High-throughput simulation of the configuration and ionisation potential of nitrogen-doped graphene

The electron emission properties of doped graphene nanoflakes can determine their suitability for a range of technological applications. Here we investigate the impact of varying the location of a substitutional nitrogen dopant on the first and second ionisation potentials of graphene nanoflakes. We use a high-throughput simulation engine in conjunction with the density functional tight binding method to calculate the properties of both armchair and zig-zag structure nanoflakes containing 1014 carbon atoms. Our results show that dopant location does affect the ionisation potentials, particularly for the armchair structure, and that there is a natural separation into interior and peripheral regions. A simple statistical analysis indicates that the resolution of electronic emissions can be maximised by restricting the nitrogen dopant to the interior region of the armchair nanoflake.     

Electronic,transport, magnetic,and optical properties of graphene nanoribbons and their optical sensing applications: A comprehensive review

Low dimensional materials have attracted great research interest from both theoretical and experimental point of views. These materials exhibit novel physical and chemical properties due to the confinement effect in low dimensions. The experimental observations of graphene open a new platform to study the physical properties of materials restricted to two dimensions. This featured article provides a review on the novel properties of quasi one-dimensional (1D) material known as graphene nanoribbon. Graphene nanoribbons can be obtained by unzipping carbon nanotubes (CNT) or cutting the graphene sheet. Alternatively, it is also called the finite termination of graphene edges. It gives rise to different edge geometries, namely zigzag and armchair, among others. There are various physical and chemical techniques to realize these materials. Depending on the edge type termination, these are called the zigzag and armchair graphene nanoribbons (ZGNR and AGNR). These edges play an important role in controlling the properties of graphene nanoribbons. The present review article provides an overview of the electronic, transport, optical, and magnetic properties of graphene nanoribbons. However, there are different ways to tune these properties for device applications. Here, some of them, such as external perturbations and chemical modifications, are highlighted. Few applications of graphene nanoribbon have also been briefly discussed.     

Modelling the effects of hydrogen passivation and strain on the field emission from armchair-graphene nanoribbon using a modified non-equilibrium Green’s function method

In this report, we introduced a modified non-equilibrium Green’s function method to investigate the structural effects on the field emission current from an armchair graphene nanoribbon. We introduce a modified self-energy which is useful to study the effects of potential barrier in the field emission devices. Investigation into the effects of hydrogen passivation and applied strain can be realised using our modified formalism. Also a practical method to consider the effect of device parameters, such as channel length, anode–cathode separation and gate potential can be provided by the proposed formalism. The quantum effects of the emitter’s structure on the field emission are achievable by our introduced method.     

Bond length pattern associated with charge carriers in armchair graphene nanoribbons

The geometry configuration of charged armchair graphene nanoribbons (AGNRs) is theoretically investigated in the framework of a two-dimensional tight-binding model that includes lattice relaxation. Our findings show that the charge distribution and, consequently, the bond length pattern is dependent on the parity of the nanoribbon width. In this sense, the lattice distortions decrease smoothly for increasingly wider GNRs. As should be expected, AGNRs belonging to a particular family present similar patterns for the bond lengths. The interplay between the electron-phonon coupling and band gap is also investigated. The results show that the electron-phonon coupling strength is fundamental to promote the transition from metallic towards semiconducting-like behavior for the band gap. Most important, such strength is crucial on defining the degree of lattice distortions in AGNRs.     

Theory of the polarization bremsstrahlung from thermal electrons scattered by the Debye sphere of an ion in a plasma

The polarization bremsstrahlung from thermal electrons scattered by the Debye sphere of an ion in a plasma is studied in the quasiclassical approximation. The model of the local plasma frequency is used to check the validity of the asymptotic expression for the polarizability of the electron cloud of an ion in the high-frequency range. This asymptotic expression is then used to derive a formula for the intensity of the total effective polarization bremsstrahlung. The R factor (the ratio of the contribution from the polarization bremsstrahlung to the contribution from conventional static bremsstrahlung) is obtained as a function of the plasma coupling parameter and electron density in order to analyze the role of the polarization bremsstrahlung in the total bremsstrahlung of the thermal plasma electrons. The spectral intensity of the effective polarization bremsstrahlung is calculated in the rotational approximation, which was previously employed in the theory of conventional static bremsstrahlung. It is shown that the spectral intensity of the polarization bremsstrahlung from thermal electrons scattered by the Debye sphere around an ion, as compared with the polarization bremsstrahlung by fast superthermal electrons, decreases more gradually with increasing frequency.     

Charge recombination and protein dynamics in bacterial photosynthetic reaction centers entrapped in a sol-gel matrix

Many proteins can be immobilized in silica hydrogel matrices without compromising their function, making this a suitable technique for biosensor applications. Immobilization will in general affect protein structure and dynamics. To study these effects, we have measured the P(+)Q(A)(-) charge recombination kinetics after laser excitation of Q(B)-depleted wild-type photosynthetic reaction centers from Rhodobacter sphaeroides in a tetramethoxysilane (TMOS) sol-gel matrix and, for comparison, also in cryosolvent. The nonexponential electron transfer kinetics observed between 10 and 300 K were analyzed quantitatively using the spin boson model for the intrinsic temperature dependence of the electron transfer and an adiabatic change of the energy gap and electronic coupling caused by protein motions in response to the altered charge distributions. The analysis reveals similarities and differences in the TMOS-matrix and bulk-solvent samples. In both preparations, electron transfer is coupled to the same spectrum of low frequency phonons. As in bulk solvent, charge-solvating protein motions are present in the TMOS matrix. Large-scale conformational changes are arrested in the hydrogel, as evident from the nonexponential kinetics even at room temperature. The altered dynamics is likely responsible for the observed changes in the electronic coupling matrix element.     

A reduced protein model with accurate native-structure identification ability

A protein model that is simple enough to be used in protein-folding simulations but accurate enough to identify a protein native fold is described. Its geometry consists of describing the residues by one, two, or three pseudoatoms, depending on the residue size. Its energy is given by a pairwise, knowledge-based potential obtained for all the pseudoatoms as a function of their relative distance. The pseudoatomic potential is also a function of the primary chain separation and residue order. The model is tested by gapless threading on a large, representative set of known protein and decoy structures obtained from the "Decoys 'R' Us" database. It is also tested by threading on gapped decoys generated for proteins with many homologs. The gapless threading tests show near 98% native-structure recognition as the lowest energy structure and almost 100% as one of the three lowest energy structures for over 2200 test proteins. In decoy threading tests, the model recognized the majority of the native structures. It is also able to recognize native structures among gapped decoys, in spite of close structural similarities. The results indicate that the pseudoatomic model has native recognition ability similar to comparable atomic-based models but much better than equivalent residue-based models.     

Electron spin polarization in photosynthesis and the mechanism of electron transfer in photosystem I. Experimental observations.

Transient electron paramagnetic resonance (EPR) methods are used to examine the spin populations of the light-induced radicals produced in spinach chloroplasts, photosystem I particles, and Chlorella pyrenoidosa. We observe both emission and enhanced absorption within the hyperfine structure of the EPR spectrum of P700+, the photooxidized reaction-center chlorophyll radical (Signal I). By using flow gradients or magnetic fields to orient the chloroplasts in the Zeeman field, we are able to influence both the magnitude and sign of the spin polarization. Identification of the polarized radical and P700+ is consistent with the effects of inhibitors, excitation light intensity and wavelength, redox potential, and fractionation of the membranes. The EPR signal of the polarized P700+ radical displays a 30% narrower line width than P700+ after spin relaxation. This suggests a magnetic interaction between P700+ and its reduced (paramagnetic) acceptor, which leads to a collapse of the P700+ hyperfine structure. Narrowing of the spectrum is evident only in the spectrum of polarized P700+, because prompt electron transfer rapidly separates the radical pair. Evidence of cross-relaxation between the adjacent radicals suggests the existence of an exchange interaction. The results indicate that polarization is produced by a radical pair mechanism between P700+ and the reduced primary acceptor of photosystem I. The orientation dependence of the spin polarization of P700+ is due to the g-tensor anisotropy of the acceptor radical to which it is exchange-coupled. The EPR spectrum of P700+ is virtually isotropic once the adjacent acceptor radical has passed the photoionized electron to a later, more remote acceptor molecule. This interpretation implies that the acceptor radical has g-tensor anisotropy significantly greater than the width of the hyperfine field on P700+ and that the acceptor is oriented with its smallest g-tensor axis along the normal to the thylakoid membranes. Both the ferredoxin-like iron-sulfur centers and the X- species observed directly by EPR at low temperatures have g-tensor anisotropy large enough to produce the observed spin polarization; however, studies on oriented chloroplasts show that the bound ferredoxin centers do not have this orientation of their g tensors. In contrast, X- is aligned with its smallest g-tensor axis predominantly normal to the plane of the thylakoid membranes. This is the same orientation predicted for the acceptor radical based on analysis of the spin polarization of P700+, and indicates that the species responsible for the anisotropy of the polarized P700+ spectrum is probably X-. The dark EPR Signal II is shown to possess anisotropic hyperfine structure (and possibly g-tensor anisotropy), which serves as a good indicator of the extent of membrane alignment.     

Spin polarization in GaAs/Al0.24Ga0.76As heterostructures

The spontaneous spin polarization of a quantum point contact (QPC) formed by the lateral confinement of a high-mobility two-dimensional electron gas in a GaAs/AlGaAs split gate heterostructure is investigated. Self consistent calculations of the electronic structure of the QPC are performed using the spin-polarized density functional formalism of Kohn and Sham. Spin polarization occurs at low electron densities and exchange interaction is found to be the dominant mechanism driving the local spin polarization within the QPC. The cascading scattering matrix approach is utilized to compute the conductance and a conductance anomaly at ～0.5 (2e ² /h) has been observed. In addition to this, the sheet density dependence of the 0.7 conduction anomaly is investigated.     

Quantum Entanglement and Spin Control in Silicon Nanocrystal

Selective coherence control and electrically mediated exchange coupling of single electron spin between triplet and singlet states using numerically derived optimal control of proton pulses is demonstrated. We obtained spatial confinement below size of the Bohr radius for proton spin chain FWHM. Precise manipulation of individual spins and polarization of electron spin states are analyzed via proton induced emission and controlled population of energy shells in pure ²⁹Si nanocrystal. Entangled quantum states of channeled proton trajectories are mapped in transverse and angular phase space of ²⁹Si axial channel alignment in order to avoid transversal excitations. Proton density and proton energy as impact parameter functions are characterized in single particle density matrix via discretization of diagonal and nearest off-diagonal elements. We combined high field and low densities (1 MeV/92 nm) to create inseparable quantum state by superimposing the hyperpolarizationed proton spin chain with electron spin of ²⁹Si. Quantum discretization of density of states (DOS) was performed by the Monte Carlo simulation method using numerical solutions of proton equations of motion. Distribution of gaussian coherent states is obtained by continuous modulation of individual spin phase and amplitude. Obtained results allow precise engineering and faithful mapping of spin states. This would provide the effective quantum key distribution (QKD) and transmission of quantum information over remote distances between quantum memory centers for scalable quantum communication network. Furthermore, obtained results give insights in application of channeled protons subatomic microscopy as a complete versatile scanning-probe system capable of both quantum engineering of charged particle states and characterization of quantum states below diffraction limit linear and in-depth resolution.PACS numbers: 03.65.Ud, 03.67.Bg, 61.85.+p, 67.30.hj     

Concentration dependence of nitroxyl spin probes in liposomal solution: electron spin resonance and overhauser-enhanced magnetic resonance studies

In this work, the detailed studies of electron spin resonance (ESR) and overhauser-enhanced magnetic resonance imaging (OMRI) were carried out for permeable nitroxyl spin probe, MC-PROXYL as a function of agent concentration in liposomal solution. In order to compare the impermeable nature of nitroxyl radical, the study was also carried out only at 2?mM concentration of carboxy-PROXYL. The ESR parameters were estimated using L-band and 300?MHz ESR spectrometers. The line width broadening was measured as a function of agent concentration in liposomal solution. The estimated rotational correlation time is proportional to the agent concentration, which indicates that less mobile nature of nitroxyl spin probe in liposomal solution. The partition parameter and permeability values indicate that the diffusion of nitroxyl spin probe distribution into the lipid phase is maximum at 2?mM concentration of MC-PROXYL. The dynamic nuclear polarization (DNP) parameters such as DNP factor, longitudinal relaxivity, saturation parameter, leakage factor and coupling factor were estimated for 2?mM MC-PROXYL in 400?mM liposomal dispersion. The spin lattice relaxation time was shortened in liposomal solution, which leads to the high relaxivity. Reduction in coupling factor is due to less interaction between the electron and nuclear spins, which causes the reduction in enhancement. The leakage factor increases with increasing agent concentration. The increase in DNP enhancement was significant up to 2?mM in liposomal solution. These results paves the way for choosing optimum agent concentration and OMRI scan parameters used in intra and extra membrane water by loading the liposome vesicles with a lipid permeable nitroxyl spin probes in OMRI experiments.     

Photoreactions of melanin: a new transient species and evidence for triplet state involvement.

The detection of a new transient species in photoirradiated natural and synthetic melanins is reported. This species decays rapidly at both ambient and cryogenic temperatures and has an electron spin resonance spectrum whose time-profile reveals spin polarization effects (chemically induced dynamic electron polarization) characteristic of triplet state involvement. A possible mechanism for light absorption and degradation by melanins is suggested.     

High frequency dynamics in hemoglobin measured by magnetic relaxation dispersion

The magnetic relaxation dispersion profiles for formate, acetate, and water protons are reported for aqueous solutions of hemoglobin singly and doubly labeled with a nitroxide and mercury(II) ion at cysteines at beta-93. Using two spin labels, one nuclear and one electron spin, a long intramolecular vector is defined between the two beta-93 positions in the protein. The paramagnetic contributions to the observed 1H spin-lattice relaxation rate constant are isolated from the magnetic relaxation dispersion profiles obtained on a dual-magnet apparatus that provides spectral density functions characterizing fluctuations sensed by intermoment dipolar interactions in the time range from the tens of microseconds to approximately 1 ps. Both formate and acetate ions are found to bind specifically within 5 angstroms of the beta-93 spin-label position and the relaxation dispersion has inflection points corresponding to correlation times of 30 ps and 4 ns for both ions. The 4-ns motion is identified with exchange of the anions from the site, whereas the 30-ps correlation time is identified with relative motions of the spin label and the bound anion in the protein environment close to beta-93. The magnetic field dependence of the paramagnetic contributions in both cases is well described by a simple Lorentzian spectral density function; no peaks in the spectral density function are observed. Therefore, the high frequency motions of the protein monitored by the intramolecular vector defined by the electron and nuclear spin are well characterized by a stationary random function of time. Attempts to examine long vector fluctuations by employing electron spin and nuclear spin double-labeling techniques did not yield unambiguous characterization of the high frequency motions of the vector between beta-93 positions on different chains.     

Hybrid Plasmonic Waveguide Based on Tapered Dielectric Nanoribbon: Excitation and Focusing

The nanofocusing of light source was proposed and simulated using the dielectric-loaded surface plasmon polariton (SPP) model with various laterally tapered planar dielectric architectures on the top surface of the metal. By using finite-difference time-domain method, enhancement factor for the local electric field under distinctive incident polarization was analyzed with different taper apexes under various incident wavelengths and incident angles of the excitation laser. The SPP dispersion and the effect of dissipation on adiabatic nanofocusing of SPP in a sharp taper structure were used to predict the optimal taper angles of the structure and to explain the phenomena of SPP wave slowing down as it propagating toward the taper end. This SPP nanofocusing process was also experimentally realized by illuminating the structure of a tapered CdS nanoribbon deposited on the Ag surface. As the emission of the focused SPP at the taper end, the proposed plasmonic structure can be severed as a light nanosource emitter in the future optical integrated circuits.     

Coarse-grained molecular simulation of self-assembly nanostructures of CTAB on nanoscale graphene

Coarse-grained molecular dynamics simulation has been performed to study the aggregated morphology of the cationic surfactant, cetyltrimethylammonium bromide (CTAB), adsorbed on nanoscale graphene surfaces. The CTAB surfactants can self-assemble on graphene to form various supramolecular morphologies and structures. The effect of packing density, thickness of graphene sheet and width of graphene nanoribbon on the CTAB–graphene self-assembly has been investigated. The buoyant densities of various graphene–CTAB assemblies were calculated, which increase with surfactant coverage and number of graphene layers. This result demonstrates that density gradient can be used to isolate graphenes with various layers. This simulation provides larger-scale microscopic insight into the supramolecular self-assembly nanostructures for the CTAB surfactants aggregated on graphene, which could be valuable to guide fabrication of graphene-based hybrid nanocomposites.     

Tunable Slow Light in Graphene Metamaterial in a Broad Terahertz Range

A graphene-based metamaterial with tunable electromagnetically induced transparency is numerically studied in this paper. The proposed structure consists of a graphene layer composed of H shape between two cut wires, by breaking symmetry can control EIT-like effects and by increasing the asymmetry in the structure has strong coupling between elements. It is important that the peak frequency of transmission window can be dynamically controlled over a broad frequency range by varying the chemical potential of graphene layer. The results show that high refractive index sensitivity and figure of merit can be achieved in asymmetrical structures which is good for sensing applications. We calculated the group delay and the results show we can control the group velocity by varying the S parameter in asymmetrical structure. The characteristics of our system indicate important potential applications in integrated optical circuits such as optical storage, ultrafast plasmonic switches, high performance filters, and slow-light devices.     

Gap junction structures: Analysis of the x-ray diffraction data

Models for the spatial distribution of protein, lipid and water in gap junction structures have been constructed from the results of the analysis of X-ray diffraction data described here and the electron microscope and chemical data presented in the preceding paper (Caspar, D. L. D., D. A. Goodenough, L. Makowski, and W.C. Phillips. 1977. 74:605-628). The continuous intensity distribution on the meridian of the X-ray diffraction pattern was measured, and corrected for the effects of the partially ordered stacking and partial orientation of the junctions in the X-ray specimens. The electron density distribution in the direction perpendicular to the plane of the junction was calculated from the meridional intensity data. Determination of the interference function for the stacking of the junctions improved the accuracy of the electron density profile. The pair-correlation function, which provides information about the packing of junctions in the specimen, was calculated from the interference function. The intensities of the hexagonal lattice reflections on the equator of the X-ray pattern were used in coordination with the electron microscope data to calculate to the two-dimensional electron density projection onto the plane of the membrane. Differences in the structure of the connexons as seen in the meridional profile and equatorial projections were shown to be correlated to changes in lattice constant. The parts of the junction structure which are variable have been distinguished from the invariant parts by comparison of the X-ray data from different specimens. The combination of these results with electron microscope and chemical data provides low resolution three- dimensional representations of the structures of gap junctions.     

Optical Near-Field Enhancement with Graphene Bowtie Antennas

In this paper, the optical near-field enhancement of graphene bowtie antennas is numerically investigated at terahertz frequencies using boundary element method. The enhanced field intensity at the gap region is a result of the mutual coupling between two triangular elements upon the excitation of graphene plasmons. Firstly, wide plasmon frequency tunability is demonstrated by changing the chemical potential of graphene without the need to alter the antenna geometry. Secondly, by varying the tip angle and radius of curvature of the graphene antennas, the field intensity enhancement at the gap center of the two-element antennas is systematically studied. It is found that graphene bowtie antennas with two round-cornered equilateral triangles have superior performance to other two-element antennas, such as ribbon pair, sharp-cornered bowtie, and disk pair antennas. Last but not least, by applying a moderate chemical potential of 0.4 eV to graphene bowtie antennas, we found that the field intensity enhancement at gap center is about 220 times as much as using gold of comparable sizes. In short, graphene bowtie antennas of rounded corners give rise to considerable near-field enhancement and are promising for a wide range of applications such as molecular sensing at terahertz frequencies.

     

The replication of kinetoplast DNA networks in Crithidia fasciculata

Kinetoplast DNA from the mitochondria of Crithidia is in the form of a two-dimensional network of thousands of minicircles each containing about 2.5 kb, and a small number of maxicircles each containing about 40 kb. Fractionation of kinetoplast DNA by equilibrium centrifugation in a CsCl-propidium dilodide gradient resolves it into three types of networks. Form I networks band at high density and contain minicircles which are covalently closed; form II networks band at low density and contain minicircles which are nicked or gapped; and replicating networks band at intermediate density and contain some minicircles of each type. Form I networks contain about 5000 minicircles; form II networks contain about 11,000; and replicating networks contain an intermediate number. When cells are pulse-labeled with ³H-thymidine, radioactivity in mitochondrial DNA is preferentially incorporated into replicating networks, but after a chase it appears first in form II networks and finally in form I. Examination of replicating networks by electron microscopy in the presence of ethidium bromide reveals that minicircles in the central region of the network are twisted and therefore covalently closed, whereas those in the peripheral region are not twisted and therefore must be nicked or gapped. The pulse-label is incorporated into the nicked or gapped minicircles of the replicating networks. These results indicate that replication of form I networks begins in peripheral minicircles and that progeny minicircles remain nicked or gapped. As replication proceeds, the size of the network increases, and the peripheral zone of nicked or gapped minicircles enlarges. Finally, when all minicircles have replicated, the network, now form II, is double the size of form I and contains only nicked or gapped minicircles. The final step in replication presumably includes both the cleavage of the network into two form I species and the covalent closure of all the minicircles.