Forces and atomic relaxations in the pSIC approach with ultrasoft pseudopotentials

We present the scheme that allows for efficient calculations of forces in the framework of pseudopotential self-interaction corrected (pSIC) formulation of the density functional theory. The scheme works with norm conserving and also with ultrasoft pseudopotentials and has been implemented in the plane-wave basis code {\sc quantum espresso}. We have performed tests of the internal consistency of the derived expressions for forces considering ZnO and CeO$_2$ crystals. Further, we have performed calculations of equilibrium geometry for LaTiO$_3$, YTiO$_3$, and LaMnO$_3$ perovskites and also for Re and Mn pairs in silicon. Comparison with standard DFT and DFT+U approaches shows that in the cases where spurious self-interaction matters, the pSIC approach predicts different geometry, very often closer to the experimental data.Comment: 11 pages, 2 figure

Smooth operator: Avoidance of subharmonic bifurcations through mechanical mechanisms simplifies song motor control in adult zebra finches

Like human infants, songbirds acquire their song by imitation and eventually generate sounds that result from complicated neural networks and intrinsically nonlinear physical processes. Signatures of low-dimensional chaos such as subharmonic bifurcations have been reported in adult and developing zebra finch song. Here, we use methods from nonlinear dynamics to test whether adult male zebra finches (Taenopygia guttata) use the intrinsic nonlinear properties of their vocal organ, the syrinx, to insert subharmonic transitions in their song. In contrast to previous data on the basis of spectrographic evidence, we show that subharmonic transitions do not occur in adult song. Subharmonic transitions also do not arise in artificially induced sound in the intact syrinx, but are commonly generated in the excised syrinx. These findings suggest that subharmonic transitions are not used to increase song complexity, and that the brain controls song in a surprisingly smooth control regimen. Fast, smooth changes in acoustic elements can be produced by direct motor control in a stereotyped fashion, which is a more reliable indicator of male fitness than abrupt acoustic changes that do not require similarly precise control. Consistent with this view is the presence of high fidelity at every level of motor control, from telencephalic premotor areas to superfast syringeal muscles

Semicircular canals circumvent Brownian Motion overload of mechanoreceptor hair cells

<p>Vertebrate semicircular canals (SCC) first appeared in the vertebrates (i.e. ancestral fish) over 600 million years ago. In SCC the principal mechanoreceptors are hair cells, which as </p><p>compared to cochlear hair cells are distinctly longer (70 vs. 7 μm), 10 times more compliant to bending (44 vs. 500 nN/m), and have a 100-fold higher tip displacement threshold (&lt; 10 μm vs. &lt;400 nm).We have developed biomechanical models of vertebrate hair cells where the </p><p>bundle is approximated as a stiff, cylindrical elastic rod subject to friction and thermal agitation. Our models suggest that the above differences aid SCC hair cells in circumventing the masking effects of Brownian motion noise of about 70 nm, and thereby permit transduction of </p><p>very low frequency (&lt;10 Hz) signals.We observe that very low frequency mechanoreception </p><p>requires increased stimulus amplitude, and argue that this is adaptive to circumvent Brownian motion overload at the hair bundles. We suggest that the selective advantage of detecting such low frequency stimuli may have favoured the evolution of large guiding structures such as semicircular canals and otoliths to overcome Brownian Motion noise at the level of the mechanoreceptors of the SCC.</p

Amplitude and frequency modulation control of sound production in a mechanical model of the avian syrinx

Birdsong has developed into one of the important models for motor control of learned behaviour and shows many parallels with speech acquisition in humans. However, there are several experimental limitations to studying the vocal organ – the syrinx – in vivo. The multidisciplinary approach of combining experimental data and mathematical modelling has greatly improved the understanding of neural control and peripheral motor dynamics of sound generation in birds. Here, we present a simple mechanical model of the syrinx that facilitates detailed study of vibrations and sound production. Our model resembles the `starling resistor', a collapsible tube model, and consists of a tube with a single membrane in its casing, suspended in an external pressure chamber and driven by various pressure patterns. With this design, we can separately control `bronchial' pressure and tension in the oscillating membrane and generate a wide variety of `syllables' with simple sweeps of the control parameters. We show that the membrane exhibits high frequency, self-sustained oscillations in the audio range (>600 Hz fundamental frequency) using laser Doppler vibrometry, and systematically explore the conditions for sound production of the model in its control space. The fundamental frequency of the sound increases with tension in three membranes with different stiffness and mass. The lower-bound fundamental frequency increases with membrane mass. The membrane vibrations are strongly coupled to the resonance properties of the distal tube, most likely because of its reflective properties to sound waves. Our model is a gross simplification of the complex morphology found in birds, and more closely resembles mathematical models of the syrinx. Our results confirm several assumptions underlying existing mathematical models in a complex geometr

Computation of correlation-induced atomic displacements and structural transformations in paramagnetic KCuF3 and LaMnO3

We present a computational scheme for ab initio total-energy calculations of materials with strongly interacting electrons using a plane-wave basis set. It combines ab initio band structure and dynamical mean-field theory and is implemented in terms of plane-wave pseudopotentials. The present approach allows us to investigate complex materials with strongly interacting electrons and is able to treat atomic displacements, and hence structural transformations, caused by electronic correlations. Here it is employed to investigate two prototypical Jahn-Teller materials, KCuF3 and LaMnO3, in their paramagnetic phases. The computed equilibrium Jahn-Teller distortion and antiferro-orbital order agree well with experiment, and the structural optimization performed for paramagnetic KCuF3 yields the correct lattice constant, equilibrium Jahn-Teller distortion and tetragonal compression of the unit cell. Most importantly, the present approach is able to determine correlation-induced structural transformations, equilibrium atomic positions and lattice structure in both strongly and weakly correlated solids in their paramagnetic phases as well as in phases with long-range magnetic order.Comment: 27 pages, 11 figure

Exceptionally strong magnetism in 4d perovskites RTcO3 (R=Ca,Sr,Ba)

The evolution of the magnetic ordering temperature of the 4d3 perovskites RTcO3 (R=Ca,Sr,Ba) and its relation with its electronic and structural properties has been studied by means of hybrid density functional theory and Monte Carlo simulations. When compared to the most widely studied 3d perovskites the large spatial extent of the 4d shells and their relatively strong hybridization with oxygen weaken the tendency to form Jahn-Teller like orbital ordering. This strengthens the superexchange interaction. The resulting insulating G-type antiferromagnetic ground state is characterized by large superexchange coupling constants (26-35 meV) and Neel temperatures (750-1200 K). These monotonically increase as a function of the R ionic radius due to the progressive enhancement of the volume and the associated decrease of the cooperative rotation of the TcO6 octahedra.Comment: 4 pages, 3 figure

Correlative Microscopy of Morphology and Luminescence of Cu porphyrin aggregates

Transfer of energy and information through molecule aggregates requires as one important building block anisotropic, cable-like structures. Knowledge on the spatial correlation of luminescence and morphology represents a prerequisite in the understanding of internal processes and will be important for architecting suitable landscapes. In this context we study the morphology, fluorescence and phosphorescence of molecule aggregate structures on surfaces in a spatially correlative way. We consider as two morphologies, lengthy strands and isotropic islands. It turns out that phosphorescence is quite strong compared to fluorescence and the spatial variation of the observed intensities is largely in line with the amount of dye. However in proportion, the strands exhibit more fluorescence than the isotropic islands suggesting weaker non-radiative channels. The ratio fluorescence to phosphorescence appears to be correlated with the degree of aggregation or internal order. The heights at which luminescence saturates is explained in the context of attenuation and emission multireflection, inside the dye. This is supported by correlative photoemission electron microscopy which is more sensitive to the surface region. The lengthy structures exhibit a pronounced polarization dependence of the luminescence with a relative dichroism up to about 60%, revealing substantial perpendicular orientation preference of the molecules with respect to the substrate and parallel with respect to the strands