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