Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “rational approximations”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

68 records · Page 4

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toughening Sm–Co sintered magnets via microstructure modification with additives

We report the mechanical properties of the brittle Smsingle bondCo permanent magnets are of great practical significance. However, studies on the magnets have mostly focused on their magnetic properties. This paper reports the modified microstructure and refined unimodal grain size, enhanced flexural strength, and magnetic properties of Sm 2 (Co,Fe,Cu,Zr) 17 sintered magnets doped with La 2 O 3 , MgO, and CaF 2 fine particulates. The correlations between microstructure, phase composition, and mechanical and magnetic properties were studied. Doping of a small amount (e.g., 0.5–3 wt%) of La 2 O 3 , MgO, or CaF 2 fine particulates could significantly refine the unimodal grain sizes of the Smsingle bondCo magnets via the Zener pinning effect. Moreover, doping significantly improved the flexural strengths σ of the magnets. For example, the σ values of the magnets with 0.5 wt% MgO, 1 wt% La 2 O 3 , and 1 wt% CaF 2 were approximately 65%, 63%, and 42% higher than that of the reference magnet, respectively. Micromechanical simulations revealed that the fine particles of La 2 O 3 could deflect crack growth, while the CaF 2 particles could attract or arrest cracks during the fracture process. The mechanical strengthening effect was mainly due to grain size refinement. The Smsingle bondCo magnets with 0.5–1.5 wt% CaF2 and 0.5 wt% La 2 O 3 exhibited excellent magnetic properties while doping 1–3 wt% La2O3 and 0.5–3 wt% MgO deteriorated magnetic performance. The rational design of CaF 2 - or La 2 O 3 -doped microstructure can be an economical and effective method for producing toughened Sm–Co sintered magnets with high magnetic performance.

36 MATERIALS SCIENCE↗

Analysis of spin frustration in an Fe III 7 cluster using a combination of computational, experimental, and magnetostructural correlation methods

The synthesis, structure, and magnetic properties are reported for [Fe 7 O 3 (O 2 C t Bu) 9 (mda) 3 (H 2 O) 3 ] ( 1 ), where mdaH 2 is N -methyldiethanolamine. 1 was prepared from the reaction of [Fe 3 O(O 2 C t Bu) 6 (H 2 O) 3 ](NO 3 ) with mdaH 2 in a 1:~3 ratio in MeCN. The core of 1 consists of a central octahedral Fe III ion held within a non-planar Fe 6 loop by three μ 3 -O 2- and three μ 2 -RO - arms from the three mda 2- chelates. Variable-temperature dc and ac magnetic susceptibility studies revealed dominant antiferromagnetic coupling, leading to a ground state spin of S = 5 / 2 . The ground state was confirmed by a fit of magnetization data collected in the 0.1–7.0 T and 1.8–10.0 K ranges. The four Fe 2 pairwise exchange parameters ( J 1 - J 4 ) were estimated by independent methods: theoretical calculations using either broken symmetry energy differences (-46.3, -16.2, -3.9, and - 28.1 cm -1 , respectively) or Green’s function approximation methods (-41.4, -14.8, -13.2, and - 24.7 cm -1 ), and a magnetostructural correlation (MSC) previously developed for high nuclearity Fe III /O complexes (-39.5, -13.8, -6.7, and - 23.5 cm -1 ). Additionally, the J 1 - J 4 obtained from the MSC and theoretical methods were used with the program PHI to both simulate χ M T vs T as well as to serve as reasonable input values to fit the experimental data (-41.0, -11.4, -5.0, and - 27.3 cm -1 ). Analysis of the J ij led to identification of the spin frustration effects operative and the resultant spin vector alignments at each Fe III ion, thus allowing for the rationalization of the experimental ground state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Skyrmions and hopfions in three-dimensional frustrated magnets

Here, a model of an inversion-symmetric frustrated spin system is introduced which hosts three-dimensional extensions of magnetic skyrmions. In the continuum approximation, this model reduces to a nonlinear sigma model on a squashed sphere that has a natural interpolating parameter. At one limit of the parameter, the model reduces to a frustrated magnetic system earlier considered by Sutcliffe as a host to hopfions, and in the other limit, it becomes very similar to the 3D Skyrme model. To better understand the relation between hopfions and 3D skyrmions, a model interpolating between the Faddeev-Niemi and the Skyrme models is reconsidered and it is shown that energies of the solitons obey a linear Bogomol'nyi-Prasad-Sommerfeld bound. The 3D skyrmions in the frustrated magnetic model are found and compared to the rational map ansatz.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Investigation of the iodate sorption mechanism by CoAl LDH through experiments and ab initio molecular dynamics simulations

Radioiodine released during the nuclear-fuel cycle constitutes a persistent radiological hazard. In this study, the IO 3 – uptake mechanism of CoAl LDH was resolved by combining pH-controlled sorption experiments, synchrotron XAFS, and DFT-based AIMD simulations. At pH close to 6, approximately 90% of IO 3 – was removed, and the equilibrium distribution coefficient reached about 1.7 × 10 4 mL g –1 . EXAFS analysis indicated an average iodine–oxygen bond length of 1.81 Å and a coordination number near 3, with the fit R-factor equal to 0.002. The simulations faithfully reproduced the experimental spectrum and revealed transient proton hopping events that generated metastable I–O–H species inside the interlayer, thereby confirming nitrate-to-iodate exchange as the controlling capture pathway. Atomic density profiles and radial distribution functions further showed that IO 3 – adopt an end-on orientation perpendicular to the hydroxide sheets, while water molecules mediate proton migration without disturbing the host lattice. In conclusion, the integrated experimental–computational evidence demonstrates that CoAl LDH can rapidly and selectively sequester IO 3 – under near-neutral conditions, offering atomic scale guidance for the rational engineering of layered sorbents for advanced radioactive-waste treatment.

Kang, Jaehyuk [Jeju National Univ. (Korea, Republi↗

Towards Realistic Models of Heterogeneous Catalysis: Simulations of Oxidation Catalysis from First Principles

Among the most significant developments in heterogeneous catalysis in the last 20 years is the emergence of microkinetic models, often parameterized from density functional theory (DFT) calculations, used to quantify observed catalyst performance and to guide the discovery of new catalytic materials. While DFT directly reports binding energies and elementary step activation energies, the free energies that enter into microkinetic models must be computed from additional approximations. Frequently these free energy approximations assume ideal behavior—that adsorbates do not interact with one another, or that adsorbates are immobile or vibrate harmonically about a binding site. These assumptions can and do have an impact on predicted catalyst performance and potentially even on predicted trends. Our work relates to three categories of non-idealities, explored in the context of nitrogen oxidation and reduction catalysis on metal surfaces. One component relates to adsorbate translational free energy, the contribution least well described by conventional models, in which we develop modeling approaches that improve accuracy with limited increase in computational expense. A second component relates adsorbate-adsorbate interactions, in which we develop benchmark on-lattice interaction models and compare kinetic predictions with conventional mean-field models, in an effort to develop more robust coverage-dependent mean field modeling approaches. The last relates the most fundamental assumption of all—that of energy equipartition—in an effort to rationalize and guide plasma-enhanced catalysis.

99 GENERAL AND MISCELLANEOUS↗

Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator

Understanding the physics of lignin will help rationalize its function in plant cell walls as well as aiding practical applications such as deriving biofuels and bioproducts. Here, in this work, we present SPRIG (Simple Polydisperse Residue Input Generator), a program for generating atomic-detail models of random polydisperse lignin copolymer melts i.e., the state most commonly found in nature. Using these models, we use all-atom molecular dynamics (MD) simulations to investigate the conformational and dynamic properties of polydisperse melts representative of switchgrass (Panicum virgatum L.) lignin. Polydispersity, branching and monolignol sequence are found to not affect the calculated glass transition temperature, T g . The Flory–Huggins scaling parameter for the segmental radius of gyration is 0.42 ± 0.02, indicating that the chains exhibit statistics that lie between a globular chain and an ideal Gaussian chain. Below T g the atomic mean squared displacements are independent of molecular weight. In contrast, above T g , they decrease with increasing molecular weight. Therefore, a monodisperse lignin melt is a good approximation to this polydisperse lignin when only static properties are probed, whereas the molecular weight distribution needs to be considered while analyzing lignin dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of edge-localized electron cyclotron current drive on edge-localized mode suppression by resonant magnetic perturbations in DIII-D

Abstract According to recent DIII-D experiments (Logan et al 2024 Nucl. Fusion 64 014003), injecting edge localized electron cyclotron current drive (ECCD) in the counter-plasma-current (counter- I p ) direction reduces the n = 3 resonant magnetic perturbation (RMP) current threshold for edge-localized mode (ELM) suppression, while co- I p ECCD during the suppressed ELM phase causes a back transition to ELMing. This paper presents nonlinear two-fluid simulations on the ECCD manipulation of edge magnetic islands induced by RMP using the TM1 code. In the presence of a magnetic island chain at the pedestal-top, co- I p ECCD is found to decrease the island width and restore the initially degraded pedestal pressure when its radial deposition location is close to the rational surface of the island. With a sufficiently strong co- I p ECCD current, the RMP-driven magnetic island can be healed, and the pedestal pressure fully recovers to its initial ELMing state. On the contrary, counter- I p ECCD is found to increase the island width and further reduce the pedestal pressure to levels significantly below the peeling-ballooning-mode limited height, leading to even stationary ELM suppression. These simulations align with the results from DIII-D experiments. However, when multiple magnetic island chains are present at the pedestal-top, the ECCD current experiences substantial broadening, and its effects on the island width and pedestal pressure become negligible. Further simulations reveal that counter- I p ECCD enhances RMP penetration by lowering the penetration threshold, with the degree of reduction proportional to the amplitude of ECCD current. For the ∼1 MW ECCD in DIII-D, the predicted decrease in the RMP penetration threshold for ELM suppression is approximately 20%, consistent with experimental observations. These simulations indicate that edge-localized ECCD can be used to either facilitate RMP-driven ELM suppression or optimize the confinement degradation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Initial study on cross section generation requirements for a PBR equilibrium core

A Serpent model of the HTR-PM equilibrium core was developed for use in cross section prepa-ration studies in order to guide methods development for the Griffin reactor multiphysics applica-tion. The model includes detailed isotopics for 10 distinct pebble burnup groups in 126 core zoneswith unique fuel and moderator temperatures obtained from a coupled neutronics-thermal-fluidsequilibrium core calculation using Griffin-Pronghorn. A sensitivity study of the fuel and mod-erator temperatures for various core regions was performed with the MOOSE stochastic tools.The results show that the uncertainties are, not unexpectedly, dominated by the value of the fluidtemperature and that the power level, heat transfer coefficient and effective conduction to neigh-boring pebbles and fluid constitute, at best, second order effects. The temperature uncertaintyrange varies from 28 K to 57 K at the core entry and exit planes, respectively, but these val-ues are probably higher. We still have to quantify the significance of these uncertainties in thepreparation of cross sections, which will be postponed for future work. In addition, we verifythat the single effective pebble approach works well for the preparation of region averaged crosssections in the infinite domain approximation. Nevertheless, there are significant discrepanciesin the cross sections when compared to the multi-pebble model. This could affect the predictionof peak values and in the depletion calculation. We conclude that is highly desirable for futurestudies with Griffin to be able to handle both the ?effective? pebble approximation and the multi-pebble approach for the various pebble burnup groups. This enables Griffin users the flexibilityto perform higher-fidelity studies. Finally, we initiate the preparation of cross sections for variouscore regions from the full core Serpent reference model. We quantify the differences in 26 groupcross sections from infinite domain models. These reference cross sections will serve to validatethe double heterogeneity, self-shielding, and spectrum-correction methods in Griffin.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Identification of and Structural Insights into Hit Compounds Targeting N -Myristoyltransferase for Cryptosporidium Drug Development

Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.

60 APPLIED LIFE SCIENCES↗

Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs

Cancer is a leading cause of death in the US, second only to heart disease. It is primarily a result of a combination of an estimated two-nine genetic mutations (multi-hit combinations). Although a body of research has identified hundreds of cancer-causing genetic mutations, we don’t know the specific combination of mutations responsible for specific instances of cancer for most cancer types. An approximate algorithm for solving the weighted set cover problem was previously adapted to identify combinations of genes with mutations that may be responsible for individual instances of cancer. However, the algorithm’s computational requirement scales exponentially with the number of genes, making it impractical for identifying more than three-hit combinations, even after the algorithm was parallelized and scaled up to a V100 GPU. Since most cancers have been estimated to require more than three hits, we scaled out the algorithm to identify combinations of four or more hits using 1000 nodes (6000 V100 GPUs with ≈48×106 processing cores) on the Summit supercomputer at Oak Ridge National Laboratory. Efficiently scaling out the algorithm required a series of algorithmic innovations and optimizations for balancing an exponentially divergent workload across processors and for minimizing memory latency and inter-node communication. We achieved an average strong scaling efficiency of 90.14% (80.96%–97.96% for 200 to 1000 nodes), compared to a 100 node run, with 84.18% scaling efficiency for 1000 nodes. With experimental validation, the multi-hit combinations identified here could provide further insight into the etiology of different cancer subtypes and provide a rational basis for targeted combination therapy.

Dash, Sajal↗

Efficient Unitary Designs from Random Sums and Permutations

A unitary k-design is an ensemble of unitaries that matches the first k moments of the Haar measure. In this work, we provide two efficient constructions of k-designs on n-qubits using new random matrix theory techniques. Our first construction is based on exponentiating sums of random i.i.d. Hermitian matrices and uses O(k2n2)-many gates. In the spirit of central limit theorems, we show that this random sum approximates the Gaussian Unitary Ensemble (GUE). We then show that the product of just two exponentiated GUE matrices is already approximately Haar random. Our second construction is based on products of exponentiated sums of random permutations and uses Õ(k poly (n)) many gates. The k dependence is optimal (up to polylogarithmic factors) and is inherited from the efficiency of existing k-wise independent permutations. Furthermore, replacing random permutations with quantum-secure pseudorandom permutations (PRPs), we also obtain a pseudorandom unitary (PRU) ensemble that is secure under nonadaptive queries. A central feature of both proofs is a new connection between the polynomial method in quantum query complexity and the large-dimension (N) expansion in random matrix theory. In particular, the first construction uses the polynomial method to control high moments of certain random matrix ensembles without requiring delicate Weingarten calculations. In doing so, we define and solve a moment problem on the unit circle, asking whether a finite number of equally weighted points can reproduce a given set of moments. In our second construction, the key step is to exhibit an orthonormal basis for irreducible representations of the partition algebra that has a low-degree large-N expansion. This allows us to show that the distinguishing probability is a low-degree rational polynomial of the dimension N.

algebra↗

Kinetics-Informed Neural Networks

Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize feed-forward artificial neural networks as basis functions to solve ordinary differential equations (ODEs) constrained by differential algebraic equations (DAEs) that describe microkinetic models (MKMs). We present an algebraic framework for the mathematical description and classification of reaction networks, types of elementary reaction, and chemical species. Under this framework, we demonstrate that the simultaneous training of neural nets and kinetic model parameters in a regularized multi-objective optimization setting leads to the solution of the inverse problem through the estimation of kinetic parameters from synthetic experimental data. We analyze a set of scenarios to establish the extent to which kinetic parameters can be retrieved from transient kinetic data, and assess the robustness of the methodology with respect to statistical noise. Furthermore, this approach to inverse kinetic ODEs can assist in the elucidation of reaction mechanisms based on transient data.

36 MATERIALS SCIENCE↗

AEOLUS: Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems

Sustained advances in the mathematics of modeling and simulation have resulted in the capability today for routine simulation of a number of large scale complex DOE-relevant systems. As remarkable as this capability for solving the so-called forward problem is, it is typically only the first step-an inner loop within an outer loop that explores the simulation model's parameter space and decision space to characterize uncertainty in the model's predictions, learn unknown model parameters from data, design the most informative experiments, determine optimal control strategies, and create optimal designs. Broadly, what unifies all of these outer loop problems is that they are, in one form or another, optimization problems over parameter/control/design space that are constrained by complex uncertain models. To fully realize the power of scientific simulation as a basis for scientific discovery, technological innovation, and rational decision-making, it is imperative to move beyond simulation to tackle the outer loop of optimization for learning from data, experimental design, and control with complex uncertain models. When the models under consideration are large-scale and complex, and when the optimization variable and uncertain parameter spaces are high (or infinite) dimensional, this constitutes a grand challenge of the highest order, and is intractable with conventional methods. To overcome these challenges, the AEOLUS Center was established to develop a unified mathematical, computational, and statistical framework for (1) Learning predictive models from complex data via Bayesian inference and optimization, and (2) Optimizing experiments, processes, and designs using the resulting uncertain models. These problems are intractable with conventional methods, for several reasons: (1) The simulation problems that govern the inner loops of the optimization problems are expensive to execute (due to severe nonlinearity, heterogeneity, multiphysics/multiscale coupling); (2) The optimization variable and uncertain parameter spaces are high dimensional, often stemming from discretizations of infinite dimensional fields such as initial conditions, sources, or material properties. We argue that the key to overcoming these challenges is to develop new mathematical, computational, and statistical methods that exploit the structure of the Bayesian inference and optimization problems mediated by their underlying complex uncertain models. This structure includes the regularity, sparsity, geometry, low intrinsic dimensionality, and multifidelity nature of the maps from uncertain parameter/optimization variable spaces to the specific objectives targeted: Bayesian inference, optimal experimental design, and optimal control design. Black box methods developed as generic tools are incapable of exploiting this structure. To be successful, we must create, integrate, and cross-fertilize ideas across multiple areas of applied math--including approximation theory, Bayesian inference, data science, experimental design, information theory, machine learning, model reduction, optimal control theory, parallel algorithms, PDE-constrained optimization, randomized algorithms, stochastic optimization, and uncertainty quantification--all while exploiting the structure of the problems at hand. With this goal in mind, we have marshaled a team of leading authorities in these areas. While the methods we develop will be broadly applicable across a wide spectrum of DOE problems in which experiments inform models and the systems those models describe must be optimized under uncertainty, we have chosen a specific area, advanced manufacturing and materials, to drive our work. AMM is characterized by complex models across multiple scales, and is a rich source of challenging problems in inference, experimental design, and optimal control, requiring multifaceted and integrated advances in applied mathematics. As such, AMM serves as an excellent vehicle to motivate and demonstrate the advances in applied mathematics developed by our center.

97 MATHEMATICS AND COMPUTING↗