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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.

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At least 91 records · Page 5

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping the Temperature-dependent and network site-specific onset of spectral diffusion at the surface of a water cluster cage

We explore the kinetic processes that sustain equilibrium in a microscopic, finite system. This is accomplished by monitoring the spontaneous, time-dependent frequency evolution (the frequency autocorrelation) of a single OH oscillator, embedded in a water cluster held in a temperature-controlled ion trap. The measurements are carried out by applying two-color, IR-IR photodissociation mass spectrometry to the D3O+?(HDO)(D2O)19 isotopologue of the “magic number” protonated water cluster, H+?(H2O)21. The OH group can occupy any one of the five spectroscopically distinct sites in the distorted pentagonal dodecahedron cage structure. The OH frequency is observed to evolve over tens of milliseconds in the temperature range (90-120 K). Starting at 100 K, large “jumps” are observed between two OH frequencies separated by ~300 cm-1 indicating migration of the OH group from the bound OH site at 3350 cm-1 to the free position at 3686 cm-1. Increasing the temperature to 110 K leads to partial interconversion among many sites. All sites are observed to interconvert at 120 K such that the distribution of the unique OH group among them adopts the form one would expect for a canonical ensemble. The spectral dynamics displayed by the clusters thus offer an unprecedented view into the molecular-level processes that drive spectral diffusion in an extended network of water molecules.

Yang, Nan↗

Coherent Phonon Dynamics in Plasmonic Gold Tetrahedral Nanoparticle Ensembles

Coherent phonon modes supported by plasmonic nanoparticles offer prospective applications in chemical and biological sensing. Whereas characterization of these phonon modes often requires single particle measurements, synthetic routes to narrow size distributions of nanoparticles permit ensemble investigations. Recently, the synthesis of highly monodisperse gold tetrahedral nanoparticles with tunable edge length and corner sharpness has been developed. Herein, we characterize a size series of these nanoparticles in colloidal dispersion via transient absorption spectroscopy to examine their mechanical and plasmonic responses upon photoexcitation. Oscillations of transient absorption signals are observed in the plasmon resonance and correspond to the lowest order radial breathing modes of the nanoparticles, the frequencies of which are affected by edge length and truncation of the corners. Furthermore, quality factor values ranging from 10 to 15 are observed for the oscillations that convey potential utility in mass-sensing and plasmon-exciton coupling photonics schemes. Finite-difference time domain and finite element analysis calculations establish the specific optically-relevant phonon modes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Realistic simulations of spin squeezing and cooperative coupling effects in large ensembles of interacting two-level systems

We describe an efficient numerical method for simulating the dynamics of interacting spin ensembles in the presence of dephasing and decay. The method builds on the discrete truncated Wigner approximation for isolated systems, which combines the mean-field dynamics of a spin ensemble with a Monte Carlo sampling of discrete initial spin values to account for quantum correlations. Here we show how this approach can be generalized for dissipative spin systems by replacing the deterministic mean-field evolution by a stochastic process, which describes the decay of coherences and populations while preserving the length of each spin. We demonstrate the application of this technique for simulating nonclassical spin-squeezing effects or the dynamics and steady states of cavity QED models with 10 5 interacting two-level systems. This opens up the possibility to perform accurate real-scale simulations of a diverse range of experiments in quantum optics or with solid-state spin ensembles under realistic laboratory conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Collective mode Brownian dynamics: A method for fast relaxation of statistical ensembles

Sampling equilibrium configurations of correlated systems of particles with long relaxation times (e.g., polymeric solutions) using conventional molecular dynamics and Monte Carlo methods can be challenging. This is especially true for systems with complicated, extended bond network topologies and other interactions that make the use and design of specialized relaxation protocols infeasible. We introduce a method based on Brownian dynamics simulations that can reduce the computational time it takes to reach equilibrium and draw decorrelated samples. Importantly, the method is completely agnostic to the particle configuration and the specifics of interparticle forces. In particular, we develop a mobility matrix that excites non-local, collective motion of N particles and can be computed efficiently in $\mathcal{O}(N)$ time. Particle motion in this scheme is computed by integrating the overdamped Langevin equation with an Euler–Maruyama scheme, in which Brownian displacements are drawn efficiently using a low-rank representation of the mobility matrix in position and wave space. We demonstrate the efficacy of the method with various examples from the realm of soft condensed matter and release a massively parallel implementation of the code as a plugin for the open-source package HOOMD-blue [J. A. Anderson et al., J. Comput. Phys. 227, 5342 (2008) and J. Glaser et al., Comput. Phys. Commun. 192, 97 (2015)] which runs on graphics processing units

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ensembles of Metastable States Govern Heterogeneous Catalysis on Dynamic Interfaces

Heterogeneous catalysis is at the heart of chemical industry. Being able to tune and design efficient catalysts for processes of interest is of an utmost importance, and for this, the molecular-level understanding of heterogeneous catalysts is the first step, and indeed a prime focus of the modern catalysis research. For a long time, a single most thermodynamically stable structure of the catalytic interface attained in reaction conditions had been envisioned as the reactive phase. However, some catalytic interfaces continue to undergo structural dynamics in the steady state, triggered by high temperatures, pressures, and binding and changing reagents. Among particularly dynamic interfaces are such widely-used catalysts as crystalline and amorphous surfaced supporting (sub-)nano metallic clusters. Recently, it became clear that this dynamic fluxionality causes the supported clusters to populate many distinct structural and stoichiometric states in catalytic conditions. Hence, the catalytic interface should be viewed as an evolving statistical ensemble of many (not one) structures. As such, every member in the ensemble contributes to the properties of the catalyst differently, and in proportion to its probability to be populated. This new notion flips the established paradigm and calls for new theory, modeling approaches, operando measurements, and updated design strategies. The statistical ensemble nature of surface-supported sub-nano cluster catalysts can be exemplified by oxide-supported and adsorbate-covered Pt, Pd, Cu, CuPd clusters, catalytic toward oxidative and non-oxidative dehydrogenation. They have access to a variety of 3D and quasi-2D shapes. The compositions of their thermal ensembles are dependent on the cluster size, leading to size-specific catalytic activities and the famous “every atom counts” phenomenon. The support and adsorbates affect catalyst structures, and state of the reacting species causes the ensemble to change in every reaction intermediate. The most stable member of the ensemble dominates the thermodynamic properties of the corresponding intermediate, whereas the kinetics can be determined by more active but less populated metastable catalyst states, and that suggests that many earlier studies might have overlooked the actual active sites. Both effects depend on the relative time-scales of catalyst restructuring and reaction dynamics. The catalyst may routinely operate off-equilibrium. Ensemble phenomena lead to surprising exceptions from established rules of catalysis, such as scaling relations, and Arrhenius behavior. Catalyst deactivation is also an ensemble property, and its extent of mitigation can be predicted through the new paradigm. These findings were enabled by advances in theory, such as global optimization and subsequent utilization of multiple local minima, and pathways sampling, as well as operando catalyst characterization. The fact that the per-site and per-species resolution is needed for the description and predicting of catalyst properties gives theory the central role in catalysis research, as most experiments provide ensemble-average information and cannot detect the crucial minority species that may be responsible for the catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theoretical quasar emission-line profiles. I - Curve-of-growth effects on observed profiles

Radiative transfer effects are examined in an investigation of the kinematics of quasar and Seyfert emission-line regions with pancake cloud geometries. Consideration is given only to the effects of limb brightening with the aspect angle of pancake clouds, assuming that all lines lie on a single portion of the curve of growth. This effect is coupled with several simple but plausible ensemble geometries and dynamics, and a number of theoretical emission-line profiles have been generated. It is shown that these profiles differ substantially depending on both the ensemble geometry and the portion of the curve of growth considered; for a given ensemble geometry, optically thick line profiles are different from optically thick profiles. It is shown that, for radiatively driven clouds, ensembles of clouds which have maximum velocities approaching the terminal velocity of the acceleration mechanism never produce acceptable profiles unless the cloud luminosity is a strongly decreasing function of radius.

Hubbard, E. N.↗

Probabilistic measures for biological adaptation and resilience

This paper introduces an approach to quantifying ecological resilience in biological systems, particularly focusing on noisy systems responding to episodic disturbances with sudden adaptations. Incorporating concepts from nonequilibrium statistical mechanics, we propose a measure termed “ecological resilience through adaptation,” specifically tailored to noisy, forced systems that undergo physiological adaptation in the face of stressful environmental changes. Randomness plays a key role, accounting for model uncertainty and the inherent variability in the dynamical response among components of biological systems. Our measure of resilience is rooted in the probabilistic description of states within these systems and is defined in terms of the dynamics of the ensemble average of a model-specific observable quantifying success or well-being. Our approach utilizes stochastic linear response theory to compute how the expected success of a system, originally in statistical equilibrium, dynamically changes in response to a environmental perturbation and a subsequent adaptation. Importantly, the resulting mathematical derivations allow for the estimation of resilience in terms of ensemble averages of simulated or experimental data. Finally, through a simple but clear conceptual example, we illustrate how our resilience measure can be interpreted and compared to other existing frameworks in the literature. The methodology is general but inspired by applications in plant systems, with the potential for broader application to complex biological processes.

60 APPLIED LIFE SCIENCES↗

Laser velocimetry measurements of oscillating airfoil dynamic stall flow field

Ensemble-averaged two-component velocity measurements over an airfoil experiencing oscillatory dynamic stall under compressibility conditions were obtained. The measurements show the formation of a separation bubble over the airfoil that persists till angles of attack close to when the dynamic stall vortex forms and convects. The fluid attains mean velocities as large as 1.6 times the free stream velocity with instantaneous values of 1.8 times the free stream velocity. The airfoil motion induces these large velocities in regions that are far removed from the surface.

Chandrasekhara, M. S.↗

Performance assessment of ensembles of in situ workflows under resource constraints

Summary Scientific breakthroughs in biomolecular methods and improvements in hardware technology have shifted from a long‐running simulation to a large set of shorter simulations running simultaneously, called an ensemble. In an ensemble, simulations are usually coupled with analyses of data produced by the simulations. In situ methods can be used to analyze large volumes of data generated by scientific simulations at runtime (i.e., simulations and analyses are performed concurrently). In this work, we study the execution of ensemble‐based simulations paired with in situ analyses using in‐memory staging methods. Using an ensemble of molecular dynamics in situ workflows with multiple simulations and analyses, we first show that collecting traditional metrics such as makespan, instructions per cycle, memory usage, or cache miss ratio is not sufficient to characterize complex behaviors of ensembles. We propose a method to evaluate the performance of ensembles of workflows that captures multiple resource usage aspects: resource efficiency, resource allocation, and resource provisioning. Experimental results demonstrate that the proposed method can effectively distinguish the performance of different component placements in an ensemble with up to 32 ensemble members. By evaluating different co‐location scenarios, our proposed performance indicators demonstrate benefits of co‐locating simulation and coupled analyses within a compute node.

Do, Tu Mai Anh↗

Dynamic Amplification of Subtropical Extreme Precipitation in a Warming Climate

Projected precipitation changes in a warming climate vary considerably, spatially, and between intensities. The changes can be greater or less than the ~7% K -1 Clausius-Clapeyron (CC) prediction, owing to dynamic effects. Using two global-climate-model large ensembles, we quantify the dynamically induced changes to precipitation extremes from the present (1996–2005) to late-21st-century (2071–2080) climates, as a function of recurrence interval, focusing on the subtropics. We separate non-CC changes into a term proportional to the present-day vertical-velocity spatial pattern (i.e., an amplification or damping thereof by a constant factor) and a residual. The amplitude term varies with recurrence interval, approximately canceling (doubling) CC for moderate (large) extremes, increasing precipitation variability. Contrastingly, the residual is quasi-uniform across recurrence intervals but spatially heterogeneous, weakening extremes over dry zones. This residual may be related to Hadley cell expansion, although this explanation is insufficient to explain many features, and other possible mechanisms are discussed.

54 ENVIRONMENTAL SCIENCES↗

Measurement-induced multipartite-entanglement regimes in collective spin systems

We study the competing effects of collective generalized measurements and interaction-induced scrambling in the dynamics of an ensemble of spin-1/2 particles at the level of quantum trajectories. This setup can be considered as analogous to the one leading to measurement-induced transitions in quantum circuits. We show that the interplay between collective unitary dynamics and measurements leads to three regimes of the average Quantum Fisher Information (QFI), which is a witness of multipartite entanglement, as a function of the monitoring strength. While both weak and strong measurements lead to extensive QFI density (i.e., individual quantum trajectories yield states displaying Heisenberg scaling), an intermediate regime of classical-like states emerges for all system sizes where the measurement effectively competes with the scrambling dynamics and precludes the development of quantum correlations, leading to sub-Heisenberg-limited states. We characterize these regimes and the crossovers between them using numerical and analytical tools, and discuss the connections between our findings, entanglement phases in monitored many-body systems, and the quantum-to-classical transition.

Physics↗

Simulating molecular polaritons in the collective regime using few-molecule models

The study of molecular polaritons beyond simple quantum emitter ensemble models (e.g., Tavis–Cummings) is challenging due to the large dimensionality of these systems and the complex interplay of molecular electronic and nuclear degrees of freedom. This complexity constrains existing models to either coarse-grain the rich physics and chemistry of the molecular degrees of freedom or artificially limit the description to a small number of molecules. In this work, we exploit permutational symmetries to drastically reduce the computational cost of ab initio quantum dynamics simulations for large N . Furthermore, we discover an emergent hierarchy of timescales present in these systems, that justifies the use of an effective single molecule to approximately capture the dynamics of the entire ensemble, an approximation that becomes exact as N → ∞. We also systematically derive finite N corrections to the dynamics and show that addition of k extra effective molecules is enough to account for phenomena whose rates scale as 𝒪( N − k ). Based on this result, we discuss how to seamlessly modify existing single-molecule strong coupling models to describe the dynamics of the corresponding ensemble. We call this approach collective dynamics using truncated equations (CUT-E), benchmark it against well-known results of polariton relaxation rates, and apply it to describe a universal cavity-assisted energy funneling mechanism between different molecular species. Beyond being a computationally efficient tool, this formalism provides an intuitive picture for understanding the role of bright and dark states in chemical reactivity, necessary to generate robust strategies for polariton chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectral broadening and ultrafast dynamics of a nitrogen-vacancy center ensemble in diamond

Abstract Many applications of nitrogen-vacancy (NV) centers in diamond crucially rely on a spectrally narrow and stable optical zero-phonon line transition. Though many impressive proof-of-principle experiments have been demonstrated, much work remains in engineering NV centers with spectral properties that are sufficiently robust for practical implementation. To elucidate the mechanisms underlying their interactions with the environment, we apply multi-dimensional coherent spectroscopy to an NV center ensemble in bulk diamond at cryogenic temperatures. Our spectra reveal thermal dephasing due to quasi-localized vibrational modes as well as ultrafast spectral diffusion on the picosecond timescale. The intrinsic, ensemble-averaged homogeneous linewidth is found to be in the tens of GHz range by extrapolating to zero temperature. We also observe a temperature-dependent Stark splitting of the excited state manifold, relevant to NV sensing protocols.

Liu, Albert (ORCID:0000000167183719)↗

Modeling Disturbance Dynamics in Transitional and Turbulent Boundary Layers

The dynamics of an ensemble of linear disturbances in boundary-layer flows at various Reynolds numbers is studied through an analysis of the transport equations for the mean disturbance kinetic energy and energy dissipation rate. Effects of adverse and favorable pressure-gradients on the disturbance dynamics are also included in the analysis. Unlike the fully turbulent regime where nonlinear phase scrambling of the fluctuations affects the flow field even in proximity to the wall, the early stage transition regime fluctuations studied here are influenced across the boundary layer by the solid boundary. In addition, the dominating dynamics in the disturbance kinetic energy equation is governed by the energy production, pressure-transport and viscous diffusion - also in contrast to the fully turbulent regime. For the disturbance dissipation rate, a dynamic balance exists between the destruction and diffusion of dissipation.

Grosch, C. E.↗

Analysis of Transition-Sensitized Turbulent Transport Equations

The dynamics of an ensemble of linear disturbances in boundary-layer flows at various Reynolds numbers is studied through an analysis of the transport equations for the mean disturbance kinetic energy and energy dissipation rate. Effects of adverse and favorable pressure-gradients on the disturbance dynamics are also included in the analysis Unlike the fully turbulent regime where nonlinear phase scrambling of the fluctuations affects the flow field even in proximity to the wall, the early stage transition regime fluctuations studied here are influenced cross the boundary layer by the solid boundary. The dominating dynamics in the disturbance kinetic energy and dissipation rate equations are described. These results are then used to formulate transition-sensitized turbulent transport equations, which are solved in a two-step process and applied to zero-pressure-gradient flow over a flat plate. Computed results are in good agreement with experimental data.

Rumsey, Christopher L.↗