Physical Sensing of Surface Properties by Microswimmers--Directing Bacterial Motion via Wall Slip.

Bacteria such as Escherichia coli swim along circular trajectories adjacent to surfaces. Thereby, the orientation (clockwise, counterclockwise) and the curvature depend on the surface properties. We employ mesoscale hydrodynamic simulations of a mechano-elastic model of E.

Spin-Flip and Element-Sensitive Electron Scattering in the BiAg2 Surface Alloy.

Heavy metal surface alloys represent model systems to study the correlation between electron scattering, spin-orbit interaction, and atomic structure. Here, we investigate the electron scattering from the atomic steps of monolayer BiAg_{2} on Ag(111) using quasiparticle interference measurements and density functional theory. We find that intraband transitions between states of opposite spin projection can occur via a spin-flip backward scattering mechanism driven by the spin-orbit interaction.

Physics of microswimmers--single particle motion and collective behavior: a review.

Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia.

Local density of states at metal-semiconductor interfaces: an atomic scale study.

We investigate low temperature grown, abrupt, epitaxial, nonintermixed, defect-free n-type and p-type Fe/GaAs(110) interfaces by cross-sectional scanning tunneling microscopy and spectroscopy with atomic resolution. The probed local density of states shows that a model of the ideal metal-semiconductor interface requires a combination of metal-induced gap states and bond polarization at the interface which is nicely corroborated by density functional calculations. A three-dimensional finite element model of the space charge region yields a precise value for the Schottky barrier height.

Generalized Pauli constraints in reduced density matrix functional theory.

Functionals of the one-body reduced density matrix (1-RDM) are routinely minimized under Coleman's ensemble N-representability conditions. Recently, the topic of pure-state N-representability conditions, also known as generalized Pauli constraints, received increased attention following the discovery of a systematic way to derive them for any number of electrons and any finite dimensionality of the Hilbert space. The target of this work is to assess the potential impact of the enforcement of the pure-state conditions on the results of reduced density-matrix functional theory calculations.

The structural impact of DNA mismatches.

The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale.

Feeding the human brain model.

The goal of the Human Brain Project is to develop, during the next decade, an infrastructure capable of simulating a draft human brain model based on available experimental data. One of the key issues is therefore to integrate and make accessible the experimental data necessary to constrain and fully specify this model. The required data covers many different spatial scales, ranging from the molecular scale to the whole brain and these data are obtained using a variety of techniques whose measurements may not be directly comparable.

Microvascular blood flow resistance: Role of red blood cell migration and dispersion.

Microvascular blood flow resistance has a strong impact on cardiovascular function and tissue perfusion. The flow resistance in microcirculation is governed by flow behavior of blood through a complex network of vessels, where the distribution of red blood cells across vessel cross-sections may be significantly distorted at vessel bifurcations and junctions. In this paper, the development of blood flow and its resistance starting from a dispersed configuration of red blood cells is investigated in simulations for different hematocrit levels, flow rates, vessel diameters, and aggregation interactions between red blood cells.

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems.

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models.

Thermostat for nonequilibrium multiparticle-collision-dynamics simulations.

Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for complex fluid, is widely employed in nonequilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization of the fluid is often required for certain MPC variants. We investigate the influence of three thermostats on the nonequilibrium properties of a MPC fluid under shear or in Poiseuille flow.

ViSAPy: a Python tool for biophysics-based generation of virtual spiking activity for evaluation of spike-sorting algorithms.

Background: New, silicon-based multielectrodes comprising hundreds or more electrode contacts offer the possibility to record spike trains from thousands of neurons simultaneously. This potential cannot be realized unless accurate, reliable automated methods for spike sorting are developed, in turn requiring benchmarking data sets with known ground-truth spike times.

New Method: We here present a general simulation tool for computing benchmarking data for evaluation of spike-sorting algorithms entitled ViSAPy (Virtual Spiking Activity in Python).

Structure and dynamics in liquid bismuth and Bi(n) clusters: a density functional study.

Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available.

Spin Hall effects in metallic antiferromagnets.

We investigate four CuAu-I-type metallic antiferromagnets for their potential as spin current detectors using spin pumping and inverse spin Hall effect. Nontrivial spin Hall effects were observed for FeMn, PdMn, and IrMn while a much higher effect was obtained for PtMn. Using thickness-dependent measurements, we determined the spin diffusion lengths of these materials to be short, on the order of 1 nm.

Dynamics of self-sustained asynchronous-irregular activity in random networks of spiking neurons with strong synapses.

Random networks of integrate-and-fire neurons with strong current-based synapses can, unlike previously believed, assume stable states of sustained asynchronous and irregular firing, even without external random background or pacemaker neurons. We analyze the mechanisms underlying the emergence, lifetime and irregularity of such self-sustained activity states. We first demonstrate how the competition between the mean and the variance of the synaptic input leads to a non-monotonic firing-rate transfer in the network.

Interplay between the Kondo effect and the Ruderman-Kittel-Kasuya-Yosida interaction.

The interplay between the Ruderman-Kittel-Kasuya-Yosida interaction and the Kondo effect is expected to provide the driving force for the emergence of many phenomena in strongly correlated electron materials. Two magnetic impurities in a metal are the smallest possible system containing all these ingredients and define a bottom-up approach towards a long-term understanding of concentrated/dense systems. Here we report on the experimental and theoretical investigation of iron dimers buried below a Cu(100) surface by means of low-temperature scanning tunnelling spectroscopy combined with density functional theory and numerical renormalization group calculations.

Dynamic stability of sequential stimulus representations in adapting neuronal networks.

The ability to acquire and maintain appropriate representations of time-varying, sequential stimulus events is a fundamental feature of neocortical circuits and a necessary first step toward more specialized information processing. The dynamical properties of such representations depend on the current state of the circuit, which is determined primarily by the ongoing, internally generated activity, setting the ground state from which input-specific transformations emerge. Here, we begin by demonstrating that timing-dependent synaptic plasticity mechanisms have an important role to play in the active maintenance of an ongoing dynamics characterized by asynchronous and irregular firing, closely resembling cortical activity in vivo.

Quasi-particle energy spectra in local reduced density matrix functional theory.

Recently, we introduced [N. N. Lathiotakis, N.

Hydrodynamics of discrete-particle models of spherical colloids: a multiparticle collision dynamics simulation study.

We investigate the hydrodynamic properties of a spherical colloid model, which is composed of a shell of point particles by hybrid mesoscale simulations, which combine molecular dynamics simulations for the sphere with the multiparticle collision dynamics approach for the fluid. Results are presented for the center-of-mass and angular velocity correlation functions. The simulation results are compared with theoretical results for a rigid colloid obtained as a solution of the Stokes equation with no-slip boundary conditions.

Comprehensive large-scale assessment of intrinsic protein disorder.

Motivation: Intrinsically disordered regions are key for the function of numerous proteins. Due to the difficulties in experimental disorder characterization, many computational predictors have been developed with various disorder flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.

Hydrodynamic correlations and diffusion coefficient of star polymers in solution.

The center-of-mass dynamics of star polymers in dilute solution is analyzed by hybrid mesoscale simulations. The fluid is modeled by the multiparticle collision dynamics approach, a particle-based hydrodynamic simulation technique, which is combined with molecular dynamics simulations for the polymers. Star polymers of various functionalities are considered.

Real-space finite-difference calculation method of generalized Bloch wave functions and complex band structures with reduced computational cost.

Generalized Bloch wave functions of bulk structures, which are composed of not only propagating waves but also decaying and growing evanescent waves, are known to be essential for defining the open boundary conditions in the calculations of the electronic surface states and scattering wave functions of surface and junction structures. Electronic complex band structures being derived from the generalized Bloch wave functions are also essential for studying bound states of the surface and junction structures, which do not appear in conventional band structures. We present a novel calculation method to obtain the generalized Bloch wave functions of periodic bulk structures by solving a generalized eigenvalue problem, whose dimension is drastically reduced in comparison with the conventional generalized eigenvalue problem derived by Fujimoto and Hirose [Phys.

Membrane-wrapping contributions to malaria parasite invasion of the human erythrocyte.

The blood stage malaria parasite, the merozoite, has a small window of opportunity during which it must successfully target and invade a human erythrocyte. The process of invasion is nonetheless remarkably rapid. To date, mechanistic models of invasion have focused predominantly on the parasite actomyosin motor contribution to the energetics of entry.