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At least 505 records · Page 28

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

59 BASIC BIOLOGICAL SCIENCES↗

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

60 APPLIED LIFE SCIENCES↗

ORNL_AISD_NiPt

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for three different sizes of the crystal structure: 256 atoms, 864 atoms, and 2,048 atoms, each of which contains 1900 configurations. For each size of the crystal structure, the data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in three compressed zipped folders: atoms256.zip, atoms864.zip, atoms2048.zip Each zipped folder contains the data that describes crystals of size 256 atoms, 864 atoms, and 2,048 atoms respectively. Each one of the three zipped folders contains the data structured in the following way: -Ni_ground_state.cfg --> atomic configuration for the pure nickel -Pt_ground_state.cfg --> atomic configuration for the pure platinum -Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder. Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms256.zip is 65,046. The total number of atomic configurations contained in atoms864.zip is 63,936. The total number of atomic configurations contained in atoms2048.zip is 61,997. The total number of atomic configurations spanned by the entire dataset is 190,979. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büccchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D

36 MATERIALS SCIENCE↗

ORNL_AISD_NiPt_108atoms

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for crystal structures with 108 atoms with 1,900 configurations. The data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system 'MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001' [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in a compressed zipped folders atoms108.zip. The zipped folder contains the data structured in the following way: - Ni_ground_state.cfg --> atomic configuration for the pure nickel - Pt_ground_state.cfg --> atomic configuration for the pure platinum - Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder - Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms108.zip is 66,132. This dataset is an extension to the dataset ORNL_AISD_NiPt [5] that has been previously released with crystal structures of 256 atoms, 864 atoms, and 2,048 atoms, with the same methodology for data collection. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D [5] M. Karabin, M. Lupo Pasini, and M. Eisenbach. ORNL_AISD_NiPt. United States: N. p., 2023. Web. doi:10.13139/OLCF/1958172.

36 MATERIALS SCIENCE↗

libEnsemble: A complete Python toolkit for dynamic ensembles of calculations

Almost all science and engineering applications eventually stop scaling: their runtime no longer decreases as available computational resources increase. Therefore, many applications will struggle to efficiently use emerging extreme-scale high-performance, parallel, and distributed systems. libEnsemble is a complete Python toolkit and workflow system for intelligently driving ensembles of experiments or simulations at massive scales. It enables and encourages multidisciplinary design, decision, and inference studies portably running on laptops, clusters, and supercomputers.

97 MATHEMATICS AND COMPUTING↗

Exascale Algorithms and Software for Lattice Field Theory in High Energy Physics: Searching Beyond the Standard Model

The Boston University component has focused on the algorithmic development of new Multigrid solver for the critical kernel for the Dirac propagators that dominated the both simulation require for lattice ensemble and the analysis of physical correlation functions. Progress on this has meet the above objects, even exceeding them a bit. The result is the beginning if multiscale lattice QCD applicable to future Exascale hardware and the development of the QUDA software for NVIDIA GPUs to give near optimal performance. As we approach exascale hardware and computation at that scale this provides the infrastructure for further advances.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nucleon valence quark distribution functions from Lattice QCD

We present results on the nucleon valence quark distribution extracted from Lattice QCD simulations, using a gauge ensemble of Nf=2+1 Wilson-Clover fermions with a pion mass of m?=350 MeV and lattice spacing of a=0.091 fm. We obtain reduced Ioffe Time Distributions (rITDs) by computing appropriate matrix elements on the lattice, and elaborate on the extraction of the desired quark distributions from the rITDs following the pseudo-PDF approach. A set of techniques are considered in order to ensure ground state dominance. Theoretical and experimental implications of our calculation are discussed.

Kallidonis, Christos↗

An overview of the Western United States Dynamically Downscaled Dataset (WUS-D3)

Abstract. Predicting future climate change over a region of complex terrain, such as the western United States (US), remains challenging due to the low resolution of global climate models (GCMs). Yet the climate extremes of recent years in this region, such as floods, wildfires, and drought, are likely to intensify further as climate warms, underscoring the need for high-quality and high-resolution predictions. Here, we present an ensemble of dynamically downscaled simulations over the western US from 1980–2100 at 9 km grid spacing, driven by 16 latest-generation GCMs. This dataset is titled the Western US Dynamically Downscaled Dataset (WUS-D3). We describe the challenges of producing WUS-D3, including GCM selection and technical issues, and we evaluate the simulations' realism by comparing historical results to temperature and precipitation observations. The future downscaled climate change signals are shaped in physically credible ways by the regional model's more realistic coastlines and topography. (1) The mean warming signals are heavily influenced by more realistic snowpack. (2) Mean precipitation changes are often consistent with wetting on the windward side of mountain complexes, as warmer, moister air masses are uplifted orographically during precipitation events. (3) There are large fractional precipitation increases on the lee side of mountain complexes, leading to potentially significant changes in water resources and ecology in these arid landscapes. (4) Increases in precipitation extremes are generally larger than in the GCMs, driven by locally intensified atmospheric updrafts tied to sharper, more realistic gradients in topography. (5) Changes in temperature extremes are different from what is expected by a shift in mean temperature and are shaped by local atmospheric dynamics and land surface feedbacks. Because of its high resolution, comprehensiveness, and representation of relevant physical processes, this dataset presents a unique opportunity to evaluate societally relevant future changes in western US climate.

Rahimi, Stefan (ORCID:0000000331884462)↗

Solar wind three; Proceedings of the Third Conference, Pacific Grove, Calif., March 25-29, 1974

Papers are presented relating to the study of solar abundances, the evolution of the solar wind, solar corona dynamics, solar wind interactions, and stellar winds. Some of the topics covered include the nuclear composition of cosmic rays, the solar wind as deduced from lunar samples, spectral characteristics of flares, numerical simulation of interplanetary shock ensembles, radial gradient of solar wind velocity from 1 to 5 AU, the enhancement of solar wind fluctuations with scale size near the proton gyroradius, solar wind-Venus interaction observed from magnetic field experiment on Mariner 10, and binary stellar winds. Individual items are announced in this issue.

Russell, C. T.↗

Semiprognostic tests of the Arakawa-Schubert cumulus parameterization using simulated data

Semiprognostic tests are performed against data simulated by a cumulus ensemble model to evaluate the Arakawa-Schubert (A-S) cumulus parametrization. It is found that the A-S cumulus parametrization is generally valid despite the existence of mesoscale organization in cumulus convection. The nondiagnostic and nondeterministic aspects of the A-S cumulus parametrization are examined by testing the sensitivity of the parametrization to the horizontal grid resolution. It is also shown that the inclusion of convective-scale downdrafts improves the results of semiprognostic tests.

Xu, Kuan-Man↗

Comparison of numerically-simulated microphysical characteristics of convective storms with multiparameter radar observations during COHMEX

The microphysical/dynamical nature and evolution of numerically simulated convective storms observed on July 11, 1986 during the Cooperative Huntsville Meteorological Experiments are investigated with the Goddard Cumulus Ensemble model. The model-simulated hydrometeor and radar reflectivity structure is verified with results derived from the multiparameter radar observations, which includes a description of the reflectivity, differential reflectivity, linear depolarization ratio, and hail signal for two thunderstorm cases analyzed by Fulton and Heymsfield (1990). Radar analysis shows the storm to split with the newer more vigorous cell in the SE quadrant. Echo tops are near 15 km while peak reflectivities exceed 50 dBZ. Preliminary model simulations likewise show a splitting storm with regeneration occurring on the SSE flank. Echo tops are around 14 km with peak reflectivities over 45 dBZ.

Tao, W.-K.↗

A Numerical Study of Tropical Sea-Air Interactions Using a Cloud Resolving Model Coupled with an Ocean Mixed-Layer Model

Coupling a cloud resolving model (CRM) with an ocean mixed layer (OML) model can provide a powerful tool for better understanding impacts of atmospheric precipitation on sea surface temperature (SST) and salinity. The objective of this study is twofold. First, by using the three dimensional (3-D) CRM-simulated (the Goddard Cumulus Ensemble model, GCE) diabatic source terms, radiation (longwave and shortwave), surface fluxes (sensible and latent heat, and wind stress), and precipitation as input for the OML model, the respective impact of individual component on upper ocean heat and salt budgets are investigated. Secondly, a two-way air-sea interaction between tropical atmospheric climates (involving atmospheric radiative-convective processes) and upper ocean boundary layer is also examined using a coupled two dimensional (2-D) GCE and OML model. Results presented here, however, only involve the first aspect. Complete results will be presented at the conference.

Shie, Chung-Lin↗

On the Causes of the 1930s Dust Bowl

During the 1930s the United States experienced one of the most devastating droughts of the last century. The drought affected almost 2/3 of the country and parts of Mexico and Canada and was infamous for the numerous dust storms that lead to the characterization of much of the Great Plains as the "Dust Bowl". Results from an ensemble of 100-year simulations with the NASA Seasonal- to-Interannual Prediction Project (NSIPP-1) atmospheric general circulation model (AGCM) forced with observed SSTs show that the model reproduces the basic features of the 1930s drought. In t h s study we exploit this realism in the model simulation to examine in more detail the role of the SST and soil moisture in the development and maintenance the 1930s drought. Results will be presented from simulations in which the SST anomalies are confined to the separate ocean basins, as well as from runs in which soil moisture feedback is turn off.

Schubert, Siegfried↗

On the Causes of the 1930s Dust Bowl

During the 1930s the United States experienced one of the most devastating droughts of the last century. The drought affected almost 2/3 of the country and parts of Mexico and Canada and was infamous for the numerous dust storms that lead to the characterization of much of the Great Plains as the 'Dust Bowl'. Results from an ensemble of 100-year simulations with the NASA Seasonal-to-Interannual Prediction Project (NSIPP-1) atmospheric general circulation model (AGCM) forced with observed SSTs show that the model reproduces the basic features of the 1930s drought. In this study we exploit this realism in the model simulation to examine in more detail the role of the SST and soil moisture in the development and maintenance the 1930s drought. Results will be presented from simulations in which the SST anomalies are confined to the separate ocean basins, as well as from runs in which soil moisture feedback is turn off.

Schubert, Siegfried↗

Addition of random run FM noise to the KPW time scale algorithm

The KPW (Kalman plus weights) time scale algorithm uses a Kalman filter to provide frequency and drift information to a basic time scale equation. This paper extends the algorithm to three-state clocks nd gives results for a simulated eight-clock ensemble.

time scale clock ensemble clock noise↗

An Update on Experimental Climate Prediction and Analysis Products Being Developed at NASA's Global Modeling and Assimilation Office

The Global Modeling and Assimilation Office at NASA's Goddard Space Flight Center is developing a number of experimental prediction and analysis products suitable for research and applications. The prediction products include a large suite of subseasonal and seasonal hindcasts and forecasts (as a contribution to the US National MME), a suite of decadal (10-year) hindcasts (as a contribution to the IPCC decadal prediction project), and a series of large ensemble and high resolution simulations of selected extreme events, including the 2010 Russian and 2011 US heat waves. The analysis products include an experimental atlas of climate (in particular drought) and weather extremes. This talk will provide an update on those activities, and discuss recent efforts by WCRP to leverage off these and similar efforts at other institutions throughout the world to develop an experimental global drought early warning system.

Schubert, Siegfried↗

Using Paleo-climate Comparisons to Constrain Future Projections in CMIP5

We present a description of the theoretical framework and best practice for using the paleo-climate model component of the Coupled Model Intercomparison Project (Phase 5) (CMIP5) to constrain future projections of climate using the same models. The constraints arise from measures of skill in hindcasting paleo-climate changes from the present over 3 periods: the Last Glacial Maximum (LGM) (21 thousand years before present, ka), the mid-Holocene (MH) (6 ka) and the Last Millennium (LM) (8501850 CE). The skill measures may be used to validate robust patterns of climate change across scenarios or to distinguish between models that have differing outcomes in future scenarios. We find that the multi-model ensemble of paleo-simulations is adequate for addressing at least some of these issues. For example, selected benchmarks for the LGM and MH are correlated to the rank of future projections of precipitationtemperature or sea ice extent to indicate that models that produce the best agreement with paleoclimate information give demonstrably different future results than the rest of the models. We also find that some comparisons, for instance associated with model variability, are strongly dependent on uncertain forcing timeseries, or show time dependent behaviour, making direct inferences for the future problematic. Overall, we demonstrate that there is a strong potential for the paleo-climate simulations to help inform the future projections and urge all the modeling groups to complete this subset of the CMIP5 runs.

paleoclimate↗