Cryo-EM map interpretation and protein model-building using iterative map segmentation.

A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a Cα model. The Cα model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo-EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps

Temperature and magnetic-field dependence of the conductivity of YBaCuO films in the vicinity of superconducting transition: Effect of Tc-inhomogeneity

Temperature and magnetic field dependences of the conductivity of YBaCuO films in the transition region are analyzed taking into account spatial inhomogeneity in transition temperature, Tc. (i) An expression for the superconducting contribution to conductivity, \sigma_s(T,H,Tc), of a homogeneous superconductor for H<<Hc2(T=0) is obtained using the solution of the Ginzburg-Landau equation in form of perturbation expansions [S.Ullah, A.T.Dorsey, PRB 44, 262 (1991)]. (ii) The error in \sigma_s(T,H,Tc) occurring due to the presence of Tc-inhomogeneity is calculated and plotted on an H-T plane diagram. These calculations use an effective medium approximation and a Gaussian distribution of Tc. (iii) Measuring the temperature dependences of a voltage, induced by a focused electron beam, we determine spatial distributions of the critical temperature for YBaCuO microbridges with a 2 micron resolution. A typical Tc-distribution dispersion is found to be approximately 1K. For such dispersion, error in \sigma_s(T,H,Tc) due to Tc-inhomogeneity exceeds 30% for magnetic fields H < 1 T and temperatures |T-Tc| < 0.5 K. (iv) Experimental R(T,H) dependences of resistance are well described by a numerical solution of a set of Kirchoff equations for the resistor network based on the measured spatial distributions of Tc and the expression for \sigma_s(T,H,Tc).Comment: REVTeX, 12 pages including 7 figures, resubmitted to Phys. Rev.

Contact force sensing in ablation of ventricular arrhythmias using a 56-hole open-irrigation catheter: a propensity-matched analysis.

PURPOSE: The effect of adding contact force (CF) sensing to 56-hole tip irrigation in ventricular arrhythmia (VA) ablation has not been previously studied. We aimed to compare outcomes with and without CF sensing in VA ablation using a 56-hole radiofrequency (RF) catheter. METHODS: A total of 164 patients who underwent first-time VA ablation using Thermocool SmartTouch Surround Flow (TC-STSF) catheter (Biosense-Webster, Diamond Bar, CA, USA) were propensity-matched in a 1:1 fashion to 164 patients who had first-time ablation using Thermocool Surround Flow (TC-SF) catheter. Patients were matched for age, gender, cardiac aetiology, ejection fraction and approach. Acute success, complications and long-term follow-up were compared. RESULTS: There was no difference between procedures utilising either TC-SF or TC-STSF in acute success (TC-SF: 134/164 (82%), TC-STSF: 141/164 (86%), p = 0.3), complications (TC-SF: 11/164 (6.7%), TC-STSF: 11/164 (6.7%), p = 1.0) or VA-free survival (TC-SF: mean arrhythmia-free survival time = 5.9 years, 95% CI = 5.4-6.4, TC-STSF: mean = 3.2 years, 95% CI = 3-3.5, log-rank p = 0.74). Fluoroscopy time was longer in normal hearts with TC-SF (19 min, IQR: 14-30) than TC-STSF (14 min, IQR: 8-25; p = 0.04). CONCLUSION: Both TC-SF and TC-STSF catheters are safe and effective in treating VAs. The use of CF sensing catheters did not improve safety or acute and long-term outcomes, but reduced fluoroscopy time in normal heart VA

Temperature dependence of the superconducting gap in high-Tc cuprates

It is proposed that (i) the temperature dependence of the superconducting gap Delta(T) in high-Tc cuprates can be predicted just from the knowledge of Delta(0) and the critical temperature Tc; and, in particular, (ii) Delta(0)/Tc > 4 implies that Delta(Tc) is not equal to zero, while Delta(0)/Tc < 4 corresponds to Delta(Tc) = 0. A number of tunneling experiments appear to support the above proposition, and, furthermore, show reasonable quantitative agreement with a model (cond-mat/0308428), which is based on the two-dimensional stripe hypothesis.Comment: Text close to the published version. Minor textual corrections in comparison to the previous versio

Inverse Iron Isotope Effect on the transition temperature of the (Ba,K)Fe2As2 superconductor

We report that (Ba,K)Fe2As2 superconductor (a transition temperature, Tc = 38 K) shows inverse Iron isotope effect (-0.18) (the sample including the larger atomic weight of Fe depicts higher Tc). Measurements of both temperature dependent magnetization and resistivity reveal a clear inverse shift by systematic studies on Tc using three types of Fe-isotopes (Fe-54, natural Fe and Fe-57). This indicates the first evidence of the inverse isotope effect in high-Tc superconductors. This atomic mass dependence on Tc implies the exotic coupling mechanism.Comment: 12 pages, 6 figure

Layered superconductors as negative-refractive-index metamaterials

We analyze the use of layered superconductors as anisotropic metamaterials. Layered superconductors can have a negative refraction index in a wide frequency range for arbitrary incident angles. Indeed, low-Tc (s-wave) superconductors allow to produce artificial heterostructures with low losses for T<<Tc. However, the real part of their in-plane effective permittivity is very large. Moreover, even at low temperatures, layered high-Tc superconductors have a large in-plane normal conductivity, producing large losses (due to d-wave symmetry). Therefore, it is difficult to enhance the evanescent modes in either low-Tc or high-Tc superconductors.Comment: 4 pages, 2 figure

Effective field approach to the Ising film in a transverse field

We study the phase transitions of the spin-1/2 Ising film in a transverse field within the framework of the effective field theory. We evaluate the critical temperature of the film as a function of the exchange interactions, the transverse field and the film thickness. We find that, if the ratio of the surface exchange interactions to the bulk ones R=Js/J is smaller than a critical value Rc, the critical temperature Tc/J of the film is smaller than the bulk critical temperature Tc^B/J and approaches Tc^B/J as R increases further. On the other hand, if R>Rc, Tc/J is larger than both the bulk Tc^B/J and the surface Tc^S/J critical temperatures of the corresponding semi-infinite system, and approaches Tc^S as R increases further.Comment: 16 pages, 5 figures, elsart.cls (included