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The internal electronic structure of single deoxyribonucleic acid (DNA) base molecules (i.e., guanine, adenine, cytosine, and thymine) adsorbed on a metallic surface of Cu (111) is determined in detail using density functional theory (DFT) computations. In contrast to the intuitive beliefs that a molecule weakly interacts with a substrate and its electronic structure is only slightly perturbed, our simulations reveal strong hybridizations and interactions between molecular and metallic states. Stipulated by the symmetries of a base molecule and the Cu(111) surface, oxygen atoms of a base approach close to the substrate, breaking the parallel orientation of the π-system with respect to the surface. Such a behavior is the most pronounced for one oxygen containing bases, leading to the chemisorption of cytosine and guanine and to stronger hybridization of their electronic states with metallic ones. Oxygen free adenine, on the other hand, lies nearly flat on a Cu substrate and interacts weakly with the surface through physisorption. The calculated local electron density of states spectra demonstrate the absence of pure localized molecular states for all four DNA bases, yet they show the smallest delocalization for adenine and thymine and the largest for guanine and cytosine. The observed diversity of the geometrical and electronic structures of the nucleobases on the Cu substrate provides guidelines for interpreting DNA tunneling spectra in the scanning tunneling microscopy (STM) measurements. Our results open a new prospective for understanding biomolecule adsorbates and have an important implication for a possible differentiation of nucleotide sequences in DNA through STM.

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We have determined the structure of AlSb and GaSb (001) surfaces prepared by molecular beam epitaxy under typical Sb-rich device growth conditions. Within the range of flux and temperature where the diffraction pattern is nominally ͑1 3 3͒, we find that there are actually three distinct, stable ͑4 3 3͒ surface reconstructions. The three structures differ from any previously proposed for these growth conditions, with two of the reconstructions incorporating mixed III-V dimers within the Sb surface layer. These heterodimers appear to play an important role in island nucleation and growth. PACS numbers: 68.35.Bs, 61.16.Ch, 73.61.Ey, 81.15.Hi The surface reconstruction on a semiconducting material is the starting point for understanding the mechanisms of growth from the vapor. The steric and energetic landscape of the surface reconstruction determines the kinetic factors for adsorption, diffusion, and desorption, and provides the template for island nucleation [1]. These factors are critical to our understanding of growth and the formation of interfaces between materials, particularly for the case of III-V semiconductor quantum heterostructures, which are key components in a wide range of optical and high frequency electronic devices under development. Many of the most promising applications require extremely thin layers, so that even submonolayer variations in film thickness and interfacial roughness can dramatically affect the ultimate device performance [2,3]. To achieve the level of morphological control needed to reproducibly fabricate optimized III-V devices, a detailed understanding of the relevant surface reconstructions and the mechanisms by which epitaxy proceeds is essential.The structure of III-As and III-P (001) surfaces under typical device growth conditions (V͞III flux . 1) has been generally established [4,5]. For the much-studied case of GaAs, the extensive experimental and theoretical knowledge accumulated about the surface structure has led to significant progress in understanding the atomistic mechanisms of growth during molecular beam epitaxy (MBE) [6,7]. In contrast, the III-Sb device surfaces are poorly understood, despite their demonstrated potential for a variety of advanced electronic and optoelectronic applications [8]. Although the surface structures have been determined for atypical, extreme Sb-rich conditions-InSb and AlSb have the c͑4 3 4͒ structure common to the arsenides, and GaSb reconstructs into unusual, metallic ͑n 3 5͒ structures [9,10]-even after more than 20 years of study [11], the atomic-scale structures under more typical growth conditions have yet to be resolved. During device growth both GaSb and AlSb usually exhibit a ͑1 3 3͒-like reflection high-energy electron diffraction (RHEED) pattern, with the GaSb RHEED further delineated into distinct c͑2 3 6͒ and ͑1 3 3͒ (higher temperature/lower Sb flux) regimes [12,13]. Simple Sb-dimer row models for these reconstructions have been proposed [13,14], but scanning tunneling microscopy (STM) studies of the III-Sb(001) surfaces...

Detailed understanding of solid-solid interface structure-function relationships is critical for the improvement and wide deployment of all-solid-state batteries. The interfaces between lithium phosphorous oxynitride (LiPON) solid electrolyte material and lithium metal anode, and between LiPON and Li CoO cathode, have been reported to generate solid-electrolyte interphase (SEI)-like products and/or disordered regions. Using electronic structure calculations and crystalline LiPON models, we predict that LiPON models with purely P-N-P backbones are kinetically inert towards lithium at room temperature. In contrast, transfer of oxygen atoms from low-energy Li CoO (104) surfaces to LiPON is much faster under ambient conditions. The mechanisms of the primary reaction steps, LiPON structural motifs that readily reacts with lithium metal, experimental results on amorphous LiPON to partially corroborate these predictions, and possible mitigation strategies to reduce degradations are discussed. LiPON interfaces are found to be useful case studies for highlighting the importance of kinetics-controlled processes during battery assembly at moderate processing temperatures.

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We discuss our new implementation of the Real-space Electronic Structure method for studying the atomic and electronic structure of infinite periodic as well as finite systems, based on density functional theory. This improved version which we call HARES (for High-performance-fortran Adaptive grid Real-space Electronic Structure) aims at making the method widely applicable and efficient, using high performance Fortran on parallel architectures. The scaling of various parts of a HARES calculation is analyzed and compared to that of plane-wave based methods. The new developments that lead to enhanced performance, and their parallel implementation, are presented in detail. We illustrate the application of HARES to the study of elemental crystalline solids, molecules and complex crystalline materials, such as blue bronze and zeolites.