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Chemical modification of graphene is a common approach to control its electronic properties and hence fabricate electronic devices with new or improved functionalities. In this work we analyze, with density functional based calculations, the effect of chemical adsorption of fluorine atoms at different coverage levels on the electronic structure of graphene.(More)
A reconstructive phase transition has been found and studied in ultrashort di- and tripeptide nanostructures, self-assembled from biomolecules of different compositions and origin such as aromatic, aliphatic, linear, and cyclic (linear FF-diphenylalanine, linear LL-dileucine, FFF-triphenylalanine, and cyclic FF-diphenylalanine). The native linear aromatic(More)
Thermally induced phase transformation in bioorganic nanotubes, which self-assembled from two ultrashort dipeptides of different origin, aromatic diphenylalanine (FF) and aliphatic dileucine (LL), is studied. In both FF and LL nanotubes, irreversible phase transformation found at 120-180 °C is governed by linear-to-cyclic dipeptide molecular modification(More)
The particle effective mass in graphene is a challenging concept because the commonly used theoretical expression is mathematically divergent. In this paper, we use basic principles to present a simple theoretical expression for the effective mass that is suitable for both parabolic and non-parabolic isotropic materials. We demonstrate that this definition(More)
In this work we show the implementation of a linear scaling algorithm for the calculation of the Poisson integral. We use domain decomposition and non-uniform auxiliary grids (NGs) to calculate the electrostatic interaction. We demonstrate the approach within the PARSEC density functional theory code and perform calculations of long 1D carbon chains and(More)
The calculation of Fock-Exchange integral is becoming an important computational challenge in solving the quantum properties of systems with many electrons. In this work we show how techniques that are used in electromagnetic simulations for the similar Poisson equation can help in accelerating the calculation of such exchange integrals. The approach we(More)
In this work, we present an all-atom molecular dynamics (MD) study of triglyme and perfluorinated carbons (PFCs) using classical atomistic force fields. Triglyme is a typical solvent used in nonaqueous Li-air battery cells. PFCs were recently reported to increase oxygen availability in such cells. We show that O2 diffusion in two specific PFC molecules(More)
We analyze with Density Functional Theory (DFT) calculations the adsorption of fluorine atoms on graphene. We show that the adsorbed atoms clustering is favored by energy considerations and show that there are long range patterns for the second atoms adsorption energy at different sites. Finally, we discuss the effect of the different adsorption patterns on(More)
The solution of the Poisson equation is an essential stage in the calculation of quantum properties of materials as it appears both in the electrostatic Hartree term and in the Fock exchange operator. We discuss here an integral method for the calculation of Poisson potential and demonstrate its integration with a Density Functional Theory (DFT) code. We(More)