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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment—simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles—using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e., a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and the shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood cells.

Biophysics↗
DOE OSTI2016

Scalable Metropolis Monte Carlo for simulation of hard shapes

We design and implement a scalable hard particle Monte Carlo simulation toolkit (HPMC), and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs and many GPUs using domain decomposition. We employ BVH trees instead of cell lists on the CPU for fast performance, especially with large particle size disparity, and optimize inner loops with SIMD vector intrinsics on the CPU. Our GPU kernel proposes many trial moves in parallel on a checkerboard and uses a block-level queue to redistribute work among threads and avoid divergence. HPMC supports a wide variety of shape classes, including spheres/disks, unions of spheres, convex polygons, convex spheropolygons, concave polygons, ellipsoids/ellipses, convex polyhedra, convex spheropolyhedra, spheres cut by planes, and concave polyhedra. NVT and NPT ensembles can be run in 2D or 3D triclinic boxes. Additional integration schemes permit Frenkel–Ladd free energy computations and implicit depletant simulations. In a benchmark system of a fluid of 4096 pentagons, HPMC performs 10 million sweeps in 10 min on 96 CPU cores on XSEDE Comet. The same simulation would take 7.6 h in serial. HPMC also scales to large system sizes, and the same benchmark with 16.8 million particles runs in 1.4 h on 2048 GPUs on OLCF Titan.

Computer Science↗
DOE OSTI2017

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to farming, forest management and climate change. X-ray computed tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and our own code was used to noninvasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure at 31µm resolution, and extract quantitative information (root volume and surface area) from the 3D data, respectively. Based on the mesh generated from the root structure, computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soil hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. The flow variability and soil water distributions under different scenarios were investigated. Parameterizations were evaluated to show their impacts on the average conductivity. The pore-scale modeling approach provides realistic simulations of rhizosphere flow processes and provides useful information that can be linked to upscaled models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Simulated aging processes of black carbon and its impact during a severe winter haze event in the Beijing-Tianjin- Hebei region

Black carbon (BC) can mitigate or worsen air pollution through perturbing meteorological conditions. BC aging processes are important for the evolution of particle size, concentration, and optical properties of BC that determines its influence on the meteorology. Here we use the online coupled Weather Research and Forecasting-Chemistry (WRF-Chem) model to quantify the role of BC aging processes, including physical processes (PP) and absorption enhancements (AE), in exerting BC-induced meteorological changes and the associated feedback to PM2.5 (particulate matter less than 2.5 µm in diameter) and O3 concentrations during a severe haze event in Beijing-Tianjin-Hebei (BTH) region during 21-27 February 2014. Our results show that, compared to the simulation without the PP treatment, the simulated near-surface BC concentration and BC mass loading in BTH region is lowered by 6.6 % and 12.1 %, respectively, during the haze event with the PP included. PP increases the proportion of large-size BC (particle diameter greater than 0.312 µm) from 28 %-33 % to 59 %-64 % below 1000 m in BTH region. Both PP and AE enhance the “dome effect” of BC. With both PP and AE considered, a reduction in PBL height due to BC-PBL interaction is 116.3 m (20.7 %), compared to 75.7 m (13.5 %) without AE and 66.6 m (11.9 %) without both PP and AE. However, during this haze event, anomalous northeasterly winds are produced by the direct radiative effect of BC, which further affects the mixing and transport of aerosols. When PBL height is decreased (from 10:00 to 21:00), combining all the impacts on multiple meteorological factors, BC effect without PP and AE, without AE, and with PP and AE, respectively, increases surface concentrations of PM2.5 by 8.3 µg m-3 (6.1 % relative to the mean value), 6.1 µg m-3 (4.5 %) and 9.6 µg m-3 (7.0 %) but decreases surface O3 concentrations by 2.8 ppbv (7.4 %), 4.0 ppbv (9.0 %) and 5.0 ppbv (10.8 %) in BTH region averaged over 21-27 February 2014. Our results highlight the importance of the aging processes and absorption enhancements of BC in simulating weather and air quality.

Chen, Donglin↗
DOE OSTI2023

Probing Accuracy-Speedup Tradeoff in Machine Learning Surrogates for Molecular Dynamics Simulations

The performance promise of machine learning surrogates of molecular dynamics simulations of soft materials is significant but generally comes at the cost of acquiring large training datasets to learn the complex relationships between input soft material attributes and output properties. Under the constraint of limited high-performance computing resources, optimizing the size of the training datasets becomes paramount. Using an artificial neural network based surrogate for molecular dynamics simulations of confined electrolytes, we explore the tradeoff between surrogate accuracy and computational gains. Accuracy is assessed by computing the root-mean-square errors between the surrogate predictions and the ground truth results obtained via molecular dynamics simulations. The computational performance is judged by evaluating the speedup which incorporates the training dataset creation time. Improvement in accuracy occurs with a loss of speedup, which scales as the inverse of the training dataset size. Furthermore, the link between surrogate generalizability and the accuracy-speedup tradeoff is assessed by examining the errors incurred in surrogate predictions on unseen, interpolated input variables and developing a net speedup metric to capture the associated gains.

Anions↗
DOE OSTI2019

Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems

We introduce a new heterogeneous CPU+GPU-enhanced DFTB approach for the routine and efficient simulation of large chemical and biological systems. Here, compared to homogenous computing with conventional CPUs, heterogeneous computing approaches exhibit substantial performance with only a modest increase in power consumption, both of which are essential to upcoming exascale computing initiatives. We show that DFTB-based molecular dynamics is a natural candidate for heterogeneous computing since the computational bottleneck in these simulations is the diagonalization of the Hamiltonian matrix, which is performed several times during a single molecular dynamics trajectory. To thoroughly test and understand the performance of our heterogeneous CPU+GPU approach, we examine a variety of algorithmic implementations, benchmarks of different hardware configurations, and applications of this methodology on several large chemical and biological systems. Finally, to demonstrate the capability of our implementation, we conclude with a large-scale DFTB MD simulation of explicitly solvated HIV protease (3,974 atoms total) as a proof-of-concept example of an extremely large/complex system which, to the best of our knowledge, is the first time that an entire explicitly-solvated protein has been treated at a quantum-based MD level of detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Quantum Simulations of Vibrational Strong Coupling via Path Integrals

A quantum simulation of vibrational strong coupling (VSC) in the collective regime via thermostated ring-polymer molecular dynamics (TRPMD) is reported. For a collection of liquid-phase water molecules resonantly coupled to a single lossless cavity mode, the simulation shows that as compared with a fully classical calculation, the inclusion of nuclear and photonic quantum effects does not lead to a change in the Rabi splitting but does broaden polaritonic line widths roughly by a factor of 2. Moreover, under thermal equilibrium, both quantum and classical simulations predict that the static dielectric constant of liquid water is largely unchanged inside vs outside the cavity. Furthermore, this result disagrees with a recent experiment demonstrating that the static dielectric constant of liquid water can be resonantly enhanced under VSC, suggesting either limitations of our approach or perhaps other experimental factors that have not yet been explored.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Interfacial Reactivity and Speciation Emerging from Na-Montmorillonite Interactions with Water and Formic Acid at 200 °C: Insights from Reactive Molecular Dynamics Simulations, Infrared Spectroscopy, and X-ray Scattering Measurements

Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. Further, we also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Evaluation of Clouds in Version 1 of E3SM Atmosphere Model with Satellite and Simulators

This study systematically evaluates clouds simulated by the Energy Exascale Earth System Model (E3SM) Atmosphere Model version one (EAMv1) against satellite and ground-based cloud observations. Both low (1°) and high (0.25°) resolution EAMv1 configurations generally underestimate clouds in low and midlatitutes and overestimate clouds in the Arctic although the error is smaller in the high-resolution model. The underestimate of clouds is due to the underestimate of optically thin to intermediate clouds. EAMv1 overestimates the optically intermediate to thick clouds. Other model errors include the largely under-predicted stratocumulus along the coasts and high clouds over the tropical deep convection regions. The underestimate of thin clouds results in too much LW radiation being emitted to space and too little SW radiation being reflected back to space while the overestimate of optically intermediate and thick clouds leads to too little LW radiation being emitted to space and too much SW radiation being reflected back to space. EAMv1 shows better skill in reproducing the observed distribution of clouds and their properties and has smaller radiatively relevant errors in the distribution of clouds than most of the CFMIP2 models. It produces more supercooled liquid cloud fraction than CAM5 and most CMIP5 models owing to a new ice nucleation scheme and a reduction of ice deposition growth rate. It simulates the diurnal variation of clouds during the summer season at SGP qualitatively well, with both the evolution of shallow clouds and the nocturnal peak in high clouds well captured, however, it largely overestimates the observed magnitude.

Zhang, Yuying↗