Structural studies and molecular dynamics simulations suggest a processive mechanism of exolytic lytic transglycosylase from Campylobacter jejuni
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
SEARCH · Engineering Papers
Results for “dynamics simulation”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
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↗
Multimode turbulent flow measurements using magnetic resonance imaging- and laser-based techniques and computational fluid dynamics simulations
We studied the flow field characteristics of a turbulent flow over a regularized cube array with a perpendicular injection flow through the floor between the second and third cubical elements, representing the complex flow interactions of a 3D jet and the wake flows behind cubical obstacles. Four different experimental measurements were performed: two magnetic resonance imaging-based measurements for three-dimensional three-component velocity (MRV) and concentration (MRC) and two laser-based techniques, particle image velocimetry (PIV) and planar laser-induced fluorescence (PLIF), for two-dimensional two-component velocity and concentration measurement, respectively. The mainstream Reynolds number is Re = 15 000, based on the primary inlet velocity U m and channel height D H , whereas the injector Reynolds number is Re j = 3400, based on the injector velocity U j and the injector's exit width D j . Numerical simulations were performed for the studied flow configuration of turbulent flow over a regularized cube array using Reynolds-averaged Navier–Stokes (RANS) and large-eddy simulation (LES) approaches. Results obtained from experimental measurements—including MRV, MRC, PIV, and PLIF—as well as RANS and LES simulations are discussed and compared along several horizontal and vertical planes of the studied configuration. In addition, 3D turbulent flow structures, such as leading-edge vortex, horseshoe vortex, and jet shear-layer vortex, and the isosurfaces of scalar concentration successfully revealed by MRV and MRC techniques were found to be in very good agreement with those 3D features extracted from RANS and LES simulations. In conclusion, the high-resolution experimental and numerical database obtained from this study could be useful for validation and verification of numerical codes.
Computational fluid dynamics↗
Machine learning molecular dynamics simulations toward exploration of high-temperature properties of nuclear fuel materials: case study of thorium dioxide
Predicting materials properties of nuclear fuel compounds is a challenging task in materials science. Their thermodynamical behaviors around and above the operational temperature are essential for the design of nuclear reactors. However, they are not easy to measure, because the target temperature range is too high to perform various standard experiments safely and accurately. Moreover, theoretical methods such as first-principles calculations also suffer from the computational limitations in calculating thermodynamical properties due to their high calculation-costs and complicated electronic structures stemming from f-orbital occupations of valence electrons in actinide elements. Here, we demonstrate, for the first time, machine-learning molecular-dynamics to theoretically explore high-temperature thermodynamical properties of a nuclear fuel material, thorium dioxide. The target compound satisfies first-principles calculation accuracy because f-electron occupation coincidentally diminishes and the scheme meets sampling sufficiency because it works at the computational cost of classical molecular-dynamics levels. We prepare a set of training data using first-principles molecular dynamics with small number of atoms, which cannot directly evaluate thermodynamical properties but captures essential atomistic dynamics at the high temperature range. Then, we construct a machine-learning molecular-dynamics potential and carry out large-scale molecular-dynamics calculations. Consequently, we successfully access two kinds of thermodynamic phase transitions, namely the melting and the anomalous λ transition induced by large diffusions of oxygen atoms. Furthermore, we quantitatively reproduce various experimental data in the best agreement manner by selecting a density functional scheme known as SCAN. Our results suggest that the present scale-up simulation-scheme using machine-learning techniques opens up a new pathway on theoretical studies of not only nuclear fuel compounds, but also a variety of similar materials that contain both heavy and light elements, like thorium dioxide.
74 ATOMIC AND MOLECULAR PHYSICS↗
Molecular dynamics simulations of reflection and sputtering behavior of boron under deuterium ion irradiation
Boronization is a commonly used method of wall conditioning in fusion reactors. The application of boron films to the plasma-facing materials results in enhanced plasma performance due to the reduction of intrinsic impurities. This is primarily driven by a reduction in oxygen content that is chemically trapped in the boron film. The reactive nature of these boron films also raises questions concerning interactions with hydrogen isotopes. In this work, boron-deuterium interactions were studied using molecular dynamics (MD). Reactive force field potentials were used to model the chemical interactions between B and D. An amorphous boron substrate was irradiated by D atoms at varying incident energies, 10 eV < E i < 150 eV and angles, 0° < α < 85°. The reflection probability was calculated and compared to results from the commonly-used binary collision approximation (BCA) method. This comparison found that the BCA underestimated the reflection probability at E i < 35 eV and α > 45 ∘ . The source of this discrepancy was found to be the surface binding energy model. The BCA calculation with an isotropic surface binding energy model was more closely aligned to the MD result. This, in combination with a correction function based on the MD results allows for corrections to the reflection probability of deuterium impinging on boron surfaces. The sputtering of the substrate material was also studied. While this study did not contain sufficient events to quantitatively describe the sputtering behavior, some qualitative results emerged: namely, chemical sputtering of B and D-containing molecules (BD, BD 2 , BD 3 ) at low ( < 20 eV) incident deuterium energies. This result suggests that chemical sputtering could be a significant factor in limiting boron coating lifetime when exposed to lower ion energies, such as those in detached plasmas. The results show that chemical interactions should be taken into account when modeling the interactions between D ions and B surfaces.
Boron↗
Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride
Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'••• O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Here, the calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational Fluid Dynamics Simulations of Glass Vitrification Refractory Coupon Tests
The Waste Treatment and Immobilization Plant (WTP) at the Hanford site is nearing the start of the Direct-Feed Low-Activity Waste (DFLAW) operations. DFLAW is destined to convert a pretreated low activity waste portion of the 56 million gallons of tank waste into a stable solid glass. In the subsequent decade completion of the high-level waste (HLW) facility is anticipated. Sustained operational missions of both LAW and HLW melter facilities are expected over multiple decades. In high-temperature glass melters, the refractory lining corrodes over time, which could potentially be an issue for longer term operations, this refractory corrosion is higher at the level of the glass-air interface due to surface tension driven flow. The glass viscosity, melt pool temperature, and glass chemical composition can impact the rate at which the refractory corrodes. This rate is important to quantify for the various waste glasses to be produced at the WTP since the integrity of the refractory should not be a limiting factor affecting the lifetime of the melter. To this end, a series of glasses representative of the first batches of waste glass produced by the WTP will be melted in small-scale crucibles with Monofrax® K-3 coupons inserted. The corrosion of the K-3 will be measured in the melt and at the meltline (or neckline). A model for the corrosion rate will be constructed and implemented into a previously developed framework for a computational fluid dynamics (CFD) model of the full-scale WTP. To assist with experimental design and validate the implementation of the model in the full-scale melter, CFD simulations of the small-scale crucible tests were performed. The bubbling that occurs in the small-scale crucible is initially validated here with a model that uses silicone oil at room temperature. The viscosity of the oil ranges from 1 to 100 Pa•s, which corresponds to operating glass pool temperatures near 1150 °C down to idling temperatures near 950 °C. The simulation results show good agreement with the bubble sizes that form during experiments. CFD modeling of the crucible setup was used to determine bubbling characteristics to match the range of near-wall velocities expected in the full-scale WTP. This study presents the initial CFD modeling results, corrosion testing plan, and some preliminary corrosion samples with an outline for the next steps for the development of the corrosion model.
Abboud, Alexander W. [Idaho National Lab]↗
All-Atom Molecular Dynamics Simulations of the Temperature Response of Densely Grafted Polyelectrolyte Brushes
Water acts a “good” solvent for most polyelectrolyte (PE) systems due to its high dielectric strength. Theoretical and experimental studies have highlighted some remarkably unconventional properties of strongly water-swollen PE brushes such as a reduction in brush height with increase in temperature. However, an understanding of the atomistic-scale response of the grafted PE chains as well as the local arrangement and organization of the brush-supported counterions and water molecules to changes in temperature is missing. Here, we conduct an all-atom molecular dynamics (MD) study to probe the influence of temperature on the “microstructure” of densely grafted, fully ionized polyacrylic acid (PAA) brushes. The atomistic insights obtained from our study shed light on prior experimental observations and elucidate the key role played by changes in hydrogen bonding network in dictating the hydrophilicity of the brushes. In addition to the temperature-mediated reduction in height of the PE brush layer, we study the influence of temperature on several properties of the brush-supported water molecules such as the number distribution and kinetics of water-water and water-PE hydrogen bonds (HBs), mass density, orientational tetrahedral order parameter, and the activation energy associated with the self-diffusion of water. The effect of temperature on the properties of the brush-trapped counterions is also quantified via changes in their solvation structure, counterion-water radial distribution function (RDF), and the translational mobility. Our findings unravel several hitherto unknown phenomena such as the enhanced propensity for attaining PE brush-induced “water-in-salt”-like scenarios at elevated temperatures, and an increase in the activation energy for the self-diffusion of water with increase in the degree of PE brush-induced nanoconfinement (from ‘bulk water’ to ‘sparsely grafted PE brushes’ to ‘densely grafted PE brushes’). Further, we anticipate that this work will be helpful in improving our predictive capabilities of the temperature response of water-swollen PE brushes, which would be instrumental for better design of several PE brush systems used in a multitude of applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Preliminary Tests and Beam Dynamics Simulations of a Straight-Merger Beamline
Beamlines capable of merging beams with different energies are critical to many applications related to advanced accelerator concepts and energy-recovery linacs (ERLs). In an ERL, a low-energy "fresh" bright bunch is generally injected into a superconducting linac for acceleration using the fields established by a decelerated "spent" beam traveling on the same axis. A straight-merger system composed of a selecting cavity with a superimposed dipole magnet was proposed and recently test at AWA. This paper reports on the experimental results obtained so far along with detailed beam dynamics investigations of the merger concept and its ability to conserve the beam brightness associated with the fresh bunch.
Al Marzouk, A. A.↗
Structure, dynamics and stability of water/scCO 2 /mineral interfaces from ab initio molecular dynamics simulations
Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivity and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO 2 . Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca 2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO 2 ) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences (R.R.), and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle. Computational resources were provided by PNNL’s Platform for Institutional Computing (PIC), the W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantum dynamical simulation of the scattering of Ar from a frozen LiF(100) surface based on a first principles interaction potential
In-plane two and three dimensional diffraction patterns are computed for the vertical scattering of an Ar atom from a frozen LiF(100) surface. Suitable collimation of the incoming wavepacket serves to reveal the quantum mechanical diffraction. The interaction potential is based on a fit to an ab initio potential calculated using density functional theory with dispersion corrections. Due to the potential coupling found between the two horizontal surface directions, there are noticeable differences between the quantum angular distributions computed for two and three dimensional scattering. The quantum results are compared to analogous classical Wigner computations on the same surface and with the same conditions. The classical dynamics largely provides the envelope for the quantum diffractive scattering. The classical results also show that the corrugation along the [110] direction of the surface is smaller than along the [100] direction, in qualitative agreement with experimental observations of unimodal and bimodal scattering for the [110] and [100] directions, respectively.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Dynamics Simulations of the Thermal Conductivity of Single-Wall Carbon Nanotubes
Carbon nanotubes (CNT) have very attractive electronic, mechanical. and thermal properties. Recently, measurements of thermal conductivity in single wall CNT mats showed estimated thermal conductivity magnitudes ranging from 17.5 to 58 W/cm-K at room temperature. which are better than bulk graphite. The cylinderical symmetry of CNT leads to large thermal conductivity along the tube axis, additionally, unlike graphite. CNTs can be made into ropes that can be used as heat conducting pipes for nanoscale applications. The thermal conductivity of several single wall carbon nanotubes has been calculated over temperature range from l00 K to 600 K using non-equilibrium molecular dynamics using Tersoff-Brenner potential for C-C interactions. Thermal conductivity of single wall CNTs shows a peaking behavior as a function of temperature. Dependence of the peak position on the chirality and radius of the tube will be discussed and explained in this presentation.
Osman, M.↗
Computational Fluid Dynamics Simulation of Dual Bell Nozzle Film Cooling
Marshall Space Flight Center (MSFC) and Armstrong Flight Research Center (AFRC) are working together to advance the technology readiness level (TRL) of the dual bell nozzle concept. Dual bell nozzles are a form of altitude compensating nozzle that consists of two connecting bell contours. At low altitude the nozzle flows fully in the first, relatively lower area ratio, nozzle. The nozzle flow separates from the wall at the inflection point which joins the two bell contours. This relatively low expansion results in higher nozzle efficiency during the low altitude portion of the launch. As ambient pressure decreases with increasing altitude, the nozzle flow will expand to fill the relatively large area ratio second nozzle. The larger area ratio of the second bell enables higher Isp during the high altitude and vacuum portions of the launch. Despite a long history of theoretical consideration and promise towards improving rocket performance, dual bell nozzles have yet to be developed for practical use and have seen only limited testing. One barrier to use of dual bell nozzles is the lack of control over the nozzle flow transition from the first bell to the second bell during operation. A method that this team is pursuing to enhance the controllability of the nozzle flow transition is manipulation of the film coolant that is injected near the inflection between the two bell contours. Computational fluid dynamics (CFD) analysis is being run to assess the degree of control over nozzle flow transition generated via manipulation of the film injection. A cold flow dual bell nozzle, without film coolant, was tested over a range of simulated altitudes in 2004 in MSFC's nozzle test facility. Both NASA centers have performed a series of simulations of that dual bell to validate their computational models. Those CFD results are compared to the experimental results within this paper. MSFC then proceeded to add film injection to the CFD grid of the dual bell nozzle. A series of nozzle pressure ratios and film coolant flow rates are investigated to determine the effect of the film injection on the nozzle flow transition behavior. The results of this CFD study of a dual bell with film injection are presented in this paper.
Braman, Kalen↗