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DOE OSTI2023

Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers

Lipid bilayers are supramolecular structures responsible for a range of processes, such as transmembrane transport of ions and solutes, and sorting and replication of genetic materials, to name just a few. Some of these processes are transient and currently, cannot be visualized in real space and time. Here, we developed an approach using 1D, 2D, and 3D Van Hove correlation functions to image collective headgroup dipole motions in zwitterionic phospholipid bilayers. We show that both 2D and 3D spatiotemporal images of headgroup dipoles are consistent with commonly understood dynamic features of fluids. However, analysis of the 1D Van Hove function reveals lateral transient and re-emergent collective dynamics of the headgroup dipoles—occurring at picosecond time scales—that transmit and dissipate heat at longer times, due to relaxation processes. At the same time, the headgroup dipoles also generate membrane surface undulations due a collective tilting of the headgroup dipoles. A continuous intensity band of headgroup dipole spatiotemporal correlations—at nanometer length and nanosecond time scales—indicates that dipoles undergo stretching and squeezing elastic deformations. Importantly, the above mentioned intrinsic headgroup dipole motions can be externally stimulated at GHz-frequency scale, enhancing their flexoelectric and piezoelectric capabilities (i.e., increased conversion efficiency of mechanical energy into electric energy). In conclusion, we discuss how lipid membranes can provide molecular-level insights about biological learning and memory, and as platforms for the development of the next generation of neuromorphic computers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Concurrent Changes in Extreme Hydroclimate Events in the Colorado River Basin

Extreme events resulting in catastrophic damage have more than doubled in the last five years, costing hundreds of lives and thousands of homes, and heavily undermining regional economic stability. At present, most of these hydroclimatic extreme events are documented by the media as individual events; however, in scientific terms, many are better understood as concurrent events—concurrent extremes of both temperature and precipitation (e.g., drought, floods). This paper considers concurrent changes in hydroclimate extremes, including heatwaves, drought, flooding, and low flows, in six historical-to-future (1970–1999, 2070–2099) Earth System Model (ESM) climate scenarios for the Colorado River basin. Results indicate that temperature-driven Impacts (heatwaves, drought) have the strongest responses while precipitation-driven Impacts have weaker responses. All Impacts exhibit an increase in magnitude from synoptic to annual time scales, with heatwaves increasing in strength about three times at the annual time scale versus the synoptic, while low flows only increase slightly. Critical watersheds in the Colorado were identified, highlighting the Blue River basin, Uncompahgre, East Taylor, Salt/Verde watersheds, locations of important water infrastructures, water resources, and hydrological research. Our results indicate that concurrent extreme hydroclimate events are projected to increase in the future and intensify within critical regions of the Colorado River basin. Considering extreme hydroclimate events concurrently is an important step towards linking economic and social effects of these events and their associated instabilities on a regional scale.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Learning Forecasts of Rare Stratospheric Transitions from Short Simulations

Abstract Rare events arising in nonlinear atmospheric dynamics remain hard to predict and attribute. We address the problem of forecasting rare events in a prototypical example, sudden stratospheric warmings (SSWs). Approximately once every other winter, the boreal stratospheric polar vortex rapidly breaks down, shifting midlatitude surface weather patterns for months. We focus on two key quantities of interest: the probability of an SSW occurring, and the expected lead time if it does occur, as functions of initial condition. These optimal forecasts concretely measure the event’s progress. Direct numerical simulation can estimate them in principle but is prohibitively expensive in practice: each rare event requires a long integration to observe, and the cost of each integration grows with model complexity. We describe an alternative approach using integrations that are short compared to the time scale of the warming event. We compute the probability and lead time efficiently by solving equations involving the transition operator, which encodes all information about the dynamics. We relate these optimal forecasts to a small number of interpretable physical variables, suggesting optimal measurements for forecasting. We illustrate the methodology on a prototype SSW model developed by Holton and Mass and modified by stochastic forcing. While highly idealized, this model captures the essential nonlinear dynamics of SSWs and exhibits the key forecasting challenge: the dramatic separation in time scales between a single event and the return time between successive events. Our methodology is designed to fully exploit high-dimensional data from models and observations, and has the potential to identify detailed predictors of many complex rare events in meteorology.

Finkel, Justin↗

DOE OSTI2025

Attosecond Transient Grating Spectroscopy with Near-Infrared Grating Pulses and an Extreme Ultraviolet Diffracted Probe

Transient grating spectroscopy has become a mainstay among metal and semiconductor characterization techniques. Here, we extend the technique toward the shortest achievable time scales by using tabletop high-harmonic generation of attosecond extreme ultraviolet (XUV) pulses that diffract from transient gratings generated with sub-5 fs near-infrared (NIR) pulses. We demonstrate the power of attosecond transient grating spectroscopy (ATGS) by investigating the ultrafast photoexcited dynamics in an Sb semimetal thin film. ATGS provides an element-specific, background-free signal unfettered by spectral congestion, in contrast to transient absorption spectroscopy. With ATGS measurements in Sb polycrystalline thin films, we observe the generation of coherent phonons and investigate the lattice and carrier dynamics. Among the latter processes, we extract carrier thermalization, hot carrier cooling, and electron-hole recombination, which are on the order of 20 fs, 50 fs, and 2 ps time scales, respectively. Furthermore, the simultaneous collection of transient absorption and transient grating data allows us to extract the total complex dielectric constant in the sample dynamics with a single measurement, including the real-valued refractive index, from which we are also able to investigate carrier-phonon interactions and longer-lived phonon dynamics. The outlined experimental technique expands the capabilities of transient grating spectroscopy and attosecond spectroscopies by providing a wealth of information concerning carrier and lattice dynamics with an element-selective technique at the shortest achievable time scales.

Quintero-Bermudez, Rafael↗

DOE OSTI2022

Department of Energy Project DE-SC0012198: Probing Electron-Molecule Scattering with HHG: Theory and Experiment (Final Report)

The study of the motion of atoms in molecules is important to understanding many areas of physical and life sciences. Such motion occurs on many different times scales, with electronic motion occurring on a sub-femtosecond time scale, and simple vibrational motion in tens to hundreds of femtoseconds. One way to follow such processes in real time is by the use of shortpulsed lasers, and in particular by studying time-resolved photoionization and the related process of high-harmonic generation (HHG). Thus there has been much effort to develop the tools necessary to probe molecular systems using short pulse lasers and understanding the sensitivity of the different possible probes to the time dependent geometric structure as well as the electronic structure of molecules. Our research has particularly focused on the connection between high-field processes and the more traditional weak field photoionization processes. Strong field and weak field processes can be connected through models that involve the same matrix elements. We have demonstrated in our study of HHG from SF 6 that the spectrum is sensitive to the interplay between the angular dependence of the ionization step and recombination step. In our study of rescattering spectroscopy, we have shown that with a combination of experiment and theory, we can use this high-field spectroscopy to determine molecular structure in molecules such as C 2 H 4 . We have also developed new computational tools based on overset grids to enable studies on larger molecular systems which use much more robust numerical approaches so that the resulting code can be a tool that non-specialists can use to study related systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Prediction of vacancy defect diffusion paths in high entropy alloys via machine learning on molecular dynamics data

Identifying the diffusion path of point defects is a critical step in understanding their evolution and the mechanisms of related phenomena. Defect diffusion occurs at small length and time scales, with impacts on material properties that may continue to evolve over ns to μs, ms, and the continuum scale (s, min, etc., and cm, m, etc.). The time scale accessible to molecular dynamics (MD) simulations is limited by small step sizes, typically in the fs range. Thus, surrogate models of MD simulations through machine learning (ML)-based algorithms are of great interest, especially for complex systems such as high entropy alloys (HEAs). In this work, dynamics governing vacancy migration in HEA were approximated with graph convolutional network (GCN) models as ansatzes for kinetic Monte Carlo (KMC) rate catalogs. Network design considered that diffusion in crystalline solids generally depends on interactions between defects and their immediate neighbor atoms. Graphs represented the vacancy surroundings, MD-generated trajectories provided training and comparison datasets, and unsupervised GCN models approximated interatomic dynamics governing vacancy migration in HEAs as ansatzes for KMC. A proof-of-concept model trained on MD data for the Fe, Ni, Cr, Co, and Cu HEA environment was used with two different neighbor interactions to assess the feasibility of training a GCN to predict vacancy defect transition rates in the HEA environment. The resulting setup rapidly generated MD-formatted synthetic trajectories based on dynamics learned from the MD training set, with a time acceleration of roughly two orders of magnitude and a similar diffusion coefficient to MD observations. Additionally, Nudged Elastic Band (NEB) calculations were performed on randomly generated FeNiCrCoCu HEA structures to determine vacancy migration barriers across nearest-neighbor sites. Transition probabilities for each jump, categorized by atomic type, were extracted from these calculations. NEB-based and GCN-based approaches led to similar outcomes.

Reimer, C↗

DOE OSTI2023

Mixed-state entanglement and information recovery in thermalized states and evaporating black holes

We study the universal behavior of quantum information-theoretic quantities in thermalized isolated quantum many-body systems and evaporating black holes. In particular, we study a genuine mixed-state entanglement measure called the logarithmic negativity, other correlation measures including the Renyi negativities and the mutual information, and a signature of multipartite entanglement called the reflected entropy. We also probe the feasibility of recovering quantum information from subsystems of a thermalized quantum many-body system or from the radiation of an evaporating black hole, using quantities such as relative entropy and Petz map fidelity. A recently developed technique called the equilibrium approximation allows us to probe these quantities at finite temperature. We find striking qualitative differences from the infinite temperature case, which has been the topic of previous studies using Haar-random states. In particular, we find regimes where the logarithmic negativity is extensive but the mutual information is sub-extensive, indicating a large amount of undistillable, bound entanglement in thermalized states. For evaporating black holes at finite temperature, both the logarithmic negativity and the Petz map fidelity reveal an important new time scale t b , which is earlier than the Page time t p by a finite fraction of the total evaporation time. We find that t b , as opposed to t p , is the time scale at which quantum entanglement between different parts of the radiation becomes extensive, and the fidelity of information recovery for a large diary thrown into the black hole starts to grow.

2D Gravity↗

DOE OSTI2024

Critical slowing of the spin and charge density wave order in thin film Cr following photoexcitation

We report on the evolution of the charge density wave (CDW) and spin density wave (SDW) orders of a chromium film following photoexcitation with an ultrafast optical laser pulse. The CDW is measured by ultrafast time-resolved x-ray diffraction of the CDW satellite that tracks the suppression and recovery of the CDW following photoexcitation. We find that as the temperature of the film approaches a discontinuous phase transition in the CDW and SDW orders, the time scales of recovery increase exponentially from the expected thermal time scales. We extend a Landau model for SDW systems to account for this critical slowing with the appropriate boundary conditions imposed by the geometry of the thin film system. This model allows us to assess the energy barrier between the available CDW/SDW states with different spatial periodicities.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Automatic Drift Correction through Nonlinear Sensing

For successful design and operation of advanced monitoring and control systems, engineers rely on high quality sensor signals that are simultaneously accurate, representative, voluminous, and timely. Unfortunately, sensor faults are common and lead to short-lived symptoms, such as outliers and spikes as well as long-lived symptoms, such as sensor drift. Sensor drift belongs to the category of incipient faults. These are particularly challenging to detect, diagnose, and correct as the time scales of these faults are typically longer than the time scales of the system dynamics that are of interest. Moreover, if sensor drift occurs as a result of exposure to measured medium, then it is likely that multiple sensors will exhibit similar drift rates, thus challenging fault management strategies based on redundancy. In this contribution, we present a first method that can handle this unique challenge.

Chowdhury, Dhruba↗

DOE OSTI2022

Implications of inertial subrange scaling for stably stratified mixing

In this work, we investigate the effects of the turbulent dynamic range on active scalar mixing in stably stratified turbulence by adapting the theoretical passive scalar modelling and demonstrating their usefulness through consideration of the results of direct numerical simulations of statistically stationary homogeneous stratified and sheared turbulence. By analysis of inertial and inertial–convective subrange scalings, we show that the relationship between the active scalar and turbulence time scales is predicted by the ratio of the Kolmogorov and Obukhov–Corrsin constants, provided mean flow parameters permit the two subrange scalings to be appropriate approximations. We use the resulting relationship between time scales to parameterise an appropriate turbulent mixing coefficient $\varGamma \equiv \chi /\epsilon$, defined here as the ratio of available potential energy ($E_p$) and turbulent kinetic energy ($E_k$) dissipation rates. With the analysis presented here, we show that $\varGamma$ can be estimated by $E_p,E_k$ and a universal constant provided an appropriate Reynolds number is sufficiently high. This large Reynolds number regime appears here to occur at $ {{Re_b}} \equiv \epsilon / \nu N^{2} \gtrapprox 300$ where $\nu$ is the kinematic viscosity and $N$ is the characteristic buoyancy frequency. We propose a model framework for irreversible diapycnal mixing with robust theoretical parametrisation and asymptotic behaviour in this high-$ {{Re_b}}$ limit.

42 ENGINEERING↗

DOE OSTI2022

Insights into the origin of halo mass profiles from machine learning

ABSTRACT The mass distribution of dark matter haloes is the result of the hierarchical growth of initial density perturbations through mass accretion and mergers. We use an interpretable machine-learning framework to provide physical insights into the origin of the spherically-averaged mass profile of dark matter haloes. We train a gradient-boosted-trees algorithm to predict the final mass profiles of cluster-sized haloes, and measure the importance of the different inputs provided to the algorithm. We find two primary scales in the initial conditions (ICs) that impact the final mass profile: the density at approximately the scale of the haloes’ Lagrangian patch RL ($R\sim 0.7\, R_L$) and that in the large-scale environment (R ∼ 1.7 RL). The model also identifies three primary time-scales in the halo assembly history that affect the final profile: (i) the formation time of the virialized, collapsed material inside the halo, (ii) the dynamical time, which captures the dynamically unrelaxed, infalling component of the halo over its first orbit, (iii) a third, most recent time-scale, which captures the impact on the outer profile of recent massive merger events. While the inner profile retains memory of the ICs, this information alone is insufficient to yield accurate predictions for the outer profile. As we add information about the haloes’ mass accretion history, we find a significant improvement in the predicted profiles at all radii. Our machine-learning framework provides novel insights into the role of the ICs and the mass assembly history in determining the final mass profile of cluster-sized haloes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Interplay between beam-driven chirping modes and plasma confinement transitions in spherical tokamak ST40

Experiments on the high field spherical tokamak ST40 have led to the recent observation of interplay between beam-driven modes of sweeping frequency (chirping modes) and transitions to the enhanced global confinement regime (H-mode) and back to the low confinement regime (L-mode). The H-modes of plasma confinement are identified from decreased intensity of D α signal and from clear distinctions in the edge gradients of the visible plasma boundary (observed as a sharp plasma edge in camera images). The beam-driven chirping modes, identified as ideal magnetohydrodynamics beta-induced Alfvén acoustic eigenmodes modes, are observed in Mirnov coil signals, interferometry, and soft x-ray diagnostics. A moderate amplitude ‘primer’ chirping mode usually precedes an H–L transition. This is followed by a ‘dominant’ chirping mode with higher amplitude during the L-mode. The L–H transition back to the improved confinement occurs on a longer time scale of tens of ms, consistent with the slowing down time scale of fast beam ions. A dramatic decrease in toroidal plasma rotation is systematically observed associated with chirping modes sweeping down to zero frequency. Resonance maps built for the beam-driven chirping modes with the ASCOT (accelerated simulation of charged particle orbits in torodoial devices) code show that the resonant beam ions have orbits near the trapped-passing boundary. The ASCOT modelling assesses how losses of the resonant fast ions caused by the chirping modes with high enough amplitude modify the torque, potentially affecting the plasma rotation.

magnetic confinement fusion↗

DOE OSTI2022

Temperature Dependence of Structural Relaxation in Glass-Forming Liquids and Polymers

Understanding the microscopic mechanism of the transition of glass remains one of the most challenging topics in Condensed Matter Physics. What controls the sharp slowing down of molecular motion upon approaching the glass transition temperature T g , whether there is an underlying thermodynamic transition at some finite temperature below T g , what the role of cooperativity and heterogeneity are, and many other questions continue to be topics of active discussions. This review focuses on the mechanisms that control the steepness of the temperature dependence of structural relaxation (fragility) in glass-forming liquids. We present a brief overview of the basic theoretical models and their experimental tests, analyzing their predictions for fragility and emphasizing the successes and failures of the models. Special attention is focused on the connection of fast dynamics on picosecond time scales to the behavior of structural relaxation on much longer time scales. A separate section discusses the specific case of polymeric glass-forming liquids, which usually have extremely high fragility. We emphasize the apparent difference between the glass transitions in polymers and small molecules. We also discuss the possible role of quantum effects in the glass transition of light molecules and highlight the recent discovery of the unusually low fragility of water. At the end, we formulate the major challenges and questions remaining in this field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Dynamic-Phasor Model of Transformer Inrush Simulation for Unbalanced Distribution System

Abstract— Power system stability is a critical concern, with respect to the increasing distributed energy resources, microgrids, and emphasis on enhancing resiliency. For stability analysis and evaluation, modeling and simulation capabilities are important. In this paper, the authors’ previous work on modeling transformer inrush dynamics is improved with a new formulation of the key equation that converts the dynamic-phasor into real-time value. Simulation results in an electromechanical time-scale are compared with PSCAD results in an electromagnetic time-scale to demonstrate the improvement. The impact of simulation step size is discussed. A bug in PSCAD transformer setting that leads to incorrect magnetizing flux and current under Delta winding type is identified and reported. In addition, explanations and analysis are provided on two modeling techniques utilized since the previous work. This work is being incorporated into the next release of GridLAB-D. The improved transformer inrush calculation enables more accurate predictions of current amplitudes for analyzing the dynamics of distribution operation and control.

power transformers, power system simulation, satur↗

DOE OSTI2020

Continuous and discrete modeling of HIV-1 decline on therapy

Mathematical models have shed light on the dynamics of HIV- 1 infection in vivo. In this paper, we generalize continuous mathematical models of drug therapy for HIV-1 by Perelson et al. (Science 271:1582–1586, 1996) and Perelson and Nelson (SIAM Rev 41:3–44, 1999) on time scales, i.e., a nonempty closed subset of real numbers in order to derive new discrete models that predict the total concentration of plasma virus as a function of time. Here, one of our main goals is to compare discrete mathematical models with the continuous model in Perelson et al. (1996) where HIV infected patients were given protease inhibitors and sampled frequently thereafter. For the comparison, we use experimental data collected in Perelson et al. (1996) and estimate the parameters such as the virion clearance rate and the rate of loss of infected cells by fitting the total concentration of plasma virus to this data set. Our results show that discrete systems describe the best fit. In the previous models of this study, the efficacy of protease inhibitor is assumed to be perfect. Motivated by Perelson and Nelson (1999), we end the paper with a mathematical model of imperfect protease inhibitor and reverse transcriptase (RT) inhibitor combination therapy of HIV-1 infection on time scales with its stability analysis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Recommendations on setup in simulating atmospheric gravity waves under conventionally neutral boundary layer conditions

Wind farm-induced atmospheric gravity waves have been the subject of recent research as they can impact wind farm performance. Pressure variations associated with gravity waves can contribute to the global blockage effect and wind farm wake recovery. Therefore, accurate numerical simulation of flow fields, where wind-farm-induced gravity waves may be produced, is important. Three main considerations in such simulations are the overall domain size, the use of Rayleigh damping near domain boundaries to dampen gravity waves, and advection damping at the inlet to prevent spurious oscillations. Often these considerations are treated ad hoc rather than systematically. This work aims to test and extend the systematic modelling of internal gravity waves proposed in a preliminary investigation to modelling of both internal and trapped gravity waves. The preliminary study identifies the length scales to set the domain and damping layer sizes and the time scale to configure the Rayleigh damping coefficient but under linearly stratified conditions. Large eddy simulations of flow through a wind farm canopy are performed under conventionally neutral boundary layer (CNBL) conditions to test the validity of proposed setups for CNBL conditions. Background atmospheric parameters, such as Froude number (Fr), inversion height (H i ), and inversion layer Froude number (Fr i ) control most of the atmospheric gravity wave characteristics. We validated for CBNL conditions that the effective wavelengths of the internal gravity waves are the correct length scale to configure the domain size and damping layer thickness. Likewise, the optimum damping coefficient to dampen the internal gravity waves relates to the free atmosphere's buoyancy frequency or buoyant perturbations' time scale. We infer that the damping coefficient in the inversion layer may relate to the inversion buoyancy frequency to effectively dampen the trapped gravity waves. Moreover, the advection damping length is linked to the horizontal wavelength of the trapped gravity waves in the inversion layer to prevent spurious waves at the inlet by retaining wave energy accumulation.

17 WIND ENERGY↗

DOE OSTI2022

Ultrafast Triplet Generation at the Lead Halide Perovskite/Rubrene Interface

Triplet sensitization of rubrene by bulk lead halide perovskites has recently resulted in efficient infrared-to-visible photon upconversion via triplet-triplet annihilation. Notably, this process can occur under solar relevant fluxes, potentially paving the way toward integration with photovoltaic devices. In order to further improve the upconversion efficiency, the fundamental photophysical pathways at the perovskite/rubrene interface must be clearly understood to maximize charge extraction. Here, we utilize ultrafast transient absorption spectroscopy to elucidate the processes underlying triplet generation at the perovskite/rubrene interface. In this work, our results point to a triplet generation mechanism based on hot carriers; thermally excited charge carriers in the perovskite cool more rapidly in the presence of rubrene, suggesting rapid extraction of these thermally excited carriers on the picosecond time scale. Subsequent triplet formation in rubrene is observed on a subnanosecond time scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗