Local Frustration Determines Molecular and Macroscopic Helix Structures

The effect of displaying cytochromes from an amyloid fibre is modelled as perturbation of -strands in a bilayer of helical -sheets, thereby explaining the spiral morphology of decorated amyloid and the dynamic response of morphology to cytochrome conformation. The morphology of the modelled fibre, which consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting units, depends primarily on the rigid constraints between units rather than the soft interactions between them. The framework is a discrete version of the bilayered frustration principle that drives morphology in Bauhinia seedpods. We show that self-assembly of frustrated long range structures can occur if the building blocks themselves are internally frustrated, e.g. amyloid morphology is governed by the conformation of the misfolded protein nucleating the fibre. Our model supports the idea that any peptide sequence can form amyloid if bilayers can form first, albeit stabilised by additional material such as chaperones or cytochromes. Analysis of experimentally derived amyloid structures supports our conclusions and suggests a range of frustration effects, which natural amyloid fibres may exploit. From this viewpoint, amyloid appears as a molecular example of a more general universal bilayered frustration principle, which may have profound implications for materials design using fibrous systems. Our model provides quantitative guidance for such applications. The relevance to longer length scales was proved by designing the morphology of a series of macroscopic magnetic stacks. Finally, this work leads to the idea of mixing controlled morphologically defined species to generate higher-order assembly and complex functional behaviour. The systematic kinking of decorated fibres and the nested frustration of the Bauhinia seed pod are two outstanding examples.

The inverse problem in magnetic force microscopy--inferring sample magnetization from MFM images.

Nanomagnetic structures have the potential to surpass silicon's scaling limitations both as elements in hybrid CMOS logic and as novel computational elements. Magnetic force microscopy (MFM) offers a convenient characterization technique for use in the design of such nanomagnetic structures. MFM measures the magnetic field and not the sample's magnetization. As such the question of the uniqueness of the relationship between an external magnetic field and a magnetization distribution is a relevant one. To study this problem we present a simple algorithm which searches for magnetization distributions consistent with an external magnetic field and solutions to the micromagnetic equations' qualitative features. The algorithm is not computationally intensive and is found to be effective for our test cases. On the basis of our results we propose a systematic approach for interpreting MFM measurements.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Effect of size, composition, and morphology on magnetic performance: First-order reversal curves evaluation of iron oxide nanoparticles

© 2014 AIP Publishing LLC. Superparamagnetic nanoparticles are employed in a broad range of applications that demand detailed magnetic characterization for superior performance, e.g., in drug delivery or cancer treatment. Magnetic hysteresis measurements provide information on saturation magnetization and coercive force for bulk material but can be equivocal for particles having a broad size distribution. Here, first-order reversal curves (FORCs) are used to evaluate the effective magnetic particle size and interaction between equally sized magnetic iron oxide (Fe2O3) nanoparticles with three different morphologies: (i) pure Fe2O3, (ii) Janus-like, and (iii) core/shell Fe2O3/SiO2synthesized using flame technology. By characterizing the distribution in coercive force and interaction field from the FORC diagrams, we find that the presence of SiO2in the core/shell structures significantly reduces the average coercive force in comparison to the Janus-like Fe2O3/SiO2and pure Fe2O3particles. This is attributed to the reduction in the dipolar interaction between particles, which in turn reduces the effective magnetic particle size. Hence, FORC analysis allows for a finer distinction between equally sized Fe2O3particles with similar magnetic hysteresis curves that can significantly influence the final nanoparticle performance.

The formation and electronic structures of 3d transition-metal atoms doped in silicon nanowires

Using first-principles methods, we systematically study the mechanism of defect formation and electronic structures for 3d transition-metal impurities (V, Cr, Mn, Fe, and Co) doped in silicon nanowires. We find that the formation energies of 3d transition-metal impurities with electrons or holes at the defect levels always increase as the diameters of silicon nanowires decrease, which suggests that self-purification, i.e., the difficulty of doping in silicon nanowires, should be an intrinsic effect. The calculated results show that the defect formation energies of Mn and Fe impurities are lower than those of V, Cr, and Co impurities in silicon nanowires. It indicates that Mn and Fe can easily occupy substitutional site in the interior of silicon nanowires. Moreover, they have larger localized moments, which means that they are good candidates for Si-based dilute magnetic semiconductor nanowires. The doping of Mn and Fe atom in silicon nanowires introduces a pair of energy levels with t(2) symmetry. One of which is dominated by 3d electrons of Mn or Fe, and the other by neighboring dangling bonds of Si vacancies. In addition, a set of nonbonding states localized on the transition-metal atom with e symmetry is also introduced. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3000445]

Correlations between electronic energy bands spin splitting and magnetic profile symmetry of magnetic superlattice

We have theoretically investigated the energy band structures of two typical magnetic superlattices formed by perpendicular or parallel magnetization ferromagnetic stripes periodically deposited on a two-dimensional electron gas (2DEG), where the magnetic profile in the perpendicular magnetization is of inversion anti-symmetry, but of inversion symmetry in parallel magnetization, respectively. We have shown that the energy bands of perpendicular magnetization display the spin-splitting and transverse wave-vector symmetry, while the energy bands of the parallel magnetization exhibit spin degeneration and transverse wave-vector asymmetry. These distinguishing spin-dependent and transverse wave-vector asymmetry features are essential for future spintronics devices applications. (c) 2008 Elsevier B.V. All rights reserved.

Tunneling magnetoresistance in CoFeB/GaAs/(Ga,Mn)As hybrid magnetic tunnel junctions

We reported the all electronic demonstration of spin injection and detection in the trilayers with hybrid structure of CoFeB/GaAs/(Ga,Mn)As (metal/insulator semiconductor) by probing the magnetoresistance at low temperature from 1.8 to 30 K. Tunneling magnetoresistance (TMR) ratios of 3.8%, 4.7%, 2.9%, and 1.4% at 1.8, 10, 20, and 30 K, respectively, were observed. Bias dependence of both the junction resistance and TMR ratio was studied systematically. V-half at which TMR drops to half of its maximum is 6.3 mV, being much smaller compared to that observed in (Ga,Mn)As/ZnSe/Fe and (Ga,Mn)As/AlAs/MnAs hybrid structures, indicating lower Fermi energy of (Ga,Mn)As.

Tunneling magnetoresistance in (Ga,Mn)As/Al-O/CoFeB hybrid structures

Tunneling magnetoresistance (TMR) in Ga(0.9)2Mn(0.08)As/Al-O/Co40Fe40B20 trilayer hybrid structure as a function of temperature from 10 to 50 K with magnetic field vertical bar H vertical bar <= 2000 Oe has been studied. TMR ratio of 1.6% at low fields at 10 K was achieved with the applied current of 1 mu A. The behavior of junction resistance was well explained by the tunneling resistance across the barrier. Strong bias dependences of magnetoresistance and junction resistance were presented. (C) 2009 American Institute of Physics. [DOI 10.1063/1.3068418]

Electric-tunable magneto resistance effect in a two-dimensional electron gas modulated by hybrid magnetic-electric barrier nanostructure

The electric-tunable spin-independent magneto resistance effect has been theoretically investigated in ballistic regime within a two-dimensional electron gas modulated by magnetic-electric barrier nanostructure. By including the omitted stray field in previous investigations oil analogous structures, it is demonstrated based on this improved approximation that the magnetoresistance ratio for the considered structure can be efficiently enhanced by a proper electric barrier up to the maximum value depending on the specific magnetic suppression. Besides, it is also shown the introduction of positive electrostatic modulation can effectively overcome the degradation of magnetoresistance ratio for asymmetric configuration and enhance the visibility of periodic pattern induced by the size effect, while for an opposite modulation the system magnetoresistance ratio concerned may change its sign. (C) 2009 Elsevier B.V. All rights reserved.

Nitrogen defects and ferromagnetism in Cr-doped dilute magnetic semiconductor AlN from first principles

High Curie temperature of 900 K has been reported in Cr-doped AlN diluted magnetic semiconductors prepared by various methods, which is exciting for spintronic applications. It is believed that N defects play important roles in achieving the high-temperature ferromagnetism in good samples. Motivated by these experimental advances, we use a full-potential density-functional-theory method and supercell approach to investigate N defects and their effects on ferromagnetism of (Al,Cr)N with N vacancies (V-N). We investigate the structural and electronic properties of V-N, single Cr atom, Cr-Cr atom pairs, Cr-V-N pairs, and so on. In each case, the most stable structure is obtained by comparing different atomic configurations optimized in terms of the total energy and the force on every atom, and then it is used to calculate the defect formation energy and study the electronic structures. Our total-energy calculations show that the nearest substitutional Cr-Cr pair with the two spins in parallel is the most favorable and the nearest Cr-V-N pair makes a stable complex. Our formation energies indicate that V-N regions can be formed spontaneously under N-poor condition because the minimal V-N formation energy equals -0.23 eV or Cr-doped regions with high enough concentrations can be formed under N-rich condition because the Cr formation energy equals 0.04 eV, and hence real Cr-doped AlN samples are formed by forming some Cr-doped regions and separated V-N regions and through subsequent atomic relaxation during annealing. Both of the single Cr atom and the N vacancy create filled electronic states in the semiconductor gap of AlN. N vacancies enhance the ferromagnetism by adding mu(B) to the Cr moment each but reduce the ferromagnetic exchange constants between the spins in the nearest Cr-Cr pairs. These calculated results are in agreement with experimental observations and facts of real Cr-doped AlN samples and their synthesis. Our first-principles results are useful to elucidate the mechanism for the ferromagnetism and to explore high-performance Cr-doped AlN diluted magnetic semiconductors.

Symmetry and optical transition rule for low-dimensional semiconductor system with spin-orbit interaction and magnetic field

Starting from effective mass Hamiltonian, we systematically investigate the symmetry of low-dimensional structures with spin-orbit interaction and transverse magnetic field. The position-dependent potentials are assumed to be space symmetric, which is ever-present in theory and experiment research. By group theory, we analyze degeneracy in different cases. Spin-orbit interaction makes the transition between Zeeman sub-levels possible, which is originally forbidden within dipole approximation. However, a transition rule given in this paper for the first time shows that the transition between some levels is forbidden for space symmetric potentials. (C) 2009 Elsevier Ltd. All rights reserved.

Electronic structure of self-assembled InAs quantum disks in an axial magnetic field and two-electron quantum-disk qubit

We have studied the single-electron and two-electron vertically assembled quantum disks in an axial magnetic field using the effective mass approximation. The electron interaction is treated accurately by the direct diagonalization of the Hamiltonian matrix. We calculate the six energy levels of the single-electron quantum disks and the two lowest energy levels of the two-electron quantum disks in an axial magnetic field. The change of the magnetic field strongly modifies the electronic structures as an effective potential, leading to the splitting of the levels and the crossings between the levels. The effect of the vertical alignment on the electronic structures is discussed. It is demonstrated that the switching of the ground-state spin exists between S=0 and S=1. The energy difference DeltaE between the lowest S=0 and S=1 states is shown as a function of the axial magnetic field. It is also found that the variation of the energy difference between the lowest S=0 and S=1 states in the strong-B S=0 state is fairly linear. Our results provide a possible realization for a qubit to be fabricated by current growth techniques. (C) 2004 American Institute of Physics.

Electronic structures of GaAs/AlxGa1-xAs quantum double

In the framework of effective mass envelope function theory, the electronic structures of GaAs/AlxGa1-xAs quantum double rings(QDRs) are studied. Our model can be used to calculate the electronic structures of quantum wells, wires, dots, and the single ring. In calculations, the effects due to the different effective masses of electrons and holes in GaAs and AlxGa1-xAs and the valence band mixing are considered. The energy levels of electrons and holes are calculated for different shapes of QDRs. The calculated results are useful in designing and fabricating the interrelated photoelectric devices. The single electron states presented here are useful for the study of the electron correlations and the effects of magnetic fields in QDRs.

Resonant tunneling theory of planar quantum dot structures

The ballistic transport in the semiconductor, planar, circular quantum dot structures is studied theoretically. The transmission probabilities show apparent resonant tunneling peaks, which correspond to energies of bound states in the dot. By use of structures with different angles between the inject and exit channels, the resonant peaks can be identified very effectively. The perpendicular magnetic field has obvious effect on the energies of bound states in the quantum dot, and thus the resonant peaks. The treatment of the boundary conditions simplifies the problem to the solution of a set of linear algebraic equations. The theoretical results in this paper can be used to design planar resonant tunneling devices, whose resonant peaks are adjustable by the angle between the inject and exit channels and the applied magnetic field. The resonant tunneling in the circular dot structures can also be used to study the bound states in the absence and presence of magnetic field.

Collective and single-particle excitations in coupled quantum wires in magnetic fields

The full spectra of magnetoplasmons and single-particle excitations are obtained of coupled one-dimensional electron gases in parallel semiconductor quantum wires with tunneling. We show the effects of the interwire Coulomb interaction and the tunneling, as well as the magnetic-field-induced localization on the elementary excitations in symmetric and asymmetric coulped quantum wire structures. The interacton and resonance between the plasmon and the intersubband single-particle excitations are found in magnetic fields.