Visual and Computational Comparison of Functionals Used in Density Functional Theory

This work presents the visual and quantitative comparison of Density Functional Theory (DFT) exchange-correlation energy Exc functionals with Coupled Cluster with Single and Double excitations (CCSD) calculations (and experiment where possible). The Exc functional is an approximate term which is a component of the total energy of a molecule. This comparison is based on visualizing the differences of computed properties, such as the charge density, geometry and other molecular properties between the functional and a CCSD calculation. In this work, this visual comparison for a set of functionals using a set of small molecules is presented to elucidate the method. Specifically, this visual comparison of the local molecular properties includes the charge density and electron localization function and global molecular properties such as molecular geometry for each DFT functional compared with a CCSD calculation. Note, that the differences of the particular computed properties are computed visually

Thermodynamic properties and phase transitions in CO<SUB>2</SUB> molecular clusters

The thermodynamic properties of (CO2)N molecular aggregates of size 2 N 13 have been investigated. These crystallites exhibit well defined orientational order-disorder rotational transitions accompanied by a structural transition into a plastic crystallite phase. In addition, they exhibit melting and disassociation transitions. It is shown that the interpretation of experimental data, based upon dimer properties, depends crucially on these results. Equilibrium structures and orientations are also given

γ Phase RDX: Initial study of geometry, spectrum and EOS

We present a full 3D periodic density functional theory study of the geometry and vibrational spectrum of γ phase nitramine, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). The B3LYP-D* functional as adjusted for molecular solids from Grimme\u27s semi-empirical approach for molecules is used to better describe the van der Waals interactions in this system. Specifically, the low terahertz portion of the spectrum is computed to determine modes that change substantially in behavior with respect to an alpha phase that is near the transition pressure for the system. These key modes provide possible clues into the nature of the α-γ phase transformation. © 2012 American Institute of Physics

Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains

Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10–15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues. SymD has proven to be a useful algorithm to detect symmetry. In this paper, we present a new parallelized algorithm called Parallel-SymD for detecting symmetry of proteins on clusters of computers. The achieved speedup of the new Parallel-SymD algorithm scales well with the number of computing processors. Scaling is better for proteins with a larger number of residues. For a protein of 509 residues, a speedup of 63 was achieved on a parallel system with 100 processors

Optical Properties of Biomass Burning Aerosols: Comparison of Experimental Measurements and T-Matrix Calculations

The refractive index (RI) is an important parameter in describing the radiative impacts of aerosols. It is important to constrain the RI of aerosol components, since there is still significant uncertainty regarding the RI of biomass burning aerosols. Experimentally measured extinction cross-sections, scattering cross-sections, and single scattering albedos for white pine biomass burning (BB) aerosols under two different burning and sampling conditions were modeled using T-matrix theory. The refractive indices were extracted from these calculations. Experimental measurements were conducted using a cavity ring-down spectrometer to measure the extinction, and a nephelometer to measure the scattering of size-selected aerosols. BB aerosols were obtained by burning white pine using (1) an open fire in a burn drum, where the aerosols were collected in distilled water using an impinger, and then re-aerosolized after several days, and (2) a tube furnace to directly introduce the BB aerosols into an indoor smog chamber, where BB aerosols were then sampled directly. In both cases, filter samples were also collected, and electron microscopy images were used to obtain the morphology and size information used in the T-matrix calculations. The effective radius of the particles collected on filter media from the open fire was approximately 245 nm, whereas it was approximately 76 nm for particles from the tube furnace burns. For samples collected in distilled water, the real part of the RI increased with increasing particle size, and the imaginary part decreased. The imaginary part of the RI was also significantly larger than the reported values for fresh BB aerosol samples. For the particles generated in the tube furnace, the real part of the RI decreased with particle size, and the imaginary part was much smaller and nearly constant. The RI is sensitive to particle size and sampling method, but there was no wavelength dependence over the range considered (500–680 nm). Our values for the RI of fresh (white pine) biomass burning aerosols ranged from 1.33 + i0.008 to 1.74 + i0.008 for 200-nm, 300-nm, and 400-nm diameter particles. These are within the range of RI values in the most recent study conducted during the Fire Laboratory at Missoula Experiments (FLAME I and II), which were 1.55 to 1.80 for the real part, and 0.01–0.50 for the imaginary part, for fresh BB aerosols with diameters of 200–570 nm. There is no clear trend on the dependence of the RI values on particle size. The RI values derived from measurements of aerosols produced from the combustion of hydrocarbons and diesel cannot be used for BB aerosols