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DOE OSTI2020

Evolving Ensembles of Spiking Neural Networks for Neuromorphic Systems

Evolutionary algorithms have been proposed as a solution to overcome many of the challenges associated with training spiking neural networks. While evolutionary optimization for spiking neural networks is very flexible, its performance has difficulty scaling to complex tasks and correspondingly complex network structures. Here we propose a method for evolving ensembles of spiking neural networks. By using ensemble learning, the flexibility of evolutionary optimization is fully preserved while scaling to more challenging tasks. We test the performance of the proposed method using handwritten digit classification. We investigate multiple strategies for constructing ensembles of spiking neural networks, and demonstrate that evolving ensembles of SNNs offers significant performance advantages over evolutionary optimization.

Elbrecht, Daniel↗

DOE OSTI2023

The yeast ALA synthase C‐terminus positively controls enzyme structure and function

Abstract 5‐Aminolevulinic acid synthase (ALAS) is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the first and rate‐limiting step of heme biosynthesis in α‐proteobacteria and several non‐plant eukaryotes. All ALAS homologs contain a highly conserved catalytic core, but eukaryotes also have a unique C‐terminal extension that plays a role in enzyme regulation. Several mutations in this region are implicated in multiple blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C‐terminal extension wraps around the homodimer core to contact conserved ALAS motifs proximal to the opposite active site. To determine the importance of these Hem1 C‐terminal interactions, we determined the crystal structure of S. cerevisiae Hem1 lacking the terminal 14 amino acids (Hem1 ΔCT). With truncation of the C‐terminal extension, we show structurally and biochemically that multiple catalytic motifs become flexible, including an antiparallel β‐sheet important to Fold‐Type I PLP‐dependent enzymes. The changes in protein conformation result in an altered cofactor microenvironment, decreased enzyme activity and catalytic efficiency, and ablation of subunit cooperativity. These findings suggest that the eukaryotic ALAS C‐terminus has a homolog‐specific role in mediating heme biosynthesis, indicating a mechanism for autoregulation that can be exploited to allosterically modulate heme biosynthesis in different organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Multivariate zeolitic imidazolate frameworks with an inverting trend in flexibility

Here, through systematic linker substitution in a flexible zeolitic imidazolate framework (ZIF) with step-shaped adsorption–desorption, structural intermediates between the known open and closed phases were isolated. Reflecting this, modulative sorption behaviour with an inverting adsorption pressure trend—in which the step pressure decreases and then increases again with increasing mixed linker concentration—is observed, highlighting how linker substitution modifies the energetic landscape of framework flexibility

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Benders Decomposition Using Graph Modeling and Multi-Parametric Programming

Benders decomposition is a widely used method for solving large and structured optimization problems, but its performance is affected by the repeated solution of subproblems. We propose a flexible and modular algorithmic framework for accelerating Benders decomposition. Specifically, we express the problem structure by using a graph-theoretic modeling abstraction in which nodes represent optimization subproblems and edges represent connectivity between subproblems. A key innovation of our approach is that we embed multiparametric programming (mp) surrogates for node subproblems, which maps the exact analytical map of the subproblem solution space. The use of mp surrogates allows us to replace subproblem solves with fast look-ups and function evaluations for primal and dual variables during the iterative Benders process. We formally show the equivalence between classical Benders cuts and those derived from the mp solution. We implement our framework in the open-source PlasmoBenders.jl software package. To demonstrate the capabilities of the proposed framework, we apply it to a two-stage stochastic programming problem, which aims to make optimal capacity expansion decisions under market uncertainty. We evaluate both single-cut and multicut variants of Benders decomposition and show that the use of mp surrogates achieves substantial speedups in subproblem solve time, while preserving the convergence guarantees of Benders decomposition. We highlight advantages in solution analysis and interpretability that is enabled by mp critical region tracking; specifically, we show that these reveal how decisions evolve geometrically across the Benders search. Our results aim to demonstrate that combining surrogate modeling with graph modeling offers a promising and extensible foundation for structure-exploiting decomposition. In addition, by decomposing the problem into more tractable subproblems, the proposed approach also aims to overcome scalability issues of mp. Finally, the use of mp surrogates provides a unifying and modular optimization framework that enables the representation of heterogeneous node subproblems as modeling objects with a homogeneous structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Mechanics of Dynamic and Deformable DNA Nanostructures

In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Design of flexible proton beam imaging energy spectrometers (PROBIES)

A simple repeating step-filtered structure has been designed and deployed for the detection of MeV-energy proton beams produced from high-intensity short-pulse laser-driven experiments. Due to the diagnostic's ability to recover energy-resolved images of proton beams, it is called the proton beam imager and energy spectrometer (or PROBIES). The flexible design has two useful applications. First, it can be fielded in a configuration with a scintillator and imaging setup in order to collect proton beam information in high-repetition rate experiments. Here we show a configuration that collects the equivalent of a nine-film radiochromic film (RCF) stack, and a technique for using a neural network (NN) to rapidly analyze the images on millisecond time-scales. Second, when using RCF stacks as the detector, the energy resolution capability is greatly increased compared to traditional RCF stacks, while simultaneously reducing the total number of films required to make each measurement. We demonstrate a configuration that provides up to 90 spatially- and energy-resolved datapoints using just ten films. Both designs presented here can be easily customized for anticipated experimental outputs and manufactured at low cost. Such designs allow for rapid prototyping using modern high-accuracy 3D printers or on-demand computer numerical control machining to reduce the reliance on time-consuming film media, analysis, or bulky electro-magnetically dispersing spectrometers. The analysis of data is discussed and a methodology for constructing a NN that is capable of rapidly analyzing data on-the-fly with greater than 95% accuracy is presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Investigation of the Effect of Framework Flexibility on CO 2 Adsorption in SIFSIX-3-Cu Using a Machine-Learned Force Field

Metal–organic frameworks (MOFs) offer promise as selective CO 2 sorbents, but successful MOF sorbent materials need high CO 2 binding affinity and selectivity for CO 2 over water. This work focuses on the use of machine-learned force fields (MLFFs) to model CO 2 adsorption in flexible MOFs, with a focus on SIFSIX-3-Cu, an anion-pillared MOF known for its high CO 2 affinity. A preliminary high-throughput screening of over 900 anion-pillared MOFs was performed using rigid UFF+DDEC6 force fields to predict zero-loading heats of adsorption for CO 2 and H 2 O. SIFSIX-3-Cu was selected for further computational study due to its predicted CO 2 heat of adsorption and experimental relevance. A DeePMD-based MLFF was trained to reproduce DFT (PBE+D3) energies and forces, with an iterative sampling scheme combining molecular dynamics, geometry optimization, random geometric insertion, and NVT Monte Carlo-based configuration generation to capture both attractive and repulsive regions of the potential energy surface. Flexibility of the MOF was explicitly included, contrasting with previous models that approximated the MOF as rigid. Hybrid Monte Carlo/molecular dynamics (MC/MD) simulations with the MLFF produced CO 2 adsorption isotherms in good agreement with experimental data at direct air capture (DAC) pressures (e.g., 40 Pa), in contrast to previous overestimations of CO 2 sorption by models with rigid structures. Bond and angle histogram analysis showed that MOF flexibility increased the variance of fluorine–fluorine diagonal distances at adsorption sites, resulting in a lower predicted sorption for flexible, asymmetric SIFSIX-3-Cu pore geometries compared to the rigid, symmetric DFT-optimized SIFSIX-3-Cu pore geometry. A detailed description of flexibility afforded by the MLFF resulted in an accurately predicted CO 2 uptake (0.88 mmol/g) at low pressure (40 Pa) compared to the experimentally measured value (1.24 mmol/g). In conclusion, these results underscore the importance of including framework flexibility when modeling adsorption phenomena in MOFs, particularly for low-pressure applications.

adsorption↗

DOE OSTI2026

Interpretable and flexible non-intrusive reduced-order models using reproducing kernel Hilbert spaces

This paper develops an interpretable, non-intrusive reduced-order modeling technique using regularized kernel interpolation. Existing non-intrusive approaches approximate the dynamics of a reduced-order model (ROM) by solving a data-driven least-squares regression problem for low-dimensional matrix operators. Our approach instead leverages regularized kernel interpolation, which yields an optimal approximation of the ROM dynamics from a user-defined reproducing kernel Hilbert space. We show that our kernel-based approach can produce interpretable ROMs whose structure mirrors full-order model structure by embedding judiciously chosen feature maps into the kernel. The approach is flexible and allows a combination of informed structure through feature maps and closure terms via more general nonlinear terms in the kernel. We also derive a computable a posteriori error bound that combines standard error estimates for intrusive projection-based ROMs and kernel interpolants. In conclusion, the approach is demonstrated in several numerical experiments that include comparisons to operator inference using both proper orthogonal decomposition and quadratic manifold dimension reduction.

Data-driven model reduction↗

DOE OSTI2024

Ultrafast structural dynamics of UV photoexcited cis , cis -1,3-cyclooctadiene observed with time-resolved electron diffraction

Conjugated diene molecules are highly reactive upon photoexcitation and can relax through multiple reaction channels that depend on the position of the double bonds and the degree of molecular rigidity. Understanding the photoinduced dynamics of these molecules is crucial for establishing general rules governing the relaxation and product formation. Here, in this study, we investigate the femtosecond time-resolved photoinduced excited-state structural dynamics of cis,cis-1,3-cyclooctadiene, a large-flexible cyclic conjugated diene molecule, upon excitation with 200 nm using mega-electron-volt ultrafast electron diffraction and trajectory surface hopping dynamics simulations. We tracked the photoinduced structural changes from the Franck–Condon region through the conical intersection seam to the ground state. Our findings revealed a novel primary reaction coordinate involving ring distortion, where the ring stretches along one axis and compresses along the perpendicular axis. The nuclear wavepacket remains compact along this reaction coordinate until it reaches the conical intersection seam, and it rapidly spreads as it approaches the ground state, where multiple products are formed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain

Ion-binding intrinsically disordered proteins (IDPs) recruit and bind to specific metal ions to perform critical biological functions. In proteins where ion binding and structural transitions are coupled, interactions with off-target toxic metals can dramatically disrupt protein structure and function, exemplified by lead and mercury poisoning. Understanding the complex mechanisms underlying how IDPs exclude or allow binding to different ionic species is crucial for addressing the origins of metal toxicity in biological systems. Here, we elucidate mechanisms of ion selectivity in an IDP that adopts a structure upon Ca 2+ binding. We probed ion-induced conformational changes of a repeats-in-toxin (RTX) protein domain in the presence of different ion ligands—Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ —with chemical similarities but drastically different ionic radii. RTX adopts ion-selective conformations measured by x-ray crystallography, small-angle x-ray scattering, and circular dichroism. High-resolution x-ray structures reveal that Sr 2+ induces a nearly identical RTX structure as natively binding Ca 2+ , enabled by the intrinsic flexibility and disorder of the protein. Small-angle x-ray scattering and circular dichroism indicate that smaller Mg 2+ does not induce a significant conformational change in RTX, whereas larger Ba 2+ induces a partially folded structure. These results highlight the importance of geometric constraints imposed by protein structure in determining metal ion selectivity, yielding insights into how off-target ion binding may result in protein misfolding and malfunction.

Gudinas, Alana P. [Stanford Univ., CA (United Stat↗

DOE OSTI2020

Containers for Massive Ensemble of I/O Bound Hierarchical Coupled Simulations

We present our experience using containers to scale up a massive ensemble of coupled I/O bound workloads on the NERSC Cori supercomputer. We describe the design of a hierarchical simulation structure using the Integrated Plasma Simulator (IPS) that enables the flexible execution of coupled simulations at the system, node, and core level using the same coupling abstraction and API. The hierarchical design allows for the node-level execution to be efficiently executed using containers while not impacting the structure of the simulation at the system level. We demonstrate the viability of the approach by presenting experimental results from applications in coupled fusion plasma simulations that illustrate the performance impact of using containers to deploy the node-level workloads, in conjunction with the user mountable XFS file systems to ameliorate the load on the Lustre parallel file system. We also present results from production runs showing the ability of the ensemble simulations to scale to hundreds of Cori Haswell nodes, with little or no overhead.

Elwasif, Wael↗

DOE OSTI2021

Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2

Peroxiredoxin 2 (Prdx2) is a thiol peroxidase with an active site Cys (C52) that reacts rapidly with H 2 O 2 and other peroxides. The sulfenic acid product condenses with the resolving Cys (C172) to form a disulfide which is recycled by thioredoxin or GSH via mixed disulfide intermediates or undergoes hyperoxidation to the sulfinic acid. C172 lies near the C terminus, outside the active site. It is not established whether structural changes in this region, such as mixed disulfide formation, affect H 2 O 2 reactivity. To investigate, we designed mutants to cause minimal (C172S) or substantial (C172D and C172W) structural disruption. Stopped flow kinetics and mass spectrometry showed that mutation to Ser had minimal effect on rates of oxidation and hyperoxidation, whereas Asp and Trp decreased both by 100-fold. To relate to structural changes, we solved the crystal structures of reduced WT and C172S Prdx2. The WT structure is highly similar to that of the published hyperoxidized form. C172S is closely related but more flexible and as demonstrated by size exclusion chromatography and analytical ultracentrifugation, a weaker decamer. Size exclusion chromatography and analytical ultracentrifugation showed that the C172D and C172W mutants are also weaker decamers than WT, and small-angle X-ray scattering analysis indicated greater flexibility with partially unstructured regions consistent with C-terminal unfolding. We propose that these structural changes around C172 negatively impact the active site geometry to decrease reactivity with H 2 O 2 . This is relevant for Prdx turnover as intermediate mixed disulfides with C172 would also be disruptive and could potentially react with peroxides before resolution is complete.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

An improved methodology for modeling short pulse buried layer x-ray emission spectra

Radiation-hydrodynamic and spectroscopic modeling are important aspects of high energy density experimental design. In this paper, we improve the performance and capabilities over those obtainable with a previous methodology used for simulating x-ray emission spectra from buried layer targets heated by short pulse lasers. The improvement incorporates post-processing HYDRA radiation-hydrodynamic output with a non-local thermodynamic equilibrium atomic-kinetics radiation transport code, Cretin. Each code uses an independent radiation field which allows decoupling HYDRA's radiation group structure from Cretin's spectral output to improve the speed and flexibility of the design methodology. The execution time decreases from 2–3 days to a few hours while the flexibility of the improved methodology allows for performing sensitivity studies including a comparison of steady-state and time-dependent atomic kinetics and differences in the radiation group structure.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Investigating the effect of screen-printed structured graphite electrodes with low tortuosity for high-capacity and fast-charging lithium-ion batteries

A flexible screen-printed graphite electrode was fabricated as an anode for developing fast-charging lithium-ion batteries with low tortuosity. A homogenous anode ink was prepared by mixing graphite as the active material, carbon black (C45) as the conductive additive, and polyvinylidene fluoride (PVDF) as the binder in N-Methyl-2-pyrrolidone (NMP) solvent. The ink was deposited on a flexible copper foil via a stainless-steel screen consisting of an array of pores, that act as secondary pore networks (SPNs), using the screen-printing process. Lithium-ion battery half-cells were assembled using the printed graphite anode, lithium metal foil as the counter electrode, and 1.2 M lithium hexafluorophosphate (LiPF 6 ) in ethyl carbonate: ethyl methyl carbonate (EC: EMC = 3:7) as the electrolyte. The effect of SPNs on the cell performance was investigated by performing formation, rate and cycling tests on the assembled cells, at different C-rates. It was observed that the cells consisting of SPNs with a pore size of 100 μm and edge-to-edge distance of 100 μm between the pores exhibited significantly higher specific capacities of 168 and 129 mAh/g when compared to reference cells without SPNs, which had capacities of 120 and 85 mAh/g, at high C-rates of 4 C and 6 C, respectively. The cells with SPNs also demonstrated excellent cycling performance with ~ 95% capacity retention after 100 cycles at 2 C.

Fast charging lithium-ion battery↗

DOE OSTI2022

Compact Peptoid Molecular Brushes for Nanoparticle Stabilization

Controlling the interfaces and interactions of colloidal nanoparticles (NPs) via tethered molecular moieties is crucial for NP applications in engineered nanomaterials, optics, catalysis, and nanomedicine. Despite a broad range of molecular types explored, there is a need for a flexible approach to rationally vary the chemistry and structure of these interfacial molecules for controlling NP stability in diverse environments, while maintaining a small size of the NP molecular shell. Here, we demonstrate that low-molecular-weight, bifunctional comb-shaped, and sequence-defined peptoids can effectively stabilize gold NPs (AuNPs). The generality of this robust functionalization strategy was also demonstrated by coating of silver, platinum, and iron oxide NPs with designed peptoids. Each peptoid (PE) is designed with varied arrangements of a multivalent AuNP-binding domain and a solvation domain consisting of oligo-ethylene glycol (EG) branches. Among designs, a peptoid (PE5) with a diblock structure is demonstrated to provide a superior nanocolloidal stability in diverse aqueous solutions while forming a compact shell (similar to 1.5 nm) on the AuNP surface. We demonstrate by experiments and molecular dynamics simulations that PE5-coated AuNPs (PE5/AuNPs) are stable in select organic solvents owing to the strong PE5 (amine)-Au binding and solubility of the oligo-EG motifs. At the vapor-aqueous interface, we show that PE5/AuNPs remain stable and can self-assemble into ordered 2D lattices. The NP films exhibit strong near-field plasmonic coupling when transferred to solid substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Combined light- and heat-induced shape memory behavior of anthracene-based epoxy elastomers

Abstract The development of multi-stimuli-responsive shape memory polymers has received increasing attention because of its scientific and technological significance. In this work, epoxy elastomers with reversible crosslinks are synthesized by polymerizing an anthracene-functionalized epoxy monomer, a diepoxy comonomer, and a dicarboxylic acid curing agent. The synthesized elastomers exhibit active responses to both light and heat enabled by the incorporated anthracene groups. When exposed to 365 nm UV light, additional crosslinking points are created by the photo-induced dimerization of pendant anthracene groups. The formation of the crosslinking points increases modulus and glass transition temperature of the elastomers, allowing for the fixation of a temporary shape at room temperature. The temporary shape remains stable until an external heat stimulus is applied to trigger the scission of the dimerized anthracene, which reduces the modulus and glass transition temperature and allows the elastomers to recover their original shapes. The effects of external stimuli on the thermal and dynamic mechanical properties of the elastomers are investigated experimentally and are correlated with molecular dynamics simulations that reveal the changes of structure and dynamics of the anthracene molecules and flexible chains.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Rheology of concentrated fiber suspensions with a load-dependent friction coefficient

Here we investigate the effects of fiber aspect ratio, roughness, flexibility, and volume fraction on the rheology of concentrated suspensions in a steady shear flow using direct numerical simulations. We model the fibers as inextensible continuous flexible slender bodies with the Euler-Bernoulli beam equation governing their dynamics suspended in an incompressible Newtonian fluid. The fiber dynamics and fluid flow coupling is achieved using the immersed boundary method. In addition, the fiber surface roughness might lead to interfiber contacts, resulting in normal and tangential forces between the fibers, which follow Coulomb’s law of friction. The surface roughness is modeled as hemispherical protrusions on the fiber surfaces. Their deformation results in a normal load-dependent friction coefficient. Our simulations accurately predict the experimentally observed shear thinning in fiber suspensions. Furthermore, we find that the suspension viscosity η increases with increasing the volume fraction, roughness, fiber rigidity, and aspect ratio. The increase in η is the macroscopic manifestation of a similar increase in the microscopic contact contribution to the total stress with these parameters. In addition, we observe positive and negative first N 1 and second N 2 normal stress differences, respectively, with |N 2 | < |N 1 |, in agreement with previous experiments. Last, we propose a modified Maron-Pierce law to quantify the reduction in the jamming volume fraction by increasing the fiber aspect ratio and roughness. Our results and analysis establish the use of fiber surface tribology to tune the suspension flow behavior.

42 ENGINEERING↗

DOE OSTI2020

Water Network Tool for Resilience (WNTR). User Manual, Version 0.2.3

The Water Network Tool for Resilience (WNTR, pronounced winter) is a Python package designed to simulate and analyze resilience of water distribution networks. Here, a network refers to the collection of pipes, pumps, valves, junctions, tanks, and reservoirs that make up a water distribution system. WNTR has an application programming interface (API) that is flexible and allows for changes to the network structure and operations, along with simulation of disruptive incidents and recovery actions. WNTR is based upon EPANET, which is a tool to simulate the movement and fate of drinking water constituents within distribution systems. Users are encouraged to be familiar with the use of EPANET and/or should have background knowledge in hydraulics and pressurized pipe network modeling before using WNTR. EPANET has a graphical user interface that might be a useful tool to facilitate the visualization of the network and the associated analysis results. Information on EPANET can be found at https://www.epa.gov/water-research/epanet. WNTR is compatible with EPANET 2.00.12 [Ross00]. In addition, users should have experience using Python, including the installation of additional Python packages. General information on Python can be found at https://www.python.org/.

54 ENVIRONMENTAL SCIENCES↗