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At least 73 records · Page 4

Non-Empirical and Self-Interaction Corrections for DFTB: Towards Accurate Quantum Simulations for Large Mesoscale Systems (Final Report)

This project was comprised of two complementary (but parallel) thrusts: (1) implementing massively-parallelized computing hardware (with new computational hardware that may replace GPUs) in the density functional tight binding (DFTB) approach and (2) developing new capabilities in DFTB to calculate the electronic structure and dynamics of large chemical systems. While classical molecular dynamics can handle hundreds of thousands of atoms, it cannot provide a first-principles based description of chemical systems at the quantum level. At the other extreme, conventional Kohn-Sham DFT methods can probe the true quantum mechanical nature of chemical systems; however, these methods cannot tackle the large sizes and length scales relevant to dynamics simulations of realistic systems. The DFTB formalism utilized in this project provides a viable approach for probing these large systems at a quantum mechanical level of detail. However, to utilize the DFTB approach for accurate calculations of electronic properties, it is crucial to incorporate quantum-based corrections in DFTB since exchange-correlation effects can still remain very strong in these large systems. At the same time, enhancing the computational efficiency of DFTB is also essential since optimal computational performance is required for addressing the large size scales associated with realistic chemical systems. As such, the new non-empirical corrections and computing hardware enhancements implemented in this project will enable accurate and computationally efficient approaches to directly probe electronic properties in these large, complex systems.

36 MATERIALS SCIENCE↗

Autonomous Operations for Advanced Reactors Utilizing Supervisory Control

Automation is a critical tenet of reactor plant operations as reliance on nuclear energy increases. Nuclear power plants require a large workforce which does not scale with output; that is, the cost per megawatt increases as reactor output becomes smaller. The economic viability of advanced reactors, particularly small modular reactors (SMRs) and microreactors, requires a significantly reduced onsite workforce. The logical solution is establishing a systematic process of elimination of reliance on human operators, and to the extent possible, replacing these actions with automated functions. In this paper, we propose a method for such transformation to establish a robust technical basis to enable transition to autonomy. Our method is based on finite state automata (FSA)—also known as finite state machines (FSMs). Relying on this method allows us to exploit the rich set of mathematical proofs available in the field of regular languages. FSA are one of the mathematical tools to model discrete event systems (DES). These properties are applied to produce an automated startup controller for the Massachusetts Institute of Technology Research Reactor (MITR). The startup procedure is captured in terms of discrete changes from one state to another while an independent supervisory control system directs the sequence of states and alerts a human in the event of an abnormal operation. First, the design and behavior of the MITR rod control system were modeled in Simulink. Then, the startup procedure was applied to the rod control system and the DES performed a startup by procedurally withdrawing rods to the subcritical position. The simulation also stops rod motion in response to an uncontrollable event and restarts rod motion once the event has been cleared.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Suppressing Polaronic Defect–Photocarrier Interaction in Halide Perovskites by Pre-distorting Its Lattice

In halide perovskites, photocarriers can have strong polaronic interactions with point defects. For iodide-deficient MAPbI 3 , we found that the Fermi level can shift significantly by 0.6–0.7 eV upon light illumination. This energy level shift is accompanied by the formation of deep electron traps. These experimental observations are consistent with the formation of a Pb–Pb dimer when photoexcited electrons are trapped at an iodide vacancy. Interestingly, we found that this polaronic interaction is suppressed when a portion of MA + cations is replaced by smaller Cs + ions. Density functional theory calculations reveal that Cs-doping can reduce the distance between two Pb atoms across an iodide vacancy, even without electron trapping. The predistortion of the lattice induced by cation replacement resembles the Pb–Pb dimer formed by electron trapping at the defect site, which explains the suppression of light-induced effects observed in the experiment. Furthermore, our finding unveils a counterintuitive strategy to enhance the photostability of halide perovskites by preintroducing distortions into its lattice.

14 SOLAR ENERGY↗

Detection of translational noncrystallographic symmetry in Patterson functions

Detection of translational noncrystallographic symmetry (TNCS) can be critical for success in crystallographic phasing, particularly when molecular-replacement models are poor or anomalous phasing information is weak. If the correct TNCS is detected then expected intensity factors for each reflection can be refined, so that the maximum-likelihood functions underlying molecular replacement and single-wavelength anomalous dispersion use appropriate structure-factor normalization and variance terms. Here, an analysis of a curated database of protein structures from the Protein Data Bank to investigate how TNCS manifests in the Patterson function is described. These studies informed an algorithm for the detection of TNCS, which includes a method for detecting the number of vectors involved in any commensurate modulation (the TNCS order). The algorithm generates a ranked list of possible TNCS associations in the asymmetric unit for exploration during structure solution.

59 BASIC BIOLOGICAL SCIENCES↗

Differentiable programming for online training of a neural artificial viscosity function within a staggered grid Lagrangian hydrodynamics scheme

Lagrangian methods to solve the inviscid Euler equations produce numerical oscillations near shock waves. A common approach to reducing these oscillations is to add artificial viscosity (AV) to the discrete equations. The AV term acts as a dissipative mechanism that attenuates oscillations by smearing the shock across a finite number of computational cells. However, AV introduces several control parameters that are not determined by the underlying physical model, and hence, in practice are tuned to the characteristics of a given problem. We seek to improve the standard quadratic-linear AV form by replacing it with a learned neural function that reduces oscillations relative to exact solutions of the Euler equations, resulting in a hybrid numerical-neural hydrodynamic solver. Because AV is an artificial construct that exists solely to improve the numerical properties of a hydrodynamic code, there is no offline ‘viscosity data’ against which a neural network can be trained before inserting into a numerical simulation, thus requiring online training. We achieve this via differentiable programming, i.e. end-to-end backpropagation or adjoint solution through both the neural and differential equation code, using automatic differentiation of the hybrid code in the Julia programming language to calculate the necessary loss function gradients. A novel offline pre-training step accelerates training by initializing the neural network to the default numerical AV scheme, which can be learned rapidly by space-filling sampling over the AV input space. We find that online training over early time steps of simulation is sufficient to learn a neural AV function that reduces numerical oscillations in long-term hydrodynamic shock simulations. These results offer an early proof-of-principle that online differentiable training of hybrid numerical schemes with novel neural network components can improve certain performance aspects existing in purely numerical schemes.

97 MATHEMATICS AND COMPUTING↗

Flexible MOFs as Pressure-Tunable Filters for Hydrocarbon Separation

Metal–organic frameworks (MOFs) hold significant promise for separating gas mixtures, especially hydrocarbons. While the main focus in the field is the development of new adsorbents for specific separations of binary mixtures, a preferable situation would be using a single framework for separating various species. This has been achieved in some flexible MOFs, where ternary mixtures can be separated at different temperatures. Here, we propose a simple yet fascinating way of utilizing the flexibility of MOFs to create tunable filters as a function of external pressure. We thus replace the more costly temperature-driven tunability with a cost-efficient external-pressure tunability. As a proof-of-concept, we select the CaMOF flexible framework for C6 hydrocarbon separation, however, our results are applicable to other flexible framework and gas molecules. Furthermore, our findings provide mechanistic insight and guidelines to engineer separation filters by designing flexible pores with critical sizes that can be effectively manipulated by external pressure.

36 MATERIALS SCIENCE↗

Understanding the Roles of Convective Trigger Functions in the Diurnal Cycle of Precipitation in the NCAR CAM5

The wrong diurnal cycle of precipitation is a common weakness of current global climate models (GCMs). To improve the simulation of the diurnal cycle of precipitation and understand what physical processes control it, we test a convective trigger function described in Xie et al. (2019) with additional optimizations in the NCAR Community Atmosphere Model version 5 (CAM5). The revised trigger function consists of three modifications: 1) replacing the Convective Available Potential Energy (CAPE) trigger with a dynamic CAPE (dCAPE) trigger, 2) allowing convection to originate above the top of planetary boundary layer (i.e., the unrestricted air parcel launch level - ULL), and 3) optimizing the entrainment rate and threshold value of the dynamic CAPE generation rate for convection onset based on observations. Results from 1°-resolution simulations show that the revised trigger can alleviate the long-standing GCM problem of too early maximum precipitation during the day and missing the nocturnal precipitation peak that is observed in many regions, including the U.S. southern Great Plains (SGP). The revised trigger also improves the simulation of the propagation of precipitation systems downstream of the Rockies and the Amazon region. A further composite analysis over the SGP unravels the mechanisms through which the revised trigger affects convection. Additional sensitivity tests show that both the peak time and the amplitude of the diurnal cycle of precipitation are sensitive to the entrainment rate and dCAPE threshold values.

54 ENVIRONMENTAL SCIENCES↗

The Concept and Role of Reference Architectures In NIF LRU Refurbishment Factories within LLNL

The National Ignition Facility (NIF) at Lawrence Livermore National Laboratory (LLNL) operates one of the most advanced laser systems in the world, relying on a vast number of optical components and Line Replaceable Units (LRUs) to maintain its functionality. Over time, these components degrade due to operational wear, necessitating refurbishment to sustain performance. However, many NIF LRU refurbishment factories have been “mothballed” or suffer from aging infrastructure, inconsistent work flows, and inefficiencies due to different approaches to production control and management. This paper explores the concept of reference architecture as a standardized framework to guide the redevelopment and restructuring of NIF LRU refurbishment factories. By establishing a common reference architecture, the refurbishment process can achieve reduced inefficiencies, produce quality products, and enhanced coordination across factories. This paper evaluates existing reference architectures, particularly those that integrate technical architecture, business architecture, customer context perspectives, and proposes tailored reference architecture for NIF LRU refurbishment factories.

42 ENGINEERING↗

Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine

Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2")-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.

59 BASIC BIOLOGICAL SCIENCES↗

Nuclear Requalification of the New ATR Core

The Advanced Test Reactor (ATR) creates a unique high neutron flux materials testing environment that subsequently causes neutron embrittlement damage to its beryllium reflector eventually requiring a replacement during a reactor Outage. Concurrently, a piece-for-piece core replacement is conducted to maintain reactor functionality called a core internals changeout (CIC). Once changeout is complete, ATR Reactor Engineering utilizes previous CIC data to model and predict criticality scenarios for the new unirradiated core. However, CIC data has been inconsistently reported over the years making it difficult to find data trends that could be useful for the modeling and prediction process. So nuclear requalification testing is conducted using different flux and irradiation tests to accurately verify the models and to recalibrate nuclear monitoring instrumentation in the ATR core allowing for safe re-start of normal operations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Nuclear Requalification of the ATR Core

The Advanced Test Reactor (ATR) creates a unique, high neutron flux materials testing environment that subsequently causes neutron embrittlement damage to its beryllium reflector. The reflector is eventually required to be replaced during a reactor Outage. Concurrently, a piece-for-piece core replacement is conducted to maintain reactor functionality called a core internals changeout (CIC). Once changeout is complete, ATR Reactor Engineering utilizes previous CIC data, notably 1977-1994 CIC data, to conduct predictive criticality analysis on the new, unirradiated core. However, CIC data has been inconsistently reported over the years making it difficult, and in some cases impossible, to utilize. These inconsistencies arise in various forms of not using correct units, inconsistent diagram usage, and not portraying the same kind of data similarly across the reports. To work around this inconsistency issue, Reactor Engineering is implementing the use of several new neutronic modeling codes that utilize modern computation speeds and methods to model the new core in different criticality environments. Further validation is then conducted by nuclear testing and bringing the reactor critical and conducting various irradiation tests. Upon completion and certification that the reactor passed all testing requirements, ATR can once again re-start normal operations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Deep-Learning Electron Diffractive Imaging

Here, we report the development of deep-learning coherent electron diffractive imaging at subangstrom resolution using convolutional neural networks (CNNs) trained with only simulated data. We experimentally demonstrate this method by applying the trained CNNs to recover the phase images from electron diffraction patterns of twisted hexagonal boron nitride, monolayer graphene, and a gold nanoparticle with comparable quality to those reconstructed by a conventional ptychographic algorithm. Fourier ring correlation between the CNN and ptychographic images indicates the achievement of a resolution in the range of 0.70 and 0.55 Å. We further develop CNNs to recover the probe function from the experimental data. The ability to replace iterative algorithms with CNNs and perform real-time atomic imaging from coherent diffraction patterns is expected to find applications in the physical and biological sciences.

47 OTHER INSTRUMENTATION↗

Four-Switch Buck-Boost Converter Based on Model Predictive Control with Smooth Mode Transition Capability

Four-switch buck-boost converter supports both voltage step-up and step-down functionalities, but it suffers from mode transfer challenge that would need reliable mode detection when designed to operate in multi different modes. In this paper, a novel control method based on model predictive current control is proposed for such converter with inherent smooth mode transfer capability without extra design on mode detection and transfer scheme. Modulator and mode detection are replaced by an optimization process through cost function. This largely simplifies the design and makes it easily implemented. Therefore, seamless transfer between buck and boost modes is achieved with many other system level benefits. Simulation and experimental results are provided to verify the effectiveness of proposed method for the four-switch buck-boost converter.

42 ENGINEERING↗

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases

The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Lignin-Derived Methoxyterephthalates for Performance-Advantaged Polymers and Plasticizers

Lignin-derived aromatic carboxylic acids can be produced from oxidative catalytic processes and are promising building blocks for performance-advantaged bioproducts that leverage their inherent heteroatom functionalities. Here, we synthesize 2-methoxyterephthalate and 2,6-dimethoxyterephthalate derivatives by electrochemical carboxylation of guaiacyl- and syringyl-derived lignin monomers obtained from the oxidative deconstruction of lignin. These methoxylated terephthalates are evaluated as comonomers in poly(ethylene terephthalate) (PET) and as plasticizers that could replace petrochemically-derived isophthalate and phthalate, respectively. Specifically, we copolymerize 2-methoxy- and 2,6-dimethoxyterephthalate with dimethyl terephthalate to form several PET copolymers, both of which enable the properties of PET to be tuned, with an incorporation beyond 25% producing amorphous polyesters. At 10 mol % loading in the copolymers, we demonstrate that the bioderived comonomers exhibit comparable behavior to isophthalic acid, a commonly used comonomer in PET, by lowering the crystallinity and melting temperature. Moreover, methoxyterephthalate esters (2-ethylhexyl and butyl) are compared to phthalate and terephthalate ester counterparts used as poly(vinyl chloride) (PVC) plasticizers. The bioderived plasticizers are comparable to the petroleum-derived incumbents in reducing the glass transition temperature and increasing the thermal stability of PVC. Furthermore, the dimethoxyterephthalic esters are expected to have an extended lifetime in the polymer matrix due to their lower volatility and lower diffusion coefficients calculated by molecular dynamic simulations. These results demonstrate that the isophthalate and phthalate components in polyesters and plasticizers, respectively, could be substituted with biobased methoxyterephthalate derivatives.

09 BIOMASS FUELS↗

Analytic gradients for compressed multistate pair-density functional theory

Photochemical reactions often involve states that are closely coupled due to near degeneracies, for example by proximity to conical intersections. Therefore, a multistate method is used to accurately describe these states; for example, ordinary perturbation theory is replaced by quasidegenerate perturbation theory. Multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to approximate the full dynamical correlation energy of strongly correlated systems, and we recently proposed compressed multistate pair-density functional theory (CMS-PDFT) to treat closely coupled states. In the present paper, we report the implementation of analytic gradients for CMS-PDFT in both OpenMolcas and PySCF, and here we illustrate the use of these gradients by applying the method to the excited states of formaldehyde and phenol.

74 ATOMIC AND MOLECULAR PHYSICS↗

Unmasking Static Correlation Error in Hybrid Kohn–Sham Density Functional Theory

To uncover the way Hartree–Fock exchange brings static correlation error into hybrid Kohn–Sham density functional theory, we compare the potential energy curves of four diatomic molecules, namely, H 2 , F 2 , HF, and NaF, using both restricted and unrestricted Kohn–Sham theory. Here, we find that increasing the percentage of Hartree–Fock exchange significantly increases the static correlation error because Hartree–Fock exchange replaces the ability of local exchange in density functionals to account for the localization effects associated with static correlation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Numerical schemes for a multi-species BGK model with velocity-dependent collision frequency

Here, we consider a kinetic description of multi-species gas mixture modeled with Bhatnagar-Gross-Krook (BGK) collision operators, in which the collision frequency varies not only in time and space but also with the microscopic velocity. In this model, the Maxwellians typically used in standard BGK operators are replaced by a generalization of such target functions, which are defined by a variational procedure. In this paper we present a numerical method for simulating this model, which uses an Implicit-Explicit (IMEX) scheme to minimize a certain potential function, mimicking the Lagrange functional that appears in the theoretical derivation. We show that theoretical properties such as conservation of mass, total momentum and total energy as well as positivity of the distribution functions are preserved by the numerical method, and illustrate its usefulness and effectiveness with numerical examples.

97 MATHEMATICS AND COMPUTING↗