Higher Order Plasmonic Modes Excited in Ag Triangular Nanoplates by an Electron Beam

Ag triangular nanoplates are known to generate strong plasmonic resonances when excited by both light and electron beams. Experimental electron energy-loss spectra (EELS) and maps were acquired using an aberration-corrected JEOL-ARM microscope. The corner, edge and centre modes that are often observed in such structures were also observed in these measurements. In addition, novel higher order internal modes were observed and were found to be well reproduced by theoretical calculations using boundary element method (BEM). These modes are “dark modes” so are not observed in the optical extinction spectra. They are confined surface propagating modes and are analogous to laser cavity modes.     

RF absorption involving biological macromolecules

The fundamental intramolecular frequency of a globular protein can be obtained from the measurements of acoustic velocities of bulk protein matter. This lowest frequency for common size molecules is shown to be above several hundred GHz. All modes below this frequency would then be intermolecular modes or bulk modes of the molecule and surrounding matter or tissue. The lowest frequency modes of an extended DNA double helix are also shown to be bulk modes because of interaction with water. Only DNA modes, whose frequency is well above 4 GHz, can be intrahelical modes, that is, confined to the helix rather than in the helix plus surroundings. Near 4 GHz, they are heavily damped and, therefore, not able to resonantly absorb. Modes that absorb radio frequency (RF) below this frequency are bulk modes of the supporting matter. Bulk modes rapidly thermalize all absorbed energy. The implication of these findings for the possibility of athermal RF effects is considered. The applicability of these findings for other biological molecules is discussed.     

Non-interacting modes for stress, strain and energy in anisotropic hard tissue.

The six non-interacting modes for stress, strain and energy in an orthotropic elastic model of human femoral cortical bone tissue are discussed and illustrated. The stress and strain modes are illustrated using the representation of the stress and strain fields around a circular hole in a flat plate of cortical bone subjected to a uniaxial field of tension as the example. The six modes play a role in the stress analysis of orthotropic elastic materials similar to the roles played by the hydrostatic and deviatoric non-interacting stress, strain and energy modes in isotropic elasticity. The biomechanical significance of the six non-interacting modes for stress, strain and energy in hard tissue is both practical and suggestive. The modes suggest a practical scheme for the representation of stress and strain fields in hard tissue. The existence of the modes suggests physical insights, for example, possible failure mechanisms or adaptation strategies possessed by the hard tissues.     

Plasmonic Modes of Ag Nanoshell Excited by Bi-Dipole

We studied plasmonic dipole, quadrupole, and sextupole modes of Ag nanoshell (NS) excited by a pair of aligned radial electric dipoles (bi-dipole) in symmetric and antisymmetric configurations by using dyadic Green’s functions. The mutual excitation rate and the radiative and nonradiative powers of bi-dipole in the presence of Ag NS were analyzed. Our results show that these modes are in accordance with the surface plasmon resonances of Ag NS irradiated by a polarized plane wave. In addition, the mutual excitation rate retains local maxima at these modes. Moreover, the quadrupole and octupole modes are only excited in the cases of the symmetric radial bi-dipole, while the dipole and sextupole modes are only excited in the cases of the antisymmetric ones. The dipole mode is broadband, while the other higher-order modes are narrowband. Moreover, all of these plasmonic modes are red-shifted as the ratio of the core radius to the shell thickness increases.     

Intermediate and stable redox states of cytochrome c studied by low temperature resonance Raman spectroscopy

Stabilized intermediate redox states of cytochrome c are generated by radiolytic reduction of initially oxidized enzyme in glass matrices at liquid nitrogen temperature. In the intermediate states the heme group is reduced by hydrated electrons, whereas the protein conformation is restrained close to its oxidized form by the low-temperature glass matrix. The intermediate and stable redox states of cytochrome c at neutral and alkaline pH are studied by low-temperature resonance Raman spectroscopy using excitations in resonance with the B (Soret) and Q1 (beta) optical transitions. The assignments of the cytochrome c resonance Raman bands are discussed. The observed spectral characteristics of the intermediate states as well as of the alkaline transition in the oxidized state are interpreted in terms of oxidation-state marker modes, spin-state marker modes, heme iron--axial ligand stretching modes, totally symmetric in-plane porphyrin modes, nontotally symmetric in-plane modes, and out-of-plane modes.     

In-Plane Plasmonic Modes in a Quasicrystalline Array of Metal Nanoparticles

We investigated the plasmonic modes in a two-dimensional quasicrystalline array of metal nanoparticles. The polarization of the modes is in the array plane. A simplified eigen-decomposition method is presented with the help of rotational symmetry. Two kinds of anti-phase ring modes with radial and tangential polarizations are of highest spatial localizations among all of plasmonic modes. For the leaky characteristic of the anti-phase ring modes, the highest fidelity mode in the quasicrystalline array is found to be tangential polarized mode, whereas normal-to-plane polarized mode in the circular ring. The leaky characteristics and spatial localizations of other plasmonic modes are also studied, for example, collective vortex mode that may be a candidate to form negative responses in plasmonic device and collective radial mode that may be used to generate light sources with radial polarizations.     

Stability of hybrid modes of a single-component electron plasma containing an admixture of background gas ions

The spectrum of eigenmodes of a waveguide completely filled with a cold electron plasma containing a small admixture of ions produced due to electron-impact ionization of background gas atoms is calculated numerically. The calculations were performed within the entire range of allowable values of the radial electric and longitudinal magnetic fields for both magnetized and unmagnetized ions by using the earlier derived nonlocal dispersion relation [Plasma Phys. Rep. 36, 563 (2010)]. The spectrum consists of three families of electron modes with frequencies equal to the Doppler-shifted upper and lower hybrid frequencies and modified ion cyclotron (MIC) modes. When the Doppler shift caused by electron rotation in the crossed electric and magnetic fields compensates for the hybrid frequency, the electron modes become low-frequency modes and interact with the ion modes. For m = 1, only the lower hybrid modes can be low-frequency ones, whereas at m ≥ 2, both lower and upper hybrid modes can be low-frequency ones. The spectrum of modes having the azimuthal number m = 2 is thoroughly analyzed. It is shown that, in this case, the lower hybrid modes behave similar to the m = 1 modes. The dispersion curves of the upper hybrid modes intersect with all harmonics of the MIC frequency (positive, negative, and zero) and are unstable in the vicinities of the intersections. The maximum value of the instability growth rate is several times higher than the ion plasma frequency. The MIC modes are unstable within a wide range of the field strengths, and their growth rates are two orders of magnitude slower. Instabilities are caused by the relative motion of electrons and ions (the transverse current) and the anisotropy of the ion distribution function.     

Alternative reproductive modes of Atlantic forest frogs

Diversity in reproductive modes is well known in amphibians, mainly among anurans, which are characterized by a diversity in breeding biology that exceeds that of any other tetrapod. Currently, 39 reproductive modes are recognized among anurans and some species display more than one mode. The breeding biology of some Brazilian Atlantic forest anurans was investigated for this study. We observed unreported reproductive modes for six species, variability in the reproductive modes of individuals of the same species (whereby some individuals of a given population displayed unusual reproductive modes when the physical conditions of the breeding site were suboptimal), and variations within the modes. These observations suggest possible evolutionary steps for the reproductive modes. Anuran breeding biology seems to be more diverse than previously reported, and a character matrix could be constructed to describe the total range of variation of the anuran reproductive modes.     

Quasi-harmonic analysis of mode coupling in fluctuating native proteins

Mode coupling and anharmonicity in a native fluctuating protein are investigated in modal space by projecting the motion along the eigenvectors of the fluctuation correlation matrix. The probability distribution of mode fluctuations is expressed in terms of tensorial Hermite polynomials. Molecular dynamics trajectories of Crambin are generated and used to evaluate the terms of the polynomials and to obtain the modal energies. The energies of a few modes exhibit large deviations from the harmonic energy of kT/2 per mode, resulting from coupling to the surroundings, or to another specific mode or to several other modes. Slowest modes have energies that are below that of the harmonic, and a few fast modes have energies significantly larger than the harmonic. Detailed analysis of the coupling of these modes to others is presented in terms of the lowest order two-mode coupling terms. Finally, the effects of mode coupling on conformational properties of the protein are investigated.     

Evolution of Protein Binding Modes in Homooligomers

The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of protein binding modes from nine families of homooligomers and mapped 60 different binding modes and oligomerization states onto the phylogenetic trees of these families. We observed a significant tendency for the same binding modes to be clustered together and conserved within clades on phylogenetic trees; this trend is especially pronounced for close homologs with 70% sequence identity or higher. Some binding modes are conserved among very distant homologs, pointing to their ancient evolutionary origin, while others are very specific for a certain phylogenetic group. Moreover, we found that the most ancient binding modes have a tendency to involve symmetrical (isologous) homodimer binding arrangements with larger interfaces, while recently evolved binding modes more often exhibit asymmetrical arrangements and smaller interfaces.     

The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies

The metabolism of a cell can be viewed as a weighted sum of elementary modes. Due to the multiplicity of modes the identification of the individual weights represents a non-trivial problem. To enable the determination of weighting factors we have identified and implemented two gene deletions in combination with defined growth conditions that limit the metabolism from 4374 original elementary modes to 24 elementary modes for a non-PHB synthesizing control and 40 modes for a PHB synthesizing strain. These remaining modes can be further grouped into five families that have the same overall stoichiometry. Thus, the complexity of the problem is significantly reduced, and weighting factors for each family of modes could be determined from the measurement of accumulation rates of metabolites. Moreover, it is shown that individual weights are inversely correlated with the entropy generated by the operation of the used pathways defined in elementary modes. This suggests that evolution developed cellular regulatory patterns that permit diversity of pathways while favoring efficient pathways with low entropy generation. Furthermore, such correlation provides a rational way of estimating metabolic fluxes based on the thermodynamic properties of elementary modes. This is demonstrated with an example in which experimentally determined, intracellular fluxes are shown to be highly correlated with fluxes computed based on elementary modes and reaction entropies. The analysis suggests that the set of elementary modes can be interpreted analogous to a metabolic ensemble of quantum states of a macroscopic system.     

Humidity levels drive reproductive modes and phylogenetic diversity of amphibians in the Brazilian Atlantic Forest

Aim The diversity of reproductive modes among amphibians constitutes a striking example of how differences in the biology of species provide important explanations for species distribution patterns on a broad scale. We hypothesize that sites with a higher humidity level will support more modes of reproduction than drier sites and will consequently exhibit a higher phylogenetic diversity. Furthermore, if there is a gradient in the tolerance of reproductive modes to desiccation, there will be a nested pattern in the composition of reproductive modes among sites. Location Twenty‐seven forest sites in the Brazilian Atlantic Forest. Methods Through a path analysis approach, we evaluated the direct and indirect effects of the humidity level on the number of reproductive modes, as well as the relative importance of both variables on amphibian phylogenetic diversity. A nestedness analysis was used to quantify the extent to which the compositions of both species and reproductive modes in drier sites correspond to subsets of those in sites with higher annual precipitation. Results We found that the reproductive modes present in drier sites are non‐random subsets of those present in sites with higher humidity levels. Because reproductive modes are phylogenetically conserved among amphibians, sites with a greater number of reproductive modes supported greater phylogenetic diversity. Sites with high precipitation throughout the year provided suitable environmental conditions for a larger number of reproductive modes, whereas sites with low precipitation and typical seasonal climates supported only those reproductive modes specialized to resist desiccation. Main conclusions Our results show that humidity‐related variables are key environmental factors related to both the richness of reproductive modes and phylogenetic diversity. Our results support the hypothesis that the higher phylogenetic diversity found in moister sites reflects differences in the tolerance to desiccation among different reproductive modes. Given that reproductive modes are associated with susceptibility to desiccation, their incorporation into explanatory models may trigger a significant advance in the understanding of the mechanisms regulating the species richness and composition of amphibian communities.     

Raman and infrared studies of nucleosides at high pressures: I. Adenosine.

Room temperature Raman and infrared (IR) spectra of crystalline adenosine at pressures between 1 atm and 10 GPa are reported. Vibrational modes were identified through assignments in the literature. Many modes were found to increase in frequency with pressure; however, some irregularities were observed. Discontinuities were observed in numerous Raman and IR modes near 2.5 GPa, indicating a phase transition. The modes associated with the glycosidic bond shift significantly down in frequency near this pressure, suggesting a weakening of the associated bond. The IR modes associated with hydrogen-stretching motions were found to decrease in frequency with pressure.     

The Relationship of Spawning Mode to Conservation of North American Minnows (Cyprinidae)

Approximately 20% of North American minnows are considered imperiled. The factors responsible for imperilment in this group are complex, but the relationship of spawning mode to conservation of North American minnows has not been explored. I provide a summary of the spawning modes of imperiled North American minnows, discuss patterns between these modes and conservation status, and predict the spawning modes for several poorly-known imperiled species. Of the 46 species of North American minnows that are imperiled, spawning modes are known for only 13 species. All spawning modes are represented in the imperiled group of minnows except mound-building and egg-clustering, and with the exception of crevice-spawners and pit-ridge-builders, the percentage of imperiled minnows in each category of spawning mode is roughly proportional to the percentage of minnows in that category overall. Species with complex spawning modes, such as mound-building, pit-building and egg-clustering, are among the most common fishes in North American streams. This pattern suggests that there is a relationship between parental care and success (lack of imperilment) in minnows. Spawning mode is an important consideration in the formulation of recovery plans and proactive conservation efforts.     

Energy landscape of a native protein: Jumping-among-minima model

We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496–517, 1998. © 1998 Wiley-Liss, Inc.     

Langevin modes of macromolecules: applications to crambin and DNA hexamers

Langevin modes describe the behavior of atoms moving on a harmonic potential surface subject to viscous damping described by a classical Langevin equation. We present applications to the protein crambin and to the DNA duplex d(CpGpCpGpCpG)2 and its complex with ethidium. Our friction matrix is weighted according to surface area exposed to solvent, and results are reported for various values of the solvent viscosity and models for hydrodynamic interactions. Even for relatively small solvent friction (eta = 0.3 cp) a substantial number of modes are overdamped, and time correlation functions decay smoothly without the oscillations characteristic of gas-phase calculations. Perturbation theory starting from the gas-phase modes is accurate for many low-frequency modes (which are overdamped in the presence of solvent), but fails badly for higher modes. For correlation functions of interest to fluorescence depolarization or nmr relaxation, the plateau values are insensitive to solvent viscosity, but the relaxation times are not. The advantages and limitations of this analysis of macromolecular motions are discussed.     

AUTECOLOGY AND THE FILLING OF ECOSPACE: KEY METAZOAN RADIATIONS

Abstract:  All possible combinations of six tiering positions in relation to the substratum/water interface, six motility levels and six feeding strategies define a complete theoretical ecospace of 216 potential modes of life for marine animals. The number of modes of life actually utilized specifies realized ecospace. Owing to constraints of effectiveness and efficiency the modern marine fauna utilizes only about half the potential number of modes of life, two-thirds of which (62 of 92) are utilized by animals with readily preserved, mineralized hard parts. Realized ecospace has increased markedly since the early evolution of animal ecosystems. The Ediacaran fauna utilized at most 12 modes of life, with just two practised by skeletal organisms. A total of 30 modes of life are recorded in the Early and Middle Cambrian, 19 of which were utilized by skeletal organisms. The other 11 are documented from soft-bodied animals preserved in the Chengjiang and Burgess Shale Konservat-Lagerstätten. The number of modes of life utilized by skeletal organisms increased by more than 50 per cent during the Ordovician radiation to a Late Ordovician total of 30. Between the Late Ordovician and the Recent the number of utilized modes of life has doubled again. The autecological and taxonomic diversity histories of the marine metazoa appear to be broadly parallel, and future studies of theoretical ecospace utilization should provide more detailed tests of pattern and process in the ecological history of the metazoa.     

Cooperative binding of polyamines induces the Escherichia coli single-strand binding protein-DNA binding mode transitions.

The Escherichia coli single-strand binding (SSB) protein is an essential protein involved in DNA replication, recombination, and repair processes. The tetrameric protein binds to ss nucleic acids in a number of different binding modes in vitro. These modes differ in the number of nucleotides occluded per SSB tetramer and in the type and degree of cooperative complexes that are formed with ss DNA. Although it is not yet known whether only one or all of these modes function in vivo, based on the dramatically different properties of the SSB tetramer in these different ss DNA binding modes, it has been suggested that the different modes may function selectively in replication, recombination, and/or repair. The transitions between these different modes are very sensitive to solution conditions, including salt (concentration, as well as cation and anion type), pH, and temperature. We have examined the effects of multivalent cations, principally the polyamine spermine, on the SSB-ss poly(dT) binding mode transitions and find that the transition from the (SSB)35 to the (SSB)56 binding mode can be induced by micromolar concentrations of polyamines as well as the inorganic cation Co(NH3)6(3+). Furthermore, these multivalent cations, as well as Mg2+, induce the binding mode transition by binding cooperatively to the SSB-poly(dT) complexes. These observations are interesting in light of the fact that polyamines, such as spermidine, are part of the ionic environment in E. coli and hence these cations are likely to affect the distribution of SSB-ss DNA binding modes in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)     

Oscillation spectrum of an electron gas with a small density fraction of ions

The problem is solved of the stability of a nonneutral plasma that completely fills a waveguide and consists of magnetized cold electrons and a small density fraction of ions produced by ionization of the atoms of the background gas. The ions are described by an anisotropic distribution function that takes into account the characteristic features of their production in crossed electric and magnetic fields. By solving a set of Vlasov-Poisson equations analytically, a dispersion equation is obtained that is valid over the entire range of allowable electric and magnetic field strengths. The solutions to the dispersion equation for the m = +1 main azimuthal mode are found numerically. The plasma oscillation spectrum consists of the families of Trivelpiece-Gould modes at frequencies equal to the frequencies of oblique Langmuir oscillations Doppler shifted by the electron rotation and also of the families of “modified” ion cyclotron (MIC) modes at frequencies close to the harmonics of the MIC frequency (the frequencies of radial ion oscillations in crossed fields). It is shown that, over a wide range of electric and magnetic field strengths, Trivelpiece-Gould modes have low frequencies and interact with MIC modes. Trivelpiece-Gould modes at frequencies close to the harmonics of the MIC frequency with nonnegative numbers are unstable. The lowest radial Trivelpiece-Gould mode at a frequency close to the zeroth harmonic of the MIC frequency has the fastest growth rate. MIC modes are unstable over a wide range of electric and magnetic field strengths and grow at far slower rates. For a low ion density, a simplified dispersion equation is derived perturbatively that accounts for the nonlocal ion contribution, but, at the same time, has the form of a local dispersion equation for a plasma with a transverse current and anisotropic ions. The solutions to the simplified dispersion equation are obtained analytically. The growth rates of the Trivelpiece-Gould modes and the behavior of the MIC modes agree with those obtained by numerical simulation.