Effect of hydrodynamic correlations on the dynamics of polymers in dilute solution.

We analyze the effect of time-dependent hydrodynamic interactions on the dynamics of flexible polymers in dilute solution. In analytical calculations, the fluctuating hydrodynamics approach is adopted to describe the fluid, and a Gaussian model to represented the polymer. Simulations are performed exploiting the multiparticle collision dynamics approach, a mesoscale hydrodynamic simulation technique, to explicitly describe the fluid.

Parity effect in the ground state localization of antiferromagnetic chains coupled to a ferromagnet.

We investigate the ground states of antiferromagnetic Mn nanochains on Ni(110) by spin-polarized scanning tunneling microscopy in combination with theory. While the ferrimagnetic linear trimer experimentally shows the predicted collinear classical ground state, no magnetic contrast was observed for dimers and tetramers where noncollinear structures were expected based on ab initio theory. This striking observation can be explained by zero-point energy motion for even-numbered chains derived within a classical equation of motion leading to nonclassical ground states.

Many-body models for molecular nanomagnets.

We present a flexible and effective ab initio scheme to build many-body models for molecular nanomagnets, and to calculate magnetic exchange couplings and zero-field splittings. It is based on using localized Foster-Boys orbitals as a one-electron basis. We apply this scheme to three paradigmatic systems, the antiferromagnetic rings Cr8 and Cr7Ni, and the single-molecule magnet Fe4.

Anisotropy of spin relaxation and transverse transport in metals.

Using first-principles methods we explore the anisotropy of the spin relaxation and transverse transport properties in bulk metals with respect to the real-space direction of the spin-quantization axis in paramagnets or of the spontaneous magnetization in ferromagnets. Owing to the presence of the spin-orbit coupling the orbital and spin character of the Bloch states depends sensitively on the orientation of the spins relative to the crystal axes. This leads to drastic changes in quantities which rely on interband mixing induced by the spin-orbit interaction.

Emergence of metachronal waves in cilia arrays.

Propulsion by cilia is a fascinating and universal mechanism in biological organisms to generate fluid motion on the cellular level. Cilia are hair-like organelles, which are found in many different tissues and many uni- and multicellular organisms. Assembled in large fields, cilia beat neither randomly nor completely synchronously--instead they display a striking self-organization in the form of metachronal waves (MCWs).

Relationships between Electroencephalographic Spectral Peaks Across Frequency Bands.

The degree to which electroencephalographic spectral peaks are independent, and the relationships between their frequencies have been debated. A novel fitting method was used to determine peak parameters in the range 2-35 Hz from a large sample of eyes-closed spectra, and their interrelationships were investigated. Findings were compared with a mean-field model of thalamocortical activity, which predicts near-harmonic relationships between peaks.

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations.

RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient.

Anisotropy of spin relaxation in metals.

The concept of anisotropy of spin relaxation in nonmagnetic metals with respect to the spin direction of the injected electrons relative to the crystal orientation is introduced. The effect is related to an anisotropy of the Elliott-Yafet parameter, arising from a modulation of the decomposition of the spin-orbit Hamiltonian into spin-conserving and spin-flip terms as the spin quantization axis is varied. This anisotropy, reaching gigantic values for uniaxial transition metals (e.

Localizing the Charged Side Chains of Ion Channels within the Crowded Charge Models.

The simplified coarse grained models of selectivity of Nonner and co-workers predict ion selectivity for a variety of different ion channels. The model includes the charged atoms of the channel's charged residues and permeant ions. However its MC implementation does not take advantage of the increasingly large body of structural information available.

Flow-induced helical coiling of semiflexible polymers in structured microchannels.

The conformations of semiflexible (bio)polymers are studied in flow-through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the narrow high-velocity region into the wide low-velocity region of the channel. The transient helix formation is the result of a nonequilibrium and nonstationary buckling transition of the semiflexible polymer, which is subjected to a compressive force originating from the fluid-velocity variation in the channel.

Local Fluctuations and Conformational Transitions in Proteins.

The intrinsic plasticity of protein residues, along with the occurrence of transitions between distinct residue conformations, plays a pivotal role in a variety of molecular recognition events in the cell. Analysis aimed at identifying both of these features has been limited so far to protein-complex structures. We present a computationally efficient tool (T-pad), which quantitatively analyzes protein residues' flexibility and detects backbone conformational transitions.

Ab initio and semi-empirical van der Waals study of graphene-boron nitride interaction from a molecular point of view.

We have performed a systematic semi-empirical and ab initio van der Waals study to investigate the bonding mechanism of benzene (C(6)H(6)), triazine (C(3)N(3)H(3)) and borazine (B(3)N(3)H(6)) adsorbed on graphene and a single boron nitride (BN) sheet. The two semi-empirical approaches used to include the van der Waals (vdW) interactions in our density functional theory (DFT) calculations suggest that the strength of the molecule-surface interaction corresponds to a strong physisorption with no net charge transfer between the molecules and the corresponding substrates. This observation is strengthened by the use of first-principles non-local correlation vdW-DF functionals which provide a sound physical basis to include vdW interactions in DFT calculations.

Magnetic adatom induced Skyrmion-like spin texture in surface electron waves.

When a foreign atom is placed on a surface of a metal, the surrounding sea of electrons responds by screening the additional charge leading to oscillations or ripples. On surfaces, those electrons are sometimes confined to two-dimensional surface states, whose spin-degeneracy is lifted due to the Rashba effect arising from the spin-orbit interaction of electrons and the inversion asymmetric environment. It is believed that at least for a single adatom scanning tunneling microscopy measurements are insensitive to the Rashba splitting; i.

Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach.

The cellular uptake of cisplatin and of other platinum-based drugs is mediated by the high-affinity copper transporter Ctr1. The eight-residue long peptide called Mets7 (MTGMKGMS) mimics one of extracellular methionine (Met)-rich motifs of Ctr1. It is an excellent model for investigating the interaction of platinum drugs with Ctr1 under in vitro and in vivo conditions.

Hybrid functionals and GW approximation in the FLAPW method.

We present recent advances in numerical implementations of hybrid functionals and the GW approximation within the full-potential linearized augmented-plane-wave (FLAPW) method. The former is an approximation for the exchange–correlation contribution to the total energy functional in density-functional theory, and the latter is an approximation for the electronic self-energy in the framework of many-body perturbation theory. All implementations employ the mixed product basis, which has evolved into a versatile basis for the products of wave functions, describing the incoming and outgoing states of an electron that is scattered by interacting with another electron.

Electrically tunable quantum anomalous Hall effect in graphene decorated by 5d transition-metal adatoms.

Based on first-principles calculations, we predict that 5d transition metals on graphene present a unique class of hybrid systems exhibiting topological transport effects that can be manipulated effectively by external electric fields. The origin of this phenomenon lies in the exceptional magnetic properties and the large spin-orbit interaction of the 5d metals leading to significant magnetic moments accompanied with colossal magnetocrystalline anisotropy energies. A strong magnetoelectric response is predicted that offers the possibility to switch the spontaneous magnetization direction by moderate electric fields, enabling an electrically tunable quantum anomalous Hall effect.

Charge Kondo anomalies in PbTe doped with Tl impurities.

We investigate the properties of PbTe doped with a small concentration x of Tl impurities acting as acceptors and described by Anderson impurities with negative onsite correlation energy. We use the numerical renormalization group method to show that the resulting charge Kondo effect naturally accounts for the unusual low temperature and doping dependence of normal state properties, including the self-compensation effect in the carrier density and the nonmagnetic Kondo anomaly in the resistivity. These are found to be in good qualitative agreement with experiment.

Margination of white blood cells in microcapillary flow.

Margination of white blood cells (WBCs) towards vessel walls is an essential precondition for their efficient adhesion to the vascular endothelium. We perform numerical simulations with a two-dimensional blood flow model to investigate the dependence of WBC margination on hydrodynamic interactions of blood cells with the vessel walls, as well as on their collective behavior and deformability. We find WBC margination to be optimal in intermediate ranges of red blood cell (RBC) volume fractions and flow rates, while, beyond these ranges, it is substantially attenuated.

Dynamic self-assembly and directed flow of rotating colloids in microchannels.

Nonequilibrium structure formation and dynamics in suspensions of superparamagnetic colloids driven by an external rotating magnetic field are studied by particle-based mesoscale hydrodynamics simulations in confined geometry. We address the fundamental question how the rotation of the colloids about their own axes can be converted into a translational motion by breaking the symmetry of the confining geometry. We study a two-dimensional system of colloids with short-range repulsive interactions, which mimics flow in shallow microchannels.

Non-planar Dzyaloshinskii spirals and magnetic domain walls in non-centrosymmetric systems with orthorhombic anisotropy.

The basic micromagnetic models of Landau, Lifshitz, and Dzyaloshinskii, are extended by an anisotropy term with two independent parameters. The resulting ground states of the magnetic domains and the domain-wall profiles are discussed for crystal lattices with orthorhombic unit cells. In these simple geometries, the magnetization is not confined to a single plane.

Predicting human blood viscosity in silico.

The viscosity of blood has long been used as an indicator in the understanding and treatment of disease, and the advent of modern viscometers allows its measurement with ever-improving clinical convenience. However, these advances have not been matched by theoretical developments that can yield a quantitative understanding of blood's microrheology and its possible connection to relevant biomolecules (e.g.

Role of spin-flip transitions in the anomalous Hall effect of FePt alloy.

We carry out ab initio calculations which demonstrate the importance of the non-spin-conserving part of the spin-orbit interaction for the intrinsic anomalous Hall conductivity of ordered FePt alloys. The impact of this interaction is strongly reduced if Pt is replaced by the lighter isoelectronic element Pd. An analysis of the interband transitions responsible for the anomalous velocity reveals that spin-flip transitions occur not only at avoided band crossings near the Fermi level, but also between well-separated pairs of bands with similar dispersions.

Anisotropic spin Hall effect from first principles.

We report on first principles calculations of the anisotropy of the intrinsic spin Hall conductivity (SHC) in nonmagnetic hcp metals and in antiferromagnetic Cr. For most of the metals of this study we find large anisotropies. We derive the general relation between the SHC vector and the direction of spin polarization and discuss its consequences for hcp metals.

Design of the local spin polarization at the organic-ferromagnetic interface.

By means of ab initio calculations and spin-polarized scanning tunneling microscopy experiments the creation of a complex energy dependent magnetic structure with a tailored spin-polarized interface is demonstrated. We show this novel effect by adsorbing organic molecules containing π(p(z)) electrons onto a magnetic surface. The hybridization of the out-of-plane p(z) atomic-type orbitals with the d states of the metal leads to the inversion of the spin polarization at the organic site due to a p(z)-d Zener exchange-type mechanism.

Nature of the Mott transition in Ca2RuO4.

We study the origin of the temperature-induced Mott transition in Ca2RuO4. As a method we use the local-density approximation+dynamical mean-field theory. We show the following.