Combined aptamer and transcriptome sequencing of single cells.

The transcriptome and proteome encode distinct information that is important for characterizing heterogeneous biological systems. We demonstrate a method to simultaneously characterize the transcriptomes and proteomes of single cells at high throughput using aptamer probes and droplet-based single cell sequencing. With our method, we differentiate distinct cell types based on aptamer surface binding and gene expression patterns. Aptamers provide advantages over antibodies for single cell protein characterization, including rapid, in vitro, and high-purity generation via SELEX, and the ability to amplify and detect them with PCR and sequencing

Questioning the existence of a unique ground state structure for Si clusters

Density functional and quantum Monte Carlo calculations challenge the existence of a unique ground state structure for certain Si clusters. For Si clusters with more than a dozen atoms the lowest ten isomers are close in energy and for some clusters entropic effects can change the energetic ordering of the configurations. Isotope pure configurations with rotational symmetry and symmetric configurations containing one additional isotope are disfavored by these effects. Comparisons with experiment are thus difficult since a mixture of configurations is to be expected at thermal equilibrium

Systematic computation of crystal field multiplets for X-ray core spectroscopies

We present a new approach to computing multiplets for core spectroscopies, whereby the crystal field is constructed explicitly from the positions and charges of surrounding atoms. The simplicity of the input allows the consideration of crystal fields of any symmetry, and in particular facilitates the study of spectroscopic effects arising from low symmetry environments. The interplay between polarization directions and crystal field can also be conveniently investigated. The determination of the multiplets proceeds from a Dirac density functional atomic calculation, followed by the exact diagonalization of the Coulomb, spin-orbit and crystal field interactions for the electrons in the open shells. The eigenstates are then used to simulate X-ray Absorption Spectroscopy and Resonant Inelastic X-ray Scattering spectra. In examples ranging from high symmetry down to low symmetry environment, comparisons with experiments are done with unadjusted model parameters as well as with semi-empirically optimized ones. Furthermore, predictions for the RIXS of low-temperature MnO and for Dy in a molecular complex are proposed.Comment: Accepted for publication in Phys. Rev.

Electronic structure and physical properties of the spinel-type phase of BeP2N4 from all-electron density functional calculations

Using density-functional-theory-based ab initio methods, the electronic structure and physical properties of the newly synthesized nitride BeP2N4 with a phenakite-type structure and the predicted high-pressure spinel phase of BeP2N4 are studied in detail. It is shown that both polymorphs are wide band-gap semiconductors with relatively small electron effective masses at the conduction-band minima. The spinel-type phase is more covalently bonded due to the increased number of P-N bonds for P at the octahedral sites. Calculations of mechanical properties indicate that the spinel-type polymorph is a promising superhard material with notably large bulk, shear, and Young’s moduli. Also calculated are the Be K, P K, P L3, and N K edges of the electron energy-loss near-edge structure for both phases. They show marked differences because of the different local environments of the atoms in the two crystalline polymorphs. These differences will be very useful for the experimental identification of the products of high-pressure syntheses targeting the predicted spinel-type phase of BeP2N4

Non-Adiabatic Potential-Energy Surfaces by Constrained Density-Functional Theory

Non-adiabatic effects play an important role in many chemical processes. In order to study the underlying non-adiabatic potential-energy surfaces (PESs), we present a locally-constrained density-functional theory approach, which enables us to confine electrons to sub-spaces of the Hilbert space, e.g. to selected atoms or groups of atoms. This allows to calculate non-adiabatic PESs for defined charge and spin states of the chosen subsystems. The capability of the method is demonstrated by calculating non-adiabatic PESs for the scattering of a sodium and a chlorine atom, for the interaction of a chlorine molecule with a small metal cluster, and for the dissociation of an oxygen molecule at the Al(111) surface.Comment: 11 pages including 7 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.htm

Evolution of the interfacial structure of LaAlO3 on SrTiO3

The evolution of the atomic structure of LaAlO3 grown on SrTiO3 was investigated using surface x-ray diffraction in conjunction with model-independent, phase-retrieval algorithms between two and five monolayers film thickness. A depolarizing buckling is observed between cation and oxygen positions in response to the electric field of polar LaAlO3, which decreases with increasing film thickness. We explain this in terms of competition between elastic strain energy, electrostatic energy, and electronic reconstructions. The findings are qualitatively reproduced by density-functional theory calculations. Significant cationic intermixing across the interface extends approximately three monolayers for all film thicknesses. The interfaces of films thinner than four monolayers therefore extend to the surface, which might affect conductivity

Evidence for coupling between collective state and phonons in two-dimensional charge-density-wave systems

We report on a Raman scattering investigation of the charge-density-wave (CDW), quasi two-dimensional rare-earth tri-tellurides $R$Te$_3$ ($R$= La, Ce, Pr, Nd, Sm, Gd and Dy) at ambient pressure, and of LaTe$_3$ and CeTe$_3$ under externally applied pressure. The observed phonon peaks can be ascribed to the Raman active modes for both the undistorted as well as the distorted lattice in the CDW state by means of a first principles calculation. The latter also predicts the Kohn anomaly in the phonon dispersion, driving the CDW transition. The integrated intensity of the two most prominent modes scales as a characteristic power of the CDW-gap amplitude upon compressing the lattice, which provides clear evidence for the tight coupling between the CDW condensate and the vibrational modes

Tunable Conductivity and Conduction Mechanism in a UV light activated electronic conductor

A tunable conductivity has been achieved by controllable substitution of a novel UV light activated electronic conductor. The transparent conducting oxide system H-doped Ca12-xMgxAl14O33 (x = 0; 0.1; 0.3; 0.5; 0.8; 1.0) presents a conductivity that is strongly dependent on the substitution level and temperature. Four-point dc-conductivity decreases with x from 0.26 S/cm (x = 0) to 0.106 S/cm (x = 1) at room temperature. At each composition the conductivity increases (reversibly with temperature) until a decomposition temperature is reached; above this value, the conductivity drops dramatically due to hydrogen recombination and loss. The observed conductivity behavior is consistent with the predictions of our first principles density functional calculations for the Mg-substituted system with x=0, 1 and 2. The Seebeck coefficient is essentially composition- and temperature-independent, the later suggesting the existence of an activated mobility associated with small polaron conduction. The optical gap measured remains constant near 2.6 eV while transparency increases with the substitution level, concomitant with a decrease in carrier content.Comment: Submitted for publicatio

Evidence for SrHo2O4 and SrDy2O4 as model J1-J2 zig-zag chain materials

Neutron diffraction and inelastic spectroscopy is used to characterize the magnetic Hamiltonian of SrHo2O4 and SrDy2O4. Through a detailed computation of the crystal-field levels we find site- dependent anisotropic single-ion magnetism in both materials and diffraction measurements show the presence of strong one-dimensional spin correlations. Our measurements indicate that competing interactions of the zig-zag chain, combined with frustrated interchain interactions, play a crucial role in stabilizing spin-liquid type correlations in this series.Comment: 5 pages, 5 figure