Influence of defect locations and nitrogen doping configurations on the mechanical properties of armchair graphene nanoribbons

The effect of defect locations on the mechanical properties of armchair graphene nanoribbons (AGNRs) and the various configurations of nitrogen (N) doping on the mechanical properties of AGNRs were examined using molecular dynamics (MD) simulations. The variation of the Young’s modulus (YM) and the ultimate tensile strength (UTS) of pyridinic-N, graphitic-N, and pyrrolic-N by increasing the concentration of N doping was investigated. The results of MD simulations show that the defect location has a significant effect on the UTS and failure strain (FS) of AGNRs in both vertical and horizontal directions. In the horizontal direction, variations of the UTS and FS are lower than in the vertical direction. On the other hand, the variations of the YM is almost similar in vertical and horizontal directions. The results of this work indicate that the UTS and FS of AGNRs are more sensitive than the YM of AGNRs for different defect directions. Pyridinic-N improves the mechanical properties of the defective AGNR and performs better YM and UTS values than the graphitic-N. Substitution N atoms, which are located at the defective sites and/or at the edges of AGNRs, are mechanically more favorable. Pyrrolic-N configuration has the lowest mechanical properties among the other configurations. Furthermore, pyrrolic-N with Stone-Wales-1 (SW-1) type of defect has higher mechanical properties than pyrrolic-N with Stone-Wales-2 (SW-2) type of defect.     

Coupled Plasmonic Cavities on Moire Surfaces

Surface plasmon polariton (SPP) waveguides formed by coupled plasmonic cavities on metallic Moire surfaces have been investigated both experimentally and numerically. The Moire surface, fabricated by interference lithography, contains periodic arrays of one-dimensional cavities. The coupling strength between the cavities has been controlled by changing the periodicities of the Moire surface. The ability to control the coupling strength allows us to tune the dispersion and the group velocity of the plasmonic coupled cavity mode. Reflection measurements and numerical simulation of the array of SPP cavities have shown a coupled resonator type plasmonic waveguide band formation within the band gap. Coupling coefficients of cavities and group velocities of SPPs are calculated for a range of cavity sizes from weakly coupled regime to strongly coupled regime.     

Homogenization of Heterogeneously Coupled Bistable ODE's—Applied to Excitation Waves in Pancreatic Islets of Langerhans

We consider a lattice of coupled identical differential equations. The coupling is between nearest neighbors and of resistance type, but the strength of coupling varies from site to site. Such a lattice can, for example, model an islet of Langerhans, where the sites in the lattice model individual but identical -cells, and the coupling between cells is made of gap junctions.By using a homogenization technique we approximate the coupled discrete equations by a PDE, basically a nonlinear heat equation (a Fisher equation). For appropriate parameters this equation is known to have wave-solutions. Of importance is the fact, that the resulting diffusion coefficient does not only depend on the average of the coupling, but also on the variance of the strength. This means that the heterogeneity of the coupling strength influences the wave velocity—the greater the variance, the slower is the wave. This result is illustrated by simulations, both of a simple prototype equation, and for a full model of coupled beta-cells in both one and two dimensions, and implies that the natural heterogeneity in the islets of Langerhans should be taken into account.     

Pigment spectra and intermolecular interaction potentials in glasses and proteins

A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and beta-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S(2) band of beta-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available.     

Covalent hybridization of CNT by thymine and uracil: A computational study

We have investigated the electronic and structural properties of covalent functionalization of the tip of (5,0) carbon nanotube (CNT) by di-keto and keto-enol forms of thymine (T) and uracil (U) nucleobases. Density functional theory (DFT) calculations have been performed to optimize the investigated structures and to calculate the properties such as dipole moment, bond length, band gap, total energy, binding energy and quadrupole coupling constant. The results indicated that, due to the functionalization of CNT by T and U, the hybrids exhibit new properties in which they are similar in both types of CNT-T and CNT-U hybrids.     

Electronic, ductile, phase transition and mechanical properties of Lu-monopnictides under high pressures

The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (B2 phase) with space group Pm-3m. Hubbard-U and spin-orbit coupling were included to predict correctly the semiconducting band gap of LuN. Under compression, these materials undergo first-order structural transitions from B1 to B2 phases at 241, 98, 56.82, 25.2 and 32.3 GPa, respectively. The computed elastic properties show that LuBi is ductile by nature. The electronic structure calculations show that LuN is semiconductor at ambient conditions with an indirect band gap of 1.55 eV while other Lu-pnictides are metallic. It was observed that LuN shows metallization at high pressures. The structural properties, viz, equilibrium lattice constant, bulk modulus and its pressure derivative, transition pressure, equation of state, volume collapse, band gap and elastic moduli, show good agreement with available data.

Cell coupling modulates the contraction of fibroblast-populated collagen lattices

Cultured dermal fibroblasts become notably elongated when incorporated into a fibroblast-populated collagen lattice (FPCL). With time these fibroblasts reorganize the collagen responsible for reduction in lattice size. In monolayer the microinjection of Lucifer Yellow (LY) into cultured human fibroblasts shows cell coupling through gap junctions. Human fibroblasts residing on the periphery of a FPCL are at high density and the microinjection of LY into one of those fibroblasts demonstrates cell coupling. Cells within the center of an FPCL are at low density and appear to be independent of one another; however, the microinjection of LY into selected fibroblasts again demonstrates cell coupling. Hence the microinjection of cells in both the center and the edge of a FPCL pass dye to numerous neighbors. Does cell coupling influence FPCL contraction? FPCL incubated with heptanol and octanol, aliphatic alcohols that uncouple cells, inhibits lattice contraction, whereas hexanol, an aliphatic alcohol that does not uncouple cells, did not alter lattice contraction. Fibroblasts derived from connexin 43 (a transmembrane protein responsible for gap junction structures) knockout mice were demonstrated to lack gap junctional communications. When incorporated into a FPCL these cells failed to elongate and demonstrated retarded lattice contraction. Hence, gap junctional communications between fibroblasts incorporated into collagen lattices appear to optimize FPCL contraction and suggest a role for gap junctions in the organization of collagen fibers.     

Effects of the nitrogen doping configuration and site on the thermal conductivity of defective armchair graphene nanoribbons

The influence of the nitrogen (N) doping configuration on the thermal conductivity (TC) of armchair graphene nanoribbons (AGNRs) of size 15.7 nm × 7.26 nm was investigated using classical molecular dynamics (MD) simulations with the optimized Tersoff potential at room temperature. The effect of changing the N-doping site in defects on the TC of AGNRs was also investigated in detail. The variations with N concentration of the TCs of AGNRs presenting graphitic N (quarternary N), pyridinic N, and pyrrolic N doping configurations were studied. Results of MD simulations showed that, among these three doping configurations, pyridinic N was associated with the highest TC, and pyrrolic N with the lowest TC. The highest TC values were obtained when the N dopant atoms were located at the edges and at defects in the AGNR. The presence of both pyrrolic N and Stone–Wales type 1 (SW-1) defects led to a higher TC than the presence of both pyrrolic N and SW-2 defects. Phonon–defect scattering was found to be influenced by changes in C–C bond orientation. SW-1 defects were found to exert a greater influence on the TC than graphitic N doping. Furthermore, the influence on the TC of the N-doping site location in SW-1 defects was examined. Doping the central sites of SW-1 defects was found to yield higher TC values than doping the edge sites of defects. Graphitic-N doping of the more central sites in a SW-1 defect led to a higher TC than the random graphitic-N doping of sites in a SW-1 defect.     

Electroic and optical properties of germanene/MoS<Subscript>2</Subscript> heterobilayers: first principles study

First principles calculations have been performed to investigate the structural, electronic, and optical properties of germanene/MoS₂ heterostructures. The results show that a weak van der Waals coupling between germanene and MoS₂ layers can lead to a considerable band-gap opening (53 meV) as well as the preserved Dirac cone with a linear band dispersion of germanene. The applied external electric filed can not only enhance the interaction strength between two layers, but also linearly control the charge transfer between germanene and MoS₂ layers, and consequently lead to a tunable band gap. Furthermore, the reduction in the optical absorption intensity of the heterostructures with respect to the separated monolayers has been predicted. These findings suggest that the Ge/MoS₂ hybrid can be designed as the device where both finite band gap and high carrier mobility are required.     

Fluorescence and absorption spectroscopy of the weakly fluorescent chlorophyll a in cytochrome b6f of Synechocystis PCC6803.

A spectroscopic characterization of the chlorophyll a (Chl) molecule in the monomeric cytochrome b6f complex (Cytb6f) isolated from the cyanobacterium Synechocystis PCC6803 is presented. The fluorescence lifetime and quantum yield have been determined, and it is shown that Chl in Cytb6f has an excited-state lifetime that is 20 times smaller than that of Chl in methanol. This shortening of the Chl excited state lifetime is not caused by an increased rate of intersystem crossing. Most probably it is due to quenching by a nearby amino acid. It is suggested that this quenching is a mechanism for preventing the formation of Chl triplets, which can lead to the formation of harmful singlet oxygen. Using site-selected fluorescence spectroscopy, detailed information on vibrational frequencies in both the ground and Qy excited states has been obtained. The vibrational frequencies indicate that the Chl molecule has one axial ligand bound to its central magnesium and accepts a hydrogen bond to its 13(1)-keto carbonyl. The results show that the Chl binds to a well-defined pocket of the protein and experiences several close contacts with nearby amino acids. From the site-selected fluorescence spectra, it is further concluded that the electron-phonon coupling is moderately strong. Simulations of both the site-selected fluorescence spectra and the temperature dependence of absorption and fluorescence spectra are presented. These simulations indicate that the Huang-Rhys factor characterizing the electron-phonon coupling strength is between 0.6 and 0.9. The width of the Gaussian inhomogeneous distribution function is 210 +/- 10 cm-1.     

Anisotropic lattice distortions in the mollusk-made aragonite: a widespread phenomenon

In this paper, we present experimental results demonstrating systematic structural distinctions between biogenic and non-biogenic calcium carbonate. Specifically we show, by high-resolution X-ray powder diffraction on dedicated synchrotron beam lines, that the orthorhombic unit cell of the mollusk-made aragonite is anisotropically distorted as compared with that one of geological aragonite. In all investigated shells, belonging to different classes (bivalve, gastropod, and cephalopod) and taken from different habitat origins (sea, fresh water, and land), the maximum elongation of about 0.1-0.2% was found along the c-axis. The lattice distortions along the a-axis were also of the positive sign (elongation) but lower than those along the c-axis, whereas lattice distortions along the b-axis were always negative (contraction). Supporting experiments, including structural analysis after a bleach procedure, measurements of temperature-dependent lattice relaxation, measurements of the CO(2) release at elevated temperatures, signify that the observed structural distinctions are most probably caused by the organic molecules intercalating into the aragonite lattice during biomineralization. Our findings show that in some sense organisms control the atomic structure of the crystals. Deeper understanding of this phenomenon will aid in the development of new approaches to grow biomimetic composites and tailor their properties on a molecular level.     

Dynamic strength of molecular adhesion bonds.

In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale of molecular motions. Using results from a simulation of biotin-avidin bonds (Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J., this issue), we describe how Brownian dynamics can help bridge the gap between molecular dynamics and probe tests.     

Ab-initio study of anisotropic and chemical surface modifications of β-SiC nanowires

The electronic band structure and electronic density of states of cubic SiC nanowires (SiCNWs) in the directions [001], [111], and [112] were studied by means of Density Functional Theory (DFT) based on the generalized gradient approximation and the supercell technique. The surface dangling bonds were passivated using hydrogen (H) atoms and OH radicals in order to study the effects of this passivation on the electronic states of the SiCNWs. The calculations show a clear dependence of the electronic properties of the SiCNWs on the quantum confinement, orientation, and chemical passivation of the surface. In general, surface passivation with either H or OH radicals removes the dangling bond states from the band gap, and OH saturation appears to produce a smaller band gap than H passivation. An analysis of the atom-resolved density of states showed that there is substantial charge transfer between the Si and O atoms in the OH-terminated case, which reduces the band gap compared to the H-terminated case, in which charge transfer mainly occurs between the Si and C atoms.     

New Insights on the Burstein-Moss Shift and Band Gap Narrowing in Indium-Doped Zinc Oxide Thin Films

The Burstein-Moss shift and band gap narrowing of sputtered indium-doped zinc oxide (IZO) thin films are investigated as a function of carrier concentrations. The optical band gap shifts below the carrier concentration of 5.61 × 10¹⁹ cm^-3 are well-described by the Burstein-Moss model. For carrier concentrations higher than 8.71 × 10¹⁹ cm^-3 the shift decreases, indicating that band gap narrowing mechanisms are increasingly significant and are competing with the Burstein-Moss effect. The incorporation of In causes the resistivity to decrease three orders of magnitude. As the mean-free path of carriers is less than the crystallite size, the resistivity is probably affected by ionized impurities as well as defect scattering mechanisms, but not grain boundary scattering. The c lattice constant as well as film stress is observed to increase in stages with increasing carrier concentration. The asymmetric XPS Zn 2p_3/2 peak in the film with the highest carrier concentration of 7.02 × 10²⁰ cm^-3 suggests the presence of stacking defects in the ZnO lattice. The Raman peak at 274 cm^-1 is attributed to lattice defects introduced by In dopants.     

Low-frequency vibrational spectra of some homopolypeptides in the solid state

Low-frequency Raman and far-infrared spectra of polyglycine, poly-L -alanine, and poly-L -valine have been measured. The Raman spectra exhibit an intense band near 100 cm^?1 for these homopolypeptides. Lattice calculations of the polyglycines are used to assign the intense Raman band to a rotary lattice mode. For homopolypeptides in the β conformation, an infrared band is observed whose frequency varies inversely with the square root of the mass of the peptide repeating unit. This infrared band is assigned to the hydrogen bond stretching lattice vibration.     

Effects of gap junction to Ca(2+) and to IP(3) on the synchronization of intercellular calcium oscillations in hepatocytes

The frequency of free cytosolic calcium concentration ([Ca(2+)]) oscillations elicited by a given agonist concentration differs between individual hepatocytes. However, in multicellular systems of rat hepatocytes and even in the intact liver, [Ca(2+)] oscillations are synchronized and highly coordinated. In this paper, we have investigated theoretically the gap junction permeable to calcium and to IP(3) on intercellular synchronization by means of a mathematical model, respectively. It is shown that gap junction permeable to calcium and to IP(3) are effective on synchronizing calcium oscillations in coupled hepatocytes. Our theoretical results are similar either for the case of Ca(2+) acting as coordinating messenger or for the case of IP(3) as coordinating messenger. There exists an optimal coupling strength for a pair of connected hepatocytes. Appropriate coupling strength and IP(3) level can induce various harmonic locking of intercellular [Ca(2+)] oscillations. Furthermore, a phase diagram in two-dimensional parameter space of the coupling strength and IP(3) level (or the velocity of IP(3) synthesis) has been predicted, in which the synchronization region is similar to Arnol'd tongue.     

FINE STRUCTURE OF THE SYNAPTIC DISCS SEPARATED FROM THE GOLDFISH MEDULLA OBLONGATA

Synaptic discs are structures localized in the club ending synapses on the Mauthner cell lateral dendrite of the goldfish medulla oblongata. The synaptic discs present a hexagonal array of particles ~8.5 nm center-to-center when observed in en face view. This lattice covers the entire surface Divalent cations are important in the stabilization of this particular hexagonal array of particles When a synaptic disc-rich fraction is treated with chelating agents (EDTA or EGTA), definite changes occur in the hexagonal lattice. First, the synaptic membranes show zones without particles interspersed with zones covered with the hexagonal array of particles Second, the synaptic discs break down and a new structure characterized by two parallel dense bands (7 nm each), separated by a 4 nm gap, is observed. The negative stain fills the gap region showing striations spaced ~10 nm center-to-center crossing the gap, but it does not penetrate the dense bands This "double band" structure is interpreted as an edge on view of a fragment of the synaptic membrane complex. Further treatment of this fraction with a chelating agent plus 0.3% deoxycholate produces an increase in the number of double band structures. However, EDTA plus Triton X-100 (a treatment known to produce solubilization of membrane proteins) never shows such double band structure An ordered material was observed associated with the cytoplasmic leaflets of the double bands This material consists of rows of beads ~4 nm in diameter and spaced at intervals of ~7 nm. Each of these beads is joined to the band by a thin stalk.     

A DFT study of the effects of donor-to-acceptor ratio on the electronic properties of copolymers based on tricyclic non-classical thiophene

The geometries and electronic properties of the 1D polymers composed of thieno[3,2-b]thiophene (TT), thiophene (T), pyrrole (P), furan (F) and tricyclic non-classical thiophenes ([1,2,5]thiadiazolo[3,4-b]thieno-[3,4-e]pyrazine, TTP) are investigated systematically by the density functional theory method at the B3LYP level with 6-31G(d) basis set. The theoretical study suggests that the ratio of donor-to-acceptor (D-A ratio) plays a crucial role in the geometric and electronic properties for the alternating donor–acceptor polymers. The increase in the D-A ratio leads to an increase in the bridge bond length and an inverse change in the bond-length alternation. Furthermore, the increase in the portion of donor units can lead to an obvious reduction in band gap for these studied polymers. The TT-containing polymer possessing the D-A ratio of 2:1 (p-BTTTTP) that is predicted to have a small band gap of 0.25 eV and a relatively small effective mass of carriers is a good candidate for an intrinsic conducting polymer. Therefore, the tricyclic non-classical thiophenes (TTP) and TT are good building blocks that can lead to small band gap polymers.     

Thermal sensitivity of the red absorption tail of the photosystem II reaction center complex.

The red tail of the absorption spectrum of the D1-D2-cytb559 complex, defined as the absorption signal not described by the two Gaussian sub-bands associated with the intense electronic transitions at 680 and 683 nm, exhibits anomalous temperature behavior. This tail was analyzed in the temperature interval between 80 and 300 K in terms of the mean square deviation (sigma2) of the total Qy absorption band and by Gaussian sub-band decomposition. The value of the average optical reorganization energy (Snum) obtained from the temperature dependence of sigma2 for the whole absorption band was 32 cm(-1), and changed to 16-20 cm(-1) after subtraction of the sub-bands describing the red tail. This latter value is in agreement with the hole burning literature data for chlorophyll bound to proteins, and indicates that the rather high value for the apparent optical reorganization energy obtained by analysis of the total Qy band of the D1-D2-cytb559 complex is determined by the temperature sensitivity of the red tail. This suggests that the long wavelength absorption tail might be due to vibrational transitions associated with vibrational modes in the range of 80-150 cm(-1) which are thermally accessible and give rise to an absorption signal on the low-energy side of the (0,0) transition. On the basis of this assumption, the electron-phonon coupling strength (S) for these modes is estimated to be in the range 0.028-0.18. This interpretation furthermore supports the idea that the electronic transition near 683 nm is that of a monomer chlorophyll.     

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of –46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X–H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent’s rule is verified for the C–H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (?²ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)₄ with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.