Gali JA, Kaxiras E, Zimanyi GT, Meng S. Effect of symmetry breaking on the optical absorption of semiconductor nanoparticles. PHYSICAL REVIEW B. 2011;84 :035325.
Melchionna S, Kaxiras E, Bernaschi M, Succi S. Endothelial shear stress from large-scale blood flow simulations. Phil. Trans. R. Soc. A. 2011;369 :2354.
Knaup JM, Li H, Vlassak JJ, Kaxiras E. Influence of CH2 content and network defects on the elastic properties of organosilicate glasses. PHYSICAL REVIEW B. 2011;83 :054204.
Zhao K, Wang WL, Gregoire J, Pharr M, Suo Z, Vlassak JJ, Kaxiras E. Lithium-Assisted Plastic Deformation of Silicon Electrodes inLithium-Ion Batteries: A First-Principles Theoretical Study. Nano Lett. 2011;11 :2962.
Kuhne TD, Pascal TA, Kaxiras E, Jung Y. New Insights into the Structure of the Vapor/WaterInterface from Large-Scale First-Principles Simulations. J. Phys. Chem. Lett. 2011;2 :105.
Maze JR, Gali A, Togan E, Chu Y, Trifonov A, Kaxiras E, Lukin MD. Properties of nitrogen-vacancy centers in diamond:the group theoretic approach. New Journal of Physics. 2011;13 :025025.
Xu B, Haubrich J, Baker TA, Kaxiras E, Friend CM. Theoretical Study of O-Assisted Selective Coupling of Methanol onAu(111). J. Phys. Chem. C. 2011;115 :3703.
Katono M, Bessho T, Meng S, Humphry-Baker R, Rothenberger G, Zakeeruddin SM, Kaxiras E, Gratzel M. D-π-A Dye System Containing Cyano-Benzoic Acid as Anchoring Group for Dye-Sensitized Solar Cells. Langmuir. 2011;27 (23) :14248–14252.
Meng S, Kaxiras E, Nazeeruddin MK, Graetzel M. Design of Dye Acceptors for Photovoltaics from First-Principles Calculations. Journal of Physical Chemistry C. 2011;115 :9276-9282.Abstract

We investigate a set of donor-π-acceptor (D-π-A) dyes with new acceptor groups for dye-sensitized solar cells, using time-dependent density-functional-theory calculations of the electronic structure and optical absorption. We considered three types of modifications on existing dye structures: (i) replacement of the side cyano group (CN) on the molecular anchor, (ii) insertion and alteration of the intermediate spacer groups, and (iii) modification of the number and positions of cyano CN groups on a phenyl-ring spacer. We find that with these modifications, the dye electronic levels and corresponding optical absorption properties can be gradually tuned, rendering possible the identification of dyes with desirable structural, electronic, and optical properties. For example, dyes with phenyl and CN-substituted phenyl groups are promising candidates for red light absorption and high molar extinction coefficients.

Heiss M, Conesa-Boj S, Ren J, Tseng H-H, Gali A, Rudolph A, Uccelli E, Peiro F, Morante JR, Schuh D, et al. Direct correlation of crystal structure and optical properties in wurtzite/zinc-blende GaAs nanowire heterostructures. Physical Review B. 2011;83 :045303.Abstract

A method for the direct correlation at the nanoscale of structural and optical properties of single GaAs nanowires is reported. Nanowires consisting of 100% wurtzite and nanowires presenting zinc-blende/wurtzite polytypism are investigated by photoluminescence spectroscopy and transmission electron microscopy. The photoluminescence of wurtzite GaAs is consistent with a band gap of 1.5 eV. In the polytypic nanowires, it is shown that the regions that are predominantly composed of either zinc-blende or wurtzite phase show photoluminescence emission close to the bulk GaAs band gap, while regions composed of a nonperiodic superlattice of wurtzite and zinc-blende phases exhibit a redshift of the photoluminescence spectra as low as 1.455 eV. The dimensions of the quantum heterostructures are correlated with the light emission, allowing us to determine the band alignment between these two crystalline phases. Our first-principles electronic structure calculations within density functional theory, employing a hybrid-exchange functional, predict band offsets and effective masses in good agreement with experimental results.

Katono M, Bessho T, Meng S, Humphry-Baker R, Rothenberger G, Zakeeruddin SM, Kaxiras E, Graetzel M. D-π-A Dye System Containing Cyano-Benzoic Acid as Anchoring Group for Dye-Sensitized Solar Cells. Langmuir. 2011;27 :14248-14252.Abstract

A D-π-A dye (KM-1) incorporating cyanobenzoic acid as a new acceptor/anchoring group has been synthesized for dye-sensitized solar cells (DSCs) with a high molar extinction coefficient of 66 700 M-1 cm-1 at 437 nm. Theoretical calculations show that the hydrogen bond between CN and surface hydroxyl leads to the most stable configuration on the surface of TiO2. In addition, the adsorption of the dye on TiO2 follows a BrunauerEmmettTeller (BET) isotherm. Multilayer adsorption of KM-1 on TiO2 seems to take place particularly at higher dye concentrations. DSC device using KM-1 reached a maximum incident photon-to-current conversion efficiency (IPCE) of 84%, with a solar to electric power conversion efficiency (PCE) of 3.3% at AM1.5 G illumination (100 mW cm-2 ). This new type of anchoring group paves a way to design new dyes that combine good visible light harvesting with strong binding to the metal oxide surface

Melchionna S, Kaxiras E, Bernaschi M, Succi S. Endothelial shear stress from large-scale blood flow simulations. Philosophical Transactions of the Royal Society A. 2011;369 :2354-2361.Abstract

We discuss the optimal evaluation of endothelial shear stress for real-life case studies based on anatomic data acquisition. The fluid dynamic simulations require smoothing of the geometric dataset to avoid major artefacts in the flow patterns, especially in the proximity of bifurcations. A systematic series of simulations at different corrugation levels shows that, below a smoothing length of about 0.5 mm, the numerical data are insensitive to further smoothing.

Mao Y, Wang WL, Wei D, Kaxiras E, Sodroski JG. Graphene Structures at an Extreme Degree of Buckling. ACS Nano. 2011;5 (2) :1395-1400.Abstract

T The distinctive properties of graphene sheets may be significantly influenced by the presence of corrugation structures. Our understanding of these graphene structures has been limited to the mesoscopic scale. Here we characterize angstrom-scale periodic buckling structures in freestanding graphene bilayers produced by liquid-phase processing in the absence of specific substrates. Monochromated, aberration-corrected transmission electron microscopy with sub-angstrom resolution revealed that the unit structures in the major buckling direction consist of only two and three unit cells of graphene's honeycomb lattice, resulting in buckling wavelengths of 3.6±0.5 and 6.4±0.8 Å, respectively. The buckling shows a strong preference of chiral direction and spontaneously chooses the orientation of the lowest deformation energy, governed by simple geometry rules agreeing with Euler buckling theory. Unexpectedly, the overall buckled structures demonstrate geometric complexity with cascaded features. First-principles calculations suggest that significant anisotropic changes in the electronic structure of graphene are induced by the buckling.

Knaup JM, Li H, Vlassak JJ, Kaxiras E. Influence of CH2 content and network defects on the elastic properties of organosilicate glasses. Physical Review B. 2011;83 :054204.Abstract

Organosilicate glasses (OSGs) are used as low-k intermetal dielectrics for advanced integrated circuits. In this application, the material must fulfill two conflicting requirements: It has to have low density to reduce the dielectric constant while being sufficiently mechanically stable to withstand thermomechanical and other stresses during subsequent steps of integrated circuit manufacture. Recent experimental advances in improving the mechanical and electrical properties of these materials have not yet been systematically studied theoretically at the ab initio level due to the large model sizes necessary to realistically describe amorphous materials. In this paper we employ the density-functional-based tight-binding method to achieve an accurate description of OSG properties at different compositions. We analyze the influence of composition and local network defects on the density and bulk modulus of nonporous OSG. We find that the dependence of density and that of mechanical stiffness on chemical composition are of different natures. This difference is traced to a transition between mechanisms of elastic deformation in silica glass and in silicon hydrocarbide, which is also the reason for the two materials’ different sensitivities to network defects.

Zhao K, Wang WL, Gregoire J, Pharr M, Suo Z, Vlassak JJ, Kaxiras E. Lithium-Assisted Plastic Deformation of Silicon Electrodes in Lithium-Ion Batteries: A First-Principles Theoretical Study. NanoLetters. 2011;11 :2962-2967.Abstract

Silicon can host a large amount of lithium, making it a promising electrode for high-capacity lithium-ion batteries. Recent experiments indicate that silicon experiences large plastic deformation upon Li absorption, which can significantly decrease the stresses induced by lithiation and thus mitigate fracture failure of electrodes. These issues become especially relevant in nanostructured electrodes with confined geometries. On the basis of first-principles calculations, we present a study of the microscopic deformation mechanism of lithiated silicon at relatively low Li concentration, which captures the onset of plasticity induced by lithiation. We find that lithium insertion leads to breaking of SiSi bonds and formation of weaker bonds between neighboring Si and Li atoms, which results in a decrease in Young’s modulus, a reduction in strength, and a brittle-to-ductile transition with increasing Li concentration. The microscopic mechanism of large plastic deformation is attributed to continuous lithium-assisted breaking and re-forming of SiSi bonds and the creation of nanopores.

Kuehne TD, Pascal TA, Kaxiras E, Jung Y. New Insights into the Structure of the Vapor/Water Interface from Large-Scale First-Principles Simulations. Journal of Physical Chemistry Letters. 2011;2 :105-113.Abstract

We present extensive ab initio simulations of the molecular arrangements at the vapor/water interface, which provide valuable insights into the interface structure. In particular, the simulations address the controversy of whether there is a significant amount of nondonor configurations at this prototypical interface, using a novel Car-Parrinello-like ab initio molecular dynamics approach. The interface is modeled by a system of 384 water molecules for 125 ps in a two-dimensional periodic slab, the most extensive ab initio molecular dynamics simulation to date. In contrast to previous theoretical simulations and X-ray absorption spectroscopy, but consistent with sum-frequency generation experiments, we observe no evidence for a significant occurrence of acceptoronly species at the vapor/water interface. Besides a distinct surface relaxation effect, we find that only the topmost layers of the interface obey structural order.

Ren J, Meng S, Wang Y-L, Ma X-C, Xue Q-K, Kaxiras E. Properties of copper (fluoro-)phthalocyanine layers deposited on epitaxial graphene. Journal of Chemical Physics. 2011;134 :194706.Abstract

We investigate the atomic structure and electronic properties of monolayers of copper phthalocyanines (CuPc) deposited on epitaxial graphene substrate. We focus in particular on hexadecafluorophthalocyanine (F16CuPc), using both theoretical and experimental (scanning tunneling microscopy – STM) studies. For the individual CuPc and F16CuPc molecules, we calculated the electronic and optical properties using density functional theory (DFT) and time-dependent DFT and found a red-shift in the absorption peaks of F16CuPc relative to those of CuPc. In F16CuPc, the electronic wavefunctions are more polarized toward the electronegative fluorine atoms and away from the Cu atom at the center of the molecule. When adsorbed on graphene, the molecules lie flat and form closely packed patterns: F16CuPc forms a hexagonal pattern with two well-ordered alternating α and β stripes while CuPc arranges into a square lattice. The competition between molecule-substrate and intermolecular van der Waals interactions plays a crucial role in establishing the molecular patterns leading to tunable electron transfer from graphene to the molecules. This transfer is controlled by the layer thickness of, or the applied voltage on, epitaxial graphene resulting in selective F16CuPc adsorption, as observed in STM experiments. In addition, phthalocyanine adsorption modifies the electronic structure of the underlying graphene substrate introducing intensity smoothing in the range of 2–3 eV below the Dirac point (ED) and a small peak in the density of states at ∼0.4 eV above ED.

Maze JR, Gali A, Togan E, Chu Y, Trifonov A, Kaxiras E, Lukin MD. Properties of nitrogen-vacancy centers in diamond: the group theoretic approach. New Journal of Physics. 2011;13 :025025.Abstract

We present a procedure that makes use of group theory to analyze and predict the main properties of the negatively charged nitrogen-vacancy (NV) center in diamond. We focus on the relatively low temperature limit where both the spin–spin and spin–orbit effects are important to consider. We demonstrate that group theory may be used to clarify several aspects of the NV structure, such as ordering of the singlets in the (e 2 ) electronic configuration and the spin–spin and spin–orbit interactions in the (ae) electronic configuration. We also discuss how the optical selection rules and the response of the center to electric field can be used for spin–photon entanglement schemes. Our general formalism is applicable to a broad class of local defects in solids. The present results have important implications for applications in quantum information science and nanomagnetometry.

Baker TA, Xu B, Jensen SC, Friend CM, Kaxiras E. Role of defects in propene adsorption and reaction on a partially O-covered Au(111) surface. Catalysis Science & Technology. 2011;1 :1166-1174.Abstract

We investigate the role of defects—adatoms, vacancies, and steps—in the bonding and reaction of propene on Au(111) containing atomic oxygen, using density functional theory (DFT) calculations. The adsorption of propene is stronger on a surface containing defects compared to the flat, bulk-terminated surface, with the largest gain in binding (~0.7 eV) on a surface with a 1/9 monolayer (ML) of Au adatoms. Charge-density difference plots reveal that the difference between defective surfaces and the bulk-terminated surface is a more pronounced depletion of electron density from the carbon–carbon p bond and a charge accumulation between the double bond and the gold atom to which the propene is bound. We calculate the energy barriers for two competing reactions that are important in determining the selectivity for propene oxidation. Allylic H abstraction by adsorbed O leads to combustion, whereas O addition to form an oxymetallacycle is the first step in propene epoxide formation. A comparison of the energetics of these two pathways on flat and defect-containing Au surfaces indicates that the reactivity depends on the nature and prevalence of surface defects. Both electronic and geometric factors, such as the path and the distance the oxygen must travel to meet the allylic hydrogen for abstraction, are important in explaining the reaction trends.

Haubrich J, Kaxiras E, Friend CM. The Role of Surface and Subsurface Point Defects for Chemical Model Studies on TiO2: A First-Principles Theoretical Study of Formaldehyde Bonding on Rutile TiO2(110). Chemistry - a European Journal. 2011;17 :4496-4506.Abstract

We report a systematic investigation of the effects of different surface and subsurface point defects on the adsorption of formaldehyde on rutile TiO2(110) surfaces using density functional theory (DFT). All point defects investigated—including surface bridging oxygen vacancies, titanium interstitials, and subsurface oxygen vacancies—stabilize the adsorption significantly by up to 56 kJ mol-1 at a coverage of 0.1 monolayer (ML). The stabilization is due to a decrease of the coordination (covalent saturation) of the surface Ti adsorption sites adjacent to the defects, which leads to a stronger molecule–surface interaction. This change in the Ti is caused by the removal of a neighboring atom (oxygen vacancies) or substantial lattice relaxations induced by the subsurface defects. On the stoichiometric reference surface, the most stable adsorption geometry of formaldehyde is a tilted η2 -dioxymethylene (with an adsorption energy Eads=-125 kJ mol-1 ), in which a bond forms to a nearby bridging O atom and the carbonyl-O atom in the formaldehyde binds to a Ti atom in the adjacent fivefold coordinated lattice site. The η1 -top configuration on fivecoordinate Ti4+ is much less favorable (Eads=-69 kJ mol-1 ). The largest stabilization is exerted by subsurface Ti interstitials between the first and second layers. These defects stabilize the η2 -dioxymethylene structure by nearly 40 kJ mol-1 to an adsorption energy of 164 kJ mol-1 . Contrary to popular belief, adsorption in a bridging oxygen vacancy (Eads=-86 kJ mol-1 ) is much less favorable for formaldehyde compared to the η2 - dioxymethylene structures. From these results we conclude that formaldehyde will bind in the η2 - dioxymethylene structure on the stoichiometric surface as well as in the presence of Ti interstitials and bridging oxygen vacancies. In the light of these substantial effects, we conclude that it is essential to include all the types of point defects present in typical, reduced rutile samples used for model studies, at realistic concentrations to obtain correct adsorption sites, structures, energetic, and chemi-physical properties.