AtomSim: web-deployed atomistic dynamics simulator

AtomSim, a collection of interfaces for computational crystallography simulations, has been developed. It uses forcefield-based dynamics through physics engines such as the General Utility Lattice Program, and can be integrated into larger computational frameworks such as the Virtual Neutron Facility for processing its dynamics into scattering functions, dynamical functions etc. It is also available as a Google App Engine-hosted web-deployed interface. Examples of a quartz molecular dynamics run and a hafnium dioxide phonon calculation are presented

Functionalized carbophenes as high-capacity versatile gas adsorbents: An ab initio study

This study employs density functional theory (DFT) and density functional tight-binding theory (DFTB) to determine the adsorption properties of carbon dioxide (CO$_2$), methane (CH$_4$), and dihydrogen (H$_2$) in carbophenes functionalized with carboxyl (COOH), amine (NH$_2$), nitro (NO$_2$), and hydroxyl (OH) groups. We demonstrate that carbophenes are promising candidates as adsorbents for these gasses. Carbophenes have larger CO$_2$ and CH$_4$ adsorption energies than other next-generation solid-state capture materials. Yet, the low predicted desorption temperatures mean they can be beneficial as air scrubbers in confined spaces. Functionalized carbophenes have H$_2$ adsorption energies usually observed in metal-containing materials. Further, the predicted desorption temperatures of H$_2$ from carbophenes lie within the DOE Technical Targets for Onboard Hydrogen Storage for Light-Duty Vehicles (DOEHST) operating temperature range. The possibility of tailoring the degree of functionalization in combination with selecting sufficiently open carbophene structures that allow for multiple strong interactions without steric hindrance (crowding) effects, added to the multiplicity of possible functional groups alone or in combination, suggests that these very light materials can be ideal adsorbates for many gases. Tailoring the design to specific adsorption or separation needs would require extensive combinatorial investigations

Low Frequency Impedance Behavior of Montmorillonite Suspensions: Polarization Mechanisms in theLow Frequency Domain

Large changes in permittivity have been observed as the frequency of an electromagnetic (EM) field applied to systems containing phases of contrasting permittivity is changed. Two mechanisms, polarization of a diffuse double layer (DDL) and polarization of the charge imbalance created by contact of two phases of different permittivity (the Maxwell-Wagner [MW] effect), are responsible for the frequency dependence of dielectric properties. To use the frequency dependence of dielectric properties to determine soil geometrical and electrochemical properties, the two mechanisms must be quantified. Three models of the frequency dependent dielectric properties, based on terms representing polarization of the electrical double layer that develops at the electrode surface, polarization of the DDL and the MW effect, were used to investigate the dielectric spectrum of montmorillonite suspensions. Dielectric spectra of suspensions of three particle-size separates (r \u3e 1.0 μm, 1.0 μm \u3e r \u3e 0.2 μm, 0.2 μm \u3e r) of homoionic (Na+ or Ca2+) were measured at a suspension density of 5.0 g of clay in 50 mL of water. Impedance plane plots suggested the contribution of three relaxation processes to the spectra. While all three models reproduced the data, they gave different interpretations of the data. Two models attributed relaxation in the kHz range to electrode polarization, relaxation at approximately 10 kHz to DDL polarization and relaxation at 1 MHz to MW polarization. The third model assigned MW polarization to the relaxation at 10 kHz and DDL polarization to the relaxation at 1 MHz

Fullerenes generated from porous structures

A class of macromolecules based on the architecture of the well-known fullerenes is theoretically investigated. The building blocks used to geometrically construct these molecules are the two dimensional structures: porous graphene and biphenylene-carbon. Density functional-based tight binding methods as well as reactive molecular dynamics methods are applied to study the electronic and structural properties of these molecules. Our calculations predict that these structures can be stable up to temperatures of 2500 K. The atomization energies of carbon structures are predicted to be in the range of 0.45 eV per atom to 12.11 eV per atom (values relative to the C60 fullerene), while the hexagonal boron nitride analogues have atomization energies between -0.17 eV per atom and 12.01 eV per atom (compared to the B12N12 fullerene). Due to their high porosity, these structures may be good candidates for gas storage and/or molecular encapsulation.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in Fireball

Fireball is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access Fireball’s unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation