Electron microscopy of frozen biological suspensions

The methodology for preparing specimens in the frozen, hydrated state has been assessed using crystals and T4 bacteriophages. The methods have also been demonstrated with lambda bacteriophages, purple membrane of Halobacterium halobium and fibres of DNA. For particles dispersed in an aqueous environment, it is shown that optimum structural preservation is obtained from a thin, quench-frozen film with the bulk aqueous medium in the vitreous state. Crystallization of the bulk water may result in solute segregation and expulsion of the specimen from the film. Contrast measurements can be used to follow directly the state of hydration of a specimen during transition from the fully hydrated to the freeze-dried state and permit direct measurement of the water content of the specimen. By changing the concentration and composition of the aqueous medium the contrast of particles in a vitreous film can be controlled and any state of negative, positive or zero contrast may be obtained. At 100 K, frozen-hydrated, freeze-dried or sugar embedded crystals can withstand a three- to four-fold increase in electron exposure for the same damage when compared with similar sugar-embedded or freeze-dried samples at room temperature

Evidence for a small hole pocket in the Fermi surface of underdoped YBa2Cu3Oy

The Fermi surface of a metal is the fundamental basis from which its properties can be understood. In underdoped cuprate superconductors, the Fermi surface undergoes a reconstruction that produces a small electron pocket, but whether there is another, as yet undetected portion to the Fermi surface is unknown. Establishing the complete topology of the Fermi surface is key to identifying the mechanism responsible for its reconstruction. Here we report the discovery of a second Fermi pocket in underdoped YBa2Cu3Oy, detected as a small quantum oscillation frequency in the thermoelectric response and in the c-axis resistance. The field-angle dependence of the frequency demonstrates that it is a distinct Fermi surface and the normal-state thermopower requires it to be a hole pocket. A Fermi surface consisting of one electron pocket and two hole pockets with the measured areas and masses is consistent with a Fermi-surface reconstruction caused by the charge-density-wave order observed in YBa2Cu3Oy, provided other parts of the reconstructed Fermi surface are removed by a separate mechanism, possibly the pseudogap.Comment: 23 pages, 5 figure

Cryo-electron microscopy of viruses

Thin vitrified layers of unfixed, unstained and unsupported virus suspensions can be prepared for observation by cryo-electron microscopy in easily controlled conditions. The viral particles appear free from the kind of damage caused by dehydration, freezing or adsorption to a support that is encountered in preparing biological samples for conventional electron microscopy. Cryo-electron microscopy of vitrified specimens offers possibilities for high resolution observations that compare favourably with any other electron microscopical method

Fermi Surface of the Electron-doped Cuprate Superconductor Nd_{2-x}Ce_xCuO_{4} Probed by High-Field Magnetotransport

We report on the study of the Fermi surface of the electron-doped cuprate superconductor Nd$_{2-x}$Ce$_x$CuO$_{4}$ by measuring the interlayer magnetoresistance as a function of the strength and orientation of the applied magnetic field. We performed experiments in both steady and pulsed magnetic fields on high-quality single crystals with Ce concentrations of $x=0.13$ to 0.17. In the overdoped regime of $x > 0.15$ we found both semiclassical angle-dependent magnetoresistance oscillations (AMRO) and Shubnikov-de Haas (SdH) oscillations. The combined AMRO and SdH data clearly show that the appearance of fast SdH oscillations in strongly overdoped samples is caused by magnetic breakdown. This observation provides clear evidence for a reconstructed multiply-connected Fermi surface up to the very end of the overdoped regime at $x\simeq 0.17$. The strength of the superlattice potential responsible for the reconstructed Fermi surface is found to decrease with increasing doping level and likely vanishes at the same carrier concentration as superconductivity, suggesting a close relation between translational symmetry breaking and superconducting pairing. A detailed analysis of the high-resolution SdH data allowed us to determine the effective cyclotron mass and Dingle temperature, as well as to estimate the magnetic breakdown field in the overdoped regime.Comment: 23 pages, 8 figure

Hall, Seebeck, and Nernst Coefficients of Underdoped HgBa2CuO4+d: Fermi-Surface Reconstruction in an Archetypal Cuprate Superconductor

Charge density-wave order has been observed in cuprate superconductors whose crystal structure breaks the square symmetry of the CuO2 planes, such as orthorhombic YBa2Cu3Oy (YBCO), but not so far in cuprates that preserve that symmetry, such as tetragonal HgBa2CuO4+d (Hg1201). We have measured the Hall (R_H), Seebeck (S), and Nernst coefficients of underdoped Hg1201 in magnetic fields large enough to suppress superconductivity. The high-field R_H(T) and S(T) are found to drop with decreasing temperature and become negative, as also observed in YBCO at comparable doping. In YBCO, the negative R_H and S are signatures of a small electron pocket caused by Fermi-surface reconstruction, attributed to charge density-wave modulations observed in the same range of doping and temperature. We deduce that a similar Fermi-surface reconstruction takes place in Hg1201, evidence that density-wave order exists in this material. A striking similarity is also found in the normal-state Nernst coefficient, further supporting this interpretation. Given the model nature of Hg1201, Fermi-surface reconstruction appears to be common to all hole-doped cuprates, suggesting that density-wave order is a fundamental property of these materials

Semiflexible chains in confined spaces

We develop an analytical method for studying the properties of a noninteracting wormlike chain (WLC) in confined geometries. The mean-field-like theory replaces the rigid constraints of confinement with average constraints, thus allowing us to develop a tractable method for treating a WLC wrapped on the surface of a sphere, and fully encapsulated within it. The efficacy of the theory is established by reproducing the exact correlation functions for a WLC confined to the surface of a sphere. In addition, the coefficients in the free energy are exactly calculated. We also describe the behavior of a surface-confined chain under external tension that is relevant for single molecule experiments on histone-DNA complexes. The force-extension curves display spatial oscillations, and the extension of the chain, whose maximum value is bounded by the sphere diameter, scales as f−1 at large forces, in contrast to the unconfined chain that approaches the contour length as f−1∕2. A WLC encapsulated in a sphere, that is relevant for the study of the viral encapsulation of DNA, can also be treated using the mean-field approach. The predictions of the theory for various correlation functions are in excellent agreement with Langevin simulations. We find that strongly confined chains are highly structured by examining the correlations using a local winding axis. The predicted pressure of the system is in excellent agreement with simulations but, as is known, is significantly lower than the pressures seen for DNA packaged in viral capsids

Coherent c-axis transport in the underdoped cuprate superconductor YBCO

The electrical resistivity rho_c of the underdoped cuprate superconductor YBCO was measured perpendicular to the CuO_2 planes on ultra-high quality single crystals in magnetic fields large enough to suppress superconductivity. The incoherent insulating-like behavior of rho_c at high temperature, characteristic of all underdoped cuprates, is found to cross over to a coherent regime of metallic behavior at low temperature. This crossover coincides with the emergence of the small electron pocket detected in the Fermi surface of YBCO via quantum oscillations, the Hall and Seebeck coefficients and with the detection of a unidirectional modulation of the charge density as seen by high-field NMR measurements. The low coherence temperature is quantitatively consistent with the small hopping integral t_perp inferred from the splitting of the quantum oscillation frequencies. We conclude that the Fermi-surface reconstruction in YBCO at dopings from p = 0.08 to at least p = 0.15, attributed to stripe order, produces a metallic state with 3D coherence deep in the underdoped regime.Comment: 7 pages, 7 figure

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

Previous studies have reported the production of malformed virus-like-particles (VLP) in recombinant host systems. Here we computationally investigate the case of a large triple-layered rotavirus VLP (RLP). In vitro assembly, disassembly and reassembly data provides strong evidence of microscopic reversibility of RLP assembly. Light scattering experimental data also evidences a slow and reversible assembly untypical of kinetic traps, thus further strengthening the fidelity of a thermodynamically controlled assembly. In silico analysis further reveals that under favourable conditions particles distribution is dominated by structural subunits and completely built icosahedra, while other intermediates are present only at residual concentrations. Except for harshly unfavourable conditions, assembly yield is maximised when proteins are provided in the same VLP protein mass composition. The assembly yield decreases abruptly due to thermodynamic equilibrium when the VLP protein mass composition is not obeyed. The latter effect is more pronounced the higher the Gibbs free energy of subunit association is and the more complex the particle is. Overall this study shows that the correct formation of complex multi-layered VLPs is restricted to a narrow range of association energies and protein concentrations, thus the choice of the host system is critical for successful assembly. Likewise, the dynamic control of intracellular protein expression rates becomes very important to minimize wasted proteins