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DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Computation of conventional and alternative jet fuel sensitivity to lean blowout

Large Eddy Simulations (LES) are performed to compute the sensitivity of a conventional (A-2) and an alternate bio-jet (C-1) fuel to Lean Blowout (LBO). A realistic aviation gas turbine engine combustor configuration is considered. Reliable experimental LBO data and OH* chemiluminescence data for the conventional and alternate jet fuel in the combustor configuration have recently become available. The present work utilizes a highly automated, on-the-fly meshing strategy, along with adaptive mesh refinement, to demonstrate the feasibility of capturing the realistic combustion processes. A Lagrangian framework, with initial conditions specified using measurements of spray statistics, is used to model the fuel spray. Newly developed compact reaction mechanisms based on fuel surrogates are validated for the A-2 and the C-1 fuels. The compact reaction mechanisms are implemented using a detailed finite rate chemistry solver. Spray statistics computed by the present LES simulations compare well with available measurements at stable flame conditions near the lean blowout limit. The computed shape of the stable flame as represented by line integrated OH concentrations compares well with the experimental OH* chemiluminescence data. Lean blowout is reached by gradually decreasing the fuel flow rate in the computations, similar to that in the experiments. The results of the LES simulations effectively capture the fuel composition effects and estimate the sensitivity of the LBO limits to the fuel type. The computed trends in LBO limits agree within engineering accuracy with the experimental results for conventional and alternative aviation fuels. The methodology for predicting the fuel composition effects on the lean blowout limits in a fully resolved realistic, complex combustor is established for the first time.

Adaptive mesh refinement↗

NASA NTRS2002

Molten-Metal Droplet Deposition on a Moving Substrate in Microgravity: Aiding the Development of Novel Technologies for Microelectronic Assembly

Driven by advancements in microelectronics manufacturing, this research investigates the oblique (non-axisymmetric) impact of liquid-metal droplets on flat substrates. The problem of interest is relevant to the development of the novel technology of on-demand dispension (printing) of microscopic solder deposits for the surface mounting of microelectronic devices. The technology, known as solder jetting, features on-demand deposition of miniature solder droplets (30 to 120 microns in diameter) in very fine, very accurate patterns using techniques analogous to those developed for the ink-jet printing industry. Despite its promise, severe limitations exist currently with regards to the throughput rates of the technology; some of these limitations are largely due to the lack of the capability for reliable prediction of solder bump positioning and shapes, especially under ballistic deposition conditions where the droplet impact phenomena are inherently three-dimensional. The study consists of a theoretical and an experimental component. The theoretical work uses a finite element formulation to simulate numerically the non-axisymmetric (3-D) fluid mechanics and heat transfer phenomena of a liquid solder droplet impacting at an angle alpha on a flat substrate. The work focuses on the pre-solidification regime. The modeling of the most challenging fluid mechanics part of the process has been completed successfully. It is based upon the full laminar Navier-Stokes equations employing a Lagrangian frame of reference. Due to the large droplet deformation, the surface (skin) as well as the volumetric mesh have to be regenerated during the calculations in order to maintain the high accuracy of the numerical scheme. The pressure and velocity fields are then interpolated on the newly created mesh. The numerical predictions are being tested against experiments, for cases where wetting phenomena are not important. For the impact parameters used in the example shown (We = 2.38, Fr = 16300, Re = 157), the droplet rolls along the substrate, but its shape remains practically axisymmetric for all impact angles within the range from 0 to 60 deg. Interestingly, the substrate/droplet contact area during the recoiling phase of the impact is not a monotonically decreasing function of time. The experimental component of the research tests the numerical predictions and provides necessary input data (contact angles) for the theoretical model. The experiments are performed in microgravity (2.2s drop tower of the NASA GRC) in order to allow for the use of mm-size solder droplets, which make feasible the performance of accurate measurements, while maintaining similitude of the relevant fluid dynamic groups (Re, Fr, We, Ste). Preliminary oblique impact experiments have been performed using water droplets in normal gravity.

Megaridis, C. M.↗

NASA NTRS1993

A survey of parametrized variational principles and applications to computational mechanics

This survey paper describes recent developments in the area of parametrized variational principles (PVP's) and selected applications to finite-element computational mechanics. A PVP is a variational principle containing free parameters that have no effect on the Euler-Lagrange equations. The theory of single-field PVP's based on gauge functions (also known as null Lagrangians) is a subset of the inverse problem of variational calculus that has limited value. On the other hand, multifield PVP's are more interesting from theoretical and practical standpoints. Following a tutorial introduction, the paper describes the recent construction of multifield PVP's in several areas of elasticity and electromagnetics. It then discusses three applications to finite-element computational mechanics: the derivation of high-performance finite elements, the development of element-level error indicators, and the constructions of finite element templates. The paper concludes with an overview of open research areas.

Felippa, Carlos A.↗

DOE OSTI2021

Quantum field theory with the generalized uncertainty principle II: Quantum Electrodynamics

Highlights: • Relativistic Generalized Uncertainty Principle gives Frame independent minimum length. • Quantum Gravity modified Dirac equation from Modified Klein–Gordon Equations. • There exists a Quantum Gravity modified Lagrangian for a spinor field theory. • Feynman vertices contain 2 fermions & up to 5 gauge bosons are allowed. • Minimum length modifies the amplitude of Electrodynamic electron–muon scattering. Continuing our earlier work on the application of the Relativistic Generalized Uncertainty Principle (RGUP) to quantum field theories, in this paper we study Quantum Electrodynamics (QED) with minimum length. We obtain expressions for the Lagrangian, Feynman rules and scattering amplitudes of the theory, and discuss their consequences for current and future high energy physics experiments. We hope this will provide an improved window for testing Quantum Gravity effects in the laboratory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1989

Dynamic analysis of a 6 DOF CKCM robot end-effector for dual-arm telerobot systems

A dynamical analysis is performed for a six DOF robot end-effector built to study telerobotic service and maintenance of NASA hardwares in space. The design of the end-effector is based on the concept of closed-kinematic chain mechanism capable of performing precise motion in a small workspace. After presenting a closed-form solution for the inverse kinematic problem, the Lagrangian approach is used to derive a set of equations of motion for the end-effector where the generalized coordinates are selected to be the Cartesian coordinates. A computer simulation study shows that the centrifugal and Coriolis terms can be neglected for slow motion.

Nguyen, Charles C.↗

DOE OSTI2023

Graph-based quantum response theory and shadow Born–Oppenheimer molecular dynamics

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born–Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. Further, the proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Mixing by internal gravity waves in stars: assessing numerical simulations against theory

ABSTRACT Here we present a study of radial chemical mixing in non-rotating massive main-sequence stars driven by internal gravity waves (IGWs), based on multidimensional hydrodynamical simulations with the fully compressible code MUSIC. We examine two proposed mechanisms of material mixing in stars by IGWs that are commonly quoted, relating to thermal diffusion and sub-wavelength shearing. Thermal diffusion provides a non-restorative effect to the waves, leaving material displaced from its previous equilibrium, while shearing arising within the waves drives weak localized flows, mixing the fluid there. Using IGW spectra from the simulations, we evaluate theoretical predictions of mixing rates due to these mechanisms. We show, for $20\, \mathrm{M}_\odot$ main-sequence stars, that neither of these mechanisms are likely to create mixing sufficient to correct inaccuracies in current stellar evolution models. Furthermore, we compare these predictions to results obtained from Lagrangian tracer particles, following a method recently used for global simulations of stellar interiors to measure mixing by IGWs in their radiative zones. We demonstrate that tracer particle methods face significant numerical challenges in measuring the small diffusion coefficients predicted by the aforementioned theories, for which they are prone to yielding artificially enhanced coefficients. Diffusion coefficients based on such methods are currently used with stellar evolution codes for asteroseismic studies, but should be viewed with caution. Finally, in a case where tracer particles do not suffer from numerical artefacts, we suggest that a diffusion model is not suitable for time-scales typically considered by 2D numerical simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Real-time evolution of texture and temperature during friction stir processing of a magnesium alloy: An operando neutron diffraction study

The real-time development of texture and the evolution of temperature during friction stir processing (FSP) of a Mg alloy were investigated using an operando neutron diffraction measurement. A novel approach was applied in this study where the real-time, quasi-steady state measurements performed as a function of position during FSP are converted to a Lagrangian dataset that reveals the transient behavior as a function of time. The in-situ FSP was carried out under two different thermo-mechanical processing conditions represented by the Zener-Hollomon parameter, Z. Further, the results show that: (i) a shear texture develops from the initial strong basal texture with the peak temperature reaching about 774 K during a low-Z processing and (ii) a strong off-normal texture develops with a peak temperature of 616 K during a high-Z processing. Moreover, time-temperature-texture diagrams were established to reveal the real-time development of the texture during the processing for both the low Z and high Z processing conditions. The changes in texture will be discussed in terms of plastic deformation mechanisms active during various stages of the FSP under the two different processing conditions.

36 MATERIALS SCIENCE↗

NASA NTRS1987

Spatially random models, estimation theory, and robot arm dynamics

Spatially random models provide an alternative to the more traditional deterministic models used to describe robot arm dynamics. These alternative models can be used to establish a relationship between the methodologies of estimation theory and robot dynamics. A new class of algorithms for many of the fundamental robotics problems of inverse and forward dynamics, inverse kinematics, etc. can be developed that use computations typical in estimation theory. The algorithms make extensive use of the difference equations of Kalman filtering and Bryson-Frazier smoothing to conduct spatial recursions. The spatially random models are very easy to describe and are based on the assumption that all of the inertial (D'Alembert) forces in the system are represented by a spatially distributed white-noise model. The models can also be used to generate numerically the composite multibody system inertia matrix. This is done without resorting to the more common methods of deterministic modeling involving Lagrangian dynamics, Newton-Euler equations, etc. These methods make substantial use of human knowledge in derivation and minipulation of equations of motion for complex mechanical systems.

Rodriguez, G.↗

NASA NTRS1985

Large-scale computations in fluid mechanics; Proceedings of the Fifteenth Summer Seminar on Applied Mathematics, University of California, La Jolla, CA, June 27-July 8, 1983. Parts 1 & 2

Papers are presented on such topics as the use of semi-Lagrangian advective schemes in meteorological modeling; computation with high-resolution upwind schemes for hyperbolic equations; dynamics of flame propagation in a turbulent field; a modified finite element method for solving the incompressible Navier-Stokes equations; computational fusion magnetohydrodynamics; and a nonoscillatory shock capturing scheme using flux-limited dissipation. Consideration is also given to the use of spectral techniques in numerical weather prediction; numerical methods for the incorporation of mountains in atmospheric models; techniques for the numerical simulation of large-scale eddies in geophysical fluid dynamics; high-resolution TVD schemes using flux limiters; upwind-difference methods for aerodynamic problems governed by the Euler equations; and an MHD model of the earth's magnetosphere.

Engquist, B. E.↗

DOE OSTI2021

The evolution dynamical processes of Ural blocking through the lens of local finite-amplitude wave activity budget analysis

Understanding the formation and evolution mechanisms of Ural blocking (UB) is of great importance for the prediction of UB and relevant extremes in east Asia. Using the 6-hourly ERA-Interim reanalysis data, this study quantifies the conservative and nonconservative processes in the lifecycle of UB through the lens of the hybrid Eulerian-Lagrangian local finite-amplitude wave activity (LWA) diagnostics. It is found that (i) as a wave activity source, eddy heat flux works to not only initiate the UB, but also prevent the wave activity of the blocking from dispersing downstream---the key characteristic of blocking; (ii) both the wave propagation and wave advection mechanisms are indispensable for the evolution of UB, playing a tug-of-war on the downstream development of wave activity; (iii) Throughout the lifespan of UB, diabatic heating provides the most important damping mechanism for the wave activity both upstream and downstream; and (IV) irreversible PV mixing appears to compensate the eddy PV flux during the wave breaking stage of blocking.

Blocking, wave activity, eddy-mean flow interactio↗

DOE OSTI2023

Re-evaluating cloud chamber constraints on depositional ice growth in cirrus clouds – Part 1: Model description and sensitivity tests

Abstract. Ice growth from vapor deposition is an important process for the evolution of cirrus clouds, but the physics of depositional ice growth at the low temperatures (<235 K) characteristic of the upper troposphere and lower stratosphere is not well understood. Surface attachment kinetics, generally parameterized as a deposition coefficient αD, control ice crystal habit and also may limit growth rates in certain cases, but significant discrepancies between experimental measurements have not been satisfactorily explained. Experiments on single ice crystals have previously indicated the deposition coefficient is a function of temperature and supersaturation, consistent with growth mechanisms controlled by the crystal's surface characteristics. Here we use observations from cloud chamber experiments in the Aerosol Interactions and Dynamics in the Atmosphere (AIDA) aerosol and cloud chamber to evaluate surface kinetic models in realistic cirrus conditions. These experiments have rapidly changing temperature, pressure, and ice supersaturation such that depositional ice growth may evolve from diffusion limited to surface kinetics limited over the course of a single experiment. In Part 1, we describe the adaptation of a Lagrangian parcel model with the Diffusion Surface Kinetics Ice Crystal Evolution (DiSKICE) model (Zhang and Harrington, 2014) to the AIDA chamber experiments. We compare the observed ice water content and saturation ratios to that derived under varying assumptions for ice surface growth mechanisms for experiments simulating ice clouds between 180 and 235 K and pressures between 150 and 300 hPa. We found that both heterogeneous and homogeneous nucleation experiments at higher temperatures (>205 K) could generally be modeled consistently with either a constant deposition coefficient or the DiSKICE model assuming growth on isometric crystals via abundant surface dislocations. Lower-temperature experiments showed more significant deviations from any depositional growth model, with different ice growth rates for heterogeneous and homogeneous nucleation experiments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Three exceptions to the Grossman-Nir bound

A bstract We show that the Grossman-Nir (GN) bound, Br( K L → $$ {\pi}^0\nu \overline{\nu} $$ π 0 ν ν ¯ ) ≤ 4 . 3 Br( K + → $$ {\pi}^{+}\nu \overline{\nu} $$ π + ν ν ¯ ), can be violated in the presence of light new physics with flavor violating couplings. We construct three sample models in which the GN bound can be violated by orders of magnitude, while satisfying all other experimental bounds. In the three models the enhanced branching ratio Br( K L → π 0 + inv) is due to K L → π 0 Φ 1, K L → π 0 Φ 1 Φ 1 , K L → $$ {\pi}^0{\psi}_1{\overline{\psi}}_1 $$ π 0 ψ 1 ψ ¯ 1 transitions, respectively, where Φ 1 ( ψ 1 ) is a light scalar (fermion) that escapes the detector. In the three models Br( K + → π + + inv) remains very close to the SM value, while Br( K L → π 0 + inv) can saturate the present KOTO bound. Besides invisible particles in the final state (which may account for dark matter) the models require additional light mediators around the GeV-scale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Detailed chemistry modeling of rotating detonations with dilute n -heptane sprays and preheated air

Utilization of liquid fuels is crucial to enabling commercialization of rotating detonation engines (RDE) in the near future. In this study, Eulerian-Lagrangian simulations are conducted for rotating detonative combustion with dilute n-heptane sprays and preheated air. Two-dimensional flattened configuration is used and a skeletal chemical mechanism with 44 species and 112 elementary reactions for n-heptane combustion is adopted. The flow structure, droplet distribution, and thermochemical parameters in the refill zone are first analyzed. It is shown that the mixture in the refill zone is heterogeneous, including evaporating droplets, vapor, and air. When the total temperature is below 950 K, the average equivalence ratio increases with the total temperature. When it is higher than 950 K, the average equivalence ratio is almost constant. Subsequently, the chemical explosive mode analysis is applied to identify the controlling reactions and dominant combustion modes in the fuel refill zone and reaction fronts. Results demonstrate that the initiation reaction (R104: n-C 7 H 16 + O 2 2-C 7 H 15 + HO 2 ) and low-temperature reaction (R107: RO 2 R'O 2 H) are dominant in the upstream and downstream of the refill zone, respectively. The intermediate species from low-temperature chemistry, R'O 2 H, is found to be important for the chemical explosive mode in the undetonated mixture. The influence of species diffusion and dispersed droplets is further analyzed. Results show that vapor autoignition facilitated by droplet evaporation occurs in the refill zone. Finally, the effects of the air total temperature on the detonation propagation speed and RDE propulsion performance are investigated. Further, it is found that the detonation propagation speed and specific impulse increase with air total temperature. The total pressure ratio first increases and then decreases as the air total temperature increases. Moreover, when the total temperature of the preheated air is above 1,300 K, the effects of low-temperature chemistry are negligible.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Effective field theory for two-body systems with shallow S -wave resonances

Resonances are of particular importance to the scattering of composite particles in quantum mechanics. We build an effective field theory for two-body scattering which includes a low-energy S-wave resonance. Our starting point is the most general Lagrangian with short-range interactions. We demonstrate that these interactions can be organized into various orders so as to generate a systematic expansion for an S matrix with two low-energy poles. The pole positions are restricted by renormalization at leading order, where the common feature is a non-positive effective range. We carry out the expansion explicitly to next-to-leading order and illustrate how it systematically accounts for the results of a toy model — a spherical well with a delta shell at its border.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

The repulsive Casimir-type forces in binary mixture of weakly interacting Bose–Einstein condensates gases

Highlights: • The equations of the state of a binary mixture weakly interacting Bose gases are established based on the Lagrangian of the system. • The formulae of the Casimir-type energy and the resulting Casimir-type force are produced from the quantum part of the grand canonical energy. • The results for the Casimir-type effect in the one-field case can be re-obtained by using the results of the two-field case. Within the framework of the quantum field theory (QFT) in the one-loop approximation, we investigate the Casimir-type effect in a mixture of two-component weakly interacting Bose-Einstein condensates (BECs) gases confined between two parallel plates at zero temperature. The Casimir-type forces in the miscible state of BECs for different boundary conditions (BCs) are discovered and compared to each other. The repulsive nature of the Casimir-type force in BECs is defined for the first time. Our calculations are finished in both grand canonical ensemble (GCE) and canonical ensemble (CE).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1993

Nonrecursive formulations of multibody dynamics and concurrent multiprocessing

Since the late 1980's, research in recursive formulations of multibody dynamics has flourished. Historically, much of this research can be traced to applications of low dimensionality in mechanism and vehicle dynamics. Indeed, there is little doubt that recursive order N methods are the method of choice for this class of systems. This approach has the advantage that a minimal number of coordinates are utilized, parallelism can be induced for certain system topologies, and the method is of order N computational cost for systems of N rigid bodies. Despite the fact that many authors have dismissed redundant coordinate formulations as being of order N(exp 3), and hence less attractive than recursive formulations, we present recent research that demonstrates that at least three distinct classes of redundant, nonrecursive multibody formulations consistently achieve order N computational cost for systems of rigid and/or flexible bodies. These formulations are as follows: (1) the preconditioned range space formulation; (2) penalty methods; and (3) augmented Lagrangian methods for nonlinear multibody dynamics. The first method can be traced to its foundation in equality constrained quadratic optimization, while the last two methods have been studied extensively in the context of coercive variational boundary value problems in computational mechanics. Until recently, however, they have not been investigated in the context of multibody simulation, and present theoretical questions unique to nonlinear dynamics. All of these nonrecursive methods have additional advantages with respect to recursive order N methods: (1) the formalisms retain the highly desirable order N computational cost; (2) the techniques are amenable to concurrent simulation strategies; (3) the approaches do not depend upon system topology to induce concurrency; and (4) the methods can be derived to balance the computational load automatically on concurrent multiprocessors. In addition to the presentation of the fundamental formulations, this paper presents new theoretical results regarding the rate of convergence of order N constraint stabilization schemes associated with the newly introduced class of methods.

Kurdila, Andrew J.↗