4,416 research outputs found
Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part II
Explicit molecular dynamics simulations were applied to a pair of amorphous
silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte.
Mean forces acting between the pair of silica nanoparticles were extracted at
four different background electrolyte concentrations. Dependence of the
inter-particle potential of mean force on the separation and the silicon to
sodium ratio, as well as on the background electrolyte concentration, are
demonstrated. The pH was indirectly accounted for via the ratio of silicon to
sodium used in the simulations. The nature of the interaction of the
counter-ions with charged silica surface sites (deprotonated silanols) was also
investigated. The effect of the sodium double layer on the water ordering was
investigated for three Si:Na+ ratios. The number of water molecules trapped
inside the nanoparticles was investigated as the Si:Na+ ratio was varied.
Differences in this number between the two nanoparticles in the simulations are
attributed to differences in the calculated electric dipole moment. The
implications of the form of the potentials for aggregation are also discussed.Comment: v1. 33 pages, 7 figures (screen-quality PDF), submitted to J. Chem.
Phys v2. 15 pages, 4 tables, 6 figures. Content, author list and title
changed; single space
A cloud platform for automating and sharing analysis of raw simulation data from high throughput polymer molecular dynamics simulations
Open material databases storing hundreds of thousands of material structures
and their corresponding properties have become the cornerstone of modern
computational materials science. Yet, the raw outputs of the simulations, such
as the trajectories from molecular dynamics simulations and charge densities
from density functional theory calculations, are generally not shared due to
their huge size. In this work, we describe a cloud-based platform to facilitate
the sharing of raw data and enable the fast post-processing in the cloud to
extract new properties defined by the user. As an initial demonstration, our
database currently includes 6286 molecular dynamics trajectories for amorphous
polymer electrolytes and 5.7 terabytes of data. We create a public analysis
library at https://github.com/TRI-AMDD/htp_md to extract multiple properties
from the raw data, using both expert designed functions and machine learning
models. The analysis is run automatically with computation in the cloud, and
results then populate a database that can be accessed publicly. Our platform
encourages users to contribute both new trajectory data and analysis functions
via public interfaces. Newly analyzed properties will be incorporated into the
database. Finally, we create a front-end user interface at
https://www.htpmd.matr.io for browsing and visualization of our data. We
envision the platform to be a new way of sharing raw data and new insights for
the computational materials science community.Comment: 21 pages, 7 figure
Simulation of Ultra-Relativistic Electrons and Positrons Channeling in Crystals with MBN Explorer
A newly developed code, implemented as a part of the \MBNExplorer package
\cite{MBN_ExplorerPaper,MBN_ExplorerSite} to simulate trajectories of an
ultra-relativistic projectile in a crystalline medium, is presented. The motion
of a projectile is treated classically by integrating the relativistic
equations of motion with account for the interaction between the projectile and
crystal atoms. The probabilistic element is introduced by a random choice of
transverse coordinates and velocities of the projectile at the crystal entrance
as well as by accounting for the random positions of the atoms due to thermal
vibrations. The simulated trajectories are used for numerical analysis of the
emitted radiation. Initial approbation and verification of the code have been
carried out by simulating the trajectories and calculating the radiation
emitted by \E=6.7 GeV and \E=855 MeV electrons and positrons in oriented
Si(110) crystal and in amorphous silicon. The calculated spectra are compared
with the experimental data and with predictions of the Bethe-Heitler theory for
the amorphous environment.Comment: 41 pages, 11 figures. Initially submitted on Dec 29, 2012 to Phys.
Rev.
Graph Dynamical Networks for Unsupervised Learning of Atomic Scale Dynamics in Materials
Understanding the dynamical processes that govern the performance of
functional materials is essential for the design of next generation materials
to tackle global energy and environmental challenges. Many of these processes
involve the dynamics of individual atoms or small molecules in condensed
phases, e.g. lithium ions in electrolytes, water molecules in membranes, molten
atoms at interfaces, etc., which are difficult to understand due to the
complexity of local environments. In this work, we develop graph dynamical
networks, an unsupervised learning approach for understanding atomic scale
dynamics in arbitrary phases and environments from molecular dynamics
simulations. We show that important dynamical information can be learned for
various multi-component amorphous material systems, which is difficult to
obtain otherwise. With the large amounts of molecular dynamics data generated
everyday in nearly every aspect of materials design, this approach provides a
broadly useful, automated tool to understand atomic scale dynamics in material
systems.Comment: 25 + 7 pages, 5 + 3 figure
Heat conductivity from energy-density fluctuations
We present a method, based on the classical Green-Kubo theory of linear
response, to compute the heat conductivity of extended systems, leveraging
energy-density, rather than energy-current, fluctuations, thus avoiding the
need to devise an analytical expression for the macroscopic energy flux. The
implementation of this method requires the evaluation of the long-wavelength
and low-frequency limits of a suitably defined correlation function, which we
perform using a combination of recently-introduced cepstral-analysis and
Bayesian extrapolation techniques. Our methodology is demonstrated against
standard current-based Green-Kubo results for liquid argon and water, and
compared with a recently proposed similar technique, which utilizes
mass-density, instead of energy-density, fluctuations.Comment: 8 pages, 5 figure
Non-additivity of pair interactions in charged colloids
It is general wisdom that the pair potential of charged colloids in a liquid
may be closely approximated by a Yukawa interaction, as predicted by the
classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. We experimentally
determine the effective forces in a binary mixture of like-charged particles,
of species 1 and 2, with blinking optical tweezers. The measured forces are
consistent with a Yukawa pair potential but the (12) cross-interaction is not
equal to the geometric mean of the (11) and (22) like-interactions, as expected
from DLVO. The deviation is a function of the electrostatic screening length
and the size ratio, with the cross-interaction measured being consistently
weaker than DLVO predictions. The corresponding non-additivity parameter is
negative and grows in magnitude with increased size asymmetry.Comment: Final versio
Explosion of Comet 17P/Holmes as revealed by the Spitzer Space Telescope
An explosion on comet 17P/Holmes occurred on 2007 Oct 23, projecting
particulate debris of a wide range of sizes into the interplanetary medium. We
observed the comet using the Spitzer spectrograph on 2007 Nov 10 and 2008 Feb
27, and the photometer, on 2008 Mar 13. The fresh ejecta have detailed
mineralogical features from small crystalline silicate grains. The 2008 Feb 27
spectra, and the central core of the 2007 Nov 10 spectral map, reveal nearly
featureless spectra, due to much larger grains that were ejected from the
nucleus more slowly. We break the infrared image into three components (size,
speed) that also explain the temporal evolution of the mm-wave flux. Optical
images were obtained on multiple dates spanning 2007 Oct 27 to 2008 Mar 10 at
the Holloway Comet Observatory and 1.5-m telescope at Palomar Observatory. The
orientation of the leading edge of the ejecta shell and the ejecta blob,
relative to the nucleus, do not change as the orientation of the Sun changes;
instead, the configuration was imprinted by the orientation of the initial
explosion. The kinetic energy of the ejecta >1e21 erg is greater than the
gravitational binding energy of the nucleus. We model the explosion as being
due to crystallization and release of volatiles from interior amorphous ice
within a subsurface cavity; once the pressure in the cavity exceeded the
surface strength, the material above the cavity was propelled from the comet.
The size of the cavity and the tensile strength of the upper layer of the
nucleus are constrained by the observed properties of the ejecta; tensile
strengths on >10 m scale must be greater than 10 kPa. The appearance of the
2007 outburst is similar to that witnessed in 1892, but the 1892 explosion was
less energetic by a factor of about 20.Comment: 51 pages. Some figures compressed (see real journal for full
quality). accepted by Icaru
Reaction Networks For Interstellar Chemical Modelling: Improvements and Challenges
We survey the current situation regarding chemical modelling of the synthesis
of molecules in the interstellar medium. The present state of knowledge
concerning the rate coefficients and their uncertainties for the major
gas-phase processes -- ion-neutral reactions, neutral-neutral reactions,
radiative association, and dissociative recombination -- is reviewed. Emphasis
is placed on those reactions that have been identified, by sensitivity
analyses, as 'crucial' in determining the predicted abundances of the species
observed in the interstellar medium. These sensitivity analyses have been
carried out for gas-phase models of three representative, molecule-rich,
astronomical sources: the cold dense molecular clouds TMC-1 and L134N, and the
expanding circumstellar envelope IRC +10216. Our review has led to the proposal
of new values and uncertainties for the rate coefficients of many of the key
reactions. The impact of these new data on the predicted abundances in TMC-1
and L134N is reported. Interstellar dust particles also influence the observed
abundances of molecules in the interstellar medium. Their role is included in
gas-grain, as distinct from gas-phase only, models. We review the methods for
incorporating both accretion onto, and reactions on, the surfaces of grains in
such models, as well as describing some recent experimental efforts to simulate
and examine relevant processes in the laboratory. These efforts include
experiments on the surface-catalysed recombination of hydrogen atoms, on
chemical processing on and in the ices that are known to exist on the surface
of interstellar grains, and on desorption processes, which may enable species
formed on grains to return to the gas-phase.Comment: Accepted for publication in Space Science Review
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