Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
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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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Cluster dynamics simulation of uranium self-diffusion during irradiation in UO 2
While fission fragments pass through UO 2 nuclear fuel, a considerable concentration of Frenkel pair defects (i.e. vacancies and interstitials) are created. The steady-state concentration of these defects leads to enhanced uranium self-diffusion, one of several fundamental kinetic parameters that control key engineering properties such as creep and fission gas swelling in UO 2 nuclear fuel. A cluster dynamics method to track point defects and defect clusters has been implemented in the MARMOT phase-field code in order to predict as-measured out-of-pile and irradiation enhanced thermal diffusivity. Here, the calculated uranium self-diffusion coefficient compares well with non-irradiated fuel measurements, and shows similar trends to those observed in irradiated fuel, which is a good result given the complexities introduced by non-stoichiometric compositions.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Application of a distributed network in computational fluid dynamic simulations
A general-purpose 3-D, incompressible Navier-Stokes algorithm is implemented on a network of concurrently operating workstations using parallel virtual machine (PVM) and compared with its performance on a CRAY Y-MP and on an Intel iPSC/860. The problem is relatively computationally intensive, and has a communication structure based primarily on nearest-neighbor communication, making it ideally suited to message passing. Such problems are frequently encountered in computational fluid dynamics (CDF), and their solution is increasingly in demand. The communication structure is explicitly coded in the implementation to fully exploit the regularity in message passing in order to produce a near-optimal solution. Results are presented for various grid sizes using up to eight processors.
Deshpande, Manish↗
Ionic Transport in Electrostatic Janus Membranes. An Explicit Solvent Molecular Dynamic Simulation
Not Available
36 MATERIALS SCIENCE↗
Molecular dynamics simulation of methane transport in confined organic nanopores with high relative roughness
Understanding and characterizing the transport of shale gas (methane) through the nanopores of kerogens are critical for the accurate prediction of shale gas recovery. However, the key factors that regulate shale gas transport through highly roughened nanopores of shale kerogens are not fully understood. Here in this work, methane transport in organic nanopores with a high relative roughness is characterized using equilibrium and non-equilibrium molecular dynamics methods. According to our results, the CH 4 mass flux has a linear relationship with the pressure gradient, consistent with previous studies, while the calculated slip lengths and gas fluxes varied with different roughness geometries in the order of sigmoidal ≥ triangular > rectangular. Surface slip flow can be a major contributor to the overall gas flux, but surprisingly, the relative contribution of surface slip flow is independent of the pressure gradient. In contrast, the contributions of both slip flow and the average gas fluxes vary strongly with pore diameters. Typical contributions of the adsorbed layer to the overall gas flux are in the range 20–40% but vary from as high as 74% in a 4-nm pore to as low as 6% in a 16-nm pore. Compared to smooth nanopores, we find that, in nanopores with realistically high degrees of relative roughness, methane confinement in cavities decouples slip flow from the flow in the pore interior, significantly reducing the overall flux.
03 NATURAL GAS↗
Evaluation of δ-Phase ZrH1.4 to ZrH1.7 Thermal Neutron Scattering Laws Using Ab Initio Molecular Dynamics Simulations
Zirconium hydride is commonly used for next-generation reactor designs due to its excellent hydrogen retention capacity at temperatures below 1000 K. These types of reactors operate at thermal neutron energies and require accurate representation of thermal scattering laws (TSLs) to optimize moderator performance and evaluate the safety indicators for reactor design. In this work, we present an atomic-scale representation of sub-stoichiometric ZrH2−x(0.3≤x≤0.6), which relies on ab initio molecular dynamics (AIMD) in tandem with velocity auto-correlation (VAC) analysis to generate phonon density of states (DOS) for TSL development. The novel NJOY+NCrystal tool, developed by the European Spallation Source community, was utilized to generate the TSL formulations in the A Compact ENDF (ACE) format for its utility in neutron transport software. First, stoichiometric zirconium hydride cross sections were benchmarked with experiments. Then sub-stoichiometric zirconium hydride TSLs were developed. Significant deviations were observed between the new δ-phase ZrH2−x TSLs and the TSLs in the current ENDF release. It was also observed that varying the hydrogen vacancy defect concentration and sites did not cause as significant a change in the TSLs (e.g., ZrH1.4 vs. ZrH1.7) as was caused by the lattice transformation from ϵ- to δ-phase.
42 ENGINEERING↗
Expansion techniques for collisionless stellar dynamical simulations
We present graphics processing unit (GPU) implementations of two fast force calculation methods based on series expansions of the Poisson equation. One method is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other method is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a 'pure' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took ∼0.1 s (depending on expansion cutoff), making simulations with as many as 10{sup 8} particles fast for a comparatively small number of nodes.
79 ASTRONOMY AND ASTROPHYSICS↗
Computational Fluid Dynamic Simulation for Electrolyte Flow in Horizontal EP of Nb SRF Elliptical Cavities
An electrolyte flow velocity on an electropolishingsurface affects a material removal rate where higherremoval is observed with a higher velocity of theelectrolyte. In horizontal EP (HEP) of an ellipticalcavity, an electrolyte flow near the equator positionmight remain slow and responsible for a lowerremoval compared to that on the iris and beam pipepositions. In order to understand the flow dynamicon an elliptical cavity surface in the horizontal EPprocess, a computational fluid dynamic simulationwas conducted. This study was conducted on 1.3GHz cavity with different cathodes and acid flowrates. Final aim of the study is to improve the flowuniformity to attain uniform removal especially inmulticell cavities.
Chouhan, V.↗
Incorporating Oxygen Uncoupling Kinetics into Computational Fluid Dynamic Simulations of a Chemical Looping System
Chemical looping with oxygen uncoupling (CLOU) is a carbon-capture technology that utilizes a metal oxide as an oxygen carrier to separate oxygen from air and releases gaseous O 2 into a reactor where fuel is fed. Earlier experimental and simulated work has been performed on systems less than 1 MW. Previous work has been limited to one-dimensional kinetic simulations. Literature kinetics were modified to work in a Barracuda-VR simulation package. A simplified spreadsheet model was used to verify the Barracuda-VR simulation adaption of the kinetics to previously published results. The simulated kinetics, literature models, and raw data matched well. The adapted kinetics were then incorporated into a 10 kW dual bubbling bed CLOU system three-dimensional simulation. The simulations predicted carbon capture efficiency similar to that reported previously for similar systems. The solid circulation rate, temperature profile, and gas concentration profiles followed the expected trends. The overall three-dimensional simulation of kinetics showed reasonable results for what has been previously reported.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A comparative study of the effectiveness of empirical potentials for molecular dynamics simulations of borosilicate glasses
Despite their practical importance, atomistic modeling of B 2 O 3 containing glasses have been challenging due to the lack of reliable empirical potentials. Fortunately, a few recent developments have shown promises to simulate these glasses where the boron coordination has complex and non-linear dependence on glass composition. This work aims to provide an evaluation of the effectiveness of three recently developed potentials by a systematic study of a series (~20) of sodium borosilicate glasses with constant K (ratio of [SiO 2 ]/[B 2 O 3 ]) =2 and varying R (ratio of [Na 2 O]/[B 2 O 3 ] ranging from 0.1 to 4) values and several sodium boroaluminosilicate glasses. A comparative assessment was established on the basis of the short- and medium-range structure features, such as boron N 4 values, total correlation functions, bond angle distribution, oxygen speciation, and mechanical properties using experimental or well-established models as criteria. Furthermore, this work provides insights on the choices of empirical potentials for MD simulations of borosilicate glasses and gives directions of future potential development and refining.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Structural studies and molecular dynamics simulations suggest a processive mechanism of exolytic lytic transglycosylase from Campylobacter jejuni
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Horizons of modern molecular dynamics simulation in digitalized solid freeform fabrication with advanced materials
Our ability to shape and finish a component by combined methods of fabrication including (but not limited to) subtractive, additive and/or no theoretical mass-loss/addition during the fabrication is now popularly known as solid free form fabrication. Fabrication of a telescope mirror is a typical example where grinding and polishing processes are first applied to shape the mirror and thereafter an optical coating is usually applied to enhance its optical performance. The area of nanomanufacturing cannot grow without a deep knowledge of the fundamentals of materials and consequently, the use of computer simulations is becoming ubiquitous. This article is intended to introduce the most recent advances in the computation benefit specific to the area of solid free form fabrication as these systems are traversing through the journey of digitalisation and Industry-4.0. Specifically, this article demonstrates that the application of the latest materials modelling approaches, based on techniques such as molecular dynamics, are enabling breakthroughs in applied precision manufacturing techniques.
36 MATERIALS SCIENCE↗
Critical interpretation of CH– and OH– stretching regions for infrared spectra of methanol clusters (CH{sub 3}OH){sub n} (n = 2–5) using self-consistent-charge density functional tight-binding molecular dynamics simulations
Vibrational infrared (IR) spectra of gas-phase O–H⋅⋅⋅O methanol clusters up to pentamer are simulated using self-consistent-charge density functional tight-binding method using two distinct methodologies: standard normal mode analysis and Fourier transform of the dipole time-correlation function. The twofold simulations aim at the direct critical assignment of the C–H stretching region of the recently recorded experimental spectra [H.-L. Han, C. Camacho, H. A. Witek, and Y.-P. Lee, J. Chem. Phys. 134, 144309 (2011)]. Both approaches confirm the previous assignment (ibid.) of the C–H stretching bands based on the B3LYP/ANO1 harmonic frequencies, showing that ν{sub 3}, ν{sub 9}, and ν{sub 2} C–H stretching modes of the proton-accepting (PA) and proton-donating (PD) methanol monomers experience only small splittings upon the cluster formation. This finding is in sharp discord with the assignment based on anharmonic B3LYP/VPT2/ANO1 vibrational frequencies (ibid.), suggesting that some procedural faults, likely related to the breakdown of the perturbational vibrational treatment, led the anharmonic calculations astray. The IR spectra based on the Fourier transform of the dipole time-correlation function include new, previously unaccounted for physical factors such as non-zero temperature of the system and large amplitude motions of the clusters. The elevation of temperature results in a considerable non-homogeneous broadening of the observed IR signals, while the presence of large-amplitude motions (methyl group rotations and PA-PD flipping), somewhat surprisingly, does not introduce any new features in the spectrum.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optimal Execution of Co-analysis for Large-scale Molecular Dynamics Simulations
The analysis of scientific simulation data enables scientists to derive insights from their simulations. This analysis of the simulation output can be performed at the same execution site as the simulation using the same resources or can be done at a different site. The optimal output frequency is challenging to decide and is often chosen empirically. We propose a mathematical formulation for choosing the optimal frequency of data transfer for analysis and the feasibility of performing the analysis, under the given resource constraints such as network bandwidth, disk space, available memory, and computation time. We propose formulations for two cases of co-analysis -- local and remote. We consider various analyses features such as computation time, input data and memory requirement, importance of the analysis and minimum frequency required for performing the analysis. We demonstrate the effectiveness of our approach using molecular dynamics applications on the Mira and Edison supercomputers.
analysis↗
Dynamical simulations of the Muon Campus at Fermilab
The Muon Campus at Fermilab is a system through which muons are delivered to the storage ring of the Muon g-2 Experiment (E989). It consists of a set of 1 km beamlines that transport and prepare a highly polarized muon beam out of secondaries produced downstream a target station. Realistic simulations of this beam delivery system (BDS) using COSY INFINITY, and presented here, contribute to the understanding and characterization of the muon beam production in relation to the statistical and systematic uncertainties of the E989 measurement, intended to be smaller than 0.14 parts per million to achieve the goals of the experiment. The impact of nonlinearities from fringe fields and high-order contributions on the BDS performance are presented, as well as detailed studies of the interactions between secondaries and the beamline elements apertures, particle decay channels, spin dynamics and beamline misalignments.
43 PARTICLE ACCELERATORS↗
Microgravity: Molecular Dynamics Simulations at the NCCS Probe the Behavior of Liquids in Low Gravity
The life of the very small, whether in something as complicated as a human cell or as simple as a drop of water, is of fundamental scientific interest: By knowing how a tiny amount of material reacts to changes in its environment, scientists maybe able to answer questions about how a bulk of material would react to comparable changes. NASA is in the forefront of computational research into a broad range of basic scientific questions about fluid dynamics and the nature of liquid boundary instability. For example, one important issue for the space program is how drops of water and other materials will behave in the low-gravity environment of space and how the low gravity will affect the transport and containment of these materials. Accurate prediction of this behavior is among the aims of a set of molecular dynamics experiments carried out on the NCCSs Cray supercomputers. In conventional computational studies of materials, matter is treated as continuous - a macroscopic whole without regard to its molecular parts - and the behavior patterns of the matter in various physical environments are studied using well-established differential equations and mathematical parameters based on physical properties such as compressibility density, heat capacity, and vapor pressure of the bulk material.
Source record↗
Simulating Dynamic Roots in the Energy Exascale Earth System Land Model
Abstract Roots are important contributors to plant development, functioning to provide nutrients and water for plant growth. However, roots and their functions are often simplified in Earth system models, which limit the feedback of root foraging strategy on plant productivity, and their impacts on the carbon cycle. The goal of this study is to introduce a new method to resolve the vertical structure of roots over time. The method allows plasticity of rooting depth distribution under nonuniform profiles of water and nitrogen, which influences aboveground dynamics. The dynamic root model optimizes root distribution for both water and nitrogen uptake but gives priority to plant water demands. I implement this new method in the Energy Exascale Earth System model. The resulting root distribution maintains agreement with observations in most ecosystems and marginally improves the gross primary productivity estimated by the model, compared to satellite observations. Increases in gross primary productivity are simulated in desert and boreal ecosystems. However, the model does not capture deep roots in the dry tropics, and therefore, productivity losses are observed in parts of the Amazon and the African savannah. I discuss details of the model algorithm, along with some sensitivity studies that shed light on the model behavior in water‐limited ecosystems. The study shows that additional model processes, such as climate dependent root depth, root hydraulics, root form and function, and better nitrogen uptake, should be considered to improve the root water uptake in the Energy Exascale Earth System Land Model (ELM).
54 ENVIRONMENTAL SCIENCES↗