution G δ (T) to the Gibbs energy G(T). From these Gibbs energies, we evaluated each compound’s stability relative to competing compounds over a wide range of conditions and show using chemical potential and composition phase diagrams that the predicted stable phases and H2 release reactions are consistent with experimental observations. This demonstrates that our approach rapidly computes the thermochemistry of hydrogen release reactions for compounds at sufficiently high accuracy relative to experiment to provide a powerful framework for analyzing hydrogen storage materials. This framework based on G(T) enables the accelerated discovery of active materials for a variety of technologies that rely on solid-state reactions involving these materials.

08 HYDROGEN↗

DOE OSTI2022

A Reversed Impedance-Based Stability Criterion for IBR Grids: Preprint

The existing impedance-based stability criterion is effective for analyzing local control interactions; however, it is difficult to scale the existing criterion to analyze wide-area control interactions among numerous IBRs through a complex power system network. The scaled version of the existing criterion requires the impedance response of each IBR in the system as well as of the network looking from all the IBRs. It is quite challenging to obtain all these impedance responses because of the computational effort and the requirement of separately scanning the impedance of the network and the IBRs. We propose a reversed criterion for the impedance-based stability analysis to address these problems. In contrast to the existing criterion, the reversed criterion analyzes the stability of a power system when an IBR is disconnected from the system. The reversed criterion estimates the impact of an IBR on the frequency and damping of power system oscillation modes using the impedance scans of only the IBR and the grid at its terminal. It can be sequentially applied at different IBRs to evaluate their impact on the power system stability. In addition to scalability, the reversed criterion gives flexibility to focus only on a few selected IBRs, depending on their rating, the magnitude of oscillations observed at their terminals, and the vendor support available for implementing stabilizing control system updates. The reversed criterion is demonstrated on a 14-bus power system with 100% IBRs.

control interactions↗

DOE OSTI2024

Spectral Analysis of Regular Material Point Method and its Application to Study High Pressure Reverse Osmosis Membrane Compaction and Embossing

Material Point Method (MPM) is gaining widespread interest in applied continuum mechanics. The fact that all the continuum properties are stored on the particles (or material points) and the governing equations are solved on these material points makes MPM extremely suited to problems involving severe material deformations, such as crack propagation, soil movement, and fluid flows. Despite its popularity, only a few studies have focused on the numerical properties of MPM. This presentation introduces a global spectral analysis of the regular material point method. Contrary to previous studies, the analysis focuses on the numerical properties of the method in the spectral space. The amplification factor is derived as a function of the non- dimensional wave numbers. It provides insights into the stability and dissipative properties of the method for various CFL and Fourier numbers. The effect of the grid shape functions, number of particles per cell and their locations inside the grid cell are also analyzed. The EXAGOOP MPM solver (https://github.com/NREL/Exagoop.git) is developed at the National Renewable Energy Laboratory as a part of the NAWI UHPRO project and is based on the AMReX framework. A single-level, uniform cartesian grid is used as the background mesh, while the particle class in AMReX is used to manage the material point operations. Linear hat and B-splines are used as grid shape functions, while the time integration is performed using explicit Euler time integration. EXAGOOP is both CPU and GPU compatible and has been demonstrated to work well on multiple compute architectures. The performance of EXAGOOP on various computing architectures is presented along with its application to study compaction and embossing of high-pressure reverse osmosis membranes. The MPM solution accurately reproduces the membrane deformation. The deformed pore size and structure simulated using MPM also agree well with experimental SEM images.

material point method↗

DOE OSTI2022

Source-to-Source Automatic Differentiation of OpenMP Parallel Loops

This article presents our work toward correct and efficient automatic differentiation of OpenMP parallel worksharing loops in forward and reverse mode. Automatic differentiation is a method to obtain gradients of numerical programs, which are crucial in optimization, uncertainty quantification, and machine learning. The computational cost to compute gradients is a common bottleneck in practice. For applications that are parallelized for multicore CPUs or GPUs using OpenMP, one also wishes to compute the gradients in parallel. Here, we propose a framework to reason about the correctness of the generated derivative code, from which we justify our OpenMP extension to the differentiation model. We implement this model in the automatic differentiation tool Tapenade and present test cases that are differentiated following our extended differentiation procedure. Performance of the generated derivative programs in forward and reverse mode is better than sequential, although our reverse mode often scales worse than the input programs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

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↗

DOE OSTI2020

High-temperature Majorana fermions in magnet-superconductor hybrid systems

Magnet-superconductor hybrid (MSH) structures represent one of the most promising platforms to realize, control, and manipulate Majorana modes using scanning tunneling methods. By depositing either chains or islands of magnetic atoms on the surface of a conventional, elemental superconductor such as Pb or Re, topological superconducting phases can emerge. They feature either localized Majorana bound states at the chain ends or dispersing chiral Majorana modes at the island's boundary. However, some of these experiments have not reached the spectral resolution to clearly distinguish between topological Majorana and trivial Shiba states due to very small superconducting gap sizes and experiments performed at sub-Kelvin temperatures. Here we consider superconducting substrates with unconventional spin-singlet pairing, including high-temperature d -wave and extended s -wave superconductors. We derive topological phase diagrams and compute edge states for cylinder and island geometries and discuss their properties. Several time-reversal invariant topological superconducting phases of the Zhang-Kane-Mele type are found and discussed. Addiotnally, we review one-dimensional MSH structures and show that parameters to realize topologically nontrivial magnetic chains embedded into a larger, two-dimensional substrate differ from the purely one-dimensional case. Quite generally we find that unconventional superconducting substrates work as well as the conventional s -wave substrates to realize topological phases. In particular, iron-based pnictide and chalcogenide superconductors are the most promising class of substrates for future high-temperature MSH systems.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Diffusioosmotic flow reversals due to ion–ion electrostatic correlations

Existing theories of diffusioosmosis have neglected ion–ion electrostatic correlations, which are important in concentrated electrolytes. Here, we develop a mathematical model to numerically compute the diffusioosmotic mobilities of binary symmetric electrolytes across low to high concentrations in a charged parallel-plate channel. We use the modified Poisson equation to model the ion–ion electrostatic correlations and the Bikerman model to account for the finite size of ions. We report two key findings. First, ion–ion electrostatic correlations can cause a unique reversal in the direction of diffusioosmosis. Such a reversal is not captured by existing theories, occurs at ≈ 0.4 M for a monovalent electrolyte, and at a much lower concentration of ≈ 0.003 M for a divalent electrolyte in a channel with the same surface charge. This highlights that diffusioosmosis of a concentrated electrolyte can be qualitatively different from that of a dilute electrolyte, not just in its magnitude but also its direction. Second, we predict a separate diffusioosmotic flow reversal, which is not due to electrostatic correlations but the competition between the underlying chemiosmosis and electroosmosis. This reversal can be achieved by varying the magnitude of the channel surface charge without changing its sign. However, electrostatic correlations can radically change how this flow reversal depends on the channel surface charge and ion diffusivity between a concentrated and a dilute electrolyte. Furthermore, the mathematical model developed here can be used to design diffusioosmosis of dilute and concentrated electrolytes, which is central to applications such as species mixing and separation, enhanced oil recovery, and reverse electrodialysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Spin Dynamics of SCRPs in ZnO Quantum Dot–Organic Molecule Conjugates Studied with Pulsed EPR

Photogenerated spin-correlated radical pairs (SCRPs) are emerging as promising new candidates for Quantum Information Science applications, where they act as electron spin qubit pairs (SQPs). Historically, these pairs have been mostly investigated in natural photosynthesis and in molecular organic donor–(linker)–acceptor systems. Recently, we have shown that these spin pairs can also be observed by time-resolved electron-paramagnetic resonance (EPR) spectroscopy in hybrid inorganic–organic conjugates. The current study builds on recent work (ACS Nano, 2025, 19, 12194–12207), in which we systematically prepared hybrid inorganic–organic molecule systems with tunable geometries that can host SCRPs/SQPs. Here, we demonstrate using pulsed EPR spectroscopy that we can generate, study, and manipulate the spins in these photogenerated SCRPs hosted on highly tailorable inorganic–organic hybrid systems. Microwave pulse-based spin manipulation is the first step toward developing quantum computing and quantum sensing applications with these promising spin-based qubit materials, which can be reversibly photogenerated in highly spin-polarized states at moderate temperatures. An attractive feature of this new class of hybrid materials is that the g-factor of the unpaired electron spin in the ZnO QD (as part of the SCRP/SQP) can be adjusted using the quantum size effect in these QDs, which allows for the selective addressability of each spin in the SCRP using microwave pulses. Additionally, we also observed a difference between the g-values of the unpaired electron in the ZnO QD in the transient SCRP state and stable photoreduced state. We hypothesize that the unpaired electron in the SCRP is delocalized as a band-like conduction electron, while in the stable photoreduced state, the electron is delocalized in a shallow electron trap state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

3D Nanomagnetism in Low Density Interconnected Nanowire Networks

Free-standing, interconnected metallic nanowire networks with densities as low as 40 mg/cm 3 have been achieved over centimeter-scale areas, using electrodeposition into polycarbonate membranes that have been ion-tracked at multiple angles. Networks of interconnected magnetic nanowires further provide an exciting platform to explore 3-dimensional nanomagnetism, where their structure, topology, and frustration may be used as additional degrees of freedom to tailor the materials properties. New magnetization reversal mechanisms in cobalt networks are captured by the first-order reversal curve method, which demonstrate the evolution from strong demagnetizing dipolar interactions to intersection-mediated domain wall pinning and propagation, and eventually to shape-anisotropy dominated magnetization reversal. These findings open up new possibilities for 3-dimensional integrated magnetic devices for memory, complex computation, and neuromorphics.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Study of wrap mode impact on Pseudomonas aeruginosa motion in the chemotactic field of fungi

An agent-based discrete computational model biologically calibrated to Pseudomonas aeruginosa migration is used to explore the impacts of bacterial reversals and wrap mode on the efficiency of motion in different environments, both with and without chemotaxis. It is first shown that wrap mode increases the exploration of continuous multimodal chemotactic profiles such as those produced by biologically relevant fungal networks. For cells undergoing a run-reverse pattern, it is shown that the bacteria are likely to remain at the first local chemoattractant maximal production site on a hypha they find. However, with wrap mode, the bacteria can more easily escape these local sites to further explore their neighboring environment along the fungi, suggesting that wrap mode may be beneficial for migration along the fungi in liquid. In a different set of simulations of bacterial motion close to an isolated chemotactic source, wrap mode is shown to increase the ability of a bacterium to reorient toward the source while reducing the overall motion required for similar chemotactic efficiency as a run-reverse strategy, suggesting a potential metabolic benefit. In contrast, model simulations show that wrap mode can increase the rate of dispersal of P. aeruginosa in a nonchemotactic environment.

Hansen, Austin [University of California, Riversid↗

DOE OSTI2022

Role of ripples in altering the electronic and chemical properties of graphene

Ripples of graphene are known to manipulate electronic and hydrogenation properties of graphitic materials. More detailed work is needed to elucidate the structure–property relationship of these systems. In this work, the density functional theory is used to compute the energy and electronic structure of the graphene models with respect to variable curvatures and hydrogen adsorption sites. The magnitude of finite bandgap opening depends on the orientation of ripples, and the hydrogen adsorption energy depends on the local curvature of graphene. An adsorbed hydrogen alters the local curvature, resulting in relatively weakened adsorption on the neighboring three sites, which gives a rationale to experimentally observed dynamic equilibrium stoichiometry (H:C = 1:4) of hydrogenated graphene. The surface diffusion transition state energy of adsorbed hydrogen is computed, which indicates that the Eley–Rideal surface recombination mechanism may be important to establish the dynamic equilibrium, instead of the commonly assumed Langmuir–Hinshelwood mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Dynamic and reversible transformations of subnanometre-sized palladium on ceria for efficient methane removal

Reversibly adjusting the active structures of supported metal catalysts in response to dynamic working conditions has long been pursued. Here we report the reaction-environment-modulated transformations of subnanometre-sized Pd on CeO 2 for efficient methane removal, leveraging the reaction environments at different stages of automotive exhaust aftertreatment. During the cold start of vehicles, inactive Pd 1 single atoms are readily transformed into PdO $x$ subnanometre clusters by CO even at room temperature with excess O 2 , resulting in boosted low-temperature CH 4 oxidation. At elevated temperatures, dispersion of PdO $x$ cluster into Pd 1 against metal sintering renders outstanding hydrothermal stability to the catalyst, to be activated during the next vehicle start. Combined experimental and computational studies elucidate the dynamically evolved Pd speciation on CeO 2 at an atomic level. In conclusion, modulating the reversible nature of supported metals helps overcome the long-existing trade-off between low-temperature activity and high-temperature stability, also providing a new paradigm for designing intelligent catalysts that brings single-atom/cluster catalysts closer to real applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

De novo design of pH-responsive self-assembling helical protein filaments

Abstract Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Computational Optimization of Room Temperature Usable Capacity for Hydrogen Storage in MFU-4-Type Metal–Organic Frameworks via Pairwise Metal Substitutions

The efficient storage of hydrogen is a critical challenge in the quest for sustainable energy solutions. Current adsorbent-based methods achieve satisfactory storage densities predominantly under cryogenic temperatures and/or high pressures, which imposes problems with cost-efficient and safe implementation of this technology. Materials that can bind hydrogen gas reversibly at ambient temperatures and more moderate pressures could play a pivotal role in enabling hydrogen-powered technologies. In this study, we use reliable computational modeling to investigate two synthetically feasible paths for tuning the enthalpy of H2 binding in MFU-4-type metal–organic frameworks (MOFs), aiming to maximize usable capacity. This study examines MIM4 IICl3(bta)6 (bta– = benzotriazolate) Kuratowski-type clusters as a model for strong binding sites in MFU-4l frameworks. We systematically evaluate the impact of separately tuning the central MII metal ion (which plays a structural role) and the peripheral MI metal ion (which binds the substrate) on the energetics of H2 binding. Our computational study reveals that H2 binding at an MI site mostly follows the trend AgI < CuI < NiI < CoI < AuI while a larger central MII site generally weakens the H2 binding at a MI site. Importantly, we have identified three new combinations of MI and MII to achieve high fractional usable capacities of the total H2 adsorbed under a pressure swing from 5 to 100 bar at room temperature. Additionally, we examine the nature of the binding interaction between the peripheral metal atom and the hydrogen molecule. While charge transfer predominantly induces this interaction, for several atom combinations, a change in the polarization (associated with variations in the ionic radius of the MI binding atom) is another important factor for adjusting the strength of the interaction. We suggest that the proposed compositions of Kuratowski-type clusters are highly desirable synthetic targets for future laboratory study.

Tkachenko, Nikolay V↗

DOE OSTI2025

Graph-based Reversible Evaluation and Tangents Library

GRETL is a C++ library for evaluation, re-evaluation and algorithmic differentiation of functional operations on an arbitrary computational graph with limited memory usage. Similar to popular machine learning frameworks in Python, like PyTorch and JAX, it tracks and stores both operations and output data as functions are evaluated. Once this composition of functions is built up, the entire chain of operations can be back propagated to compute sensitivities of the final result with respect to any number of inputs. In contrast to most machine learning applications, memory usage becomes the bottleneck for back propagation in many physics applications, especially for time-dependent PDEs. Dynamic check pointing becomes essential. An important distinguishing feature of GRETL is its ability to limit the maximum memory usage by automatically dynamic checkpointing the data output for each graph operation (see Wang, Moin, Iaccarino, 2009). During backpropagation, parts of the graph that are no longer in memory are automatically re-evaluated from upstream checkpointed states as needed for derivative sensitivity calculations (or more precisely, for vector-Jacobian products). GRETL is particularly beneficial for applications, such as coupled multi-physics, where deriving adjoint-based sensitivities and managing checkpoint memory across modules becomes onerous. Cases which can be readily handled by the GRETL library include: different time-integration algorithms per physics (e.g., coupled predictor-corrector algorithms, IMEX, etc.), sub-cycling, asynchronous integrators, state dependent timestep sizes, iterative solvers and coupling algorithms, controller algorithms, and more.

Tupek, MichaelR [Lawrence Livermore National Labor↗