Author Correction: Universality of defect-skyrmion interaction profiles.

The original version of this Article contained an error in the Acknowledgements, which incorrectly omitted from the end the following: 'We acknowledge the computing time granted by the JARA-HPC Vergabegremium and VSR commission on the supercomputer JURECA at Forschungszentrum Jülich.' This has been corrected in both the PDF and HTML versions of the Article.

Distinct modes of top-down cognitive processing in the ventral visual cortex.

Top-down cognitive control leads to changes in the sensory processing of the brain. In visual perception such changes can take place in the ventral visual cortex altering the functional asymmetry in forward and backward connections. Here we used fixation-related evoked responses of EEG measurement and dynamic causal modeling to examine hierarchical forward-backward asymmetry, while twenty-six healthy adults performed cognitive tasks that require different types of top-down cognitive control (memorizing or searching visual objects embedded in a natural scene image).

Active Brownian ring polymers.

The conformational and dynamical properties of semiflexible active Brownian ring polymers are investigated analytically. A ring is described by the Gaussian semiflexible polymer model accounting for the finite contour length. Activity is implemented by a Gaussian, non-Markovian stochastic process resembling either an external nonthermal force or a local self-propulsion velocity as for an active Ornstein-Uhlenbeck particle.

Influence of bonded interactions on structural phases of flexible polymers.

We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states obtained in advanced replica-exchange Monte Carlo simulations is analyzed by employing the recently developed generalized microcanonical inflection-point analysis method, which enables the identification of diverse structural phases and the construction of a suitably parameterized hyperphase diagram. It reveals that icosahedral phases dominate for polymers with asymmetric and narrow bond potentials, whereas polymers with symmetric and more elastic bonds tend to form amorphous structures with non-icosahedral cores.

Traction force microscopy with optimized regularization and automated Bayesian parameter selection for comparing cells.

Adherent cells exert traction forces on to their environment which allows them to migrate, to maintain tissue integrity, and to form complex multicellular structures during developmental morphogenesis. Traction force microscopy (TFM) enables the measurement of traction forces on an elastic substrate and thereby provides quantitative information on cellular mechanics in a perturbation-free fashion. In TFM, traction is usually calculated via the solution of a linear system, which is complicated by undersampled input data, acquisition noise, and large condition numbers for some methods.

Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data.

Computational neuroscience relies on simulations of neural network models to bridge the gap between the theory of neural networks and the experimentally observed activity dynamics in the brain. The rigorous validation of simulation results against reference data is thus an indispensable part of any simulation workflow. Moreover, the availability of different simulation environments and levels of model description require also validation of model implementations against each other to evaluate their equivalence.

Chronology of motor-mediated microtubule streaming.

We introduce a filament-based simulation model for coarse-grained, effective motor-mediated interaction between microtubule pairs to study the time-scales that compose cytoplasmic streaming. We characterise microtubule dynamics in two-dimensional systems by chronologically arranging five distinct processes of varying duration that make up streaming, from microtubule pairs to collective dynamics. The structures found were polarity sorted due to the propulsion of antialigned microtubules.

Structural Determinants of the Prion Protein N-Terminus and Its Adducts with Copper Ions.

The N-terminus of the prion protein is a large intrinsically disordered region encompassing approximately 125 amino acids. In this paper, we review its structural and functional properties, with a particular emphasis on its binding to copper ions. The latter is exploited by the region's conformational flexibility to yield a variety of biological functions.

Rigorous Neural Network Simulations: A Model Substantiation Methodology for Increasing the Correctness of Simulation Results in the Absence of Experimental Validation Data.

The reproduction and replication of scientific results is an indispensable aspect of good scientific practice, enabling previous studies to be built upon and increasing our level of confidence in them. However, reproducibility and replicability are not sufficient: an incorrect result will be accurately reproduced if the same incorrect methods are used. For the field of simulations of complex neural networks, the causes of incorrect results vary from insufficient model implementations and data analysis methods, deficiencies in workmanship (e.

Weak Shape Anisotropy Leads to a Nonmonotonic Contribution to Crowding, Impacting Protein Dynamics under Physiologically Relevant Conditions.

The effect of a nonspherical particle shape on the dynamics in crowded solutions presents a significant challenge for a comprehensive understanding of interaction and structural relaxation in biological and soft matter. We report that small deviations from a spherical shape induce a nonmonotonic contribution to the crowding effect on the short-time cage diffusion compared with spherical systems, using molecular dynamics simulations with mesoscale hydrodynamics of a multiparticle collision dynamics fluid in semidilute systems with volume fractions smaller than 0.35.

Duplication, Collapse, and Escape of Magnetic Skyrmions Revealed Using a Systematic Saddle Point Search Method.

Various transitions that a magnetic Skyrmion can undergo are found in calculations using a method for climbing up the energy surface and converging onto first order saddle points. In addition to collapse and escape through a boundary, the method identifies a transition where the Skyrmion divides and forms two Skyrmions. The activation energy for this duplication process can be similar to that of collapse and escape.

Heavy Physics Contributions to Neutrinoless Double Beta Decay from QCD.

Observation of neutrinoless double beta decay, a lepton number violating process that has been proposed to clarify the nature of neutrino masses, has spawned an enormous world-wide experimental effort. Relating nuclear decay rates to high-energy, beyond the standard model (BSM) physics requires detailed knowledge of nonperturbative QCD effects. Using lattice QCD, we compute the necessary matrix elements of short-range operators, which arise due to heavy BSM mediators, that contribute to this decay via the leading order π^{-}→π^{+} exchange diagrams.

Spin-Resolved Electronic Response to the Phase Transition in MoTe_{2}.

The semimetal MoTe_{2} is studied by spin- and angle-resolved photoemission spectroscopy across the centrosymmetry-breaking structural transition temperature of the bulk. A three-dimensional spin-texture is observed in the bulk Fermi surface in the low temperature, noncentrosymmetric phase that is consistent with first-principles calculations. The spin texture and two types of surface Fermi arc are not completely suppressed above the bulk transition temperature.

Universality of defect-skyrmion interaction profiles.

Magnetic skyrmions are prime candidates for future spintronic devices. However, incorporating them as information carriers hinges on their interaction with defects ubiquitous in any device. Here we map from first-principles, the energy profile of single skyrmions interacting with single-atom impurities, establishing a generic shape as function of the defect's electron filling.

Modification of Dzyaloshinskii-Moriya-Interaction-Stabilized Domain Wall Chirality by Driving Currents.

We measure and analyze the chirality of Dzyaloshinskii-Moriya-interaction (DMI) stabilized spin textures in multilayers of Ta|Co_{20}F_{60}B_{20}|MgO. The effective DMI is measured experimentally using domain wall motion measurements, both in the presence (using spin-orbit torques) and absence of driving currents (using magnetic fields). We observe that the current-induced domain wall motion yields a change in effective DMI magnitude and opposite domain wall chirality when compared to field-induced domain wall motion (without current).

A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas.

Cortical activity has distinct features across scales, from the spiking statistics of individual cells to global resting-state networks. We here describe the first full-density multi-area spiking network model of cortex, using macaque visual cortex as a test system. The model represents each area by a microcircuit with area-specific architecture and features layer- and population-resolved connectivity between areas.

Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study.

Human G-protein coupled receptors (GPCRs) are important targets for pharmaceutical intervention against neurological diseases. Here, we use molecular simulation to investigate the key step in ligand recognition governed by the extracellular domains in the neuronal adenosine receptor type 2A (hAR), a target for neuroprotective compounds. The ligand is the high-affinity antagonist (4-(2-(7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-ylamino)ethyl)phenol), embedded in a neuronal membrane mimic environment.

Flow-Induced Transitions of Red Blood Cell Shapes under Shear.

A recent study of red blood cells (RBCs) in shear flow [Lanotte et al., Proc. Natl.

Collective behavior of self-propelled rods with quorum sensing.

Active agents-like phoretic particles, bacteria, sperm, and cytoskeletal filaments in motility assays-show a large variety of motility-induced collective behaviors, such as aggregation, clustering, and phase separation. The behavior of dense suspensions of engineered phoretic particles and of bacteria during biofilm formation is determined by two qualitatively different physical mechanisms: (i) volume exclusion (short-range steric repulsion) and (ii) quorum sensing (longer-range reduced propulsion due to alteration of the local chemical environment). To systematically characterize such systems, we study semi-penetrable self-propelled rods in two dimensions, with a propulsion force that decreases with increasing local rod density, by employing Brownian dynamics simulations.

Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models.

Any modeler who has attempted to reproduce a spiking neural network model from its description in a paper has discovered what a painful endeavor this is. Even when all parameters appear to have been specified, which is rare, typically the initial attempt to reproduce the network does not yield results that are recognizably akin to those in the original publication. Causes include inaccurately reported or hidden parameters (e.

Criteria on Balance, Stability, and Excitability in Cortical Networks for Constraining Computational Models.

During ongoing and Up state activity, cortical circuits manifest a set of dynamical features that are conserved across these states. The present work systematizes these phenomena by three notions: excitability, the ability to sustain activity without external input; balance, precise coordination of excitatory and inhibitory neuronal inputs; and stability, maintenance of activity at a steady level. Slice preparations exhibiting Up states demonstrate that balanced activity can be maintained by small local circuits.

Effect of spectrin network elasticity on the shapes of erythrocyte doublets.

Red blood cell (RBC) aggregates play an important role in determining blood rheology. RBCs in plasma or polymer solution interact attractively to form various shapes of RBC doublets, where the attractive interactions can be varied by changing the solution conditions. A systematic numerical study on RBC doublet formation is performed, which takes into account the shear elasticity of the RBC membrane due to the spectrin cytoskeleton, in addition to the membrane bending rigidity.

Bimetallic NiMoN Nanowires with a Preferential Reactive Facet: An Ultraefficient Bifunctional Electrocatalyst for Overall Water Splitting.

Faceted nanomaterials with highly reactive exposed facets have been the target of intense researches owing to their significantly enhanced catalytic performance. NiMoN nanowires with the (100) facet preferentially exposed were prepared by an in situ N/O exchange and the morphology tuned by using a rationally designed NiMoO precursor. The facet-tuned NiMoN nanowires exhibited excellent electrocatalytic activity for the hydrogen evolution reaction (HER) under both alkaline and acidic conditions that was comparable to that of noble metal platinum.

Corrigendum: Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers.

[This corrects the article DOI: 10.3389/fninf.2018.