arXiv subjects

Nan Xu

Publications and source records attributed to Nan Xu.

116 records · Page 7Linked to original sources

arXiv2017

Initial validation for the estimation of resting-state fMRI effective connectivity by a generalization of the correlation approach

Resting-state functional MRI (rs-fMRI) is widely used to noninvasively study human brain networks. Network functional connectivity is often estimated by calculating the timeseries correlation between blood-oxygen-level dependent (BOLD) signal from different regions of interest. However, standard correlation cannot characterize the direction of information flow between regions. In this paper, we introduce and test a new concept, prediction correlation, to estimate effective connectivity in functional brain networks from rs-fMRI. In this approach, the correlation between two BOLD signals is replaced by a correlation between one BOLD signal and a prediction of this signal via a causal system driven by another BOLD signal. Three validations are described: (1) Prediction correlation performed well on simulated data where the ground truth was known, and outperformed four other methods. (2) On simulated data designed to display the "common driver" problem, prediction correlation did not introduce false connections between non-interacting driven ROIs. (3) On experimental data, prediction correlation recovered the previously identified network organization of human brain. Prediction correlation scales well to work with hundreds of ROIs, enabling it to assess whole brain interregional connectivity at the single subject level. These results provide an initial validation that prediction correlation can capture the direction of information flow and estimate the duration of extended temporal delays in information flow between regions of interest based on BOLD signal. This approach not only maintains the high sensitivity to network connectivity provided by the correlation analysis, but also performs well in the estimation of causal information flow in the brain.

q-bio.QM↗

arXiv2016

3D Reconstruction of Heterogeneous Virus Particles with Statistical Geometric Symmetry

In 3-D reconstruction problems, the image data obtained from cryo electron microscopy is the projection of many heterogeneous instances of the object under study (e.g., a virus). When the object is heterogeneous but has an overall symmetry, it is natural to describe the object as stochastic with symmetrical statistics. This paper presents a maximum likelihood reconstruction approach which allows each object to lack symmetry while constraining the {\it statistics} of the ensemble of objects to have symmetry. This algorithm is demonstrated on bacteriophage HK97 and is contrasted with an existing algorithm in which each object, while still heterogeneous, has the symmetry. Reconstruction results show that the proposed algorithm eliminates long-standing distortions in previous heterogeneity calculations associated with symmetry axes, and provides estimates that make more biologically sense than the estimates of existing algorithms.

q-bio.QM↗

arXiv2016

Real basis functions of polyhedral groups

The basis of the identity representation of a polyhedral group is able to describe functions with symmetries of a platonic solid, i.e., 3-D objects which geometrically obey the cubic symmetries. However, to describe the dynamic of assembles of heterogeneous 3-D structures, a situation that each object lacks the symmetries but obeys the symmetries on a level of statistics, the basis of all representations of a group is required. While those 3-D objects are often transformed to real functions on $L_2$ space, it is desirable to generate a complete basis on real space. This paper deduces the existence of a basis on real space for each polyhedral group, and introduces a novel approach to explicitly compute these real basis functions, of which properties are further explored.

math.GR↗

arXiv2015

Micro-metric electronic patterning of a topological band structure using a photon beam

In an ideal 3D topological insulator (TI), the bulk is insulating and the surface conducting due to the existence of metallic states that are localized on the surface; these are the topological surface states. Quaternary Bi-based compounds of Bi$_{2-x}$Sb$_{x}$Te$_{3-y}$Se$_{y}$ with finely-tuned bulk stoichiometries are good candidates for realizing ideal 3D TI behavior due to their bulk insulating character. However, despite its insulating bulk in transport experiments, the surface region of Bi$_{2-x}$Sb$_{x}$Te$_{3-y}$Se$_{y}$ crystals cleaved in ultrahigh vacuum also exhibits occupied states originating from the bulk conduction band. This is due to adsorbate-induced downward band-bending, a phenomenon known from other Bi-based 3D TIs. Here we show, using angle-resolved photoemission, how an EUV light beam of moderate flux can be used to exclude these topologically trivial states from the Fermi level of Bi$_{1.46}$Sb$_{0.54}$Te$_{1.7}$Se$_{1.3}$ single crystals, thereby re-establishing the purely topological character of the low lying electronic states of the system. We furthermore prove that this process is highly local in nature in this bulk-insulating TI, and are thus able to imprint structures in the spatial energy landscape at the surface. We illustrate this by `writing' micron-sized letters in the Dirac point energy of the system.

cond-mat.mtrl-sci↗

arXiv2015

Dirac states with knobs on: interplay of external parameters and the surface electronic properties of 3D topological insulators

Topological insulators are a novel materials platform with high applications potential in fields ranging from spintronics to quantum computation. In the ongoing scientific effort to demonstrate controlled manipulation of their electronic structure by external means, stoichiometric variation and surface decoration are two effective approaches that have been followed. In ARPES experiments, both approaches are seen to lead to electronic band structure changes. Such approaches result in variations of the energy position of bulk and surface-related features and the creation of two-dimensional electron gases.The data presented here demonstrate that a third manipulation handle is accessible by utilizing the amount of illumination a topological insulator surface has been exposed to under typical experimental ARPES conditions. Our results show that this new, third, knob acts on an equal footing with stoichiometry and surface decoration as a modifier of the electronic band structure, and that it is in continuous competition with the latter. The data clearly point towards surface photovoltage and photo-induced desorption as the physical phenomena behind modifications of the electronic band structure under exposure to high-flux photons. We show that the interplay of these phenomena can minimize and even eliminate the adsorbate-related surface band bending on typical binary, ternary and quaternary Bi-based topological insulators. Including the influence of the sample temperature, these data set up a framework for the external control of the electronic band structure in topological insulator compounds in an ARPES setting. Four external knobs are available: bulk stoichiometry, surface decoration, temperature and photon exposure. These knobs can be used in conjunction to tune the band energies near the surface and consequently influence the topological properties of the relevant electronic states.

cond-mat.mtrl-sci↗

arXiv2014

Dynamical correlations and screened exchange on the experimental bench: spectral properties of the cobalt pnictide BaCo2As2

Understanding the Fermi surface and low-energy excitations of iron or cobalt pnictides is crucial for assessing electronic instabilities such as magnetic or superconducting states. Here, we propose and implement a new approach to compute the low-energy properties of correlated electron materials, taking into account both screened exchange beyond the local density approximation and local dynamical correlations. The scheme allows us to resolve the puzzle of BaCo2As2, for which standard electronic structure techniques predict a ferromagnetic instability not observed in nature.

cond-mat.str-el↗

arXiv2014

Correlation-induced self-doping in intercalated iron-pnictide superconductor Ba2Ti2Fe2As4O

The electronic structure of the intercalated iron-based superconductor Ba2Ti2Fe2As4O (Tc - 21.5 K) has been investigated by using angle-resolved photoemission spectroscopy and combined local density approximation and dynamical mean field theory calculations. The electronic states near the Fermi level are dominated by both the Fe 3d and Ti 3d orbitals, indicating that the spacing layers separating different FeAs layers are also metallic. By counting the enclosed volumes of the Fermi surface sheets, we observe a large self-doping effect, i.e. 0.25 electrons per unit cell are transferred from the FeAs layer to the Ti2As2O layer, leaving the FeAs layer in a hole-doped state. This exotic behavior is successfully reproduced by our dynamical mean field calculations, in which the self-doping effect is attributed to the electronic correlations in the Fe 3d shell. Our work provides an alternative route of effective doping without element substitution for iron-based superconductors.

cond-mat.supr-con↗

arXiv2011

Unconventional superconducting gap in NaFe$_{0.95}$Co$_{0.05}$As observed by angle-resolved photoemission spectroscopy

We have performed high resolution angle-resolved photoemission measurements on superconducting electron-doped NaFe$_{0.95}$Co$_{0.05}$As ($T_{c}\sim$18 K). We observed a hole-like Fermi surface around the zone center and two electron-like Fermi surfaces around the M point which can be connected by the $Q=(π, π)$ wavevector, suggesting that scattering over the near-nested Fermi surfaces is important to the superconductivity of this "111" pnicitide. Nearly isotropic superconducting gaps with sharp coherent peaks are observed below $T_c$ on all three Fermi surfaces. Upon increasing temperature through $T_c$, the gap size shows little change while the coherence vanishes. Large ratios of $2Δ/k_{B}T_{c}\sim8$ are observed for all the bands, indicating a strong coupling in this system. These results are not expected from a classical phonon-mediated pairing mechanism.

cond-mat.supr-con↗