Monosodium iodoacetate-induced inflammation and joint pain are reduced in TRPA1 deficient mice--potential role of TRPA1 in osteoarthritis.

OBJECTIVES: Intra-articularly injected monosodium iodoacetate (MIA) induces joint pathology mimicking osteoarthritis (OA) and it is a widely used experimental model of OA. MIA induces acute inflammation, cartilage degradation and joint pain. Transient Receptor Potential Ankyrin 1 (TRPA1) is an ion channel known to mediate nociception and neurogenic inflammation. Here, we tested the hypothesis that TRPA1 would be involved in the development of MIA-induced acute inflammation, cartilage changes and joint pain. METHODS: The effects of pharmacological blockade (by TCS 5861528) and genetic depletion of TRPA1 were studied in MIA-induced acute paw inflammation. Cartilage changes (histological scoring) and joint pain (weight-bearing test) in MIA-induced experimental OA were compared between wild type and TRPA1 deficient mice. The effects of MIA were also studied in primary human OA chondrocytes and in mouse cartilage. RESULTS: MIA evoked acute inflammation, degenerative cartilage changes and joint pain in wild type mice. Interestingly, these responses were attenuated in TRPA1 deficient animals. MIA-induced paw inflammation was associated with increased tissue levels of substance P; and the inflammatory edema was reduced by pretreatment with catalase, with the TRPA1 antagonist TCS 5861528 and with the neurokinin 1 receptor antagonist L703,606. In chondrocytes, MIA enhanced interleukin-1 induced cyclooxygenase-2 (COX-2) expression, an effect that was blunted by pharmacological inhibition and genetic depletion of TRPA1. CONCLUSIONS: TRPA1 was found to mediate acute inflammation and the development of degenerative cartilage changes and joint pain in MIA-induced experimental OA in the mouse. The results reveal TRPA1 as a potential mediator and drug target in OA.

van der Waals bonding in layered compounds from advanced density-functional first-principles calculations.

Although the precise microscopic knowledge of van der Waals interactions is crucial for understanding bonding in weakly bonded layered compounds, very little quantitative information on the strength of interlayer interaction in these materials is available, either from experiments or simulations. Here, using many-body perturbation and advanced density-functional theory techniques, we calculate the interlayer binding and exfoliation energies for a large number of layered compounds and show that, independent of the electronic structure of the material, the energies for most systems are around 20 meV/Å2. This universality explains the successful exfoliation of a wide class of layered materials to produce two-dimensional systems, and furthers our understanding the properties of layered compounds in general.

d0 ferromagnetic interface between nonmagnetic perovskites.

We use computational and experimental methods to study d(0) ferromagnetism at a charge-imbalanced interface between two perovskites. In SrTiO(3)/KTaO(3) superlattice calculations, the charge imbalance introduces holes in the SrTiO(3) layer, inducing a d(0) ferromagnetic half-metallic 2D hole gas at the interface oxygen 2p orbitals. The charge imbalance overrides doping by vacancies at realistic concentrations. Varying the constituent materials shows ferromagnetism to be a general property of hole-type d(0) perovskite interfaces. Atomically sharp epitaxial d(0) SrTiO(3)/KTaO(3), SrTiO(3)/KNbO(3), and SrTiO(3)/NaNbO(3) interfaces are found to exhibit ferromagnetic hysteresis at room temperature. We suggest that the behavior is due to the high density of states and exchange coupling at the oxygen t(1g) band in comparison with the more studied d band t(2g) symmetry electron gas.

Evidence for strain-induced ferroelectric order in epitaxial thin-film KTaO3.

In perovskite-structure epitaxial films, it has been theoretically predicted that the polarization and the coherence of polar order can increase with increasing crystallographic strain. Experimental evidence of strain-induced long-range ferroelectric order has not been obtained thus far, posing the fundamental question of whether or not strain can induce the long-range polar order. Here we demonstrate the existence of strain-induced ferroelectric order in quantum paraelectric KTaO3 by combining experimental investigations of epitaxial KTaO3 films and density-functional-theory calculations. The long-range ferroelectric order does exist under a large enough epitaxial strain. We suggest that a region of short-range polar order might appear between paraelectric and ferroelectric states in the strain-temperature phase diagrams.

The factors behind the morphotropic phase boundary in piezoelectric perovskites.

The best piezoelectric materials are solid solutions in the vicinity of the steep morphotropic phase boundary (MPB) separating rhombohedral and tetragonal phases in the composition-temperature plane. A classical example is the lead zirconate titanate [Pb(Zr(x)Ti(1-x))O(3), PZT] system, with x approximately 0.52, where the two phases are separated by a boundary extending from the lowest temperatures up to several hundred degrees. The origin of the boundary has been under keen studies for 40 years. Recent interest is largely due to the need to develop new, lead-free piezoelectrics, for which a natural starting point is to understand the properties of the present systems. Here, we demonstrate, through high-pressure (up to 8 GPa) neutron powder diffraction experiments and density functional theory computations on lead titanate (PbTiO(3), PT), that it is the competition between two factors which determines the MPB. The first is the oxygen octahedral tilting, giving advantage for the rhombohedral R3c phase, and the second is the entropy, which in the vicinity of the MPB favors the tetragonal phase above 130 K. If the two factors are in balance over a large temperature range, a steep phase boundary results in the pressure-temperature plane.

C20 based polymers: electronic and elastic properties and stability studies.

In this paper we propose several new C20 polymer structures, whose properties were studied using density-functional theory based calculations. New structures predicted in this work are shown to be energetically more favourable and stable than previously found structures in computational studies. The new carbon structure which we have named as a quasi-graphite phase with fcc type structures was found to be the most energetically favourable polymer structures. Stability of the polymers was studied using constant temperature and constant pressure techniques. All the predicted structures demonstrate high stability with respect to high temperatures and external loads. The elastic and electronic properties of the proposed structures are discussed.

Multiscale study of hydrogen diffusion and clustering on carbon nanotube.

In this paper we report the results of a multiscale study of hydrogen clusterization at the surface of (10,0) carbon nanotube. For this purpose, a systematic study of the binding energies and migration barriers of hydrogen adatom and various close adatom pairs of has been undertaken using density-functional theory approach. The interaction between hydrogen atoms on the surface of nanotube is shown to be long ranged and anisotropic. On applying the obtained potential energy surfaces for lattice kinetic Monte Carlo simulations of chemisorbed hydrogen annealihg, a noticeable influence of the annealing conditions on cluster sizes, shapes and relative populations has bean revealed, which opens a possibility for the control of hydrogen clusterization kinetics. The effect on carbon nanotube electronic structure from hydrogen dimers and trimers most frequently met in lattice kinetic Monte Carlo simulations is discussed.

Vacancies in wurtzite GaN and AlN.

Vacancies in wurtzite GaN and AlN are studied using a computational method which is based on the density functional theory (DFT) and takes into account the errors arising from use of finite-sized supercells and the DFT band gap underestimation. Negatively charged N vacancies in GaN and AlN are found to be stable, with formation energies similar to and higher than those of Ga and Al vacancies in n-type material under Ga- and Al-rich growth conditions, respectively. The localization and energies of the defect levels close to the computational conduction band edge are considered in detail.

Nitrogen interstitial defects in GaAs.

We have studied nitrogen interstitial defects in GaAs with first-principles calculations. On the basis of calculated formation energies we have determined the most common nitrogen defects and the transition levels for various charge states. The lowest energy interstitial-type defects are found to be N-N and N-As split interstitials for most of the experimentally relevant conditions. We have also compared two different methods of obtaining the potential correction needed in an accurate calculation of the formation energies and transition levels.

Pressure-induced phase transitions in PbTiO3: a query for the polarization rotation theory.

Our first-principles computations show that the ground state of PbTiO3 under hydrostatic pressure transforms discontinuously from P4mm to R3c at 9 GPa. Spontaneous polarization decreases with increasing pressure so that the R3c phase transforms to the centrosymmetric Rc phase at around 27 GPa. The first-order phase transition between the tetragonal and rhombohedral phases is exceptional since there is no evidence for a bridging phase. The essential feature of the R3c and Rc phases is that they allow the oxygen octahedron to increase its volume VB at the expense of the cuboctahedral volume VA around a Pb ion. This is further supported by the fact that neither the R3m nor Cm phase, which keep the VA/VB ratio constant, is a ground state within the pressure range between 0 and 40 GPa. Thus, tetragonal strain is dominant up to 9 GPa, whereas at higher pressures, efficient compression through oxygen octahedra tilting plays the central role for PbTiO3. Previously predicted pressure induced colossal enhancement of piezoelectricity in PbTiO3 corresponds to unstable Cm and R3m phases. This suggests that the phase instability, in contrast to the polarization rotation, is responsible for the large piezoelectric properties observed in systems like Pb(Zr,Ti)O3 in the vicinity of the morphotropic phase boundary.

Substitutional carbon doping of free-standing and Ru-supported BN sheets: a first-principles study.

The development of spatially homogeneous mixed structures with boron (B), nitrogen (N) and carbon (C) atoms arranged in a honeycomb lattice is highly desirable, as they open the possibility of creating stable two-dimensional materials with tunable band gaps. However, at least in the free-standing form, the mixed BCN system is energetically driven towards phase segregation to graphene and hexagonal BN. It is possible to overcome the segregation when BCN material is grown on a particular metal substrate, for example Ru(0 0 0 1), but the stabilization mechanism is still unknown. With the use of density-functional theory we study the energetics of BN/Ru slabs, with different types of configurations of C substitutional defects introduced to the h-BN overlayer. The results are compared to the energetics of free-standing BCN materials. We found that the substrate facilitates the C substitution process in the h-BN overlayer. Thus, more homogeneous BCN material can be grown, overcoming the segregation into graphene and h-BN. In addition, we investigate the electronic and transport gaps in free-standing BCN structures, and assess their mechanical properties and stability. The band gap in mixed BCN free-standing material depends on the concentration of the constituent elements and ranges from zero in pristine graphene to nearly 5 eV in free-standing h-BN. This makes BCN attractive for application in modern electronics.

Probing organic layers on the TiO2(110) surface.

In this work, we use first principles simulations to provide features of the dynamic scanning force microscopy imaging of adsorbed organic layers on insulating surfaces. We consider monolayers of formic (HCOOH) and acetic (CH(3)COOH) acid and a mixed layer of acetic and trifluoroacetic acids (CF(3)COOH) on the TiO(2)(110) surface and study their interaction with a silicon dangling bond tip. The results demonstrate that the silicon tip interacts more strongly with the substrate and the COO(-) group than the adsorbed acid headgroups, and, therefore, molecules would appear dark in images. The pattern of contrast and apparent height of molecules is determined by the repulsion between the tip and the molecular headgroups and by significant deformation of the monolayer and individual molecules. The height of the molecule on the surface and the size of the headgroup play a large role in determining access of the tip to the substrate and, hence, the contrast in images. Direct imaging of the molecules themselves could be obtained by providing a functionalized tip with attraction to the molecular headgroups, for example, a positive potential tip.

Relation between macroscopic and microscopic activation energies in nonequilibrium surface processing.

Realistic Monte Carlo simulations show that the apparent macroscopic activation energy is only partially explained by the expected expression for the average over the microscopic activation energies for surface processing. An additional term accounting for the existence of fluctuations in the fractions of particles has to be taken into account. In all cases considered, the additional term can be accurately estimated by a posteriori analysis of the temperature dependence of the surface densities. In addition, we demonstrate that the relative contribution of the different competing microscopic processes to the macroscopic activation energy can be accurately obtained during the simulations, allowing for the unambiguous identification of the particular surface species which effectively control the process. As an example of the nonequilibrium open interfaces to which the results apply, the case of wet chemical etching of crystalline silicon is considered. The results can be directly applied to surface growth.

Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states.

Density-functional theory (DFT) calculations utilizing the Becke 3LYP hybrid functional have been carried out for N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA), vibrational circular dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers of the small alanine peptide, especially in the gas phase.

Formation, migration, and clustering of point defects in CuInSe2 from first principles.

The electronic properties of high-efficiency CuInSe(2) (CIS)-based solar cells are affected by the microstructural features of the absorber layer, such as point defect types and their distribution. Recently, there has been controversy over whether some of the typical point defects in CIS--V(Cu), V(Se), In(Cu), Cu(In)--can form stable complexes in the material. In this work, we demonstrate that the presence of defect complexes during device operational time can be justified by taking into account the thermodynamic and kinetic driving forces acting behind defect microstructure formation. Our conclusions are backed up by thorough state-of-the-art calculations of defect interaction potentials as well as the activation barriers surrounding the complexes. Defect complexes such as In(Cu)-2V(Cu), In(Cu)-Cu(In), and V(Se)-V(Cu) are shown to be stable against thermal dissociation at device operating temperatures, but can anneal out within tens of minutes at temperatures higher than 150-200 °C (V(Cu)-related complexes) or 400 °C (antisite pair). Our results suggest that the presence of these complexes can be controlled via growth temperatures, which provides a mechanism for tuning the electronic activity of defects and the device altogether.

First-principles study of layered antiferromagnetic CuCrX2 (X = S, Se and Te).

We present detailed electronic band-structure calculations for antiferromagnetic chromium compounds, CuCrX(2) (X = S, Se or Te), carried out using spin-polarized density functional theory within the generalized-gradient approximation (GGA). A narrow-band semiconductor-to-metal transition is observed upon replacement of S or Se by Te. The indirect bandgap is found at 0.58 eV and 0.157 eV for CuCrS(2) and CuCrSe(2), respectively. The results for our theoretical calculations are well in line with the electronic transport properties experimentally observed for CuCrS(2) and CuCrSe(2).

Are we van der Waals ready?

We apply a range of density-functional-theory-based methods capable of describing van der Waals interactions with weakly bonded layered solids in order to investigate their accuracy for extended systems. The methods under investigation are the local-density approximation, semi-empirical force fields, non-local van der Waals density functionals and the random-phase approximation. We investigate the equilibrium geometries, elastic constants and binding energies of a large and diverse set of compounds and arrive at conclusions about the reliability of the different methods. The study also points to some directions of further development for the non-local van der Waals density functionals.

Effect of gating and pressure on the electronic transport properties of crossed nanotube junctions: formation of a Schottky barrier.

The electronic transport properties of crossed carbon nanotube junctions are investigated using ab initio methods. The optimal atomic structures and the intertube distances of the junctions are obtained using van der Waals corrected density functional theory. The effect of gating on the intertube conductance of the junctions is explored, showing the charge accumulation to the nanotube contact and the charge depletion region at the metal-semiconductor Schottky contact. Finally, it is shown how the conductance of the junctions under the gate voltage is affected by pressure applied to the nanotube film.

Vacancies in CuInSe2: new insights from hybrid-functional calculations.

We calculate the energetics of vacancies in CuInSe(2) using a hybrid functional (HSE06, HSE standing for Heyd, Scuseria and Ernzerhof), which gives a better description of the band gap compared to (semi)local exchange-correlation functionals. We show that, contrary to present beliefs, copper and indium vacancies induce no defect levels within the band gap and therefore cannot account for any experimentally observed levels. The selenium vacancy is responsible for only one level, namely, a deep acceptor level ε(0/2-). We find strong preference for V(Cu) and V(Se) over V(In) under practically all chemical conditions.

Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method.

Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, ΔSCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.