Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER

Single particle analysis has become a key structural biology technique. Experimental images are extremely noisy, and during iterative refinement it is possible to stably incorporate noise into the reconstruction. Such “over-fitting” can lead to misinterpretation of the structure and flawed biological results. Several strategies are routinely used to prevent over-fitting, the most common being independent refinement of two sides of a split dataset. In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise, despite independent refinement of half datasets. We propose a modification of the refinement process through the application of a local signal-to-noise filter: SIDESPLITTER. We show that our approach can reduce over-fitting for both idealised and experimental data while maintaining independence between the two sides of a split refinement. SIDESPLITTER refinement leads to improved density, and can also lead to improvement of the final resolution in extreme cases where datasets are prone to severe over-fitting, such as small membrane proteins

Adaptive Optical Phase Estimation Using Time-Symmetric Quantum Smoothing

Quantum parameter estimation has many applications, from gravitational wave detection to quantum key distribution. We present the first experimental demonstration of the time-symmetric technique of quantum smoothing. We consider both adaptive and non-adaptive quantum smoothing, and show that both are better than their well-known time-asymmetric counterparts (quantum filtering). For the problem of estimating a stochastically varying phase shift on a coherent beam, our theory predicts that adaptive quantum smoothing (the best scheme) gives an estimate with a mean-square error up to $2\sqrt{2}$ times smaller than that from non-adaptive quantum filtering (the standard quantum limit). The experimentally measured improvement is $2.24 \pm 0.14$

Doping-dependence of nodal quasiparticle properties in high-TcT_{\rm c} cuprates studied by laser-excited angle-resolved photoemission spectroscopy

We investigate the doping dependent low energy, low temperature ($T$ = 5 K) properties of nodal quasiparticles in the d-wave superconductor Bi$_{2.1}$Sr$_{1.9}$CaCu$_2$O$_{8+\delta}$ (Bi2212). By utilizing ultrahigh resolution laser-excited angle-resolved photoemission spectroscopy, we obtain precise band dispersions near $E_{F}$, mean free paths and scattering rates ($\Gamma$) of quasiparticles. For optimally and overdoped, we obtain very sharp quasiparticle peaks of 8 meV and 6 meV full-width at half-maximum, respectively, in accord with terahertz conductivity. For all doping levels, we find the energy-dependence of $\Gamma \sim |\omega |$, while $\Gamma$($\omega =0$) shows a monotonic increase from overdoping to underdoping. The doping dependence suggests the role of electronic inhomogeneity on the nodal quasiparticle scattering at low temperature (5 K \lsim 0.07T_{\rm c}), pronounced in the underdoped region

Impurity scattering in unconventional density waves

We have investigated the effect of nonmagnetic impurities on the quasi-one-dimensional unconventional density wave (UDW) ground state. The thermodynamics were found to be close to those of a d-wave superconductor in the Born limit. Four different optical conductivity curves were found depending on the direction of the applied electric field and on the wavevector dependence of the gap.Comment: 14 pages, 9 figure

Layer-specific hole concentrations in Bi2Sr2(Y1-xCax)Cu208+[delta] as probed by XANES spectroscopy and coulometric redox analysis

Induction of holes not only in the superconductive CuO2 plane but also in the Bi2O2+δ charge reservoir of the Bi2Sr2(Y1-xCax)Cu2O8+δ superconductor upon CaII-for-YIII substitution is evidenced by means of two independent techniques, i.e., high-resolution x-ray-absorption near-edge structure (XANES) spectroscopy measurements and coulometric redox titrations. The absolute values derived for the CuO2-plane hole concentration from the Cu L2,3-edge XANES spectra are in good agreement with those obtained from the coulometric redox analysis. The CuO2-plane hole concentration is found to increase from 0.03 to 0.14 concomitantly with the increase in the BiO1+δ/2-layer hole concentration from 0.00 to 0.13 as the Ca-substitution level, x, increases from 0 to 1. The threshold CuO2-plane hole concentration for the appearance of superconductivity is determined at 0.06, while the highest Tc is obtained at the hole concentration of 0.12. In the O K-edge XANES spectrum, the increases in the CuO2-plane and BiO1+δ/2-layer hole concentrations with increasing x are seen as enhancement in the relative intensities of the pre-edge peaks at ∼528.3 and ∼530.5 eV, respectively.Peer reviewe

Layered-specific hole concentrations in Bi2Sr2(Y1-xCax)Cu2O8+d as probed by XANES spectroscopy and coulometric redox analysis

Induction of holes not only in the superconductive CuO2 plane but also in the Bi2O2+d charge reservoir of the Bi2Sr2(Y1-xCax)Cu2O8+d superconductor upon CaII-for-YIII substitution is evidenced by means of two independent techniques, i.e., high-resolution x-ray-absorption near-edge structure (XANES) spectroscopy measurements and coulometric redox titrations. The absolute values derived for the CuO2-plane hole concentration from the Cu L2,3-edge XANES spectra are in good agreement with those obtained from the coulometric redox analysis. The CuO2-plane hole concentration is found to increase from 0.03 to 0.14 concomitantly with the increase in the BiO1+d/2-layer hole concentration from 0.00 to 0.13 as the Ca-substitution level, x, increases from 0 to 1. The threshold CuO2-plane hole concentration for the appearance of superconductivity is determined at 0.06, while the highest Tc is obtained at the hole concentration of 0.12. In the O K-edge XANES spectrum, the increases in the CuO2-plane and BiO1+d/2-layer hole concentrations with increasing x are seen as enhancement in the relative intensities of the pre-edge peaks at ~528.3 and \~530.5 eV, respectively.Comment: 12 pages, 6 figures, to appear in Phys. Rev.