Antiparallel Ones Research Articles

Real-Time Observation of Charge-Spin Cooperative Dynamics Driven by a Nonequilibrium Phonon Environment.

We report on experimental observations of charge-spin cooperative dynamics of two-electron states in a GaAs double quantum dot located in a nonequilibrium phonon environment. When the phonon energy exceeds the lowest excitation energy in the quantum dot, the spin-flip rate of a single electron strongly enhances. In addition, originated from the spatial gradient of phonon density between the dots, the parallel spin states become more probable than the antiparallel ones. These results indicate that spin is essential for further demonstrations of single-electron thermodynamic systems driven by phonons, which will greatly contribute to understanding of the fundamental physics of thermoelectric devices.

Diversity of Parallel Guanine Quadruplexes Induced by Guanine Substitutions.

Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating agents. As a possible cause, we proposed a difference in the sensitivity of parallel and antiparallel quadruplexes to the guanine substitutions in the resulting thermodynamic stability. Reports on the influence of guanine substitutions on the biophysical properties of intramolecular parallel quadruplexes are rare. Moreover, such reports are often complicated by the multimerisation tendencies of parallel quadruplexes. To address this incomplete knowledge, we employed circular dichroism spectroscopy (CD), both as stopped-flow-assisted fast kinetics measurements and end-point measurements, accompanied by thermodynamic analyses, based on UV absorption melting profiles, and electrophoretic methods. We showed that parallel quadruplexes are significantly more sensitive towards guanine substitutions than antiparallel ones. Furthermore, guanine-substituted variants, which in principle might correspond to native genomic sequences, distinctly differ in their biophysical properties, indicating that the four guanines in each tetrad of parallel quadruplexes are not equal. In addition, we were able to distinguish by CD an intramolecular G4 from intermolecular ones resulting from multimerisation mediated by terminal tetrad association, but not from intermolecular G4s formed due to inter-strand Hoogsteen hydrogen bond formation. In conclusion, our study indicates significant variability in parallel quadruplex structures, otherwise disregarded without detailed experimental analysis.

Intrinsically Disordered Domain of Kinesin-3 Kif14 Enables Unique Functional Diversity

In addition to their force-generating motor domains, kinesin motor proteins feature various accessory domains enabling them to fulfill a variety of functions in the cell. Human kinesin-3, Kif14, localizes to the midbody of the mitotic spindle and is involved in the progression of cytokinesis. The specific motor properties enabling Kif14's cellular functions, however, remain unknown. Here, we show invitro that the intrinsically disordered N-terminal domain of Kif14 enables unique functional diversity of the kinesin. Using single molecule TIRF microscopy, we found that Kif14 exists either as a diffusible monomer or as processive dimer and that the disordered domain (1) enables diffusibility of the monomeric Kif14, (2) renders the dimeric Kif14 super-processive and enables the kinesin to pass through highly crowded areas, (3) enables robust, autonomous Kif14 tracking of growing microtubule tips, independent of microtubule end-binding (EB) proteins, and (4) is sufficient to enable crosslinking of parallel microtubules and necessary to enable Kif14-driven sliding of antiparallel ones. We explain these features of Kif14 by the observed diffusible interaction of the disordered domain with the microtubule lattice and the observed increased affinity of the disordered domain for GTP-bound tubulin. We suggest that the disordered domain tethers the motor domain to the microtubule providing a diffusible foothold and a regulatory hub, tuning the kinesin's interaction with microtubules. Our findings thus exemplify pliable protein tethering as a fundamental mechanism of molecular motor regulation.

Quantum correlation swapping in parallel and antiparallel two-qubit mixed states

Quantum correlations (QCs) in some mixed states are thought as important resources in performing certain quantum communication tasks. Recently, it is found that (Azam et al. in Phys Rev A 91:012304, 2015) separable two-qubit states with maximally mixed marginals can be divided into two classes, i.e., parallel and antiparallel two-qubit mixed states. Moreover, a profound difference between their QCs quantified by more probing measures is revealed. In this paper, we study the swapping of QCs in these two classes of states. To be concrete, before the swapping, the two initial states are selected as two parallel two-qubit mixed states, or two antiparallel ones, or a parallel one and an antiparallel one. It is found that, according to two QC quantifiers, i.e., OQD (Ollivier and Zurek in Phys Rev Lett 88:017901, 2001) and LQU (Girolami et al. in Phys Rev Lett 110:240402, 2013), although QCs in the two parallel initial states are different from those in the two antiparallel initial states, the differences are eliminated after the QC swapping. However, if the initial states are selected as a parallel one and an antiparallel one, contrast to the case of two parallel ones as initial states, then after QC swapping, differences emerge.

Mitotic kinesins in action: diffusive searching, directional switching, and ensemble coordination.

Mitotic spindle assembly requires the collective action of multiple microtubule motors that coordinate their activities in ensembles. However, despite significant advances in our understanding of mitotic kinesins at the single-motor level, multi-motor systems are challenging to reconstitute in vitro and thus less well understood. Recent findings highlighted in this perspective demonstrate how various properties of kinesin-5 and -14 motors—diffusive searching, directional switching, and multivalent interactions—allow them to achieve their physiological roles of cross-linking parallel microtubules and sliding antiparallel ones during cell division. Additionally, we highlight new experimental techniques that will help bridge the gap between in vitro biophysical studies and in vivo cell biology investigations and provide new insights into how specific single-molecule mechanisms generate complex cellular behaviors.

Assessing the Structure of Octastate Molecular Switches Using 1H NMR Density Functional Theory Calculations

Density functional theory calculations are used to reveal the relationships between the structures, energies, and NMR signatures of an octastate molecular switch composed of a dithienylethene (DTE) unit covalently linked to an indolino[2,1-b]oxazolidine (BOX) moiety through an ethylenic junction. Both the DTE and BOX moieties can adopt open or closed forms. The ethylenic junction can be Z or E, but the latter has been confirmed to be, by far, more stable than the former for all BOX/DTE combinations. In addition, when the DTE is open, the two thienyl units can fold to form parallel conformers, by opposition to the antiparallel or unfolded conformers. Usually parallel conformers present a higher energy than the antiparallel ones, but in the case of compound 2 having a bulky substituent (R = pPh-SMe) on the terminal thienyl group, the enthalpy of one conformer is very close (1–2 kJ mol–1) to that of the most stable antiparallel one, making photocyclization less efficient. These conformational differences and...

Self-Assembled Donor–Acceptor Chromophores: Evident Layer Effect on the First Hyperpolarizability and Two-Dimensional Charge Transfer Character

Self-assembled donor–acceptor chromophores have extensive applications in photofunctional devices owing to their unique charge transport properties. To explore the possibility of improving nonlinear optical (NLO) properties by self-assembly to multilayer complexes, we theoretically investigated the geometric and electronic structures, interlayer weak interactions, absorption spectra, charge transfer properties, polarizabilities (α), and first hyperpolarizabilities (β) of naphthalimide, -phenyl, and -naphthyl monomers, dimers, and trimers by increasing the layer number n (n = 1, 2, 3). Different stacking patterns of their dimers were also taken into account. These show that parallel stacking patterns are conducive to maximizing overlap with respect to antiparallel ones due to the concept of optimal π-orbital overlap is more vast than purely maximizing cofacial overlap to improve charge transport. The decreases in band gap for the di/trimeric versus monomeric naphthalimide, -phenyl, and -naphthyl monomers i...

Stereoblock-like Brush Copolymers Consisting of Poly(l-lactide) and Poly(d-lactide) Side Chains along Poly(norbornene) Backbone: Synthesis, Stereocomplex Formation, and Structure–Property Relationship

Random and block copolymerizations of poly(l-lactide) (PLLA) and poly(d-lactide) (PDLA) macromonomers having an exo-norbornene group at the α- or ω-chain end (D/L ratio = 1/1, Mn = ca. 5000 g mol–1) were performed via ring-opening metathesis polymerization to produce the brush random and block copolymers consisting of parallel or antiparallel aligned PLLA and PDLA side chains on a poly(norbornene) backbone. The molecular weight and polydispersity index of the brush copolymers were in the range of 40 300–458 000 g mol–1 and 1.03–1.14, respectively. Despite such high molecular weights, these brush copolymers formed a stereocomplex without homochiral crystallization. The melting temperature (Tm) and crystallinity (X) of the resulting stereocomplex varied depending on the backbone length, relative chain direction, and distribution of the PLLA/PDLA side chains. The parallel brush copolymers showed significantly higher Tm and X values than the antiparallel ones.

Induced spin-accumulation and spin-polarization in a quantum-dot ring by using magnetic quantum dots and Rashba spin-orbit effect

The effect of magnetic contacts on spin-dependent electron transport and spin-accumulation in a quantum ring, which is threaded by a magnetic flux, is studied. The quantum ring is made up of four quantum dots, where two of them possess magnetic structure and other ones are subjected to the Rashba spin-orbit coupling. The magnetic quantum dots, referred to as magnetic quantum contacts, are connected to two external leads. Two different configurations of magnetic moments of the quantum contacts are considered; the parallel and the anti-parallel ones. When the magnetic moments are parallel, the degeneracy between the transmission coefficients of spin-up and spin-down electrons is lifted and the system can be adjusted to operate as a spin-filter. In addition, the accumulation of spin-up and spin-down electrons in non-magnetic quantum dots are different in the case of parallel magnetic moments. When the intra-dot Coulomb interaction is taken into account, we find that the electron interactions participate in separation between the accumulations of electrons with different spin directions in non-magnetic quantum dots. Furthermore, the spin-accumulation in non-magnetic quantum dots can be tuned in the both parallel and anti-parallel magnetic moments by adjusting the Rashba spin-orbit strength and the magnetic flux. Thus, the quantum ring with magnetic quantum contacts could be utilized to create tunable local magnetic moments which can be used in designing optimized nanodevices.

Atomistic organization and characterization of tube-like assemblies comprising peptide–polymer conjugates: computer simulation studies

The structure and stability of the nanotube obtained by assembling peptide-polymer conjugates consisting of two poly(n-butyl acrylate) blocks coupled to the cyclic (D-alt-L)-octapeptide cyc[(L-Gln-D-Ala-L-Lys-D-Ala)2], have been investigated at the molecular level using atomistic molecular dynamics simulations. The effect of the wrapping polymer shells in the tube-like core, which consists of stacked beta-sheet cyclopeptides, has been examined by simulating assemblies of both unsubstituted cyclopeptides, and conjugates in chloroform and N,N-dimethylformamide solutions. Furthermore, the influence of the environment has been investigated by comparing conjugate assemblies in solution with those deposited on mica. In addition, nanotubes stabilized by beta-sheet-like hydrogen bonds between both parallel and antiparallel oriented cyclopeptides have been considered in all cases. The results, which have been analysed in terms of energy contributions, partial radial distribution functions, inter-subunit distances, shape of the cyclopeptide ring, internal van der Waals diameters, and both height and width of the nanostructures deposited on mica, have provided important microscopic insights. For example, analysis of both the energy terms and the structural dynamics obtained for the different assemblies indicate that the mica surface interacts more favourably with the parallel assembly than with the antiparallel ones, whereas the only configuration that is structurally stable in solution is the latter. Furthermore, adsorption onto the solid substrate produces a small deformation of the cylindrical molecular system.

Parallel G-Quadruplex-Specific Fluorescent Probe for Monitoring DNA Structural Changes and Label-Free Detection of Potassium Ion

Here we demonstrate an anionic porphyrin, protoporphyrin IX (PPIX), as a parallel G-quadruplex-specific fluorescent probe for monitoring DNA structural changes and utilize it to develop a DNA-based K(+) sensor. The interactions of PPIX with different DNA structures in K(+) or Na(+) solution are investigated by using circular dichroism, fluorescence, and UV-vis spectroscopy. The observations reveal that PPIX has an ∼100-fold selectivity for parallel G-quadruplexes against duplexes and antiparallel G-quadruplexes. Meanwhile, the fluorescence intensity of PPIX increases by over 10-fold upon binding to parallel G-quadruplexes. On the basis of the selectivity and fluorescence property of PPIX, we introduce a facile, label-free approach to monitoring DNA structural changes via fluorescence signal readout that is tuned by PPIX binding and release. To illustrate it, we utilize PPIX and a G-rich DNA PS2.M to construct a fluorescent K(+) sensor based on an antiparallel-to-parallel conformation transition of the G-quadruplex. PS2.M adopts an antiparallel quadruplex structure in Na(+) solution, whereas it gradually converts into a parallel G-quadruplex upon addition of increasing K(+). This conformational change is indicated by a sharp increase in the fluorescence intensity of PPIX, owing to the good ability of PPIX to discriminate parallel G-quadruplexes from antiparallel ones. Even in the presence of 100 mM Na(+), such a "turn-on" fluorescent sensor can respond to low concentrations of K(+), with a limit of detection (0.5 mM) for K(+) analysis. In addition, this sensor exhibits a high selectivity for K(+) over other common metal ions, which ensures its practical applications to real samples. These results reveal that PPIX is promising for use as a specific DNA structural probe in sensing applications.

Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine

At the core of amyloid fibrils is the cross-β spine, a long tape of β-sheets formed by the constituent proteins. Recent high-resolution x-ray studies show that the unit of this filamentous structure is a β-sheet bilayer with side chains within the bilayer forming a tightly interdigitating “steric zipper” interface. However, for a given peptide, different bilayer patterns are possible, and no quantitative explanation exists regarding which pattern is selected or under what condition there can be more than one pattern observed, exhibiting molecular polymorphism. We address the structural selection mechanism by performing molecular dynamics simulations to calculate the free energy of incorporating a peptide monomer into a β-sheet bilayer. We test filaments formed by several types of peptides including GNNQQNY, NNQQ, VEALYL, KLVFFAE and STVIIE, and find that the patterns with the lowest binding free energy correspond to available atomistic structures with high accuracy. Molecular polymorphism, as exhibited by NNQQ, is likely because there are more than one most stable structures whose binding free energies differ by less than the thermal energy. Detailed analysis of individual energy terms reveals that these short peptides are not strained nor do they lose much conformational entropy upon incorporating into a β-sheet bilayer. The selection of a bilayer pattern is determined mainly by the van der Waals and hydrophobic forces as a quantitative measure of shape complementarity among side chains between the β-sheets. The requirement for self-complementary steric zipper formation supports that amyloid fibrils form more easily among similar or same sequences, and it also makes parallel β-sheets generally preferred over anti-parallel ones. But the presence of charged side chains appears to kinetically drive anti-parallel β-sheets to form at early stages of assembly, after which the bilayer formation is likely driven by energetics.

Fast growing instabilities for non-parallel flows

Unstable modes growing when two plasma shells cross over a background plasma at arbitrary angle θ, are investigated using a non-relativistic three cold fluids model. Parallel flows with θ = 0 are slightly more unstable than anti-parallel ones with θ = π . The case θ = π / 2 is as unstable as the θ = 0 one, but the fastest growing modes are oblique. While the most unstable wave vector varies with orientation, its growth rate slightly evolves and there is no such thing as a stable configuration. A number of exact results can be derived, especially for the θ = π / 2 case.

Spin Torque in Double Planar Tunnel Junctions

Transport in a double planar tunnel junction with ferromagnetic electrodes is analyzed theoretically in the zero-temperature limit. The in-plane and out-of-plane components of the spin torque exerted on magnetic moment of the central layer are determined as a function of the angle θ between magnetic moments of one of the external electrodes and of the central layer. Two configurations of the magnetic moments of external electrodes are considered, i.e. parallel and antiparallel ones. It is found that both torque components depend strongly on the thickness of the central layer, especially in junctions with a relatively thin central layer, where enhancement of the torque or a change of its sign can be observed for specific layer thicknesses. In junctions with thick central layer and in the limit of small bias voltage applied to the junction, the in-plane torque is generally smaller in the parallel configuration than in the antiparallel one. The opposite relation is observed for the normal torque.

Yohkoh SXT Full-Resolution Observations of Sigmoids: Structure, Formation, and Eruption

We study the structure of 107 bright sigmoids using full-resolution (2.5'' pixels) images from the Yohkoh Soft X-Ray Telescope (SXT) obtained between 1991 December and 2001 December. We find that none of these sigmoids are made of single loops of S or inverse-S shape; all comprise a pattern of multiple loops. We also find that all S-shaped sigmoids are made of right-bearing loops and all inverse-S-shaped sigmoids of left-bearing loops, without exception. We co-align the SXT images with Kitt Peak magnetograms to determine the magnetic field directions in each sigmoid. We use a potential-field source surface model to determine the direction of the overlying magnetic field. We find that sigmoids for which the relative orientation of these two fields has a parallel component outnumber antiparallel ones by more than an order of magnitude. We find that the number of sigmoids per active region varies with the solar cycle in a manner that is consistent with this finding. Finally, those few sigmoids that are antiparallel erupt roughly twice as often as those that are parallel. We briefly discuss the implications of these results in terms of formation and eruption mechanisms of flux tubes and sigmoids.

Molecular Dynamics Simulations on the Oligomer-Formation Process of the GNNQQNY Peptide from Yeast Prion Protein Sup35

Oligomeric intermediates are possible cytotoxic species in diseases associated with amyloid deposits. Understanding the early steps of fibril formation at atomic details may provide useful information for the rational therapeutic design. In this study, using the heptapeptide GNNQQNY from the yeast prion-like protein Sup35 as a model system, for which a detailed atomic structure of the fibril formed has been determined by x-ray microcrystallography, we investigated its oligomer-formation process from monomer to tetramer at the atomistic level by means of a molecular dynamics simulation with explicit water. Although the number of simulations was limited, the qualitative statistical data gave some interesting results, which indicated that the oligomer formation might start from antiparallel β-sheet-like dimers. When a new single peptide strand was added to the preformed dimers to form trimers and then tetramers, the transition time from disorder aggregates to regular ones for the parallel alignment was found to be obviously much less than for the antiparallel one. Moreover, the parallel pattern also statistically stayed longer, providing more chances for oligomer extending, although the number of parallel stack events was almost equal to antiparallel ones. Therefore, our simulations showed that new strands might prefer to extend in a parallel arrangement to form oligomers, which agrees with the microcrystal structure of the amyloid fibril formed by this peptide. In addition, analysis of the π- π stacking of aromatic residues showed that this type of interaction did not play an important role in giving directionality for β-strand alignment but played a great influence on stabilizing the structures formed in the oligomer-formation process.

Line vortex pinning and spacing in a three-dimensional ordered Josephson medium

A method of calculating the configuration of two line vortices interacting in a three-dimensional ordered Josephson medium and a minimal distance between them at a given pinning parameter is proposed. The axes of the vortices lie in the middle row of an infinite slab 9 or 13 cells thick with different conditions at the boundaries of the slab. Away from the centers of the vortices, the system of finite-difference equations becomes linear. Fluxoid quantization conditions in cells near the centers of the vortices serve as boundary conditions. An exact solution is approached by iterations in those phase discontinuities which cannot be considered small. This technique provides a much higher calculation accuracy and offers a wider domain of applicability than the earlier methods. Critical values I d of the pinning parameter at which two initial vortices keep given spacing d between them are calculated. For various vortex configurations, maximal pinning forces are calculated as functions of the pinning parameter and the distance to the nearest vortices. It is shown that the pinning force decreases near parallel vortices and increases near antiparallel ones.

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water–K +–TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT.

Parallel and antiparallel G*G.C base triplets in pur*pur.pyr triple helices formed with (GA) third strands

Triple helices with G*G.C and A*A.T base triplets with third GA strands either parallel or antiparallel with respect to the homologous duplex strand have been formed in presence of Na+ or Mg2+ counterions. Antiparallel triplexes are more stable and can be obtained even in presence of only monovalent Na+ counterions. A biphasic melting has been observed, reflecting third strand separation around 20°C followed by the duplex -> coil transition around 63°C. Parallel triplexes are far less stable than the antiparallel ones. Their formation requires divalent ions and is observed at low temperature and in high concentration conditions. Different FTIR signatures of G*G.C triplets in parallel and antiparallel triple helices with GA rich third strands have been obtained allowing the identification of such base triplets in triplexes formed by nucleic acids with heterogenous compositions. Only S-type sugars are found in the antiparallel triplex while some N-type sugar conformation is detected in the parallel triplex.

Density functional study of intramolecular ferromagnetic interaction through m-phenylene coupling unit (I): UBLYP, UB3LYP, and UHF calculations

Polyradicals comprised of m-phenylene-bridged organic radicals are well known as building blocks of organic ferromagnets, in which radical groups are connected with each other at the meta position in the benzene ring, and the parallel-spin configurations between radical sites are more stabilized than the antiparallel ones. Topological rules for spin alignments enable us to design organic high-spin dendrimers and polymers with the ferromagnetic ground states by linking various radical species through an m-phenylene unit. However, no systematic ab initio treatment of such spin dendrimers and magnetic polymers has been reported until now, though experimental studies on these materials have been performed extensively in the past ten years. As a first step to examine the possibilities of ferromagnetic dendrimers and polymers constructed of m-phenylene units with organic radicals, we report density functional and molecular orbital calculations of six m-phenylene biradical units with radical substituents and polycarbenes linked with an m-phenylene-type network. The relative stability between the spin states and spin density population are estimated by BLYP or B3LYP and Hartree–Fock calculations in order to clarify their utility for constructions of large spin denderimers and periodic magnetic polymers, which are final targets in this series of papers. It is shown that neutral polyradicals with an m-phenylene bridge are predicted as high-spin ground-state molecules by the computations, while m-phenylene-bridged ion-radical species formed by doping may have the low-spin ground states if zwitterionic configurations play significant roles to stabilize low-spin states. Ab initio computations also show an important role of conformations of polyradicals for stabilization of their high-spin states. The computational results are applied to molecular design of high-spin dendrimers and polymers. Implications of them are also discussed in relation to recent experimental results for high-spin organic molecules.