Spatial Coherence Conversion with Surface Plasmons Using a Three-slit Interferometer

It has been demonstrated recently that surface plasmons can change the state of coherence of light emanating from a Young’s double-slit interferometer. This suggests the possibility of developing a “coherence-converting” device with a large array of subwavelength holes in a metal plate. We have taken an intermediate approach by considering a three-slit geometry, in which we investigated the effects on the modulation of the spatial coherence when an additional slit is placed between the pair of Young’s slits. Our results show that the amount of modulation (enhancement or suppression) can be increased or decreased in the three-slit geometry, compared to the double-slit configuration. This is promising for achieving coherence converting optical devices with suitable arrays of subwavelength holes.     

Quantifying Neural Oscillatory Synchronization: A Comparison between Spectral Coherence and Phase-Locking Value Approaches

Synchronization or phase-locking between oscillating neuronal groups is considered to be important for coordination of information among cortical networks. Spectral coherence is a commonly used approach to quantify phase locking between neural signals. We systematically explored the validity of spectral coherence measures for quantifying synchronization among neural oscillators. To that aim, we simulated coupled oscillatory signals that exhibited synchronization dynamics using an abstract phase-oscillator model as well as interacting gamma-generating spiking neural networks. We found that, within a large parameter range, the spectral coherence measure deviated substantially from the expected phase-locking. Moreover, spectral coherence did not converge to the expected value with increasing signal-to-noise ratio. We found that spectral coherence particularly failed when oscillators were in the partially (intermittent) synchronized state, which we expect to be the most likely state for neural synchronization. The failure was due to the fast frequency and amplitude changes induced by synchronization forces. We then investigated whether spectral coherence reflected the information flow among networks measured by transfer entropy (TE) of spike trains. We found that spectral coherence failed to robustly reflect changes in synchrony-mediated information flow between neural networks in many instances. As an alternative approach we explored a phase-locking value (PLV) method based on the reconstruction of the instantaneous phase. As one approach for reconstructing instantaneous phase, we used the Hilbert Transform (HT) preceded by Singular Spectrum Decomposition (SSD) of the signal. PLV estimates have broad applicability as they do not rely on stationarity, and, unlike spectral coherence, they enable more accurate estimations of oscillatory synchronization across a wide range of different synchronization regimes, and better tracking of synchronization-mediated information flow among networks.     

Defect formation of lytic peptides in lipid membranes and their influence on the thermodynamic properties of the pore environment

We present an experimental study of the pore formation processes of small amphipathic peptides in model phosphocholine lipid membranes. We used atomic force microscopy to characterize the spatial organization and structure of alamethicin- and melittin-induced defects in lipid bilayer membranes and the influence of the peptide on local membrane properties. Alamethicin induced holes in gel DPPC membranes were directly visualized at different peptide concentrations. We found that the thermodynamic state of lipids in gel membranes can be influenced by the presence of alamethicin such that nanoscopic domains of fluid lipids form close to the peptide pores, and that the elastic constants of the membrane are altered in their vicinity. Melittin-induced holes were visualized in DPPC and DLPC membranes at room temperature in order to study the influence of the membrane state on the peptide induced hole formation. Also differential scanning calorimetry was used to investigate the effect of alamethicin on the lipid membrane phase behaviour.     

睡眠剥夺对脑电活动相位相干性的影响研究

将小波变换和相位相干分析应用到事件相关电位实验的脑电信号中。在正常状态和一夜睡眠剥夺状态下提取12名受试者的视觉ERP,进行30～60Hz的小波变换,以此计算前额叶区域的导联内相位相干,以及枕叶和前额叶之间的相位相干性。发现睡眠剥夺引起前额叶的导联内相位相干活动减少和延迟,表明大脑维持完成任务的能力下降;枕叶与前额叶之间的gamma波段相位相干活动减少,表明功能区域之间的电活动传递效应减弱。基于小波变换的相位相干分析可以得到脑电的同步活动,为更好地理解睡眠的机制和评价睡眠剥夺对认知的影响提供了一条思路。     

A simple, selective method for freeze-fracturing spherical cells

A simple and selective method for freeze-fracturing spherical cells is described. The cells are loaded into the holes of a thin nickel screen. A metal hat is applied to the cell monolayer and the whole assembly, hat-cells-screen, is frozen and then fractured by ripping the hat off. The fractured face on the screen is replicated. By varying the size of the screen holes and by applying the hat to either side of the screen, this method can selectively expose the E face (or the outer half of plasma membrane), the P face (or the inner half of the plasma membrane), or the cytoplasm of the cells. It also provides a means to produce fractures at a preselected area on the cell, if the cells can be loaded onto the screen in an oriented fashion.     

Defect formation of lytic peptides in lipid membranes and their influence on the thermodynamic properties of the pore environment

We present an experimental study of the pore formation processes of small amphipathic peptides in model phosphocholine lipid membranes. We used atomic force microscopy to characterize the spatial organization and structure of alamethicin- and melittin-induced defects in lipid bilayer membranes and the influence of the peptide on local membrane properties. Alamethicin induced holes in gel DPPC membranes were directly visualized at different peptide concentrations. We found that the thermodynamic state of lipids in gel membranes can be influenced by the presence of alamethicin such that nanoscopic domains of fluid lipids form close to the peptide pores, and that the elastic constants of the membrane are altered in their vicinity. Melittin-induced holes were visualized in DPPC and DLPC membranes at room temperature in order to study the influence of the membrane state on the peptide induced hole formation. Also differential scanning calorimetry was used to investigate the effect of alamethicin on the lipid membrane phase behaviour.     

Surface Plasmon Resonance on the V-Type Microstructured Optical Fiber Embedded with Dual Copper Wires

Plasmonics - Microstructured optical fiber can be used as polarized filters by filling the metal into the air holes in cladding to generate surface plasmon resonance. In this paper, we present a...     

A quantum mechanical model of adaptive mutation

The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings. Using a very simple model we estimate the decoherence times for protons within DNA and demonstrate that quantum coherence may be maintained for biological time-scales. Interaction of the coherent genome wave function with environments containing utilisable substrate will induce rapid decoherence and thereby destroy the superposition of mutant and non-mutant states. We show that this accelerated rate of decoherence may significantly increase the rate of production of the mutated state.     

Cell motility as an entangled quantum coherence.

Cell motility underlying muscle contraction is imputed to a macroscopic quantum mechanical coherence actualized locally in the body of a biological organism. Actin-activated myosin ATPase activity functions as a heat sink operating effectively at an extremely low temperature. Extraction of heat energy from the actin filament can help condensing the atomic degrees of freedom constituting the filament into a macroscopic quantum state carrying a nonvanishing linear momentum. Sliding movement of an actin filament on myosin molecules while hydrolyzing ATP molecules is a consequence of the quantum mechanical coherence due to an extremely slow release of energy stored in an ATP molecule.     

Tunable Extraordinary Optical Transmission in a Metal Film Perforated with Two-Level Subwavelength Cylindrical Holes

We propose a novel plasmonic metal structure composed of a silver film perforated with a two-dimensional square array of two-level cylindrical holes on a silica substrate. The transmission properties of this structure are theoretically calculated by the finite-difference time-domain (FDTD) method. Double-enhanced transmission peaks are achieved in the visible and infrared regions, which mainly originate from the excitation of localized surface plasmon resonances (LSPRs), the hybridization of plasmon modes, and the optical cavity mode formed in the holes. The enhanced transmission behaviors can be effectively tailored by changing the geometrical parameters and dielectric materials filled in the holes. These findings indicate that our proposed structure has potential applications in highly integrated optoelectronic devices.     

An Air‐Stable and Dendrite‐Free Li Anode for Highly Stable All‐Solid‐State Sulfide‐Based Li Batteries

Li metal is a promising anode material for all‐solid‐state batteries, owing to its high specific capacity and low electrochemical potential. However, direct contact of Li metal with most solid‐state electrolytes induces severe side reactions that can lead to dendrite formation and short circuits. Moreover, Li metal is unstable when exposed to air, leading to stringent processing requirements. Herein, it is reported that the Li₃PS₄/Li interface in all‐solid‐state batteries can be stabilized by an air‐stable Li_xSiS_y protection layer that is formed in situ on the surface of Li metal through a solution‐based method. Highly stable Li cycling for over 2000 h in symmetrical cells and a lifetime of over 100 cycles can be achieved for an all‐solid‐state LiCoO₂/Li₃PS₄/Li cell. Synchrotron‐based high energy X‐ray photoelectron spectroscopy in‐depth analysis demonstrates the distribution of different components within the protection layer. The in situ formation of an electronically insulating Li_xSiS_y protection layer with highly ionic conductivity provides an effective way to prevent Li dendrite formation in high‐energy all‐solid‐state Li metal batteries.     

Conformations consistent with charge migration observed in DNA and RNA X-ray structures

Electron holes are known to migrate along the DNA or RNA duplexes and to localize preferentially on successive guanines. The stationary point conformations of Gua pairs that can trap or let pass these holes have been characterized by quantum chemistry calculations. Here we show their recurrent occurrence in DNA and RNA X-ray structures, often in quadruplex conformations or in interaction with proteins, ligands or metal ions. These findings give support to the biological, possibly regulatory, roles of charge migration in cell functioning.     

Interpreting the visible absorption bands of 1,4-(dihydroxy)-9,10-anthraquinone and its metal chelates

The visible absorption spectra of 1,4-(dihydroxy)-9,10-anthraquinone and of Co(II), Ni(II), Cu(II) and Zn(II) chelates have been studied in different organic solvents. This system provides a model for the anthracycline antibiotics and their metal chelates. The band structure of the spectrum has been determined using the second and fourth derivatives of the spectrum. The visible absorption band of the parent molecule can be assigned to a single electronic state with a reduced dipole moment in the excited state; structure in this band is ascribed to two overlapping vibrational progressions. In contrast, the dianion (hydroxy protons removed) shows a single electronic state with an increased dipole moment in the excited state; structure in this band can be assigned to a single vibrational progression. All of the metal chelates show spectra which are similar in appearance to that of the dianion although the identity of the metal determines the bathochromic shift of the absorption band. Titration of 1,4-dihydroxyanthraquinone with Cu(ClO4)2.6H2O demonstrates that three chelates with metal-to-ligand ratios of 1:2, 1:1 and 2:1 can form depending on the identity of the metal, ratio of metal to ligand, and donor character of the solvent.     

Conformations Consistent with Charge Migration Observed in DNA and RNA X-ray Structures

Abstract

Electron holes are known to migrate along the DNA or RNA duplexes and to localize preferentially on successive guanines. The stationary point conformations of Gua pairs that can trap or let pass these holes have been characterized by quantum chemistry calculations. Here we show their recurrent occurrence in DNA and RNA X-ray structures, often in quadruplex conformations or in interaction with proteins, ligands or metal ions. These findings give support to the biological, possibly regulatory, roles of charge migration in cell functioning.     

Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase

Two divalent metal ions are required for primer‐extension catalyzed by DNA polymerases. One metal ion brings the 3′‐hydroxyl of the primer terminus and the α‐phosphorus atom of incoming dNTP together for bond formation so that the catalytically relevant conformation of the triphosphate tail of the dNTP is in an α,β,γ‐tridentate coordination complex with the second metal ion required for proper substrate alignment. A probable base selectivity mechanism derived from structural studies on Dpo4 suggests that the inability of mispaired dNTPs to form a substrate‐aligned, tridentate coordination complex could effectively cause the mispaired dNTPs to be rejected before catalysis. Nevertheless, we found that mispaired dNTPs can actually form a properly aligned tridentate coordination complex. However, complementary dNTPs occasionally form misaligned complexes with mutant RB69 DNA polymerases (RB69pols) that are not in a tridentate coordination state. Here, we report finding a β,γ‐bidentate coordination complex that contained the complementary dUpNpp opposite dA in the structure of a ternary complex formed by the wild type RB69pol at 1.88 Å resolution. Our observations suggest that several distinct metal‐ion coordination states can exist at the ground state in the polymerase active site and that base selectivity is unlikely to be based on metal‐ion coordination alone.     

A Manipulated Extraordinary Optical Transmission Filter Composed with Subwavelength Hole Complex Arrays

We present a new style extraordinary optical transmission (EOT) nano optical filter combined by two kinds of subwavelength holes array on a gold film. In the design, a square array of non-penetrating holes (hollow holes) inlays into another square array of penetrating holes ordered by a central arrange mode. We numerically calculated the transmission spectra of the patterned gold films by finite-difference time-domain (FDTD) method. Results show that the transmission of the filter can be manipulated by changing the depth of non-penetrating holes. The (1, 1) peak can be enhanced when the incident light normally illuminates one side of the filter with the hollow holes, yet the (1, 1) peak can be suppressed when the light illuminates the other side without hollow holes. It also depicts that the hollow hole array results in energy level splitting of (1, 0) mode propagating on the surface of the filter. What’s more, the splitting can be eliminated by modulating the depth of the hollow holes. Our study further reveals the role of suface plasmon effect in the EOT.     

X-ray absorption spectroscopy (XAS) of toxic metal mineral transformations by fungi

Fungi can be highly efficient biogeochemical agents and accumulators of soluble and particulate forms of metals. This work aims to understand some of the physico-chemical mechanisms involved in toxic metal transformations focusing on the speciation of metals accumulated by fungi and mycorrhizal associations. The amorphous state or poor crystallinity of metal complexes within biomass and relatively low metal concentrations make the determination of metal speciation in biological systems a challenging problem but this can be overcome by using synchrotron-based element-specific X-ray absorption spectroscopy (XAS) techniques. In this research, we have exposed fungi and ectomycorrhizas to a variety of copper-, zinc- and lead-containing minerals. X-ray absorption spectroscopy studies revealed that oxygen ligands (phosphate, carboxylate) played a major role in toxic metal coordination within the fungal and ectomycorrhizal biomass during the accumulation of mobilized toxic metals. Coordination of toxic metals within biomass depended on the fungal species, initial mineral composition, the nitrogen source, and the physiological state/age of the fungal mycelium.     

Functional role of water in membranes updated: A tribute to Träuble

The classical view of a cell membrane is as a hydrophobic slab in which only nonpolar solutes can dissolve and permeate. However, water-soluble non-electrolytes such as glycerol, erythritol, urea and others can permeate lipid membranes in the liquid crystalline state. Moreover, recently polar amino acid's penetration has been explained by means of molecular dynamics in which appearance of water pockets is postulated. According to Träuble (1971), water diffuses across the lipid membranes by occupying holes formed in the lipid matrix due to fluctuations of the acyl chain trans–gauche isomers. These holes, named “kinks” have the molecular dimension of CH₂ vacancies. The condensation of kinks may form aqueous spaces into which molecular species of the size of low molecular weight can dissolve. This molecular view can explain permeability properties considering that water may be distributed along the hydrocarbon chains in the lipid matrix. The purpose of this review is to consolidate the mechanism anticipated by Träuble by discussing recent data in literature that directly correlates the molecular state of methylene groups of the lipids with the state of water in each of them. In addition, the structural properties of water near the lipid residues can be related with the water activity triggering kink formation by changes in the head group conformation that induces the propagation along the acyl chains and hence to the diffusion of water.