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

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

Mice produce ultrasonic vocalizations by intra-laryngeal planar impinging jets

Rodent ultrasonic vocalizations (USVs) are a vital tool for linking gene mutations to behavior in mouse models of communication disorders, such as autism [1. However, we currently lack an understanding of how physiological and physical mechanisms combine to generate acoustic features of the vocalizations, and thus cannot meaningfully relate those features to experimental treatments. Here we test and provide evidence against the two leading hypotheses explaining USV production: superficial vocal fold vibrations [2, and a hole-tone whistle [3. Instead, we propose and provide theoretical and experimental evidence for an alternative and novel vocal production mechanism: a glottal jet impinging onto the laryngeal inner planar wall. Our data provide a framework for future research on the neuromuscular control of mouse vocal production and for interpreting mouse vocal behavior phenotypes.National Science Foundation (Grant ID: IOS 1257768), Danish Research Council, Carlsberg Foundatio

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

LiFE Assessment Tool

As part of an ongoing study to construct a molecular Turing machine in which a polymer chain is encoded via allosteric information transfer between macrocyclic complexes, we describe the thermodynamic and kinetic characterization of a multicomponent self-assembled system based on a zinc porphyrin macrocyclic compound, a bidentate ligand (1,4-diazabicyclo[2.2.2]octane, DABCO), and a viologen-substituted polymer guest. Initial addition of DABCO to the porphyrin macrocycle in chloroform solution leads to the formation of a stable 2:1 (porphyrin:DABCO) dimeric complex, even under dilute conditions, by means of strong cooperative interactions involving hydrogen and metal-ligand bonds. Further titration of the porphyrin-DABCO mixtures with the polymer gives rise to a complex array of species in the solution. The system is analyzed in detail by a combination of spectroscopic measurements and computational modeling. Each association constant in the binding scheme and the fraction of each individual complex that is formed in solution are determined precisely using a mass-balance model. Kinetic studies revealed that the rates of the polymer threading and dethreading in and out of the dimeric system are remarkably slow, indicating that the polymer is locked inside the cavity of the stable 2:1 dimeric complex as a result of strong allosteric interactions

Effect of Chirality on the Binding of Viologen Guests in Porphyrin Macrocycles

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Topological defects and shape of aromatic self-assembled vesicles

We show that the stacking of flat aromatic molecules on a curved surface results in topological defects. We consider, as an example, spherical vesicles, self-assembled from molecules with 5- and 6-thiophene cores. We predict that the symmetry of the molecules influences the number of topological defects and the resulting equilibrium shape.Comment: accepted as a Letter in the J. Phys. Chem.

Aerodynamics and motor control of ultrasonic vocalizations for social communication in mice and rats.

BACKGROUND: Rodent ultrasonic vocalizations (USVs) are crucial to their social communication and a widely used translational tool for linking gene mutations to behavior. To maximize the causal interpretation of experimental treatments, we need to understand how neural control affects USV production. However, both the aerodynamics of USV production and its neural control remain poorly understood. RESULTS: Here, we test three intralaryngeal whistle mechanisms-the wall and alar edge impingement, and shallow cavity tone-by combining in vitro larynx physiology and individual-based 3D airway reconstructions with fluid dynamics simulations. Our results show that in the mouse and rat larynx, USVs are produced by a glottal jet impinging on the thyroid inner wall. Furthermore, we implemented an empirically based motor control model that predicts motor gesture trajectories of USV call types. CONCLUSIONS: Our results identify wall impingement as the aerodynamic mechanism of USV production in rats and mice. Furthermore, our empirically based motor control model shows that both neural and anatomical components contribute to USV production, which suggests that changes in strain specific USVs or USV changes in disease models can result from both altered motor programs and laryngeal geometry. Our work provides a quantitative neuromechanical framework to evaluate the contributions of brain and body in shaping USVs and a first step in linking descending motor control to USV production

Two-Dimensional Molecular Patterning by Surface-Enhanced Zn-Porphyrin Coordination

In this contribution, we show how zinc-5,10,15,20-meso-tetradodecylporphyrins (Zn-TDPs) self-assemble into stable organized arrays on the surface of graphite, thus positioning their metal center at regular distances from each other, creating a molecular pattern, while retaining the possibility to coordinate additional ligands. We also demonstrate that Zn-TDPs coordinated to 3-nitropyridine display a higher tendency to be adsorbed at the surface of highly oriented pyrolytic graphite (HOPG) than noncoordinated ones. In order to investigate the two-dimensional (2D) self-assembly of coordinated Zn-TDPs, solutions with different relative concentrations of 3-nitropyridine and Zn-TDP were prepared and deposited on the surface of HOPG. STM measurements at the liquid-solid interface reveal that the ratio of coordinated Zn-TDPs over noncoordinated Zn-TDPs is higher at the n-tetradecane/HOPG interface than in n-tetradecane solution. This enhanced binding of the axial ligand at the liquid/solid interface is likely related to the fact that physisorbed Zn-TDPs are better binding sites for nitropyridines.