Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ≈0.75, a value that is similar to close packing of equal-sized spheres. ...
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Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ≈0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ≈0.56, which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.
Cholesteric liquid crystals can potentially provide a means for tunable self-organization of colloidal particles. However, the structures of particle-induced defects and the ensuing elasticity-mediated colloidal inter...
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Cholesteric liquid crystals can potentially provide a means for tunable self-organization of colloidal particles. However, the structures of particle-induced defects and the ensuing elasticity-mediated colloidal interactions in these media remain much less explored and understood as compared to their nematic liquid crystal counterparts. Here we demonstrate how colloidal microspheres of varying diameter relative to the helicoidal pitch can induce dipolelike director field configurations in cholesteric liquid crystals, where these particles are accompanied by point defects and a diverse variety of nonsingular line defects forming closed loops. Using laser tweezers and nonlinear optical microscopy, we characterize the ensuing medium-mediated elastic interactions and three-dimensional colloidal assemblies. Experimental findings show a good agreement with numerical modeling based on minimization of the Landau–de Gennes free energy and promise both practical applications in the realization of colloidal composite materials and a means of controlling nonsingular topological defects that attract a great deal of fundamental interest.
The spin superfluid analogy can be extended to include Josephson-like oscillations of the spin current. In a system of two antiferromagnetic insulators (AFMIs) separated by a thin metallic spacer, a threshold spin che...
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The spin superfluid analogy can be extended to include Josephson-like oscillations of the spin current. In a system of two antiferromagnetic insulators (AFMIs) separated by a thin metallic spacer, a threshold spin chemical potential established perpendicular to the direction of the Néel vector field drives terahertz oscillations of the spin current. This spin current also has a nonlinear, time-averaged component which provides a “smoking gun” signature of spin superfluidity. The time-averaged spin current can be detected via the inverse spin Hall effect in a metallic spacer with large spin-orbit coupling. The physics illustrated here with AFMIs also applies to easy-plane ferromagnetic insulators. These findings may provide a new approach for experimental verification of spin superfluidity and realization of a terahertz spin oscillator.
The perovskite SrIrO3 is an exotic narrow-band metal owing to a confluence of the strengths of the spin-orbit coupling (SOC) and the electron-electron correlations. It has been proposed that topological and magnetic i...
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The perovskite SrIrO3 is an exotic narrow-band metal owing to a confluence of the strengths of the spin-orbit coupling (SOC) and the electron-electron correlations. It has been proposed that topological and magnetic insulating phases can be achieved by tuning the SOC, Hubbard interactions, and/or lattice symmetry. Here, we report that the substitution of nonmagnetic, isovalent Sn4+ for Ir4+ in the SrIr1−xSnxO3 perovskites synthesized under high pressure leads to a metal-insulator transition to an antiferromagnetic (AF) phase at TN≥225 K. The continuous change of the cell volume as detected by x-ray diffraction and the λ-shape transition of the specific heat on cooling through TN demonstrate that the metal-insulator transition is of second order. Neutron powder diffraction results indicate that the Sn substitution enlarges an octahedral-site distortion that reduces the SOC relative to the spin-spin exchange interaction and results in the type-G AF spin ordering below TN. Measurement of high-temperature magnetic susceptibility shows the evolution of magnetic coupling in the paramagnetic phase typical of weak itinerant-electron magnetism in the Sn-substituted samples. A reduced structural symmetry in the magnetically ordered phase leads to an electron gap opening at the Brillouin zone boundary below TN in the same way as proposed by Slater.
In this work, we show that Cu-Sn based nanowires can be used as a one-dimensional (1-D) diffusion couple to study the atomic diffusion. In order to control the nano-soldering process and form reliable nano-joints (nan...
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In this work, we show that Cu-Sn based nanowires can be used as a one-dimensional (1-D) diffusion couple to study the atomic diffusion. In order to control the nano-soldering process and form reliable nano-joints (nanoscale interconnects between nanowires), fundamental study of wetting and intermetallic diffusion at the small dimension is necessary. An electrodeposition method is used to synthesize multisegmented nanowires in nanoporous templates in the diameter range of 15-200 nm and length up to 20 μm. By choosing two-segment Sn-Cu nanowires and symmetric three-segment Sn-Cu-Sn nanowires as the model systems in which Sn acts as the solder element and Cu serves as a functional element, we aim to understand the nanoscale soldering reaction along the one-dimension. The morphological evolutions of Sn and Cu segments and Kirkendall void formation in the Cu segment during the oven based soldering process have been observed. The fundamental principles of diffusion kinetics, primarily at a phenomenological level, are discussed. These studies and results provide important understanding in the design, assembly and integration of functional nanowires into nanoelectronics and nanodevices.
The growth of Co-substituted BaTiO3 (BTO) films on Ge(001) substrates by molecular beam epitaxy is demonstrated. Energy-dispersive x-ray spectroscopy and transmission electron microscopy images confirm the uniform Co ...
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The growth of Co-substituted BaTiO3 (BTO) films on Ge(001) substrates by molecular beam epitaxy is demonstrated. Energy-dispersive x-ray spectroscopy and transmission electron microscopy images confirm the uniform Co distribution. However, no evidence of magnetic ordering is observed in samples grown for Co concentrations between 2% and 40%. Piezoresponse force microscopy measurements show that a 5% Co-substituted BTO sample exhibits ferroelectric behavior. First-principles calculations indicate that while Co atoms couple ferromagnetically in the absence of oxygen vacancies, the occurrence of oxygen vacancies leads to locally antiferromagnetically coupled complexes with relatively strong spin coupling. The presence of a significant amount of oxygen vacancies is suggested by x-ray photoelectron spectroscopy measurements.
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