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DOE OSTI2020

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data

The dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D fast Fourier transforms, correlation, and pair distribution functions are explored using the unsupervised linear unmixing, demonstrating the presence of static ordered and dynamic disordered phases and establishing their time dynamics. Here, the deep learning (DL)-based workflow is developed to analyze detailed particle dynamics and explore the evolution of local geometries. Finally, we use a combination of DL feature extraction and mixture modeling to define particle neighborhoods free of physics constraints, allowing for a separation of possible classes of particle behavior and identification of the associated transitions. Overall, this work establishes the workflow for the analysis of the self-organization processes in complex systems from observational data and provides insight into the fundamental mechanisms.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Autoregressive Neural Network for Simulating Open Quantum Systems via a Probabilistic Formulation

The theory of open quantum systems lays the foundation for a substantial part of modern research in quantum science and engineering. Rooted in the dimensionality of their extended Hilbert spaces, the high computational complexity of simulating open quantum systems calls for the development of strategies to approximate their dynamics. In this Letter, we present an approach for tackling open quantum system dynamics. Using an exact probabilistic formulation of quantum physics based on positive operator-valued measure, we compactly represent quantum states with autoregressive neural networks; such networks bring significant algorithmic flexibility due to efficient exact sampling and tractable density. We further introduce the concept of string states to partially restore the symmetry of the autoregressive neural network and improve the description of local correlations. Efficient algorithms have been developed to simulate the dynamics of the Liouvillian superoperator using a forward-backward trapezoid method and find the steady state via a variational formulation. Our approach is benchmarked on prototypical one-dimensional and two-dimensional systems, finding results which closely track the exact solution and achieve higher accuracy than alternative approaches based on using Markov chain Monte Carlo method to sample restricted Boltzmann machines. Our Letter provides general methods for understanding quantum dynamics in various contexts, as well as techniques for solving high-dimensional probabilistic differential equations in classical setups.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Polar state reversal in active fluids

Spontaneous emergence of correlated states such as flocks and vortices is a prime example of collective dynamics and self-organization observed in active matter. In geometrically confined systems, the formation of globally correlated polar states proceeds through the emergence of a macroscopic steadily rotating vortex, which spontaneously selects a clockwise or counterclockwise global chiral state. In this work, we reveal that a global vortex formed by colloidal rollers exhibits polar state reversal and that a subsequent formation of the collective states upon re-energizing the system is not random. We combine experiments and simulations to elucidate how a combination of hydrodynamic and electrostatic interactions leads to hidden asymmetries in the local particle positional order, reflecting the chiral state of the system. These asymmetries can be exploited to systematically command subsequent polar states of active liquids through temporal control of the activity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Isolation and phase-space energization analysis of the instabilities in collisionless shocks

We analyse the generation of kinetic instabilities and their effect on the energization of ions in non-relativistic, oblique collisionless shocks using a 3D-3V (three spatial with three velocity components) simulation by dHybridR, a hybrid particle-in-cell code. At sufficiently high Mach number, quasi-perpendicular and oblique shocks can experience rippling of the shock surface caused by kinetic instabilities arising from free energy in the ion velocity distribution due to the combination of the incoming ion beam and the population of ions reflected at the shock front. To understand the role of the ripple on particle energization, we devise a new instability isolation method to identify the unstable modes underlying the ripple and interpret the results in terms of the governing kinetic instability. We generate velocity-space signatures using the field–particle correlation technique to look at energy transfer in phase space from the isolated instability driving the shock ripple, providing a viewpoint on the different dynamics of distinct populations of ions in phase space. Together, the field–particle correlation technique and our new instability isolation method provide a unique viewpoint on the different dynamics of distinct populations of ions in phase space and allow us to completely characterize the energetics of the collisionless shock under investigation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Connecting Femtosecond Transient Absorption Microscopy with Spatially Coregistered Time Averaged Optical Imaging Modalities

Multimodal all-optical imaging involving coregistered femtosecond transient absorption microscopy (TAM), time-integrated photoluminescence (PL), and steady-state modalities such as confocal reflectance and transmission offers an appealing approach to gain a comprehensive understanding of complex electronic excited-state phenomena in spatially heterogeneous systems. A unique combination of these modalities allows us to unravel not only the competing electronic excited-state dynamical processes but also the underlying morphological information with simultaneous high temporal and spatial resolution. However, correlating the various images obtained from time-resolved and time-independent modalities is generally nontrivial and particularly challenging when the electronic dynamics under study evolve in both time and space. Here, we demonstrate a new approach for rationally correlating time-resolved microscopy with coregistered time-integrated or steady-state modalities. Specifically, our approach involves an extended global lifetime analysis of the time-resolved microscopic data set to separate distinct dynamical processes taking place on commensurate time scales, and the resulting decay-associated amplitude maps (DAAMs) were applied to explore correlations with the images acquired using time-independent modalities. The feasibility of our approach was validated through analyzing a multimodal data set acquired from a thin film of chloride-containing mixed lead halide perovskites (CH 3 NH 3 PbI 3–x Cl x ) using femtosecond transient absorption, time-integrated PL, and confocal reflectance microscopies. Analysis of the results obtained enable us to gain new insight into the complex ultrafast relaxation dynamics in this highly heterogeneous system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Ultrafast Electron Correlations and Memory Effects at Work: Femtosecond Demagnetization in Ni

Experimental observations of the ultrafast (less than 50 fs) demagnetization of Ni have so far defied theoretical explanations particularly since its spin-flipping time is much less than that resulting from spin-orbit and electron-lattice interactions. Through the application of an approach that benefits from spin-flip time-dependent density-functional theory and dynamical mean-field theory, we show that proper inclusion of electron correlations and memory (time dependence of electron-electron interaction) effects leads to demagnetization at the femtosecond scale, in good agreement with experimental observations. Furthermore, our calculations reveal that this ultrafast demagnetization results mainly from spin-flip transitions from occupied to unoccupied orbitals implying a dynamical reduction of exchange splitting. In this work, these conclusions are found to be valid for a wide range of laser pulse amplitudes. They also pave the way for ab initio investigations of ultrafast charge and spin dynamics in a variety of quantum materials in which electron correlations may play a definitive role.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

The nature of dynamic local order in CH 3 NH 3 PbI 3 and CH 3 NH 3 PbBr 3

Hybrid organic-inorganic lead-halide perovskites (LHPs) are a class of semiconductors with remarkable properties relevant to optoelectronic applications. The structure-property-function relationship in LHPs, however, is poorly understood, leading to incomplete descriptions of optoelectronic properties and a persistent problem of device degradation due to ion migration. Here, we reveal the true structure to contain an assembly of dynamic, two-dimensional short-range structural correlations in the lead-halide octahedral sublattice, with additional correlations between organic molecules. Here, we propose that these correlations are the origin of large-amplitude halide displacements, which govern charge carrier mobility and the sharpness of the absorption edge. Correlations between organic molecules may introduce regions of transient ferroelectricity or antiferroelectricity, which increase charge carrier lifetime. Finally, the correlations introduce an ion diffusion barrier that is static on the timescale of diffusive jumps.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Scalable learning of potentials to predict time-dependent Hartree–Fock dynamics

We propose a framework to learn the time-dependent Hartree–Fock (TDHF) inter-electronic potential of a molecule from its electron density dynamics. Although the entire TDHF Hamiltonian, including the inter-electronic potential, can be computed from first principles, we use this problem as a testbed to develop strategies that can be applied to learn a priori unknown terms that arise in other methods/approaches to quantum dynamics, e.g., emerging problems such as learning exchange–correlation potentials for time-dependent density functional theory. We develop, train, and test three models of the TDHF inter-electronic potential, each parameterized by a four-index tensor of size up to 60 × 60 × 60 × 60. Two of the models preserve Hermitian symmetry, while one model preserves an eight-fold permutation symmetry that implies Hermitian symmetry. Across seven different molecular systems, we find that accounting for the deeper eight-fold symmetry leads to the best-performing model across three metrics: training efficiency, test set predictive power, and direct comparison of true and learned inter-electronic potentials. All three models, when trained on ensembles of field-free trajectories, generate accurate electron dynamics predictions even in a field-on regime that lies outside the training set. To enable our models to scale to large molecular systems, we derive expressions for Jacobian-vector products that enable iterative, matrix-free training.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1994

An investigation of angular stiffness and damping coefficients of an axial spline coupling in high-speed rotating machinery

This paper provided an opportunity to quantify the angular stiffness and equivalent viscous damping coefficients of an axial spline coupling used in high-speed turbomachinery. A unique test methodology and data reduction procedures were developed. The bending moments and angular deflections transmitted across an axial spline coupling were measured while a nonrotating shaft was excited by an external shaker. A rotor dynamics computer program was used to simulate the test conditions and to correlate the angular stiffness and damping coefficients. In addition, sensitivity analyses were performed to show that the accuracy of the dynamic coefficients do not rely on the accuracy of the data reduction procedures.

Ku, C.-P. Roger↗

NASA NTRS1988

A study of helicopter stability and control including blade dynamics

A linearized model of rotorcraft dynamics has been developed through the use of symbolic automatic equation generating techniques. The dynamic model has been formulated in a unique way such that it can be used to analyze a variety of rotor/body coupling problems including a rotor mounted on a flexible shaft with a number of modes as well as free-flight stability and control characteristics. Direct comparison of the time response to longitudinal, lateral and directional control inputs at various trim conditions shows that the linear model yields good to very good correlation with flight test. In particular it is shown that a dynamic inflow model is essential to obtain good time response correlation, especially for the hover trim condition. It also is shown that the main rotor wake interaction with the tail rotor and fixed tail surfaces is a significant contributor to the response at translational flight trim conditions. A relatively simple model for the downwash and sidewash at the tail surfaces based on flat vortex wake theory is shown to produce good agreement. Then, the influence of rotor flap and lag dynamics on automatic control systems feedback gain limitations is investigated with the model. It is shown that the blade dynamics, especially lagging dynamics, can severly limit the useable values of the feedback gain for simple feedback control and that multivariable optimal control theory is a powerful tool to design high gain augmentation control system. The frequency-shaped optimal control design can offer much better flight dynamic characteristics and a stable margin for the feedback system without need to model the lagging dynamics.

Zhao, Xin↗

DOE OSTI2023

Correlation-temperature phase diagram of prototypical infinite layer rare earth nickelates

The discovery of superconductivity in hole-doped infinite layer nickelates, RNiO 2 (R = Nd, Pr, La) has resulted in sustained interest in the field. A definitive picture of low-energy many-body states has not yet emerged. Here we provide insights into the low-energy physics, based on our embedded dynamical mean-field theory calculations, and propose a correlation (U)-temperature (T) phase diagram. The key features are a low-T Fermi liquid (FL) phase, a high-T Curie-Weiss regime, and an antiferromagnetic phase in a narrow U-T region. We associate the onset of the FL phase with partial screening of Ni-d moments; however, full screening occurs at lower temperatures. This may be related to insufficiency of conduction electrons to effectively screen the Ni-d moments, suggestive of Nozieres Exhaustion Principle. Our results suggest that RNiO 2 are in the paramagnetic state, close to an antiferromagnetic dome, making magnetic fluctuations feasible. This may be consequential for superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Sequence-defined Pareto frontier of a copolymer structure

The correlations between the sequence of monomers in a macromolecule and its three-dimensional (3D) structure is a grand challenge in polymer science. The properties and functions of macromolecules depend on their 3D shape that has appeared to be dictated by their monomer sequence. However, the progress towards understanding the sequence–structure-property correlations and their utilization in materials engineering are slow because it is almost impossible to characterize an astronomically large number of possible sequences of a copolymer using traditional experimental and simulation methods. To address this problem, here, we combine evolutionary computing and coarse-grained molecular dynamics (CGMD) simulation and study the sequence-structure correlations of a model AB-type copolymer in a solution and assess the impact of sequence on the packing density in its bulk phase. The CGMD-based evolutionary algorithm (EA) screens the sequence space of a single chain copolymer efficiently and identifies a wide range of single-molecule structures including extremal radii of gyration. The data are utilized to estimate the Pareto front of the structure-space of a binary copolymer as a function of its composition. The monomer packings in single-molecule solution phase and multimolecular bulk phase are found to be identical. Finally, this work highlights the opportunities of sequence-specific control of macromolecular structure for designing target materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled–coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled–coil hydrogel design. Using Rosetta energy scores and Poisson–Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled–coil proteins while simultaneously exploring five new coiled–coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled–coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled–coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled–coil fiber formation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Vortical interactions in turbulent thermoacoustic systems

This study examines the dynamics of vortical interactions and their implications for mitigating thermoacoustic instability in a turbulent combustor. The regions of intense vortical interactions are identified as vortical communities in the network space of weighted directed vortical networks constructed from two-dimensional experimental velocity data. One can expect vortical interactions in the combustor to be strongest near the moment of vortex shedding, as the shed vortices gradually weaken due to dissipation while convecting downstream. However, we show that, during the state of thermoacoustic instability, there is a non-trivial consistent phase lag of approximately 52° between the shedding of the coherent structures from the backward-facing step and the time instant when the vortical interactions attain their local maximum value. We explain this phase lag by investigating the correlation between acoustic pressure fluctuations, spatio-temporal dynamics of coherent structures and vortical interactions in the reaction field of the combustor. We also show the aperiodic variation of vortical interactions during the states of combustion noise and aperiodic epochs of intermittency. Furthermore, the spatio-temporal evolution of pairs of vortical communities with the maximum inter-community interactions provides insight into explaining the critical regions detected in the reaction field during the states of intermittency and thermoacoustic instability, also identified in previous studies. As a result, we further show that the most efficient suppression of thermoacoustic instability via air microjet injection is achieved when steady air jets are introduced to disrupt the maximum inter-community interactions present during the state of thermoacoustic instability.

Sahay, Ankit [Indian Institute of Technology Madra↗

NASA NTRS1990

A chaotic attractor in timing noise from the Vela pulsar?

Fourteen years of timing residual data from the Vela pulsar have been analyzed in order to determine if a chaotic dynamical process is the origin of timing noise. Using the correlation sum technique, a dimension of about 1.5 is obtained. This low dimension indicates underlying structure in the phase residuals which may be evidence for a chaotic attractor. It is therefore possible that nonlinear dynamics intrinsic to the spin-down may be the cause of the timing noise in the Vela pulsar. However, it has been found that the stimulated random walks in frequency and frequency derivative often used to model pulsar timing noise also have low fractal dimension, using the same analysis technique. Recent work suggesting that random processes with steep power spectra can mimic strange attractors seems to be confirmed in the case of these random walks. It appears that the correlation sum estimator for dimension is unable to distinguish between chaotic and random processes.

Harding, Alice K.↗

NASA NTRS2019

A 10,000-solar-mass black hole in the nucleus of a bulgeless dwarf galaxy

The motions of gas and stars in the nuclei of nearby galaxies have demonstrated that massive black holes are common1 and that their masses correlate with the stellar velocity dispersion σ⁎ of the bulge. This correlation suggests that massive black holes and galaxies influence each other’s growth. Dynamical measurements are less reliable when the sphere of influence is unresolved; thus, it remains unknown whether this correlation exists in galaxies much smaller than the Milky Way. Light echoes from photoionized clouds around accreting black holes, in combination with the velocity of these clouds, yield a direct mass measurement that circumvents this difficulty. Here we report an exceptionally low reverberation delay of 83 ± 14 min between variability in the accretion disk and Hα emission from the nucleus of the dwarf galaxy NGC 4395. Combined with the Hα velocity dispersion σline = 426 ± 1 km/s, this lag determines a mass of about 10,000 M⊙ for the black hole (M(BH)). This mass is among the smallest central black hole masses reported, near the low end of expected masses for heavy ‘seeds’, and the best direct mass measurement for a galaxy of this size. Despite the lack of a bulge, NGC 4395 is consistent with the M(BH–σ⁎) relation, indicating that the relation need not originate from hierarchical galaxy assembly nor from black hole feedback.

Jong-Hak Woo↗

DOE OSTI2021

Laser-Induced Cooperative Transition in Molecular Electronic Crystal

The competing and non-equilibrium phase transitions, involving dynamic tunability of cooperative electronic and magnetic states in strongly correlated materials, show great promise in quantum sensing and information technology. To date, the stabilization of transient states is still in the preliminary stage, particularly with respect to molecular electronic solids. Here, a dynamic and cooperative phase in potassium-7,7,8,8-tetracyanoquinodimethane (K-TCNQ) with the control of pulsed electromagnetic excitation is demonstrated. Simultaneous dynamic and coherent lattice perturbation with 8 ns pulsed laser (532 nm, 15 MW cm -2 , 10 Hz) in such a molecular electronic crystal initiates a stable long-lived (over 400 days) conducting paramagnetic state (≈42 Ωcm), showing the charge–spin bistability over a broad temperature range from 2 to 360 K. Comprehensive noise spectroscopy, in situ high-pressure measurements, electron spin resonance (ESR), theoretical model, and scanning tunneling microscopy/spectroscopy (STM/STS) studies provide further evidence that such a transition is cooperative, requiring a dedicated charge–spin–lattice decoupling to activate and subsequently stabilize nonequilibrium phase. Finally, the cooperativity triggered by ultrahigh-strain-rate (above 10 6 s -1 ) pulsed excitation offers a collective control toward the generation and stabilization of strongly correlated electronic and magnetic orders in molecular electronic solids and offers unique electro-magnetic phases with technological promises.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Topological order and entanglement dynamics in the measurement-only XZZX quantum code

We examine the dynamics of a ( 1 + 1 ) -dimensional measurement-only circuit defined by the stabilizers of the [[5,1,3]] quantum error correcting code interrupted by single-qubit Pauli measurements. The code corrects arbitrary single-qubit errors and it stabilizes an area law entangled state with a D 2 = Z 2 × Z 2 symmetry protected topological (SPT) order, as well as a symmetry breaking (SB) order from a twofold bulk degeneracy. The Pauli measurements break the topological order and induce a phase transition into a trivial area law phase. Allowing more than one type of Pauli measurement increases the measurement-induced frustration and the SPT and SB order can be broken either simultaneously or separately at nonzero measurement rate. This yields a rich phase diagram and unanticipated critical behavior at the phase transitions. Although the correlation length exponent ν = 4 3 and the dynamical critical exponent z = 1 are consistent with bond percolation, the prefactor of the logarithmic entanglement growth may take noninteger multiples of the percolation value. Remarkably, we identify a robust transient scaling regime for the purification dynamics of L qubits. It reveals a modified dynamical critical exponent z * ≠ z , which is observable up to times t ~ L z * and is reminiscent of the relaxation of critical systems into a prethermal state.

36 MATERIALS SCIENCE↗