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At least 1,765 records · Page 98
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Constraint methods that accelerate free-energy simulations of biomolecules

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Mean flows and blob velocities in scrape-off layer (SOLT) simulations of an L-mode discharge on Alcator C-Mod

Two-dimensional scrape-off layer turbulence (SOLT) code simulations are compared with an L-mode discharge on the Alcator C-Mod tokamak [M. Greenwald, et al., Phys. Plasmas 21, 110501 (2014)]. Density and temperature profiles for the simulations were obtained by smoothly fitting Thomson scattering and mirror Langmuir probe (MLP) data from the shot. Simulations differing in turbulence intensity were obtained by varying a dissipation parameter. Mean flow profiles and density fluctuation amplitudes are consistent with those measured by MLP in the experiment and with a Fourier space diagnostic designed to measure poloidal phase velocity. Blob velocities in the simulations were determined from the correlation function for density fluctuations, as in the analysis of gas-puff-imaging (GPI) blobs in the experiment. In the simulations, it was found that larger blobs moved poloidally with the ExB flow velocity, v E , in the near-SOL, while smaller fluctuations moved with the group velocity of the dominant linear (interchange) mode, v E + 1/2 v di , where v di is the ion diamagnetic drift velocity. Comparisons are made with the measured GPI correlation velocity for the discharge. The saturation mechanisms operative in the simulation of the discharge are also discussed. In conclusion, it is found that neither sheared flow nor pressure gradient modification can be excluded as saturation mechanisms.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2 × 2 × 2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquidlike motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intraprotein) and between different protein molecules (interprotein). The interprotein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intraprotein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally, the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall, our findings increase our understanding of the connection between molecular motions and diffraction data and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparison of edge turbulence characteristics between DIII-D and C-Mod simulations with XGC1

The physical processes taking place at the separatrix and scrape-off layer regions are crucial for the operation of tokamaks as they govern the interaction of hot plasma with the vessel walls. Numerical modeling of the edge with state-of-the-art codes attempts to elucidate the complex interactions between neoclassical drifts, turbulence, poloidal and parallel flows that control the physical set-up of the SOL region. Here, we present post-processing analysis of simulation results from the gyrokinetic code XGC1, comparing and contrasting edge turbulence characteristics from a simulation of the DIII-D tokamak against a simulation of the Alcator C-Mod tokamak. We find that the equilibrium ExB flux across the separatrix has a similar poloidal pattern in both discharges which can be explained by rB-drifts and trapped ion excursions. Furthermore, collisionality is noted to play a major role in the way that it prevents local charge accumulations from having more global effects in the C-Mod case. In both cases, turbulent electron heat flux is observed to be higher than the ion one and is possibly related to the need of electrons to maintain quasineutrality through the only channel available to them for exiting the confinement. By Fourier analysis, we identify turbulent frequencies and growth rates of the dominant mode in both simulations. In the case of C-Mod, these numbers point to the presence of a drift wave. In the DIII-D case, further linear simulations with the Gene code reveal a trapped electron mode. Furthermore, using a blob detection and tracking tool, we present the amplitude and size distributions of the blobs from both simulations. The amplitude distributions are in qualitative agreement with experimental observations while the size distributions are consistent with the fact that most of the blobs are not connecting to the divertor plates and suggest that they are generated by the shearing of the turbulent modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Gyrokinetic simulations of momentum flux parasitic to free-energy transfer

Ion Landau damping interacts with a portion of the E × B drift to cause a nondiffusive outward flux of co-current toroidal angular momentum. Quantitative evaluation of this momentum flux requires nonlinear simulations to determine f L , the fraction of fluctuation free energy that passes through ion Landau damping, in fully developed turbulence. Nonlinear gyrokinetic simulations with the GKW code confirm the presence of the systematic symmetry-breaking momentum flux. For simulations with adiabatic electrons, f L scales inversely with the ion temperature gradient, because only the ion curvature drift can transfer free energy to the electrostatic potential. Although kinetic electrons should, in principle, relax this restriction, the ion Landau damping measured in collisionless kinetic-electron simulations remained at low levels comparable with ion-curvature-drift transfer, except when magnetic shear $\hat{s}$ was strong. A set of simulations scanning the electron pitch-angle scattering rate showed only a weak variation of f L with the electron collisionality. Still, collisional-electron simulations with electron temperature greater than ion temperature unambiguously showed electron-curvature-drift transfer supporting ion Landau damping, leading to a corresponding enhancement of the symmetry-breaking momentum flux.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Effect of neutral interactions on parallel transport and blob dynamics in gyrokinetic scrape-off layer simulations

The effect of neutral interactions on scrape-off layer (SOL) turbulence is investigated in a continuum gyrokinetic code that has been coupled to a continuum kinetic model of neutral transport. This extends the work of a previous paper, which compared two NSTX SOL simulations in simple helical geometry, one with neutrals and one without. The former included electron-impact ionization, charge exchange, and wall recycling. Here, the case with neutrals is compared to a gyrokinetic-only simulation that includes an effective ionization source to separate the effect of sourcing from charge exchange collisions. It is observed that sourcing accounts for many features of the simulated SOL with neutrals, including density and temperature magnitudes and reduced normalized density fluctuations, but differences persist. In particular, a flatter density profile results due to changes in parallel transport when neutral collisions are included, illustrating the importance of neutral drag on global plasma properties. An analysis of coherent turbulent structures, or blobs, in these simulations demonstrates the case with neutrals has slower and larger blobs. Here, a series of seeded blob simulations corroborates the blob velocity observation. In general, the blob motion does not contribute significantly to radial transport in these simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Nonplanar effects in simulations of laser-driven ejecta microjet experiments

Recent experiments of laser-driven ejecta microjets performed at OMEGA 60 reveal tortuous jets whereby the jets appear to deviate from their initial trajectory as they travel in vacuum. To understand these data, we perform two dimensional numerical simulations, considering different target thicknesses, pressures, and models of the drive conditions. In particular, modeling the finite laser spot size appears essential in reproducing qualitatively the non-planar shock observed in the experiment. Simulations capture jet deflection by accounting for a slight misalignment of the laser pointing with respect to the groove axis along with spatial variation of the laser pulse intensity. The principal physical mechanism appears to be that lateral momentum is imparted by release waves arising from the non-planar drive. The induced off-axis velocity is small in comparison to the jet axial velocity but integrates into a pronounced deflection over the course of the experiment. The analysis of jet axial and lateral mass distributions is found to be reproduced reasonably by the simulations. Simulated radiographs are in qualitative agreement with the experiments, though their differences point to potential shortcomings in modeling strictly three-dimensional experiments using two-dimensional hydrodynamic simulations. The simple analysis is able to explain part of the observed discrepancy in simulated vs experimental jet masses.

42 ENGINEERING↗
DOE OSTI2024

Verification of electromagnetic simulation capabilities in global gyrokinetic particle-in-cell code GTS

Recently, the numerical scheme presented by Mishchenko et al. enabled explicit gyrokinetic simulations of low-frequency electromagnetic instabilities in tokamaks at experimentally relevant values of plasma β⁠. This scheme resolved the long-standing cancellation problem that previously hindered gyrokinetic particle-in-cell code simulations of magnetohydrodynamic phenomena with inherently small parallel electric fields. Moreover, the scheme did not employ approximations that eliminate critical tearing-type instabilities. Here, we report on the implementation of this numerical scheme in the global gyrokinetic particle-in-cell code GTS. This implementation allows for a more complete and accurate picture of interaction between small scale turbulence and MHD modes in tokamaks. Additionally, we present a comprehensive set of verification simulations of numerous electromagnetic instabilities relevant to present-day tokamaks. These simulations encompass the kinetic ballooning mode, the internal kink mode, the tearing mode, the micro-tearing mode, and the toroidal Alfven eigenmode destabilized by energetic ions, which are all instrumental in understanding tokamak physics. We will also showcase the preliminary nonlinear simulations of kinetic ballooning instabilities and (2,1) island formation due to tearing mode instability. These simulations validate the accuracy of the scheme implementation and pave the way for studying how these instabilities affect plasma confinement and performance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Axisymmetric gyrokinetic simulation of ASDEX-Upgrade scrape-off layer using a conservative implicit BGK collision operator

Collisions play an important role in turbulence and transport of fusion plasmas. For kinetic simulations, as the collisionality increases in the domain of interest, the size of the time step to resolve the collisional physics can become overly restrictive in an explicit time integration scheme, leading to high computational cost. With the aim of overcoming such restriction, we have implemented an implicit Bhatnagar–Gross–Krook (BGK) collision operator for use in the discontinuous Galerkin full-f gyrokinetic solver within the Gkeyll framework, which, when combined with Gkeyll's traditional explicit time integrator for collisionless advection, can significantly increase the time step in gyrokinetic simulations of highly collisional regimes. To ensure conservation of density, momentum, and energy, we utilize an iterative scheme to correct the discretized approximation to the equilibrium Maxwellian distribution to which the BGK collision operator relaxes. We have further generalized the BGK infrastructure, both the implicit scheme and the correction routine, to handle cross-species collisions. This improved implicit and conservative BGK operator is benchmarked against the more accurate but more computationally expensive Lenard–Bernstein–Dougherty (LBD) operator, which has been utilized in prior studies with Gkeyll. The implicit BGK operator enables 2D axisymmetric simulations of the ASDEX-Upgrade scrape-off layer to run 56 times faster to completion than the simulations with the LBD operator, because the BGK operator is more robust and converges at a lower resolution than is required by the LBD operator. Additionally, in this more collisional limit, we demonstrate that the results of our simulations utilizing the implicit BGK operator agreed well with simulations utilizing the more computationally expensive LBD operator.

Gyrokinetic simulations↗
DOE OSTI2026

Accelerating kinetic plasma simulations with machine-learning-generated initial conditions

Computational models of plasma technologies often solve for the system operating conditions by time-stepping an initial value problem to a quasi-steady solution. However, the strongly nonlinear and multi-timescale nature of plasma dynamics often necessitate millions, or even hundreds of millions, of steps to reach convergence, reducing the effectiveness of these simulations for computer-aided engineering. We consider acceleration of kinetic plasma simulations via data-driven machine-learning-generated initial conditions, which initialize the simulations close to their final quasi-steady-state, thereby reducing the number of steps to reach convergence. Three machine-learning models are developed to predict the density and ion kinetic profiles of capacitively coupled plasma discharges relevant to the microelectronics industry. The models are trained on kinetic simulations over a range of device operating frequencies and pressures. Best performance was observed when simulations were initialized with ion kinetic profiles generated by a convolutional neural network, reducing the mean number of steps to reach convergence by 17.1× when compared to initialization with a zero-dimensional global model. We also outline a workflow for continuous data-driven model improvement and simulation speedup, with the aim of generating sufficient data for full device digital twins.

Artificial neural networks↗
DOE OSTI2026

MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations

We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.

chemical physics↗
DOE OSTI2018

An effective online data monitoring and saving strategy for large-scale climate simulations

Large-scale climate simulation models have been developed and widely used to generate historical data and study future climate scenarios. These simulation models often have to run for a couple of months to understand the changes in the global climate over the course of decades. This long-duration simulation process creates a huge amount of data with both high temporal and spatial resolution information; however, how to effectively monitor and record the climate changes based on these large-scale simulation results that are continuously produced in real time still remains to be resolved. Due to the slow process of writing data to disk, the current practice is to save a snapshot of the simulation results at a constant, slow rate although the data generation process runs at a very high speed. This study proposes an effective online data monitoring and saving strategy over the temporal and spatial domains with the consideration of practical storage and memory capacity constraints. Finally, our proposed method is able to intelligently select and record the most informative extreme values in the raw data generated from real-time simulations in the context of better monitoring climate changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Acceleration of the matrix multiplication of Radiance three phase daylighting simulations with parallel computing on heterogeneous hardware of personal computer

Building designers are increasingly relying on complex fenestration systems to reduce energy consumed for lighting and HVAC in low energy buildings. Radiance, a lighting simulation program, has been used to conduct daylighting simulations for complex fenestration systems. Depending on the configurations, the simulation can take hours or even days using a personal computer. This paper describes how to accelerate the matrix multiplication portion of a Radiance three-phase daylight simulation by conducting parallel computing on heterogeneous hardware of a personal computer. The algorithm was optimized and the computational part was implemented in parallel using OpenCL. The speed of new approach was evaluated using various daylighting simulation cases on a multicore central processing unit and a graphics processing unit. Based on the measurements and analysis of the time usage for the Radiance daylighting simulation, further speedups can be achieved by using fast I/O devices and storing the data in a binary format.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2013

PHYSICS OF A PARTIALLY IONIZED GAS RELEVANT TO GALAXY FORMATION SIMULATIONS-THE IONIZATION POTENTIAL ENERGY RESERVOIR

Simulation codes for galaxy formation and evolution take on board as many physical processes as possible beyond the standard gravitational and hydrodynamical physics. Most of this extra physics takes place below the resolution level of the simulations and is added in a ''sub-grid'' fashion. However, these sub-grid processes affect the macroscopic hydrodynamical properties of the gas and thus couple to the ''on-grid'' physics that is explicitly integrated during the simulation. In this paper, we focus on the link between partial ionization and the hydrodynamical equations. We show that the energy stored in ions and free electrons constitutes a potential energy term which breaks the linear dependence of the internal energy on temperature. Correctly taking into account ionization hence requires modifying both the equation of state and the energy-temperature relation. We implemented these changes in the cosmological simulation code GADGET2. As an example of the effects of these changes, we study the propagation of Sedov-Taylor shock waves through an ionizing medium. This serves as a proxy for the absorption of supernova feedback energy by the interstellar medium. Depending on the density and temperature of the surrounding gas, we find that up to 50% of the feedback energy is spent ionizing the gas rather than heating it. Thus, it can be expected that properly taking into account ionization effects in galaxy evolution simulations will drastically reduce the effects of thermal feedback. To the best of our knowledge, this potential energy term is not used in current simulations of galaxy formation and evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

A DETAILED COMPARISON BETWEEN THE OBSERVED AND SYNTHESIZED PROPERTIES OF A SIMULATED TYPE II SPICULE

We have performed a three-dimensional radiative MHD simulation of the solar atmosphere. This simulation shows a jet-like feature that shows similarities to the type II spicules observed for the first time with Hinode's Solar Optical Telescope. Rapid blueshifted events (RBEs) on the solar disk are associated with these spicules. Observational results suggest they may contribute significantly in supplying the corona with hot plasma. We perform a detailed comparison of the properties of the simulated jet with those of type II spicules (observed with Hinode) and RBEs (with ground-based instruments). We analyze a wide variety of synthetic emission and absorption lines from the simulations including chromospheric (Ca II 8542 A, Ca II H, and H{alpha}) to transition region and coronal temperatures (10,000 K to several million K). We compare their synthetic intensities, line profiles, Doppler shifts, line widths, and asymmetries with observations from Hinode/SOT and EIS, SOHO/SUMER, the Swedish 1 m Solar Telescope, and SDO/AIA. Many properties of the synthetic observables resemble the observations, and we describe in detail the physical processes that lead to these observables. Detailed analysis of the synthetic observables provides insight into how observations should be analyzed to derive information about physical variables in such a dynamic event. For example, we find that line-of-sight superposition in the optically thin atmosphere requires the combination of Doppler shifts and spectral line asymmetry to determine the velocity in the jet. In our simulated type II spicule, the lifetime of the asymmetry of the transition region lines is shorter than that of the coronal lines. Other properties differ from the observations, especially in the chromospheric lines. The mass density of the part of the spicule with a chromospheric temperature is too low to produce significant opacity in chromospheric lines. The synthetic Ca II 8542 A and H{alpha} profiles therefore do not show signal resembling RBEs. These and other discrepancies are described in detail, and we discuss which mechanisms and physical processes may need to be included in the MHD simulations to mimic the thermodynamic processes of the chromosphere and corona, in particular to reproduce type II spicules.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

THE ACCELERATION OF THERMAL PROTONS AT PARALLEL COLLISIONLESS SHOCKS: THREE-DIMENSIONAL HYBRID SIMULATIONS

We present three-dimensional hybrid simulations of collisionless shocks that propagate parallel to the background magnetic field to study the acceleration of protons that forms a high-energy tail on the distribution. We focus on the initial acceleration of thermal protons and compare it with results from one-dimensional simulations. We find that for both one- and three-dimensional simulations, particles that end up in the high-energy tail of the distribution later in the simulation gained their initial energy right at the shock. This confirms previous results but is the first to demonstrate this using fully three-dimensional fields. The result is not consistent with the ''thermal leakage'' model. We also show that the gyrocenters of protons in the three-dimensional simulation can drift away from the magnetic field lines on which they started due to the removal of ignorable coordinates that exist in one- and two-dimensional simulations. Our study clarifies the injection problem for diffusive shock acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

GIANT MOLECULAR CLOUD FORMATION IN DISK GALAXIES: CHARACTERIZING SIMULATED VERSUS OBSERVED CLOUD CATALOGS

We present the results of a study of simulated giant molecular clouds (GMCs) formed in a Milky Way-type galactic disk with a flat rotation curve. This simulation, which does not include star formation or feedback, produces clouds with masses ranging between 10{sup 4} M{sub ☉} and 10{sup 7} M{sub ☉}. We compare our simulated cloud population to two observational surveys: the Boston University-Five College Radio Astronomy Observatory Galactic Ring Survey and the BIMA All-Disk Survey of M33. An analysis of the global cloud properties as well as a comparison of Larson's scaling relations is carried out. We find that simulated cloud properties agree well with the observed cloud properties, with the closest agreement occurring between the clouds at comparable resolution in M33. Our clouds are highly filamentary—a property that derives both from their formation due to gravitational instability in the sheared galactic environment, as well as to cloud-cloud gravitational encounters. We also find that the rate at which potentially star-forming gas accumulates within dense regions—wherein n{sub thresh} ≥ 10{sup 4} cm{sup –3}—is 3% per 10 Myr, in clouds of roughly 10{sup 6} M{sub ☉}. This suggests that star formation rates in observed clouds are related to the rates at which gas can be accumulated into dense subregions within GMCs via filamentary flows. The most internally well-resolved clouds are chosen for listing in a catalog of simulated GMCs—the first of its kind. The cataloged clouds are available as an extracted data set from the global simulation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

DIRECT NUMERICAL SIMULATIONS OF REFLECTION-DRIVEN, REDUCED MAGNETOHYDRODYNAMIC TURBULENCE FROM THE SUN TO THE ALFVÉN CRITICAL POINT

We present direct numerical simulations of inhomogeneous reduced magnetohydrodynamic (RMHD) turbulence between the Sun and the Alfvén critical point. These are the first such simulations that take into account the solar-wind outflow velocity and the radial inhomogeneity of the background solar wind without approximating the nonlinear terms in the governing equations. RMHD turbulence is driven by outward-propagating Alfvén waves (z {sup +} fluctuations) launched from the Sun, which undergo partial non-WKB reflection to produce sunward-propagating Alfvén waves (z {sup –} fluctuations). We present 10 simulations with different values of the correlation time τ{sub c{sub sun}{sup +}} and perpendicular correlation length L{sub ☉} of outward-propagating Alfvén waves at the coronal base. We find that between 15% and 33% of the z {sup +} energy launched into the corona dissipates between the coronal base and Alfvén critical point. Between 33% and 40% of this input energy goes into work on the solar-wind outflow, and between 22% and 36% escapes as z {sup +} fluctuations through the simulation boundary at r = r{sub A}. The z {sup ±} power spectra scale like k{sub perpendicular}{sup -α{sup ±}}, where k is the wavenumber in the plane perpendicular to B{sub 0}. In our simulation with the smallest value of τ{sub c{sub sun}{sup +}} (∼2 minutes) and largest value of L{sub ☉} (2 × 10{sup 4} km), we find that α{sup +} decreases approximately linearly with increasing ln (r), reaching a value of 1.3 at r = 11.1 R{sub ☉}. Our simulations with larger values of τ{sub c{sub sun}{sup +}} exhibit alignment between the contours of constant φ{sup +}, φ{sup –}, Ω{sub 0}{sup +}, and Ω{sub 0}{sup -}, where φ{sup ±} are the Elsässer potentials and Ω{sub 0}{sup ±} are the outer-scale parallel Elsässer vorticities.

79 ASTRONOMY AND ASTROPHYSICS↗