Sample records for all-atom normal mode

  1. Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution.

    PubMed

    Chen, Xuehui; Sun, Yunxiang; An, Xiongbo; Ming, Dengming

    2011-10-14

    Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another. © 2011 American Institute of Physics

  2. Normal Mode Analysis of Polytheonamide B

    NASA Astrophysics Data System (ADS)

    Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

    2007-09-01

    Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

  3. Normal mode analysis and applications in biological physics.

    PubMed

    Dykeman, Eric C; Sankey, Otto F

    2010-10-27

    Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.

  4. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme.

    PubMed

    Levitt, M; Sander, C; Stern, P S

    1985-02-05

    We have developed a new method for modelling protein dynamics using normal-mode analysis in internal co-ordinates. This method, normal-mode dynamics, is particularly well suited for modelling collective motion, makes possible direct visualization of biologically interesting modes, and is complementary to the more time-consuming simulation of molecular dynamics trajectories. The essential assumption and limitation of normal-mode analysis is that the molecular potential energy varies quadratically. Our study starts with energy minimization of the X-ray co-ordinates with respect to the single-bond torsion angles. The main technical task is the calculation of second derivative matrices of kinetic and potential energy with respect to the torsion angle co-ordinates. These enter into a generalized eigenvalue problem, and the final eigenvalues and eigenvectors provide a complete description of the motion in the basic 0.1 to 10 picosecond range. Thermodynamic averages of amplitudes, fluctuations and correlations can be calculated efficiently using analytical formulae. The general method presented here is applied to four proteins, trypsin inhibitor, crambin, ribonuclease and lysozyme. When the resulting atomic motion is visualized by computer graphics, it is clear that the motion of each protein is collective with all atoms participating in each mode. The slow modes, with frequencies of below 10 cm-1 (a period of 3 ps), are the most interesting in that the motion in these modes is segmental. The root-mean-square atomic fluctuations, which are dominated by a few slow modes, agree well with experimental temperature factors (B values). The normal-mode dynamics of these four proteins have many features in common, although in the larger molecules, lysozyme and ribonuclease, there is low frequency domain motion about the active site.

  5. Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

    PubMed Central

    Zheng, Wenjun

    2010-01-01

    Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

  6. Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor

    NASA Astrophysics Data System (ADS)

    Brooks, Bernard; Karplus, Martin

    1983-11-01

    A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.

  7. Normalized modes at selected points without normalization

    NASA Astrophysics Data System (ADS)

    Kausel, Eduardo

    2018-04-01

    As every textbook on linear algebra demonstrates, the eigenvectors for the general eigenvalue problem | K - λM | = 0 involving two real, symmetric, positive definite matrices K , M satisfy some well-defined orthogonality conditions. Equally well-known is the fact that those eigenvectors can be normalized so that their modal mass μ =ϕT Mϕ is unity: it suffices to divide each unscaled mode by the square root of the modal mass. Thus, the normalization is the result of an explicit calculation applied to the modes after they were obtained by some means. However, we show herein that the normalized modes are not merely convenient forms of scaling, but that they are actually intrinsic properties of the pair of matrices K , M, that is, the matrices already "know" about normalization even before the modes have been obtained. This means that we can obtain individual components of the normalized modes directly from the eigenvalue problem, and without needing to obtain either all of the modes or for that matter, any one complete mode. These results are achieved by means of the residue theorem of operational calculus, a finding that is rather remarkable inasmuch as the residues themselves do not make use of any orthogonality conditions or normalization in the first place. It appears that this obscure property connecting the general eigenvalue problem of modal analysis with the residue theorem of operational calculus may have been overlooked up until now, but which has in turn interesting theoretical implications.Á

  8. iMODS: internal coordinates normal mode analysis server.

    PubMed

    López-Blanco, José Ramón; Aliaga, José I; Quintana-Ortí, Enrique S; Chacón, Pablo

    2014-07-01

    Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Principal Component Relaxation Mode Analysis of an All-Atom Molecular Dynamics Simulation of Human Lysozyme

    NASA Astrophysics Data System (ADS)

    Nagai, Toshiki; Mitsutake, Ayori; Takano, Hiroshi

    2013-02-01

    A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

  10. Instantaneous Normal Modes and the Protein Glass Transition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schulz, Roland; Krishnan, Marimuthu; Daidone, Isabella

    2009-01-01

    In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at ~ 220more » K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.« less

  11. Instantaneous Normal Modes and the Protein Glass Transition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schultz, Roland; Krishnan, Marimuthu; Daidone, Isabella

    2009-01-01

    In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at 220 K.more » The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.« less

  12. Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids

    NASA Astrophysics Data System (ADS)

    Moreno-Herrero, F.; Colchero, J.; Gómez-Herrero, J.; Baró, A. M.

    2004-03-01

    The capabilities of the atomic force microscope for imaging biomolecules under physiological conditions has been systematically investigated. Contact, dynamic, and jumping modes have been applied to four different biological systems: DNA, purple membrane, Alzheimer paired helical filaments, and the bacteriophage φ29. These samples have been selected to cover a wide variety of biological systems in terms of sizes and substrate contact area, which make them very appropriate for the type of comparative studies carried out in the present work. Although dynamic mode atomic force microscopy is clearly the best choice for imaging soft samples in air, in liquids there is not a leading technique. In liquids, the most appropriate imaging mode depends on the sample characteristics and preparation methods. Contact or dynamic modes are the best choices for imaging molecular assemblies arranged as crystals such as the purple membrane. In this case, the advantage of image acquisition speed predominates over the disadvantage of high lateral or normal force. For imaging individual macromolecules, which are weakly bonded to the substrate, lateral and normal forces are the relevant factors, and hence the jumping mode, an imaging mode which minimizes lateral and normal forces, is preferable to other imaging modes.

  13. Population of collective modes in light scattering by many atoms

    NASA Astrophysics Data System (ADS)

    Guerin, William; Kaiser, Robin

    2017-05-01

    The interaction of light with an atomic sample containing a large number of particles gives rise to many collective (or cooperative) effects, such as multiple scattering, superradiance, and subradiance, even if the atomic density is low and the incident optical intensity weak (linear optics regime). Tracing over the degrees of freedom of the light field, the system can be well described by an effective atomic Hamiltonian, which contains the light-mediated dipole-dipole interaction between atoms. This long-range interaction is at the origin of the various collective effects, or of collective excitation modes of the system. Even though an analysis of the eigenvalues and eigenfunctions of these collective modes does allow distinguishing superradiant modes, for instance, from other collective modes, this is not sufficient to understand the dynamics of a driven system, as not all collective modes are significantly populated. Here, we study how the excitation parameters, i.e., the driving field, determines the population of the collective modes. We investigate in particular the role of the laser detuning from the atomic transition, and demonstrate a simple relation between the detuning and the steady-state population of the modes. This relation allows understanding several properties of cooperative scattering, such as why superradiance and subradiance become independent of the detuning at large enough detuning without vanishing, and why superradiance, but not subradiance, is suppressed near resonance. We also show that the spatial properties of the collective modes allow distinguishing diffusive modes, responsible for radiation trapping, from subradiant modes.

  14. Line splitting and modified atomic decay of atoms coupled with N quantized cavity modes

    NASA Astrophysics Data System (ADS)

    Zhu, Yifu

    1992-05-01

    We study the interaction of a two-level atom with N non-degenerate quantized cavity modes including dissipations from atomic decay and cavity damps. In the strong coupling regime, the absorption or emission spectrum of weakly excited atom-cavity system possesses N + 1 spectral peaks whose linewidths are the weighted averages of atomic and cavity linewidths. The coupled system shows subnatural (supernatural) atomic decay behavior if the photon loss rates from the N cavity modes are smaller (larger) than the atomic decay rate. If N cavity modes are degenerate, they can be treated effectively as a single mode. In addition, we present numerical calculations for N = 2 to characterize the system evolution from the weak coupling to strong coupling limits.

  15. Normal mode-guided transition pathway generation in proteins

    PubMed Central

    Lee, Byung Ho; Seo, Sangjae; Kim, Min Hyeok; Kim, Youngjin; Jo, Soojin; Choi, Moon-ki; Lee, Hoomin; Choi, Jae Boong

    2017-01-01

    The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this. PMID:29020017

  16. Hydrodynamics of Normal Atomic Gases with Spin-orbit Coupling

    PubMed Central

    Hou, Yan-Hua; Yu, Zhenhua

    2015-01-01

    Successful realization of spin-orbit coupling in atomic gases by the NIST scheme opens the prospect of studying the effects of spin-orbit coupling on many-body physics in an unprecedentedly controllable way. Here we derive the linearized hydrodynamic equations for the normal atomic gases of the spin-orbit coupling by the NIST scheme with zero detuning. We show that the hydrodynamics of the system crucially depends on the momentum susceptibilities which can be modified by the spin-orbit coupling. We reveal the effects of the spin-orbit coupling on the sound velocities and the dipole mode frequency of the gases by applying our formalism to the ideal Fermi gas. We also discuss the generalization of our results to other situations. PMID:26483090

  17. Hydrodynamics of Normal Atomic Gases with Spin-orbit Coupling.

    PubMed

    Hou, Yan-Hua; Yu, Zhenhua

    2015-10-20

    Successful realization of spin-orbit coupling in atomic gases by the NIST scheme opens the prospect of studying the effects of spin-orbit coupling on many-body physics in an unprecedentedly controllable way. Here we derive the linearized hydrodynamic equations for the normal atomic gases of the spin-orbit coupling by the NIST scheme with zero detuning. We show that the hydrodynamics of the system crucially depends on the momentum susceptibilities which can be modified by the spin-orbit coupling. We reveal the effects of the spin-orbit coupling on the sound velocities and the dipole mode frequency of the gases by applying our formalism to the ideal Fermi gas. We also discuss the generalization of our results to other situations.

  18. Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.

    PubMed

    Farag, Marwa H; Zúñiga, José; Requena, Alberto; Bastida, Adolfo

    2013-05-28

    Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ~85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.

  19. Helicon normal modes in Proto-MPEX

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Piotrowicz, Pawel A.; Caneses, Juan F.; Green, David L.

    Here, the Proto-MPEX helicon source has been operating in a high electron density 'helicon-mode'. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the 'helicon-mode'. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besidesmore » directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region.« less

  20. Helicon normal modes in Proto-MPEX

    DOE PAGES

    Piotrowicz, Pawel A.; Caneses, Juan F.; Green, David L.; ...

    2018-05-22

    Here, the Proto-MPEX helicon source has been operating in a high electron density 'helicon-mode'. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the 'helicon-mode'. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besidesmore » directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region.« less

  1. Low frequency mechanical modes of viruses with atomic detail

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric; Sankey, Otto

    2008-03-01

    The low frequency mechanical modes of viruses can provide important insights into the large global motions that a virus may exhibit. Recently it has been proposed that these large global motions may be excited using impulsive stimulated Raman scattering producing permanent damage to the virus. In order to understand the coupling of external probes to the capsid, vibrational modes with atomic detail are essential. The standard approach to find the atomic modes of a molecule with N atoms requires the formation and diagonlization of a 3Nx3N matrix. As viruses have 10^5 or more atoms, the standard approach is difficult. Using ideas from electronic structure theory, we have developed a method to construct the mechanical modes of large molecules such as viruses with atomic detail. Application to viruses such as the cowpea chlorotic mottle virus, satellite tobacco necrosis virus, and M13 bacteriophage show a fairly complicated picture of the mechanical modes.

  2. All-optical transistor based on Rydberg atom-assisted optomechanical system.

    PubMed

    Liu, Yi-Mou; Tian, Xue-Dong; Wang, Jing; Fan, Chu-Hui; Gao, Feng; Bao, Qian-Qian

    2018-04-30

    We study the optical response of a double optomechanical cavity system assisted by two Rydberg atoms. The target atom is only coupled with one side cavity by a single cavity mode, and gate one is outside the cavities. It has been realized that a long-range manipulation of optical properties of a hybrid system, by controlling the Rydberg atom decoupled with the optomechanical cavity. Switching on the coupling between atoms and cavity mode, the original spatial inversion symmetry of the double cavity structure has been broken. Combining the controllable optical non-reciprocity with the coherent perfect absorption/transmission/synthesis effect (CPA/CPT/CPS reported by [ X.-B.Yan Opt. Express 22, 4886 (2014)], we put forward the theoretical schemes of an all-optical transistor which contains functions such as a controllable diode, rectifier, and amplifier by controlling a single gate photon.

  3. Normal modes of weak colloidal gels

    NASA Astrophysics Data System (ADS)

    Varga, Zsigmond; Swan, James W.

    2018-01-01

    The normal modes and relaxation rates of weak colloidal gels are investigated in calculations using different models of the hydrodynamic interactions between suspended particles. The relaxation spectrum is computed for freely draining, Rotne-Prager-Yamakawa, and accelerated Stokesian dynamics approximations of the hydrodynamic mobility in a normal mode analysis of a harmonic network representing several colloidal gels. We find that the density of states and spatial structure of the normal modes are fundamentally altered by long-ranged hydrodynamic coupling among the particles. Short-ranged coupling due to hydrodynamic lubrication affects only the relaxation rates of short-wavelength modes. Hydrodynamic models accounting for long-ranged coupling exhibit a microscopic relaxation rate for each normal mode, λ that scales as l-2, where l is the spatial correlation length of the normal mode. For the freely draining approximation, which neglects long-ranged coupling, the microscopic relaxation rate scales as l-γ, where γ varies between three and two with increasing particle volume fraction. A simple phenomenological model of the internal elastic response to normal mode fluctuations is developed, which shows that long-ranged hydrodynamic interactions play a central role in the viscoelasticity of the gel network. Dynamic simulations of hard spheres that gel in response to short-ranged depletion attractions are used to test the applicability of the density of states predictions. For particle concentrations up to 30% by volume, the power law decay of the relaxation modulus in simulations accounting for long-ranged hydrodynamic interactions agrees with predictions generated by the density of states of the corresponding harmonic networks as well as experimental measurements. For higher volume fractions, excluded volume interactions dominate the stress response, and the prediction from the harmonic network density of states fails. Analogous to the Zimm model in polymer

  4. Molecular structure, natural bond analysis, vibrational and electronic spectra, surface enhanced Raman scattering and Mulliken atomic charges of the normal modes of [Mn(DDTC)2] complex.

    PubMed

    Téllez S, Claudio A; Costa, Anilton C; Mondragón, M A; Ferreira, Glaucio B; Versiane, O; Rangel, J L; Lima, G Müller; Martin, A A

    2016-12-05

    Theoretical and experimental bands have been assigned for the Fourier Transform Infrared and Raman spectra of the bis(diethyldithiocarbamate)Mn(II) complex, [Mn(DDTC)2]. The calculations have been based on the DFT/B3LYP method, second derivative spectra and band deconvolution analysis. The UV-vis experimental spectra were measured in acetonitrile solution, and the calculated electronic spectrum was obtained using the TD/B3LYP method with 6-311G(d, p) basis set for all atoms. Charge transfer bands and those d-d spin forbidden were assigned in the UV-vis spectrum. The natural bond orbital analysis was carried out using the DFT/B3LYP method and the Mn(II) hybridization leading to the planar geometry of the framework was discussed. Surface enhanced Raman scattering (SERS) was also performed. Mulliken charges of the normal modes were obtained and related to the SERS enhanced bands. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Dynamics of mode-coupling-induced microresonator frequency combs in normal dispersion

    NASA Astrophysics Data System (ADS)

    Jang, Jae K.; Okawachi, Yoshitomo; Yu, Mengjie; Luke, Kevin; Ji, Xingchen; Lipson, Michal; Gaeta, Alexander L.

    2016-12-01

    We experimentally and theoretically investigate the dynamics of microresonator-based frequency comb generation assisted by mode coupling in the normal group-velocity dispersion (GVD) regime. We show that mode coupling can initiate intracavity modulation instability (MI) by directly perturbing the pump-resonance mode. We also observe the formation of a low-noise comb as the pump frequency is tuned further into resonance from the MI point. We determine the phase-matching conditions that accurately predict all the essential features of the MI and comb spectra, and extend the existing analogy between mode coupling and high-order dispersion to the normal GVD regime. We discuss the applicability of our analysis to the possibility of broadband comb generation in the normal GVD regime.

  6. Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation.

    PubMed

    Tang, Ping-Han; Wu, Ten-Ming; Yen, Tsung-Wen; Lai, S K; Hsu, P J

    2011-09-07

    We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat. © 2011 American Institute of Physics

  7. Normal mode study of the earth's rigid body motions

    NASA Technical Reports Server (NTRS)

    Chao, B. F.

    1983-01-01

    In this paper it is shown that the earth's rigid body (rb) motions can be represented by an analytical set of eigensolutions to the equation of motion for elastic-gravitational free oscillations. Thus each degree of freedom in the rb motion is associated with a rb normal mode. Cases of both nonrotating and rotating earth models are studied, and it is shown that the rb modes do incorporate neatly into the earth's system of normal modes of free oscillation. The excitation formula for the rb modes are also obtained, based on normal mode theory. Physical implications of the results are summarized and the fundamental differences between rb modes and seismic modes are emphasized. In particular, it is ascertained that the Chandler wobble, being one of the rb modes belonging to the rotating earth, can be studied using the established theory of normal modes.

  8. Helicon normal modes in Proto-MPEX

    NASA Astrophysics Data System (ADS)

    Piotrowicz, P. A.; Caneses, J. F.; Green, D. L.; Goulding, R. H.; Lau, C.; Caughman, J. B. O.; Rapp, J.; Ruzic, D. N.

    2018-05-01

    The Proto-MPEX helicon source has been operating in a high electron density ‘helicon-mode’. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the ‘helicon-mode’. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besides directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region. ).

  9. High-Frequency Normal Mode Propagation in Aluminum Cylinders

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2009-01-01

    Acoustic measurements made using compressional-wave (P-wave) and shear-wave (S-wave) transducers in aluminum cylinders reveal waveform features with high amplitudes and with velocities that depend on the feature's dominant frequency. In a given waveform, high-frequency features generally arrive earlier than low-frequency features, typical for normal mode propagation. To analyze these waveforms, the elastic equation is solved in a cylindrical coordinate system for the high-frequency case in which the acoustic wavelength is small compared to the cylinder geometry, and the surrounding medium is air. Dispersive P- and S-wave normal mode propagations are predicted to exist, but owing to complex interference patterns inside a cylinder, the phase and group velocities are not smooth functions of frequency. To assess the normal mode group velocities and relative amplitudes, approximate dispersion relations are derived using Bessel functions. The utility of the normal mode theory and approximations from a theoretical and experimental standpoint are demonstrated by showing how the sequence of P- and S-wave normal mode arrivals can vary between samples of different size, and how fundamental normal modes can be mistaken for the faster, but significantly smaller amplitude, P- and S-body waves from which P- and S-wave speeds are calculated.

  10. Normal modes of a small gamelan gong.

    PubMed

    Perrin, Robert; Elford, Daniel P; Chalmers, Luke; Swallowe, Gerry M; Moore, Thomas R; Hamdan, Sinin; Halkon, Benjamin J

    2014-10-01

    Studies have been made of the normal modes of a 20.7 cm diameter steel gamelan gong. A finite-element model has been constructed and its predictions for normal modes compared with experimental results obtained using electronic speckle pattern interferometry. Agreement was reasonable in view of the lack of precision in the manufacture of the instrument. The results agree with expectations for an axially symmetric system subject to small symmetry breaking. The extent to which the results obey Chladni's law is discussed. Comparison with vibrational and acoustical spectra enabled the identification of the small number of modes responsible for the sound output when played normally. Evidence of non-linear behavior was found, mainly in the form of subharmonics of true modes. Experiments using scanning laser Doppler vibrometry gave satisfactory agreement with the other methods.

  11. Two-mode mazer injected with V-type three-level atoms

    NASA Astrophysics Data System (ADS)

    Liang, Wen-Qing; Zhang, Zhi-Ming; Xie, Sheng-Wu

    2003-12-01

    The properties of the two-mode mazer operating on V-type three-level atoms are studied. The effect of the one-atom pumping on the two modes of the cavity field in number-state is asymmetric, that is, the atom emits a photon into one mode with some probability and absorbs a photon from the other mode with some other probability. This effect makes the steady-state photon distribution and the steady-state photon statistics asymmetric for the two modes. The diagram of the probability currents for the photon distribution, given by the analysis of the master equation, reveals that there is no detailed balance solution for the master equation. The computations show that the photon statistics of one mode or both modes can be sub-Poissonian, that the two modes can have anticorrelation or correlation, that the photon statistics increases with the increase of thermal photons and that the resonant position and strength of the photon statistics are influenced by the ratio of the two coupling strengths of the two modes. These properties are also discussed physically.

  12. Relating normal vibrational modes to local vibrational modes with the help of an adiabatic connection scheme

    NASA Astrophysics Data System (ADS)

    Zou, Wenli; Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2012-08-01

    Information on the electronic structure of a molecule and its chemical bonds is encoded in the molecular normal vibrational modes. However, normal vibrational modes result from a coupling of local vibrational modes, which means that only the latter can provide detailed insight into bonding and other structural features. In this work, it is proven that the adiabatic internal coordinate vibrational modes of Konkoli and Cremer [Int. J. Quantum Chem. 67, 29 (1998)], 10.1002/(SICI)1097-461X(1998)67:1<29::AID-QUA3>3.0.CO;2-0 represent a unique set of local modes that is directly related to the normal vibrational modes. The missing link between these two sets of modes are the compliance constants of Decius, which turn out to be the reciprocals of the local mode force constants of Konkoli and Cremer. Using the compliance constants matrix, the local mode frequencies of any molecule can be converted into its normal mode frequencies with the help of an adiabatic connection scheme that defines the coupling of the local modes in terms of coupling frequencies and reveals how avoided crossings between the local modes lead to changes in the character of the normal modes.

  13. Three key regimes of single pulse generation per round trip of all-normal-dispersion fiber lasers mode-locked with nonlinear polarization rotation.

    PubMed

    Smirnov, Sergey; Kobtsev, Sergey; Kukarin, Sergey; Ivanenko, Aleksey

    2012-11-19

    We show experimentally and numerically new transient lasing regime between stable single-pulse generation and noise-like generation. We characterize qualitatively all three regimes of single pulse generation per round-trip of all-normal-dispersion fiber lasers mode-locked due to effect of nonlinear polarization evolution. We study spectral and temporal features of pulses produced in all three regimes as well as compressibility of such pulses. Simple criteria are proposed to identify lasing regime in experiment.

  14. Dual-Mode Operation of an Optical Lattice Clock Using Strontium and Ytterbium Atoms.

    PubMed

    Akamatsu, Daisuke; Kobayashi, Takumi; Hisai, Yusuke; Tanabe, Takehiko; Hosaka, Kazumoto; Yasuda, Masami; Hong, Feng-Lei

    2018-06-01

    We have developed an optical lattice clock that can operate in dual modes: a strontium (Sr) clock mode and an ytterbium (Yb) clock mode. Dual-mode operation of the Sr-Yb optical lattice clock is achieved by alternately cooling and trapping 87 Sr and 171 Yb atoms inside the vacuum chamber of the clock. Optical lattices for Sr and Yb atoms were arranged with horizontal and vertical configurations, respectively, resulting in a small distance of the order of between the trapped Sr and Yb atoms. The 1 S 0 - 3 P 0 clock transitions in the trapped atoms were interrogated in turn and the clock lasers were stabilized to the transitions. We demonstrated the frequency ratio measurement of the Sr and Yb clock transitions by using the dual-mode operation of the Sr-Yb optical lattice clock. The dual-mode operation can reduce the uncertainty of the blackbody radiation shift in the frequency ratio measurement, because both Sr and Yb atoms share the same blackbody radiation.

  15. Normal modes of the shallow water system on the cubed sphere

    NASA Astrophysics Data System (ADS)

    Kang, H. G.; Cheong, H. B.; Lee, C. H.

    2017-12-01

    Spherical harmonics expressed as the Rossby-Haurwitz waves are the normal modes of non-divergent barotropic model. Among the normal modes in the numerical models, the most unstable mode will contaminate the numerical results, and therefore the investigation of normal mode for a given grid system and a discretiztaion method is important. The cubed-sphere grid which consists of six identical faces has been widely adopted in many atmospheric models. This grid system is non-orthogonal grid so that calculation of the normal mode is quiet challenge problem. In the present study, the normal modes of the shallow water system on the cubed sphere discretized by the spectral element method employing the Gauss-Lobatto Lagrange interpolating polynomials as orthogonal basis functions is investigated. The algebraic equations for the shallow water equation on the cubed sphere are derived, and the huge global matrix is constructed. The linear system representing the eigenvalue-eigenvector relations is solved by numerical libraries. The normal mode calculated for the several horizontal resolution and lamb parameters will be discussed and compared to the normal mode from the spherical harmonics spectral method.

  16. Mean flow generation mechanism by inertial waves and normal modes

    NASA Astrophysics Data System (ADS)

    Will, Andreas; Ghasemi, Abouzar

    2016-04-01

    The mean flow generation mechanism by nonlinearity of the inertial normal modes and inertial wave beams in a rotating annular cavity with longitudinally librating walls in stable regime is discussed. Inertial normal modes (standing waves) are excited when libration frequency matches eigenfrequencies of the system. Inertial wave beams are produced by Ekman pumping and suction in a rotating cylinder and form periodic orbits or periodic ray trajectories at selected frequencies. Inertial wave beams emerge as concentrated shear layers in a librating annular cavity, while normal modes appear as global recirculation cells. Both (inertial wave beam and mode) are helical and thus intrinsically non-linear flow structures. No second mode or wave is necessary for non-linearity. We considered the low order normal modes (1,1), (2,1) and (2,2) which are expected to be excited in the planetary objects and investigate the mean flow generation mechanism using two independent solutions: 1) analytical solution (Borcia 2012) and 2) the wave component of the flow (ω0 component) obtained from the direct numerical simulation (DNS). It is well known that a retrograde bulk mean flow is generated by the Ekman boundary layer and E1/4-Stewartson layer close to the outer cylinder side wall due to libration. At and around the normal mode resonant frequencies we found additionally a prograde azimuthal mean flow (Inertial Normal Mode Mean Flow: INMMF) in the bulk of the fluid. The fluid in the bulk is in geostrophic balance in the absence of the inertial normal modes. However, when INMMF is excited, we found that the geostrophic balance does not hold in the region occupied by INMMF. We hypothesize that INMMF is generated by the nonlinearity of the normal modes or by second order effects. Expanding the velocity {V}(u_r,u_θ,u_z) and pressure (p) in a power series in ɛ (libration amplitude), the Navier-Stokes equations are segregated into the linear and nonlinear parts at orders ɛ1 and ɛ^2

  17. A new method to real-normalize measured complex modes

    NASA Technical Reports Server (NTRS)

    Wei, Max L.; Allemang, Randall J.; Zhang, Qiang; Brown, David L.

    1987-01-01

    A time domain subspace iteration technique is presented to compute a set of normal modes from the measured complex modes. By using the proposed method, a large number of physical coordinates are reduced to a smaller number of model or principal coordinates. Subspace free decay time responses are computed using properly scaled complex modal vectors. Companion matrix for the general case of nonproportional damping is then derived in the selected vector subspace. Subspace normal modes are obtained through eigenvalue solution of the (M sub N) sup -1 (K sub N) matrix and transformed back to the physical coordinates to get a set of normal modes. A numerical example is presented to demonstrate the outlined theory.

  18. Normal modes and mode transformation of pure electron vortex beams

    PubMed Central

    Thirunavukkarasu, G.; Mousley, M.; Babiker, M.

    2017-01-01

    Electron vortex beams constitute the first class of matter vortex beams which are currently routinely produced in the laboratory. Here, we briefly review the progress of this nascent field and put forward a natural quantum basis set which we show is suitable for the description of electron vortex beams. The normal modes are truncated Bessel beams (TBBs) defined in the aperture plane or the Fourier transform of the transverse structure of the TBBs (FT-TBBs) in the focal plane of a lens with the said aperture. As these modes are eigenfunctions of the axial orbital angular momentum operator, they can provide a complete description of the two-dimensional transverse distribution of the wave function of any electron vortex beam in such a system, in analogy with the prominent role Laguerre–Gaussian (LG) beams played in the description of optical vortex beams. The characteristics of the normal modes of TBBs and FT-TBBs are described, including the quantized orbital angular momentum (in terms of the winding number l) and the radial index p>0. We present the experimental realization of such beams using computer-generated holograms. The mode analysis can be carried out using astigmatic transformation optics, demonstrating close analogy with the astigmatic mode transformation between LG and Hermite–Gaussian beams. This article is part of the themed issue ‘Optical orbital angular momentum’. PMID:28069769

  19. Normal modes and mode transformation of pure electron vortex beams.

    PubMed

    Thirunavukkarasu, G; Mousley, M; Babiker, M; Yuan, J

    2017-02-28

    Electron vortex beams constitute the first class of matter vortex beams which are currently routinely produced in the laboratory. Here, we briefly review the progress of this nascent field and put forward a natural quantum basis set which we show is suitable for the description of electron vortex beams. The normal modes are truncated Bessel beams (TBBs) defined in the aperture plane or the Fourier transform of the transverse structure of the TBBs (FT-TBBs) in the focal plane of a lens with the said aperture. As these modes are eigenfunctions of the axial orbital angular momentum operator, they can provide a complete description of the two-dimensional transverse distribution of the wave function of any electron vortex beam in such a system, in analogy with the prominent role Laguerre-Gaussian (LG) beams played in the description of optical vortex beams. The characteristics of the normal modes of TBBs and FT-TBBs are described, including the quantized orbital angular momentum (in terms of the winding number l) and the radial index p>0. We present the experimental realization of such beams using computer-generated holograms. The mode analysis can be carried out using astigmatic transformation optics, demonstrating close analogy with the astigmatic mode transformation between LG and Hermite-Gaussian beams.This article is part of the themed issue 'Optical orbital angular momentum'. © 2017 The Author(s).

  20. Normal-mode selectivity in ultrafast Raman excitations in C60

    NASA Astrophysics Data System (ADS)

    Zhang, G. P.; George, Thomas F.

    2006-01-01

    Ultrafast Raman spectra are a powerful tool to probe vibrational excitations, but inherently they are not normal-mode specific. For a system as complicated as C60 , there is no general rule to target a specific mode. A detailed study presented here aims to investigate normal-mode selectivity in C60 by an ultrafast laser. To accurately measure mode excitation, we formally introduce the kinetic-energy-based normal-mode analysis which overcomes the difficulty with the strong lattice anharmonicity and relaxation. We first investigate the resonant excitation and find that mode selectivity is normally difficult to achieve. However, for off-resonant excitations, it is possible to selectively excite a few modes in C60 by properly choosing an optimal laser pulse duration, which agrees with previous experimental and theoretical findings. Going beyond the phenomenological explanation, our study shines new light on the origin of the optimal duration: The phase matching between the laser field and mode vibration determines which mode is strongly excited or suppressed. This finding is very robust and should be a useful guide for future experimental and theoretical studies in more complicated systems.

  1. Normal mode selectivity in ultrafast Raman excitations in C60

    NASA Astrophysics Data System (ADS)

    Zhang, Guoping; George, Thomas F.

    2006-05-01

    Ultrafast Raman spectra are a powerful tool to probe vibrational excitations, but inherently they are not normal-mode specific. For a system as complicated as C60, there is no general rule to target a specific mode. A detailed study presented here aims to investigate normal mode selectivity in C60 by an ultrafast laser. To accurately measure mode excitation, we formally introduce the kinetic energy-based normal mode analysis which overcomes the difficulty with the strong lattice anharmonicity and relaxation. We first investigate the resonant excitation and find that mode selectivity is normally difficult to achieve. However, for off-resonant excitations, it is possible to selectively excite a few modes in C60 by properly choosing an optimal laser pulse duration, which agrees with previous experimental and theoretical findings. Going beyond the phenomenological explanation, our study shines new light on the origin of the optimal duration: The phase matching between laser field and mode vibration determines which mode is strongly excited or suppressed. This finding is very robust and may be a useful guide for future experimental and theoretical studies in more complicated systems.

  2. Quasi-Normal Modes of Stars and Black Holes.

    PubMed

    Kokkotas, Kostas D; Schmidt, Bernd G

    1999-01-01

    Perturbations of stars and black holes have been one of the main topics of relativistic astrophysics for the last few decades. They are of particular importance today, because of their relevance to gravitational wave astronomy. In this review we present the theory of quasi-normal modes of compact objects from both the mathematical and astrophysical points of view. The discussion includes perturbations of black holes (Schwarzschild, Reissner-Nordström, Kerr and Kerr-Newman) and relativistic stars (non-rotating and slowly-rotating). The properties of the various families of quasi-normal modes are described, and numerical techniques for calculating quasi-normal modes reviewed. The successes, as well as the limits, of perturbation theory are presented, and its role in the emerging era of numerical relativity and supercomputers is discussed.

  3. Normal modes and frequencies from covariances in molecular dynamics or Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Strachan, Alejandro

    2004-01-01

    We propose a simple method to obtain normal modes (NMs) and their characteristic frequencies from molecular dynamics or Monte Carlo simulations at any temperature. The resulting NM are consistent with the vibrational density of states (DOS) (every feature of the DOS can be attributed to one or few NMs). At low temperatures they coincide with the ones obtained from the Hessian matrix. We define the NMs (ρi) by imposing the condition that their velocities be uncorrelated to each other: <ρ˙i(t)ρ˙j(t)>∝δij, where < > denotes time average and δij is Kronecker's delta. With this definition the modes are the eigenvectors of the matrix Kijv=1/2<√mimj vivj> [i, j=1,…,3N (N being the number of atoms); m are masses and v atomic velocities]. The eigenvalues of Kijv, λiv, represent the kinetic energy in each NM. The ratio between the eigenvalues (λiv) and those obtained using positions (λir), accelerations (λia) in Kijv instead of velocities are a very good approximation to the mode frequencies: 2πνi˜(λiv/λix)(1/2)˜(λia/λix)(1/4). We demonstrate the new method using with two cases: an isolated water molecule and a crystalline polymer.

  4. An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sibaev, M.; Crittenden, D. L., E-mail: deborah.crittenden@canterbury.ac.nz

    In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm{sup −1} in fundamental frequencies, on average, across a sizable testmore » set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/.« less

  5. Excitation of trapped modes from a metasurface composed of only Z-shaped meta-atoms

    NASA Astrophysics Data System (ADS)

    Dhouibi, Abdallah; Nawaz Burokur, Shah; Lupu, Anatole; de Lustrac, André; Priou, Alain

    2013-10-01

    A printed planar Z-shaped meta-atom has recently been proposed as an alternative design to the conventional electric-LC resonator for achieving negative permittivity. Transforming the LC topology of the resonator helps to facilitate transposition of geometrical parameters for the optical regime and also to improve the metamaterial homogeneity. In this work, we discuss about the excitation of a dark or trapped mode in such Z-shaped meta-atom. The electromagnetic behavior of the meta-atom has been investigated through both simulations and experiments in the microwave regime. Our results show that the Z meta-atom exhibits a trapped mode resonance. Depending on the orientation of the polarized electromagnetic field with respect to the Z atom topology and the incident plane, the excitation of the dark mode can lead either to a narrowband resonance in reflection or to a very asymmetric Fano-like resonance in transmission, analog of electromagnetically induced transparency. Compared to other structures, the Z meta-atom presents the advantage of having the dark mode resonance spectrally spaced with respect to the bright mode resonances, which could simplify the observation of the dark mode at much shorter wavelengths.

  6. Intertwined and vestigial order with ultracold atoms in multiple cavity modes

    NASA Astrophysics Data System (ADS)

    Gopalakrishnan, Sarang; Shchadilova, Yulia E.; Demler, Eugene

    2017-12-01

    Atoms in transversely pumped optical cavities "self-organize" by forming a density wave and emitting superradiantly into the cavity mode(s). For a single-mode cavity, the properties of this self-organization transition are well characterized both theoretically and experimentally. Here, we explore the self-organization of a Bose-Einstein condensate in the presence of two cavity modes—a system that recently was realized experimentally [Léonard et al., Nature (London) 543, 87 (2017), 10.1038/nature21067]. We argue that this system can exhibit a "vestigially ordered" phase in which neither cavity mode exhibits superradiance but the cavity modes are mutually phase locked by the atoms. We argue that this vestigially ordered phase should generically be present in multimode cavity geometries.

  7. Normal mode Rossby waves observed in the upper stratosphere

    NASA Technical Reports Server (NTRS)

    Hirooka, T.; Hirota, I.

    1985-01-01

    In recent years, observational evidence has been obtained for westward traveling planetary waves in the middle atmosphere with the aid of global data from satellites. There is no doubt that the fair portion of the observed traveling waves can be understood as the manifestation of the normal mode Rossby waves which are theoretically derived from the tidal theory. Some observational aspects of the structure and behavior of the normal model Rossby waves in the upper stratosphere are reported. The data used are the global stratospheric geopotential thickness and height analyses which are derived mainly from the Stratospheric Sounding Units (SSUs) on board TIROS-N and NOAA satellites. A clear example of the influence of the normal mode Rossby wave on the mean flow is reported. The mechanism considered is interference between the normal mode Rossby wave and the quasi-stationary wave.

  8. Improved Root Normal Size Distributions for Liquid Atomization

    DTIC Science & Technology

    2015-11-01

    Jackson, Primary Breakup of Round Aerated- Liquid Jets in Supersonic Crossflows, Atomization and Sprays, 16(6), 657-672, 2006 H. C. Simmons, The...Breakup in Liquid - Gas Mixing Layers, Atomization and Sprays, 1, 421-440, 1991 P.-K. Wu, L.-K. Tseng, and G. M. Faeth, Primary Breakup in Gas / Liquid ...Improved Root Normal Size Distributions for Liquid Atomization Distribution Statement A. Approved for public release; distribution is unlimited

  9. Quasi-normal modes from non-commutative matrix dynamics

    NASA Astrophysics Data System (ADS)

    Aprile, Francesco; Sanfilippo, Francesco

    2017-09-01

    We explore similarities between the process of relaxation in the BMN matrix model and the physics of black holes in AdS/CFT. Focusing on Dyson-fluid solutions of the matrix model, we perform numerical simulations of the real time dynamics of the system. By quenching the equilibrium distribution we study quasi-normal oscillations of scalar single trace observables, we isolate the lowest quasi-normal mode, and we determine its frequencies as function of the energy. Considering the BMN matrix model as a truncation of N=4 SYM, we also compute the frequencies of the quasi-normal modes of the dual scalar fields in the AdS5-Schwarzschild background. We compare the results, and we finda surprising similarity.

  10. Atom guidance in the TE01 donut mode of a large-core hollow fiber

    NASA Astrophysics Data System (ADS)

    Pechkis, J. A.; Fatemi, F. K.

    2011-05-01

    We report on our progress towards low-light-level nonlinear optics experiments by optically guiding atoms in the TE01 donut mode of a hollow fiber. Atoms are transported over 12 cm from a ``source'' magneto-optical trap (MOT) through a 100- μm-diameter hollow fiber and are recaptured by a ``collection'' MOT situated directly below the fiber. For red-detuned guiding, we compare the guiding efficiency between the fundamental (Gaussian-like) mode and this donut mode, which has a larger guiding area but lower peak intensity. We also discuss our progress in transporting atoms in the dark core of this mode using blue-detuned light, which has more stringent constraints to atom guidance compared to red-detuned light. This work is supported by ONR.

  11. Fast Eigensolver for Computing 3D Earth's Normal Modes

    NASA Astrophysics Data System (ADS)

    Shi, J.; De Hoop, M. V.; Li, R.; Xi, Y.; Saad, Y.

    2017-12-01

    We present a novel parallel computational approach to compute Earth's normal modes. We discretize Earth via an unstructured tetrahedral mesh and apply the continuous Galerkin finite element method to the elasto-gravitational system. To resolve the eigenvalue pollution issue, following the analysis separating the seismic point spectrum, we utilize explicitly a representation of the displacement for describing the oscillations of the non-seismic modes in the fluid outer core. Effectively, we separate out the essential spectrum which is naturally related to the Brunt-Väisälä frequency. We introduce two Lanczos approaches with polynomial and rational filtering for solving this generalized eigenvalue problem in prescribed intervals. The polynomial filtering technique only accesses the matrix pair through matrix-vector products and is an ideal candidate for solving three-dimensional large-scale eigenvalue problems. The matrix-free scheme allows us to deal with fluid separation and self-gravitation in an efficient way, while the standard shift-and-invert method typically needs an explicit shifted matrix and its factorization. The rational filtering method converges much faster than the standard shift-and-invert procedure when computing all the eigenvalues inside an interval. Both two Lanczos approaches solve for the internal eigenvalues extremely accurately, comparing with the standard eigensolver. In our computational experiments, we compare our results with the radial earth model benchmark, and visualize the normal modes using vector plots to illustrate the properties of the displacements in different modes.

  12. Design of a linear projector for use with the normal modes of the GLAS 4th order GCM

    NASA Technical Reports Server (NTRS)

    Bloom, S. C.

    1984-01-01

    The design of a linear projector for use with the normal modes of a model of atmospheric circulation is discussed. A central element in any normal mode initialization scheme is the process by which a set of data fields - winds, temperatures or geopotentials, and surface pressures - are expressed ("projected') in terms of the coefficients of a model's normal modes. This process is completely analogous to the Fourier decomposition of a single field (indeed a FFT applied in the zonal direction is a part of the process). Complete separability in all three spatial dimensions is assumed. The basis functions for the modal expansion are given. An important feature of the normal modes is their coupling of the structures of different fields, thus a coefficient in a normal mode expansion would contain both mass and momentum information.

  13. The Multiphoton Interaction of Lambda Model Atom and Two-Mode Fields

    NASA Technical Reports Server (NTRS)

    Liu, Tang-Kun

    1996-01-01

    The system of two-mode fields interacting with atom by means of multiphotons is addressed, and the non-classical statistic quality of two-mode fields with interaction is discussed. Through mathematical calculation, some new rules of non-classical effects of two-mode fields which evolue with time, are established.

  14. Vocal fold contact patterns based on normal modes of vibration.

    PubMed

    Smith, Simeon L; Titze, Ingo R

    2018-05-17

    The fluid-structure interaction and energy transfer from respiratory airflow to self-sustained vocal fold oscillation continues to be a topic of interest in vocal fold research. Vocal fold vibration is driven by pressures on the vocal fold surface, which are determined by the shape of the glottis and the contact between vocal folds. Characterization of three-dimensional glottal shapes and contact patterns can lead to increased understanding of normal and abnormal physiology of the voice, as well as to development of improved vocal fold models, but a large inventory of shapes has not been directly studied previously. This study aimed to take an initial step toward characterizing vocal fold contact patterns systematically. Vocal fold motion and contact was modeled based on normal mode vibration, as it has been shown that vocal fold vibration can be almost entirely described by only the few lowest order vibrational modes. Symmetric and asymmetric combinations of the four lowest normal modes of vibration were superimposed on left and right vocal fold medial surfaces, for each of three prephonatory glottal configurations, according to a surface wave approach. Contact patterns were generated from the interaction of modal shapes at 16 normalized phases during the vibratory cycle. Eight major contact patterns were identified and characterized by the shape of the flow channel, with the following descriptors assigned: convergent, divergent, convergent-divergent, uniform, split, merged, island, and multichannel. Each of the contact patterns and its variation are described, and future work and applications are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Effects of mode profile on tunneling and traversal of ultracold atoms through vacuum-induced potentials

    NASA Astrophysics Data System (ADS)

    Badshah, Fazal; Irfan, Muhammad; Qamar, Sajid; Qamar, Shahid

    2016-04-01

    We consider the resonant interaction of an ultracold two-level atom with an electromagnetic field inside a high-Q micromaser cavity. In particular, we study the tunneling and traversal of ultracold atoms through vacuum-induced potentials for secant hyperbolic square and sinusoidal cavity mode functions. The phase time which may be considered as an appropriate measure of the time required for the atoms to cross the cavity, significantly modifies with the change of cavity mode profile. For example, switching between the sub and superclassical behaviors in phase time can occur due to the mode function. Similarly, negative phase time appears for the transmission of the two-level atoms in both excited and ground states for secant hyperbolic square mode function which is in contrast to the mesa mode case.

  16. Stability of strongly nonlinear normal modes

    NASA Astrophysics Data System (ADS)

    Recktenwald, Geoffrey; Rand, Richard

    2007-10-01

    It is shown that a transformation of time can allow the periodic solution of a strongly nonlinear oscillator to be written as a simple cosine function. This enables the stability of strongly nonlinear normal modes in multidegree of freedom systems to be investigated by standard procedures such as harmonic balance.

  17. Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis.

    PubMed

    Demerdash, Omar N A; Mitchell, Julie C

    2012-07-01

    Normal mode analysis has emerged as a useful technique for investigating protein motions on long time scales. This is largely due to the advent of coarse-graining techniques, particularly Hooke's Law-based potentials and the rotational-translational blocking (RTB) method for reducing the size of the force-constant matrix, the Hessian. Here we present a new method for domain decomposition for use in RTB that is based on hierarchical clustering of atomic density gradients, which we call Density-Cluster RTB (DCRTB). The method reduces the number of degrees of freedom by 85-90% compared with the standard blocking approaches. We compared the normal modes from DCRTB against standard RTB using 1-4 residues in sequence in a single block, with good agreement between the two methods. We also show that Density-Cluster RTB and standard RTB perform well in capturing the experimentally determined direction of conformational change. Significantly, we report superior correlation of DCRTB with B-factors compared with 1-4 residue per block RTB. Finally, we show significant reduction in computational cost for Density-Cluster RTB that is nearly 100-fold for many examples. Copyright © 2012 Wiley Periodicals, Inc.

  18. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  19. An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

    PubMed Central

    Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

    2012-01-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  20. Cooling flexural modes of a mechanical oscillator by magnetically trapped Bose-Einstein-condensate atoms

    NASA Astrophysics Data System (ADS)

    Xu, Donghong; Xue, Fei

    2017-12-01

    We theoretically study cooling of flexural modes of a mechanical oscillator by Bose-Einstein-condensate (BEC) atoms (Rb87) trapped in a magnetic trap. The mechanical oscillator with a tiny magnet attached on one of its free ends produces an oscillating magnetic field. When its oscillating frequency matches certain hyperfine Zeeman energy of Rb87 atoms, the trapped BEC atoms are coupled out of the magnetic trap by the mechanical oscillator, flying away from the trap with stolen energy from the mechanical oscillator. Thus the mode temperature of the mechanical oscillator is reduced. The mode temperature of the steady state of mechanical oscillator, measured by the mean steady-state phonon number in the flexural mode of the mechanical oscillator, is analyzed. It is found that ground state (phonon number less than 1) may be accessible with optimal parameters of the hybrid system of mechanical oscillator and trapped BEC atoms.

  1. Acyl carrier protein structural classification and normal mode analysis

    PubMed Central

    Cantu, David C; Forrester, Michael J; Charov, Katherine; Reilly, Peter J

    2012-01-01

    All acyl carrier protein primary and tertiary structures were gathered into the ThYme database. They are classified into 16 families by amino acid sequence similarity, with members of the different families having sequences with statistically highly significant differences. These classifications are supported by tertiary structure superposition analysis. Tertiary structures from a number of families are very similar, suggesting that these families may come from a single distant ancestor. Normal vibrational mode analysis was conducted on experimentally determined freestanding structures, showing greater fluctuations at chain termini and loops than in most helices. Their modes overlap more so within families than between different families. The tertiary structures of three acyl carrier protein families that lacked any known structures were predicted as well. PMID:22374859

  2. Nonlinear normal modes in electrodynamic systems: A nonperturbative approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kudrin, A. V., E-mail: kud@rf.unn.ru; Kudrina, O. A.; Petrov, E. Yu.

    2016-06-15

    We consider electromagnetic nonlinear normal modes in cylindrical cavity resonators filled with a nonlinear nondispersive medium. The key feature of the analysis is that exact analytic solutions of the nonlinear field equations are employed to study the mode properties in detail. Based on such a nonperturbative approach, we rigorously prove that the total energy of free nonlinear oscillations in a distributed conservative system, such as that considered in our work, can exactly coincide with the sum of energies of the normal modes of the system. This fact implies that the energy orthogonality property, which has so far been known tomore » hold only for linear oscillations and fields, can also be observed in a nonlinear oscillatory system.« less

  3. Normal-Mode Splitting in a Weakly Coupled Optomechanical System

    NASA Astrophysics Data System (ADS)

    Rossi, Massimiliano; Kralj, Nenad; Zippilli, Stefano; Natali, Riccardo; Borrielli, Antonio; Pandraud, Gregory; Serra, Enrico; Di Giuseppe, Giovanni; Vitali, David

    2018-02-01

    Normal-mode splitting is the most evident signature of strong coupling between two interacting subsystems. It occurs when two subsystems exchange energy between themselves faster than they dissipate it to the environment. Here we experimentally show that a weakly coupled optomechanical system at room temperature can manifest normal-mode splitting when the pump field fluctuations are antisquashed by a phase-sensitive feedback loop operating close to its instability threshold. Under these conditions the optical cavity exhibits an effectively reduced decay rate, so that the system is effectively promoted to the strong coupling regime.

  4. Spatial-mode switchable ring fiber laser based on low mode-crosstalk all-fiber mode MUX/DEMUX

    NASA Astrophysics Data System (ADS)

    Ren, Fang; Yu, Jinyi; Wang, Jianping

    2018-05-01

    We report an all-fiber ring laser that emits linearly polarized (LP) modes based on the intracavity all-fiber mode multiplexer/demultiplexer (MUX/DEMUX). Multiple LP modes in ring fiber laser are generated by taking advantage of mode MUX/DEMUX. The all-fiber mode MUX/DEMUX are composed of cascaded mode-selective couplers (MSCs). The output lasing mode of the ring fiber laser can be switched among the three lowest-order LP modes by employing combination of a mode MUX and a simple N × 1 optical switch. The slope efficiencies, optical spectra and mode profiles are measured.

  5. An approach to the quantization of black hole quasi-normal modes

    NASA Astrophysics Data System (ADS)

    Pal, Soham; Rajeev, Karthik; Shankaranarayanan, S.

    2015-07-01

    In this work, we derive the asymptotic quasi-normal modes of a Banados-Teitelboim-Zanelli (BTZ) black hole using a quantum field theoretic Lagrangian. The BTZ black hole is a very popular system in the context of 2 + 1-dimensional quantum gravity. However, to our knowledge the quasi-normal modes of the BTZ black hole have been studied only in the classical domain. Here we show a way to quantize the quasi-normal modes of the BTZ black hole by mapping it to the Bateman-Feschbach-Tikochinsky oscillator and the Caldirola-Kanai oscillator. We have also discussed a couple of other black hole potentials to which this method can be applied.

  6. Normal Mode Analysis on the Relaxation of AN Excited Nitromethane Molecule in Argon Bath

    NASA Astrophysics Data System (ADS)

    Rivera-Rivera, Luis A.; Wagner, Albert F.

    2017-06-01

    In our previous work [Rivera-Rivera et al. J. Chem. Phys. 142, 014303 (2015).] classical molecular dynamics simulations followed, in an Ar bath, the relaxation of nitromethane (CH_3NO_2) instantaneously excited by statistically distributing 50 kcal/mol among all its internal degrees of freedom. The 300 K Ar bath was at pressures of 10 to 400 atm. Both rotational and vibrational energies exhibited multi-exponential decay. This study explores mode-specific mechanisms at work in the decay process. With the separation of rotation and vibration developed by Rhee and Kim [J. Chem. Phys. 107, 1394 (1997).], one can show that the vibrational kinetic energy decomposes only into vibrational normal modes while the rotational and Coriolis energies decompose into both vibrational and rotational normal modes. Then the saved CH_3NO_2 positions and momenta can be converted into mode-specific energies whose decay over 1000 ps can be monitored. The results identify vibrational and rotational modes that promote/resist energy lost and drive multi-exponential behavior. In addition to mode-specificity, the results show disruption of IVR with increasing pressure.

  7. Plantar fascia softening in plantar fasciitis with normal B-mode sonography.

    PubMed

    Wu, Chueh-Hung; Chen, Wen-Shiang; Wang, Tyng-Guey

    2015-11-01

    To investigate plantar fascia elasticity in patients with typical clinical manifestations of plantar fasciitis but normal plantar fascia morphology on B-mode sonography. Twenty patients with plantar fasciitis (10 unilateral and 10 bilateral) and 30 healthy volunteers, all with normal plantar fascia morphology on B-mode sonography, were included in the study. Plantar fascia elasticity was evaluated by sonoelastographic examination. All sonoelastograms were quantitatively analyzed, and less red pixel intensity was representative of softer tissue. Pixel intensity was compared among unilateral plantar fasciitis patients, bilateral plantar fasciitis patients, and healthy volunteers by one-way ANOVA. A post hoc Scheffé's test was used to identify where the differences occurred. Compared to healthy participants (red pixel intensity: 146.9 ± 9.1), there was significantly less red pixel intensity in the asymptomatic sides of unilateral plantar fasciitis (140.4 ± 7.3, p = 0.01), symptomatic sides of unilateral plantar fasciitis (127.1 ± 7.4, p < 0.001), and both sides of bilateral plantar fasciitis (129.4 ± 7.5, p < 0.001). There were no significant differences in plantar fascia thickness or green or blue pixel intensity among these groups. Sonoelastography revealed that the plantar fascia is softer in patients with typical clinical manifestations of plantar fasciitis, even if they exhibit no abnormalities on B-mode sonography.

  8. A theory for protein dynamics: Global anisotropy and a normal mode approach to local complexity

    NASA Astrophysics Data System (ADS)

    Copperman, Jeremy; Romano, Pablo; Guenza, Marina

    2014-03-01

    We propose a novel Langevin equation description for the dynamics of biological macromolecules by projecting the solvent and all atomic degrees of freedom onto a set of coarse-grained sites at the single residue level. We utilize a multi-scale approach where molecular dynamic simulations are performed to obtain equilibrium structural correlations input to a modified Rouse-Zimm description which can be solved analytically. The normal mode solution provides a minimal basis set to account for important properties of biological polymers such as the anisotropic global structure, and internal motion on a complex free-energy surface. This multi-scale modeling method predicts the dynamics of both global rotational diffusion and constrained internal motion from the picosecond to the nanosecond regime, and is quantitative when compared to both simulation trajectory and NMR relaxation times. Utilizing non-equilibrium sampling techniques and an explicit treatment of the free-energy barriers in the mode coordinates, the model is extended to include biologically important fluctuations in the microsecond regime, such as bubble and fork formation in nucleic acids, and protein domain motion. This work supported by the NSF under the Graduate STEM Fellows in K-12 Education (GK-12) program, grant DGE-0742540 and NSF grant DMR-0804145, computational support from XSEDE and ACISS.

  9. Heavy Atom Vibrational Modes and Low-Energy Vibrational Autodetachment in Nitromethane Anions

    NASA Astrophysics Data System (ADS)

    Thompson, Michael C.; Baraban, Joshua H.; Stanton, John F.; Weber, J. Mathias

    2015-06-01

    We use Ar predissociation and vibrational autodetachment below 2100 wn to obtain vibrational spectra of the low-energy modes of nitromethane anion. We interpret the spectra using anharmonic calculations, which reveal strong mode coupling and Fermi resonances. Not surprisingly, the number of evaporated Ar atoms varies with photon energy, and we follow the propensity of evaporating two versus one Ar atoms as photon energy increases. The photodetachment spectrum is discussed in the context of threshold effects and the importance of hot bands.

  10. Normal Modes Expose Active Sites in Enzymes.

    PubMed

    Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

    2016-12-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

  11. Normal Modes Expose Active Sites in Enzymes

    PubMed Central

    Glantz-Gashai, Yitav; Samson, Abraham O.

    2016-01-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

  12. Phenomenology of break-up modes in contact free externally heated nanoparticle laden fuel droplets

    NASA Astrophysics Data System (ADS)

    Pathak, Binita; Basu, Saptarshi

    2016-12-01

    We study thermally induced atomization modes in contact free (acoustically levitated) nanoparticle laden fuel droplets. The initial droplet size, external heat supplied, and suspended particle concentration (wt. %) in droplets govern the stability criterion which ultimately determines the dominant mode of atomization. Pure fuel droplets exhibit two dominant modes of breakup namely primary and secondary. Primary modes are rather sporadic and normally do not involve shape oscillations. Secondary atomization however leads to severe shape deformations and catastrophic intense breakup of the droplets. The dominance of these modes has been quantified based on the external heat flux, dynamic variation of surface tension, acoustic pressure, and droplet size. Addition of particles alters the regimes of the primary and secondary atomization and introduces bubble induced boiling and bursting. We analyze this new mode of atomization and estimate the time scale of bubble growth up to the point of bursting using energy balance to determine the criterion suitable for parent droplet rupture. All the three different modes of breakup have been well identified in a regime map determined in terms of Weber number and the heat utilization rate which is defined as the energy utilized for transient heating, vaporization, and boiling in droplets.

  13. Normal modes of synchronous rotation

    NASA Astrophysics Data System (ADS)

    Varadi, Ferenc; Musotto, Susanna; Moore, William; Schubert, Gerald

    2005-07-01

    The dynamics of synchronous rotation and physical librations are revisited in order to establish a conceptually simple and general theoretical framework applicable to a variety of problems. Our motivation comes from disagreements between the results of numerical simulations and those of previous theoretical studies, and also because different theoretical studies disagree on basic features of the dynamics. We approach the problem by decomposing the orientation matrix of the body into perfectly synchronous rotation and deviation from the equilibrium state. The normal modes of the linearized equations are computed in the case of a circular satellite orbit, yielding both the periods and the eigenspaces of three librations. Libration in longitude decouples from the other two, vertical modes. There is a fast vertical mode with a period very close to the average rotational period. It corresponds to tilting the body around a horizontal axis while retaining nearly principal-axis rotation. In the inertial frame, this mode appears as nutation and free precession. The other vertical mode, a slow one, is the free wobble. The effects of the nodal precession of the orbit are investigated from the point of view of Cassini states. We test our theory using numerical simulations of the full equations of the dynamics and discuss the disagreements among our study and previous ones. The numerical simulations also reveal that in the case of eccentric orbits large departures from principal-axis rotation are possible due to a resonance between free precession and wobble. We also revisit the history of the Moon's rotational state and show that it switched from one Cassini state to another when it was at 46.2 Earth radii. This number disagrees with the value 34.2 derived in a previous study.

  14. Nonlinear normal modes modal interactions and isolated resonance curves

    DOE PAGES

    Kuether, Robert J.; Renson, L.; Detroux, T.; ...

    2015-05-21

    The objective of the present study is to explore the connection between the nonlinear normal modes of an undamped and unforced nonlinear system and the isolated resonance curves that may appear in the damped response of the forced system. To this end, an energy balance technique is used to predict the amplitude of the harmonic forcing that is necessary to excite a specific nonlinear normal mode. A cantilever beam with a nonlinear spring at its tip serves to illustrate the developments. Furthermore, the practical implications of isolated resonance curves are also discussed by computing the beam response to sine sweepmore » excitations of increasing amplitudes.« less

  15. Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes

    DOE PAGES

    Kuether, Robert J.; Deaner, Brandon J.; Hollkamp, Joseph J.; ...

    2015-09-15

    Several reduced-order modeling strategies have been developed to create low-order models of geometrically nonlinear structures from detailed finite element models, allowing one to compute the dynamic response of the structure at a dramatically reduced cost. But, the parameters of these reduced-order models are estimated by applying a series of static loads to the finite element model, and the quality of the reduced-order model can be highly sensitive to the amplitudes of the static load cases used and to the type/number of modes used in the basis. Our paper proposes to combine reduced-order modeling and numerical continuation to estimate the nonlinearmore » normal modes of geometrically nonlinear finite element models. Not only does this make it possible to compute the nonlinear normal modes far more quickly than existing approaches, but the nonlinear normal modes are also shown to be an excellent metric by which the quality of the reduced-order model can be assessed. Hence, the second contribution of this work is to demonstrate how nonlinear normal modes can be used as a metric by which nonlinear reduced-order models can be compared. Moreover, various reduced-order models with hardening nonlinearities are compared for two different structures to demonstrate these concepts: a clamped–clamped beam model, and a more complicated finite element model of an exhaust panel cover.« less

  16. Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model

    NASA Technical Reports Server (NTRS)

    Dong, Zhengchao; Zhao, Yonglin

    1996-01-01

    In this paper, we study the atomic dipole squeezing in the correlated two-mode two-photon JC model with the field initially in the correlated two-mode SU(1,1) coherent state. The effects of detuning, field intensity and number difference between the two field modes are investigated through numerical calculation.

  17. Fast normal mode computations of capsid dynamics inspired by resonance

    NASA Astrophysics Data System (ADS)

    Na, Hyuntae; Song, Guang

    2018-07-01

    Increasingly more and larger structural complexes are being determined experimentally. The sizes of these systems pose a formidable computational challenge to the study of their vibrational dynamics by normal mode analysis. To overcome this challenge, this work presents a novel resonance-inspired approach. Tests on large shell structures of protein capsids demonstrate that there is a strong resonance between the vibrations of a whole capsid and those of individual capsomeres. We then show how this resonance can be taken advantage of to significantly speed up normal mode computations.

  18. Wormhole potentials and throats from quasi-normal modes

    NASA Astrophysics Data System (ADS)

    Völkel, Sebastian H.; Kokkotas, Kostas D.

    2018-05-01

    Exotic compact objects refer to a wide class of black hole alternatives or effective models to describe phenomenologically quantum gravitational effects on the horizon scale. In this work we show how the knowledge of the quasi-normal mode spectrum of non-rotating wormhole models can be used to reconstruct the effective potential that appears in perturbation equations. From this it is further possible to obtain the parameters that characterize the specific wormhole model, which in this paper was chosen to be the one by Damour and Solodukhin. We also address the question whether one can distinguish such type of wormholes from ultra compact stars, if only the quasi-normal mode spectrum is known. We have proven that this is not possible by using the trapped modes only, but requires additional information. The inverse method presented here is an extension of work that has previously been developed and applied to the oscillation spectra of ultra compact stars and gravastars. However, it is not limited to the study of exotic compact objects, but applicable to symmetric double barrier potentials that appear in one-dimensional wave equations. Therefore we think it can be of interest for other fields too.

  19. Large-amplitude nonlinear normal modes of the discrete sine lattices.

    PubMed

    Smirnov, Valeri V; Manevitch, Leonid I

    2017-02-01

    We present an analytical description of the large-amplitude stationary oscillations of the finite discrete system of harmonically coupled pendulums without any restrictions on their amplitudes (excluding a vicinity of π). Although this model has numerous applications in different fields of physics, it was studied earlier in the infinite limit only. The discrete chain with a finite length can be considered as a well analytical analog of the coarse-grain models of flexible polymers in the molecular dynamics simulations. The developed approach allows to find the dispersion relations for arbitrary amplitudes of the nonlinear normal modes. We emphasize that the long-wavelength approximation, which is described by well-known sine-Gordon equation, leads to an inadequate zone structure for the amplitudes of about π/2 even if the chain is long enough. An extremely complex zone structure at the large amplitudes corresponds to multiple resonances between nonlinear normal modes even with strongly different wave numbers. Due to the complexity of the dispersion relations the modes with shorter wavelengths may have smaller frequencies. The stability of the nonlinear normal modes under condition of the resonant interaction are discussed. It is shown that this interaction of the modes in the vicinity of the long wavelength edge of the spectrum leads to the localization of the oscillations. The thresholds of instability and localization are determined explicitly. The numerical simulation of the dynamics of a finite-length chain is in a good agreement with obtained analytical predictions.

  20. Nonlinear normal vibration modes in the dynamics of nonlinear elastic systems

    NASA Astrophysics Data System (ADS)

    Mikhlin, Yu V.; Perepelkin, N. V.; Klimenko, A. A.; Harutyunyan, E.

    2012-08-01

    Nonlinear normal modes (NNMs) are a generalization of the linear normal vibrations. By the Kauderer-Rosenberg concept in the regime of the NNM all position coordinates are single-values functions of some selected position coordinate. By the Shaw-Pierre concept, the NNM is such a regime when all generalized coordinates and velocities are univalent functions of a couple of dominant (active) phase variables. The NNMs approach is used in some applied problems. In particular, the Kauderer-Rosenberg NNMs are analyzed in the dynamics of some pendulum systems. The NNMs of forced vibrations are investigated in a rotor system with an isotropic-elastic shaft. A combination of the Shaw-Pierre NNMs and the Rauscher method is used to construct the forced NNMs and the frequency responses in the rotor dynamics.

  1. Relationships between nonlinear normal modes and response to random inputs

    NASA Astrophysics Data System (ADS)

    Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

    2017-02-01

    The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). This work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing. Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.

  2. Relationships between nonlinear normal modes and response to random inputs

    DOE PAGES

    Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

    2016-07-25

    The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). Here, this work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing.more » Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.« less

  3. Comparative study of various normal mode analysis techniques based on partial Hessians.

    PubMed

    Ghysels, An; Van Speybroeck, Veronique; Pauwels, Ewald; Catak, Saron; Brooks, Bernard R; Van Neck, Dimitri; Waroquier, Michel

    2010-04-15

    Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein. 2009 Wiley Periodicals, Inc.

  4. Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians

    PubMed Central

    GHYSELS, AN; VAN SPEYBROECK, VERONIQUE; PAUWELS, EWALD; CATAK, SARON; BROOKS, BERNARD R.; VAN NECK, DIMITRI; WAROQUIER, MICHEL

    2014-01-01

    Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein. PMID:19813181

  5. All-fiber nonlinearity- and dispersion-managed dissipative soliton nanotube mode-locked laser

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Z.; Nanjing University of Posts and Communications, Nanjing 210003; Popa, D., E-mail: dp387@cam.ac.uk

    We report dissipative soliton generation from an Yb-doped all-fiber nonlinearity- and dispersion-managed nanotube mode-locked laser. A simple all-fiber ring cavity exploits a photonic crystal fiber for both nonlinearity enhancement and dispersion compensation. The laser generates stable dissipative solitons with large linear chirp in the net normal dispersion regime. Pulses that are 8.7 ps long are externally compressed to 118 fs, outperforming current nanotube-based Yb-doped fiber laser designs.

  6. Three-mode mode-division-multiplexing passive optical network over 12-km low mode-crosstalk FMF using all-fiber mode MUX/DEMUX

    NASA Astrophysics Data System (ADS)

    Ren, Fang; Li, Juhao; Wu, Zhongying; Hu, Tao; Yu, Jinyi; Mo, Qi; He, Yongqi; Chen, Zhangyuan; Li, Zhengbin

    2017-01-01

    We propose three-mode mode-division-multiplexing passive optical network (MDM-PON) based on low mode-crosstalk few-mode fiber (FMF) and all-fiber mode multiplexer/demultiplexer (MUX/DEMUX). The FMF with step-index profile is designed and fabricated for effectively three-independent-spatial-mode transmission and low mode-crosstalk for MDM-PON transmission. The all-fiber mode MUX/DEMUX are composed of cascaded mode selective couplers (MSCs), which simultaneously multiplex or demultiplex multiple modes. Based on the low mode-crosstalk of the FMF and all-fiber mode MUX/DEMUX, each optical network unit (ONU) communicates with the optical line terminal (OLT) independently utilizing a different optical linearly polarized (LP) spatial mode in MDM-PON system. We experimentally demonstrate MDM-PON transmission of three independent-spatial-modes over 12-km FMF with 10-Gb/s optical on-off keying (OOK) signal and direct detection.

  7. Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric C.; Sankey, Otto F.

    2010-02-01

    We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

  8. Scissors Mode of Dipolar Quantum Droplets of Dysprosium Atoms

    NASA Astrophysics Data System (ADS)

    Ferrier-Barbut, Igor; Wenzel, Matthias; Böttcher, Fabian; Langen, Tim; Isoard, Mathieu; Stringari, Sandro; Pfau, Tilman

    2018-04-01

    We report on the observation of the scissors mode of a single dipolar quantum droplet. The existence of this mode is due to the breaking of the rotational symmetry by the dipole-dipole interaction, which is fixed along an external homogeneous magnetic field. By modulating the orientation of this magnetic field, we introduce a new spectroscopic technique for studying dipolar quantum droplets. This provides a precise probe for interactions in the system, allowing us to extract a background scattering length for 164Dy of 69 (4 )a0 . Our results establish an analogy between quantum droplets and atomic nuclei, where the existence of the scissors mode is also only due to internal interactions. They further open the possibility to explore physics beyond the available theoretical models for strongly dipolar quantum gases.

  9. S-Wave Normal Mode Propagation in Aluminum Cylinders

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2010-01-01

    Large amplitude waveform features have been identified in pulse-transmission shear-wave measurements through cylinders that are long relative to the acoustic wavelength. The arrival times and amplitudes of these features do not follow the predicted behavior of well-known bar waves, but instead they appear to propagate with group velocities that increase as the waveform feature's dominant frequency increases. To identify these anomalous features, the wave equation is solved in a cylindrical coordinate system using an infinitely long cylinder with a free surface boundary condition. The solution indicates that large amplitude normal-mode propagations exist. Using the high-frequency approximation of the Bessel function, an approximate dispersion relation is derived. The predicted amplitude and group velocities using the approximate dispersion relation qualitatively agree with measured values at high frequencies, but the exact dispersion relation should be used to analyze normal modes for full ranges of frequency of interest, particularly at lower frequencies.

  10. Normal modes of the world's oceans: A numerical investigation using Proudman functions

    NASA Technical Reports Server (NTRS)

    Sanchez, Braulio V.; Morrow, Dennis

    1993-01-01

    The numerical modeling of the normal modes of the global oceans is addressed. The results of such modeling could be expected to serve as a guide in the analysis of observations and measurements intended to detect these modes. The numerical computation of normal modes of the global oceans is a field in which several investigations have obtained results during the past 15 years. The results seem to be model-dependent to an unsatisfactory extent. Some modeling areas, such as higher resolution of the bathymetry, inclusion of self-attraction and loading, the role of the Arctic Ocean, and systematic testing by means of diagnostic models are addressed. The results show that the present state of the art is such that a final solution to the normal mode problem still lies in the future. The numerical experiments show where some of the difficulties are and give some insight as to how to proceed in the future.

  11. Normal mode analysis on the relaxation of an excited nitromethane molecule in argon bath

    NASA Astrophysics Data System (ADS)

    Rivera-Rivera, Luis; Wagner, Albert

    In our previous work [J. Chem. Phys. 142, 014303 (2015)] classical molecular dynamics simulations followed in an Ar bath the relaxation of nitromethane (CH3NO2) instantaneously excited by statistically distributing 50 kcal/mol among all its internal degrees of freedom. The 300 K Ar bath was at pressures of 10 to 400 atm, a range spanning the breakdown of the isolated binary collision approximation. Both rotational and vibrational energies exhibit multi-exponential decay. This study explores mode-specific mechanisms at work in the decay process. With the separation of rotation and vibration developed by Rhee and Kim [J. Chem. Phys. 107, 1394 (1997)], one can show that the vibrational kinetic energy decomposes only into vibrational normal modes while the rotational and Coriolis energies decompose into both vibrational and rotational normal modes. Then the saved CH3NO2 positions and momenta can be converted into mode-specific energies whose decay over 1000 ps can be monitored. The results identify vibrational and rotational modes that promote/resist energy lost and drive multi-exponential behavior. Increasing pressure can be shown to increasingly interfere with post-collision IVR. The work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

  12. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    NASA Astrophysics Data System (ADS)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  13. Computational aspects of the nonlinear normal mode initialization of the GLAS 4th order GCM

    NASA Technical Reports Server (NTRS)

    Navon, I. M.; Bloom, S. C.; Takacs, L.

    1984-01-01

    Using the normal modes of the GLAS 4th Order Model, a Machenhauer nonlinear normal mode initialization (NLNMI) was carried out for the external vertical mode using the GLAS 4th Order shallow water equations model for an equivalent depth corresponding to that associated with the external vertical mode. A simple procedure was devised which was directed at identifying computational modes by following the rate of increase of BAL sub M, the partial (with respect to the zonal wavenumber m) sum of squares of the time change of the normal mode coefficients (for fixed vertical mode index) varying over the latitude index L of symmetric or antisymmetric gravity waves. A working algorithm is presented which speeds up the convergence of the iterative Machenhauer NLNMI. A 24 h integration using the NLNMI state was carried out using both Matsuno and leap-frog time-integration schemes; these runs were then compared to a 24 h integration starting from a non-initialized state. The maximal impact of the nonlinear normal mode initialization was found to occur 6-10 hours after the initial time.

  14. 152 fs nanotube-mode-locked thulium-doped all-fiber laser

    PubMed Central

    Wang, Jinzhang; Liang, Xiaoyan; Hu, Guohua; Zheng, Zhijian; Lin, Shenghua; Ouyang, Deqin; Wu, Xu; Yan, Peiguang; Ruan, Shuangchen; Sun, Zhipei; Hasan, Tawfique

    2016-01-01

    Ultrafast fiber lasers with broad bandwidth and short pulse duration have a variety of applications, such as ultrafast time-resolved spectroscopy and supercontinuum generation. We report a simple and compact all-fiber thulium-doped femtosecond laser mode-locked by carbon nanotubes. The oscillator operates in slightly normal cavity dispersion at 0.055 ps2, and delivers 152 fs pulses with 52.8 nm bandwidth and 0.19 nJ pulse energy. This is the shortest pulse duration and the widest spectral width demonstrated from Tm-doped all-fiber lasers based on 1 or 2 dimensional nanomaterials, underscoring their growing potential as versatile saturable absorber materials. PMID:27374764

  15. Isotope effect in normal-to-local transition of acetylene bending modes

    DOE PAGES

    Ma, Jianyi; Xu, Dingguo; Guo, Hua; ...

    2012-01-01

    The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helpsmore » to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans and normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.« less

  16. Wavelength-independent all-fiber mode converters.

    PubMed

    Lai, K; Leon-Saval, S G; Witkowska, A; Wadsworth, W J; Birks, T A

    2007-02-15

    We have used two different photonic crystal fiber (PCF) techniques to make all-fiber mode converters. An LP(01) to LP(11) mode converter was made by the ferrule technique on a drawing tower, and an LP(01) to LP(02) mode converter was made by controlled hole inflation of an existing PCF on a tapering rig. Both devices rely on adiabatic propagation rather than resonant coupling; so high extinction was achieved across a wide wavelength range.

  17. Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations

    NASA Astrophysics Data System (ADS)

    Hicks, Stephen D.; Henley, C. L.

    2010-03-01

    Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamics simulations of one pair of units at a time. The computed relaxation times of this pair give a consistency check for the simulation, and we can also find the corrective force needed to null systematic drifts. As a first application we predict the stiffness of an HIV capsid layer and the relaxation time for its breathing mode.

  18. Linear perturbations of black holes: stability, quasi-normal modes and tails

    NASA Astrophysics Data System (ADS)

    Zhidenko, Alexander

    2009-03-01

    Black holes have their proper oscillations, which are called the quasi-normal modes. The proper oscillations of astrophysical black holes can be observed in the nearest future with the help of gravitational wave detectors. Quasi-normal modes are also very important in the context of testing of the stability of black objects, the anti-de Sitter/Conformal Field Theory (AdS/CFT) correspondence and in higher dimensional theories, such as the brane-world scenarios and string theory. This dissertation reviews a number of works, which provide a thorough study of the quasi-normal spectrum of a wide class of black holes in four and higher dimensions for fields of various spin and gravitational perturbations. We have studied numerically the dependance of the quasi-normal modes on a number of factors, such as the presence of the cosmological constant, the Gauss-Bonnet parameter or the aether in the space-time, the dependance of the spectrum on parameters of the black hole and fields under consideration. By the analysis of the quasi-normal spectrum, we have studied the stability of higher dimensional Reissner-Nordstrom-de Sitter black holes, Kaluza-Klein black holes with squashed horizons, Gauss-Bonnet black holes and black strings. Special attention is paid to the evolution of massive fields in the background of various black holes. We have considered their quasi-normal ringing and the late-time tails. In addition, we present two new numerical techniques: a generalisation of the Nollert improvement of the Frobenius method for higher dimensional problems and a qualitatively new method, which allows to calculate quasi-normal frequencies for black holes, which metrics are not known analytically.

  19. Topography-coupled resonance between Mars normal-modes and the tidal force of the Phobos

    NASA Astrophysics Data System (ADS)

    Tian, Y.; Zheng, Y.

    2016-12-01

    Phobos is the largest moon of Mars. The gravity attraction of Phobos to Mars is a periodic force, which may excite seismic waves inside Mars. Since Phobos is below the synchronous orbit, its orbit is continuously decreasing due to the tidal effect. This will result in a monotonic increase in its orbital frequency, which may eventually intrude into the seismic normal-mode frequency range to cause resonance. The objective of this research is to investigate whether such a resonance phenomenon can occur and what the consequence is. As we know, resonance happens when the periodic tidal force has a similar frequency as that of martian normal modes. It can be shown that such a resonance will not occur if Mars is perfectly spherical because the tidal force can only excite modes of the same angular order. For the same angular order, the tidal force frequencies are always smaller than those of the normal modes. However, when we consider the effect of topography of Mars, the resonance can occur because of coupling of normal modes. We use numerical method to calculate when the resonance will occur. We firstly solve for the normal modes of Mars by idealizing it as a solid elastic sphere. At the second step, we calculate the excitation effect of gravitational force from Phobos on each individual normal mode. For example, the gravity tidal force F at L=5, m=5 F55 can excite a normal mode 0S5 which can be coupled to 0T2. The third step is to calculate the frequency that the resonance will happen. For example, when the rotation frequency of Phobos increase to 0.8 mRad/s, the tidal force at L=5, m=5 can reach 4mRad/s which is the eigen-frequency of 0T2. Since we have calculated the coupling factors between each individual mode, the amplitude coefficients can be solved by a linear equation. We can observe a 100 times of amplitude increase of mode 0T2, which convince us the resonance will happen. The resonance may cause large amplitude of ground vibration of Mars. From our calculation

  20. Atomic torsional modal analysis for high-resolution proteins.

    PubMed

    Tirion, Monique M; ben-Avraham, Daniel

    2015-03-01

    We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier one-parameter formulation [M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996)] that characterized the slow modes associated with protein data bank structures. Here we develop that empirical potential function that is minimized at the outset to include two features essential to reproduce the eigenspectra and associated density of states in the 0 to 300cm-1 frequency range, not merely the slow modes. First, introduction of preferred dihedral-angle configurations via use of torsional stiffness constants eliminates anomalous dispersion characteristics due to insufficiently bound surface side chains and helps fix the spectrum thin tail frequencies (100-300cm-1). Second, we take into account the atomic identities and the distance of separation of all pairwise interactions, improving the spectrum distribution in the 20 to 300cm-1 range. With these modifications, not only does the spectrum reproduce that of full atomic potentials, but we obtain stable reliable eigenmodes for the slow modes and over a wide range of frequencies.

  1. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

    PubMed

    Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

    2012-09-21

    Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Normal Modes of a Lagrangian System Constrained in a Potential Well.

    DTIC Science & Technology

    1983-12-01

    A’ -137 948 NORMAL MODES OF A LFHbRANGIAN SYSTEM CONSTRAINED INvi P0TENTIAL WELL(U WISCONSNN UNIV-MADISON MATHEMATICS RESEARCH CENTER V EN DEC F1...Carolina 27709 DT FLE OP Y UNIVERSITY OF WISCONSIN-MADISON MATHEMATICS RESEARCH CENTER NORMAL MODES OF A LAGRANGIAN SYSTEM CONSTRAINED IN A POTENTIAL WELL...respect to the norm lYE [f i + 2 yi )dtl/ 0 Since H I(S’ 1 n’) C CO(S, fle ), then the set A 1 0 is an open set in H1 (lf’) The periodic solution of

  3. Simultaneous multielement atomic absorption spectrometry with graphite furnace atomization

    NASA Astrophysics Data System (ADS)

    Harnly, James M.; Miller-Ihli, Nancy J.; O'Haver, Thomas C.

    The extended analytical range capability of a simultaneous multielement atomic absorption continuum source spectrometer (SIMAAC) was tested for furnace atomization with respect to the signal measurement mode (peak height and area), the atomization mode (from the wall or from a platform), and the temperature program mode (stepped or ramped atomization). These parameters were evaluated with respect to the shapes of the analytical curves, the detection limits, carry-over contamination and accuracy. Peak area measurements gave more linear calibration curves. Methods for slowing the atomization step heating rate, the use of a ramped temperature program or a platform, produced similar calibration curves and longer linear ranges than atomization with a stepped temperature program. Peak height detection limits were best using stepped atomization from the wall. Peak area detection limits for all atomization modes were similar. Carry-over contamination was worse for peak area than peak height, worse for ramped atomization than stepped atomization, and worse for atomization from a platform than from the wall. Accurate determinations (100 ± 12% for Ca, Cu, Fe, Mn, and Zn in National Bureau of Standards' Standard Reference Materials Bovine Liver 1577 and Rice Flour 1568 were obtained using peak area measurements with ramped atomization from the wall and stepped atomization from a platform. Only stepped atomization from a platform gave accurate recoveries for K. Accurate recoveries, 100 ± 10%, with precisions ranging from 1 to 36 % (standard deviation), were obtained for the determination of Al, Co, Cr, Fe, Mn, Mo, Ni. Pb, V and Zn in Acidified Waters (NBS SRM 1643 and 1643a) using stepped atomization from a platform.

  4. Global measurements of coarse-mode aerosol size distributions - first results from the Atmospheric Tomography Mission (ATom)

    NASA Astrophysics Data System (ADS)

    Weinzierl, B.; Dollner, M.; Schuh, H.; Brock, C. A.; Bui, T. V.; Gasteiger, J.; Froyd, K. D.; Schwarz, J. P.; Spanu, A.; Murphy, D. M.; Katich, J. M.; Kupc, A.; Williamson, C.

    2016-12-01

    Although coarse-mode aerosol (>1 µm diameter), composed mainly of mineral dust and sea-salt, is highly abundant over large regions of the world, these particles form a particularly poorly understood and characterized subset of atmospheric aerosol constituents. The NASA-sponsored Atmospheric Tomography Mission (ATom) is an unprecedented field program that investigates how human emissions affect air quality and climate change. ATom provides a singular opportunity to characterize the global coarse-mode size distribution by continuously profiling between 0.2 and 13 km with the NASA DC-8 research aircraft while traveling from the high Arctic down south the middle of the Pacific Ocean, to the Southern Ocean and back north over the Atlantic Ocean basin in four seasons. For ATom, the DC-8 aircraft has been equipped with multiple instruments to observe the composition of the air. The coarse mode and cloud particle size distribution is measured in-situ with a Cloud, Aerosol, and Precipitation Spectrometer (CAPS) mounted under the wing of the DC-8 research aircraft. The CAPS consists of an optical spectrometer providing size distributions in the size range between 0.5 and 50 µm and an imager detecting number concentration, size and shape of particles between 15 and 930 µm diameter. Early ATom flights indicated complicated vertical layering: over the sea, we regularly observed sea salt aerosol which extended from the ground up to 0.6-1 km altitude. In addition - depending on the location of the measurements - we frequently found layers with coarse mode aerosol originating from deserts and biomass burning aerosol aloft. In this study, we will present first results of coarse mode aerosol observations from the entire first ATom deployment in summer 2016. We will show vertical profiles of coarse mode aerosol number concentration, discuss their interhemispheric differences, and look into the question how frequently coarse-mode aerosol is externally mixed with submicron black

  5. Evaluation of diaphragmatic motion in normal and diaphragmatic paralyzed dogs using M-mode ultrasonography.

    PubMed

    Choi, Mihyun; Lee, Namsoon; Kim, Ahyoung; Keh, Seoyeon; Lee, Jinsoo; Kim, Hyunwook; Choi, Mincheol

    2014-01-01

    Diagnosis of unilateral diaphragmatic paralysis in dogs is currently based on fluoroscopic detection of unequal movement between the crura. Bilateral paralysis may be more difficult to confirm with fluoroscopy because diaphragmatic movement is sometimes produced by compensatory abdominal muscle contractions. The purpose of this study was to develop a new method to evaluate diaphragmatic movement using M-mode ultrasonography and to describe findings for normal and diaphragmatic paralyzed dogs. Fifty-five clinically normal dogs and two dogs with diaphragmatic paralysis were recruited. Thoracic radiographs were acquired for all dogs and fluoroscopy studies were also acquired for clinically affected dogs. Two observers independently measured diaphragmatic direction of motion and amplitude of excursion using M-mode ultrasonography for dogs meeting study inclusion criteria. Eight of the clinically normal dogs were excluded due to abnormal thoracic radiographic findings. For the remaining normal dogs, the lower limit values of diaphragmatic excursion were 2.85-2.98 mm during normal breathing. One dog with bilateral diaphragmatic paralysis showed paradoxical movement of both crura at the end of inspiration. One dog with unilateral diaphragmatic paralysis had diaphragmatic excursion values of 2.00 ± 0.42 mm on the left side and 4.05 ± 1.48 mm on the right side. The difference between left and right diaphragmatic excursion values was 55%. Findings indicated that M-mode ultrasonography is a relatively simple and objective method for measuring diaphragmatic movement in dogs. Future studies are needed in a larger number of dogs with diaphragmatic paralysis to determine the diagnostic sensitivity of this promising new technique. © 2013 American College of Veterinary Radiology.

  6. Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands.

    PubMed

    Shen, Zhanhang; Mulholland, Kelly A; Zheng, Yujun; Wu, Chun

    2017-09-01

    DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG) 2 ) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT) 4 ) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.

  7. Wave Propagation and Localization via Quasi-Normal Modes and Transmission Eigenchannels

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Shi, Zhou; Davy, Matthieu; Genack, Azriel Z.

    2013-10-01

    Field transmission coefficients for microwave radiation between arrays of points on the incident and output surfaces of random samples are analyzed to yield the underlying quasi-normal modes and transmission eigenchannels of each realization of the sample. The linewidths, central frequencies, and transmitted speckle patterns associated with each of the modes of the medium are found. Modal speckle patterns are found to be strongly correlated leading to destructive interference between modes. This explains distinctive features of transmission spectra and pulsed transmission. An alternate description of wave transport is obtained from the eigenchannels and eigenvalues of the transmission matrix. The maximum transmission eigenvalue, τ1 is near unity for diffusive waves even in turbid samples. For localized waves, τ1 is nearly equal to the dimensionless conductance, which is the sum of all transmission eigenvalues, g = Στn. The spacings between the ensemble averages of successive values of lnτn are constant and equal to the inverse of the bare conductance in accord with predictions by Dorokhov. The effective number of transmission eigenvalues Neff determines the contrast between the peak and background of radiation focused for maximum peak intensity. The connection between the mode and channel approaches is discussed.

  8. Wave Propagation and Localization via Quasi-Normal Modes and Transmission Eigenchannels

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Shi, Zhou; Davy, Matthieu; Genack, Azriel Z.

    Field transmission coefficients for microwave radiation between arrays of points on the incident and output surfaces of random samples are analyzed to yield the underlying quasi-normal modes and transmission eigenchannels of each realization of the sample. The linewidths, central frequencies, and transmitted speckle patterns associated with each of the modes of the medium are found. Modal speckle patterns are found to be strongly correlated leading to destructive interference between modes. This explains distinctive features of transmission spectra and pulsed transmission. An alternate description of wave transport is obtained from the eigenchannels and eigenvalues of the transmission matrix. The maximum transmission eigenvalue, τ1 is near unity for diffusive waves even in turbid samples. For localized waves, τ1 is nearly equal to the dimensionless conductance, which is the sum of all transmission eigenvalues, g = Στn. The spacings between the ensemble averages of successive values of lnτn are constant and equal to the inverse of the bare conductance in accord with predictions by Dorokhov. The effective number of transmission eigenvalues Neff determines the contrast between the peak and background of radiation focused for maximum peak intensity. The connection between the mode and channel approaches is discussed.

  9. Anisotropy of the innermost inner core from body wave and normal mode observations

    NASA Astrophysics Data System (ADS)

    Deuss, A. F.; Smink, M.; Bouwman, D.; Ploegstra, J.; van Tent, R.

    2016-12-01

    It has been known for a long time that the Earth's inner core is cylindrically anisotropic, with waves that travel in the direction of the Earth's rotation axis arriving several seconds before waves travelling in the equatorial direction. Recently, several studies have suggested that the Earth's rotation axis may not be the fast anisotropy direction in the innermost inner core. Beghein and Trampert (2003) found that the Earth's rotation axis is slow, with the equatorial plane being fast. Wang et al (2015) found instead that the fast symmetry axis is in the equatorial plane. Here, we use both body wave and normal mode observations to test these two different hypotheses. Similar to Wang, we correct body wave PKIKP data for anisotropy in the upper inner core, and investigate if there is any anisotropy remaining in the innermost inner core. We find that the results strongly depend on the very limited number of polar direction waves with angle less than 25 degrees. With the limited data it is difficult to distinguish between the two different hypotheses, and if any tilted anisotropy is required at all. Normal modes see inner core anisotropy with north-south symmetry axis as anomalous zonal coefficients. We will show theoretically that if the anisotropy symmetry axis is tilted, non-zonal coefficients will also become anomalous. We search consistent anomalous non-zonal coefficients for modes sensitive to the innermost inner core. If the symmetry axis is still north south, but this is now the slow direction and the equatorial plane fast, then we predict negative zonal coefficients. This is observed for some normal modes, explaining why Beghein and Trampert (2003) found this type of anisotropy in the innermost inner core.

  10. Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses.

    PubMed

    Ahmed, Aqeel; Villinger, Saskia; Gohlke, Holger

    2010-12-01

    A large-scale comparison of essential dynamics (ED) modes from molecular dynamic simulations and normal modes from coarse-grained normal mode methods (CGNM) was performed on a dataset of 335 proteins. As CGNM methods, the elastic network model (ENM) and the rigid cluster normal mode analysis (RCNMA) were used. Low-frequency normal modes from ENM correlate very well with ED modes in terms of directions of motions and relative amplitudes of motions. Notably, a similar performance was found if normal modes from RCNMA were used, despite a higher level of coarse graining. On average, the space spanned by the first quarter of ENM modes describes 84% of the space spanned by the five ED modes. Furthermore, no prominent differences for ED and CGNM modes among different protein structure classes (CATH classification) were found. This demonstrates the general potential of CGNM approaches for describing intrinsic motions of proteins with little computational cost. For selected cases, CGNM modes were found to be more robust among proteins that have the same topology or are of the same homologous superfamily than ED modes. In view of recent evidence regarding evolutionary conservation of vibrational dynamics, this suggests that ED modes, in some cases, might not be representative of the underlying dynamics that are characteristic of a whole family, probably due to insufficient sampling of some of the family members by MD. Copyright © 2010 Wiley-Liss, Inc.

  11. Conjugate gradient filtering of instantaneous normal modes, saddles on the energy landscape, and diffusion in liquids.

    PubMed

    Chowdhary, J; Keyes, T

    2002-02-01

    Instantaneous normal modes (INM's) are calculated during a conjugate-gradient (CG) descent of the potential energy landscape, starting from an equilibrium configuration of a liquid or crystal. A small number (approximately equal to 4) of CG steps removes all the Im-omega modes in the crystal and leaves the liquid with diffusive Im-omega which accurately represent the self-diffusion constant D. Conjugate gradient filtering appears to be a promising method, applicable to any system, of obtaining diffusive modes and facilitating INM theory of D. The relation of the CG-step dependent INM quantities to the landscape and its saddles is discussed.

  12. Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies.

    PubMed

    De Moor, Bart A; Ghysels, An; Reyniers, Marie-Françoise; Van Speybroeck, Veronique; Waroquier, Michel; Marin, Guy B

    2011-04-12

    An efficient procedure for normal-mode analysis of extended systems, such as zeolites, is developed and illustrated for the physisorption and chemisorption of n-octane and isobutene in H-ZSM-22 and H-FAU using periodic DFT calculations employing the Vienna Ab Initio Simulation Package. Physisorption and chemisorption entropies resulting from partial Hessian vibrational analysis (PHVA) differ at most 10 J mol(-1) K(-1) from those resulting from full Hessian vibrational analysis, even for PHVA schemes in which only a very limited number of atoms are considered free. To acquire a well-conditioned Hessian, much tighter optimization criteria than commonly used for electronic energy calculations in zeolites are required, i.e., at least an energy cutoff of 400 eV, maximum force of 0.02 eV/Å, and self-consistent field loop convergence criteria of 10(-8) eV. For loosely bonded complexes the mobile adsorbate method is applied, in which frequency contributions originating from translational or rotational motions of the adsorbate are removed from the total partition function and replaced by free translational and/or rotational contributions. The frequencies corresponding with these translational and rotational modes can be selected unambiguously based on a mobile block Hessian-PHVA calculation, allowing the prediction of physisorption entropies within an accuracy of 10-15 J mol(-1) K(-1) as compared to experimental values. The approach presented in this study is useful for studies on other extended catalytic systems.

  13. Freeze-all cycle for all normal responders?

    PubMed

    Roque, Matheus; Valle, Marcello; Guimarães, Fernando; Sampaio, Marcos; Geber, Selmo

    2017-02-01

    The purpose of this study is to evaluate the freeze-all strategy in subgroups of normal responders, to assess whether this strategy is beneficial regardless of ovarian response, and to evaluate the possibility of implementing an individualized embryo transfer (iET) based on ovarian response. This was an observational, cohort study performed in a private IVF center. A total of 938 IVF cycles were included in this study. The patients were submitted to controlled ovarian stimulation (COS) with a gonadotropin-releasing hormone (GnRH) antagonist protocol and a cleavage-stage day 3 embryo transfer. We performed a comparison of outcomes between the fresh embryo transfer (n = 523) and the freeze-all cycles (n = 415). The analysis was performed in two subgroups of patients based on the number of retrieved oocytes: Group 1 (4-9 oocytes) and Group 2 (10-15 oocytes). In Group 1 (4-9 retrieved oocytes), the implantation rates (IR) were 17.9 and 20.5% (P = 0.259) in the fresh and freeze-all group, respectively; the ongoing pregnancy rates (OPR) were 31 and 33% (P = 0.577) in the fresh and freeze-all group, respectively. In Group 2 (10-15 oocytes), the IR were 22.1 and 30.1% (P = 0.028) and the OPR were 34 and 47% (P = 0.021) in the fresh and freeze-all groups, respectively. Although the freeze-all policy may be related to better in vitro fertilization (IVF) outcomes in normal responders, these potential advantages decrease with worsening ovarian response. Patients with poorer ovarian response do not benefit from the freeze-all strategy.

  14. Diffracted field distributions from the HE11 mode in a hollow optical fibre for an atomic funnel

    NASA Astrophysics Data System (ADS)

    Ni, Yun; Liu, Nanchun; Yin, Jianping

    2003-06-01

    The diffracted near field distribution from an LP01 mode in a hollow optical fibre was recently calculated using a scalar model based on the weakly waveguiding approximation (Yoo et al 1999 J. Opt. B: Quantum Semiclass. Opt. 1 364). It showed a dominant Gaussian-like distribution with an increased axial intensity in the central region (not a doughnut-like distribution), so the diffracted output beam from the hollow fibre cannot be used to form an atomic funnel. Using exact solutions of the Maxwell equations based on a vector model, however, we calculate the electric field and intensity distributions of the HE11 mode in the same hollow fibre and study the diffracted near- and far-field distributions of the HE11-mode output beam under the Fresnel approximation. We analyse and compare the differences between the output beams from the HE11 and LP01 modes. Our study shows that both the near- and far-field intensity distributions of the HE11-mode output beam are doughnut-like and can be used to form a simple atomic funnel. However, it is not suitable to use the weakly waveguiding approximation to calculate the diffracted near-field distribution of the hollow fibre due to the greater refractive-index difference between the hollow region (n0 = 1) and the core (n1 = 1.45 or 1.5). Finally, the 3D intensity distribution of the HE11-mode output beam is modelled and the corresponding optical potentials for cold atoms are calculated. Some potential applications of the HE11-mode output beam in an atomic guide and funnel are briefly discussed.

  15. Vibrational dynamics of vocal folds using nonlinear normal modes.

    PubMed

    Pinheiro, Alan P; Kerschen, Gaëtan

    2013-08-01

    Many previous works involving physical models, excised and in vivo larynges have pointed out nonlinear vibration in vocal folds during voice production. Moreover, theoretical studies involving mechanical modeling of these folds have tried to gain a profound understanding of the observed nonlinear phenomena. In this context, the present work uses the nonlinear normal mode theory to investigate the nonlinear modal behavior of 16 subjects using a two-mass mechanical modeling of the vocal folds. The free response of the conservative system at different energy levels is considered to assess the impact of the structural nonlinearity of the vocal fold tissues. The results show very interesting and complex nonlinear phenomena including frequency-energy dependence, subharmonic regimes and, in some cases, modal interactions, entrainment and bifurcations. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

  16. Normal modes in an overmoded circular waveguide coated with lossy material

    NASA Technical Reports Server (NTRS)

    Lee, C. S.; Lee, S. W.; Chuang, S. L.

    1985-01-01

    The normal modes in an overmoded waveguide coated with a lossy material are analyzed, particularly for their attenuation properties as a function of coating material, layer thickness, and frequency. When the coating material is not too lossy, the low-order modes are highly attenuated even with a thin layer of coating. This coated guide serves as a mode suppressor of the low-order modes, which can be particularly useful for reducing the radar cross section (RCS) of a cavity structure such as a jet inlet. When the coating material is very lossy, low-order modes fall into two distinct groups: highly and lowly attenuated modes. However, as a/lambda (a = radius of the cylinder; lambda = the free-space wavelength) increases, the separation between these two groups becomes less distinctive. The attenuation constants of most of the low-order modes become small, and decrease as a function of lambda sup 2/a sup 3.

  17. Higher order mode couplers for normal conducting DORIS 5-cell cavities

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dewersteg, B.; Seesselberg, E.; Zolfaghari, A.

    1985-10-01

    The beam intensity of the DORIS e -e storage ring is limited to about 100 mA average circulation current as a result of instabilities driven by higher order rf cavity modes. Thus an investigation has been made of the higher order mode impedances of the DORIS rf accelerator cavities. These cavities are the same as the normally conducting inductively coupled 500 MHz 5-cell structures used in PETRA. The results of the investigation were applied for the construction of inductive and capacitive attenuation antennae corresponding to specific mode spectra and mode impedances. The antennae must fit into the existing 35 mmmore » pick up flanges of the cavities and in spite of these size and position limitations they must be efficient in reducing the shunt impedances of the dangerous modes.« less

  18. Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mortisugu, Kei; Njunda, Brigitte; Smith, Jeremy C

    2009-12-01

    The change of protein vibrations on ligand binding is of functional and thermodynamic importance. Here, this process is characterized using a simple analytical 'ball-and-spring' model and all-atom normal-mode analysis (NMA) of the binding of the cancer drug, methotrexate (MTX) to its target, dihydrofolate reductase (DHFR). The analytical model predicts that the coupling between protein vibrations and ligand external motion generates entropy-rich, low-frequency vibrations in the complex. This is consistent with the atomistic NMA which reveals vibrational softening in forming the DHFR-MTX complex, a result also in qualitative agreement with neutron-scattering experiments. Energy minimization of the atomistic bound-state (B) structure whilemore » gradually decreasing the ligand interaction to zero allows the generation of a hypothetical 'intermediate' (I) state, without the ligand force field but with a structure similar to that of B. In going from I to B, it is found that the vibrational entropies of both the protein and MTX decrease while the complex structure becomes enthalpically stabilized. However, the relatively weak DHFR:MTX interaction energy results in the net entropy gain arising from coupling between the protein and MTX external motion being larger than the loss of vibrational entropy on complex formation. This, together with the I structure being more flexible than the unbound structure, results in the observed vibrational softening on ligand binding.« less

  19. Imaging modes of atomic force microscopy for application in molecular and cell biology.

    PubMed

    Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

    2017-04-06

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  20. Demonstration of the Jaynes-Cummings ladder with Rydberg-dressed atoms

    DOE PAGES

    Lee, Jongmin; Martin, Michael J.; Jau, Yuan-Yu; ...

    2017-04-06

    Here, we observe the nonlinearity of the Jaynes-Cummings (JC) ladder in the Autler-Townes spectroscopy of the hyperfine ground states for a Rydberg-dressed two-atom system. The role of the two-level system in the JC model is played by the presence or absence of a collective Rydberg excitation, and the bosonic mode manifests as the number n of single-atom spin flips, symmetrically distributed between the atoms. We also measure the normal-mode splitting and √ n nonlinearity as a function of detuning and Rabi frequency, thereby experimentally establishing the isomorphism with the JC model.

  1. Mixing induced by a propagating normal mode in long term experiments

    NASA Astrophysics Data System (ADS)

    Dossmann, Yvan; Pollet, Florence; Odier, Philippe; Dauxois, Thierry

    2017-04-01

    The energy pathways from propagating internal waves to the scales of irreversible mixing in the ocean are numerous. The triadic resonant instability (TRI) is an intrinsic destabilization process that can lead to mixing away from topographies. It consists in the destabilization of a primary internal wave generation leading to the radiation of two secondary waves of lower frequencies and different wave vectors. In the process, internal wave energy is carried down to smaller scales. A previous study focused on the assessment of instantaneous turbulent fluxes fields associated with the TRI process in laboratory experiments [1]. The present study investigates the integrated impact of mixing processes induced by a propagative normal mode over long term experiments using a similar setup. Configurations for which the TRI process is either favored or inhibited are tackled. Optical measurements using the light attenuation technique allow to follow the internal waves dynamics and the evolution of the density profile between two runs of one hour typical duration. The horizontally averaged turbulent diffusivity Kt(z) and the mixing efficiency Γ are assessed. One finds values up to Kt = 10-6 m2/s and Γ = 11 %, with slightly larger values in the presence of TRI. The maximum value for Kt is measured at the position(s) of the maximum shear normal mode shear for both normal modes 1 and 2. The development of staircases in the density profile is observed after several hours of forcing. This mechanism can be explained by Phillips' argument by which sharp interfaces can form due to vertical variations of the buoyancy flux. The staircases are responsible for large variations in the vertical distribution of turbulent diffusivity. These results could help to refine parameterizations of the impact of low order normal modes in ocean mixing. Reference : [1] Dossmann et al. 2016, Mixing by internal waves quantified using combined PIV/PLIF technique, Experiments in Fluids, 57, 132.

  2. High-frequency Born synthetic seismograms based on coupled normal modes

    USGS Publications Warehouse

    Pollitz, Fred F.

    2011-01-01

    High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ∼4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD).

  3. High-frequency Born synthetic seismograms based on coupled normal modes

    USGS Publications Warehouse

    Pollitz, F.

    2011-01-01

    High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ~4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD). ?? The Author Geophysical Journal International ?? 2011 RAS.

  4. Near-Field Acoustical Imaging using Lateral Bending Mode of Atomic Force Microscope Cantilevers

    NASA Astrophysics Data System (ADS)

    Caron, A.; Rabe, U.; Rödel, J.; Arnold, W.

    Scanning probe microscopy techniques enable one to investigate surface properties such as contact stiffness and friction between the probe tip and a sample with nm resolution. So far the bending and the torsional eigenmodes of an atomic force microscope cantilever have been used to image variations of elasticity and shear elasticity, respectively. Such images are near-field images with the resolution given by the contact radius typically between 10 nm and 50 nm. We show that the flexural modes of a cantilever oscillating in the width direction and parallel to the sample surface can also be used for imaging. Additional to the dominant in-plane component of the oscillation, the lateral modes exhibit a vertical component as well, provided there is an asymmetry in the cross-section of the cantilever or in its suspension. The out-of-plane deflection renders the lateral modes detectable by the optical position sensors used in atomic force microscopes. We studied cracks which were generated by Vickers indents, in submicro- and nanocrystalline ZrO2. Images of the lateral contact stiffness were obtained by vibrating the cantilever close to a contact-resonance frequency. A change in contact stiffness causes a shift of the resonant frequency and hence a change of the cantilever vibration amplitude. The lateral contact-stiffness images close to the crack faces display a contrast that we attribute to altered elastic properties indicating a process zone. This could be caused by a stress-induced phase transformation during crack propagation. Using the contact mode of an atomic force microscope, we measured the crack-opening displacement as a function of distance from the crack tip, and we determined the crack-tip toughness Ktip. Furthermore, K1c was inferred from the length of radial cracks of Vickers indents that were measured using classical scanning acoustic microscopy

  5. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

    PubMed Central

    Qin, Feng

    2015-01-01

    The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

  6. Entanglement Criteria of Two Two-Level Atoms Interacting with Two Coupled Modes

    NASA Astrophysics Data System (ADS)

    Baghshahi, Hamid Reza; Tavassoly, Mohammad Kazem; Faghihi, Mohammad Javad

    2015-08-01

    In this paper, we study the interaction between two two-level atoms and two coupled modes of a quantized radiation field in the form of parametric frequency converter injecting within an optical cavity enclosed by a medium with Kerr nonlinearity. It is demonstrated that, by applying the Bogoliubov-Valatin canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes-Cummings model. Then, under particular initial conditions for the atoms (in a coherent superposition of its ground and upper states) and the fields (in a standard coherent state) which may be prepared, the time evolution of state vector of the entire system is analytically evaluated. In order to understand the degree of entanglement between subsystems (atom-field and atom-atom), the dynamics of entanglement through different measures, namely, von Neumann reduced entropy, concurrence and negativity is evaluated. In each case, the effects of Kerr nonlinearity and detuning parameter on the above measures are numerically analyzed, in detail. It is illustrated that the amount of entanglement can be tuned by choosing the evolved parameters, appropriately.

  7. Quantum control of the normal modes of benzene with ultrafast laser pulses

    NASA Astrophysics Data System (ADS)

    Sauer, Petra; Dou, Yusheng; Torralva, Ben; Allen, Roland

    2005-03-01

    Remarkable innovations in laser technology have made it possible to create laser pulses with ultrashort durations (below 100 femtoseconds) and ultrahigh intensities (above 1 terawatt per cm^2). To understand the behavior of complex molecules and materials in this new regime of physics, chemistry, biology, and materials science requires innovative techniques which complement experiment and standard theory, and which can treat situations in which conventional approximations like the Born- Oppenheimer approximation, the Franck-Condon principle, and Fermi's golden rule are no longer valid. In this talk we describe a method that we are developing, semiclassical electron-radiation-ion dyanmics (SERID), which can be used to perform simulations of the coupled dynamics of electrons and nuclei in an intense radiation field. We have employed this technique in studying the normal modes of benzene, and the possibility of controlling these modes by optimizing the laser pulses that are applied to the molecule. Animations will be shown of particular normal modes, including the breathing and beating modes, illustrating their symmetries and other properties, and of the photodissociation of benzene when the laser pulse exceeds a threshold intensity.

  8. Quasi-normal modes of extremal BTZ black holes in TMG

    NASA Astrophysics Data System (ADS)

    Afshar, Hamid R.; Alishahiha, Mohsen; Mosaffa, Amir E.

    2010-08-01

    We study the spectrum of tensor perturbations on extremal BTZ black holes in topologically massive gravity for arbitrary values of the coefficient of the Chern-Simons term, μ. Imposing proper boundary conditions at the boundary of the space and at the horizon, we find that the spectrum contains quasi-normal modes.

  9. Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit.

    PubMed

    Skjaerven, Lars; Martinez, Aurora; Reuter, Nathalie

    2011-01-01

    Principal component analysis (PCA) and normal mode analysis (NMA) have emerged as two invaluable tools for studying conformational changes in proteins. To compare these approaches for studying protein dynamics, we have used a subunit of the GroEL chaperone, whose dynamics is well characterized. We first show that both PCA on trajectories from molecular dynamics (MD) simulations and NMA reveal a general dynamical behavior in agreement with what has previously been described for GroEL. We thus compare the reproducibility of PCA on independent MD runs and subsequently investigate the influence of the length of the MD simulations. We show that there is a relatively poor one-to-one correspondence between eigenvectors obtained from two independent runs and conclude that caution should be taken when analyzing principal components individually. We also observe that increasing the simulation length does not improve the agreement with the experimental structural difference. In fact, relatively short MD simulations are sufficient for this purpose. We observe a rapid convergence of the eigenvectors (after ca. 6 ns). Although there is not always a clear one-to-one correspondence, there is a qualitatively good agreement between the movements described by the first five modes obtained with the three different approaches; PCA, all-atoms NMA, and coarse-grained NMA. It is particularly interesting to relate this to the computational cost of the three methods. The results we obtain on the GroEL subunit contribute to the generalization of robust and reproducible strategies for the study of protein dynamics, using either NMA or PCA of trajectories from MD simulations. © 2010 Wiley-Liss, Inc.

  10. Earth's Outer Core Properties Estimated Using Bayesian Inversion of Normal Mode Eigenfrequencies

    NASA Astrophysics Data System (ADS)

    Irving, J. C. E.; Cottaar, S.; Lekic, V.

    2016-12-01

    The outer core is arguably Earth's most dynamic region, and consists of an iron-nickel liquid with an unknown combination of lighter alloying elements. Frequencies of Earth's normal modes provide the strongest constraints on the radial profiles of compressional wavespeed, VΦ, and density, ρ, in the outer core. Recent great earthquakes have yielded new normal mode measurements; however, mineral physics experiments and calculations are often compared to the Preliminary reference Earth model (PREM), which is 35 years old and does not provide uncertainties. Here we investigate the thermo-elastic properties of the outer core using Earth's free oscillations and a Bayesian framework. To estimate radial structure of the outer core and its uncertainties, we choose to exploit recent datasets of normal mode centre frequencies. Under the self-coupling approximation, centre frequencies are unaffected by lateral heterogeneities in the Earth, for example in the mantle. Normal modes are sensitive to both VΦ and ρ in the outer core, with each mode's specific sensitivity depending on its eigenfunctions. We include a priori bounds on outer core models that ensure compatibility with measurements of mass and moment of inertia. We use Bayesian Monte Carlo Markov Chain techniques to explore different choices in parameterizing the outer core, each of which represents different a priori constraints. We test how results vary (1) assuming a smooth polynomial parametrization, (2) allowing for structure close to the outer core's boundaries, (3) assuming an Equation-of-State and adiabaticity and inverting directly for thermo-elastic parameters. In the second approach we recognize that the outer core may have distinct regions close to the core-mantle and inner core boundaries and investigate models which parameterize the well mixed outer core separately from these two layers. In the last approach we seek to map the uncertainties directly into thermo-elastic parameters including the bulk

  11. Functional Dynamics of PDZ Binding Domains: A Normal-Mode Analysis

    PubMed Central

    De Los Rios, Paolo; Cecconi, Fabio; Pretre, Anna; Dietler, Giovanni; Michielin, Olivier; Piazza, Francesco; Juanico, Brice

    2005-01-01

    Postsynaptic density-95/disks large/zonula occludens-1 (PDZ) domains are relatively small (80–120 residues) protein binding modules central in the organization of receptor clusters and in the association of cellular proteins. Their main function is to bind C-terminals of selected proteins that are recognized through specific amino acids in their carboxyl end. Binding is associated with a deformation of the PDZ native structure and is responsible for dynamical changes in regions not in direct contact with the target. We investigate how this deformation is related to the harmonic dynamics of the PDZ structure and show that one low-frequency collective normal mode, characterized by the concerted movements of different secondary structures, is involved in the binding process. Our results suggest that even minimal structural changes are responsible for communication between distant regions of the protein, in agreement with recent NMR experiments. Thus, PDZ domains are a very clear example of how collective normal modes are able to characterize the relation between function and dynamics of proteins, and to provide indications on the precursors of binding/unbinding events. PMID:15821164

  12. Tapping mode imaging and measurements with an inverted atomic force microscope.

    PubMed

    Chan, Sandra S F; Green, John-Bruce D

    2006-07-18

    This report demonstrates the successful use of the inverted atomic force microscope (i-AFM) for tapping mode AFM imaging of cantilever-supported samples. i-AFM is a mode of AFM operation in which a sample supported on a tipless cantilever is imaged by one of many tips in a microfabricated tip array. Tapping mode is an intermittent contact mode whereby the cantilever is oscillated at or near its resonance frequency, and the amplitude and/or phase are used to image the sample. In the process of demonstrating that tapping mode images could be obtained in the i-AFM design, it was observed that the amplitude of the cantilever oscillation decreased markedly as the cantilever and tip array were approached. The source of this damping of the cantilever oscillations was identified to be the well-known "squeeze film damping", and the extent of damping was a direct consequence of the relatively shorter tip heights for the tip arrays, as compared to those of commercially available tapping mode cantilevers with integrated tips. The functional form for the distance dependence of the damping coefficient is in excellent agreement with previously published models for squeeze film damping, and the values for the fitting parameters make physical sense. Although the severe damping reduces the cantilever free amplitude substantially, we found that we were still able to access the low-amplitude regime of oscillation necessary for attractive tapping mode imaging of fragile molecules.

  13. Normal Modes of Magnetized Finite Two-Dimensional Yukawa Crystals

    NASA Astrophysics Data System (ADS)

    Marleau, Gabriel-Dominique; Kaehlert, Hanno; Bonitz, Michael

    2009-11-01

    The normal modes of a finite two-dimensional dusty plasma in an isotropic parabolic confinement, including the simultaneous effects of friction and an external magnetic field, are studied. The ground states are found from molecular dynamics simulations with simulated annealing, and the influence of screening, friction, and magnetic field on the mode frequencies is investigated in detail. The two-particle problem is solved analytically and the limiting cases of weak and strong magnetic fields are discussed.[4pt] [1] C. Henning, H. K"ahlert, P. Ludwig, A. Melzer, and M.Bonitz. J. Phys. A 42, 214023 (2009)[2] B. Farokhi, M. Shahmansouri, and P. K. Shukla. Phys.Plasmas 16, 063703 (2009)[3] L. Cândido, J.-P. Rino, N. Studart, and F. M. Peeters. J. Phys.: Condens. Matter 10, 11627--11644 (1998)

  14. Soft Vibrational Modes Predict Breaking Events during Force-Induced Protein Unfolding.

    PubMed

    Habibi, Mona; Plotkin, Steven S; Rottler, Jörg

    2018-02-06

    We investigate the correlation between soft vibrational modes and unfolding events in simulated force spectroscopy of proteins. Unfolding trajectories are obtained from molecular dynamics simulations of a Gō model of a monomer of a mutant of superoxide dismutase 1 protein containing all heavy atoms in the protein, and a normal mode analysis is performed based on the anisotropic network model. We show that a softness map constructed from the superposition of the amplitudes of localized soft modes correlates with unfolding events at different stages of the unfolding process. Soft residues are up to eight times more likely to undergo disruption of native structure than the average amino acid. The memory of the softness map is retained for extensions of up to several nanometers, but decorrelates more rapidly during force drops. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. All-fiber-based selective mode multiplexer and demultiplexer for weakly-coupled mode-division multiplexed systems

    NASA Astrophysics Data System (ADS)

    Igarashi, Koji; Park, Kyung Jun; Tsuritani, Takahiro; Morita, Itsuro; Kim, Byoung Yoon

    2018-02-01

    We show all-fiber-based selective mode multiplexers and demultiplexers for weakly-coupled mode-division multiplexed systems. We fabricate a set of six-mode multiplexer and demultiplexer based on fiber mode selective couplers, and experimentally evaluate the performance for the six-mode dual-polarization (DP) quadrature phase shift keying (QPSK) optical signals. In the mode multiplexer and demultiplexer, the mode couplings between the lower three modes and the higher three modes are suppressed to be less than -20 dB, which enables us to apply partial 6 ×6 MIMO equalizers even for the six-mode demultiplexing. For the six-mode DP-QPSK signals, the penalty of optical signal-to-noise ratio by replacing the full 12 ×12MIMO to the partial 6 ×6 MIMO is suppressed by less than 1 dB.

  16. Tunable and switchable dual-wavelength dissipative soliton generation in an all-normal-dispersion Yb-doped fiber laser with birefringence fiber filter.

    PubMed

    Zhang, Z X; Xu, Z W; Zhang, L

    2012-11-19

    We report the generation of tunable single- and dual-wavelength dissipative solitons in an all-normal-dispersion mode-locked Yb-doped fiber laser, to the best of our knowledge, for the first time. Besides single-wavelength mode-locking, dual-wavelength mode-locking was achieved using an in-line birefringence fiber filter with periodic multiple passbands, which not only allows multiple wavelengths to oscillate simultaneously but also performs spectrum modulation on highly chirped dissipative pulse. Furthermore, taking advantage of the tunability of the birefringence fiber filter, wavelength tuning for both single- and dual-wavelength dissipative soliton mode-locking was realized. The dual-wavelength operation is also switchable. The all-fiber dissipative laser with flexible outputs can meet diverse application needs.

  17. Effectiveness of Modal Decomposition for Tapping Atomic Force Microscopy Microcantilevers in Liquid Environment.

    PubMed

    Kim, Il Kwang; Lee, Soo Il

    2016-05-01

    The modal decomposition of tapping mode atomic force microscopy microcantilevers in liquid environments was studied experimentally. Microcantilevers with different lengths and stiffnesses and two sample surfaces with different elastic moduli were used in the experiment. The response modes of the microcantilevers were extracted as proper orthogonal modes through proper orthogonal decomposition. Smooth orthogonal decomposition was used to estimate the resonance frequency directly. The effects of the tapping setpoint and the elastic modulus of the sample under test were examined in terms of their multi-mode responses with proper orthogonal modes, proper orthogonal values, smooth orthogonal modes and smooth orthogonal values. Regardless of the stiffness of the microcantilever under test, the first mode was dominant in tapping mode atomic force microscopy under normal operating conditions. However, at lower tapping setpoints, the flexible microcantilever showed modal distortion and noise near the tip when tapping on a hard sample. The stiff microcantilever had a higher mode effect on a soft sample at lower tapping setpoints. Modal decomposition for tapping mode atomic force microscopy can thus be used to estimate the characteristics of samples in liquid environments.

  18. The study of the plasmon modes of square atomic clusters based on the eigen-oscillation equation of charge under the free-electron gas model

    NASA Astrophysics Data System (ADS)

    Xue, Hong-Jie; Wu, Reng-Lai; Hu, Cheng-Xi; Zhang, Ming

    2018-04-01

    In atomic clusters, plasmon modes are generally gained by the resonant responses for external fields. However, these resonant methods still carry some defects: some plasmon modes may not have been found as that may not have been excited by the external fields. Recently, by employing the extended Hubbard model to describe electron systems of atomic clusters, we have presented the eigen-oscillation equation of charge to study plasmon modes. In this work, based on the free-electron gas model, we further explore the eigen-equation method. Under different external electric fields, some of the plasmon mode spectrums with obvious differences are found, which display the defects of the resonant methods. All the plasmon modes obtained by the resonant methods are predicted by the eigen-equation method. This effectively shows that the eigen-equation method is feasible and reliable in the process of finding plasmon. In addition, various kinds of plasmons are displayed by charge distributions, and the evolution features of plasmon with system parameters are gained by the energy absorption spectrum.

  19. Free and forced Rossby normal modes in a rectangular gulf of arbitrary orientation

    NASA Astrophysics Data System (ADS)

    Graef, Federico

    2016-09-01

    A free Rossby normal mode in a rectangular gulf of arbitrary orientation is constructed by considering the reflection of a Rossby mode in a channel at the head of the gulf. Therefore, it is the superposition of four Rossby waves in an otherwise unbounded ocean with the same frequency and wavenumbers perpendicular to the gulf axis whose difference is equal to 2mπ/W, where m is a positive integer and W the gulf's width. The lower (or higher) modes with small m (or large m) are oscillatory (evanescent) in the coordinate along the gulf; these are elucidated geometrically. However for oceanographically realistic parameter values, most of the modes are evanescent. When the gulf is forced at the mouth with a single Fourier component, the response is in general an infinite sum of modes that are needed to match the value of the streamfunction at the gulf's entrance. The dominant mode of the response is the resonant one, which corresponds to forcing with a frequency ω and wavenumber normal to the gulf axis η appropriate to a gulf mode: η =- β sin α/(2ω) ± Mπ/W, where α is the angle between the gulf's axis and the eastern direction (+ve clockwise) and M the resonant's mode number. For zonal gulfs ω drops out of the resonance condition. For the special cases η = 0 in which the free surface goes up and down at the mouth with no flow through it, or a flow with a sinusoidal profile, resonant modes can get excited for very specific frequencies (only for non-zonal gulfs in the η = 0 case). The resonant mode is around the annual frequency for a wide range of gulf orientations α ∈ [40°, 130°] or α ∈ [220°, 310°] and gulf widths between 150 and 200 km; these include the Gulf of California and the Adriatic Sea. If η is imaginary, i.e. a flow with an exponential profile, there is no resonance. In general less modes get excited if the gulf is zonally oriented.

  20. A normal mode treatment of semi-diurnal body tides on an aspherical, rotating and anelastic Earth

    NASA Astrophysics Data System (ADS)

    Lau, Harriet C. P.; Yang, Hsin-Ying; Tromp, Jeroen; Mitrovica, Jerry X.; Latychev, Konstantin; Al-Attar, David

    2015-08-01

    Normal mode treatments of the Earth's body tide response were developed in the 1980s to account for the effects of Earth rotation, ellipticity, anelasticity and resonant excitation within the diurnal band. Recent space-geodetic measurements of the Earth's crustal displacement in response to luni-solar tidal forcings have revealed geographical variations that are indicative of aspherical deep mantle structure, thus providing a novel data set for constraining deep mantle elastic and density structure. In light of this, we make use of advances in seismic free oscillation literature to develop a new, generalized normal mode theory for the tidal response within the semi-diurnal and long-period tidal band. Our theory involves a perturbation method that permits an efficient calculation of the impact of aspherical structure on the tidal response. In addition, we introduce a normal mode treatment of anelasticity that is distinct from both earlier work in body tides and the approach adopted in free oscillation seismology. We present several simple numerical applications of the new theory. First, we compute the tidal response of a spherically symmetric, non-rotating, elastic and isotropic Earth model and demonstrate that our predictions match those based on standard Love number theory. Second, we compute perturbations to this response associated with mantle anelasticity and demonstrate that the usual set of seismic modes adopted for this purpose must be augmented by a family of relaxation modes to accurately capture the full effect of anelasticity on the body tide response. Finally, we explore aspherical effects including rotation and we benchmark results from several illustrative case studies of aspherical Earth structure against independent finite-volume numerical calculations of the semi-diurnal body tide response. These tests confirm the accuracy of the normal mode methodology to at least the level of numerical error in the finite-volume predictions. They also demonstrate

  1. Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation.

    PubMed

    Karasawa, N; Mitsutake, A; Takano, H

    2017-12-01

    Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n]polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μs molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

  2. Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

    NASA Astrophysics Data System (ADS)

    Karasawa, N.; Mitsutake, A.; Takano, H.

    2017-12-01

    Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n ] polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μ s molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

  3. Tip Effect of the Tapping Mode of Atomic Force Microscope in Viscous Fluid Environments.

    PubMed

    Shih, Hua-Ju; Shih, Po-Jen

    2015-07-28

    Atomic force microscope with applicable types of operation in a liquid environment is widely used to scan the contours of biological specimens. The contact mode of operation allows a tip to touch a specimen directly but sometimes it damages the specimen; thus, a tapping mode of operation may replace the contact mode. The tapping mode triggers the cantilever of the microscope approximately at resonance frequencies, and so the tip periodically knocks the specimen. It is well known that the cantilever induces extra liquid pressure that leads to drift in the resonance frequency. Studies have noted that the heights of protein surfaces measured via the tapping mode of an atomic force microscope are ~25% smaller than those measured by other methods. This discrepancy may be attributable to the induced superficial hydrodynamic pressure, which is worth investigating. In this paper, we introduce a semi-analytical method to analyze the pressure distribution of various tip geometries. According to our analysis, the maximum hydrodynamic pressure on the specimen caused by a cone-shaped tip is ~0.5 Pa, which can, for example, pre-deform a cell by several nanometers in compression before the tip taps it. Moreover, the pressure calculated on the surface of the specimen is 20 times larger than the pressure without considering the tip effect; these results have not been motioned in other papers. Dominating factors, such as surface heights of protein surface, mechanical stiffness of protein increasing with loading velocity, and radius of tip affecting the local pressure of specimen, are also addressed in this study.

  4. Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution.

    PubMed

    Jelsch, C

    2001-09-01

    The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 A resolution, the elements are reduced by two orders of magnitude for distances above 1.5 A. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.

  5. Calculation of normal modes of the closed waveguides in general vector case

    NASA Astrophysics Data System (ADS)

    Malykh, M. D.; Sevastianov, L. A.; Tiutiunnik, A. A.

    2018-04-01

    The article is devoted to the calculation of normal modes of the closed waveguides with an arbitrary filling ɛ, μ in the system of computer algebra Sage. Maxwell equations in the cylinder are reduced to the system of two bounded Helmholtz equations, the notion of weak solution of this system is given and then this system is investigated as a system of ordinary differential equations. The normal modes of this system are an eigenvectors of a matrix pencil. We suggest to calculate the matrix elements approximately and to truncate the matrix by usual way but further to solve the truncated eigenvalue problem exactly in the field of algebraic numbers. This approach allows to keep the symmetry of the initial problem and in particular the multiplicity of the eigenvalues. In the work would be presented some results of calculations.

  6. Polyad breaking phenomenon associated with a local-to-normal mode transition and suitability to estimate force constants

    NASA Astrophysics Data System (ADS)

    Bermúdez-Montaña, M.; Lemus, R.; Castaños, O.

    2017-12-01

    In a system of two interacting harmonic oscillators a local-to-normal mode transition is manifested as a polyad breaking phenomenon. This phenomenon is associated with the suitability to estimate zeroth-order force constants in the framework of a local mode description. This transition is also exhibited in two interacting Morse oscillators. To study this case, an appropriate parameterisation going from a molecule with local mode behaviour (H2O) to a molecule presenting a normal mode behaviour (CO2) is introduced. Concepts from quantum mechanics like fidelity, entropy and probability density, as well from nonlinear classical mechanics like Poincaré sections are used to detect the transition region. It is found that fidelity and entropy are sensitive complementary properties to detect the local-to-normal transition. Poincaré sections allow the local-to-normal transition to be detected through the appearance of chaos as a consequence of the polyad breaking phenomenon. In addition, two kinds of avoided energy crossings are identified in accordance with the different regions of the spectrum.

  7. All-fiber orbital angular momentum mode generation and transmission system

    NASA Astrophysics Data System (ADS)

    Heng, Xiaobo; Gan, Jiulin; Zhang, Zhishen; Qian, Qi; Xu, Shanhui; Yang, Zhongmin

    2017-11-01

    We proposed and demonstrated an all-fiber system for generating and transmitting orbital angular momentum (OAM) mode light. A specially designed multi-core fiber (MCF) was used to endow with guide modes different phase change and two tapered transition regions were used for providing low-loss interfaces between different fiber structures. By arranging the refractive index distribution among the multi-cores and controlling the length of MCF, which essentially change the phase difference between the neighboring cores, OAM modes with different topological charge l can be generated selectively. Through two tapered transition regions, the non-OAM mode light can be effectively injected into the MCF and the generated OAM mode light can be easily launched into OAM mode supporting fiber for long distance and high purity transmission. Such an all-fiber OAM mode generation and transmission system owns the merits of flexibility, compactness, portability, and would have practical application value in OAM optical fiber communication systems.

  8. Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the 199Hg Atom

    NASA Astrophysics Data System (ADS)

    Sahoo, B. K.; Das, B. P.

    2018-05-01

    Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P ,T -odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P ,T -odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to 199Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

  9. Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the ^{199}Hg Atom.

    PubMed

    Sahoo, B K; Das, B P

    2018-05-18

    Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P,T-odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P,T-odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to ^{199}Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

  10. ECHOCARDIOGRAPHIC FINDINGS OF BIDIMENSIONAL MODE, M-MODE, AND DOPPLER OF CLINICALLY NORMAL BLACK-RUMPED AGOUTI (DASYPROCTA PRYMNOLOPHA, WAGLER 1831).

    PubMed

    Diniz, Anaemilia das Neves; Pessoa, Gerson Tavares; da Silva Moura, Laecio; de Sousa, André Braga; Sousa, Francisco das Chagas Araújo; de Sá Rodrigues, Renan Paraguassu; da Silva Barbosa, Maria Angélica Parente; de Almeida, Hatawa Melo; Freire, Larisse Danielle Silva; Sanches, Marina Pinto; Júnior, Antônio Augusto Nascimento Machado; Guerra, Porfírio Candanedo; Neves, Willams Costa; de Sousa, João Macedo; Bolfer, Luiz; Giglio, Robson Fortes; Alves, Flávio Ribeiro

    2017-06-01

    The black-rumped agouti ( Dasyprocta prymnolopha , Wagler 1831) is currently under intense ecologic pressure, which has resulted in its disappearance from some regions of Brazil. Echocardiography is widely used in veterinary medicine but it is not yet part of the clinical routine for wild animals. The objective of the present study was to assess the applicability of the echocardiographic exam in nonanesthetized agouti and to establish normal reference values for echocardiographic measurements in bidimensional mode (2D), M-mode, and Doppler for this species, and a lead II electrocardiogram was simultaneously recorded. Twenty agouti were used in this study. All the echocardiographic measurements were positively correlated with weight (P < 0.05), and there were no significant differences between sexes (P > 0.05). Blood flow velocities in the pulmonary and aortic artery ranged from 67.32-71.28 cm/sec and 79.22-101.84 cm/sec, respectively. The isovolumic relaxation time was assessed in all the animals and ranged from 38.5 to 56.6 ms. The maximum value for the nonfused E and A waves and the Et and At waves was 158 beats/min for both. The results obtained for the morphologic and heart hemodynamic measurements can guide future studies and help in the clinical management of these animals in captivity.

  11. Estimation of splitting functions from Earth's normal mode spectra using the neighbourhood algorithm

    NASA Astrophysics Data System (ADS)

    Pachhai, Surya; Tkalčić, Hrvoje; Masters, Guy

    2016-01-01

    The inverse problem for Earth structure from normal mode data is strongly non-linear and can be inherently non-unique. Traditionally, the inversion is linearized by taking partial derivatives of the complex spectra with respect to the model parameters (i.e. structure coefficients), and solved in an iterative fashion. This method requires that the earthquake source model is known. However, the release of energy in large earthquakes used for the analysis of Earth's normal modes is not simple. A point source approximation is often inadequate, and a more complete account of energy release at the source is required. In addition, many earthquakes are required for the solution to be insensitive to the initial constraints and regularization. In contrast to an iterative approach, the autoregressive linear inversion technique conveniently avoids the need for earthquake source parameters, but it also requires a number of events to achieve full convergence when a single event does not excite all singlets well. To build on previous improvements, we develop a technique to estimate structure coefficients (and consequently, the splitting functions) using a derivative-free parameter search, known as neighbourhood algorithm (NA). We implement an efficient forward method derived using the autoregresssion of receiver strips, and this allows us to search over a multiplicity of structure coefficients in a relatively short time. After demonstrating feasibility of the use of NA in synthetic cases, we apply it to observations of the inner core sensitive mode 13S2. The splitting function of this mode is dominated by spherical harmonic degree 2 axisymmetric structure and is consistent with the results obtained from the autoregressive linear inversion. The sensitivity analysis of multiple events confirms the importance of the Bolivia, 1994 earthquake. When this event is used in the analysis, as little as two events are sufficient to constrain the splitting functions of 13S2 mode. Apart from

  12. Imaging surface nanobubbles at graphite-water interfaces with different atomic force microscopy modes.

    PubMed

    Yang, Chih-Wen; Lu, Yi-Hsien; Hwang, Ing-Shouh

    2013-05-08

    We have imaged nanobubbles on highly ordered pyrolytic graphite (HOPG) surfaces in pure water with different atomic force microscopy (AFM) modes, including the frequency-modulation, the tapping, and the PeakForce techniques. We have compared the performance of these modes in obtaining the surface profiles of nanobubbles. The frequency-modulation mode yields a larger height value than the other two modes and can provide more accurate measurement of the surface profiles of nanobubbles. Imaging with PeakForce mode shows that a nanobubble appears smaller and shorter with increasing peak force and disappears above a certain peak force, but the size returns to the original value when the peak force is reduced. This indicates that imaging with high peak forces does not cause gas removal from the nanobubbles. Based on the presented findings and previous AFM observations, the existing models for nanobubbles are reviewed and discussed. The model of gas aggregate inside nanobubbles provides a better explanation for the puzzles of the high stability and the contact angle of surface nanobubbles.

  13. Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion

    NASA Astrophysics Data System (ADS)

    Faghihi, M. J.; Tavassoly, M. K.; Hatami, M.

    In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a Λ-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering ‘atomic population inversion’ and two different measures of entanglement, i.e., ‘von Neumann entropy’ and ‘idempotency defect’ is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter p and the detuning parameters.

  14. Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.

    PubMed

    Sorzano, Carlos Oscar S; de la Rosa-Trevín, José Miguel; Tama, Florence; Jonić, Slavica

    2014-11-01

    This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Analysis of dynamic cantilever behavior in tapping mode atomic force microscopy.

    PubMed

    Deng, Wenqi; Zhang, Guang-Ming; Murphy, Mark F; Lilley, Francis; Harvey, David M; Burton, David R

    2015-10-01

    Tapping mode atomic force microscopy (AFM) provides phase images in addition to height and amplitude images. Although the behavior of tapping mode AFM has been investigated using mathematical modeling, comprehensive understanding of the behavior of tapping mode AFM still poses a significant challenge to the AFM community, involving issues such as the correct interpretation of the phase images. In this paper, the cantilever's dynamic behavior in tapping mode AFM is studied through a three dimensional finite element method. The cantilever's dynamic displacement responses are firstly obtained via simulation under different tip-sample separations, and for different tip-sample interaction forces, such as elastic force, adhesion force, viscosity force, and the van der Waals force, which correspond to the cantilever's action upon various different representative computer-generated test samples. Simulated results show that the dynamic cantilever displacement response can be divided into three zones: a free vibration zone, a transition zone, and a contact vibration zone. Phase trajectory, phase shift, transition time, pseudo stable amplitude, and frequency changes are then analyzed from the dynamic displacement responses that are obtained. Finally, experiments are carried out on a real AFM system to support the findings of the simulations. © 2015 Wiley Periodicals, Inc.

  16. Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

    PubMed

    Zheng, Wenjun; Brooks, Bernard R

    2006-06-15

    Recently we have developed a normal-modes-based algorithm that predicts the direction of protein conformational changes given the initial state crystal structure together with a small number of pairwise distance constraints for the end state. Here we significantly extend this method to accurately model both the direction and amplitude of protein conformational changes. The new protocol implements a multisteps search in the conformational space that is driven by iteratively minimizing the error of fitting the given distance constraints and simultaneously enforcing the restraint of low elastic energy. At each step, an incremental structural displacement is computed as a linear combination of the lowest 10 normal modes derived from an elastic network model, whose eigenvectors are reorientated to correct for the distortions caused by the structural displacements in the previous steps. We test this method on a list of 16 pairs of protein structures for which relatively large conformational changes are observed (root mean square deviation >3 angstroms), using up to 10 pairwise distance constraints selected by a fluctuation analysis of the initial state structures. This method has achieved a near-optimal performance in almost all cases, and in many cases the final structural models lie within root mean square deviation of 1 approximately 2 angstroms from the native end state structures.

  17. Superradiance for Atoms Trapped along a Photonic Crystal Waveguide

    NASA Astrophysics Data System (ADS)

    Goban, A.; Hung, C.-L.; Hood, J. D.; Yu, S.-P.; Muniz, J. A.; Painter, O.; Kimble, H. J.

    2015-08-01

    We report observations of superradiance for atoms trapped in the near field of a photonic crystal waveguide (PCW). By fabricating the PCW with a band edge near the D1 transition of atomic cesium, strong interaction is achieved between trapped atoms and guided-mode photons. Following short-pulse excitation, we record the decay of guided-mode emission and find a superradiant emission rate scaling as Γ¯SR∝N ¯Γ1 D for average atom number 0.19 ≲N ¯≲2.6 atoms, where Γ1 D/Γ'=1.0 ±0.1 is the peak single-atom radiative decay rate into the PCW guided mode, and Γ' is the radiative decay rate into all the other channels. These advances provide new tools for investigations of photon-mediated atom-atom interactions in the many-body regime.

  18. Strain partitioning and deformation mode analysis of the normal faults at Red Mountain, Birmingham, Alabama

    NASA Astrophysics Data System (ADS)

    Wu, Schuman

    1989-12-01

    In a low-temperature environment, the thin-section scale rock-deformation mode is primarily a function of confining pressure and total strain at geological strain rates. A deformation mode diagram is constructed from published experimental data by plotting the deformation mode on a graph of total strain versus the confining pressure. Four deformation modes are shown on the diagram: extensional fracturing, mesoscopic faulting, incipient faulting, and uniform flow. By determining the total strain and the deformation mode of a naturally deformed sample, the confining pressure and hence the depth at which the rock was deformed can be evaluated. The method is applied to normal faults exposed on the gently dipping southeast limb of the Birmingham anticlinorium in the Red Mountain expressway cut in Birmingham, Alabama. Samples of the Ordovician Chickamauga Limestone within and adjacent to the faults contain brittle structures, including mesoscopic faults and veins, and ductile deformation features including calcite twins, intergranular and transgranular pressure solution, and deformed burrows. During compaction, a vertical shortening of about 45 to 80% in shale is indicated by deformed burrows and relative compaction of shale to burrows, about 6% in limestone by stylolites. The normal faults formed after the Ordovician rocks were consolidated because the faults and associated veins truncate the deformed burrows and stylolites, which truncate the calcite cement. A total strain of 2.0% was caused by mesoscopic faults during normal faulting. A later homogenous deformation, indicated by the calcite twins in veins, cement and fossil fragments, has its major principal shortening strain in the dip direction at a low angle (about 22°) to bedding. The strain magnitude is about 2.6%. By locating the observed data on the deformation mode diagram, it is found that the normal faulting characterized by brittle deformation occurred under low confining pressure (< 18 MPa) at shallow

  19. Time-dependent local-to-normal mode transition in triatomic molecules

    NASA Astrophysics Data System (ADS)

    Cruz, Hans; Bermúdez-Montaña, Marisol; Lemus, Renato

    2018-01-01

    Time-evolution of the vibrational states of two interacting harmonic oscillators in the local mode scheme is presented. A local-to-normal mode transition (LNT) is identified and studied from temporal perspective through time-dependent frequencies of the oscillators. The LNT is established as a polyad-breaking phenomenon from the local standpoint for the stretching degrees of freedom in a triatomic molecule. This study is carried out in the algebraic representation of bosonic operators. The dynamics of the states are determined via the solutions of the corresponding nonlinear Ermakov equation and a local time-dependent polyad is obtained as a tool to identify the LNT. Applications of this formalism to H2O, CO2, O3 and NO2 molecules in the adiabatic, sudden and linear regime are considered.

  20. On-site monitoring of atomic density number for an all-optical atomic magnetometer based on atomic spin exchange relaxation.

    PubMed

    Zhang, Hong; Zou, Sheng; Chen, Xiyuan; Ding, Ming; Shan, Guangcun; Hu, Zhaohui; Quan, Wei

    2016-07-25

    We present a method for monitoring the atomic density number on site based on atomic spin exchange relaxation. When the spin polarization P ≪ 1, the atomic density numbers could be estimated by measuring magnetic resonance linewidth in an applied DC magnetic field by using an all-optical atomic magnetometer. The density measurement results showed that the experimental results the theoretical predictions had a good consistency in the investigated temperature range from 413 K to 463 K, while, the experimental results were approximately 1.5 ∼ 2 times less than the theoretical predictions estimated from the saturated vapor pressure curve. These deviations were mainly induced by the radiative heat transfer efficiency, which inevitably leaded to a lower temperature in cell than the setting temperature.

  1. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

    PubMed Central

    Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.

    2012-01-01

    Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983

  2. Microcavities coupled to multilevel atoms

    NASA Astrophysics Data System (ADS)

    Schmid, Sandra Isabelle; Evers, Jörg

    2011-11-01

    A three-level atom in the Λ configuration coupled to a microcavity is studied. The two transitions of the atom are assumed to couple to different counterpropagating mode pairs in the cavity. We analyze the dynamics both in the strong-coupling and the bad-cavity limits. We find that, compared to a two-level setup, the third atomic state and the additional control field modes crucially modify the system dynamics and enable more advanced control schemes. All results are explained using appropriate dressed-state and eigenmode representations. As potential applications, we discuss optical switching and turnstile operations and detection of particles close to the resonator surface.

  3. Widely tunable Tm-doped mode-locked all-fiber laser

    PubMed Central

    Yan, Zhiyu; Sun, Biao; Li, Xiaohui; Luo, Jiaqi; Shum, Perry Ping; Yu, Xia; Zhang, Ying; Wang, Qi Jie

    2016-01-01

    We demonstrated a widely tunable Tm-doped mode-locked all-fiber laser, with the widest tunable range of 136 nm, from 1842 to 1978 nm. Nonlinear polarization evolution (NPE) technique is employed to enable mode-locking and the wavelength-tunable operation. The widely tunable range attributes to the NPE-induced transmission modulation and bidirectional pumping mechanism. Such kind of tunable mode-locked laser can find various applications in optical communications, spectroscopy, time-resolved measurement, and among others. PMID:27263655

  4. Atmospheric resonances of the Rayleigh and tsunami normal modes and its sensitivity to local time and geographical location.

    NASA Astrophysics Data System (ADS)

    Rakoto, V.; Astafyeva, E.; Lognonne, P. H.

    2017-12-01

    It is known that natural hazard events, such as earthquakes, tsunamis, volcano eruptions, etc. can generate atmospheric/ionospheric perturbations. During earthquakes, vertical displacements of the ground or of the ocean floor generate acoustic-gravity waves that further propagate upward in the upper atmosphere and ionosphere. In turn, tsunamis propagating in the open sea, generate gravity waves which propagate obliquely and reach the ionosphere in 45-60 min. The properties of the atmospheric "channel" in the vertical and oblique propagation depend on a variety of factors such as solar and geomagnetic conditions, latitude, local time, season, and their influence on propagation and properties of co-seismic and co-tsunamic perturbations is not well understood yet. In this work, we use present a detailed study of the coupling efficiency between solid earth, ocean and atmosphere. For this purpose, we use the normal mode technique extended to the whole solid Earth-ocean-atmosphere system. In our study, we focus on the Rayleigh modes (solid modes) and tsunami modes (oceanic modes). As the normal modes amplitude are also depending on the spatial and temporal variation of the structure of the atmosphere, we also performed a sensitivity study location of the normal modes amplitude with local time and geographical position.

  5. Optimization of electrothermal atomization parameters for simultaneous multielement atomic absorption spectrometry

    USGS Publications Warehouse

    Harnly, J.M.; Kane, J.S.

    1984-01-01

    The effect of the acid matrix, the measurement mode (height or area), the atomizer surface (unpyrolyzed and pyrolyzed graphite), the atomization mode (from the wall or from a platform), and the atomization temperature on the simultaneous electrothermal atomization of Co, Cr, Cu, Fe, Mn, Mo, Ni, V, and Zn was examined. The 5% HNO3 matrix gave rise to severe irreproducibility using a pyrolyzed tube unless the tube was properly "prepared". The 5% HCl matrix did not exhibit this problem, and no problems were observed with either matrix using an unpyrolized tube or a pyrolyzed platform. The 5% HCl matrix gave better sensitivities with a pyrolyzed tube but the two matrices were comparable for atomization from a platform. If Mo and V are to be analyzed with the other seven elements, a high atomization temperature (2700??C or greater) is necessary regardless of the matrix, the measurement mode, the atomization mode, or the atomizer surface. Simultaneous detection limits (peak height with pyrolyzed tube atomization) were comparable to those of conventional atomic absorption spectrometry using electrothermal atomization above 280 nm. Accuracies and precisions of ??10-15% were found in the 10 to 120 ng mL-1 range for the analysis of NBS acidified water standards.

  6. Phase-synchroniser based on gm-C all-pass filter chain with sliding mode control

    NASA Astrophysics Data System (ADS)

    Mitić, Darko B.; Jovanović, Goran S.; Stojčev, Mile K.; Antić, Dragan S.

    2015-03-01

    Phase-synchronisers have many applications in VLSI circuit designs. They are used in CMOS RF circuits including phase (de)modulators, phase recovery circuits, multiphase synthesis, etc. In this article, a phase-synchroniser based on gm-C all-pass filter chain with sliding mode control is presented. The filter chain provides good controllable delay characteristics over the full range of phase and frequency regulation, without deterioration of input signal amplitude and waveform, while the sliding mode control enables us to achieve fast and predetermined finite locking time. IHP 0.25 µm SiGe BiCMOS technology has been used in design and verification processes. The circuit operates in the frequency range from 33 MHz up to 150 MHz. Simulation results indicate that it is possible to achieve very fast synchronisation time period, which is approximately four time intervals of the input signal during normal operation, and 20 time intervals during power-on.

  7. Quantized edge modes in atomic-scale point contacts in graphene

    NASA Astrophysics Data System (ADS)

    Kinikar, Amogh; Phanindra Sai, T.; Bhattacharyya, Semonti; Agarwala, Adhip; Biswas, Tathagata; Sarker, Sanjoy K.; Krishnamurthy, H. R.; Jain, Manish; Shenoy, Vijay B.; Ghosh, Arindam

    2017-07-01

    The zigzag edges of single- or few-layer graphene are perfect one-dimensional conductors owing to a set of gapless states that are topologically protected against backscattering. Direct experimental evidence of these states has been limited so far to their local thermodynamic and magnetic properties, determined by the competing effects of edge topology and electron-electron interaction. However, experimental signatures of edge-bound electrical conduction have remained elusive, primarily due to the lack of graphitic nanostructures with low structural and/or chemical edge disorder. Here, we report the experimental detection of edge-mode electrical transport in suspended atomic-scale constrictions of single and multilayer graphene created during nanomechanical exfoliation of highly oriented pyrolytic graphite. The edge-mode transport leads to the observed quantization of conductance close to multiples of G0 = 2e2/h. At the same time, conductance plateaux at G0/2 and a split zero-bias anomaly in non-equilibrium transport suggest conduction via spin-polarized states in the presence of an electron-electron interaction.

  8. Quantized edge modes in atomic-scale point contacts in graphene.

    PubMed

    Kinikar, Amogh; Phanindra Sai, T; Bhattacharyya, Semonti; Agarwala, Adhip; Biswas, Tathagata; Sarker, Sanjoy K; Krishnamurthy, H R; Jain, Manish; Shenoy, Vijay B; Ghosh, Arindam

    2017-07-01

    The zigzag edges of single- or few-layer graphene are perfect one-dimensional conductors owing to a set of gapless states that are topologically protected against backscattering. Direct experimental evidence of these states has been limited so far to their local thermodynamic and magnetic properties, determined by the competing effects of edge topology and electron-electron interaction. However, experimental signatures of edge-bound electrical conduction have remained elusive, primarily due to the lack of graphitic nanostructures with low structural and/or chemical edge disorder. Here, we report the experimental detection of edge-mode electrical transport in suspended atomic-scale constrictions of single and multilayer graphene created during nanomechanical exfoliation of highly oriented pyrolytic graphite. The edge-mode transport leads to the observed quantization of conductance close to multiples of G 0  = 2e 2 /h. At the same time, conductance plateaux at G 0 /2 and a split zero-bias anomaly in non-equilibrium transport suggest conduction via spin-polarized states in the presence of an electron-electron interaction.

  9. On the identification of normal modes of oscillation from observations of the solar periphery

    NASA Technical Reports Server (NTRS)

    Gough, D. O.; Latour, J.

    1984-01-01

    The decomposition of solar oscillations into their constituent normal modes requires a knowledge of both the spatial and temporal variation of the perturbation to the sun's surface. The task can be especially difficult when only limited spatial information is available. Observations of the limb-darkening function, for example, are probably sensitive to too large a number of modes to permit most of the modes to be identified in a power spectrum of measurements at only a few points on the limb, unless the results are combined with other data. In this paper a procedure is considered by which the contributions from quite small groups of modes to spatially well resolved data obtained at any instant can be extracted from the remaining modes. Combining these results with frequency information then permits the modes to be identified, at least if their frequencies are low enough to ensure that modes of high degree do not contribute substantially to the signal.

  10. On the identification of normal modes of oscillation from observations of the solar periphery

    NASA Technical Reports Server (NTRS)

    Gough, D. D.; Latour, J.

    1984-01-01

    The decomposition of solar oscillations into their constituent normal modes requires a knowledge of both the spatial and temporal variation of the perturbation to the Sun's surface. The task is especially difficult when only limited spatial information is available. Observations of the limb darkening function, for example, are probably sensitive to too large a number of modes to permit most of the modes to be identified in a power spectrum of measurements at only a few points on the limb, unless the results are combined with other data. A procedure was considered by which the contributions from quite small groups of modes to spatially well resolved data obtained at any instant can be extracted from the remaining modes. Combining these results with frequency information then permits the modes to be identified, at least if their frequencies are low enough to ensure that modes of high degree do not contribute substantially to the signal.

  11. Learning about Modes in Atomic Force Microscopy by Means of Hands-On Activities Based on a Simple Apparatus

    ERIC Educational Resources Information Center

    Phuapaiboon, Unchada; Panijpan, Bhinyo; Osotchan, Tanakorn

    2009-01-01

    This study was conducted to examine the results of using a low-cost hands-on setup in combination with accompanying activities to promote understanding of the contact mode of atomic force microscopy (AFM). This contact mode setup enabled learners to study how AFM works by hand scanning using probing cantilevers with different characteristics on…

  12. Comparison of the quantitative analysis performance between pulsed voltage atom probe and pulsed laser atom probe.

    PubMed

    Takahashi, J; Kawakami, K; Raabe, D

    2017-04-01

    The difference in quantitative analysis performance between the voltage-mode and laser-mode of a local electrode atom probe (LEAP3000X HR) was investigated using a Fe-Cu binary model alloy. Solute copper atoms in ferritic iron preferentially field evaporate because of their significantly lower evaporation field than the matrix iron, and thus, the apparent concentration of solute copper tends to be lower than the actual concentration. However, in voltage-mode, the apparent concentration was higher than the actual concentration at 40K or less due to a detection loss of matrix iron, and the concentration decreased with increasing specimen temperature due to the preferential evaporation of solute copper. On the other hand, in laser-mode, the apparent concentration never exceeded the actual concentration, even at lower temperatures (20K), and this mode showed better quantitative performance over a wide range of specimen temperatures. These results indicate that the pulsed laser atom probe prevents both detection loss and preferential evaporation under a wide range of measurement conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Atmospheric Excitation of Planetary Normal Modes

    NASA Technical Reports Server (NTRS)

    Tanimoto, Toshiro

    2001-01-01

    The objectives of this study were to: (1) understand the phenomenon of continuous free oscillations of the Earth and (2) examine the idea of using this phenomenon for planetary seismology. We first describe the results on (1) and present our evaluations of the idea (2) in the final section. In 1997, after almost forty years since the initial attempt by Benioff et al, continuous free oscillations of the Earth were discovered. Spheroidal fundamental modes between 2 and 7 millihertz are excited continuously with acceleration amplitudes of about 0.3-0.5 nanogals. The signal is now commonly found in virtually all data recorded by STS-1 type broadband seismometers at quiet sites. Seasonal variation in amplitude and the existence of two coupled modes between the atmosphere and the solid Earth support that these oscillations are excited by the atmosphere. Stochastic excitation due to atmospheric turbulence is a favored mechanism, providing a good match between theory and data. The atmosphere has ample energy to support this theory because excitation of these modes require only 500-10000 W whereas the atmosphere contains about 117 W of kinetic energy. An application of this phenomenon includes planetary seismology, because other planets may be oscillating due to atmospheric excitation. The interior structure of planets could be learned by determining the eigenfrequencies in the continuous free oscillations. It is especially attractive to pursue this idea for tectonically quiet planets, since quakes may be too infrequent to be recorded by seismic instruments.

  14. Passive microrheology of normal and cancer cells after ML7 treatment by atomic force microscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lyapunova, Elena, E-mail: lyapunova@icmm.ru; Ural Federal University, Kuibyishev Str. 48, Ekaterinburg, 620000; Nikituk, Alexander, E-mail: nas@icmm.ru

    Mechanical properties of living cancer and normal thyroidal cells were investigated by atomic force microscopy (AFM). Cell mechanics was compared before and after treatment with ML7, which is known to reduce myosin activity and induce softening of cell structures. We recorded force curves with extended dwell time of 6 seconds in contact at maximum forces from 500 pN to 1 nN. Data were analyzed within different frameworks: Hertz fit was applied in order to evaluate differences in Young’s moduli among cell types and conditions, while the fluctuations of the cantilever in contact with cells were analyzed with both conventional algorithmsmore » (probability density function and power spectral density) and multifractal detrended fluctuation analysis (MF-DFA). We found that cancer cells were softer than normal cells and ML7 had a substantial softening effect on normal cells, but only a marginal one on cancer cells. Moreover, we observed that all recorded signals for normal and cancer cells were monofractal with small differences between their scaling parameters. Finally, the applicability of wavelet-based methods of data analysis for the discrimination of different cell types is discussed.« less

  15. A haptic model of vibration modes in spherical geometry and its application in atomic physics, nuclear physics and beyond

    NASA Astrophysics Data System (ADS)

    Ubben, Malte; Heusler, Stefan

    2018-07-01

    Vibration modes in spherical geometry can be classified based on the number and position of nodal planes. However, the geometry of these planes is non-trivial and cannot be easily displayed in two dimensions. We present 3D-printed models of those vibration modes, enabling a haptic approach for understanding essential features of bound states in quantum physics and beyond. In particular, when applied to atomic physics, atomic orbitals are obtained in a natural manner. Applied to nuclear physics, the same patterns of vibration modes emerge as cornerstone for the nuclear shell model. These applications of the very same model in a range of more than 5 orders of magnitude in length scales leads to a general discussion of the applicability and limits of validity of physical models in general.

  16. Combined inelastic neutron scattering and solid state DFT study of dynamics of hydrogen atoms in trioctahedral 1M phlogopite

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smrčok, Ľubomír; Kolesnikov, Alexander I; Rieder, Milan

    2012-01-01

    Inelastic neutron scattering (INS) was used to study vibrational dynamics of the hydrogen atoms in natural trioctahedral phlogopite, K0.93Na0.03(Mg2.47Fe0.22Al0.16Fe0.04Tl0.06)[Si2.84Al1.16]O10OH1.71F0.28Cl0.01, within the 50-1000 cm-1 energy range. The INS spectra collected using direct geometry spectrometer SEQUOIA at ORNL were interpreted by means of the solid-state DFT calculations covering both normal mode analysis and molecular dynamics. To optimize the structure and to calculate the vibrational modes under harmonic approximation both a hybrid PBE0 and the AM05 functional were used, while the molecular dynamics calculations (60ps/1fs) were performed only with the computationally less-demanding AM05 functional. The main contributions to the dominant band within ~750-550more » cm-1 are symmetric and antisymmetric Mg-O-H bending modes, overlapping with the skeletal stretching and bending modes causing weaker secondary movements of H atoms of inner hydroxyl groups. Signatures of the Mg-O-H bending modes appear down to ~400 cm-1, where a region of octahedra deformation modes starts. These deformations cause just shallow movements of the hydrogen atoms and are mirrored by the modes with close vibrational energies. The region from ~330 cm-1 down to the low energy end of the spectrum portrays induced vibrations of the H atoms caused by deformation of individual polyhedra, translational vibrations of the parts of the 2:1 layer relative one to another, and librational and translational vibrations of the layer. The main difference between the INS spectrum of dioctahedral Al-muscovite and trioctahedral Mg-phlogopite is that the Mg-O-H modes are all assigned to in-plane vibrations of the respective hydrogen atoms.« less

  17. Combined inelastic neutron scattering and solid-state DFT study of dynamics of hydrogen atoms in trioctahedral 1 M phlogopite

    NASA Astrophysics Data System (ADS)

    Smrčok, L'ubomír; Kolesnikov, Alexander I.; Rieder, Milan

    2012-10-01

    Inelastic neutron scattering (INS) was used to study the vibrational dynamics of the hydrogen atoms in natural trioctahedral phlogopite, K0.93Na0.03(Mg2.47Fe0.22Al0.16Fe0.04Tl0.06)[Si2.84Al1.16]O10OH1.71F0.28Cl0.01, within the 50-1,000 cm-1 energy range. The INS spectra collected using direct geometry spectrometer SEQUOIA (ORNL) were interpreted by means of the solid-state DFT calculations covering both normal mode analysis and molecular dynamics. To optimize the structure and to calculate the vibrational modes under harmonic approximation, both a hybrid PBE0 and the AM05 functional were used, while the molecular dynamics calculations (60 ps/1 fs) were performed only with the computationally less-demanding AM05 functional. The main contributions to the dominant band within ~750-550 cm-1 are symmetric and antisymmetric Mg-O-H bending modes, overlapping with the skeletal stretching and bending modes causing weaker secondary movements of H atoms of inner hydroxyl groups. Signatures of the Mg-O-H bending modes appear down to ~400 cm-1, where a region of octahedra deformation modes starts. These deformations cause just shallow movements of the hydrogen atoms and are mirrored by the modes with close vibrational energies. The region from ~330 cm-1 down to the low-energy end of the spectrum portrays induced vibrations of the H atoms caused by deformation of individual polyhedra, translational vibrations of the parts of the 2:1 layer relative one to another, and librational and translational vibrations of the layer. The main difference between the INS spectrum of dioctahedral Al-muscovite and trioctahedral Mg-phlogopite is that the Mg-O-H modes are all assigned to in-plane vibrations of the respective hydrogen atoms.

  18. Controllable optical bistability in a three-mode optomechanical system with atom-cavity-mirror couplings

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Wang, Xiao-Fang; Yan, Jia-Kai; Zhu, Xiao-Fei; Jiang, Cheng

    2018-01-01

    We theoretically investigate the optical bistable behavior in a three-mode optomechanical system with atom-cavity-mirror couplings. The effects of the cavity-pump detuning and the pump power on the bistable behavior are discussed detailedly, the impacts of the atom-pump detuning and the atom-cavity coupling strength on the bistability of the system are also explored, and the influences of the cavity-resonator coupling strength and the cavity decay rate are also taken into consideration. The numerical results demonstrate that by tuning these parameters the bistable behavior of the system can be freely switched on or off, and the threshold of the pump power for the bistability as well as the bistable region width can also be effectively controlled. These results can find potential applications in optical bistable switch in the quantum information processing.

  19. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    PubMed

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  20. Search for Long Period Solar Normal Modes in Ambient Seismic Noise

    NASA Astrophysics Data System (ADS)

    Caton, R.; Pavlis, G. L.

    2016-12-01

    We search for evidence of solar free oscillations (normal modes) in long period seismic data through multitaper spectral analysis of array stacks. This analysis is similar to that of Thomson & Vernon (2015), who used data from the most quiet single stations of the global seismic network. Our approach is to use stacks of large arrays of noisier stations to reduce noise. Arrays have the added advantage of permitting the use of nonparametic statistics (jackknife errors) to provide objective error estimates. We used data from the Transportable Array, the broadband borehole array at Pinyon Flat, and the 3D broadband array in Homestake Mine in Lead, SD. The Homestake Mine array has 15 STS-2 sensors deployed in the mine that are extremely quiet at long periods due to stable temperatures and stable piers anchored to hard rock. The length of time series used ranged from 50 days to 85 days. We processed the data by low-pass filtering with a corner frequency of 10 mHz, followed by an autoregressive prewhitening filter and median stack. We elected to use the median instead of the mean in order to get a more robust stack. We then used G. Prieto's mtspec library to compute multitaper spectrum estimates on the data. We produce delete-one jackknife error estimates of the uncertainty at each frequency by computing median stacks of all data with one station removed. The results from the TA data show tentative evidence for several lines between 290 μHz and 400 μHz, including a recurring line near 379 μHz. This 379 μHz line is near the Earth mode 0T2 and the solar mode 5g5, suggesting that 5g5 could be coupling into the Earth mode. Current results suggest more statistically significant lines may be present in Pinyon Flat data, but additional processing of the data is underway to confirm this observation.

  1. Comments on compressible effects on Alfven normal modes in nonuniform plasmas

    NASA Technical Reports Server (NTRS)

    Mok, Y.; Einaudi, G.

    1990-01-01

    The paper discusses the regime of validity of the theory of dissipative Alfven normal modes presented by Mok and Einaudi (1985) and Einaudi and Mok (1985), which was based on the incompressible closure of the system of ideal MHD equations. Some simple extensions of the earlier results to the compressible case are described. In addition, certain misunderstandings of this work, which have appeared in other papers, are clarified.

  2. Toward single mode, atomic size electron vortex beams.

    PubMed

    Krivanek, Ondrej L; Rusz, Jan; Idrobo, Juan-Carlos; Lovejoy, Tracy J; Dellby, Niklas

    2014-06-01

    We propose a practical method of producing a single mode electron vortex beam suitable for use in a scanning transmission electron microscope (STEM). The method involves using a holographic "fork" aperture to produce a row of beams of different orbital angular momenta, as is now well established, magnifying the row so that neighboring beams are separated by about 1 µm, selecting the desired beam with a narrow slit, and demagnifying the selected beam down to 1-2 Å in size. We show that the method can be implemented by adding two condenser lenses plus a selection slit to a straight-column cold-field emission STEM. It can also be carried out in an existing instrument, the monochromated Nion high-energy-resolution monochromated electron energy-loss spectroscopy-STEM, by using its monochromator in a novel way. We estimate that atom-sized vortex beams with ≥ 20 pA of current should be attainable at 100-200 keV in either instrument.

  3. NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

    PubMed

    Krüger, Dennis M; Ahmed, Aqeel; Gohlke, Holger

    2012-07-01

    The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. On a data set of proteins with experimentally observed conformational changes, the NMSim approach has been shown to be a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or more sophisticated sampling techniques. The web server output is a trajectory of generated conformations, Jmol representations of the coarse-graining and a subset of the trajectory and data plots of structural analyses. The NMSim webserver, accessible at http://www.nmsim.de, is free and open to all users with no login requirement.

  4. Dynamic evolution of double Λ five-level atom interacting with one-mode electromagnetic cavity field

    NASA Astrophysics Data System (ADS)

    Abdel-Wahab, N. H.; Salah, Ahmed

    2017-12-01

    In this paper, the model describing a double Λ five-level atom interacting with a single mode electromagnetic cavity field in the (off) non-resonate case is studied. We obtained the constants of motion for the considered model. Also, the state vector of the wave function is given by using the Schrödinger equation when the atom is initially prepared in its excited state. The dynamical evolutions for the collapse revivals, the antibunching of photons and the field squeezing phenomena are investigated when the field is considered in a coherent state. The influence of detuning parameters on these phenomena is investigated. We noticed that the atom-field properties are influenced by changing the detuning parameters. The investigation of these aspects by numerical simulations is carried out using the Quantum Toolbox in Python (QuTip).

  5. High-latitude filtering in a global grid-point model using model normal modes. [Fourier filters for synoptic weather forecasting

    NASA Technical Reports Server (NTRS)

    Takacs, L. L.; Kalnay, E.; Navon, I. M.

    1985-01-01

    A normal modes expansion technique is applied to perform high latitude filtering in the GLAS fourth order global shallow water model with orography. The maximum permissible time step in the solution code is controlled by the frequency of the fastest propagating mode, which can be a gravity wave. Numerical methods are defined for filtering the data to identify the number of gravity modes to be included in the computations in order to obtain the appropriate zonal wavenumbers. The performances of the model with and without the filter, and with a time tendency and a prognostic field filter are tested with simulations of the Northern Hemisphere winter. The normal modes expansion technique is shown to leave the Rossby modes intact and permit 3-5 day predictions, a range not possible with the other high-latitude filters.

  6. Density and spin modes in imbalanced normal Fermi gases from collisionless to hydrodynamic regime

    NASA Astrophysics Data System (ADS)

    Narushima, Masato; Watabe, Shohei; Nikuni, Tetsuro

    2018-03-01

    We study the mass- and population-imbalance effect on density (in-phase) and spin (out-of-phase) collective modes in a two-component normal Fermi gas. By calculating the eigenmodes of the linearized Boltzmann equation as well as the density/spin dynamic structure factor, we show that mass- and population-imbalance effects offer a variety of collective mode crossover behaviors from collisionless to hydrodynamic regimes. The mass-imbalance effect shifts the crossover regime to the higher-temperature, and a significant peak of the spin dynamic structure factor emerges only in the collisionless regime. This is in contrast to the case of mass- and population-balanced normal Fermi gases, where the spin dynamic response is always absent. Although the population-imbalance effect does not shift the crossover regime, the spin dynamic structure factor survives both in the collisionless and hydrodynamic regimes.

  7. Non-local electron transport through normal and topological ladder-like atomic systems

    NASA Astrophysics Data System (ADS)

    Kurzyna, Marcin; Kwapiński, Tomasz

    2018-05-01

    We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

  8. [Raman, FTIR spectra and normal mode analysis of acetanilide].

    PubMed

    Liang, Hui-Qin; Tao, Ya-Ping; Han, Li-Gang; Han, Yun-Xia; Mo, Yu-Jun

    2012-10-01

    The Raman and FTIR spectra of acetanilide (ACN) were measured experimentally in the regions of 3 500-50 and 3 500-600 cm(-1) respectively. The equilibrium geometry and vibration frequencies of ACN were calculated based on density functional theory (DFT) method (B3LYP/6-311G(d, p)). The results showed that the theoretical calculation of molecular structure parameters are in good agreement with previous report and better than the ones calculated based on 6-31G(d), and the calculated frequencies agree well with the experimental ones. Potential energy distribution of each frequency was worked out by normal mode analysis, and based on this, a detailed and accurate vibration frequency assignment of ACN was obtained.

  9. All-fiber mode converter based on superimposed long period fiber gratings

    NASA Astrophysics Data System (ADS)

    Xue, Yan-ru; Bi, Wei-hong; Jin, Wa; Tian, Peng-fei; Jiang, Peng; Liu, Qiang; Jin, Yun

    2018-03-01

    In this paper, a novel broadband all-fiber mode converter is proposed and experimentally demonstrated. Through writing a pair of superimposed long period fiber gratings (SLPFGs) in tow-mode fiber (TMF) with a CO2 laser, the mode converter can realize the conversion from LP01 to LP11 owing to the phase matching condition. Numerical and experimental results show that the bandwidth of this mode converter is 3 times broader than that of a single grating converter. The converter has low loss, high coupling efficiency, small size and is easy to fabricate, so it can be widely used in mode-division multiplexing.

  10. Possibility of observation of polaron normal modes at the far-infrared spectrum of acetanilide and related organics

    NASA Astrophysics Data System (ADS)

    Kalosakas, G.; Aubry, S.; Tsironis, G. P.

    1998-10-01

    We use a stationary and normal mode analysis of the semiclassical Holstein model in order to connect the low-frequency linear polaron modes to low-lying far-infrared lines of the acetanilide spectrum and through parameter fitting we comment on the validity of the polaron results in this system.

  11. Normal Mode Derived Models of the Physical Properties of Earth's Outer Core

    NASA Astrophysics Data System (ADS)

    Irving, J. C. E.; Cottaar, S.; Lekic, V.; Wu, W.

    2017-12-01

    Earth's outer core, the largest reservoir of metal in our planet, is comprised of an iron alloy of an uncertain composition. Its dynamical behaviour is responsible for the generation of Earth's magnetic field, with convection driven both by thermal and chemical buoyancy fluxes. Existing models of the seismic velocity and density of the outer core exhibit some variation, and there are only a small number of models which aim to represent the outer core's density.It is therefore important that we develop a better understanding of the physical properties of the outer core. Though most of the outer core is likely to be well mixed, it is possible that the uppermost outer core is stably stratified: it may be enriched in light elements released during the growth of the solid, iron enriched, inner core; by elements dissolved from the mantle into the outer core; or by exsolution of compounds previously dissolved in the liquid metal which will eventually be swept into the mantle. The stratified layer may host MAC or Rossby waves and it could impede communication between the chemically differentiated mantle and outer core, including screening out some of the geodynamo's signal. We use normal mode center frequencies to estimate the physical properties of the outer core in a Bayesian framework. We estimate the mineral physical parameters needed to best produce velocity and density models of the outer core which are consistent with the normal mode observations. We require that our models satisfy realistic physical constraints. We create models of the outer core with and without a distinct uppermost layer and assess the importance of this region.Our normal mode-derived models are compared with observations of body waves which travel through the outer core. In particular, we consider SmKS waves which are especially sensitive to the uppermost outer core and are therefore an important way to understand the robustness of our models.

  12. High-power, cladding-pumped all-fiber laser with selective transverse mode generation property.

    PubMed

    Li, Lei; Wang, Meng; Liu, Tong; Leng, Jinyong; Zhou, Pu; Chen, Jinbao

    2017-06-10

    We demonstrate, to the best of our knowledge, the first cladding-pumped all-fiber oscillator configuration with selective transverse mode generation based on a mode-selective fiber Bragg grating pair. Operating in the second-order (LP 11 ) mode, maximum output power of 4.2 W is obtained with slope efficiency of about 38%. This is the highest reported output power of single higher-order transverse mode generation in an all-fiber configuration. The intensity distribution profile and spectral evolution have also been investigated in this paper. Our work suggests the potential of realizing higher power with selective transverse mode operation based on a mode-selective fiber Bragg grating pair.

  13. Black phosphorus as a saturable absorber for generating mode-locked fiber laser in normal dispersion regime

    NASA Astrophysics Data System (ADS)

    Latiff, A. A.; Rusdi, M. F. M.; Hisyam, M. B.; Ahmad, H.; Harun, S. W.

    2016-11-01

    This paper reports a few-layer black phosphorus (BP) as a saturable absorber (SA) or phase-locker in generating modelocked pulses from a double-clad ytterbium-doped fiber laser (YDFL). We mechanically exfoliated the BP flakes from BP crystal through a scotch tape, and repeatedly press until the flakes thin and spread homogenously. Then, a piece of BP tape was inserted in the cavity between two fiber connectors end facet. Under 810 mW to 1320 mW pump power, stable mode-locked operation at 1085 nm with a repetition rate of 13.4 MHz is successfully achieved in normal dispersion regime. Before mode-locked operation disappears above maximum pump, the output power and pulse energy is about 80 mW and 6 nJ, respectively. This mode-locked laser produces peak power of 0.74 kW. Our work may validates BP SA as a phase-locker related to two-dimensional nanomaterials and pulsed generation in normal dispersion regime.

  14. Lattice vibration modes in type-II superlattice InAs/GaSb with no-common-atom interface and overlapping vibration spectra

    NASA Astrophysics Data System (ADS)

    Liu, Henan; Yue, Naili; Zhang, Yong; Qiao, Pengfei; Zuo, Daniel; Kesler, Ben; Chuang, Shun Lien; Ryou, Jae-Hyun; Justice, James D.; Dupuis, Russell

    2015-06-01

    Heterostructures like InAs /GaSb superlattices (SLs) are distinctly different from well-studied ones like GaAs /AlAs SLs in terms of band alignment, common interface atom, and phonon spectrum overlapping of the constituents, which manifests as stark differences in their electronic and vibrational properties. This paper reports a comprehensive examination of all four types of phonon modes (confined, quasiconfined, extended, and interface) that have long been predicted for the InAs /GaSb SL, with the observation and interpretation of a set of phonon modes by performing cleaved edge μ -Raman study with polarization analysis. Furthermore, we show a signature of symmetry reduction from D2 d for GaAs /AlAs SL to C2 v for InAs/GaSb SL revealed as a phonon-polariton effect.

  15. Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions

    NASA Astrophysics Data System (ADS)

    Thompson, Michael C.; Baraban, Joshua H.; Matthews, Devin A.; Stanton, John F.; Weber, J. Mathias

    2015-06-01

    We report infrared spectra of nitromethane anion, CH3NO2-, in the region 700-2150 cm-1, obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

  16. Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions.

    PubMed

    Thompson, Michael C; Baraban, Joshua H; Matthews, Devin A; Stanton, John F; Weber, J Mathias

    2015-06-21

    We report infrared spectra of nitromethane anion, CH3NO2 (-), in the region 700-2150 cm(-1), obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

  17. On the mode-coupling treatment of collective density fluctuations for quantum liquids: para-hydrogen and normal liquid helium.

    PubMed

    Kletenik-Edelman, Orly; Reichman, David R; Rabani, Eran

    2011-01-28

    A novel quantum mode coupling theory combined with a kinetic approach is developed for the description of collective density fluctuations in quantum liquids characterized by Boltzmann statistics. Three mode-coupling approximations are presented and applied to study the dynamic response of para-hydrogen near the triple point and normal liquid helium above the λ-transition. The theory is compared with experimental results and to the exact imaginary time data generated by path integral Monte Carlo simulations. While for liquid para-hydrogen the combination of kinetic and quantum mode-coupling theory provides semi-quantitative results for both short and long time dynamics, it fails for normal liquid helium. A discussion of this failure based on the ideal gas limit is presented.

  18. Mode synthesizing atomic force microscopy and mode-synthesizing sensing

    DOEpatents

    Passian, Ali; Thundat, Thomas George; Tetard, Laurene

    2013-05-17

    A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

  19. Mode-synthesizing atomic force microscopy and mode-synthesizing sensing

    DOEpatents

    Passain, Ali; Thundat, Thomas George; Tetard, Laurene

    2014-07-22

    A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

  20. Large-mode-area single-mode-output Neodymium-doped silicate glass all-solid photonic crystal fiber

    PubMed Central

    Li, Wentao; Chen, Danping; Qinling, Zhou; Hu, Lili

    2015-01-01

    We have demonstrated a 45 μm core diameter Neodymium-doped all-solid silicate glass photonic crystal fiber laser with a single mode laser output. The structure parameters and modes information of the fiber are both demonstrated by theoretical calculations using Finite Difference Time Domain (FDTD) method and experimental measurements. Maximum 0.8 W output power limited by launched pump power has been generated in 1064 nm with laser beam quality factor M2 1.18. PMID:26205850

  1. An approach to detect afterslips in giant earthquakes in the normal-mode frequency band

    NASA Astrophysics Data System (ADS)

    Tanimoto, Toshiro; Ji, Chen; Igarashi, Mitsutsugu

    2012-08-01

    An approach to detect afterslips in the source process of giant earthquakes is presented in the normal-mode frequency band (0.3-2.0 mHz). The method is designed to avoid a potential systematic bias problem in the determination of earthquake moment by a typical normal-mode approach. The source of bias is the uncertainties in Q (modal attenuation parameter) which varies by up to about ±10 per cent among published studies. A choice of Q values within this range affects amplitudes in synthetic seismograms significantly if a long time-series of about 5-7 d is used for analysis. We present an alternative time-domain approach that can reduce this problem by focusing on a shorter time span with a length of about 1 d. Application of this technique to four recent giant earthquakes is presented: (1) the Tohoku, Japan, earthquake of 2011 March 11, (2) the 2010 Maule, Chile earthquake, (3) the 2004 Sumatra-Andaman earthquake and (4) the Solomon earthquake of 2007 April 1. The Global Centroid Moment Tensor (GCMT) solution for the Tohoku earthquake explains the normal-mode frequency band quite well. The analysis for the 2010 Chile earthquake indicates that the moment is about 7-10 per cent higher than the moment determined by its GCMT solution but further analysis shows that there is little evidence of afterslip; the deviation in moment can be explained by an increase of the dip angle from 18° in the GCMT solution to 19°. This may be a simple trade-off problem between the moment and dip angle but it may also be due to a deeper centroid in the normal-mode frequency band data, as a deeper source could have steeper dip angle due to changes in geometry of the Benioff zone. For the 2004 Sumatra-Andaman earthquake, the five point-source solution by Tsai et al. explains most of the signals but a sixth point-source with long duration improves the fit to the normal-mode frequency band data. The 2007 Solomon earthquake shows that the high-frequency part of our analysis (above 1 mHz) is

  2. Mode-locking of an InAs Quantum Dot Based Vertical External Cavity Surface Emitting Laser Using Atomic Layer Graphene

    DTIC Science & Technology

    2015-07-16

    SECURITY CLASSIFICATION OF: The InAs quantum dot (QD) grown on GaAs substrates represents a highly performance active region in the 1 - 1.3 µm...2015 Approved for Public Release; Distribution Unlimited Final Report: Mode-locking of an InAs Quantum Dot Based Vertical External Cavity Surface...ABSTRACT Final Report: Mode-locking of an InAs Quantum Dot Based Vertical External Cavity Surface Emitting Laser Using Atomic Layer Graphene Report

  3. AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.

    PubMed

    Greener, Joe G; Sternberg, Michael J E

    2015-10-23

    Despite being hugely important in biological processes, allostery is poorly understood and no universal mechanism has been discovered. Allosteric drugs are a largely unexplored prospect with many potential advantages over orthosteric drugs. Computational methods to predict allosteric sites on proteins are needed to aid the discovery of allosteric drugs, as well as to advance our fundamental understanding of allostery. AlloPred, a novel method to predict allosteric pockets on proteins, was developed. AlloPred uses perturbation of normal modes alongside pocket descriptors in a machine learning approach that ranks the pockets on a protein. AlloPred ranked an allosteric pocket top for 23 out of 40 known allosteric proteins, showing comparable and complementary performance to two existing methods. In 28 of 40 cases an allosteric pocket was ranked first or second. The AlloPred web server, freely available at http://www.sbg.bio.ic.ac.uk/allopred/home, allows visualisation and analysis of predictions. The source code and dataset information are also available from this site. Perturbation of normal modes can enhance our ability to predict allosteric sites on proteins. Computational methods such as AlloPred assist drug discovery efforts by suggesting sites on proteins for further experimental study.

  4. The signal of mantle anisotropy in the coupling of normal modes

    NASA Astrophysics Data System (ADS)

    Beghein, Caroline; Resovsky, Joseph; van der Hilst, Robert D.

    2008-12-01

    We investigate whether the coupling of normal mode (NM) multiplets can help us constrain mantle anisotropy. We first derive explicit expressions of the generalized structure coefficients of coupled modes in terms of elastic coefficients, including the Love parameters describing radial anisotropy and the parameters describing azimuthal anisotropy (Jc, Js, Kc, Ks, Mc, Ms, Bc, Bs, Gc, Gs, Ec, Es, Hc, Hs, Dc and Ds). We detail the selection rules that describe which modes can couple together and which elastic parameters govern their coupling. We then focus on modes of type 0Sl - 0Tl+1 and determine whether they can be used to constrain mantle anisotropy. We show that they are sensitive to six elastic parameters describing azimuthal anisotropy, in addition to the two shear-wave elastic parameters L and N (i.e. VSV and VSH). We find that neither isotropic nor radially anisotropic mantle models can fully explain the observed degree two signal. We show that the NM signal that remains after correction for the effect of the crust and mantle radial anisotropy can be explained by the presence of azimuthal anisotropy in the upper mantle. Although the data favour locating azimuthal anisotropy below 400km, its depth extent and distribution is still not well constrained by the data. Consideration of NM coupling can thus help constrain azimuthal anisotropy in the mantle, but joint analyses with surface-wave phase velocities is needed to reduce the parameter trade-offs and improve our constraints on the individual elastic parameters and the depth location of the azimuthal anisotropy.

  5. Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Thompson, Michael C.; Weber, J. Mathias, E-mail: weberjm@jila.colorado.edu; Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215UCB, Boulder, Colorado 80309-0215

    2015-06-21

    We report infrared spectra of nitromethane anion, CH{sub 3}NO{sub 2}{sup −}, in the region 700–2150 cm{sup −1}, obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

  6. A Free-Energy Approach for All-Atom Protein Simulation

    PubMed Central

    Verma, Abhinav; Wenzel, Wolfgang

    2009-01-01

    All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 Å to the native conformation and an average Z-score of −3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded β-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger ββα motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 Å to their respective experimental conformations. PMID:19413955

  7. A free-energy approach for all-atom protein simulation.

    PubMed

    Verma, Abhinav; Wenzel, Wolfgang

    2009-05-06

    All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 A to the native conformation and an average Z-score of -3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded beta-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger beta beta alpha motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 A to their respective experimental conformations.

  8. Quantum entanglement and position-momentum entropic squeezing of a moving Lambda-type three-level atom interacting with a single-mode quantized field with intensity-dependent coupling

    NASA Astrophysics Data System (ADS)

    Faghihi, M. J.; Tavassoly, M. K.

    2013-07-01

    In this paper, we study the interaction between a moving Λ-type three-level atom and a single-mode cavity field in the presence of intensity-dependent atom-field coupling. After obtaining the state vector of the entire system explicitly, we study the nonclassical features of the system such as quantum entanglement, position-momentum entropic squeezing, quadrature squeezing and sub-Poissonian statistics. According to the obtained numerical results we illustrate that the squeezed period, the duration of entropy squeezing and the maximal squeezing can be controlled by choosing the appropriate nonlinearity function together with entering the atomic motion effect by the suitable selection of the field-mode structure parameter. Also, the atomic motion, as well as the nonlinearity function, leads to the oscillatory behaviour of the degree of entanglement between the atom and field.

  9. Extending Mode Areas of Single-mode All-solid Photonic Bandgap Fibers

    DTIC Science & Technology

    2015-04-02

    T. Tunnermann, R. Iliew, F. Lederer, J. Broeng, G. Vienne, A. Petersson, and C. Jakobsen, “High-power air-clad large-mode-area photonic crystal ...Yvernault, and F. Salin, “Extended single-mode photonic crystal fiber lasers,” Opt. Express 14(7), 2715–2720 (2006). 10. L. Dong, T. Wu, H. McKay, L. Fu...progress in mode area scaling of optical fibers. One notable area is in photonic crystal fibers (PCF) [3–5, 8, 9]. The short straight PCF rods used in

  10. Part of evanescent modes in the normally incident gravity surface wave's energy layout around a submerged obstacle

    NASA Astrophysics Data System (ADS)

    Charland, J.; Rey, V.; Touboul, J.

    2012-04-01

    Part of evanescent modes in the normally incident gravity surface wave's energy layout around a submerged obstacle Jenna Charland *1, Vincent Rey *2, Julien Touboul *2 *1 Mediterraneen Institute of Oceanography. Institut des Sciences de l'Ingénieur Toulon-Var. Avenue Georges Pompidou, BP 56, 83162 La Valette du Var Cedex, France. Centre National de la Recherche Scientifique, Délégation Normandie. Projet soutenu financièrement par la Délégation Générale de l'Armement. *2 Mediterraneen Institute of Oceanography. Institut des Sciences de l'Ingénieur Toulon-Var. Avenue Georges Pompidou, BP 56, 83162 La Valette du Var Cedex, France. During the last decades various studies have been performed to understand the wave propagation over varying bathymetries. Few answers related to this non linear problem were given by the Patarapanich's studies which described the reflection coefficient of a submerged plate as a function of the wavelength. Later Le-Thi-Minh [2] demonstrated the necessity of taking into account the evanescent modes to better describe the propagation of waves over a varying bathymetry. However, all these studies stare at pseudo-stationary state that allows neither the comprehension of the transient behaviour of propagative modes nor the role of the evanescent modes in this unstationnary process. Our study deals with the wave establishment over a submerged plate or step and focuses on the evanescent modes establishment. Rey [3] described the propagation of a normally incident surface gravity wave over a varying topography on the behaviour of the fluid using a linearized potential theory solved by a numerical model using an integral method. This model has a large field of application and has been adapted to our case. This code still solves a stationary problem but allows us to calculate the contribution of the evanescent modes in the energy layout around a submerged plate or a submerged step. The results will show the importance of the trapped energy

  11. Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis

    PubMed Central

    Dorner, Mariah E; McMunn, Ryan D; Bartholow, Thomas G; Calhoon, Brecken E; Conlon, Michelle R; Dulli, Jessica M; Fehling, Samuel C; Fisher, Cody R; Hodgson, Shane W; Keenan, Shawn W; Kruger, Alyssa N; Mabin, Justin W; Mazula, Daniel L; Monte, Christopher A; Olthafer, Augustus; Sexton, Ashley E; Soderholm, Beatrice R; Strom, Alexander M; Hati, Sanchita

    2015-01-01

    Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide-range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of pro are based on the canonical paradigm that attributes proteins' function to their three-dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in Cα atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes. PMID:26130403

  12. Computational modes and the Machenauer N.L.N.M.I. of the GLAS 4th order model. [NonLinear Normal Mode Initialization in numerical weather forecasting

    NASA Technical Reports Server (NTRS)

    Navon, I. M.; Bloom, S.; Takacs, L. L.

    1985-01-01

    An attempt was made to use the GLAS global 4th order shallow water equations to perform a Machenhauer nonlinear normal mode initialization (NLNMI) for the external vertical mode. A new algorithm was defined for identifying and filtering out computational modes which affect the convergence of the Machenhauer iterative procedure. The computational modes and zonal waves were linearly initialized and gravitational modes were nonlinearly initialized. The Machenhauer NLNMI was insensitive to the absence of high zonal wave numbers. The effects of the Machenhauer scheme were evaluated by performing 24 hr integrations with nondissipative and dissipative explicit time integration models. The NLNMI was found to be inferior to the Rasch (1984) pseudo-secant technique for obtaining convergence when the time scales of nonlinear forcing were much smaller than the time scales expected from the natural frequency of the mode.

  13. All-optical wavelength conversion for mode division multiplexed superchannels.

    PubMed

    Gong, Jiaxin; Xu, Jing; Luo, Ming; Li, Xiang; Qiu, Ying; Yang, Qi; Zhang, Xinliang; Yu, Shaohua

    2016-04-18

    We report in this work the first all-optical wavelength conversion (AOWC) of a mode division multiplexed (MDM) superchannel consisting of 2N modes by dividing the superchannel into N single-mode (SM) tributaries, wavelength converting N SM signals using well developed SM-AOWC techniques, and finally combining the N SM tributaries back to an MDM superchannel at the converted wavelength, inspired by the idea of using SM filtering techniques to filter multimode signals in astronomy. The conversions between multimode and SM are realized by 3D laser-writing photonic lanterns and SM-AOWCs are realized based on polarization insensitive four wave mixing (FWM) configuration in N semiconductor optical amplifiers (SOAs). As a proof of concept demonstration, the conversion of a 6-mode MDM superchannel with each mode modulated with orthogonal frequency division multiplexed (OFDM) quadrature phase-shift keying (QPSK)/16 quadrature amplitude modulation (QAM) signals is demonstrated in this work, indicating that the scheme is transparent to data format, polarization and compatible with multi-carrier signals. Data integrity of the converted superchannel has been verified by using coherent detection and digital signal processing (DSP). Bit error rates (BERs) below the forward error correction (FEC) hard limit (3.8 × 10-3) have been obtained for QPSK modulation at a net bitrate of 104.2 Gbit/s and BERs below the soft decision FEC threshold (1.98 × 10-2) have been achieved for 16-QAM format, giving a total aggregate bit rate of 185.8 Gbit/s when taking 20% coding overhead into account. Add and drop functionalities that usually come along with wavelength conversion in flexible network nodes have also been demonstrated. The working conditions of the SOAs, especially the pump and signal power levels, are critical for the quality of the converted signal and have been thoroughly discussed. The impact of imbalanced FWM conversion efficiency among different SM

  14. Identification of nonlinear normal modes of engineering structures under broadband forcing

    NASA Astrophysics Data System (ADS)

    Noël, Jean-Philippe; Renson, L.; Grappasonni, C.; Kerschen, G.

    2016-06-01

    The objective of the present paper is to develop a two-step methodology integrating system identification and numerical continuation for the experimental extraction of nonlinear normal modes (NNMs) under broadband forcing. The first step processes acquired input and output data to derive an experimental state-space model of the structure. The second step converts this state-space model into a model in modal space from which NNMs are computed using shooting and pseudo-arclength continuation. The method is demonstrated using noisy synthetic data simulated on a cantilever beam with a hardening-softening nonlinearity at its free end.

  15. Theory of psychological adaptive modes.

    PubMed

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

    PubMed Central

    Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

    2009-01-01

    Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all-atom distance-dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT-TS score, but decreased the Z-score of the native structure. The attractiveness of potential improved both the correlation and Z-score for template-based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states. PMID:19588493

  17. A Pictorial Visualization of Normal Mode Vibrations of the Fullerene (C[subscript 60]) Molecule in Terms of Vibrations of a Hollow Sphere

    ERIC Educational Resources Information Center

    Dunn, Janette L.

    2010-01-01

    Understanding the normal mode vibrations of a molecule is important in the analysis of vibrational spectra. However, the complicated 3D motion of large molecules can be difficult to interpret. We show how images of normal modes of the fullerene molecule C[subscript 60] can be made easier to understand by superimposing them on images of the normal…

  18. Switchable Q-switched and modelocked operation in ytterbium doped fiber laser under all-normal-dispersion configuration

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mukhopadhyay, Pranb K., E-mail: pkm@rrcat.gov.in; Gupta, Pradeep K.; Singh, Chandra Pal

    2015-03-15

    We have constructed an Yb-doped fiber laser in all-normal-dispersion configuration which can be independently operated in Q-switched or modelocked configuration with the help of a simple fiber optic ring resonator (FORR). In the presence of FORR, the laser operates in Q-switched mode producing stable pulses in the range of 1 μs-200 ns with repetition rate in the range of 45 kHz-82 kHz. On the other hand, the laser can be easily switched to mode-locked operation by disjoining the FORR loop producing train of ultrashort pulses of ∼5 ps duration (compressible to ∼150 fs) at ∼38 MHz repetition rate. The transmissionmore » characteristics of FORR in combination with the nonlinear polarization rotation for passive Q-switching operation is numerically investigated and experimentally verified. The laser can serve as a versatile seed source for power amplifier which can be easily configured for application in the fields that require different pulsed fiber lasers.« less

  19. Coherent all-optical control of ultracold atoms arrays in permanent magnetic traps.

    PubMed

    Abdelrahman, Ahmed; Mukai, Tetsuya; Häffner, Hartmut; Byrnes, Tim

    2014-02-10

    We propose a hybrid architecture for quantum information processing based on magnetically trapped ultracold atoms coupled via optical fields. The ultracold atoms, which can be either Bose-Einstein condensates or ensembles, are trapped in permanent magnetic traps and are placed in microcavities, connected by silica based waveguides on an atom chip structure. At each trapping center, the ultracold atoms form spin coherent states, serving as a quantum memory. An all-optical scheme is used to initialize, measure and perform a universal set of quantum gates on the single and two spin-coherent states where entanglement can be generated addressably between spatially separated trapped ultracold atoms. This allows for universal quantum operations on the spin coherent state quantum memories. We give detailed derivations of the composite cavity system mediated by a silica waveguide as well as the control scheme. Estimates for the necessary experimental conditions for a working hybrid device are given.

  20. Quasi-regenerative mode locking in a compact all-polarisation-maintaining-fibre laser

    NASA Astrophysics Data System (ADS)

    Nyushkov, B. N.; Ivanenko, A. V.; Kobtsev, S. M.; Pivtsov, V. S.; Farnosov, S. A.; Pokasov, P. V.; Korel, I. I.

    2017-12-01

    A novel technique of mode locking in erbium-doped all-polarisation-maintaining-fibre laser has been developed and preliminary investigated. The proposed quasi-regenerative technique combines the advantages of conventional active mode locking (when an intracavity modulator is driven by an independent RF oscillator) and regenerative mode locking (when a modulator is driven by an intermode beat signal from the laser itself). This scheme is based on intracavity intensity modulation driven by an RF oscillator being phase-locked to the actual intermode frequency of the laser. It features also possibilities of operation at multiple frequencies and harmonic mode-locking operation.

  1. Bi-harmonic cantilever design for improved measurement sensitivity in tapping-mode atomic force microscopy.

    PubMed

    Loganathan, Muthukumaran; Bristow, Douglas A

    2014-04-01

    This paper presents a method and cantilever design for improving the mechanical measurement sensitivity in the atomic force microscopy (AFM) tapping mode. The method uses two harmonics in the drive signal to generate a bi-harmonic tapping trajectory. Mathematical analysis demonstrates that the wide-valley bi-harmonic tapping trajectory is as much as 70% more sensitive to changes in the sample topography than the standard single-harmonic trajectory typically used. Although standard AFM cantilevers can be driven in the bi-harmonic tapping trajectory, they require large forcing at the second harmonic. A design is presented for a bi-harmonic cantilever that has a second resonant mode at twice its first resonant mode, thereby capable of generating bi-harmonic trajectories with small forcing signals. Bi-harmonic cantilevers are fabricated by milling a small cantilever on the interior of a standard cantilever probe using a focused ion beam. Bi-harmonic drive signals are derived for standard cantilevers and bi-harmonic cantilevers. Experimental results demonstrate better than 30% improvement in measurement sensitivity using the bi-harmonic cantilever. Images obtained through bi-harmonic tapping exhibit improved sharpness and surface tracking, especially at high scan speeds and low force fields.

  2. Influence of Mixed Mode I-Mode II Loading on Fatigue Delamination Growth Characteristics of a Graphite Epoxy Tape Laminate

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.; Johnston, William M., Jr.

    2014-01-01

    Mixed mode I-mode II interlaminar tests were conducted on IM7/8552 tape laminates using the mixed-mode bending test. Three mixed mode ratios, G(sub II)/G(sub T) = 0.2, 0.5, and 0.8, were considered. Tests were performed at all three mixed-mode ratios under quasi-static and cyclic loading conditions, where the former static tests were used to determine initial loading levels for the latter fatigue tests. Fatigue tests at each mixed-mode ratio were performed at four loading levels, Gmax, equal to 0.5G(sub c), 0.4G(sub c), 0.3G(sub c), and 0.2G(sub c), where G(sub c) is the interlaminar fracture toughness of the corresponding mixed-mode ratio at which a test was performed. All fatigue tests were performed using constant-amplitude load control and delamination growth was automatically documented using compliance solutions obtained from the corresponding quasi-static tests. Static fracture toughness data yielded a mixed-mode delamination criterion that exhibited monotonic increase in Gc with mixed-mode ratio, G(sub II)/G(sub T). Fatigue delamination onset parameters varied monotonically with G(sub II)/G(sub T), which was expected based on the fracture toughness data. Analysis of non-normalized data yielded a monotonic change in Paris law exponent with mode ratio. This was not the case when normalized data were analyzed. Fatigue data normalized by the static R-curve were most affected in specimens tested at G(sub II)/G(sub T)=0.2 (this process has little influence on the other data). In this case, the normalized data yielded a higher delamination growth rate compared to the raw data for a given loading level. Overall, fiber bridging appeared to be the dominant mechanism, affecting delamination growth rates in specimens tested at different load levels and differing mixed-mode ratios.

  3. Normal mode analysis of the IUS/TDRS payload in a payload canister/transporter environment

    NASA Technical Reports Server (NTRS)

    Meyer, K. A.

    1980-01-01

    Special modeling techniques were developed to simulate an accurate mathematical model of the transporter/canister/payload system during ground transport of the Inertial Upper Stage/Tracking and Data Relay Satellite (IUS/TDRS) payload. The three finite element models - the transporter, the canister, and the IUS/TDRS payload - were merged into one model and used along with the NASTRAN normal mode analysis. Deficiencies were found in the NASTRAN program that make a total analysis using modal transient response impractical. It was also discovered that inaccuracies may exist for NASTRAN rigid body modes on large models when Given's method for eigenvalue extraction is employed. The deficiencies as well as recommendations for improving the NASTRAN program are discussed.

  4. Normal co-ordinate analysis of 1, 8-dibromooctane

    NASA Astrophysics Data System (ADS)

    Singh, Devinder; Jaggi, Neena; Singh, Nafa

    2010-02-01

    The organic compound 1,8-dibromooctane (1,8-DBO) exists in liquid phase at ambient temperatures and has versatile synthetic applications. In its liquid phase 1,8-DBO has been expected to exist in four most probable conformations, with all its carbon atoms in the same plane, having symmetries C 2h , C i , C 2 and C 1 . In the present study a detailed vibrational analysis in terms of assignment of Fourier transform infrared (FT-IR) and Raman bands of this molecule using normal co-ordinate calculations has been done. A systematic set of symmetry co-ordinates has been constructed for this molecule and normal co-ordinate analysis is carried out using the computer program MOLVIB. The force-field transferred from already studied lower chain bromo-alkanes is subjected to refinement so as to fit the observed infrared and Raman frequencies with those of calculated ones. The potential energy distribution (PED) has also been calculated for each mode of vibration of the molecule for the assumed conformations.

  5. Quasi-normal modes of holographic system with Weyl correction and momentum dissipation

    NASA Astrophysics Data System (ADS)

    Wu, Jian-Pin; Liu, Peng

    2018-05-01

    We study the charge response in complex frequency plane and the quasi-normal modes (QNMs) of the boundary quantum field theory with momentum dissipation dual to a probe generalized Maxwell system with Weyl correction. When the strength of the momentum dissipation α ˆ is small, the pole structure of the conductivity is similar to the case without the momentum dissipation. The qualitative correspondence between the poles of the real part of the conductivity of the original theory and the ones of its electromagnetic (EM) dual theory approximately holds when γ → - γ with γ being the Weyl coupling parameter. While the strong momentum dissipation alters the pole structure such that most of the poles locate at the purely imaginary axis. At this moment, the correspondence between the poles of the original theory and its EM dual one is violated when γ → - γ. In addition, for the dominant pole, the EM duality almost holds when γ → - γ for all α ˆ except for a small region of α ˆ .

  6. Quantum coherent tractor beam effect for atoms trapped near a nanowaveguide

    PubMed Central

    Sadgrove, Mark; Wimberger, Sandro; Nic Chormaic, Síle

    2016-01-01

    We propose several schemes to realize a tractor beam effect for ultracold atoms in the vicinity of a few-mode nanowaveguide. Atoms trapped near the waveguide are transported in a direction opposite to the guided mode propagation direction. We analyse three specific examples for ultracold 23Na atoms trapped near a specific nanowaveguide (i.e. an optical nanofibre): (i) a conveyor belt-type tractor beam effect, (ii) an accelerator tractor beam effect, and (iii) a quantum coherent tractor beam effect, all of which can effectively pull atoms along the nanofibre toward the light source. This technique provides a new tool for controlling the motion of particles near nanowaveguides with potential applications in the study of particle transport and binding as well as atom interferometry. PMID:27440516

  7. Detecting atmospheric normal modes with periods less than 6 h by barometric observations

    NASA Astrophysics Data System (ADS)

    Ermolenko, S. I.; Shved, G. M.; Jacobi, Ch.

    2018-04-01

    The theory of atmospheric normal modes (ANMs) predicts the existence of relatively short-period gravity-inertia ANMs. Simultaneous observations of surface air-pressure variations by barometers at distant stations of the Global Geodynamics Project network during an interval of 6 months were used to detect individual gravity-inertia ANMs with periods of ∼2-5 h. Evidence was found for five ANMs with a lifetime of ∼10 days. The data of the stations, which are close in both latitude and longitude, were utilized for deriving the phases of the detected ANMs. The phases revealed wave propagation to the west and increase of zonal wavenumbers with frequency. As all the detected gravity-inertia ANMs are westward propagating, they are suggested to be generated due to the breakdown of migrating solar tides and/or large-scale Rossby waves. The existence of an ANM background will complicate the detection of the translational motions of the Earth's inner core.

  8. Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales.

    PubMed

    Huang, Shiping

    2017-11-13

    The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

  9. Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales

    NASA Astrophysics Data System (ADS)

    Huang, Shiping

    2017-11-01

    The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

  10. All-fiber bandpass filter based on asymmetrical modes exciting and coupling

    NASA Astrophysics Data System (ADS)

    Zhang, Qiang; Zhu, Tao; Shi, Leilei; Liu, Min

    2013-01-01

    A low cost all-fiber bandpass filter is demonstrated by fabricating an asymmetric long-period fiber grating (LPFG) in an off-set splicing fiber structure of two single mode fibers in this paper. The main principle of the filter is that the asymmetric LPFG written by single-side CO2 laser irradiation is used to couple the asymmetric cladding modes excited by the offset-coupling of the splicing point between the single mode fiber and the grating, and the left core mode of the splicing point cannot be coupled to the right fiber core, hence the interference effect is avoided. So the bandpass characteristics in the transmission spectrum are achieved. The designed filter exhibits a pass band at a central wavelength of 1565.0 nm with a full-width at half-maximum bandwidth of 12.3 nm.

  11. Generalization of soft phonon modes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rudin, Sven P.

    Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

  12. Generalization of soft phonon modes

    DOE PAGES

    Rudin, Sven P.

    2018-04-27

    Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

  13. Generalization of soft phonon modes

    NASA Astrophysics Data System (ADS)

    Rudin, Sven P.

    2018-04-01

    Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. Here, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system with N atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, PVM0, represents the 3 N -dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, PVM0 serves as a generalization of soft phonon modes. At low temperatures, PVM0 reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case PVM0 culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, PVM0 can be equally well calculated on either side of the structural phase transition. Two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the β phase of uranium, the higher-symmetry structure of which stabilizes with temperature.

  14. All-optical laser spectral narrowing and line fixing at atomic absorption transition by injection competition and gain knock-down techniques

    NASA Astrophysics Data System (ADS)

    Gacheva, Lazarina I.; Deneva, Margarita A.; Kalbanov, Mihail H.; Nenchev, Marin N.

    2008-12-01

    We present two original, all optical techniques, to produce a narrowline laser light, fixed at the frequency of a chosen reference atomic absorption transition. The first type of systems is an essential improvement of our method 3,4 for laser spectral locking using a control by two frequency scanned, competitive injections with disturbed power ratio by the absorption at the reference line. The new development eliminates the narrowing limiting problem, related with the fixed laser longitudinal mode structure. We have proposed an original new technique for continuously tunable single mode laser operation in combination with synchronously and equal continuous tuning of the modes of the amplifier. By adapting the laser differential rate equations, the system is analyzed theoretically in details and is shown its feasibility. The results are in agreement with previous our experiments. The essential advantage, except simplicity of realization, is that the laser line can be of order of magnitude and more narrowed than the absorption linewidth. The second system is based of the laser amplifier arrangement with a gain knock-down from the competitive frequency scanned pulse, except at the wavelength of the desired absorption reference line. The essential advantages of the last system are that the problem of fixing laser mode presence is naturally avoided. The theoretical modeling and the numerical investigations show the peculiarity and advantages of the system proposed. The developed approaches are of interest for applications in spectroscopy, in DIAL monitoring of the atmospheric pollutants, in isotope separation system and potentially - for creation of simple, all optical, frequency standards for optical communications. Also, the continuously tunable single mode laser (and the combination with the simultaneously tunable amplifier) presents itself the interest for many practical applications in spectroscopy, metrology, and holography. We compare the action and the

  15. Time-domain study of acoustic pulse propagation in an ocean waveguide using a new normal mode model

    NASA Astrophysics Data System (ADS)

    Sidorovskaia, Natalia Anatol'evna

    1997-11-01

    This study is focused on issues of numerical modeling of sound propagation in diverse ocean waveguides. A new normal mode acoustical model (Shallow Water Acoustic Mode Propagation-SWAMP) has been developed. The algorithm for obtaining the vertical modal solution is based on a warping matrix transformation of the solution of an isovelocity (reference) waveguide to one of arbitrary velocity profile. An efficient mode coupling scheme with an adaptive step-size in range has been implemented for range-dependent environments. The new algorithm allows fairly arbitrary ocean layering and readily works at high frequency. An important advantage of the new procedure is that vertical modal eigenfunctions can easily be transformed to a spherical representation suitable for coupling in object scattering problems. Benchmarking results of the new code against established acoustic models based on parabolic equation and existing normal mode approaches show good agreement for range-independent and up-slope and down-slope bathymetries and a very competitive calculation speed. Broad-band pulse propagation in deep and shallow water with double (surface and bottom) ducts has been modeled using the new normal mode model for a variety of ocean waveguide parameters and different frequency bands. The surface duct generates a series of the surface-duct-trapped- modes, which form amplitude-modulated precursors in the far field pulse response. It has been found that the arrival times of the precursors could not be explained by the conventional concept of group velocity so that a more general principle based on the rate of energy transfer has been used. The Airy function solution was found to explain the amplitude modulation of the precursors. It has been learned from the numerical simulation that for a range-independent environment the time separation between precursors is fixed and any variations from this have been a result of range-dependence and mode coupling in the model. The time

  16. An instrument for direct observations of seismic and normal-mode rotational oscillations of the Earth

    PubMed Central

    Cowsik, R.

    2007-01-01

    The rotations around the vertical axis associated with the normal mode oscillations of the Earth and those induced by the seismic and other disturbances have been very difficult to observe directly. Such observations will provide additional information for 3D modeling of the Earth and for understanding earthquakes and other underground explosions. In this paper, we describe the design of an instrument capable of measuring the rotational motions associated with the seismic oscillations of the Earth, including the lowest frequency normal mode at ν ≈ 3.7 × 10−4 Hz. The instrument consists of a torsion balance with a natural frequency of ν0 ≈ 1.6 × 10−4 Hz, which is observed by an autocollimating optical lever of high angular resolution and dynamic range. Thermal noise limits the sensitivity of the apparatus to amplitudes of ≈ 1.5 × 10−9 rad at the lowest frequency normal mode and the sensitivity improves as ν−3/2 with increasing frequency. Further improvements in sensitivity by about two orders of magnitude may be achieved by operating the balance at cryogenic temperatures. Alternatively, the instrument can be made more robust with a reduced sensitivity by increasing ν0 to ≈10−2 Hz. This instrument thus complements the ongoing effort by Igel and others to study rotational motions using ring laser gyroscopes and constitutes a positive response to the clarion call for developments in rotation seismology by Igel, Lee, and Todorovska [H. Igel, W.H.K. Lee and M.I. Todorovska, AGU Fall Meeting 2006, Rotational Seismology Sessions: S22A,S23B, Inauguration of the International Working Group on Rotational Seismology (IWGoRS)]. PMID:17438268

  17. Identification of nonlinear modes using phase-locked-loop experimental continuation and normal form

    NASA Astrophysics Data System (ADS)

    Denis, V.; Jossic, M.; Giraud-Audine, C.; Chomette, B.; Renault, A.; Thomas, O.

    2018-06-01

    In this article, we address the model identification of nonlinear vibratory systems, with a specific focus on systems modeled with distributed nonlinearities, such as geometrically nonlinear mechanical structures. The proposed strategy theoretically relies on the concept of nonlinear modes of the underlying conservative unforced system and the use of normal forms. Within this framework, it is shown that without internal resonance, a valid reduced order model for a nonlinear mode is a single Duffing oscillator. We then propose an efficient experimental strategy to measure the backbone curve of a particular nonlinear mode and we use it to identify the free parameters of the reduced order model. The experimental part relies on a Phase-Locked Loop (PLL) and enables a robust and automatic measurement of backbone curves as well as forced responses. It is theoretically and experimentally shown that the PLL is able to stabilize the unstable part of Duffing-like frequency responses, thus enabling its robust experimental measurement. Finally, the whole procedure is tested on three experimental systems: a circular plate, a chinese gong and a piezoelectric cantilever beam. It enable to validate the procedure by comparison to available theoretical models as well as to other experimental identification methods.

  18. A real-time all-atom structural search engine for proteins.

    PubMed

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

    2014-07-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

  19. Even and odd normalized zero modes in random interacting Majorana models respecting the parity P and the time-reversal-symmetry T

    NASA Astrophysics Data System (ADS)

    Monthus, Cécile

    2018-06-01

    For random interacting Majorana models where the only symmetries are the parity P and the time-reversal-symmetry T, various approaches are compared to construct exact even and odd normalized zero modes Γ in finite size, i.e. Hermitian operators that commute with the Hamiltonian, that square to the identity, and that commute (even) or anticommute (odd) with the parity P. Even normalized zero-modes are well known under the name of ‘pseudo-spins’ in the field of many-body-localization or more precisely ‘local integrals of motion’ (LIOMs) in the many-body-localized-phase where the pseudo-spins happens to be spatially localized. Odd normalized zero-modes are popular under the name of ‘Majorana zero modes’ or ‘strong zero modes’. Explicit examples for small systems are described in detail. Applications to real-space renormalization procedures based on blocks containing an odd number of Majorana fermions are also discussed.

  20. Extensions to the instantaneous normal mode analysis of cluster dynamics: Diffusion constants and the role of rotations in clusters

    NASA Astrophysics Data System (ADS)

    Adams, John E.; Stratt, Richard M.

    1990-08-01

    For the instantaneous normal mode analysis method to be generally useful in studying the dynamics of clusters of arbitrary size, it ought to yield values of atomic self-diffusion constants which agree with those derived directly from molecular dynamics calculations. The present study proposes that such agreement indeed can be obtained if a sufficiently sophisticated formalism for computing the diffusion constant is adopted, such as the one suggested by Madan, Keyes, and Seeley [J. Chem. Phys. 92, 7565 (1990)]. In order to implement this particular formalism, however, we have found it necessary to pay particular attention to the removal from the computed spectra of spurious rotational contributions. The utility of the formalism is demonstrated via a study of small argon clusters, for which numerous results generated using other approaches are available. We find the same temperature dependence of the Ar13 self-diffusion constant that Beck and Marchioro [J. Chem. Phys. 93, 1347 (1990)] do from their direct calculation of the velocity autocorrelation function: The diffusion constant rises quickly from zero to a liquid-like value as the cluster goes through (the finite-size equivalent of) the melting transition.

  1. Ab initio folding of proteins using all-atom discrete molecular dynamics

    PubMed Central

    Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

    2008-01-01

    Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374

  2. Comparative analysis of guide mode of government - oriented industry guidance funds under china’s new normal of economic growth

    NASA Astrophysics Data System (ADS)

    Sun, Chunling; Cheng, Xuemei

    2017-11-01

    The government-oriented industry guidance Funds solve the problem of financing difficulty and high innovation under the background of China’s new normal. Through the provinces and cities of the policies and regulations of the collation and comparative analysis, it will be divided into three modes. And then compare among three modes and analyze applicability to guide the construction of provinces and cities.

  3. Sensing mode atomic force microscope

    DOEpatents

    Hough, Paul V. C.; Wang, Chengpu

    2003-01-01

    An atomic force microscope utilizes a pulse release system and improved method of operation to minimize contact forces between a probe tip affixed to a flexible cantilever and a specimen being measured. The pulse release system includes a magnetic particle affixed proximate the probe tip and an electromagnetic coil. When energized, the electromagnetic coil generates a magnetic field which applies a driving force on the magnetic particle sufficient to overcome adhesive forces exhibited between the probe tip and specimen. The atomic force microscope includes two independently displaceable piezo elements operable along a Z-axis. A controller drives the first Z-axis piezo element to provide a controlled approach between the probe tip and specimen up to a point of contact between the probe tip and specimen. The controller then drives the first Z-axis piezo element to withdraw the cantilever from the specimen. The controller also activates the pulse release system which drives the probe tip away from the specimen during withdrawal. Following withdrawal, the controller adjusts the height of the second Z-axis piezo element to maintain a substantially constant approach distance between successive samples.

  4. On the origin of amplitude reduction mechanism in tapping mode atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Keyvani, Aliasghar; Sadeghian, Hamed; Goosen, Hans; van Keulen, Fred

    2018-04-01

    The origin of amplitude reduction in Tapping Mode Atomic Force Microscopy (TM-AFM) is typically attributed to the shift in resonance frequency of the cantilever due to the nonlinear tip-sample interactions. In this paper, we present a different insight into the same problem which, besides explaining the amplitude reduction mechanism, provides a simple reasoning for the relationship between tip-sample interactions and operation parameters (amplitude and frequency). The proposed formulation, which attributes the amplitude reduction to an interference between the tip-sample and dither force, only deals with the linear part of the system; however, it fully agrees with experimental results and numerical solutions of the full nonlinear model of TM-AFM.

  5. Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule.

    PubMed

    Matsumoto, Atsushi; Tobias, Irwin; Olson, Wilma K

    2005-01-01

    Fine structural and energetic details embedded in the DNA base sequence, such as intrinsic curvature, are important to the packaging and processing of the genetic material. Here we investigate the internal dynamics of a 200 bp closed circular molecule with natural curvature using a newly developed normal-mode treatment of DNA in terms of neighboring base-pair "step" parameters. The intrinsic curvature of the DNA is described by a 10 bp repeating pattern of bending distortions at successive base-pair steps. We vary the degree of intrinsic curvature and the superhelical stress on the molecule and consider the normal-mode fluctuations of both the circle and the stable figure-8 configuration under conditions where the energies of the two states are similar. To extract the properties due solely to curvature, we ignore other important features of the double helix, such as the extensibility of the chain, the anisotropy of local bending, and the coupling of step parameters. We compare the computed normal modes of the curved DNA model with the corresponding dynamical features of a covalently closed duplex of the same chain length constructed from naturally straight DNA and with the theoretically predicted dynamical properties of a naturally circular, inextensible elastic rod, i.e., an O-ring. The cyclic molecules with intrinsic curvature are found to be more deformable under superhelical stress than rings formed from naturally straight DNA. As superhelical stress is accumulated in the DNA, the frequency, i.e., energy, of the dominant bending mode decreases in value, and if the imposed stress is sufficiently large, a global configurational rearrangement of the circle to the figure-8 form takes place. We combine energy minimization with normal-mode calculations of the two states to decipher the configurational pathway between the two states. We also describe and make use of a general analytical treatment of the thermal fluctuations of an elastic rod to characterize the

  6. Modeling guided wave excitation in plates with surface mounted piezoelectric elements: coupled physics and normal mode expansion

    NASA Astrophysics Data System (ADS)

    Ren, Baiyang; Lissenden, Cliff J.

    2018-04-01

    Guided waves have been extensively studied and widely used for structural health monitoring because of their large volumetric coverage and good sensitivity to defects. Effectively and preferentially exciting a desired wave mode having good sensitivity to a certain defect is of great practical importance. Piezoelectric discs and plates are the most common types of surface-mounted transducers for guided wave excitation and reception. Their geometry strongly influences the proportioning between excited modes as well as the total power of the excited modes. It is highly desirable to predominantly excite the selected mode while the total transduction power is maximized. In this work, a fully coupled multi-physics finite element analysis, which incorporates the driving circuit, the piezoelectric element and the wave guide, is combined with the normal mode expansion method to study both the mode tuning and total wave power. The excitation of circular crested waves in an aluminum plate with circular piezoelectric discs is numerically studied for different disc and adhesive thicknesses. Additionally, the excitation of plane waves in an aluminum plate, using a stripe piezoelectric element is studied both numerically and experimentally. It is difficult to achieve predominant single mode excitation as well as maximum power transmission simultaneously, especially for higher order modes. However, guidelines for designing the geometry of piezoelectric elements for optimal mode excitation are recommended.

  7. Tailoring properties of lossy-mode resonance optical fiber sensors with atomic layer deposition technique

    NASA Astrophysics Data System (ADS)

    Kosiel, Kamil; Koba, Marcin; Masiewicz, Marcin; Śmietana, Mateusz

    2018-06-01

    The paper shows application of atomic layer deposition (ALD) technique as a tool for tailoring sensorial properties of lossy-mode-resonance (LMR)-based optical fiber sensors. Hafnium dioxide (HfO2), zirconium dioxide (ZrO2), and tantalum oxide (TaxOy), as high-refractive-index dielectrics that are particularly convenient for LMR-sensor fabrication, were deposited by low-temperature (100 °C) ALD ensuring safe conditions for thermally vulnerable fibers. Applicability of HfO2 and ZrO2 overlays, deposited with ALD-related atomic level thickness accuracy for fabrication of LMR-sensors with controlled sensorial properties was presented. Additionally, for the first time according to our best knowledge, the double-layer overlay composed of two different materials - silicon nitride (SixNy) and TaxOy - is presented for the LMR fiber sensors. The thin films of such overlay were deposited by two different techniques - PECVD (the SixNy) and ALD (the TaxOy). Such approach ensures fast overlay fabrication and at the same time facility for resonant wavelength tuning, yielding devices with satisfactory sensorial properties.

  8. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  9. Control of atomic transition rates via laser-light shaping

    NASA Astrophysics Data System (ADS)

    Jáuregui, R.

    2015-04-01

    A modular systematic analysis of the feasibility of modifying atomic transition rates by tailoring the electromagnetic field of an external coherent light source is presented. The formalism considers both the center of mass and internal degrees of freedom of the atom, and all properties of the field: frequency, angular spectrum, and polarization. General features of recoil effects for internal forbidden transitions are discussed. A comparative analysis of different structured light sources is explicitly worked out. It includes spherical waves, Gaussian beams, Laguerre-Gaussian beams, and propagation invariant beams with closed analytical expressions. It is shown that increments in the order of magnitude of the transition rates for Gaussian and Laguerre-Gaussian beams, with respect to those obtained in the paraxial limit, require waists of the order of the wavelength, while propagation invariant modes may considerably enhance transition rates under more favorable conditions. For transitions that can be naturally described as modifications of the atomic angular momentum, this enhancement is maximal (within propagation invariant beams) for Bessel modes, Mathieu modes can be used to entangle the internal and center-of-mass involved states, and Weber beams suppress this kind of transition unless they have a significant component of odd modes. However, if a recoil effect of the transition with an adequate symmetry is allowed, the global transition rate (center of mass and internal motion) can also be enhanced using Weber modes. The global analysis presented reinforces the idea that a better control of the transitions between internal atomic states requires both a proper control of the available states of the atomic center of mass, and shaping of the background electromagnetic field.

  10. Motions in the interiors and atmospheres of Jupiter and Saturn. II - Barotropic instabilities and normal modes of an adiabatic planet

    NASA Technical Reports Server (NTRS)

    Ingersoll, A. P.; Miller, R. L.

    1986-01-01

    A rotating and adiabatic inviscid fluid planet possesses low frequency motions that are barotropic, quasi-geostrophic and quasi-columnar. The limiting curvature at which flow becomes unstable upon projection onto the planetary surface is negative, with an amplitude that is 3-4 times that for thin atmospheres, in planets in which density linearly decreases to zero at the surface. This result is shown to hold for all quasi-columnar perturbations. Both the phase speed of the normal mode oscillations and the barotropic stability criterion have features in common with Saturn and Jupiter oscillations.

  11. All-optical switch using optically controlled two mode interference coupler.

    PubMed

    Sahu, Partha Pratim

    2012-05-10

    In this paper, we have introduced optically controlled two-mode interference (OTMI) coupler having silicon core and GaAsInP cladding as an all-optical switch. By taking advantage of refractive index modulation by launching optical pulse into cladding region of TMI waveguide, we have shown optically controlled switching operation. We have studied optical pulse-controlled coupling characteristics of the proposed device by using a simple mathematical model on the basis of sinusoidal modes. The device length is less than that of previous work. It is also seen that the cross talk of the OTMI switch is not significantly increased with fabrication tolerances (±δw) in comparison with previous work.

  12. Normal-mode-based analysis of electron plasma waves with second-order Hermitian formalism

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ramos, J. J.; White, R. L.

    The classic problem of the dynamic evolution and Landau damping of linear Langmuir electron waves in a collisionless plasma with Maxwellian background is cast as a second-order, self-adjoint problem with a continuum spectrum of real and positive squared frequencies. The corresponding complete basis of singular normal modes is obtained, along with their orthogonality relation. This yields easily the general expression of the time-reversal-invariant solution for any initial-value problem. Examples are then given for specific initial conditions that illustrate different behaviors of the Landau-damped macroscopic moments of the perturbations.

  13. Normal-mode-based analysis of electron plasma waves with second-order Hermitian formalism

    DOE PAGES

    Ramos, J. J.; White, R. L.

    2018-03-01

    The classic problem of the dynamic evolution and Landau damping of linear Langmuir electron waves in a collisionless plasma with Maxwellian background is cast as a second-order, self-adjoint problem with a continuum spectrum of real and positive squared frequencies. The corresponding complete basis of singular normal modes is obtained, along with their orthogonality relation. This yields easily the general expression of the time-reversal-invariant solution for any initial-value problem. Examples are then given for specific initial conditions that illustrate different behaviors of the Landau-damped macroscopic moments of the perturbations.

  14. All fiber passively mode locked zirconium-based erbium-doped fiber laser

    NASA Astrophysics Data System (ADS)

    Ahmad, H.; Awang, N. A.; Paul, M. C.; Pal, M.; Latif, A. A.; Harun, S. W.

    2012-04-01

    All passively mode locked erbium-doped fiber laser with a zirconium host is demonstrated. The fiber laser utilizes the Non-Linear Polarization Rotation (NPR) technique with an inexpensive fiber-based Polarization Beam Splitter (PBS) as the mode-locking element. A 2 m crystalline Zirconia-Yttria-Alumino-silicate fiber doped with erbium ions (Zr-Y-Al-EDF) acts as the gain medium and generates an Amplified Spontaneous Emission (ASE) spectrum from 1500 nm to 1650 nm. The generated mode-locked pulses have a spectrum ranging from 1548 nm to more than 1605 nm, as well as a 3-dB bandwidth of 12 nm. The mode-locked pulse train has an average output power level of 17 mW with a calculated peak power of 1.24 kW and energy per pulse of approximately 730 pJ. The spectrum also exhibits a Signal-to-Noise Ratio (SNR) of 50 dB as well as a repetition rate of 23.2 MHz. The system is very stable and shows little power fluctuation, in addition to being repeatable.

  15. Surface normal velocity distribution of sputtered Zr-atoms for light-ion irradiation

    NASA Astrophysics Data System (ADS)

    Bay, H. L.; Berres, W.; Hintz, E.

    1982-03-01

    The velocity distribution of sputtered Zr-atoms has been measured for 8 keV Ar + and He + ions and 2.5 keV D + ion irradiation at normal incidence. The measurements were performed with the aid of laser induced fluorescence spectroscopy (LIFS) using a CW-laser pumped dye-laser. The influence of the measuring geometry was investigated and found to be in good agreement with calculation. For light-ion sputtering the collision-cascade theory is no longer applicable. Here a distinct shift in the velocity distributions towards lower velocities compared with the Ar results was found. The shift can be correlated to anisotropic effects in connection with the change in the maximum recoil energy Tm in the cascade.

  16. Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

    PubMed

    Schug, Alexander; Herges, Thomas; Verma, Abhinav; Lee, Kyu Hwan; Wenzel, Wolfgang

    2005-12-09

    The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.

  17. Tunable-Range, Photon-Mediated Atomic Interactions in Multimode Cavity QED

    NASA Astrophysics Data System (ADS)

    Vaidya, Varun D.; Guo, Yudan; Kroeze, Ronen M.; Ballantine, Kyle E.; Kollár, Alicia J.; Keeling, Jonathan; Lev, Benjamin L.

    2018-01-01

    Optical cavity QED provides a platform with which to explore quantum many-body physics in driven-dissipative systems. Single-mode cavities provide strong, infinite-range photon-mediated interactions among intracavity atoms. However, these global all-to-all couplings are limiting from the perspective of exploring quantum many-body physics beyond the mean-field approximation. The present work demonstrates that local couplings can be created using multimode cavity QED. This is established through measurements of the threshold of a superradiant, self-organization phase transition versus atomic position. Specifically, we experimentally show that the interference of near-degenerate cavity modes leads to both a strong and tunable-range interaction between Bose-Einstein condensates (BECs) trapped within the cavity. We exploit the symmetry of a confocal cavity to measure the interaction between real BECs and their virtual images without unwanted contributions arising from the merger of real BECs. Atom-atom coupling may be tuned from short range to long range. This capability paves the way toward future explorations of exotic, strongly correlated systems such as quantum liquid crystals and driven-dissipative spin glasses.

  18. Two-Particle Four-Mode Interferometer for Atoms

    NASA Astrophysics Data System (ADS)

    Dussarrat, Pierre; Perrier, Maxime; Imanaliev, Almazbek; Lopes, Raphael; Aspect, Alain; Cheneau, Marc; Boiron, Denis; Westbrook, Christoph I.

    2017-10-01

    We present a free-space interferometer to observe two-particle interference of a pair of atoms with entangled momenta. The source of atom pairs is a Bose-Einstein condensate subject to a dynamical instability, and the interferometer is realized using Bragg diffraction on optical lattices, in the spirit of our recent Hong-Ou-Mandel experiment. We report on an observation ruling out the possibility of a purely mixed state at the input of the interferometer. We explain how our current setup can be extended to enable a test of a Bell inequality on momentum observables.

  19. Atomic-scale origin of dynamic viscoelastic response and creep in disordered solids

    NASA Astrophysics Data System (ADS)

    Milkus, Rico; Zaccone, Alessio

    2017-02-01

    Viscoelasticity has been described since the time of Maxwell as an interpolation of purely viscous and purely elastic response, but its microscopic atomic-level mechanism in solids has remained elusive. We studied three model disordered solids: a random lattice, the bond-depleted fcc lattice, and the fcc lattice with vacancies. Within the harmonic approximation for central-force lattices, we applied sum rules for viscoelastic response derived on the basis of nonaffine atomic motions. The latter motions are a direct result of local structural disorder, and in particular, of the lack of inversion symmetry in disordered lattices. By defining a suitable quantitative and general atomic-level measure of nonaffinity and inversion symmetry, we show that the viscoelastic responses of all three systems collapse onto a master curve upon normalizing by the overall strength of inversion-symmetry breaking in each system. Close to the isostatic point for central-force lattices, power-law creep G (t ) ˜t-1 /2 emerges as a consequence of the interplay between soft vibrational modes and nonaffine dynamics, and various analytical scalings, supported by numerical calculations, are predicted by the theory.

  20. Selection and amplification of a single optical frequency comb mode for laser cooling of the strontium atoms in an optical clock

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Hui; School of Physics, University of Chinese Academy of Sciences, Beijing 100049; Yin, Mojuan

    2015-10-12

    In this paper, we report on the active filtering and amplification of a single mode from an optical femtosecond laser comb with mode spacing of 250 MHz by optical injection of two external-cavity diode lasers operating in cascade to build a narrow linewidth laser for laser cooling of the strontium atoms in an optical lattice clock. Despite the low injection of individual comb mode of approximately 50 nW, a single comb line at 689 nm could be filtered and amplified to reach as high as 10 mW with 37 dB side mode suppression and a linewidth of 240 Hz. This method could be appliedmore » over a broad spectral band to build narrow linewidth lasers for various applications.« less

  1. Interaction of human synovial phospholipase A2 with mixed lipid bilayers: a coarse-grain and all-atom molecular dynamics simulation study.

    PubMed

    Qin, Shan-Shan; Yu, Yang-Xin; Li, Qi-Kai; Yu, Zhi-Wu

    2013-02-26

    Human secreted phospholipase A2s have been shown to promote inflammation in mammals by catalyzing the first step of the arachidonic acid pathway by breaking down phospholipids, producing fatty acids, including arachidonic acid. They bind to the membrane water interface to access their phospholipid substrates from the membrane. Their binding modes on membrane surfaces are regulated by diverse factors, including membrane charge, fluidity, and heterogeneity. The influence of these factors on the binding modes of the enzymes is not well understood. Here we have studied several human synovial phospholipase A2 (hs-PLA2)/mixed bilayer systems through a combined coarse-grain and all-atom molecular dynamics simulation. It was found that hydrophobic residues Leu2, Val3, Ala18, Leu19, Phe23, Gly30, and Phe63 that form the edge of the entrance of the hydrophobic binding pocket in hs-PLA2 tend to penetrate into the hydrophobic area of lipid bilayers, and more than half of the total amino acid residues make contact with the lipid headgroups. Each enzyme molecule forms 19-38 hydrogen bonds with the bilayer to which it binds, most of which are with the phosphate groups. Analysis of the root-mean-square deviation (rmsd) shows that residues Val30-Thr40, Tyr66-Gln80, and Lys107-Arg118 have relatively large rmsds during all-atom molecular dynamics simulations, in accordance with the observation of an enlarged entrance region of the hydrophobic binding pocket. The amino acid sequences forming the entrance of the binding pocket prefer to interact with lipid molecules that are more fluid or negatively charged, and the opening of the binding pocket would be larger when the lipid components are more fluid.

  2. Reliable before-fabrication forecasting of normal and touch mode MEMS capacitive pressure sensor: modeling and simulation

    NASA Astrophysics Data System (ADS)

    Jindal, Sumit Kumar; Mahajan, Ankush; Raghuwanshi, Sanjeev Kumar

    2017-10-01

    An analytical model and numerical simulation for the performance of MEMS capacitive pressure sensors in both normal and touch modes is required for expected behavior of the sensor prior to their fabrication. Obtaining such information should be based on a complete analysis of performance parameters such as deflection of diaphragm, change of capacitance when the diaphragm deflects, and sensitivity of the sensor. In the literature, limited work has been carried out on the above-stated issue; moreover, due to approximation factors of polynomials, a tolerance error cannot be overseen. Reliable before-fabrication forecasting requires exact mathematical calculation of the parameters involved. A second-order polynomial equation is calculated mathematically for key performance parameters of both modes. This eliminates the approximation factor, and an exact result can be studied, maintaining high accuracy. The elimination of approximation factors and an approach of exact results are based on a new design parameter (δ) that we propose. The design parameter gives an initial hint to the designers on how the sensor will behave once it is fabricated. The complete work is aided by extensive mathematical detailing of all the parameters involved. Next, we verified our claims using MATLAB® simulation. Since MATLAB® effectively provides the simulation theory for the design approach, more complicated finite element method is not used.

  3. Intrinsic hybrid modes in a corrugated conical horn

    NASA Astrophysics Data System (ADS)

    Dendane, A.; Arnold, J. M.

    1988-08-01

    Computational requirements for the generation of intrinsic modes in a nonseparable waveguide geometry requiring a full vector field description with anistropic impedance boundaries were derived. Good agreement is shown between computed and measured radiation patterns in copolar and crosspolar configurations. This agreement establishes that the intrinsic mode correctly accounts for the local normal mode conversion which takes place along the horn in a conventional mode coupling scheme, at least for cone semiangles up to 15 deg. The advantage of the intrinsic mode formulation over the conventional mode-coupling theory is that, to construct a single intrinsic mode throughout the horn, only one local normal mode field is required at each cross section, whereas mode conversion from the HE11 mode would require all the HE1n modes to be known at each cross section. The intrinsic mode accounts also for fields which would appear as backward modes in coupled-mode theory. A complete coupled-mode theory solution requires the inversion of a large matrix at each cross section, whereas the intrinsic mode can be constructed explicitly using a simple Fourier-like integral; the perturbation solution of Dragone (1977) is difficult to make rigorous.

  4. All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins

    PubMed Central

    Guttman, Miklos; Weinkam, Patrick; Sali, Andrej; Lee, Kelly K.

    2013-01-01

    Summary The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small Angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern, and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins, but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a webserver at http://modbase.compbio.ucsf.edu/allosmod-foxs. PMID:23473666

  5. Mitral annulus motion as determined by M-mode echocardiography in normal dogs and dogs with cardiac disease.

    PubMed

    Schober, K E; Fuentes, V L

    2001-01-01

    M-mode echocardiography was used to assess apical mitral annulus motion (MAM) in 103 normal dogs and 101 dogs with cardiac disease, to obtain information on systolic left ventricular long axis function. In normal dogs, a close relationship was found between MAM and body weight (r = 0.80, P < 0.001). There was a weak correlation between MAM and heart rate (r = -0.25, P < 0.05), but no correlation between MAM and age or left ventricular shortening fraction (P > 0.05). Mean MAM (95% confidence intervals) were established for normal dogs of differing body weight, and were 0.70 cm (0.65 to 0.75) in dogs < 15 kg, 1.08 cm (1.03 to 1.13) in dogs weighing 15 to 40 kg, and 1.51 cm (1.21 to 1.81) in dogs > 40 kg. "Cut-off" values to define decreased MAM for normal dogs of differing body weight were 0.45 cm (dogs < 15 kg), 0.80 cm (dogs 15-40 kg), and 1.20 cm (dogs > 40 kg). In dogs with cardiac disease, median MAM was normal in mitral valve endocardiosis or aortic stenosis, but significantly decreased (P < 0.05) in dilated cardiomyopathy. All dogs with mitral valve endocardiosis (n = 54) or aortic stenosis (n = 26) had MAM above the above-mentioned "cut-off" values, suggesting normal or increased left ventricular longitudinal systolic shortening, whereas 81% (17/21) of dogs with dilated cardiomyopathy had MAM below the "cut-off" value, indicating decreased long axis systolic function. It is concluded that MAM may be used to evaluate systolic left ventricular long axis performance in dogs and may add useful information on global left ventricular contraction dynamics.

  6. Hierarchical atom type definitions and extensible all-atom force fields.

    PubMed

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  7. Evidence for Radial Anisotropy in Earth's Upper Inner Core from Normal Modes

    NASA Astrophysics Data System (ADS)

    Lythgoe, K.; Deuss, A. F.

    2017-12-01

    The structure of the uppermost inner core is related to solidification of outer core material at the inner core boundary. Previous seismic studies using body waves indicate an isotropic upper inner core, although radial anisotropy has not been considered since it cannot be uniquely determined by body waves. Normal modes, however, do constrain radial anisotropy in the inner core. Centre frequency measurements indicate 2-5 % radial anisotropy in the upper 100 km of the inner core, with a fast direction radially outwards and a slow direction along the inner core boundary. This seismic structure provides constraints on solidification processes at the inner core boundary and appears consistent with texture predicted due to anisotropic inner core growth.

  8. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.

    PubMed

    Erban, Radek

    2016-02-01

    Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl - ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  9. Stability branching induced by collective atomic recoil in an optomechanical ring cavity

    NASA Astrophysics Data System (ADS)

    Ian, Hou

    2017-02-01

    In a ring cavity filled with an atomic condensate, self-bunching of atoms due to the cavity pump mode produce an inversion that re-emits into the cavity probe mode with an exponential gain, forming atomic recoil lasing. An optomechanical ring cavity is formed when one of the reflective mirrors is mounted on a mechanical vibrating beam. In this paper, we extend studies on the stability of linear optomechanical cavities to such ring cavities with two counter-propagating cavity modes, especially when the forward propagating pump mode is taken to its weak coupling limit. We find that when the atomic recoil is in action, stable states of the mechanical mode of the mirror converge into branch cuts, where the gain produced by the recoiling strikes balance with the multiple decay sources, such as cavity leakage in the optomechanical system. This balance is obtained when the propagation delay in the dispersive atomic medium matches in a periodic pattern to the frequencies and linewidths of the cavity mode and the collective bosonic mode of the atoms. We show an input-output hysteresis cycle between the atomic mode and the cavity mode to verify the multi-valuation of the stable states after branching at the weak coupling limit.

  10. Continuous all-optical deceleration of molecular beams and demonstration with Rb atoms

    NASA Astrophysics Data System (ADS)

    Long, Xueping; Jayich, Andrew; Campbell, Wesley

    2017-04-01

    Ultracold samples of molecules are desirable for a variety of applications, such as many-body physics, precision measurement and quantum information science. However, the pursuit of ultracold molecules has achieved limited success: spontaneous emission into many different dark states makes it hard to optically decelerate molecules to trappable speed. We propose to address this problem with a general optical deceleration technique that exploits a pump-dump pulse pair from a mode-locked laser. A molecular beam is first excited by a counter-propagating ``pump'' pulse. The molecular beam is then driven back to the initial ground state by a co-propagating ``dump'' pulse via stimulated emission. The delay between the pump and dump pulse is set to be shorter than the excited state lifetimes in order to limit decays to dark states. We report progress benchmarking this stimulated force by accelerating a cold sample of neutral Rb atoms.

  11. Continuous parametric feedback cooling of a single atom in an optical cavity

    NASA Astrophysics Data System (ADS)

    Sames, C.; Hamsen, C.; Chibani, H.; Altin, P. A.; Wilk, T.; Rempe, G.

    2018-05-01

    We demonstrate a feedback algorithm to cool a single neutral atom trapped inside a standing-wave optical cavity. The algorithm is based on parametric modulation of the confining potential at twice the natural oscillation frequency of the atom, in combination with fast and repetitive atomic position measurements. The latter serve to continuously adjust the modulation phase to a value for which parametric excitation of the atomic motion is avoided. Cooling is limited by the measurement backaction which decoheres the atomic motion after only a few oscillations. Nonetheless, applying this feedback scheme to an ˜5 -kHz oscillation mode increases the average storage time of a single atom in the cavity by a factor of 60 to more than 2 s. In contrast to previous feedback schemes, our algorithm is also capable of cooling a much faster ˜500 -kHz oscillation mode within just microseconds. This demonstrates that parametric cooling is a powerful technique that can be applied in all experiments where optical access is limited.

  12. Fluorescence quenching and the "ring-mode" to "red-mode" transition in alkali inductively coupled plasmas

    NASA Astrophysics Data System (ADS)

    Huang, M.; Bazurto, R.; Camparo, J.

    2018-01-01

    The ring-mode to red-mode transition in alkali metal inductively coupled plasmas (ICPs) (i.e., rf-discharge lamps) is perhaps the most important physical phenomenon affecting these devices as optical pumping light sources for atomic clocks and magnetometers. It sets the limit on useful ICP operating temperature, thereby setting a limit on ICP light output for atomic-clock/magnetometer signal generation, and it is a temperature region of ICP operation associated with discharge instability. Previous work has suggested that the mechanism driving the ring-mode to red-mode transition is associated with radiation trapping, but definitive experimental evidence validating that hypothesis has been lacking. Based on that hypothesis, one would predict that the introduction of an alkali-fluorescence quenching gas (i.e., N2) into the ICP would increase the ring-mode to red-mode transition temperature. Here, we test that prediction, finding direct evidence supporting the radiation-trapping hypothesis.

  13. Correlation of atomic packing with the boson peak in amorphous alloys

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, W. M.; Key Laboratory of Magnetic Materials and Devices, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201; School of Materials Science and Engineering, Southeast University, Nanjing 211189

    2014-09-28

    Boson peaks (BP) have been observed from phonon specific heats in 10 studied amorphous alloys. Two Einstein-type vibration modes were proposed in this work and all data can be fitted well. By measuring and analyzing local atomic structures of studied amorphous alloys and 56 reported amorphous alloys, it is found that (a) the BP originates from local harmonic vibration modes associated with the lengths of short-range order (SRO) and medium-range order (MRO) in amorphous alloys, and (b) the atomic packing in amorphous alloys follows a universal scaling law, i.e., the ratios of SRO and MRO lengths to solvent atomic diametermore » are 3 and 7, respectively, which exact match with length ratios of BP vibration frequencies to Debye frequency for the studied amorphous alloys. This finding provides a new perspective for atomic packing in amorphous materials, and has significant implications for quantitative description of the local atomic orders and understanding the structure-property relationship.« less

  14. Atom-atom interactions around the band edge of a photonic crystal waveguide

    NASA Astrophysics Data System (ADS)

    Hood, Jonathan D.; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E.; Kimble, H. J.

    2016-09-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxxE(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e-normal">κx|x|E(x)∝e-κx|x| within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the normal">D1D1 line of atomic cesium for N¯=3.0±0.5

  15. All-fiber radially/azimuthally polarized lasers based on mode coupling of tapered fibers.

    PubMed

    Mao, Dong; He, Zhiwen; Lu, Hua; Li, Mingkun; Zhang, Wending; Cui, Xiaoqi; Jiang, Biqiang; Zhao, Jianlin

    2018-04-01

    We demonstrate a mode converter with an insertion loss of 0.36 dB based on mode coupling of tapered single-mode and two-mode fibers, and realize all-fiber flexible cylindrical vector lasers at 1550 nm. Attributing to the continuous distribution of a tangential electric field at taper boundaries, the laser is switchable between the radially and azimuthally polarized states by adjusting the input polarization. In the temporal domain, the operation is controllable among continuous-wave, Q-switched, and mode-locked statuses by changing the saturable absorber or pump strength. The duration of Q-switched radially/azimuthally polarized laser spans from 10.4/10.8 to 6/6.4 μs at the pump range of 38 to 58 mW, while that of the mode-locked pulse varies from 39.2/31.9 to 5.6/5.2 ps by controlling the laser bandwidth. The proposed laser combines the features of a cylindrical vector beam, a fiber laser, and an ultrafast pulse, providing a special and cost-effective source for practical applications.

  16. Majorana spin in magnetic atomic chain systems

    NASA Astrophysics Data System (ADS)

    Li, Jian; Jeon, Sangjun; Xie, Yonglong; Yazdani, Ali; Bernevig, B. Andrei

    2018-03-01

    In this paper, we establish that Majorana zero modes emerging from a topological band structure of a chain of magnetic atoms embedded in a superconductor can be distinguished from trivial localized zero energy states that may accidentally form in this system using spin-resolved measurements. To demonstrate this key Majorana diagnostics, we study the spin composition of magnetic impurity induced in-gap Shiba states in a superconductor using a hybrid model. By examining the spin and spectral densities in the context of the Bogoliubov-de Gennes (BdG) particle-hole symmetry, we derive a sum rule that relates the spin densities of localized Shiba states with those in the normal state without superconductivity. Extending our investigations to a ferromagnetic chain of magnetic impurities, we identify key features of the spin properties of the extended Shiba state bands, as well as those associated with a localized Majorana end mode when the effect of spin-orbit interaction is included. We then formulate a phenomenological theory for the measurement of the local spin densities with spin-polarized scanning tunneling microscopy (STM) techniques. By combining the calculated spin densities and the measurement theory, we show that spin-polarized STM measurements can reveal a sharp contrast in spin polarization between an accidental-zero-energy trivial Shiba state and a Majorana zero mode in a topological superconducting phase in atomic chains. We further confirm our results with numerical simulations that address generic parameter settings.

  17. Proximity-induced superconductivity in all-silicon superconductor /normal-metal junctions

    NASA Astrophysics Data System (ADS)

    Chiodi, F.; Duvauchelle, J.-E.; Marcenat, C.; Débarre, D.; Lefloch, F.

    2017-07-01

    We have realized laser-doped all-silicon superconducting (S)/normal metal (N) bilayers of tunable thickness and dopant concentration. We observed a strong reduction of the bilayers' critical temperature when increasing the normal metal thickness, a signature of the highly transparent S/N interface associated to the epitaxial sharp laser doping profile. We extracted the interface resistance by fitting with the linearized Usadel equations, demonstrating a reduction of 1 order of magnitude from previous superconductor/doped Si interfaces. In this well-controlled crystalline system we exploited the low-resistance S/N interfaces to elaborate all-silicon lateral SNS junctions with long-range proximity effect. Their dc transport properties, such as the critical and retrapping currents, could be well understood in the diffusive regime. Furthermore, this work led to the estimation of important parameters in ultradoped superconducting Si, such as the Fermi velocity, the coherence length, or the electron-phonon coupling constant, fundamental to conceive all-silicon superconducting electronics.

  18. Plasma Modes

    NASA Astrophysics Data System (ADS)

    Dubin, D. H. E.

    This chapter explores several aspects of the linear electrostatic normal modes of oscillation for a single-species non-neutral plasma in a Penning trap. Linearized fluid equations of motion are developed, assuming the plasma is cold but collisionless, which allow derivation of the cold plasma dielectric tensor and the electrostatic wave equation. Upper hybrid and magnetized plasma waves in an infinite uniform plasma are described. The effect of the plasma surface in a bounded plasma system is considered, and the properties of surface plasma waves are characterized. The normal modes of a cylindrical plasma column are discussed, and finally, modes of spheroidal plasmas, and finite temperature effects on the modes, are briefly described.

  19. "Good Vibrations": A workshop on oscillations and normal modes

    NASA Astrophysics Data System (ADS)

    Barbieri, Sara; Carpineti, Marina; Giliberti, Marco; Rigon, Enrico; Stellato, Marco; Tamborini, Marina

    2016-05-01

    We describe some theatrical strategies adopted in a two hour workshop in order to show some meaningful experiments and the underlying useful ideas to describe a secondary school path on oscillations, that develops from harmonic motion to normal modes of oscillations, and makes extensive use of video analysis, data logging, slow motions and applet simulations. Theatre is an extremely useful tool to stimulate motivation starting from positive emotions. That is the reason why the theatrical approach to the presentation of physical themes has been explored by the group "Lo spettacolo della Fisica" (http://spettacolo.fisica.unimi.it) of the Physics Department of University of Milano for the last ten years (Carpineti et al., JCOM, 10 (2011) 1; Nuovo Cimento B, 121 (2006) 901) and has been inserted also in the European FP7 Project TEMI (Teaching Enquiry with Mysteries Incorporated, see http://teachingmysteries.eu/en) which involves 13 different partners coming from 11 European countries, among which the Italian (Milan) group. According to the TEMI guidelines, this workshop has a written script based on emotionally engaging activities of presenting mysteries to be solved while participants have been involved in nice experiments following the developed path.

  20. All-polymer whispering gallery mode sensor system.

    PubMed

    Petermann, Ann Britt; Varkentin, Arthur; Roth, Bernhard; Morgner, Uwe; Meinhardt-Wollweber, Merve

    2016-03-21

    Sensors based on whispering gallery modes have been extensively investigated with respect to their possible application as physical or biological sensors. Instead of using a single resonator, we use an all polymer resonator array as sensing element. A tunable narrowband laser is coupled into a PMMA plate serving as an optical wave guide. PMMA spheres are placed in the evanescent field on the surface of the plate. Due to small size variations, some spheres are in resonance at a given wavelength while others are not. We show that this device is well suited for the determination of an unknown wavelength or for temperature measurements. Moreover, we discuss several general aspects of the sensor concept such as the number and size of sensing elements which are necessary for a correct measurement result, or the maximum acceptable linewidth of the laser.

  1. All-fiber broadband supercontinuum generation in a single-mode high nonlinear silica fiber

    NASA Astrophysics Data System (ADS)

    Gao, Weiqing; Liao, Meisong; Yang, Lingzhen; Yan, Xin; Suzuki, Takenobu; Ohishi, Yasutake

    2012-06-01

    We demonstrate an all-fiber broadband supercontinuum (SC) source with high efficiency in a single-mode high nonlinear silica fiber. The SC is pumped by the 1557 nm sub-picosecond pulse, which is generated by a homemade passively mode-locked fiber laser, amplified by an EDFA and compressed to 600 fs. The high nonlinear fiber used in experiments has the zero-dispersion wavelength of 1584 nm with low dispersion slope. The pump pulse is in the normal dispersion region and the SC generation is initiated by the SPM effect. When the long-wave band of the spectrum is extended to the anomalous dispersion region, the soliton effects and intra-pulse Raman effects extend the spectrum further. Meanwhile, the dispersive waves shorter than 1100 nm begin to emerge because the phase matching condition is satisfied and the intensity increases with increasing the pump intensity. The broad SC spectrum with the spectral range from 840 to 2390 nm is obtained at the pump peak power of 46.71 kW, and the 10 dB bandwidth from 1120 nm to 2245 nm of the SC covers one octave assuming the peak near 1550 nm is filtered. The temporal trace of the SC has the repetition rate of 16.7 MHz, and some satellite pulses are generated during the nonlinear process. The SC source system is constructed by all-fiber components, which can be fusion spliced together directly with low loss less than 0.1 dB and improves the energy transfer efficiency from the pump source to the SC greatly. The maximum SC average power of 332 mW is obtained for the total spectral range, and the slop efficiency to the pump source is about 70.3%, which will be lower when the peaks near 1550 nm are filtered, but is higher than those in PCFs. The spectral density for the 10 dB bandwidth is in the range from -17.3 to -7.3 dBm/nm.

  2. Unified Description of the Optical Phonon Modes in N-Layer MoTe2

    NASA Astrophysics Data System (ADS)

    Froehlicher, Guillaume; Lorchat, Etienne; Fernique, François; Joshi, Chaitanya; Molina-Sánchez, Alejandro; Wirtz, Ludger; Berciaud, Stéphane

    N -layer transition metal dichalcogenides (denoted MX2) provide a unique platform to investigate the evolution of the physical properties between the bulk (3D) and monolayer (quasi-2D) limits. Here, we present a unified analysis of the optical phonon modes in N-layer 2 H -MX2. The 2 H -phase (or hexagonal phase) is the most common polytype for semiconducting MX2 (such as MoS2). Using Raman spectroscopy, we have measured the manifold of low-frequency (rigid layer), mid-frequency (involving intralayer displacement of the chalcogen atoms only), and high-frequency (involving intralayer displacements of all atoms) Raman-active modes in N = 1 to 12 layer 2 H -molybdenenum ditelluride (MoTe2). For each monolayer mode, the N-dependent phonon frequencies give rise to fan diagrams that are quantitatively fit to a force constant model. This analysis allows us to deduce the frequencies of all the bulk (including silent) optical phonon modes.

  3. A hierarchical coarse-grained (all-atom to all residue) approach to peptides (P1, P2) binding with a graphene sheet

    NASA Astrophysics Data System (ADS)

    Pandey, Ras; Kuang, Zhifeng; Farmer, Barry; Kim, Sang; Naik, Rajesh

    2012-02-01

    Recently, Kim et al. [1] have found that peptides P1: HSSYWYAFNNKT and P2: EPLQLKM bind selectively to graphene surfaces and edges respectively which are critical in modulating both the mechanical as well as electronic transport properties of graphene. Such distinctions in binding sites (edge versus surface) observed in electron micrographs were verified by computer simulation by an all-atomic model that captures the pi-pi bonding. We propose a hierarchical approach that involves input from the all-atom Molecular Dynamics (MD) study (with atomistic detail) into a coarse-grained Monte Carlo simulation to extend this study further to a larger scale. The binding energy of a free amino acid with the graphene sheet from all-atom simulation is used in the interaction parameter for the coarse-grained approach. Peptide chain executes its stochastic motion with the Metropolis algorithm. We investigate a number of local and global physical quantities and find that peptide P1 is likely to bind more strongly to graphene sheet than P2 and that it is anchored by three residues ^4Y^5W^6Y. [1] S.N. Kim et al J. Am. Chem. Soc. 133, 14480 (2011).

  4. Zero group velocity longitudinal modes in an isotropic cylinder

    NASA Astrophysics Data System (ADS)

    Hussain, Takasar; Ahmad, Faiz; Ozair, Muhammad

    2018-06-01

    Zero group velocity (ZGV) modes are studied in an isotropic cylinder. The L(0, 2) mode behaves anomalously for the materials with a value of the bulk velocity ratio, κ , in the range √{2}<κ <2.64 and normally otherwise. All higher modes, except the first few, have no ZGV point for all isotropic materials. This is explained analytically by finding the slope of phase velocity dispersion curves of modes first when the phase velocity equals κ and then at their initial state.

  5. An exact variational method to calculate vibrational energies of five atom molecules beyond the normal mode approach

    DOE PAGES

    Yu, Hua-Gen

    2002-01-01

    We present a full dimensional variational algorithm to calculate vibrational energies of penta-atomic molecules. The quantum mechanical Hamiltonian of the system for J=0 is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame without any dynamical approximation. Moreover, the vibrational Hamiltonian has been obtained in an explicitly Hermitian form. Variational calculations are performed in a direct product discrete variable representation basis set. The sine functions are used for the radial coordinates, whereas the Legendre polynomials are employed for the polar angles. For the azimuthal angles, the symmetrically adapted Fourier–Chebyshev basis functions are utilized. The eigenvalue problem ismore » solved by a Lanczos iterative diagonalization algorithm. The preliminary application to methane is given. Ultimately, we made a comparison with previous results.« less

  6. All optical mode controllable Er-doped random fiber laser with distributed Bragg gratings.

    PubMed

    Zhang, W L; Ma, R; Tang, C H; Rao, Y J; Zeng, X P; Yang, Z J; Wang, Z N; Gong, Y; Wang, Y S

    2015-07-01

    An all-optical method to control the lasing modes of Er-doped random fiber lasers (RFLs) is proposed and demonstrated. In the RFL, an Er-doped fiber (EDF) recoded with randomly separated fiber Bragg gratings (FBG) is used as the gain medium and randomly distributed reflectors, as well as the controllable element. By combining random feedback of the FBG array and Fresnel feedback of a cleaved fiber end, multi-mode coherent random lasing is obtained with a threshold of 14 mW and power efficiency of 14.4%. Moreover, a laterally-injected control light is used to induce local gain perturbation, providing additional gain for certain random resonance modes. As a result, active mode selection of the RFL is realized by changing locations of the laser cavity that is exposed to the control light.

  7. Self-organization of atoms coupled to a chiral reservoir

    NASA Astrophysics Data System (ADS)

    Eldredge, Zachary; Solano, Pablo; Chang, Darrick; Gorshkov, Alexey V.

    2016-11-01

    Tightly confined modes of light, as in optical nanofibers or photonic crystal waveguides, can lead to large optical coupling in atomic systems, which mediates long-range interactions between atoms. These one-dimensional systems can naturally possess couplings that are asymmetric between modes propagating in different directions. Strong long-range interaction among atoms via these modes can drive them to a self-organized periodic distribution. In this paper, we examine the self-organizing behavior of atoms in one dimension coupled to a chiral reservoir. We determine the solution to the equations of motion in different parameter regimes, relative to both the detuning of the pump laser that initializes the atomic dipole-dipole interactions and the degree of reservoir chirality. In addition, we calculate possible experimental signatures such as reflectivity from self-organized atoms and motional sidebands.

  8. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-08

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups.

  9. All-fiber mode-locked laser oscillator with pulse energy of 34 nJ using a single-walled carbon nanotube saturable absorber.

    PubMed

    Jeong, Hwanseong; Choi, Sun Young; Rotermund, Fabian; Cha, Yong-Ho; Jeong, Do-Young; Yeom, Dong-Il

    2014-09-22

    We demonstrate a dissipative soliton fiber laser with high pulse energy (>30 nJ) based on a single-walled carbon nanotube saturable absorber (SWCNT-SA). In-line SA that evanescently interacts with the high quality SWCNT/polymer composite film was fabricated under optimized conditions, increasing the damage threshold of the saturation fluence of the SA to 97 mJ/cm(2). An Er-doped mode-locked all-fiber laser operating at net normal intra-cavity dispersion was built including the fabricated in-line SA. The laser stably delivers linearly chirped pulses with a pulse duration of 12.7 ps, and exhibits a spectral bandwidth of 12.1 nm at the central wavelength of 1563 nm. Average power of the laser output is measured as 335 mW at an applied pump power of 1.27 W. The corresponding pulse energy is estimated to be 34 nJ at the fundamental repetition rate of 9.80 MHz; this is the highest value, to our knowledge, reported in all-fiber Er-doped mode-locked laser using an SWCNT-SA.

  10. A nanowaveguide platform for collective atom-light interaction

    NASA Astrophysics Data System (ADS)

    Meng, Y.; Lee, J.; Dagenais, M.; Rolston, S. L.

    2015-08-01

    We propose a nanowaveguide platform for collective atom-light interaction through evanescent field coupling. We have developed a 1 cm-long silicon nitride nanowaveguide can use evanescent fields to trap and probe an ensemble of 87Rb atoms. The waveguide has a sub-micrometer square mode area and was designed with tapers for high fiber-to-waveguide coupling efficiencies at near-infrared wavelengths (750 nm to 1100 nm). Inverse tapers in the platform adiabatically transfer a weakly guided mode of fiber-coupled light into a strongly guided mode with an evanescent field to trap atoms and then back to a weakly guided mode at the other end of the waveguide. The coupling loss is -1 dB per facet (˜80% coupling efficiency) at 760 nm and 1064 nm, which is estimated by a propagation loss measurement with waveguides of different lengths. The proposed platform has good thermal conductance and can guide high optical powers for trapping atoms in ultra-high vacuum. As an intermediate step, we have observed thermal atom absorption of the evanescent component of a nanowaveguide and have demonstrated the U-wire mirror magneto-optical trap that can transfer atoms to the proximity of the surface.

  11. Noise squeezing of fields that bichromatically excite atoms in a cavity.

    PubMed

    Li, Lingchao; Hu, Xiangming; Rao, Shi; Xu, Jun

    2016-11-14

    It is well known that bichromatic excitation on one common transition can tune the emission or absorption spectra of atoms due to the modulation frequency dependent non-linearities. However little attention has been focused on the quantum dynamics of fields under bichromatic excitation. Here we present dissipative effects on noise correlations of fields in bichromatic interactions with atoms in cavities. We first consider an ensemble of two-level atoms that interacts with the two cavity fields of different frequencies and considerable amplitudes. By transferring the atom-field nonlinearities to the dressed atoms we separate out the dissipative interactions of Bogoliubov modes with the dressed atoms. The Bogoliubov mode dissipation establishes stable two-photon processes of two involved fields and therefore leads to two-mode squeezing. As a generalization, we then consider an ensemble of three-level Λ atoms for cascade bichromatic interactions. We extract the Bogoliubov-like four-mode interactions, which establish a quadrilateral of the two-photon processes of four involved fields and thus result in four-mode squeezing.

  12. Sensing mode atomic force microscope

    DOEpatents

    Hough, Paul V. C.; Wang, Chengpu

    2006-08-22

    An atomic force microscope is described having a cantilever comprising a base and a probe tip on an end opposite the base; a cantilever drive device connected to the base; a magnetic material coupled to the probe tip, such that when an incrementally increasing magnetic field is applied to the magnetic material an incrementally increasing force will be applied to the probe tip; a moveable specimen base; and a controller constructed to obtain a profile height of a specimen at a point based upon a contact between the probe tip and a specimen, and measure an adhesion force between the probe tip and the specimen by, under control of a program, incrementally increasing an amount of a magnetic field until a release force, sufficient to break the contact, is applied. An imaging method for atomic force microscopy involving measuring a specimen profile height and adhesion force at multiple points within an area and concurrently displaying the profile and adhesion force for each of the points is also described. A microscope controller is also described and is constructed to, for a group of points, calculate a specimen height at a point based upon a cantilever deflection, a cantilever base position and a specimen piezo position; calculate an adhesion force between a probe tip and a specimen at the point by causing an incrementally increasing force to be applied to the probe tip until the probe tip separates from a specimen; and move the probe tip to a new point in the group.

  13. Sensing mode atomic force microscope

    DOEpatents

    Hough, Paul V.; Wang, Chengpu

    2004-11-16

    An atomic force microscope is described having a cantilever comprising a base and a probe tip on an end opposite the base; a cantilever drive device connected to the base; a magnetic material coupled to the probe tip, such that when an incrementally increasing magnetic field is applied to the magnetic material an incrementally increasing force will be applied to the probe tip; a moveable specimen base; and a controller constructed to obtain a profile height of a specimen at a point based upon a contact between the probe tip and a specimen, and measure an adhesion force between the probe tip and the specimen by, under control of a program, incrementally increasing an amount of a magnetic field until a release force, sufficient to break the contact, is applied. An imaging method for atomic force microscopy involving measuring a specimen profile height and adhesion force at multiple points within an area and concurrently displaying the profile and adhesion force for each of the points is also described. A microscope controller is also described and is constructed to, for a group of points, calculate a specimen height at a point based upon a cantilever deflection, a cantilever base position and a specimen piezo position; calculate an adhesion force between a probe tip and a specimen at the point by causing an incrementally increasing force to be applied to the probe tip until the probe tip separates from a specimen; and move the probe tip to a new point in the group.

  14. Probabilistic estimation of splitting coefficients of normal modes of the Earth, and their uncertainties, using an autoregressive technique

    NASA Astrophysics Data System (ADS)

    Pachhai, S.; Masters, G.; Laske, G.

    2017-12-01

    Earth's normal-mode spectra are crucial to studying the long wavelength structure of the Earth. Such observations have been used extensively to estimate "splitting coefficients" which, in turn, can be used to determine the three-dimensional velocity and density structure. Most past studies apply a non-linear iterative inversion to estimate the splitting coefficients which requires that the earthquake source is known. However, it is challenging to know the source details, particularly for big events as used in normal-mode analyses. Additionally, the final solution of the non-linear inversion can depend on the choice of damping parameter and starting model. To circumvent the need to know the source, a two-step linear inversion has been developed and successfully applied to many mantle and core sensitive modes. The first step takes combinations of the data from a single event to produce spectra known as "receiver strips". The autoregressive nature of the receiver strips can then be used to estimate the structure coefficients without the need to know the source. Based on this approach, we recently employed a neighborhood algorithm to measure the splitting coefficients for an isolated inner-core sensitive mode (13S2). This approach explores the parameter space efficiently without any need of regularization and finds the structure coefficients which best fit the observed strips. Here, we implement a Bayesian approach to data collected for earthquakes from early 2000 and more recent. This approach combines the data (through likelihood) and prior information to provide rigorous parameter values and their uncertainties for both isolated and coupled modes. The likelihood function is derived from the inferred errors of the receiver strips which allows us to retrieve proper uncertainties. Finally, we apply model selection criteria that balance the trade-offs between fit (likelihood) and model complexity to investigate the degree and type of structure (elastic and anelastic

  15. All-optical atom trap as a target for MOTRIMS-like collision experiments

    NASA Astrophysics Data System (ADS)

    Sharma, S.; Acharya, B. P.; De Silva, A. H. N. C.; Parris, N. W.; Ramsey, B. J.; Romans, K. L.; Dorn, A.; de Jesus, V. L. B.; Fischer, D.

    2018-04-01

    Momentum-resolved scattering experiments with laser-cooled atomic targets have been performed since almost two decades with magneto-optical trap recoil ion momentum spectroscopy (MOTRIMS) setups. Compared to experiments with gas-jet targets, MOTRIMS features significantly lower target temperatures allowing for an excellent recoil ion momentum resolution. However, the coincident and momentum-resolved detection of electrons was long rendered impossible due to incompatible magnetic field requirements. Here we report on an experimental approach which is based on an all-optical 6Li atom trap that—in contrast to magneto-optical traps—does not require magnetic field gradients in the trapping region. Atom temperatures of about 2 mK and number densities up to 109 cm-3 make this trap ideally suited for momentum-resolved electron-ion coincidence experiments. The overall configuration of the trap is very similar to conventional magneto-optical traps. It mainly requires small modifications of laser beam geometries and polarization which makes it easily implementable in other existing MOTRIMS experiments.

  16. Simultaneous chiral discrimination of multiple profens by cyclodextrin-modified capillary electrophoresis in normal and reversed polarity modes.

    PubMed

    La, Sookie; Kim, Jiyung; Kim, Jung-Han; Goto, Junichi; Kim, Kyoung-Rae

    2003-08-01

    Simultaneous enantioseparations of nine profens for their accurate chiral discrimination were achieved by capillary electrophoresis (CE) in the normal polarity (NP) mode with a single cyclodextrin (CD) system and in the reversed polarity (RP) mode with a dual CD system. The single CD system in the NP mode employed heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TMbetaCD) added at 75 mM-100 mM 2-(N-morpholino)ethanesulfonic acid buffer (pH 6.0) as the optimum run buffer. The dual CD system operated in the RP mode used 30 mM TMbetaCD and 1.0% anionic carboxymethyl-beta-cyclodextrin dissolved in pH 3.0, 100 mM phosphoric acid-triethanolamine buffer containing 0.01% hexadimethrine bromide added to reverse the electroosmotic flow. Fairly good enantiomeric resolutions and the opposite enantiomer migration orders were achieved in the two modes. Relative migration times to internal standard under respective optimum conditions were characteristic of each enantiomer with good precision (< 2% relative standard deviation, RSD), thereby enabling to crosscheck the chemical identification of profens and also their accurate chiralities. The method linearity in the two modes was found to be adequate (r > or = 0.9991) for the chiral assay of the profens investigated. Simultaneous enantiomeric purity test of ibuprofen, ketoprofen and flurbiprofen in a mixture was feasible in a single analysis by the present method.

  17. Vibrational normal modes of diazo-dimedone: A comparative study by Fourier infrared/Raman spectroscopies and conformational analysis by MM/QM

    NASA Astrophysics Data System (ADS)

    Téllez Soto, C. A.; Ramos, J. M.; Rianelli, R. S.; de Souza, M. C. B. V.; Ferreira, V. F.

    2007-07-01

    The 2-diazo-5,5-dimethyl-cyclohexane-1,3-dione ( 3) was synthesized and the FT-IR/Raman spectra were measured with the purpose of obtain a full assignment of the vibrational modes. Singular aspects concerning the -C dbnd N dbnd N oscillator are discussed in view of two strong bands observed in the region of 2300-2100 cm -1 in both, Infrared and Raman spectra. The density functional theory (DFT) was used to obtain the geometrical structure and for assisting in the vibrational assignment joint to the traditional normal coordinate analysis (NCA). The observed wavenumbers at 2145 (IR), 2144(R) are assigned as the coupled ν(N dbnd N) + ν(C dbnd N) vibrational mode with higher participation of the N dbnd N stretching. A 2188 cm -1 (IR) and at 2186 cm -1 (R) can be assigned as a overtone of one of ν(CC) normal mode or to a combination band of the fundamentals δ(CCH) found at 1169 cm -1 and the δ (CC dbnd N) found at 1017 cm -1 enhanced by Fermi resonance.

  18. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    PubMed Central

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems. PMID:23665897

  19. Differential Lipid Profiles of Normal Human Brain Matter and Gliomas by Positive and Negative Mode Desorption Electrospray Ionization – Mass Spectrometry Imaging

    PubMed Central

    Pirro, Valentina; Hattab, Eyas M.; Cohen-Gadol, Aaron A.; Cooks, R. Graham

    2016-01-01

    Desorption electrospray ionization—mass spectrometry (DESI-MS) imaging was used to analyze unmodified human brain tissue sections from 39 subjects sequentially in the positive and negative ionization modes. Acquisition of both MS polarities allowed more complete analysis of the human brain tumor lipidome as some phospholipids ionize preferentially in the positive and others in the negative ion mode. Normal brain parenchyma, comprised of grey matter and white matter, was differentiated from glioma using positive and negative ion mode DESI-MS lipid profiles with the aid of principal component analysis along with linear discriminant analysis. Principal component–linear discriminant analyses of the positive mode lipid profiles was able to distinguish grey matter, white matter, and glioma with an average sensitivity of 93.2% and specificity of 96.6%, while the negative mode lipid profiles had an average sensitivity of 94.1% and specificity of 97.4%. The positive and negative mode lipid profiles provided complementary information. Principal component–linear discriminant analysis of the combined positive and negative mode lipid profiles, via data fusion, resulted in approximately the same average sensitivity (94.7%) and specificity (97.6%) of the positive and negative modes when used individually. However, they complemented each other by improving the sensitivity and specificity of all classes (grey matter, white matter, and glioma) beyond 90% when used in combination. Further principal component analysis using the fused data resulted in the subgrouping of glioma into two groups associated with grey and white matter, respectively, a separation not apparent in the principal component analysis scores plots of the separate positive and negative mode data. The interrelationship of tumor cell percentage and the lipid profiles is discussed, and how such a measure could be used to measure residual tumor at surgical margins. PMID:27658243

  20. Multi-frequency tapping-mode atomic force microscopy beyond three eigenmodes in ambient air

    PubMed Central

    An, Sangmin; Long, Christian J

    2014-01-01

    Summary We present an exploratory study of multimodal tapping-mode atomic force microscopy driving more than three cantilever eigenmodes. We present tetramodal (4-eigenmode) imaging experiments conducted on a thin polytetrafluoroethylene (PTFE) film and computational simulations of pentamodal (5-eigenmode) cantilever dynamics and spectroscopy, focusing on the case of large amplitude ratios between the fundamental eigenmode and the higher eigenmodes. We discuss the dynamic complexities of the tip response in time and frequency space, as well as the average amplitude and phase response. We also illustrate typical images and spectroscopy curves and provide a very brief description of the observed contrast. Overall, our findings are promising in that they help to open the door to increasing sophistication and greater versatility in multi-frequency AFM through the incorporation of a larger number of driven eigenmodes, and in highlighting specific future research opportunities. PMID:25383276

  1. Modes competition in superradiant emission from an inverted sub-wavelength thick slab of two-level atoms

    NASA Astrophysics Data System (ADS)

    Manassah, Jamal T.

    2016-08-01

    Using the expansion in the eigenmodes of 1-D Lienard-Wiechert kernel, the temporal and spectral profiles of the radiation emitted by a fully inverted collection of two-level atoms in a sub-wavelength slab geometry are computed. The initial number of amplifying modes determine the specific regime of radiation. In particular, the temporal profile of the field intensity is oscillatory and the spectral profile is non-Lorentzian with two unequal height peaks in a narrow band centered at the slab thickness value at which the real parts of the lowest order odd and even eigenvalues are equal.

  2. Geiger-Mode Avalanche Photodiode Arrays Integrated to All-Digital CMOS Circuits.

    PubMed

    Aull, Brian

    2016-04-08

    This article reviews MIT Lincoln Laboratory's work over the past 20 years to develop photon-sensitive image sensors based on arrays of silicon Geiger-mode avalanche photodiodes. Integration of these detectors to all-digital CMOS readout circuits enable exquisitely sensitive solid-state imagers for lidar, wavefront sensing, and passive imaging.

  3. Reduction of timing jitter and intensity noise in normal-dispersion passively mode-locked fiber lasers by narrow band-pass filtering.

    PubMed

    Qin, Peng; Song, Youjian; Kim, Hyoji; Shin, Junho; Kwon, Dohyeon; Hu, Minglie; Wang, Chingyue; Kim, Jungwon

    2014-11-17

    Fiber lasers mode-locked with normal cavity dispersion have recently attracted great attention due to large output pulse energy and femtosecond pulse duration. Here we accurately characterized the timing jitter of normal-dispersion fiber lasers using a balanced cross-correlation method. The timing jitter characterization experiments show that the timing jitter of normal-dispersion mode-locked fiber lasers can be significantly reduced by using narrow band-pass filtering (e.g., 7-nm bandwidth filtering in this work). We further identify that the timing jitter of the fiber laser is confined in a limited range, which is almost independent of cavity dispersion map due to the amplifier-similariton formation by insertion of the narrow bandpass filter. The lowest observed timing jitter reaches 0.57 fs (rms) integrated from 10 kHz to 10 MHz Fourier frequency. The rms relative intensity noise (RIN) is also reduced from 0.37% to 0.02% (integrated from 1 kHz to 5 MHz Fourier frequency) by the insertion of narrow band-pass filter.

  4. Thermal transport in bismuth telluride quintuple layer: mode-resolved phonon properties and substrate effects

    PubMed Central

    Shao, Cheng; Bao, Hua

    2016-01-01

    The successful exfoliation of atomically-thin bismuth telluride (Bi2Te3) quintuple layer (QL) attracts tremendous research interest in this strongly anharmonic quasi-two-dimensional material. The thermal transport properties of this material are not well understood, especially the mode-wise properties and when it is coupled with a substrate. In this work, we have performed molecular dynamics simulations and normal mode analysis to study the mode-resolved thermal transport in freestanding and supported Bi2Te3 QL. The detailed mode-wise phonon properties are calculated and the accumulated thermal conductivities with respect to phonon mean free path (MFP) are constructed. It is shown that 60% of the thermal transport is contributed by phonons with MFP longer than 20 nm. Coupling with a-SiO2 substrate leads to about 60% reduction of thermal conductivity. Through varying the interfacial coupling strength and the atomic mass of substrate, we also find that phonon in Bi2Te3 QL is more strongly scattered by interfacial potential and its transport process is less affected by the dynamics of substrate. Our study provides an in-depth understanding of heat transport in Bi2Te3 QL and is helpful in further tailoring its thermal property through nanostructuring. PMID:27263656

  5. Weather and atmosphere observation with the ATOM all-sky camera

    NASA Astrophysics Data System (ADS)

    Jankowsky, Felix; Wagner, Stefan

    2015-03-01

    The Automatic Telescope for Optical Monitoring (ATOM) for H.E.S.S. is an 75 cm optical telescope which operates fully automated. As there is no observer present during observation, an auxiliary all-sky camera serves as weather monitoring system. This device takes an all-sky image of the whole sky every three minutes. The gathered data then undergoes live-analysis by performing astrometric comparison with a theoretical night sky model, interpreting the absence of stars as cloud coverage. The sky monitor also serves as tool for a meteorological analysis of the observation site of the the upcoming Cherenkov Telescope Array. This overview covers design and benefits of the all-sky camera and additionally gives an introduction into current efforts to integrate the device into the atmosphere analysis programme of H.E.S.S.

  6. Signature of nonadiabatic coupling in excited-state vibrational modes.

    PubMed

    Soler, Miguel A; Nelson, Tammie; Roitberg, Adrian E; Tretiak, Sergei; Fernandez-Alberti, Sebastian

    2014-11-13

    Using analytical excited-state gradients, vibrational normal modes have been calculated at the minimum of the electronic excited-state potential energy surfaces for a set of extended conjugated molecules with different coupling between them. Molecular model systems composed of units of polyphenylene ethynylene (PPE), polyphenylenevinylene (PPV), and naphthacene/pentacene (NP) have been considered. In all cases except the NP model, the influence of the nonadiabatic coupling on the excited-state equilibrium normal modes is revealed as a unique highest frequency adiabatic vibrational mode that overlaps with the coupling vector. This feature is removed by using a locally diabatic representation in which the effect of NA interaction is removed. Comparison of the original adiabatic modes with a set of vibrational modes computed in the locally diabatic representation demonstrates that the effect of nonadiabaticity is confined to only a few modes. This suggests that the nonadiabatic character of a molecular system may be detected spectroscopically by identifying these unique state-specific high frequency vibrational modes.

  7. Linear entropy and collapse–revival phenomenon for a general formalism N-type four-level atom interacting with a single-mode field

    NASA Astrophysics Data System (ADS)

    Eied, A. A.

    2018-05-01

    In this paper, the linear entropy and collapse-revival phenomenon through the relation (< {\\hat{a}}+{\\hat{a}} > -{\\bar{n}}) in a system of N-configuration four-level atom interacting with a single-mode field with additional forms of nonlinearities of both the field and the intensity-dependent atom-field coupling functional are investigated. A factorization of the initial density operator is assumed, considering the field to be initially in a squeezed coherent states and the atom initially in its most upper excited state. The dynamical behavior of the linear entropy and the time evolution of (< {\\hat{a}}+ {\\hat{a}} > -{\\bar{n}}) are analyzed. In particular, the effects of the mean photon number, detuning, Kerr-like medium and the intensity-dependent coupling functional on the entropy and the evolution of (< {\\hat{a}}+ {\\hat{a}} > -{\\bar{n}}) are examined.

  8. All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

    PubMed Central

    2017-01-01

    Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

  9. SLAC All Access: Atomic, Molecular and Optical Science Instrument

    ScienceCinema

    Bozek, John

    2018-02-13

    John Bozek, a staff scientist at SLAC's Linac Coherent Light Source (LCLS) X-ray laser who manages the LCLS Soft X-ray Department, takes us behind the scenes at the Atomic, Molecular and Optical Science (AMO) instrument, the first of six experimental stations now operating at LCLS. Samples used in AMO experiments include atoms, molecules, clusters, and nanoscale objects such as protein crystals or viruses. Science performed at AMO includes fundamental studies of light-matter interactions in the extreme X-ray intensity of the LCLS pules, time-resolved studies of increasingly charged states of atoms and molecules, X-ray diffraction imaging of nanocrystals, and single-shot imaging of a variety of objects.

  10. A Novel Method to Reconstruct the Force Curve by Higher Harmonics of the First Two Flexural Modes in Frequency Modulation Atomic Force Microscope (FM-AFM).

    PubMed

    Zhang, Suoxin; Qian, Jianqiang; Li, Yingzi; Zhang, Yingxu; Wang, Zhenyu

    2018-06-04

    Atomic force microscope (AFM) is an idealized tool to measure the physical and chemical properties of the sample surfaces by reconstructing the force curve, which is of great significance to materials science, biology, and medicine science. Frequency modulation atomic force microscope (FM-AFM) collects the frequency shift as feedback thus having high force sensitivity and it accomplishes a true noncontact mode, which means great potential in biological sample detection field. However, it is a challenge to establish the relationship between the cantilever properties observed in practice and the tip-sample interaction theoretically. Moreover, there is no existing method to reconstruct the force curve in FM-AFM combining the higher harmonics and the higher flexural modes. This paper proposes a novel method that a full force curve can be reconstructed by any order higher harmonics of the first two flexural modes under any vibration amplitude in FM-AFM. Moreover, in the small amplitude regime, short range forces are reconstructed more accurately by higher harmonics analysis compared with fundamental harmonics using the Sader-Jarvis formula.

  11. Atom detection and photon production in a scalable, open, optical microcavity.

    PubMed

    Trupke, M; Goldwin, J; Darquié, B; Dutier, G; Eriksson, S; Ashmore, J; Hinds, E A

    2007-08-10

    A microfabricated Fabry-Perot optical resonator has been used for atom detection and photon production with less than 1 atom on average in the cavity mode. Our cavity design combines the intrinsic scalability of microfabrication processes with direct coupling of the cavity field to single-mode optical waveguides or fibers. The presence of the atom is seen through changes in both the intensity and the noise characteristics of probe light reflected from the cavity input mirror. An excitation laser passing transversely through the cavity triggers photon emission into the cavity mode and hence into the single-mode fiber. These are first steps toward building an optical microcavity network on an atom chip for applications in quantum information processing.

  12. Determination of low-frequency normal modes and structure coefficients using optimal sequence stacking method and autoregressive method in frequency domain

    NASA Astrophysics Data System (ADS)

    Majstorovic, J.; Rosat, S.; Lambotte, S.; Rogister, Y. J. G.

    2017-12-01

    Although there are numerous studies about 3D density Earth model, building an accurate one is still an engaging challenge. One procedure to refine global 3D Earth density models is based on unambiguous measurements of Earth's normal mode eigenfrequencies. To have unbiased eigenfrequency measurements one needs to deal with a variety of time records quality and especially different noise sources, while standard approaches usually include signal processing methods such as Fourier transform. Here we present estimate of complex eigenfrequencies and structure coefficients for several modes below 1 mHz (0S2, 2S1, etc.). Our analysis is performed in three steps. The first step includes the use of stacking methods to enhance specific modes of interest above the observed noise level. Out of three trials the optimal sequence estimation turned out to be the foremost compared to the spherical harmonic stacking method and receiver strip method. In the second step we apply an autoregressive method in the frequency domain to estimate complex eigenfrequencies of target modes. In the third step we apply the phasor walkout method to test and confirm our eigenfrequencies. Before conducting an analysis of time records, we evaluate how the station distribution and noise levels impact the estimate of eigenfrequencies and structure coefficients by using synthetic seismograms calculated for a 3D realistic Earth model, which includes Earth's ellipticity and lateral heterogeneity. Synthetic seismograms are computed by means of normal mode summation using self-coupling and cross-coupling of modes up to 1 mHz. Eventually, the methods tested on synthetic data are applied to long-period seismometer and superconducting gravimeter data recorded after six mega-earthquakes of magnitude greater than 8.3. Hence, we propose new estimates of structure coefficients dependent on the density variations.

  13. Principle and Reconstruction Algorithm for Atomic-Resolution Holography

    NASA Astrophysics Data System (ADS)

    Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

    2018-06-01

    Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

  14. Normal modes from the 2013 Sea of Okhotsk earthquake, the largest deep event ever recorded

    NASA Astrophysics Data System (ADS)

    Okal, E. A.

    2013-12-01

    With a moment of 4.1 10**28 dyn*cm, the Sea of Okhotsk earthquake of 24 May 2013 is the largest deep event ever recorded. This provides a unique opportunity to study the excitation of low-frequency normal modes, including overtone and radial ones. The principal questions addressed will be the possible existence of a slow component to the source, which is not warranted by preliminary results; and the possible presence of an isotropic component to the moment tensor of its source. The latter was strongly debated in the case of the 1970 Colombian event (Gilbert and Dziewonski, 1973; Okal and Geller, 1979), and clearly found absent from the source of the 1994 Bolivian one (Kikuchi and Kanamori, 1994; Okal, 1996). Critical in this respect will be the investigation of the relative excitation of the the radial modes, and in particular, the fundamental 0s0, for which a sufficiently long (90 days) time series was not available by the submission deadline.

  15. All-Atom Molecular-Level Computational Analyses of Polyurea/Fused-Silica Interfacial Decohesion Caused by Impinging Tensile Stress-Waves

    DTIC Science & Technology

    2014-01-01

    glass, the polyhedron -center atoms are all silicon and each silicon atom is surrounded by four oxygen atoms (while each oxygen atom is connected to...of non-bridging (connected to only a single network forming cation) oxygen atoms per network polyhedron and takes on a zero value in the case of...network polyhedron and takes on a value of 4.0 in the case of fused silica. In addition to the three parameters mentioned above, the “seemingly

  16. Sub-femtosecond timing jitter, all-fiber, CNT-mode-locked Er-laser at telecom wavelength.

    PubMed

    Kim, Chur; Bae, Sangho; Kieu, Khanh; Kim, Jungwon

    2013-11-04

    We demonstrate a 490-attosecond timing jitter (integration bandwidth: 10 kHz - 39.4 MHz) optical pulse train from a 78.7-MHz repetition rate, all-fiber soliton Er laser mode-locked by a fiber tapered carbon nanotube saturable absorber (ft-CNT-SA). To achieve this jitter performance, we searched for a net cavity dispersion condition where the Gordon-Haus jitter is minimized while maintaining stable soliton mode-locking. Our result shows that optical pulse trains with well below a femtosecond timing jitter can be generated from a self-starting and robust all-fiber laser operating at telecom wavelength.

  17. Optical ferris wheel for ultracold atoms

    NASA Astrophysics Data System (ADS)

    Franke-Arnold, S.; Leach, J.; Padgett, M. J.; Lembessis, V. E.; Ellinas, D.; Wright, A. J.; Girkin, J. M.; Ohberg, P.; Arnold, A. S.

    2007-07-01

    We propose a versatile optical ring lattice suitable for trapping cold and quantum degenerate atomic samples. We demonstrate the realisation of intensity patterns from pairs of Laguerre-Gauss (exp(iℓө) modes with different ℓ indices. These patterns can be rotated by introducing a frequency shift between the modes. We can generate bright ring lattices for trapping atoms in red-detuned light, and dark ring lattices suitable for trapping atoms with minimal heating in the optical vortices of blue-detuned light. The lattice sites can be joined to form a uniform ring trap, making it ideal for studying persistent currents and the Mott insulator transition in a ring geometry.

  18. 978-nm square-wave in an all-fiber single-mode ytterbium-doped fiber laser

    NASA Astrophysics Data System (ADS)

    Li, Shujie; Xu, Lixin; Gu, Chun

    2018-01-01

    A 978 nm single mode passively mode-locked all-fiber laser delivering square-wave pulses was demonstrated using a figure-8 cavity and a 75 cm commercial double-clad ytterbium-doped fiber. We found the three-level system near 978 nm was able to operate efficiently under clad pumping, simultaneously oscillation around 1030 nm well inhibited. The optimized nonlinear amplifying loop mirror made the mode locking stable and performed the square-pulses shaping. To the best of our knowledge, it is the first time to report the square-wave pulse fiber laser operating at 980 nm. The spectral width of the 978 mode-locked square pulses was about 4 nm, far greater than that of the mode-locked square pulses around 1060 nm reported before, which would be helpful to deeply understand the various square-wave pulses' natures and forming mechanisms. Compared with modulated single-mode or multimode 980 nm LDs, this kind of 980 nm square-wave sources having higher brightness, more steeper rising and falling edge and shorter pulse width, might have potential applications in pumping nanosecond ytterbium or erbium fiber lasers and amplifiers.

  19. Low-emittance tuning of storage rings using normal mode beam position monitor calibration

    NASA Astrophysics Data System (ADS)

    Wolski, A.; Rubin, D.; Sagan, D.; Shanks, J.

    2011-07-01

    We describe a new technique for low-emittance tuning of electron and positron storage rings. This technique is based on calibration of the beam position monitors (BPMs) using excitation of the normal modes of the beam motion, and has benefits over conventional methods. It is relatively fast and straightforward to apply, it can be as easily applied to a large ring as to a small ring, and the tuning for low emittance becomes completely insensitive to BPM gain and alignment errors that can be difficult to determine accurately. We discuss the theory behind the technique, present some simulation results illustrating that it is highly effective and robust for low-emittance tuning, and describe the results of some initial experimental tests on the CesrTA storage ring.

  20. A simulation of atomic force microscope microcantilever in the tapping mode utilizing couple stress theory.

    PubMed

    Abbasi, Mohammad

    2018-04-01

    The nonlinear vibration behavior of a Tapping mode atomic force microscopy (TM-AFM) microcantilever under acoustic excitation force has been modeled and investigated. In dynamic AFM, the tip-surface interactions are strongly nonlinear, rapidly changing and hysteretic. First, the governing differential equation of motion and boundary conditions for dynamic analysis are obtained using the modified couple stress theory. Afterwards, closed-form expressions for nonlinear frequency and effective nonlinear damping ratio are derived utilizing perturbation method. The effect of tip connection position on the vibration behavior of the microcantilever are also analyzed. The results show that nonlinear frequency is size dependent. According to the results, an increase in the equilibrium separation between the tip and the sample surface reduces the overall effect of van der Waals forces on the nonlinear frequency, but its effect on the effective nonlinear damping ratio is negligible. The results also indicate that both the change in the distance between tip and cantilever free end and the reduction of tip radius have significant effects on the accuracy and sensitivity of the TM-AFM in the measurement of surface forces. The hysteretic behavior has been observed in the near resonance frequency response due to softening and hardening of the forced vibration response. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Optical-bistability-enabled control of resonant light transmission for an atom-cavity system

    NASA Astrophysics Data System (ADS)

    Sawant, Rahul; Rangwala, S. A.

    2016-02-01

    The control of light transmission through a standing-wave Fabry-Pérot cavity containing atoms is theoretically and numerically investigated, when the cavity mode beam and an intersecting control beam are both close to specific atomic resonances. A four-level atomic system is considered and its interaction with the cavity mode is studied by solving for the cavity field and atomic state populations. The conditions for optical bistability of the atom-cavity system are obtained. The response of the intracavity intensity to an intersecting beam on atomic resonance is understood in the presence of stationary atoms (closed system) and nonstatic atoms (open system) in the cavity. The nonstatic system of atoms is modelled by adjusting the atomic state populations to represent the exchange of atoms in the cavity mode, which corresponds to a thermal environment where atoms are moving in and out of the cavity mode volume. The control behavior with three- and two-level atomic systems is also studied, and the rich physics arising out of these systems for closed and open atomic systems is discussed. The solutions to the models are used to interpret the steady-state and transient behavior observed by Sharma et al. [Phys. Rev. A 91, 043824 (2015)], 10.1103/PhysRevA.91.043824.

  2. Atom-atom interactions around the band edge of a photonic crystal waveguide.

    PubMed

    Hood, Jonathan D; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E; Kimble, H J

    2016-09-20

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  3. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

    PubMed Central

    Davis, Ian W.; Leaver-Fay, Andrew; Chen, Vincent B.; Block, Jeremy N.; Kapral, Gary J.; Wang, Xueyi; Murray, Laura W.; Arendall, W. Bryan; Snoeyink, Jack; Richardson, Jane S.; Richardson, David C.

    2007-01-01

    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu. PMID:17452350

  4. Metastable Atom-Activated Dissociation Mass Spectrometry of Phosphorylated and Sulfonated Peptides in Negative Ion Mode

    NASA Astrophysics Data System (ADS)

    Cook, Shannon L.; Jackson, Glen P.

    2011-06-01

    The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were Cα - C peptide backbone cleavages and neutral losses of CO2, H2O, and [CO2 + H2O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

  5. Goldstone and Higgs modes of photons inside a cavity

    NASA Astrophysics Data System (ADS)

    Yi-Xiang, Yu; Ye, Jinwu; Liu, Wu-Ming

    2013-12-01

    Goldstone and Higgs modes have been detected in various condensed matter, cold atom and particle physics experiments. Here, we demonstrate that the two modes can also be observed in optical systems with only a few (artificial) atoms inside a cavity. We establish this connection by studying the U(1)/Z2 Dicke model where N qubits (atoms) coupled to a single photon mode. We determine the Goldstone and Higgs modes inside the super-radiant phase and their corresponding spectral weights by performing both 1/J = 2/N expansion and exact diagonalization (ED) study at a finite N. We find nearly perfect agreements between the results achieved by the two approaches when N gets down even to N = 2. The quantum finite size effects at a few qubits make the two modes quite robust against an effectively small counterrotating wave term. We present a few schemes to reduce the critical coupling strength, so the two modes can be observed in several current available experimental systems by just conventional optical measurements.

  6. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

    PubMed

    Ahmed, Aqeel; Rippmann, Friedrich; Barnickel, Gerhard; Gohlke, Holger

    2011-07-25

    A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 Å) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.

  7. Hybrid mode-locked erbium-doped all-fiber soliton laser with a distributed polarizer.

    PubMed

    Chernykh, D S; Krylov, A A; Levchenko, A E; Grebenyukov, V V; Arutunyan, N R; Pozharov, A S; Obraztsova, E D; Dianov, E M

    2014-10-10

    A soliton-type erbium-doped all-fiber ring laser hybrid mode-locked with a co-action of arc-discharge single-walled carbon nanotubes (SWCNTs) and nonlinear polarization evolution (NPE) is demonstrated. For the first time, to the best of our knowledge, boron nitride-doped SWCNTs were used as a saturable absorber for passive mode-locking initiation. Moreover, the NPE was introduced through the implementation of the short-segment polarizing fiber. Owing to the NPE action in the laser cavity, significant pulse length shortening as well as pulse stability improvement were observed as compared with a SWCNTs-only mode-locked laser. The shortest achieved pulse width of near transform-limited solitons was 222 fs at the output average power of 9.1 mW and 45.5 MHz repetition frequency, corresponding to the 0.17 nJ pulse energy.

  8. Entanglement between collective fields via atomic coherence effects

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang Xiu; Department of Physics, Xiaogan University, Xiaogan 432000; Hu Xiangming

    2010-01-15

    We explore the quantum entanglement between two collective fields via atomic coherence effects. For three-level atoms in V configuration driven by two applied fields on two-photon resonance, one coherent superposition of the excited states is not excited, which is the counterpart of coherent population trapping. The coherence-induced depopulation makes two cavity fields in each collection combine into a quantum-beat, i.e., equivalently, the difference mode of the two components decouples from the driven atoms. The two sum modes, when they are arranged in the four-wave mixinglike interactions, can be prepared in Einstein-Podolsky-Rosen entangled state. Correspondingly, any two individual fields from differentmore » collective modes are entangled with each other. Furthermore, the effects of thermal reservoir and laser linewidths are discussed, and a generalization is given to the case in which each quantum beat involves more than two modes.« less

  9. Normal vibrational modes of phospholipid bilayers observed by low-frequency Raman scattering

    NASA Astrophysics Data System (ADS)

    Surovtsev, N. V.; Dmitriev, A. A.; Dzuba, S. A.

    2017-03-01

    Low-frequency Raman spectra of multilamellar vesicles made either of 1-palmitoyl-2-oleoyl-s n -glycero-3-phosphocholine (POPC) or 1,2-dipalmitoyl-s n -glycero-3-phosphocholine (DPPC) have been studied in a wide temperature range. Below 0 ∘C two peaks are found at frequencies around 8-9 and 14 -17 c m -1 and attributed to the normal vibrational modes of the phospholipid bilayer, which are determined by the bilayer thickness and stiffness (elastic modulus). The spectral positions of the peaks depend on the temperature and the bilayer composition. It is suggested that the ratio of the intensities of the first and second peaks can serve as a measure of the interleaflet elastic coupling. The addition of cholesterol to the phospholipid bilayer leads to peak shift and broadening, which may be assigned to the composition heterogeneities commonly attributed to the lipid raft formation.

  10. Broadband features of passively harmonic mode locking in dispersion-managed erbium-doped all-fiber lasers

    NASA Astrophysics Data System (ADS)

    Geng, Y.; Li, L.; Shu, C. J.; Wang, Y. F.; Tang, D. Y.; Zhao, L. M.

    2018-06-01

    Broadband features of passively harmonic mode locking (HML) in dispersion-managed erbium-doped all-fiber lasers are explored. The bandwidth of HML state is generally narrower than that of fundamental mode locking before pulse breaking occurs. There exists a broadest bandwidth versus the order of HML. HML state with bandwidth up to 61.5 nm is obtained.

  11. Extending of flat normal dispersion profile in all-solid soft glass nonlinear photonic crystal fibres

    NASA Astrophysics Data System (ADS)

    Siwicki, Bartłomiej; Kasztelanic, Rafał; Klimczak, Mariusz; Cimek, Jarosław; Pysz, Dariusz; Stępień, Ryszard; Buczyński, Ryszard

    2016-06-01

    The bandwidth of coherent supercontinuum generated in optical fibres is strongly determined by the all-normal dispersion characteristic of the fibre. We investigate all-normal dispersion limitations in all-solid oxide-based soft glass photonic crystal fibres with various relative inclusion sizes and lattice constants. The influence of material dispersion on fibre dispersion characteristics for a selected pair of glasses is also examined. A relation between the material dispersion of the glasses and the fibre dispersion has been described. We determined the parameters which limit the maximum range of flattened all-normal dispersion profile achievable for the considered pair of heavy-metal-oxide soft glasses.

  12. Exponential protection of zero modes in Majorana islands.

    PubMed

    Albrecht, S M; Higginbotham, A P; Madsen, M; Kuemmeth, F; Jespersen, T S; Nygård, J; Krogstrup, P; Marcus, C M

    2016-03-10

    Majorana zero modes are quasiparticle excitations in condensed matter systems that have been proposed as building blocks of fault-tolerant quantum computers. They are expected to exhibit non-Abelian particle statistics, in contrast to the usual statistics of fermions and bosons, enabling quantum operations to be performed by braiding isolated modes around one another. Quantum braiding operations are topologically protected insofar as these modes are pinned near zero energy, with the departure from zero expected to be exponentially small as the modes become spatially separated. Following theoretical proposals, several experiments have identified signatures of Majorana modes in nanowires with proximity-induced superconductivity and atomic chains, with small amounts of mode splitting potentially explained by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced superconducting Coulomb island (a 'Majorana island') that is isolated from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy Majorana modes. We observe exponential suppression of energy splitting with increasing wire length. For short devices of a few hundred nanometres, sub-gap state energies oscillate as the magnetic field is varied, as is expected for hybridized Majorana modes. Splitting decreases by a factor of about ten for each half a micrometre of increased wire length. For devices longer than about one micrometre, transport in strong magnetic fields occurs through a zero-energy state that is energetically isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance peaks, consistent with teleportation via Majorana modes. Our results help to explain the trivial-to-topological transition in finite systems and to quantify the scaling of topological protection with end-mode separation.

  13. The Use of Contact Mode Atomic Force Microscopy in Aqueous Medium for Structural Analysis of Spinach Photosynthetic Complexes

    DOE PAGES

    Phuthong, Witchukorn; Huang, Zubin; Wittkopp, Tyler M.; ...

    2015-07-28

    To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach ( Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsicmore » domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Furthermore, our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.« less

  14. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Comandi, G.L.; Chiofalo, M.L.; Toncelli, R.

    Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration {eta} between two test bodies-of different compositions, falling in the gravitational field of a source mass--if the measurement is made to the level of {eta}{approx_equal}10{sup -13} or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report onmore » the progress made with the 'Galileo Galilei on the ground' (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation-in particular, its normal modes (Part I) and rejection of common mode effects (Part II)-can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.« less

  15. Quantized mode of a leaky cavity

    NASA Astrophysics Data System (ADS)

    Dutra, S. M.; Nienhuis, G.

    2000-12-01

    We use Thomson's classical concept of mode of a leaky cavity to develop a quantum theory of cavity damping. This theory generalizes the conventional system-reservoir theory of high-Q cavity damping to arbitrary Q. The small system now consists of damped oscillators corresponding to the natural modes of the leaky cavity rather than undamped oscillators associated with the normal modes of a fictitious perfect cavity. The formalism unifies semiclassical Fox-Li modes and the normal modes traditionally used for quantization. It also lays the foundations for a full quantum description of excess noise. The connection with Siegman's semiclassical work is straightforward. In a wider context, this theory constitutes a radical departure from present models of dissipation in quantum mechanics: unlike conventional models, system and reservoir operators no longer commute with each other. This noncommutability is an unavoidable consequence of having to use natural cavity modes rather than normal modes of a fictitious perfect cavity.

  16. Redistribution of carbonyl stretch mode energy in isolated and solvated N-methylacetamide: kinetic energy spectral density analyses.

    PubMed

    Jeon, Jonggu; Cho, Minhaeng

    2011-12-07

    The vibrational energy transfer from the excited carbonyl stretch mode in N-deuterated N-methylacetamide (NMA-d), both in isolation and in a heavy water cluster, is studied with nonequilibrium molecular dynamics (NEMD) simulations, employing a quantum mechanical/molecular mechanical (QM∕MM) force field at the semiempirical PM3 level. The nonequilibrium ensemble of vibrationally excited NMA-d is prepared by perturbing the positions and velocities of the carbonyl C and O atoms and its NEMD trajectories are obtained with a leap-frog algorithm properly modified for the initial perturbation. In addition to the time-domain analysis of the kinetic and potential energies, a novel method for the spectral analysis of the atomic kinetic energies is developed, in terms of the spectral density of kinetic energy, which provides the time-dependent changes of the frequency-resolved kinetic energies without the complications of normal mode analysis at every MD time step. Due to the QM description of the solute electronic structure, the couplings among the normal modes are captured more realistically than with classical force fields. The energy transfer in the isolated NMA-d is found to proceed first from the carbonyl bond to other modes with time scales of 3 ps or less, and then among the other modes over 3-21 ps. In the solvated NMA-d, most of the excess energy is first transferred to other intramolecular modes within 5 ps, which is subsequently dissipated to solvent with 7-19 ps time scales. The contribution of the direct energy transfer from the carbonyl bond to solvent was only 5% with ~7 ps time scale. Solvent reorganization that leads to destabilization of the electrostatic interactions is found to be crucial in the long time relaxation of the excess energy, while the water intramolecular modes do not contribute significantly. Detailed mode-specific energy transfer pathways are deduced for the isolated and solvated NMA-d and they show that the energy transfer in NMA-d is a

  17. A latest developed all permanent magnet ECRIS for atomic physics research at IMP

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sun, L.T.; Zhao, H.W.; Zhang, Z.M.

    2006-03-15

    Electron cyclotron resonance (ECR) ion sources have been used for atomic physics research for a long time. With the development of atomic physics research in the Institute of Modern Physics (IMP), additional high performance experimental facilities are required. A 300 kV high voltage (HV) platform has been under construction since 2003, and an all permanent magnet ECR ion source is supposed to be put on the platform. Lanzhou all permanent magnet ECR ion source No. 2 (LAPECR2) is a latest developed all permanent magnet ECRIS. It is a 900 kg weight and null-set 650 mmx562 mm outer dimension (magnetic body)more » ion source. The injection magnetic field of the source is 1.28 T and the extraction magnetic field is 1.07 T. This source is designed to be running at 14.5 GHz. The high magnetic field inside the plasma chamber enables the source to give good performances at 14.5 GHz. LAPECR2 source is now under commissioning in IMP. In this article, the typical parameters of the source LAPECR2 are listed, and the typical results of the preliminary commissioning are presented.« less

  18. Wide range local resistance imaging on fragile materials by conducting probe atomic force microscopy in intermittent contact mode

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vecchiola, Aymeric; Concept Scientific Instruments, ZA de Courtaboeuf, 2 rue de la Terre de Feu, 91940 Les Ulis; Unité Mixte de Physique CNRS-Thales UMR 137, 1 avenue Augustin Fresnel, 91767 Palaiseau

    An imaging technique associating a slowly intermittent contact mode of atomic force microscopy (AFM) with a home-made multi-purpose resistance sensing device is presented. It aims at extending the widespread resistance measurements classically operated in contact mode AFM to broaden their application fields to soft materials (molecular electronics, biology) and fragile or weakly anchored nano-objects, for which nanoscale electrical characterization is highly demanded and often proves to be a challenging task in contact mode. Compared with the state of the art concerning less aggressive solutions for AFM electrical imaging, our technique brings a significantly wider range of resistance measurement (over 10more » decades) without any manual switching, which is a major advantage for the characterization of materials with large on-sample resistance variations. After describing the basics of the set-up, we report on preliminary investigations focused on academic samples of self-assembled monolayers with various thicknesses as a demonstrator of the imaging capabilities of our instrument, from qualitative and semi-quantitative viewpoints. Then two application examples are presented, regarding an organic photovoltaic thin film and an array of individual vertical carbon nanotubes. Both attest the relevance of the technique for the control and optimization of technological processes.« less

  19. Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.

    PubMed

    Machado, Agnes Thiane Pereira; Fonseca, Emanuella Maria Barreto; Reis, Marcelo Augusto Dos; Saraiva, Antonio Marcos; Santos, Clelton Aparecido Dos; de Toledo, Marcelo Augusto Szymanski; Polikarpov, Igor; de Souza, Anete Pereira; Aparicio, Ricardo; Iulek, Jorge

    2017-10-01

    Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein. © 2017 Wiley Periodicals, Inc.

  20. Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

    PubMed

    Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

    2014-07-24

    Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

  1. Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C.

    2014-06-25

    Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagatesmore » into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Furthermore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.« less

  2. High Energy, Single-Mode, All-Solid-State Nd:YAG Laser

    NASA Technical Reports Server (NTRS)

    Prasad, Narasimha S.; Singh, Upendra N.; Hovis, Floyd

    2006-01-01

    In this paper, recent progress made in the design and development of an all-solid-state, single longitudinal mode, conductively cooled Nd:YAG laser operating at 1064 nm wavelength for UV lidar for ozone sensing applications is presented. Currently, this pump laser provides an output pulse energy of greater than 1.1 J/pulse at 50 Hz PRF and a pulsewidth of 22 ns. The spatial profile of the output beam is a rectangular super Gaussian. Electrical-to-optical system efficiency of greater than 7% and a minimum M(sup 2) value of less than 2 have been achieved.

  3. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

    PubMed

    Wang, Jinan; Shao, Qiang; Xu, Zhijian; Liu, Yingtao; Yang, Zhuo; Cossins, Benjamin P; Jiang, Hualiang; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang

    2014-01-09

    Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.

  4. The study on the nanomachining property and cutting model of single-crystal sapphire by atomic force microscopy.

    PubMed

    Huang, Jen-Ching; Weng, Yung-Jin

    2014-01-01

    This study focused on the nanomachining property and cutting model of single-crystal sapphire during nanomachining. The coated diamond probe is used to as a tool, and the atomic force microscopy (AFM) is as an experimental platform for nanomachining. To understand the effect of normal force on single-crystal sapphire machining, this study tested nano-line machining and nano-rectangular pattern machining at different normal force. In nano-line machining test, the experimental results showed that the normal force increased, the groove depth from nano-line machining also increased. And the trend is logarithmic type. In nano-rectangular pattern machining test, it is found when the normal force increases, the groove depth also increased, but rather the accumulation of small chips. This paper combined the blew by air blower, the cleaning by ultrasonic cleaning machine and using contact mode probe to scan the surface topology after nanomaching, and proposed the "criterion of nanomachining cutting model," in order to determine the cutting model of single-crystal sapphire in the nanomachining is ductile regime cutting model or brittle regime cutting model. After analysis, the single-crystal sapphire substrate is processed in small normal force during nano-linear machining; its cutting modes are ductile regime cutting model. In the nano-rectangular pattern machining, due to the impact of machined zones overlap, the cutting mode is converted into a brittle regime cutting model. © 2014 Wiley Periodicals, Inc.

  5. Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study

    DOE PAGES

    Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; ...

    2015-07-29

    Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

  6. Chemical bond imaging using higher eigenmodes of tuning fork sensors in atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ebeling, Daniel; Zhong, Qigang; Ahles, Sebastian; Chi, Lifeng; Wegner, Hermann A.; Schirmeisen, André

    2017-05-01

    We demonstrate the ability of resolving the chemical structure of single organic molecules using non-contact atomic force microscopy with higher normal eigenmodes of quartz tuning fork sensors. In order to achieve submolecular resolution, CO-functionalized tips at low temperatures are used. The tuning fork sensors are operated in ultrahigh vacuum in the frequency modulation mode by exciting either their first or second eigenmode. Despite the high effective spring constant of the second eigenmode (on the order of several tens of kN/m), the force sensitivity is sufficiently high to achieve atomic resolution above the organic molecules. This is observed for two different tuning fork sensors with different tip geometries (small tip vs. large tip). These results represent an important step towards resolving the chemical structure of single molecules with multifrequency atomic force microscopy techniques where two or more eigenmodes are driven simultaneously.

  7. Notch strengthening or weakening governed by transition of shear failure to normal mode fracture

    PubMed Central

    Lei, Xianqi; Li, Congling; Shi, Xinghua; Xu, Xianghong; Wei, Yujie

    2015-01-01

    It is generally observed that the existence of geometrical discontinuity like notches in materials will lead to strength weakening, as a resultant of local stress concentration. By comparing the influence of notches to the strength of three typical materials, aluminum alloys with intermediate tensile ductility, metallic glasses with no tensile ductility, and brittle ceramics, we observed strengthening in aluminum alloys and metallic glasses: Tensile strength of the net section in circumferentially notched cylinders increases with the constraint quantified by the ratio of notch depth over notch root radius; in contrast, the ceramic exhibit notch weakening. The strengthening in the former two is due to resultant deformation transition: Shear failure occurs in intact samples while samples with deep notches break in normal mode fracture. No such deformation transition was observed in the ceramic, and stress concentration leads to its notch weakening. The experimental results are confirmed by theoretical analyses and numerical simulation. The results reported here suggest that the conventional criterion to use brittleness and/or ductility to differentiate notch strengthening or weakening is not physically sound. Notch strengthening or weakening relies on the existence of failure mode transition and materials exhibiting shear failure while subjected to tension will notch strengthen. PMID:26022892

  8. Finite element normal mode analysis of resistance welding jointed of dissimilar plate hat structure

    NASA Astrophysics Data System (ADS)

    Nazri, N. A.; Sani, M. S. M.

    2017-10-01

    Structural joints offer connection between structural element (beam, plate, solid etc.) in order to build a whole assembled structure. The complex behaviour of connecting elements plays a valuable role in characteristics of dynamic such as natural frequencies and mode shapes. In automotive structures, the trustworthiness arrangement of the structure extremely depends on joints. In this paper, top hat structure is modelled and designed with spot welding joint using dissimilar materials which is mild steel 1010 and stainless steel 304, using finite element software. Different types of connector elements such as rigid body element (RBE2), welding joint element (CWELD), and bar element (CBAR) are applied to represent real connection between two dissimilar plates. Normal mode analysis is simulated with different types of joining element in order to determine modal properties. Natural frequencies using RBE2, CBAR and CWELD are compared to equivalent rigid body method. Connection that gives the lowest percentage error among these three will be selected as the most reliable joining for resistance spot weld. From the analysis, it is shown that CWELD is better compared to others in term of weld joining among dissimilar plate materials. It is expected that joint modelling of finite element plays significant role in structural dynamics.

  9. Normal modes of a superconducting transmission-line resonator with embedded lumped element circuit components

    NASA Astrophysics Data System (ADS)

    Mortensen, Henrik Lund; Mølmer, Klaus; Andersen, Christian Kraglund

    2016-11-01

    We present a method to identify the coupled, normal modes of a superconducting transmission line with an embedded lumped element circuit. We evaluate the effective transmission-line nonlinearities in the case of Kerr-like Josephson interactions in the circuit and in the case where the embedded circuit constitutes a qubit degree of freedom, which is Rabi coupled to the field in the transmission line. Our theory quantitatively accounts for the very high and positive Kerr nonlinearities observed in a recent experiment [M. Rehák, P. Neilinger, M. Grajcar, G. Oelsner, U. Hübner, E. Il'ichev, and H.-G. Meyer, Appl. Phys. Lett. 104, 162604 (2014), 10.1063/1.4873719], and we can evaluate the accomplishments of modified versions of the experimental circuit.

  10. Measurement of nonlinear normal modes using multi-harmonic stepped force appropriation and free decay

    NASA Astrophysics Data System (ADS)

    Ehrhardt, David A.; Allen, Matthew S.

    2016-08-01

    Nonlinear Normal Modes (NNMs) offer tremendous insight into the dynamic behavior of a nonlinear system, extending many concepts that are familiar in linear modal analysis. Hence there is interest in developing methods to experimentally and numerically determine a system's NNMs for model updating or simply to characterize its dynamic response. Previous experimental work has shown that a mono-harmonic excitation can be used to isolate a system's dynamic response in the neighborhood of a NNM along the main backbones of a system. This work shows that a multi-harmonic excitation is needed to isolate a NNM when well separated linear modes of a structure couple to produce an internal resonance. It is shown that one can tune the multiple harmonics of the input excitation using a plot of the input force versus the response velocity until the area enclosed by the force-velocity curve is minimized. Once an appropriated NNM is measured, one can increase the force level and retune the frequency to obtain a NNM at a higher amplitude or remove the excitation and measure the structure's decay down a NNM backbone. This work explores both methods using simulations and measurements of a nominally-flat clamped-clamped beam excited at a single point with a magnetic force. Numerical simulations are used to validate the method in a well defined environment and to provide comparison with the experimentally measured NNMs. The experimental results seem to produce a good estimate of two NNMs along their backbone and part of an internal resonance branch. Full-field measurements are then used to further explore the couplings between the underlying linear modes along the identified NNMs.

  11. Scheme for approximate conditional teleportation of an unknown atomic state without the Bell-state measurement

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zheng Shibiao

    2004-06-01

    We propose a scheme for approximately and conditionally teleporting an unknown atomic state in cavity QED. Our scheme does not involve the Bell-state measurement and thus an additional atom is unnecessary. Only two atoms and one single-mode cavity are required. The scheme may be used to teleport the state of a cavity mode to another mode using a single atom. The idea may also be used to teleport the state of a trapped ion.

  12. All-solid-state single longitudinal mode MOPA laser system

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang; Gu, Haidong; Hu, Wenhua; Ren, Shilong

    2018-03-01

    Side diode pumped electro-optical Q Switching Nd: YAG is demonstrated as master oscillator. F-P etalon and twisted-mode cavity combined configuration is introduced to select longitudinal modes. The seed light experiences a round trip through the two flash pump amplifiers, in this device, the 4f image transmission system and SBS phase conjugate mirror is adopted in order to improved beam quality, by compensating the heat depolarization effect and eliminate wave-front distortion. In the condition of 1 or 5 repetitions of the wavelength at 1064nm, it produces the pulse energy of 300mJ, pulse width of 12ns, and energy instability (RMS) below 3% in single longitudinal mode operation. With a type two-phase matched KTP crystal, 532nm green light is yielded, at 1 Hz repetition rate, the pulse energy of green light is more than 150mJ.

  13. Guided-mode interactions in thin films with surface corrugation

    NASA Astrophysics Data System (ADS)

    Seshadri, S. R.

    1994-12-01

    The guided modes in a thin-film planar dielectric waveguide sandwiched between a cover and a substrate (two different dielectrics) are considered. The interface between the cover and the film has a smooth corrugation in the longitudinal direction. For weak corrugations, the guided-mode interactions are investigated using the expansion in terms of ideal normal modes. A corresponding treament is given for the not-so-weak corrugations using the expansion in terms of local normal modes. The coupling coefficients are evaluated and reduced to simple forms. The theories are specialized for the treatment of contradirectional coupling between two guided modes taking place selectively in the neighborhood of the Bragg frequency. The coupled-mode equations governing the contradirectional interaction obtained from the local normal mode expansion procedure, in the limit of weak periodic corrugations, are identical to those deduced directly using the ideal normal mode expansion technique. The treatments for both the transverse electric and the transvers magnetic modes are included.

  14. All-fiber Yb-doped fiber laser passively mode-locking by monolayer MoS2 saturable absorber

    NASA Astrophysics Data System (ADS)

    Zhang, Yue; Zhu, Jianqi; Li, Pingxue; Wang, Xiaoxiao; Yu, Hua; Xiao, Kun; Li, Chunyong; Zhang, Guangyu

    2018-04-01

    We report on an all-fiber passively mode-locked ytterbium-doped (Yb-doped) fiber laser with monolayer molybdenum disulfide (ML-MoS2) saturable absorber (SA) by three-temperature zone chemical vapor deposition (CVD) method. The modulation depth, saturation fluence, and non-saturable loss of this ML-MoS2 are measured to be 3.6%, 204.8 μJ/cm2 and 6.3%, respectively. Based on this ML-MoS2SA, a passively mode-locked Yb-doped fiber laser has been achieved at 979 nm with pulse duration of 13 ps and repetition rate of 16.51 MHz. A mode-locked fiber laser at 1037 nm is also realized with a pulse duration of 475 ps and repetition rate of 26.5 MHz. To the best of our knowledge, this is the first report that the ML-MoS2 SA is used in an all-fiber Yb-doped mode-locked fiber laser at 980 nm. Our work further points the excellent saturable absorption ability of ML-MoS2 in ultrafast photonic applications.

  15. Toward Single Atom Chains with Exfoliated Tellurium.

    PubMed

    Churchill, Hugh O H; Salamo, Gregory J; Yu, Shui-Qing; Hironaka, Takayuki; Hu, Xian; Stacy, Jeb; Shih, Ishiang

    2017-08-10

    We demonstrate that the atom chain structure of Te allows it to be exfoliated as ultra-thin flakes and nanowires. Atomic force microscopy of exfoliated Te shows that thicknesses of 1-2 nm and widths below 100 nm can be exfoliated with this method. The Raman modes of exfoliated Te match those of bulk Te, with a slight shift (4 cm -1 ) due to a hardening of the A 1 and E modes. Polarized Raman spectroscopy is used to determine the crystal orientation of exfoliated Te flakes. These experiments establish exfoliation as a route to achieve nanoscale trigonal Te while also demonstrating the potential for fabrication of single atom chains of Te.

  16. Vertical normal modes of a mesoscale model using a scaled height coordinate

    NASA Technical Reports Server (NTRS)

    Lipton, A. E.; Pielke, R. A.

    1986-01-01

    Vertical modes were derived for a version of the Colorado State Regional Atmospheric Mesoscale Modeling System. The impacts of three options for dealing with the upper boundary of the model were studied. The standard model formulation holds pressure constant at a fixed altitude near the model top, and produces a fastest mode with a speed of about 90 m/sec. An alternative formulation, which allows for an external mode, could require recomputation of vertical modes for every surface elevation on the horizontal grid unless the modes are derived in a particular way. These results have bearing on the feasibility of applying vertical mode initialization to models with scaled height coordinates.

  17. Modeling the Internal Structure of Mars Using Normal Mode Relaxation Theory

    NASA Astrophysics Data System (ADS)

    Pithawala, T. M.; Ghent, R. R.; Bills, B. G.

    2010-12-01

    We seek to resolve an apparent paradox between two sets of observations, which seem to suggest quite different thermal structures for the deep interior of Mars. The orbit of Phobos is observed to be accelerating along-track at a rate of (273.4 ± 1.2) 10^(-5) deg/yr^(2), which implies that the orbit is shrinking at (4.03 ± 0.03) cm/yr, and losing energy at a rate of 3.4 MW. The most likely sink for that energy is tidal dissipation within Mars, seemingly requiring a warm interior. However, static support of the gravity and topography of Mars requires a thick elastic lithosphere, indicating a relatively cool (and therefore stiff) mantle. Using normal mode relaxation theory we model the internal viscosity structure of Mars by analyzing its response to tidal forcing from Phobos. We investigate spherical axisymmetric layered viscoelastic models, seeking to satisfy what is known about planetary differentiation, to support large-scale topography via a thick elastic lithosphere, and to yield the observed tidal dissipation rate. We present a family of 4-layer models (core, mantle, lithosphere, and thin weak layer) that satisfy these constraints, and discuss the implications for Mars’ internal structure.

  18. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

  19. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Perilla, Juan R.; Schulten, Klaus

    2017-07-01

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

  20. The all-too-flexible abductive method: ATOM's normative status.

    PubMed

    Romeijn, Jan-Willem

    2008-09-01

    The author discusses the abductive theory of method (ATOM) by Brian Haig from a philosophical perspective, connecting his theory with a number of issues and trends in contemporary philosophy of science. It is argued that as it stands, the methodology presented by Haig is too permissive. Both the use of analogical reasoning and the application of exploratory factor analysis leave us with too many candidate theories to choose from, and explanatory coherence cannot be expected to save the day. The author ends with some suggestions to remedy the permissiveness and lack of normative force in ATOM, deriving from the experimental practice within which psychological data are produced.

  1. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

    NASA Astrophysics Data System (ADS)

    Reinhardt, Aleks; Doye, Jonathan P. K.; Noya, Eva G.; Vega, Carlos

    2012-11-01

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

  2. High-Q lattice mode matched structural resonances in terahertz metasurfaces

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xu, Ningning; Zhang, Weili, E-mail: weili.zhang@okstate.edu; Singh, Ranjan, E-mail: ranjans@ntu.edu.sg

    2016-07-11

    The quality (Q) factor of metamaterial resonances is limited by the radiative and non-radiative losses. At terahertz frequencies, the dominant loss channel is radiative in nature since the non-radiative losses are low due to high conductivity of metals. Radiative losses could be suppressed by engineering the meta-atom structure. However, such suppression usually occurs at the fundamental resonance mode which is typically a closed mode resonance such as an inductive-capacitive resonance or a Fano resonance. Here, we report an order of magnitude enhancement in Q factor of all the structural eigenresonances of a split-ring resonator fueled by the lattice mode matching.more » We match the fundamental order diffractive mode to each of the odd and even eigenresonances, thus leading to a tremendous line-narrowing of all the resonances. Such precise tailoring and control of the structural resonances in a metasurface lattice could have potential applications in low-loss devices, sensing, and design of high-Q metamaterial cavities.« less

  3. Three-mode all-optical (de)multiplexing on a SOI chip

    NASA Astrophysics Data System (ADS)

    Le, Yan-Si; Wang, Zhi; Li, Zhi-Yong; Li, Ying; Li, Qiang; Cui, Can; Wu, Chong-Qing

    2018-01-01

    An on-chip three-mode division multiplexing circuit using a simple ADC-based TE0 & TE1 & TE2 (de)multiplexer is demonstrated to improve the link capacity of on-chip optical interconnects. The proposed (de)multiplexer does not contain any tapered waveguide which is different from the previous mode (de)multiplexer based on ADCs. Here, we choose multimode waveguide width first and then confirm corresponding width of the other two waveguides. Thus the bus waveguide without any tapers can not only reduce complexity of (de)multiplexer but also reduce difficulty of the fabrication. Our simulation results show that the hybrid multiplexer has relatively low loss and low crosstalk about -40 dB, -26.99 dB and -28.72 dB for each mode around 1550 nm with a width-variation w =± 25 nm. These properties make the proposed mode-(de)multiplexer suitable for application in high-capacity data transmission.

  4. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

    PubMed

    Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

    2015-05-12

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from

  5. A control approach to cross-coupling compensation of piezotube scanners in tapping-mode atomic force microscope imaging.

    PubMed

    Wu, Ying; Shi, Jian; Su, Chanmin; Zou, Qingze

    2009-04-01

    In this article, an approach based on the recently developed inversion-based iterative control (IIC) to cancel the cross-axis coupling effect of piezoelectric tube scanners (piezoscanners) in tapping-mode atomic force microscope (AFM) imaging is proposed. Cross-axis coupling effect generally exists in piezoscanners used for three-dimensional (x-y-z axes) nanopositioning in applications such as AFM, where the vertical z-axis movement can be generated by the lateral x-y axes scanning. Such x/y-to-z cross-coupling becomes pronounced when the scanning is at large range and/or at high speed. In AFM applications, the coupling-caused position errors, when large, can generate various adverse effects, including large imaging and topography distortions, and damage of the cantilever probe and/or the sample. This paper utilizes the IIC technique to obtain the control input to precisely track the coupling-caused x/y-to-z displacement (with sign-flipped). Then the obtained input is augmented as a feedforward control to the existing feedback control in tapping-mode imaging, resulting in the cancellation of the coupling effect. The proposed approach is illustrated through two exemplary applications in industry, the pole-tip recession examination, and the nanoasperity measurement on hard-disk drive. Experimental results show that the x/y-to-z coupling effect in large-range (20 and 45 microm) tapping-mode imaging at both low to high scan rates (2, 12.2 to 24.4 Hz) can be effectively removed.

  6. Arc plasma generator of atomic driver for steady-state negative ion source.

    PubMed

    Ivanov, A A; Belchenko, Yu I; Davydenko, V I; Ivanov, I A; Kolmogorov, V V; Listopad, A A; Mishagin, V V; Putvinsky, S V; Shulzhenko, G I; Smirnov, A

    2014-02-01

    The paper reviews the results of development of steady-state arc-discharge plasma generator with directly heated LaB6 cathode. This arc-discharge plasma generator produces a plasma jet which is to be converted into an atomic one after recombination on a metallic plate. The plate is electrically biased relative to the plasma in order to control the atom energies. Such an intensive jet of hydrogen atoms can be used in negative ion sources for effective production of negative ions on a cesiated surface of plasma grid. All elements of the plasma generator have an augmented water cooling to operate in long pulse mode or in steady state. The thermo-mechanical stresses and deformations of the most critical elements of the plasma generator were determined by simulations. Magnetic field inside the discharge chamber was optimized to reduce the local power loads. The first tests of the steady-state arc plasma generator prototype have performed in long-pulse mode.

  7. Trapped atoms along nanophotonic resonators

    NASA Astrophysics Data System (ADS)

    Fields, Brian; Kim, May; Chang, Tzu-Han; Hung, Chen-Lung

    2017-04-01

    Many-body systems subject to long-range interactions have remained a very challenging topic experimentally. Ultracold atoms trapped in extreme proximity to the surface of nanophotonic structures provides a dynamic system combining the strong atom-atom interactions mediated by guided mode photons with the exquisite control implemented with trapped atom systems. The hybrid system promises pair-wise tunability of long-range interactions between atomic pseudo spins, allowing studies of quantum magnetism extending far beyond nearest neighbor interactions. In this talk, we will discuss our current status developing high quality nanophotonic ring resonators, engineered on CMOS compatible optical chips with integrated nanostructures that, in combination with a side illuminating beam, can realize stable atom traps approximately 100nm above the surface. We will report on our progress towards loading arrays of cold atoms near the surface of these structures and studying atom-atom interaction mediated by photons with high cooperativity.

  8. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent.

    PubMed

    Mulholland, Kelly; Siddiquei, Farzana; Wu, Chun

    2017-07-19

    RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence. The most stable binding mode identified for the duplex, parallel, antiparallel and hybrid G-quadruplexes is an intercalation, bottom stacking, top intercalation and bottom intercalation mode, respectively. The intercalation mode with similar binding strength to both the duplex and the G-quadruplexes, explains the lack of binding selectivity of RHPS4 to the G-quadruplex form. Therefore, a ligand modification that destabilizes the duplex intercalation mode but stabilizes the G-quadruplex intercalation mode will improve the binding selectivity toward G-quadruplex. The intercalation mode of RHPS4 to both the duplex and the antiparallel and the hybrid G-quadruplex follows a base flipping-insertion mechanism rather than an open-insertion mechanism. The groove binding, the side binding and the intercalation with flipping out of base were observed to be intermediate states before the full intercalation state with paired bases.

  9. Self-organization of atoms coupled to a chiral reservoir

    NASA Astrophysics Data System (ADS)

    Eldredge, Zachary; Jarzynski, Christopher; Chang, Darrick; Gorshkov, Alexey

    2016-05-01

    Tightly confined modes of light, as in optical nanofibers or photonics crystal waveguides, can lead to large optical coupling in atomic systems, which mediates long-range interactions between atoms. These one-dimensional systems can naturally possess couplings which are asymmetric between modes in different directions. In this poster, we examine the self-organizing behavior of atoms in one dimension coupled to a chiral reservoir. We determine the behavior of the self-organized solution to the equations of motion in different parameter regimes, relative to both the detuning of the pump laser and the degree of reservoir chirality. In addition to the spatial configuration of self-organized atoms, we calculate possible experimental signatures.

  10. Causality analysis of leading singular value decomposition modes identifies rotor as the dominant driving normal mode in fibrillation

    NASA Astrophysics Data System (ADS)

    Biton, Yaacov; Rabinovitch, Avinoam; Braunstein, Doron; Aviram, Ira; Campbell, Katherine; Mironov, Sergey; Herron, Todd; Jalife, José; Berenfeld, Omer

    2018-01-01

    Cardiac fibrillation is a major clinical and societal burden. Rotors may drive fibrillation in many cases, but their role and patterns are often masked by complex propagation. We used Singular Value Decomposition (SVD), which ranks patterns of activation hierarchically, together with Wiener-Granger causality analysis (WGCA), which analyses direction of information among observations, to investigate the role of rotors in cardiac fibrillation. We hypothesized that combining SVD analysis with WGCA should reveal whether rotor activity is the dominant driving force of fibrillation even in cases of high complexity. Optical mapping experiments were conducted in neonatal rat cardiomyocyte monolayers (diameter, 35 mm), which were genetically modified to overexpress the delayed rectifier K+ channel IKr only in one half of the monolayer. Such monolayers have been shown previously to sustain fast rotors confined to the IKr overexpressing half and driving fibrillatory-like activity in the other half. SVD analysis of the optical mapping movies revealed a hierarchical pattern in which the primary modes corresponded to rotor activity in the IKr overexpressing region and the secondary modes corresponded to fibrillatory activity elsewhere. We then applied WGCA to evaluate the directionality of influence between modes in the entire monolayer using clear and noisy movies of activity. We demonstrated that the rotor modes influence the secondary fibrillatory modes, but influence was detected also in the opposite direction. To more specifically delineate the role of the rotor in fibrillation, we decomposed separately the respective SVD modes of the rotor and fibrillatory domains. In this case, WGCA yielded more information from the rotor to the fibrillatory domains than in the opposite direction. In conclusion, SVD analysis reveals that rotors can be the dominant modes of an experimental model of fibrillation. Wiener-Granger causality on modes of the rotor domains confirms their

  11. Resistive edge mode instability in stellarator and tokamak geometries

    NASA Astrophysics Data System (ADS)

    Mahmood, M. Ansar; Rafiq, T.; Persson, M.; Weiland, J.

    2008-09-01

    Geometrical effects on linear stability of electrostatic resistive edge modes are investigated in the three-dimensional Wendelstein 7-X stellarator [G. Grieger et al., Plasma Physics and Controlled Nuclear Fusion Research 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525] and the International Thermonuclear Experimental Reactor [Progress in the ITER Physics Basis, Nucl. Fusion 7, S1, S285 (2007)]-like equilibria. An advanced fluid model is used for the ions together with the reduced Braghinskii equations for the electrons. Using the ballooning mode representation, the drift wave problem is set as an eigenvalue equation along a field line and is solved numerically using a standard shooting technique. A significantly larger magnetic shear and a less unfavorable normal curvature in the tokamak equilibrium are found to give a stronger finite-Larmor radius stabilization and a more narrow mode spectrum than in the stellarator. The effect of negative global magnetic shear in the tokamak is found to be stabilizing. The growth rate on a tokamak magnetic flux surface is found to be comparable to that on a stellarator surface with the same global magnetic shear but the eigenfunction in the tokamak is broader than in the stellarator due to the presence of large negative local magnetic shear (LMS) on the tokamak surface. A large absolute value of the LMS in a region of unfavorable normal curvature is found to be stabilizing in the stellarator, while in the tokamak case, negative LMS is found to be stabilizing and positive LMS destabilizing.

  12. The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.

    PubMed

    Linhananta, Apichart; Boer, Jesse; MacKay, Ian

    2005-03-15

    The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

  13. All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

    PubMed

    Masso, Majid

    2018-09-14

    Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Drive-amplitude-modulation atomic force microscopy: From vacuum to liquids

    PubMed Central

    Jaafar, Miriam; Cuenca, Mariano; Melcher, John; Raman, Arvind

    2012-01-01

    Summary We introduce drive-amplitude-modulation atomic force microscopy as a dynamic mode with outstanding performance in all environments from vacuum to liquids. As with frequency modulation, the new mode follows a feedback scheme with two nested loops: The first keeps the cantilever oscillation amplitude constant by regulating the driving force, and the second uses the driving force as the feedback variable for topography. Additionally, a phase-locked loop can be used as a parallel feedback allowing separation of the conservative and nonconservative interactions. We describe the basis of this mode and present some examples of its performance in three different environments. Drive-amplutide modulation is a very stable, intuitive and easy to use mode that is free of the feedback instability associated with the noncontact-to-contact transition that occurs in the frequency-modulation mode. PMID:22563531

  15. Elastic parabolic equation and normal mode solutions for seismo-acoustic propagation in underwater environments with ice covers.

    PubMed

    Collis, Jon M; Frank, Scott D; Metzler, Adam M; Preston, Kimberly S

    2016-05-01

    Sound propagation predictions for ice-covered ocean acoustic environments do not match observational data: received levels in nature are less than expected, suggesting that the effects of the ice are substantial. Effects due to elasticity in overlying ice can be significant enough that low-shear approximations, such as effective complex density treatments, may not be appropriate. Building on recent elastic seafloor modeling developments, a range-dependent parabolic equation solution that treats the ice as an elastic medium is presented. The solution is benchmarked against a derived elastic normal mode solution for range-independent underwater acoustic propagation. Results from both solutions accurately predict plate flexural modes that propagate in the ice layer, as well as Scholte interface waves that propagate at the boundary between the water and the seafloor. The parabolic equation solution is used to model a scenario with range-dependent ice thickness and a water sound speed profile similar to those observed during the 2009 Ice Exercise (ICEX) in the Beaufort Sea.

  16. Quantum oscillations of nitrogen atoms in uranium nitride

    NASA Astrophysics Data System (ADS)

    Aczel, A. A.; Granroth, G. E.; MacDougall, G. J.; Buyers, W. J. L.; Abernathy, D. L.; Samolyuk, G. D.; Stocks, G. M.; Nagler, S. E.

    2012-10-01

    The vibrational excitations of crystalline solids corresponding to acoustic or optic one-phonon modes appear as sharp features in measurements such as neutron spectroscopy. In contrast, many-phonon excitations generally produce a complicated, weak and featureless response. Here we present time-of-flight neutron scattering measurements for the binary solid uranium nitride, showing well-defined, equally spaced, high-energy vibrational modes in addition to the usual phonons. The spectrum is that of a single atom, isotropic quantum harmonic oscillator and characterizes independent motions of light nitrogen atoms, each found in an octahedral cage of heavy uranium atoms. This is an unexpected and beautiful experimental realization of one of the fundamental, exactly solvable problems in quantum mechanics. There are also practical implications, as the oscillator modes must be accounted for in the design of generation IV nuclear reactors that plan to use uranium nitride as a fuel.

  17. Quantum oscillations of nitrogen atoms in uranium nitride.

    PubMed

    Aczel, A A; Granroth, G E; Macdougall, G J; Buyers, W J L; Abernathy, D L; Samolyuk, G D; Stocks, G M; Nagler, S E

    2012-01-01

    The vibrational excitations of crystalline solids corresponding to acoustic or optic one-phonon modes appear as sharp features in measurements such as neutron spectroscopy. In contrast, many-phonon excitations generally produce a complicated, weak and featureless response. Here we present time-of-flight neutron scattering measurements for the binary solid uranium nitride, showing well-defined, equally spaced, high-energy vibrational modes in addition to the usual phonons. The spectrum is that of a single atom, isotropic quantum harmonic oscillator and characterizes independent motions of light nitrogen atoms, each found in an octahedral cage of heavy uranium atoms. This is an unexpected and beautiful experimental realization of one of the fundamental, exactly solvable problems in quantum mechanics. There are also practical implications, as the oscillator modes must be accounted for in the design of generation IV nuclear reactors that plan to use uranium nitride as a fuel.

  18. Nonlinear acoustic experiments for landmine detection: the significance of the top-plate normal modes

    NASA Astrophysics Data System (ADS)

    Korman, Murray S.; Alberts, W. C. K., II; Sabatier, James M.

    2004-09-01

    In nonlinear acoustic detection experiments involving a buried inert VS 2.2 anti-tank landmine, airborne sound at two closely spaced primary frequencies f1 and f2 couple into the ground and interact nonlinearly with the soil-top pressure plate interface. Scattering generates soil vibration at the surface at the combination frequencies | m f1 +- n f2 | , where m and n are integers. The normal component of the particle velocity at the soil surface has been measured with a laser Doppler velocimeter (LDV) and with a geophone by Sabatier et. al. [SPIE Proceedings Vol. 4742, (695-700), 2002; Vol. 5089, (476-486), 2003] at the gravel lane test site. Spatial profiles of the particle velocity measured for both primary components and for various combination frequencies indicate that the modal structure of the mine is playing an important role. Here, an experimental modal analysis is performed on a VS 1.6 inert anti-tank mine that is resting on sand but is not buried. Five top-plate mode shapes are described. The mine is then buried in dry finely sifted natural loess soil and excited at f1 = 120 Hz and f2 = 130 Hz. Spatial profiles at the primary components and the nonlinearly generated f1 - (f2 - f1) component are characterized by a single peak. For the 2f1+f2 and 2f2 + f1 components, the doubly peaked profiles can be attributed to the familiar mode shape of a timpani drum (that is shifted lower in frequency due to soil mass loading). Other nonlinear profiles appear to be due to a mixture of modes. This material is based upon work supported by the U. S. Army RDECOM CERDEC Night Vision and Electronic Sensors Directorate under Contract DAAB15-02-C-0024.

  19. Observable cosmological vector mode in the dark ages

    NASA Astrophysics Data System (ADS)

    Saga, Shohei

    2016-09-01

    The second-order vector mode is inevitably induced from the coupling of first-order scalar modes in cosmological perturbation theory and might hinder a possible detection of primordial gravitational waves from inflation through 21 cm lensing observations. Here, we investigate the weak lensing signal in 21 cm photons emitted by neutral hydrogen atoms in the dark ages induced by the second-order vector mode by decomposing the deflection angle of the 21 cm lensing signal into the gradient and curl modes. The curl mode is a good tracer of the cosmological vector and tensor modes since the scalar mode does not induce the curl one. By comparing angular power spectra of the 21 cm lensing curl mode induced by the second-order vector mode and primordial gravitational waves whose amplitude is parametrized by the tensor-to-scalar ratio r , we find that the 21 cm curl mode from the second-order vector mode dominates over that from primordial gravitational waves on almost all scales if r ≲10-5. If we use the multipoles of the power spectrum up to ℓmax=1 05 and 1 06 in reconstructing the curl mode from 21 cm temperature maps, the signal-to-noise ratios of the 21 cm curl mode from the second-order vector mode achieve S /N ≈0.46 and 73, respectively. Observation of 21 cm radiation is, in principle, a powerful tool to explore not only the tensor mode but also the cosmological vector mode.

  20. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Perilla, Juan R.; Schulten, Klaus

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

  1. Free-energy landscape of the villin headpiece in an all-atom force field.

    PubMed

    Herges, Thomas; Wenzel, Wolfgang

    2005-04-01

    We investigate the landscape of the internal free-energy of the 36 amino acid villin headpiece with a modified basin hopping method in the all-atom force field PFF01, which was previously used to predictively fold several helical proteins with atomic resolution. We identify near native conformations of the protein as the global optimum of the force field. More than half of the twenty best simulations started from random initial conditions converge to the folding funnel of the native conformation, but several competing low-energy metastable conformations were observed. From 76,000 independently generated conformations we derived a decoy tree which illustrates the topological structure of the entire low-energy part of the free-energy landscape and characterizes the ensemble of metastable conformations. These emerge as similar in secondary content, but differ in tertiary arrangement.

  2. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    DOE PAGES

    Perilla, Juan R.; Schulten, Klaus

    2017-07-19

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

  3. Potential surfaces for O atom-polymer reactions

    NASA Technical Reports Server (NTRS)

    Laskowski, B. C.; Jaffe, R. L.

    1987-01-01

    Ab initio quantum chemistry methods are used to study the energetics of interactions of O atoms with organic compounds. Polyethylene (CH2)n has been chosen as the model system to study the interactions of O(3P) and O(1D) atoms with polymers. In particular, H abstraction is investigated and polyethylene is represented by a C3 (propane) oligomeric model. The gradient method, as implemented in the GRADSCF package of programs, is used to determine the geometries and energies of products and reactants. The saddle point, barrier geometry is determined by minimizing the squares of the gradients of the potential with respect to the internal coordinates. To correctly describe the change in bonding during the reaction at least a two configuration MCSCF (multiconfiguration self consistent field) or GVB (generalized valence bond) wave function has to be used. Basis sets include standard Pople and Dunning sets, however, increased with polarization functions and diffuse p functions on both the C and O atoms. The latter is important due to the O(-) character of the wave function at the saddle point and products. Normal modes and vibrational energy levels are given for the reactants, saddle points and products. Finally, quantitative energetics are obtained by implementing a small CAS (complete active space) approach followed by limited configuration interaction (CI) calculations. Comparisons are made with available experimental data.

  4. Structural characterization of synthetic and protein-bound porphyrins in terms of the lowest-frequency normal coordinates of the macrocycle

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jentzen, W.; Song, X.Z.; Shelnutt, J.A.

    1997-02-27

    The X-ray crystal structures of synthetic and protein-bound metalloporphyrins are analyzed using a new normal structural decomposition method for classifying and quantifying their out-of-plane and in-plane distortions. These distortions are characterized in terms of equivalent displacements along the normal coordinates of the D{sub 4h}-symmetric porphyrin macrocycle (normal deformations). It is shown that the macrocyclic structure is, even in highly distorted porphyrins, accurately represented by displacements along only the lowest-frequency normal coordinates. Accordingly, the macrocyclic structure obtained from just the out-of-plane normal deformations of the saddling (sad, B{sub 2u})-, ruffling (ruf, B{sub 1u})-, doming (dom, A{sub 2u})-, waving [wav(x), wav(y); E{submore » g}]-, and propellering (pro, A{sub 1u})-type essentially simulates the out-of-plane distortion of the X-ray crystal structure. Similarly, the observed in-plane distortions are decomposed into in-plane normal deformations corresponding to the lowest-frequency vibrational modes including macrocycle stretching in the direction of the meso-carbon atoms (meso-str, B{sub 2g}), stretching in the direction of the nitrogen atoms (N-str, B{sub 1g}), x and y pyrrole translations [trn(x), trn(y); E{sub u}], macrocycle breathing (bre, A{sub 1g}), and pyrrole rotation (rot, A{sub 2g}). 71 refs., 9 figs., 4 tabs.« less

  5. High Energy, Single-Mode, All-Solid-State and Tunable UV Laser Transmitter

    NASA Technical Reports Server (NTRS)

    Prasad, Narasimha S.; Singh, Upendra N.; Hovis, FLoyd

    2007-01-01

    A high energy, single mode, all solid-state Nd:YAG laser primarily for pumping an UV converter is developed. Greater than 1 J/pulse at 50 HZ PRF and pulse widths around 22 ns have been demonstrated. Higher energy, greater efficiency may be possible. Refinements are known and practical to implement. Technology Demonstration of a highly efficient, high-pulse-energy, single mode UV wavelength generation using flash lamp pumped laser has been achieved. Greater than 90% pump depletion is observed. 190 mJ extra-cavity SFG; IR to UV efficiency > 21% (> 27% for 1 mJ seed). 160 mJ intra-cavity SFG; IR to UV efficiency up to 24% Fluence < 1 J/sq cm for most beams. The pump beam quality of the Nd:YAG pump laser is being refined to match or exceed the above UV converter results. Currently the Nd:YAG pump laser development is a technology demonstration. System can be engineered for compact packaging.

  6. A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

    PubMed Central

    Frappier, Vincent; Najmanovich, Rafael J.

    2014-01-01

    Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569

  7. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

    NASA Astrophysics Data System (ADS)

    Kitao, Akio; Hirata, Fumio; Gō, Nobuhiro

    1991-12-01

    The effects of solvent on the conformation and dynamics of protein is studied by computer simulation. The dynamics is studied by focusing mainly on collective motions of the protein molecule. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water are applied to melittin, the major component of bee venom. To define collective motions principal, component analysis as well as normal mode analysis has been carried out. The principal components with large fluctuation amplitudes have a very good correspondence with the low-frequency normal modes. Trajectories of the molecular dynamics simulation are projected onto the principal axes. From the projected motions time correlation functions are calculated. The results indicate that the very-low-frequency modes, whose frequencies are less than ≈ 50 cm -1, are overdamping in water with relaxation times roushly twice as long as the period of the oscillatory motion. Effective Langevin mode analysis is carried out by using the friction coefficient matrix determined from the velocity correlation function calculated from the molecular dynamics trajectory in water. This analysis reproduces the results of the simulation in water reasonably well. The presence of the solvent water is found also to affect the shape of the potential energy surface in such a way that it produces many local minima with low-energy barriers in between, the envelope of which is given by the surface in vacuum. Inter-minimum transitions endow the conformational dynamics of proteins in water another diffusive character, which already exists in the intra-minimum collective motions.

  8. All-angle Negative Reflection with An Ultrathin Acoustic Gradient Metasurface: Floquet-Bloch Modes Perspective and Experimental Verification.

    PubMed

    Liu, Bingyi; Zhao, Jiajun; Xu, Xiaodong; Zhao, Wenyu; Jiang, Yongyuan

    2017-10-23

    Metasurface with gradient phase response offers new alternative for steering the propagation of waves. Conventional Snell's law has been revised by taking the contribution of local phase gradient into account. However, the requirement of momentum matching along the metasurface sets its nontrivial beam manipulation functionality within a limited-angle incidence. In this work, we theoretically and experimentally demonstrate that the acoustic gradient metasurface supports the negative reflection for all-angle incidence. The mode expansion theory is developed to help understand how the gradient metasurface tailors the incident beams, and the all-angle negative reflection occurs when the first negative order Floquet-Bloch mode dominates inside the metasurface slab. The coiling-up space structures are utilized to build desired acoustic gradient metasurface, and the all-angle negative reflections have been perfectly verified by experimental measurements. Our work offers the Floquet-Bloch modes perspective for qualitatively understanding the reflection behaviors of the acoustic gradient metasurface, and the all-angle negative reflection characteristic possessed by acoustic gradient metasurface could enable a new degree of the acoustic wave manipulating and be applied in the functional diffractive acoustic elements, such as the all-angle acoustic back reflector.

  9. Antidepressants normalize the default mode network in patients with dysthymia.

    PubMed

    Posner, Jonathan; Hellerstein, David J; Gat, Inbal; Mechling, Anna; Klahr, Kristin; Wang, Zhishun; McGrath, Patrick J; Stewart, Jonathan W; Peterson, Bradley S

    2013-04-01

    The default mode network (DMN) is a collection of brain regions that reliably deactivate during goal-directed behaviors and is more active during a baseline, or so-called resting, condition. Coherence of neural activity, or functional connectivity, within the brain's DMN is increased in major depressive disorder relative to healthy control (HC) subjects; however, whether similar abnormalities are present in persons with dysthymic disorder (DD) is unknown. Moreover, the effect of antidepressant medications on DMN connectivity in patients with DD is also unknown. To use resting-state functional-connectivity magnetic resonance imaging (MRI) to study (1) the functional connectivity of the DMN in subjects with DD vs HC participants and (2) the effects of antidepressant therapy on DMN connectivity. After collecting baseline MRI scans from subjects with DD and HC participants, we enrolled the participants with DD into a 10-week prospective, double-blind, placebo-controlled trial of duloxetine and collected MRI scans again at the conclusion of the study. Enrollment occurred between 2007 and 2011. University research institute. Volunteer sample of 41 subjects with DD and 25 HC participants aged 18 to 53 years. Control subjects were group matched to patients with DD by age and sex. We used resting-state functional-connectivity MRI to measure the functional connectivity of the brain's DMN in persons with DD compared with HC subjects, and we examined the effects of treatment with duloxetine vs placebo on DMN connectivity. Of the 41 subjects with DD, 32 completed the clinical trial and MRI scans, along with the 25 HC participants. At baseline, we found that the coherence of neural activity within the brain's DMN was greater in persons with DD compared with HC subjects. Following a 10-week clinical trial, we found that treatment with duloxetine, but not placebo, normalized DMN connectivity. The baseline imaging findings are consistent with those found in patients with major

  10. Antidepressants Normalize the Default Mode Network in Patients With Dysthymia

    PubMed Central

    Posner, Jonathan; Hellerstein, David J.; Gat, Inbal; Mechling, Anna; Klahr, Kristin; Wang, Zhishun; McGrath, Patrick J.; Stewart, Jonathan W.; Peterson, Bradley S.

    2014-01-01

    Importance The default mode network (DMN) is a collection of brain regions that reliably deactivate during goal-directed behaviors and is more active during a baseline, or so-called resting, condition. Coherence of neural activity, or functional connectivity, within the brain’s DMN is increased in major depressive disorder relative to healthy control (HC) subjects; however, whether similar abnormalities are present in persons with dysthymic disorder (DD) is unknown. Moreover, the effect of antidepressant medications on DMN connectivity in patients with DD is also unknown. Objective To use resting-state functional-connectivity magnetic resonance imaging (MRI) to study (1) the functional connectivity of the DMN in subjects with DD vs HC participants and (2) the effects of antidepressant therapy on DMN connectivity. Design After collecting baseline MRI scans from subjects with DD and HC participants, we enrolled the participants with DD into a 10-week prospective, double-blind, placebo-controlled trial of duloxetine and collected MRI scans again at the conclusion of the study. Enrollment occurred between 2007 and 2011. Setting University research institute. Participants Volunteer sample of 41 subjects with DD and 25 HC participants aged 18 to 53 years. Control subjects were group matched to patients with DD by age and sex. Main Outcome Measures We used resting-state functional-connectivity MRI to measure the functional connectivity of the brain’s DMN in persons with DD compared with HC subjects, and we examined the effects of treatment with duloxetine vs placebo on DMN connectivity. Results Of the 41 subjects with DD, 32 completed the clinical trial and MRI scans, along with the 25 HC participants. At baseline, we found that the coherence of neural activity within the brain’s DMN was greater in persons with DD compared with HC subjects. Following a 10-week clinical trial, we found that treatment with duloxetine, but not placebo, normalized DMN connectivity

  11. Bonds Between Metal Atoms: A New Mode of Transition Metal Chemistry.

    ERIC Educational Resources Information Center

    Cotton, F. Albert; Chisholm, Malcolm H.

    1982-01-01

    Discusses polynuclear metal clusters (containing two or more metal atoms bonded to one another as well as to nonmetallic elements), including their formation and applications. Studies of bonds between metal atoms reveal superconductors, organic-reaction catalysts, and photosensitive complexes that may play a role in solar energy. (JN)

  12. Study of different HILIC, mixed-mode, and other aqueous normal-phase approaches for the liquid chromatography/mass spectrometry-based determination of challenging polar pesticides.

    PubMed

    Vass, Andrea; Robles-Molina, José; Pérez-Ortega, Patricia; Gilbert-López, Bienvenida; Dernovics, Mihaly; Molina-Díaz, Antonio; García-Reyes, Juan F

    2016-07-01

    The aim of the study was to evaluate the performance of different chromatographic approaches for the liquid chromatography/mass spectrometry (LC-MS(/MS)) determination of 24 highly polar pesticides. The studied compounds, which are in most cases unsuitable for conventional LC-MS(/MS) multiresidue methods were tested with nine different chromatographic conditions, including two different hydrophilic interaction liquid chromatography (HILIC) columns, two zwitterionic-type mixed-mode columns, three normal-phase columns operated in HILIC-mode (bare silica and two silica-based chemically bonded columns (cyano and amino)), and two standard reversed-phase C18 columns. Different sets of chromatographic parameters in positive (for 17 analytes) and negative ionization modes (for nine analytes) were examined. In order to compare the different approaches, a semi-quantitative classification was proposed, calculated as the percentage of an empirical performance value, which consisted of three main features: (i) capacity factor (k) to characterize analyte separation from the void, (ii) relative response factor, and (iii) peak shape based on analytes' peak width. While no single method was able to provide appropriate detection of all the 24 studied species in a single run, the best suited approach for the compounds ionized in positive mode was based on a UHPLC HILIC column with 1.8 μm particle size, providing appropriate results for 22 out of the 24 species tested. In contrast, the detection of glyphosate and aminomethylphosphonic acid could only be achieved with a zwitterionic-type mixed-mode column, which proved to be suitable only for the pesticides detected in negative ion mode. Finally, the selected approach (UHPLC HILIC) was found to be useful for the determination of multiple pesticides in oranges using HILIC-ESI-MS/MS, with limits of quantitation in the low microgram per kilogram in most cases. Graphical Abstract HILIC improves separation of multiclass polar pesticides.

  13. Discrimination of bladder cancer cells from normal urothelial cells with high specificity and sensitivity: combined application of atomic force microscopy and modulated Raman spectroscopy.

    PubMed

    Canetta, Elisabetta; Riches, Andrew; Borger, Eva; Herrington, Simon; Dholakia, Kishan; Adya, Ashok K

    2014-05-01

    Atomic force microscopy (AFM) and modulated Raman spectroscopy (MRS) were used to discriminate between living normal human urothelial cells (SV-HUC-1) and bladder tumour cells (MGH-U1) with high specificity and sensitivity. MGH-U1 cells were 1.5-fold smaller, 1.7-fold thicker and 1.4-fold rougher than normal SV-HUC-1 cells. The adhesion energy was 2.6-fold higher in the MGH-U1 cells compared to normal SV-HUC-1 cells, which possibly indicates that bladder tumour cells are more deformable than normal cells. The elastic modulus of MGH-U1 cells was 12-fold lower than SV-HUC-1 cells, suggesting a higher elasticity of the bladder cancer cell membranes. The biochemical fingerprints of cancer cells displayed a higher DNA and lipid content, probably due to an increase in the nuclear to cytoplasm ratio. Normal cells were characterized by higher protein contents. AFM studies revealed a decrease in the lateral dimensions and an increase in thickness of cancer cells compared to normal cells; these studies authenticate the observations from MRS. Nanostructural, nanomechanical and biochemical profiles of bladder cells provide qualitative and quantitative markers to differentiate between normal and cancerous cells at the single cellular level. AFM and MRS allow discrimination between adhesion energy, elasticity and Raman spectra of SV-HUC-1 and MGH-U1 cells with high specificity (83, 98 and 95%) and sensitivity (97, 93 and 98%). Such single-cell-level studies could have a pivotal impact on the development of AFM-Raman combined methodologies for cancer profiling and screening with translational significance. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  14. Cortical Thinning in Network-Associated Regions in Cognitively Normal and Below-Normal Range Schizophrenia

    PubMed Central

    Pinnock, Farena; Parlar, Melissa; Hawco, Colin; Hanford, Lindsay; Hall, Geoffrey B.

    2017-01-01

    This study assessed whether cortical thickness across the brain and regionally in terms of the default mode, salience, and central executive networks differentiates schizophrenia patients and healthy controls with normal range or below-normal range cognitive performance. Cognitive normality was defined using the MATRICS Consensus Cognitive Battery (MCCB) composite score (T = 50 ± 10) and structural magnetic resonance imaging was used to generate cortical thickness data. Whole brain analysis revealed that cognitively normal range controls (n = 39) had greater cortical thickness than both cognitively normal (n = 17) and below-normal range (n = 49) patients. Cognitively normal controls also demonstrated greater thickness than patients in regions associated with the default mode and salience, but not central executive networks. No differences on any thickness measure were found between cognitively normal range and below-normal range controls (n = 24) or between cognitively normal and below-normal range patients. In addition, structural covariance between network regions was high and similar across subgroups. Positive and negative symptom severity did not correlate with thickness values. Cortical thinning across the brain and regionally in relation to the default and salience networks may index shared aspects of the psychotic psychopathology that defines schizophrenia with no relation to cognitive impairment. PMID:28348889

  15. High quality-factor quartz tuning fork glass probe used in tapping mode atomic force microscopy for surface profile measurement

    NASA Astrophysics Data System (ADS)

    Chen, Yuan-Liu; Xu, Yanhao; Shimizu, Yuki; Matsukuma, Hiraku; Gao, Wei

    2018-06-01

    This paper presents a high quality-factor (Q-factor) quartz tuning fork (QTF) with a glass probe attached, used in frequency modulation tapping mode atomic force microscopy (AFM) for the surface profile metrology of micro and nanostructures. Unlike conventionally used QTFs, which have tungsten or platinum probes for tapping mode AFM, and suffer from a low Q-factor influenced by the relatively large mass of the probe, the glass probe, which has a lower density, increases the Q-factor of the QTF probe unit allowing it to obtain better measurement sensitivity. In addition, the process of attaching the probe to the QTF with epoxy resin, which is necessary for tapping mode AFM, is also optimized to further improve the Q-factor of the QTF glass probe. The Q-factor of the optimized QTF glass probe unit is demonstrated to be very close to that of a bare QTF without a probe attached. To verify the effectiveness and the advantages of the optimized QTF glass probe unit, the probe unit is integrated into a home-built tapping mode AFM for conducting surface profile measurements of micro and nanostructures. A blazed grating with fine tool marks of 100 nm, a microprism sheet with a vertical amplitude of 25 µm and a Fresnel lens with a steep slope of 90 degrees are used as measurement specimens. From the measurement results, it is demonstrated that the optimized QTF glass probe unit can achieve higher sensitivity as well as better stability than conventional probes in the measurement of micro and nanostructures.

  16. Exact mode volume and Purcell factor of open optical systems

    NASA Astrophysics Data System (ADS)

    Muljarov, E. A.; Langbein, W.

    2016-12-01

    The Purcell factor quantifies the change of the radiative decay of a dipole in an electromagnetic environment relative to free space. Designing this factor is at the heart of photonics technology, striving to develop ever smaller or less lossy optical resonators. The Purcell factor can be expressed using the electromagnetic eigenmodes of the resonators, introducing the notion of a mode volume for each mode. This approach allows an analytic treatment, reducing the Purcell factor and other observables to sums over eigenmode resonances. Calculating the mode volumes requires a correct normalization of the modes. We introduce an exact normalization of modes, not relying on perfectly matched layers. We present an analytic theory of the Purcell effect based on this exact mode normalization and the resulting effective mode volume. We use a homogeneous dielectric sphere in vacuum, which is analytically solvable, to exemplify these findings. We furthermore verify the applicability of the normalization to numerically determined modes of a finite dielectric cylinder.

  17. Functional dependence of resonant harmonics on nanomechanical parameters in dynamic mode atomic force microscopy.

    PubMed

    Gramazio, Federico; Lorenzoni, Matteo; Pérez-Murano, Francesc; Rull Trinidad, Enrique; Staufer, Urs; Fraxedas, Jordi

    2017-01-01

    We present a combined theoretical and experimental study of the dependence of resonant higher harmonics of rectangular cantilevers of an atomic force microscope (AFM) as a function of relevant parameters such as the cantilever force constant, tip radius and free oscillation amplitude as well as the stiffness of the sample's surface. The simulations reveal a universal functional dependence of the amplitude of the 6th harmonic (in resonance with the 2nd flexural mode) on these parameters, which can be expressed in terms of a gun-shaped function. This analytical expression can be regarded as a practical tool for extracting qualitative information from AFM measurements and it can be extended to any resonant harmonics. The experiments confirm the predicted dependence in the explored 3-45 N/m force constant range and 2-345 GPa sample's stiffness range. For force constants around 25 N/m, the amplitude of the 6th harmonic exhibits the largest sensitivity for ultrasharp tips (tip radius below 10 nm) and polymers (Young's modulus below 20 GPa).

  18. Einstein-Podolsky-Rosen paradox and quantum steering in a three-mode optomechanical system

    NASA Astrophysics Data System (ADS)

    He, Qiongyi; Ficek, Zbigniew

    2014-02-01

    We study multipartite entanglement, the generation of Einstein-Podolsky-Rosen (EPR) states, and quantum steering in a three-mode optomechanical system composed of an atomic ensemble located inside a single-mode cavity with a movable mirror. The cavity mode is driven by a short laser pulse, has a nonlinear parametric-type interaction with the mirror and a linear beam-splitter-type interaction with the atomic ensemble. There is no direct interaction of the mirror with the atomic ensemble. A threshold effect for the dynamics of the system is found, above which the system works as an amplifier and below which as an attenuator of the output fields. The threshold is determined by the ratio of the coupling strengths of the cavity mode to the mirror and to the atomic ensemble. It is shown that above the threshold, the system effectively behaves as a two-mode system in which a perfect bipartite EPR state can be generated, while it is impossible below the threshold. Furthermore, a fully inseparable tripartite entanglement and even further a genuine tripartite entanglement can be produced above and below the threshold. In addition, we consider quantum steering and examine the monogamy relations that quantify the amount of bipartite steering that can be shared between different modes. It is found that the mirror is more capable for steering of entanglement than the cavity mode. The two-way steering is found between the mirror and the atomic ensemble despite the fact that they are not directly coupled to each other, while it is impossible between the output of cavity mode and the ensemble which are directly coupled to each other.

  19. Integrated optical dipole trap for cold neutral atoms with an optical waveguide coupler

    NASA Astrophysics Data System (ADS)

    Lee, J.; Park, D. H.; Mittal, S.; Dagenais, M.; Rolston, S. L.

    2013-04-01

    An integrated optical dipole trap uses two-color (red and blue-detuned) traveling evanescent wave fields for trapping cold neutral atoms. To achieve longitudinal confinement, we propose using an integrated optical waveguide coupler, which provides a potential gradient along the beam propagation direction sufficient to confine atoms. This integrated optical dipole trap can support an atomic ensemble with a large optical depth due to its small mode area. Its quasi-TE0 waveguide mode has an advantage over the HE11 mode of a nanofiber, with little inhomogeneous Zeeman broadening at the trapping region. The longitudinal confinement eliminates the need for a one dimensional optical lattice, reducing collisional blockaded atomic loading, potentially producing larger ensembles. The waveguide trap allows for scalability and integrability with nano-fabrication technology. We analyze the potential performance of such integrated atom traps.

  20. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

    PubMed Central

    Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

    2016-01-01

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

  1. Single-beam, dark toroidal optical traps for cold atoms

    NASA Astrophysics Data System (ADS)

    Fatemi, Fredrik K.; Olson, Spencer E.; Bashkansky, Mark; Dutton, Zachary; Terraciano, Matthew

    2007-02-01

    We demonstrate the generation of single-beam dark toroidal optical intensity distributions, which are of interest for neutral atom storage and atom interferometry. We demonstrate experimentally and numerically optical potentials that contain a ring-shaped intensity minimum, bounded in all directions by higher intensity. We use a spatial light modulator to alter the phase of an incident laser beam, and analyze the resulting optical propagation characteristics. For small toroidal traps (< 50 μm diameter), we find an optimal superposition of Laguerre-Gaussian modes that allows the formation of single-beam toroidal traps. We generate larger toroidal bottle traps by focusing hollow beams with toroidal lenses imprinted onto the spatial light modulator.

  2. On the tunability of quality-factor for optical Tamm plasmon modes

    NASA Astrophysics Data System (ADS)

    Kumar, Samir; Das, Ritwick

    2017-09-01

    We present a comprehensive investigation to ascertain the impact of gold and silver films on modifying the quality-factor (Q-factor) of optical Tamm-plasmon (OTP) resonance in a metal-distributed Bragg reflector (M-DBR) geometry. Here, OTP mode is excited using direct incidence of white-light-source at normal incidence as well as oblique incidence on M-DBR geometry. The lifetime of OTP in gold and silver deposited films on DBR mirror was determined from OTP resonance linewidth. The lifetime and the Q-factor of OTP modes are found to depend on DBR bilayers, metal film thickness as well as on different plasmon active metals. This finding would facilitate tuning the Q-factor and consequently, the lifetime of OTP modes for various applications in all-optical switches and modulators. In addition, we discuss the spectral characteristics of OTP modes excited using normal and oblique incident of source.

  3. Phase modulation atomic force microscope with true atomic resolution

    NASA Astrophysics Data System (ADS)

    Fukuma, Takeshi; Kilpatrick, Jason I.; Jarvis, Suzanne P.

    2006-12-01

    We have developed a dynamic force microscope (DFM) working in a novel operation mode which is referred to as phase modulation atomic force microscopy (PM-AFM). PM-AFM utilizes a fixed-frequency excitation signal to drive a cantilever, which ensures stable imaging even with occasional tip crash and adhesion to the surface. The tip-sample interaction force is detected as a change of the phase difference between the cantilever deflection and excitation signals and hence the time response is not influenced by the Q factor of the cantilever. These features make PM-AFM more suitable for high-speed imaging than existing DFM techniques such as amplitude modulation and frequency modulation atomic force microscopies. Here we present the basic principle of PM-AFM and the theoretical limit of its performance. The design of the developed PM-AFM is described and its theoretically limited noise performance is demonstrated. Finally, we demonstrate the true atomic resolution imaging capability of the developed PM-AFM by imaging atomic-scale features of mica in water.

  4. Finite element modeling of trolling-mode AFM.

    PubMed

    Sajjadi, Mohammadreza; Pishkenari, Hossein Nejat; Vossoughi, Gholamreza

    2018-06-01

    Trolling mode atomic force microscopy (TR-AFM) has overcome many imaging problems in liquid environments by considerably reducing the liquid-resonator interaction forces. The finite element model of the TR-AFM resonator considering the effects of fluid and nanoneedle flexibility is presented in this research, for the first time. The model is verified by ABAQUS software. The effect of installation angle of the microbeam relative to the horizon and the effect of fluid on the system behavior are investigated. Using the finite element model, frequency response curve of the system is obtained and validated around the frequency of the operating mode by the available experimental results, in air and liquid. The changes in the natural frequencies in the presence of liquid are studied. The effects of tip-sample interaction on the excitation of higher order modes of the system are also investigated in air and liquid environments. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Tunable all-fiber dissipative-soliton laser with a multimode interference filter.

    PubMed

    Zhang, Lei; Hu, Jinmeng; Wang, Jianhua; Feng, Yan

    2012-09-15

    We report on a tunable all-fiber dissipative-soliton laser with a multimode interference filter that consists of a multimode fiber spliced between two single-mode fibers. By carefully selecting the fiber parameters, a filter with a central wavelength at 1032 nm and a bandwidth of 7.6 nm is constructed and used for spectral filtering in an all-normal-dispersion mode-locked ytterbium-doped fiber laser based on nonlinear polarization evolution. The laser delivers 31 mW of average output power with positively chirped 7 ps pulses. The repetition rate of the pulses is 15.3 MHz, and pulse energy is 2.1 nJ. Tunable dissipative-soliton over 12 nm is achieved by applying tension to the single-mode-multimode-single-mode filter.

  6. Atomic motion from the mean square displacement in a monatomic liquid

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wallace, Duane C.; De Lorenzi-Venneri, Giulia; Chisolm, Eric D.

    V-T theory is constructed in the many-body Hamiltonian formulation, and is being developed as a novel approach to liquid dynamics theory. In this theory the liquid atomic motion consists of two contributions, normal mode vibrations in a single representative potential energy valley, and transits, which carry the system across boundaries between valleys. The mean square displacement time correlation function (the MSD) is a direct measure of the atomic motion, and our goal is to determine if the V-T formalism can produce a physically sensible account of this motion. We employ molecular dynamics (MD) data for a system representing liquid Na,more » and find the motion evolves in three successive time intervals: on the first 'vibrational' interval, the vibrational motion alone gives a highly accurate account of the MD data; on the second 'crossover' interval, the vibrational MSD saturates to a constant while the transit motion builds up from zero; on the third 'random walk' interval, the transit motion produces a purely diffusive random walk of the vibrational equilibrium positions. Furthermore, this motional evolution agrees with, and adds refinement to, the MSD atomic motion as described by current liquid dynamics theories.« less

  7. Atomic motion from the mean square displacement in a monatomic liquid

    DOE PAGES

    Wallace, Duane C.; De Lorenzi-Venneri, Giulia; Chisolm, Eric D.

    2016-04-08

    V-T theory is constructed in the many-body Hamiltonian formulation, and is being developed as a novel approach to liquid dynamics theory. In this theory the liquid atomic motion consists of two contributions, normal mode vibrations in a single representative potential energy valley, and transits, which carry the system across boundaries between valleys. The mean square displacement time correlation function (the MSD) is a direct measure of the atomic motion, and our goal is to determine if the V-T formalism can produce a physically sensible account of this motion. We employ molecular dynamics (MD) data for a system representing liquid Na,more » and find the motion evolves in three successive time intervals: on the first 'vibrational' interval, the vibrational motion alone gives a highly accurate account of the MD data; on the second 'crossover' interval, the vibrational MSD saturates to a constant while the transit motion builds up from zero; on the third 'random walk' interval, the transit motion produces a purely diffusive random walk of the vibrational equilibrium positions. Furthermore, this motional evolution agrees with, and adds refinement to, the MSD atomic motion as described by current liquid dynamics theories.« less

  8. Observations of the azimuthal dependence of normal mode coupling below 4 mHz at the South Pole and its nearby stations: Insights into the anisotropy beneath the Transantarctic Mountains

    NASA Astrophysics Data System (ADS)

    Hu, Xiao Gang

    2016-08-01

    Normal mode coupling pair 0S26-0T26 and 0S27-0T27 are significantly present at the South Pole station QSPA after the 2011/03/11 Mw9.1 Tohoku earthquake. In an attempt to determine the mechanisms responsible for the coupling pairs, I first investigate mode observations at 43 stations distributed along the polar great-circle path for the earthquake and observations at 32 Antarctic stations. I rule out the effect of Earth's rotation as well as the effect of global large-scale lateral heterogeneity, but argue instead for the effect of small-scale local azimuthal anisotropy in a depth extent about 300 km. The presence of quasi-Love waveform in 2-5 mHz at QSPA and its nearby stations confirms the predication. Secondly, I analyze normal mode observations at the South Pole location after 28 large earthquakes from 1998 to 2015. The result indicates that the presence of the mode coupling is azimuthal dependent, which is related to event azimuths in -46° to -18°. I also make a comparison between the shear-wave splitting measurements of previous studies and the mode coupling observations of this study, suggesting that their difference can be explained by a case that the anisotropy responsible for the mode coupling is not just below the South Pole location but located below region close to the Transantarctic Mountains (TAM). Furthermore, more signals of local azimuthal anisotropy in normal-mode observations at QSPA and SBA, such as coupling of 0S12-0T11 and vertical polarization anomaly for 0T10, confirms the existence of deep anisotropy close to TAM, which may be caused by asthenospheric mantle flow and edge convection around cratonic keel of TAM.

  9. Atomization of Impinging Droplets on Superheated Superhydrophobic Surfaces

    NASA Astrophysics Data System (ADS)

    Emerson, Preston; Crockett, Julie; Maynes, Daniel

    2017-11-01

    Water droplets impinging smooth superheated surfaces may be characterized by dynamic vapor bubbles rising to the surface, popping, and causing a spray of tiny droplets to erupt from the droplet. This spray is called secondary atomization. Here, atomization is quantified experimentally for water droplets impinging superheated superhydrophobic surfaces. Smooth hydrophobic and superhydrophobic surfaces with varying rib and post microstructuring were explored. Each surface was placed on an aluminum heating block, and impingement events were captured with a high speed camera at 3000 fps. For consistency among tests, all events were normalized by the maximum atomization found over a range of temperatures on a smooth hydrophobic surface. An estimate of the level of atomization during an impingement event was created by quantifying the volume of fluid present in the atomization spray. Droplet diameter and Weber number were held constant, and atomization was found for a range of temperatures through the lifetime of the impinging droplet. The Leidenfrost temperature was also determined and defined to be the lowest temperature at which atomization ceases to occur. Both atomization and Leidenfrost temperature increase with decreasing pitch (distance between microstructures).

  10. Calculations of atomic magnetic nuclear shielding constants based on the two-component normalized elimination of the small component method

    NASA Astrophysics Data System (ADS)

    Yoshizawa, Terutaka; Zou, Wenli; Cremer, Dieter

    2017-04-01

    A new method for calculating nuclear magnetic resonance shielding constants of relativistic atoms based on the two-component (2c), spin-orbit coupling including Dirac-exact NESC (Normalized Elimination of the Small Component) approach is developed where each term of the diamagnetic and paramagnetic contribution to the isotropic shielding constant σi s o is expressed in terms of analytical energy derivatives with regard to the magnetic field B and the nuclear magnetic moment 𝝁 . The picture change caused by renormalization of the wave function is correctly described. 2c-NESC/HF (Hartree-Fock) results for the σiso values of 13 atoms with a closed shell ground state reveal a deviation from 4c-DHF (Dirac-HF) values by 0.01%-0.76%. Since the 2-electron part is effectively calculated using a modified screened nuclear shielding approach, the calculation is efficient and based on a series of matrix manipulations scaling with (2M)3 (M: number of basis functions).

  11. Image routing via atomic spin coherence

    PubMed Central

    Wang, Lei; Sun, Jia-Xiang; Luo, Meng-Xi; Sun, Yuan-Hang; Wang, Xiao-Xiao; Chen, Yi; Kang, Zhi-Hui; Wang, Hai-Hua; Wu, Jin-Hui; Gao, Jin-Yue

    2015-01-01

    Coherent storage of optical image in a coherently-driven medium is a promising method with possible applications in many fields. In this work, we experimentally report a controllable spatial-frequency routing of image via atomic spin coherence in a solid-state medium driven by electromagnetically induced transparency (EIT). Under the EIT-based light-storage regime, a transverse spatial image carried by the probe field is stored into atomic spin coherence. By manipulating the frequency and spatial propagation direction of the read control field, the stored image is transferred into a new spatial-frequency channel. When two read control fields are used to retrieve the stored information, the image information is converted into a superposition of two spatial-frequency modes. Through this technique, the image is manipulated coherently and all-optically in a controlled fashion. PMID:26658846

  12. Entanglement analysis of a two-atom nonlinear Jaynes-Cummings model with nondegenerate two-photon transition, Kerr nonlinearity, and two-mode Stark shift

    NASA Astrophysics Data System (ADS)

    Baghshahi, H. R.; Tavassoly, M. K.; Faghihi, M. J.

    2014-12-01

    An entangled state, as an essential tool in quantum information processing, may be generated through the interaction between light and matter in cavity quantum electrodynamics. In this paper, we study the interaction between two two-level atoms and a two-mode field in an optical cavity enclosed by a medium with Kerr nonlinearity in the presence of a detuning parameter and Stark effect. It is assumed that the atom-field coupling and third-order susceptibility of the Kerr medium depend on the intensity of the light. In order to investigate the dynamics of the introduced system, we obtain the exact analytical form of the state vector of the considered atom-field system under initial conditions which may be prepared for the atoms (in a coherent superposition of their ground and upper states) and the fields (in a standard coherent state). Then, in order to evaluate the degree of entanglement between the subsystems, we investigate the dynamics of the entanglement by employing the entanglement of formation. Finally, we analyze in detail the influences of the Stark shift, the deformed Kerr medium, the intensity-dependent coupling, and also the detuning parameter on the behavior of this measure for different subsystems. The numerical results show that the amount of entanglement between the different subsystems can be controlled by choosing the evolved parameters appropriately.

  13. Robust Seismic Normal Modes Computation in Radial Earth Models and A Novel Classification Based on Intersection Points of Waveguides

    NASA Astrophysics Data System (ADS)

    Ye, J.; Shi, J.; De Hoop, M. V.

    2017-12-01

    We develop a robust algorithm to compute seismic normal modes in a spherically symmetric, non-rotating Earth. A well-known problem is the cross-contamination of modes near "intersections" of dispersion curves for separate waveguides. Our novel computational approach completely avoids artificial degeneracies by guaranteeing orthonormality among the eigenfunctions. We extend Wiggins' and Buland's work, and reformulate the Sturm-Liouville problem as a generalized eigenvalue problem with the Rayleigh-Ritz Galerkin method. A special projection operator incorporating the gravity terms proposed by de Hoop and a displacement/pressure formulation are utilized in the fluid outer core to project out the essential spectrum. Moreover, the weak variational form enables us to achieve high accuracy across the solid-fluid boundary, especially for Stoneley modes, which have exponentially decaying behavior. We also employ the mixed finite element technique to avoid spurious pressure modes arising from discretization schemes and a numerical inf-sup test is performed following Bathe's work. In addition, the self-gravitation terms are reformulated to avoid computations outside the Earth, thanks to the domain decomposition technique. Our package enables us to study the physical properties of intersection points of waveguides. According to Okal's classification theory, the group velocities should be continuous within a branch of the same mode family. However, we have found that there will be a small "bump" near intersection points, which is consistent with Miropol'sky's observation. In fact, we can loosely regard Earth's surface and the CMB as independent waveguides. For those modes that are far from the intersection points, their eigenfunctions are localized in the corresponding waveguides. However, those that are close to intersection points will have physical features of both waveguides, which means they cannot be classified in either family. Our results improve on Okal

  14. Bimodal atomic force microscopy driving the higher eigenmode in frequency-modulation mode: Implementation, advantages, disadvantages and comparison to the open-loop case.

    PubMed

    Ebeling, Daniel; Solares, Santiago D

    2013-01-01

    We present an overview of the bimodal amplitude-frequency-modulation (AM-FM) imaging mode of atomic force microscopy (AFM), whereby the fundamental eigenmode is driven by using the amplitude-modulation technique (AM-AFM) while a higher eigenmode is driven by using either the constant-excitation or the constant-amplitude variant of the frequency-modulation (FM-AFM) technique. We also offer a comparison to the original bimodal AFM method, in which the higher eigenmode is driven with constant frequency and constant excitation amplitude. General as well as particular characteristics of the different driving schemes are highlighted from theoretical and experimental points of view, revealing the advantages and disadvantages of each. This study provides information and guidelines that can be useful in selecting the most appropriate operation mode to characterize different samples in the most efficient and reliable way.

  15. Local vibrational modes of the water dimer - Comparison of theory and experiment

    NASA Astrophysics Data System (ADS)

    Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D.

    2012-12-01

    Local and normal vibrational modes of the water dimer are calculated at the CCSD(T)/CBS level of theory. The local H-bond stretching frequency is 528 cm-1 compared to a normal mode stretching frequency of just 143 cm-1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to mass coupling, a change in the anharmonicity, and coupling with the local HOH bending modes. The local mode stretching force constant is related to the strength of the H-bond whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the H-bond strength.

  16. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  17. Comparing mode-crosstalk and mode-dependent loss of laterally displaced orbital angular momentum and Hermite-Gaussian modes for free-space optical communication.

    PubMed

    Ndagano, Bienvenu; Mphuthi, Nokwazi; Milione, Giovanni; Forbes, Andrew

    2017-10-15

    There is interest in using orbital angular momentum (OAM) modes to increase the data speed of free-space optical communication. A prevalent challenge is the mitigation of mode-crosstalk and mode-dependent loss that is caused by the modes' lateral displacement at the data receiver. Here, the mode-crosstalk and mode-dependent loss of laterally displaced OAM modes (LG 0,+1 , LG 0,-1 ) are experimentally compared to that of a Hermite-Gaussian (HG) mode subset (HG 0,1 , HG 1,0 ). It is shown, for an aperture larger than the modes' waist sizes, some of the HG modes can experience less mode-crosstalk and mode-dependent loss when laterally displaced along a symmetry axis. It is also shown, over a normal distribution of lateral displacements whose standard deviation is 2× the modes' waist sizes, on average, the HG modes experience 66% less mode-crosstalk and 17% less mode-dependent loss.

  18. Qubit-loss-free fusion of atomic W states via photonic detection

    NASA Astrophysics Data System (ADS)

    Ding, Cheng-Yun; Kong, Fan-Zhen; Yang, Qing; Yang, Ming; Cao, Zhuo-Liang

    2018-06-01

    In this paper, we propose two new qubit-loss-free (QLF) fusion schemes for W states in cavity QED system. Resonant interactions between atoms and single cavity mode constitute the main fusion mechanism, with which atomic |W_{n+m}> and |W_{n+m+q}> states can be generated, respectively, from a |Wn> and a |Wm>; and from a |Wn>, a |Wm> and a |Wq>, by detecting the cavity mode. The QLF property of the schemes makes them more efficient and simpler than the currently existing ones, and fewer intermediate steps and memory resources are required for generating a target large-scale W state. Furthermore, the fusion of atomic states can be realized via the detection on cavity mode rather than the much complicated atomic detection, which makes our schemes feasible. In addition, the analyses of the optimal resource cost and the experimental feasibility indicate that the present schemes are simple and efficient, and maybe implementable within the current experimental techniques.

  19. Time reversal imaging and cross-correlations techniques by normal mode theory

    NASA Astrophysics Data System (ADS)

    Montagner, J.; Fink, M.; Capdeville, Y.; Phung, H.; Larmat, C.

    2007-12-01

    Time-reversal methods were successfully applied in the past to acoustic waves in many fields such as medical imaging, underwater acoustics, non destructive testing and recently to seismic waves in seismology for earthquake imaging. The increasing power of computers and numerical methods (such as spectral element methods) enables one to simulate more and more accurately the propagation of seismic waves in heterogeneous media and to develop new applications, in particular time reversal in the three-dimensional Earth. Generalizing the scalar approach of Draeger and Fink (1999), the theoretical understanding of time-reversal method can be addressed for the 3D- elastic Earth by using normal mode theory. It is shown how to relate time- reversal methods on one hand, with auto-correlation of seismograms for source imaging and on the other hand, with cross-correlation between receivers for structural imaging and retrieving Green function. The loss of information will be discussed. In the case of source imaging, automatic location in time and space of earthquakes and unknown sources is obtained by time reversal technique. In the case of big earthquakes such as the Sumatra-Andaman earthquake of december 2004, we were able to reconstruct the spatio-temporal history of the rupture. We present here some new applications at the global scale of these techniques on synthetic tests and on real data.

  20. Using Atomic Orbitals and Kinesthetic Learning to Authentically Derive Molecular Stretching Vibrations

    ERIC Educational Resources Information Center

    Bridgeman, Adam J.; Schmidt, Timothy W.; Young, Nigel A.

    2013-01-01

    The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many…

  1. Molecules Without Atoms

    NASA Astrophysics Data System (ADS)

    Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

    We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

  2. Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results.

    PubMed

    Hahn, Seungsoo

    2016-10-28

    The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.

  3. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

    PubMed

    Higo, Junichi; Umezawa, Koji

    2014-01-01

    We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

  4. Single atom emission in an optical resonator

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Childs, J.J.; An, K.; Dasari, R.R.

    A single atom coupled to a single mode of a radiation field is a fundamental system for studying the interaction of radiation with matter. The study of such systems has come to be called cavity quantum electrodynamics (QED). Atoms coupled to a single mode of a resonator have been studied experimentally and theoretically in several interesting regimes since this basic system was first considered theoretically by Janes and Cummings. The objective of the present chapter is to provide a theoretical framework and present a unifying picture of the various phenomena which can occur in such a system. 35 refs., 11more » figs.« less

  5. Integrated Optical Dipole Trap for Cold Neutral Atoms with an Optical Waveguide Coupler

    NASA Astrophysics Data System (ADS)

    Lee, J.; Park, D. H.; Mittal, S.; Meng, Y.; Dagenais, M.; Rolston, S. L.

    2013-05-01

    Using an optical waveguide, an integrated optical dipole trap uses two-color (red and blue-detuned) traveling evanescent wave fields for trapping cold neutral atoms. To achieve longitudinal confinement, we propose using an integrated optical waveguide coupler, which provides a potential gradient along the beam propagation direction sufficient to confine atoms. This integrated optical dipole trap can support an atomic ensemble with a large optical depth due to its small mode area. Its quasi-TE0 waveguide mode has an advantage over the HE11 mode of a nanofiber, with little inhomogeneous Zeeman broadening at the trapping region. The longitudinal confinement eliminates the need for a 1D optical lattice, reducing collisional blockaded atomic loading, potentially producing larger ensembles. The waveguide trap allows for scalability and integrability with nano-fabrication technology. We analyze the potential performance of such integrated atom traps and present current research progress towards a fiber-coupled silicon nitride optical waveguide integrable with atom chips. Work is supported by the ARO Atomtronics MURI. Work is supported by the ARO Atomtronics MURI.

  6. Discrimination Between Cervical Cancer Cells and Normal Cervical Cells Based on Longitudinal Elasticity Using Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Zhao, Xueqin; Zhong, Yunxin; Ye, Ting; Wang, Dajing; Mao, Bingwei

    2015-12-01

    The mechanical properties of cells are considered promising biomarkers for the early diagnosis of cancer. Recently, atomic force microscopy (AFM)-based nanoindentation technology has been utilized for the examination of cell cortex mechanics in order to distinguish malignant cells from normal cells. However, few attempts to evaluate the biomechanical properties of cells have focused on the quantification of the non-homogeneous longitudinal elasticity of cellular structures. In the present study, we applied a variation of the method of Carl and Schillers to investigate the differences between longitudinal elasticity of human cervical squamous carcinoma cells (CaSki) and normal cervical epithelial cells (CRL2614) using AFM. The results reveal a three-layer heterogeneous structure in the probing volume of both cell types studied. CaSki cells exhibited a lower whole-cell stiffness and a softer nuclei zone compared to the normal counterpart cells. Moreover, a better differentiated cytoskeleton was found in the inner cytoplasm/nuclei zone of the normal CRL2614 cells, whereas a deeper cytoskeletal distribution was observed in the probing volume of the cancerous counterparts. The sensitive cortical panel of CaSki cells, with a modulus of 0.35~0.47 kPa, was located at 237~225 nm; in normal cells, the elasticity was 1.20~1.32 kPa at 113~128 nm. The present improved method may be validated using the conventional Hertz-Sneddon method, which is widely reported in the literature. In conclusion, our results enable the quantification of the heterogeneous longitudinal elasticity of cancer cells, in particular the correlation with the corresponding depth. Preliminary results indicate that our method may potentially be applied to improve the detection of cancerous cells and provide insights into the pathophysiology of the disease.

  7. Approximate solution of the mode-mode coupling integral: Application to cytosine and its deuterated derivative.

    PubMed

    Rasheed, Tabish; Ahmad, Shabbir

    2010-10-01

    Ab initio Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset (MP2) methods were used to perform harmonic and anharmonic calculations for the biomolecule cytosine and its deuterated derivative. The anharmonic vibrational spectra were computed using the vibrational self-consistent field (VSCF) and correlation-corrected vibrational self-consistent field (CC-VSCF) methods. Calculated anharmonic frequencies have been compared with the argon matrix spectra reported in literature. The results were analyzed with focus on the properties of anharmonic couplings between pair of modes. A simple and easy to use formula for calculation of mode-mode coupling magnitudes has been derived. The key element in present approach is the approximation that only interactions between pairs of normal modes have been taken into account, while interactions of triples or more are neglected. FTIR and Raman spectra of solid state cytosine have been recorded in the regions 400-4000 cm(-1) and 60-4000 cm(-1), respectively. Vibrational analysis and assignments are based on calculated potential energy distribution (PED) values. Copyright 2010 Elsevier B.V. All rights reserved.

  8. Few-Photon Nonlinearity with an Atomic Ensemble in an Optical Cavity

    NASA Astrophysics Data System (ADS)

    Tanji, Haruka

    2011-12-01

    This thesis investigates the effect of the cavity vacuum field on the dispersive properties of an atomic ensemble in a strongly coupled high-finesse cavity. In particular, we demonstrate vacuum-induced transparency (VIT). The light absorption by the ensemble is suppressed by up to 40% in the presence of a cavity vacuum field. The sharp transparency peak is accompanied by the reduction in the group velocity of a light pulse, measured to be as low as 1800 m/s. This observation is a large step towards the realization of photon number-state filters, recently proposed by Nikoghosyan et al. Furthermore, we demonstrate few-photon optical nonlinearity, where the transparency is increased from 40% to 80% with ˜12 photons in the cavity mode. The result may be viewed as all-optical switching, where the transmission of photons in one mode may be controlled by 12 photons in another. These studies point to the possibility of nonlinear interaction between photons in different free-space modes, a scheme that circumvents cavity-coupling losses that plague cavity-based quantum information processing. Potential applications include advanced quantum devices such as photonic quantum gates, photon-number resolving detectors, and single-photon transistors. In the efforts leading up to these results, we investigate the collective enhancement of atomic coupling to a single mode of a low-finesse cavity. With the strong collective coupling, we obtain exquisite control of quantum states in the atom-photon coupled system. In this system, we demonstrate a heralded single-photon source with 84% conditional efficiency, a quantum bus for deterministic entanglement of two remote ensembles, and heralded polarization-state quantum memory with fidelity above 90%.

  9. Number-phase entropic squeezing and nonclassical properties of a three-level atom interacting with a two-mode field: intensity-dependent coupling, deformed Kerr medium, and detuning effects

    NASA Astrophysics Data System (ADS)

    Faghihi, Mohammad Javad; Tavassoly, Mohammad Kazem

    2013-11-01

    In this paper, we follow our presented model in J. Opt. Soc. Am. B {\\bf 30}, 1109--1117 (2013), in which the interaction between a $\\Lambda$-type three-level atom and a quantized two-mode radiation field in a cavity in the presence of nonlinearities is studied. After giving a brief review on the procedure of obtaining the state vector of the atom-field system, some further interesting and important physical features (which are of particular interest in the quantum optics field of research) of the whole system state, i.e., the number-phase entropic uncertainty relation (based on the two-mode Pegg-Barnett formalism) and some of the nonclassicality signs consist of sub-Poissonian statistics, Cauchy-Schwartz inequality and two kinds of squeezing phenomenon are investigated. During our presentation, the effects of intensity-dependent coupling, deformed Kerr medium and the detuning parameters on the depth and domain of each of the mentioned nonclassical criteria of the considered quantum system are studied, in detail. It is shown that each of the mentioned nonclassicality aspects can be obtained by appropriately choosing the related parameters.

  10. Toward quantitative estimation of material properties with dynamic mode atomic force microscopy: a comparative study.

    PubMed

    Ghosal, Sayan; Gannepalli, Anil; Salapaka, Murti

    2017-08-11

    In this article, we explore methods that enable estimation of material properties with the dynamic mode atomic force microscopy suitable for soft matter investigation. The article presents the viewpoint of casting the system, comprising of a flexure probe interacting with the sample, as an equivalent cantilever system and compares a steady-state analysis based method with a recursive estimation technique for determining the parameters of the equivalent cantilever system in real time. The steady-state analysis of the equivalent cantilever model, which has been implicitly assumed in studies on material property determination, is validated analytically and experimentally. We show that the steady-state based technique yields results that quantitatively agree with the recursive method in the domain of its validity. The steady-state technique is considerably simpler to implement, however, slower compared to the recursive technique. The parameters of the equivalent system are utilized to interpret storage and dissipative properties of the sample. Finally, the article identifies key pitfalls that need to be avoided toward the quantitative estimation of material properties.

  11. Mode Locking of Lasers with Atomic Layer Graphene

    DTIC Science & Technology

    2012-07-01

    polarization components. As in order to obtain the vector soliton operation in a mode locked fiber laser no any polarization ...oscilloscope traces of a polarization locked vector soliton operation state. Figure 21: Oscilloscope traces of pulse train in a phase locked vector ... locked vector solitons , where the polarization of the solitons emitted by the laser is fixed, the polarization of the

  12. Internal Spin Control, Squeezing and Decoherence in Ensembles of Alkali Atomic Spins

    NASA Astrophysics Data System (ADS)

    Norris, Leigh Morgan

    particular, we find that state preparation using control of the internal hyperfine spin increases the entangling power of squeezing protocols when f>1/2. Post-processing of the ensemble using additional internal spin control converts this entanglement into metrologically useful spin squeezing. By employing a variation of the Holstein-Primakoff approximation, in which the collective spin observables of the atomic ensemble are treated as quadratures of a bosonic mode, we model entanglement generation, spin squeezing and the effects of internal spin control. The Holstein-Primakoff formalism also enables us to take into account the decoherence of the ensemble due to optical pumping. While most works ignore or treat optical pumping phenomenologically, we employ a master equation derived from first principles. Our analysis shows that state preparation and the hyperfine spin size have a substantial impact upon both the generation of spin squeezing and the decoherence of the ensemble. Through a numerical search, we determine state preparations that enhance squeezing protocols while remaining robust to optical pumping. Finally, most work on spin squeezing in atomic ensembles has treated the light as a plane wave that couples identically to all atoms. In the final part of this dissertation, we go beyond the customary plane wave approximation on the light and employ focused paraxial beams, which are more efficiently mode matched to the radiation pattern of the atomic ensemble. The mathematical formalism and the internal spin control techniques that we applied in the plane wave case are generalized to accommodate the non-homogeneous paraxial probe. We find the optimal geometries of the atomic ensemble and the probe for mode matching and generation of spin squeezing.

  13. Internal Spin Control, Squeezing and Decoherence in Ensembles of Alkali Atomic Spins

    NASA Astrophysics Data System (ADS)

    Norris, Leigh Morgan

    particular, we find that state preparation using control of the internal hyperfine spin increases the entangling power of squeezing protocols when f >1/2. Post-processing of the ensemble using additional internal spin control converts this entanglement into metrologically useful spin squeezing. By employing a variation of the Holstein-Primakoff approximation, in which the collective spin observables of the atomic ensemble are treated as quadratures of a bosonic mode, we model entanglement generation, spin squeezing and the effects of internal spin control. The Holstein-Primakoff formalism also enables us to take into account the decoherence of the ensemble due to optical pumping. While most works ignore or treat optical pumping phenomenologically, we employ a master equation derived from first principles. Our analysis shows that state preparation and the hyperfine spin size have a substantial impact upon both the generation of spin squeezing and the decoherence of the ensemble. Through a numerical search, we determine state preparations that enhance squeezing protocols while remaining robust to optical pumping. Finally, most work on spin squeezing in atomic ensembles has treated the light as a plane wave that couples identically to all atoms. In the final part of this dissertation, we go beyond the customary plane wave approximation on the light and employ focused paraxial beams, which are more efficiently mode matched to the radiation pattern of the atomic ensemble. The mathematical formalism and the internal spin control techniques that we applied in the plane wave case are generalized to accommodate the non-homogeneous paraxial probe. We find the optimal geometries of the atomic ensemble and the probe for mode matching and generation of spin squeezing.

  14. Higher order microfibre modes for dielectric particle trapping and propulsion

    PubMed Central

    Maimaiti, Aili; Truong, Viet Giang; Sergides, Marios; Gusachenko, Ivan; Nic Chormaic, Síle

    2015-01-01

    Optical manipulation in the vicinity of optical micro- and nanofibres has shown potential across several fields in recent years, including microparticle control, and cold atom probing and trapping. To date, most work has focussed on the propagation of the fundamental mode through the fibre. However, along the maximum mode intensity axis, higher order modes have a longer evanescent field extension and larger field amplitude at the fibre waist compared to the fundamental mode, opening up new possibilities for optical manipulation and particle trapping. We demonstrate a microfibre/optical tweezers compact system for trapping and propelling dielectric particles based on the excitation of the first group of higher order modes at the fibre waist. Speed enhancement of polystyrene particle propulsion was observed for the higher order modes compared to the fundamental mode for particles ranging from 1 μm to 5 μm in diameter. The optical propelling velocity of a single, 3 μm polystyrene particle was found to be 8 times faster under the higher order mode than the fundamental mode field for a waist power of 25 mW. Experimental data are supported by theoretical calculations. This work can be extended to trapping and manipulation of laser-cooled atoms with potential for quantum networks. PMID:25766925

  15. All-atom molecular dynamics of virus capsids as drug targets

    DOE PAGES

    Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

    2016-04-29

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

  16. All-atom molecular dynamics of virus capsids as drug targets

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

  17. Coherent quantum depletion of an interacting atom condensate

    PubMed Central

    Kira, M.

    2015-01-01

    Sufficiently strong interactions promote coherent quantum transitions in spite of thermalization and losses, which are the adversaries of delicate effects such as reversibility and correlations. In atomic Bose–Einstein condensates (BECs), strong atom–atom interactions can eject atoms from the BEC to the normal component, yielding quantum depletion instead of temperature depletion. A recent experiment has already been verified to overcome losses. Here I show that it also achieves coherent quantum-depletion dynamics in a BEC swept fast enough from weak to strong atom–atom interactions. The elementary coherent process first excites the normal component into a liquid state that evolves into a spherical shell state, where the atom occupation peaks at a finite momentum to shield 50% of the BEC atoms from annihilation. The identified coherent processes resemble ultrafast semiconductor excitations expanding the scope of BEC explorations to many-body non-equilibrium studies. PMID:25767044

  18. The equilibrium properties and folding kinetics of an all-atom Go xAF model of the Trp-cage

    NASA Astrophysics Data System (ADS)

    Linhananta, Apichart; Boer, Jesse; MacKay, Ian

    2005-03-01

    The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go ¯ model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial α-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

  19. Nanosystem self-assembly pathways discovered via all-atom multiscale analysis.

    PubMed

    Pankavich, Stephen D; Ortoleva, Peter J

    2012-07-26

    We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an N-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the classical Liouville equation. From a reduced statistical framework, rigorous stochastic equations for population levels of beginning, intermediate, and final aggregates are also derived. It is shown that the definition of an assembly type is a self-consistency criterion that must strike a balance between precision and the need for population levels to be slowly varying relative to the time scale of atomic motion. The deductive multiscale approach is complemented by a qualitative notion of multicomponent association and the ensemble of exact atomic-level configurations consistent with them. In processes such as viral self-assembly from proteins and RNA or DNA, there are many possible intermediates, so that it is usually difficult to predict the most efficient assembly pathway. However, in the current study, rates of assembly of each possible intermediate can be predicted. This avoids the need, as in a phenomenological approach, for recalibration with each new application. The method accounts for the feedback across scales in space and time that is fundamental to nanosystem self-assembly. The theory has applications to bionanostructures, geomaterials, engineered composites, and nanocapsule therapeutic delivery systems.

  20. Entanglement between two spatially separated atomic modes

    NASA Astrophysics Data System (ADS)

    Lange, Karsten; Peise, Jan; Lücke, Bernd; Kruse, Ilka; Vitagliano, Giuseppe; Apellaniz, Iagoba; Kleinmann, Matthias; Tóth, Géza; Klempt, Carsten

    2018-04-01

    Modern quantum technologies in the fields of quantum computing, quantum simulation, and quantum metrology require the creation and control of large ensembles of entangled particles. In ultracold ensembles of neutral atoms, nonclassical states have been generated with mutual entanglement among thousands of particles. The entanglement generation relies on the fundamental particle-exchange symmetry in ensembles of identical particles, which lacks the standard notion of entanglement between clearly definable subsystems. Here, we present the generation of entanglement between two spatially separated clouds by splitting an ensemble of ultracold identical particles prepared in a twin Fock state. Because the clouds can be addressed individually, our experiments open a path to exploit the available entangled states of indistinguishable particles for quantum information applications.

  1. Electronic control of different generation regimes in mode-locked all-fibre F8 laser

    NASA Astrophysics Data System (ADS)

    Kobtsev, Sergey; Ivanenko, Aleksey; Kokhanovskiy, Alexey; Smirnov, Sergey

    2018-04-01

    We demonstrate for the first time an electronically controlled realisation of markedly different generation regimes in a mode-locked all-fibre figure-eight (F8) Yb-doped laser. Electronic adjustment of the ratio of pumping powers of two amplification stages in a nonlinear amplifying loop mirror enables the establishment of stable pulse generation regimes with different degrees of coherence and control over their parameters within relatively broad limits, with the pulse duration range exceeding a factor of two in the picosecond domain for coherent and incoherent pulses, the energy range exceeding an order of magnitude for incoherent pulses (2.2-24.8 nJ) and over a factor of 8 for coherent pulses (1.9-16.2 nJ). Adjustment of the pumping powers allows one to maintain the duration of the coherent pulses and to set their peak power in the range of 32.5-292.5 W. The proposed configuration of electronic control over the radiation parameters of a mode-locked all-fibre F8 laser enables reproducible generation of pulses of different types with specified parameters within a broad range of values.

  2. Kelvin waves: a comparison study between SABER and normal mode analysis of ECMWF data

    NASA Astrophysics Data System (ADS)

    Blaauw, Marten; Garcia, Rolando; Zagar, Nedjeljka; Tribbia, Joe

    2014-05-01

    Equatorial Kelvin waves spectra are sensitive to the multi-scale variability of their source of tropical convective forcing. Moreover, Kelvin wave spectra are modified upward by changes in the background winds and stability. Recent high resolution data from observations as well as analyses are capable of resolving the slower Kelvin waves with shorter vertical wavelength near the tropical tropopause. In this presentation, results from a quantitive comparison study of stratospheric Kelvin waves in satellite data (SABER) and analysis data from the ECMWF operational archive will be shown. Temperature data from SABER is extracted over a six year period (2007-2012) with an effective vertical resolution of 2 km. Spectral power of stratospheric Kelvin waves in SABER data is isolated by selecting symmetric and eastward spectral components in the 8-20 days range. Global data from ECMWF operational analysis is extracted for the same six years on 91 model levels (top level at 0.01 hPa) and 25 km horizontal resolution. Using three-dimensional orthogonal normal-mode expansions, the input mass and wind data from ECMWF is projected onto balanced rotational modes and unbalanced inertia-gravity modes, including spectral data for pure Kelvin waves. The results show good agreement between Kelvin waves in SABER and ECMWF analyses data for: (i) the frequency shift of Kelvin wave variance with height and (ii) vertical wavelengths. Variability with respect to QBO will also be discussed. In a previous study, discrepancies in the upper stratosphere were found to be 60% and are found here to be 10% (8-20 day averaged value), which can be explained by the better stratosphere representation in the 91 model level version of the ECMWF operational model. New discrepancies in Kelvin wave variance are found in the lower stratosphere at 20 km. Averaged spectral power over the 8-20 day range is found to be 35% higher in ECMWF compared to SABER data. We compared results at 20 km with additional

  3. Tungsten devices in analytical atomic spectrometry

    NASA Astrophysics Data System (ADS)

    Hou, Xiandeng; Jones, Bradley T.

    2002-04-01

    Tungsten devices have been employed in analytical atomic spectrometry for approximately 30 years. Most of these atomizers can be electrically heated up to 3000 °C at very high heating rates, with a simple power supply. Usually, a tungsten device is employed in one of two modes: as an electrothermal atomizer with which the sample vapor is probed directly, or as an electrothermal vaporizer, which produces a sample aerosol that is then carried to a separate atomizer for analysis. Tungsten devices may take various physical shapes: tubes, cups, boats, ribbons, wires, filaments, coils and loops. Most of these orientations have been applied to many analytical techniques, such as atomic absorption spectrometry, atomic emission spectrometry, atomic fluorescence spectrometry, laser excited atomic fluorescence spectrometry, metastable transfer emission spectroscopy, inductively coupled plasma optical emission spectrometry, inductively coupled plasma mass spectrometry and microwave plasma atomic spectrometry. The analytical figures of merit and the practical applications reported for these techniques are reviewed. Atomization mechanisms reported for tungsten atomizers are also briefly summarized. In addition, less common applications of tungsten devices are discussed, including analyte preconcentration by adsorption or electrodeposition and electrothermal separation of analytes prior to analysis. Tungsten atomization devices continue to provide simple, versatile alternatives for analytical atomic spectrometry.

  4. Phonon Transport at Crystalline Si/Ge Interfaces: The Role of Interfacial Modes of Vibration

    PubMed Central

    Gordiz, Kiarash; Henry, Asegun

    2016-01-01

    We studied the modal contributions to heat conduction at crystalline Si and crystalline Ge interfaces and found that more than 15% of the interface conductance arises from less than 0.1% of the modes in the structure. Using the recently developed interface conductance modal analysis (ICMA) method along with a new complimentary methodology, we mapped the correlations between modes, which revealed that a small group of interfacial modes, which exist between 12–13 THz, exhibit extremely strong correlation with other modes in the system. It is found that these interfacial modes (e.g., modes with large eigen vectors for interfacial atoms) are enabled by the degree of anharmonicity near the interface, which is higher than in the bulk, and therefore allows this small group of modes to couple to all others. The analysis sheds light on the nature of localized vibrations at interfaces and can be enlightening for other investigations of localization. PMID:26979787

  5. First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction

    NASA Astrophysics Data System (ADS)

    Zhao, Xiu-Qin; Liu, Ni; Liang, Jiu-Qing

    2017-05-01

    In this article, we use the spin coherent state transformation and the ground state variational method to theoretically calculate the ground function. In order to consider the influence of the atom-atom interaction on the extended Dicke model’s ground state properties, the mean photon number, the scaled atomic population and the average ground energy are displayed. Using the self-consistent field theory to solve the atom-atom interaction, we discover the system undergoes a first-order quantum phase transition from the normal phase to the superradiant phase, but a famous Dicke-type second-order quantum phase transition without the atom-atom interaction. Meanwhile, the atom-atom interaction makes the phase transition point shift to the lower atom-photon collective coupling strength. Supported by the National Natural Science Foundation of China under Grant Nos. 11275118, 11404198, 91430109, 61505100, 51502189, and the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi Province (STIP) under Grant No. 2014102, and the Launch of the Scientific Research of Shanxi University under Grant No. 011151801004, and the National Fundamental Fund of Personnel Training under Grant No. J1103210. The Natural Science Foundation of Shanxi Province under Grant No. 2015011008

  6. Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals.

    PubMed

    Viñes, Francesc; Illas, Francesc

    2017-03-30

    The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects, calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ∼0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ∼0.25 eV smaller than equivalent nonrelativistic all electron PBE0 calculations indicating possible sources of error in nonrelativistic all electron density functional calculations for systems containing elements with relatively high atomic number. The oxygen vacancy formation energy converges rather fast with the supercell size, the predicted value agrees with previously hybrid density functional calculations and analysis of the electronic structure evidences the presence of localized electrons at the vacancy site with a concomitant well localized peak in the density of states ∼0.5 eV above the top of the valence band and a significant relaxation of the Zn atoms near to the oxygen vacancy. Finally, present work shows that accurate results can be obtained in systems involving large supercells containing up to ∼450 atoms using a numeric atomic-centered orbital basis set within a full all electron description including scalar relativistic effects at an affordable cost. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Nanophotonic Optical Isolator Controlled by the Internal State of Cold Atoms

    NASA Astrophysics Data System (ADS)

    Sayrin, Clément; Junge, Christian; Mitsch, Rudolf; Albrecht, Bernhard; O'Shea, Danny; Schneeweiss, Philipp; Volz, Jürgen; Rauschenbeutel, Arno

    2015-10-01

    The realization of nanophotonic optical isolators with high optical isolation even at ultralow light levels and low optical losses is an open problem. Here, we employ the link between the local polarization of strongly confined light and its direction of propagation to realize low-loss nonreciprocal transmission through a silica nanofiber at the single-photon level. The direction of the resulting optical isolator is controlled by the spin state of cold atoms. We perform our experiment in two qualitatively different regimes, i.e., with an ensemble of cold atoms where each atom is weakly coupled to the waveguide and with a single atom strongly coupled to the waveguide mode. In both cases, we observe simultaneously high isolation and high forward transmission. The isolator concept constitutes a nanoscale quantum optical analog of microwave ferrite resonance isolators, can be implemented with all kinds of optical waveguides and emitters, and might enable novel integrated optical devices for fiber-based classical and quantum networks.

  8. Dynamics of entropy and nonclassical properties of the state of a Λ-type three-level atom interacting with a single-mode cavity field with intensity-dependent coupling in a Kerr medium

    NASA Astrophysics Data System (ADS)

    Faghihi, M. J.; Tavassoly, M. K.

    2012-02-01

    In this paper, we study the interaction between a three-level atom and a quantized single-mode field with ‘intensity-dependent coupling’ in a ‘Kerr medium’. The three-level atom is considered to be in a Λ-type configuration. Under particular initial conditions, which may be prepared for the atom and the field, the dynamical state vector of the entire system will be explicitly obtained, for the arbitrary nonlinearity function f(n) associated with any physical system. Then, after evaluating the variation of the field entropy against time, we will investigate the quantum statistics as well as some of the nonclassical properties of the introduced state. During our calculations we investigate the effects of intensity-dependent coupling, Kerr medium and detuning parameters on the depth and domain of the nonclassicality features of the atom-field state vector. Finally, we compare our obtained results with those of V-type three-level atoms.

  9. Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule

    NASA Astrophysics Data System (ADS)

    Takahashi, Takuya; Sugiura, Junnnosuke; Nagayama, Kuniaki

    2002-05-01

    To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high

  10. Chains of benzenes with lithium-atom adsorption: Vibrations and spontaneous symmetry breaking

    NASA Astrophysics Data System (ADS)

    Ortiz, Yenni P.; Stegmann, Thomas; Klein, Douglas J.; Seligman, Thomas H.

    2017-09-01

    We study effects of different configurations of adsorbates on the vibrational modes as well as symmetries of polyacenes and poly-p-phenylenes focusing on lithium atom adsorption. We found that the spectra of the vibrational modes distinguish the different configurations. For more regular adsorption schemes the lowest states are bending and torsion modes of the skeleton, which are essentially followed by the adsorbate. On poly-p-phenylenes we found that lithium adsorption reduces and often eliminates the torsion between rings thus increasing symmetry. There is spontaneous symmetry breaking in poly-p-phenylenes due to double adsorption of lithium atoms on alternating rings.

  11. Quantitative comparison of two independent lateral force calibration techniques for the atomic force microscope.

    PubMed

    Barkley, Sarice S; Deng, Zhao; Gates, Richard S; Reitsma, Mark G; Cannara, Rachel J

    2012-02-01

    Two independent lateral-force calibration methods for the atomic force microscope (AFM)--the hammerhead (HH) technique and the diamagnetic lateral force calibrator (D-LFC)--are systematically compared and found to agree to within 5 % or less, but with precision limited to about 15 %, using four different tee-shaped HH reference probes. The limitations of each method, both of which offer independent yet feasible paths toward traceable accuracy, are discussed and investigated. We find that stiff cantilevers may produce inconsistent D-LFC values through the application of excessively high normal loads. In addition, D-LFC results vary when the method is implemented using different modes of AFM feedback control, constant height and constant force modes, where the latter is more consistent with the HH method and closer to typical experimental conditions. Specifically, for the D-LFC apparatus used here, calibration in constant height mode introduced errors up to 14 %. In constant force mode using a relatively stiff cantilever, we observed an ≈ 4 % systematic error per μN of applied load for loads ≤ 1 μN. The issue of excessive load typically emerges for cantilevers whose flexural spring constant is large compared with the normal spring constant of the D-LFC setup (such that relatively small cantilever flexural displacements produce relatively large loads). Overall, the HH method carries a larger uncertainty, which is dominated by uncertainty in measurement of the flexural spring constant of the HH cantilever as well as in the effective length dimension of the cantilever probe. The D-LFC method relies on fewer parameters and thus has fewer uncertainties associated with it. We thus show that it is the preferred method of the two, as long as care is taken to perform the calibration in constant force mode with low applied loads.

  12. Atomic force microscopy as a tool for the investigation of living cells.

    PubMed

    Morkvėnaitė-Vilkončienė, Inga; Ramanavičienė, Almira; Ramanavičius, Arūnas

    2013-01-01

    Atomic force microscopy is a valuable and useful tool for the imaging and investigation of living cells in their natural environment at high resolution. Procedures applied to living cell preparation before measurements should be adapted individually for different kinds of cells and for the desired measurement technique. Different ways of cell immobilization, such as chemical fixation on the surface, entrapment in the pores of a membrane, or growing them directly on glass cover slips or on plastic substrates, result in the distortion or appearance of artifacts in atomic force microscopy images. Cell fixation allows the multiple use of samples and storage for a prolonged period; it also increases the resolution of imaging. Different atomic force microscopy modes are used for the imaging and analysis of living cells. The contact mode is the best for cell imaging because of high resolution, but it is usually based on the following: (i) image formation at low interaction force, (ii) low scanning speed, and (iii) usage of "soft," low resolution cantilevers. The tapping mode allows a cell to behave like a very solid material, and destructive shear forces are minimized, but imaging in liquid is difficult. The force spectroscopy mode is used for measuring the mechanical properties of cells; however, obtained results strongly depend on the cell fixation method. In this paper, the application of 3 atomic force microscopy modes including (i) contact, (ii) tapping, and (iii) force spectroscopy for the investigation of cells is described. The possibilities of cell preparation for the measurements, imaging, and determination of mechanical properties of cells are provided. The applicability of atomic force microscopy to diagnostics and other biomedical purposes is discussed.

  13. Entanglement dynamics and position-momentum entropic uncertainty relation of a Λ-type three-level atom interacting with a two-mode cavity field in the presence of nonlinearities

    NASA Astrophysics Data System (ADS)

    Faghihi, M. J.; Tavassoly, M. K.; Hooshmandasl, M. R.

    2013-05-01

    In this paper, the interaction between a $\\Lambda$-type three-level atom and two-mode cavity field is discussed. The detuning parameters and cross-Kerr nonlinearity are taken into account and it is assumed that atom-field coupling and Kerr medium to be $f$-deformed. Even though the system seems to be complicated, the analytical form of the state vector of the entire system for considered model is exactly obtained. The time evolution of nonclassical properties such as quantum entanglement and position-momentum entropic uncertainty relation (entropy squeezing) of the field are investigated. In each case, the influences of the detuning parameters, generalized Kerr medium and intensity-dependent coupling on the latter nonclassicality signs are analyzed, in detail.

  14. Functionalization of Carbon Nanotubes using Atomic Hydrogen

    NASA Technical Reports Server (NTRS)

    Khare, Bishun N.; Cassell, Alan M.; Nguyen, Cattien V.; Meyyappan, M.; Han, Jie; Arnold, Jim (Technical Monitor)

    2001-01-01

    We have investigated the irradiation of multi walled and single walled carbon nanotubes (SWNTs) with atomic hydrogen. After irradiating the SWNT sample, a band at 2940/cm (3.4 microns) that is characteristic of the C-H stretching mode is observed using Fourier transform infrared (FTIR) spectroscopy. Additional confirmation of SWNT functionalization is tested by irradiating with atomic deuterium. A weak band in the region 1940/cm (5.2 micron) to 2450/cm (4.1 micron) corresponding to C-D stretching mode is also observed in the FTIR spectrum. This technique provides a clean gas phase process for the functionalization of SWNTs, which could lead to further chemical manipulation and/or the tuning of the electronic properties of SWNTs for nanodevice applications.

  15. 980 nm all-fiber NPR mode-locking Yb-doped phosphate fiber oscillator and its amplifier

    NASA Astrophysics Data System (ADS)

    Li, Pingxue; Yao, Yifei; Chi, Junjie; Hu, Haowei; Yang, Chun; Zhao, Ziqiang; Zhang, Guangju

    2014-12-01

    We report on a 980 nm all-fiber passively mode-locking Yb-doped phosphate fiber oscillator with the nonlinear polarization rotation (NPR) technique and its amplifier. In order to obtaining the stable self-starting mode-locking oscillator at 980 nm, a bandpass filter with 30 nm transmission bandwidth around 980 nm is inserted into the cavity. The oscillator generates the average output power of 26.1 mW with the repetition rate of 20.38 MHz, corresponding to the single pulse energy of 1.28 nJ. The pulse width is 159.48 ps. The output spectrum of the pulses is centered at 977 nm with a full width half maximum (FWHM) of 10 nm and has the characteristic steep spectral edges of dissipative soliton. No undesired ASE and harmful oscillation around 1030 nm is observed. Moreover, through two stage all-fiber-integrated amplifier by using the 980 nm oscillator as seed source, an amplified output power of 205 mW at 980 nm and pulse duration of 178.10 ps is achieved.

  16. Frequency stability degradation of an oscillator slaved to a periodically interrogated atomic resonator.

    PubMed

    Santarelli, G; Audoin, C; Makdissi, A; Laurent, P; Dick, G J; Clairon, A

    1998-01-01

    Atomic frequency standards using trapped ions or cold atoms work intrinsically in a pulsed mode. Theoretically and experimentally, this mode of operation has been shown to lead to a degradation of the frequency stability due to the frequency noise of the interrogation oscillator. In this paper a physical analysis of this effect has been made by evaluating the response of a two-level atom to the interrogation oscillator phase noise in Ramsey and multi-Rabi interrogation schemes using a standard quantum mechanical approach. This response is then used to calculate the degradation of the frequency stability of a pulsed atomic frequency standard such as an atomic fountain or an ion trap standard. Comparison is made to an experimental evaluation of this effect in the LPTF Cs fountain frequency standard, showing excellent agreement.

  17. High power laser source for atom cooling based on reliable telecoms technology with all fibre frequency stabilisation

    NASA Astrophysics Data System (ADS)

    Legg, Thomas; Farries, Mark

    2017-02-01

    Cold atom interferometers are emerging as important tools for metrology. Designed into gravimeters they can measure extremely small changes in the local gravitational field strength and be used for underground surveying to detect buried utilities, mineshafts and sinkholes prior to civil works. To create a cold atom interferometer narrow linewidth, frequency stabilised lasers are required to cool the atoms and to setup and measure the atom interferometer. These lasers are commonly either GaAs diodes, Ti Sapphire lasers or frequency doubled InGaAsP diodes and fibre lasers. The InGaAsP DFB lasers are attractive because they are very reliable, mass-produced, frequency controlled by injection current and simply amplified to high powers with fibre amplifiers. In this paper a laser system suitable for Rb atom cooling, based on a 1560nm DFB laser and erbium doped fibre amplifier, is described. The laser output is frequency doubled with fibre coupled periodically poled LiNbO3 to a wavelength of 780nm. The output power exceeds 1 W at 780nm. The laser is stabilised at 1560nm against a fibre Bragg resonator that is passively temperature compensated. Frequency tuning over a range of 1 GHz is achieved by locking the laser to sidebands of the resonator that are generated by a phase modulator. This laser design is attractive for field deployable rugged systems because it uses all fibre coupled components with long term proven reliability.

  18. Whistler mode waves observed by MGF search coil magnetometer -Polarization and wave normal features of upstream waves near the bow-shock

    NASA Astrophysics Data System (ADS)

    Hayashi, K.; Matsui, H.; Kawano, H.; Yamamoto, T.; Kokubun, S.

    1994-12-01

    Whistler mode waves observed in the upstream region very close to the bow-shock is focused from the initial survey for magnetic fed data in a frequency range between 1Hz and 50Hz observed by the search coil magnetometer on board the Geotail satellite. Based on the three component wave form data polarization and wave-normal characteristics of foreshock waves is first shown as dynamic spectra for the whole Fourier components of the 50 Hz band width. Intense whistler mode waves generated in the foot region of the bow-shock are found strongly controlled in the observed polarization dependent on the angle between directions of the wave propagation and the solar wind flow but not very dependent on frequency. Our simple scheme to derive the ware characteristics which is effective to survey large amount of data continuously growing is also introduced.

  19. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  20. An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

    PubMed

    Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah

    2014-09-04

    Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

  1. Precisely detecting atomic position of atomic intensity images.

    PubMed

    Wang, Zhijun; Guo, Yaolin; Tang, Sai; Li, Junjie; Wang, Jincheng; Zhou, Yaohe

    2015-03-01

    We proposed a quantitative method to detect atomic position in atomic intensity images from experiments such as high-resolution transmission electron microscopy, atomic force microscopy, and simulation such as phase field crystal modeling. The evaluation of detection accuracy proves the excellent performance of the method. This method provides a chance to precisely determine atomic interactions based on the detected atomic positions from the atomic intensity image, and hence to investigate the related physical, chemical and electrical properties. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. A Comparison of the Bounded Derivative and the Normal Mode Initialization Methods Using Real Data

    NASA Technical Reports Server (NTRS)

    Semazzi, F. H. M.; Navon, I. M.

    1985-01-01

    Browning et al. (1980) proposed an initialization method called the bounded derivative method (BDI). They used analytical data to test the new method. Kasahara (1982) theoretically demonstrated the equivalence between BDI and the well known nonlinear normal mode initialization method (NMI). The purposes of this study are the extension of the application of BDI to real data and comparison with NMI. The unbalanced initial state (UBD) is data of January, 1979 OOZ which were interpolated from the adjacent sigma levels of the GLAS GCM to the 300 mb surface. The global barotropic model described by Takacs and Balgovind (1983) is used. Orographic forcing is explicitly included in the model. Many comparisons are performed between various quantities. However, we only present a comparison of the time evolution at two grid points A(50 S, 90 E) and B(10 S, 20 E) which represent low and middle latitude locations. To facilitate a more complete comparison an initialization experiment based on the classical balance equation (CBE) was also included.

  3. Mode coupling in vortex beams

    NASA Astrophysics Data System (ADS)

    Eyyuboğlu, Halil T.

    2018-05-01

    We examine the mode coupling in vortex beams. Mode coupling also known as the crosstalk takes place due to turbulent characteristics of the atmospheric communication medium. This way, the transmitted intrinsic mode of the vortex beam leaks power to other extrinsic modes, thus preventing the correct detection of the transmitted symbol which is usually encoded into the mode index or the orbital angular momentum state of the vortex beam. Here we investigate the normalized power mode coupling ratios of several types of vortex beams, namely, Gaussian vortex beam, Bessel Gaussian beam, hypergeometric Gaussian beam and Laguerre Gaussian beam. It is found that smaller mode numbers lead to less mode coupling. The same is partially observed for increasing source sizes. Comparing the vortex beams amongst themselves, it is seen that hypergeometric Gaussian beam is the one retaining the most power in intrinsic mode during propagation, but only at lowest mode index of unity. At higher mode indices this advantage passes over to the Gaussian vortex beam.

  4. Representing Chemistry: How Instructional Use of Symbolic, Microscopic, and Macroscopic Mode Influences Student Conceptual Understanding in Chemistry

    NASA Astrophysics Data System (ADS)

    Wood, Lorelei

    Chemistry as a subject is difficult to learn and understand, due in part to the specific language used by practitioners in their professional and scientific communications. The language and ways of representing chemical interactions have been grouped into three modes of representation used by chemistry instructors, and ultimately by students in understanding the discipline. The first of these three modes of representation is the symbolic mode, which uses a standard set of rules for chemical nomenclature set out by the IUPAC. The second mode of representation is that of microscopic, which depicts chemical compounds as discrete units made up of atoms and molecules, with a particular ratio of atoms to a molecule or formula unit. The third mode of representation is macroscopic, what can be seen, experienced, or measured directly, like ice melting or a color change during a chemical reaction. Recent evidence suggests that chemistry instructors can assist their students in making the connections between the modes of representation by incorporating all three modes into their teaching and discussions, and overtly connecting the modes during instruction. In this research, chemistry teachers at the community college level were observed over the course of an entire semester, to evaluate their instructional use of mode of representation. The students of these teachers were tested prior to and after a semester's worth of instruction, and changes in the basic chemistry conceptual knowledge of these students were compared. Additionally, a subset of the overall population that was pre- and post-tested was interviewed at length using demonstrations of chemical phenomenon that students were asked to translate using all three modes of representation. Analysis of the instruction of three community college teachers shows there were significant differences among these teachers in their instructional use of mode of representation. Additionally, the students of these three teachers had

  5. Compact all-fiber figure-9 dissipative soliton resonance mode-locked double-clad Er:Yb laser.

    PubMed

    Krzempek, Karol; Sotor, Jaroslaw; Abramski, Krzysztof

    2016-11-01

    The first demonstration of a compact all-fiber figure-9 double-clad erbium-ytterbium laser working in the dissipative soliton resonance (DSR) regime is presented. Mode-locking was achieved using a nonlinear amplifying loop (NALM) resonator configuration. The laser was assembled with an additional 475 m long spool of SMF28 fiber in the NALM loop in order to obtain large net-anomalous cavity dispersion (-10.4  ps2), and therefore ensure that DSR would be the dominant mode-locking mechanism. At maximum pump power (4.78 W) the laser generated rectangular-shaped pulses with 455 ns duration and an average power of 950 mW, which at a repetition frequency of 412 kHz corresponds to a record energy of 2.3 μJ per pulse.

  6. "I Treat Him as a Normal Patient": Unveiling the Normalization Coping Strategy Among Formal Caregivers of Persons With Dementia and Its Implications for Person-Centered Care.

    PubMed

    Bentwich, Miriam Ethel; Dickman, Nomy; Oberman, Amitai; Bokek-Cohen, Ya'arit

    2017-11-01

    Currently, 47 million people have dementia, worldwide, often requiring paid care by formal caregivers. Research regarding family caregivers suggests normalization as a model for coping with negative emotional outcomes in caring for a person with dementia (PWD). The study aims to explore whether normalization coping mechanism exists among formal caregivers, reveal differences in its application among cross-cultural caregivers, and examine how this coping mechanism may be related to implementing person-centered care for PWDs. Content analysis of interviews with 20 formal caregivers from three cultural groups (Jews born in Israel [JI], Arabs born in Israel [AI], Russian immigrants [RI]), attending to PWDs. We extracted five normalization modes, revealing AI caregivers had substantially more utterances of normalization expressions than their colleagues. The normalization modes most commonly expressed by AI caregivers relate to the personhood of PWDs. These normalization modes may enhance formal caregivers' ability to employ person-centered care.

  7. Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

    PubMed

    Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

    2013-04-01

    When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Quantum theory of atoms in molecules charge-charge flux-dipole flux models for the infrared intensities of X(2)CY (X = H, F, Cl; Y = O, S) molecules.

    PubMed

    Faria, Sergio H D M; da Silva, João Viçozo; Haiduke, Roberto L A; Vidal, Luciano N; Vazquez, Pedro A M; Bruns, Roy E

    2007-08-16

    The molecular dipole moments, their derivatives, and the fundamental IR intensities of the X2CY (X = H, F, Cl; Y = O, S) molecules are determined from QTAIM atomic charges and dipoles and their fluxes at the MP2/6-311++G(3d,3p) level. Root-mean-square errors of +/-0.03 D and +/-1.4 km mol(-1) are found for the molecular dipole moments and fundamental IR intensities calculated using quantum theory of atoms in molecules (QTAIM) parameters when compared with those obtained directly from the MP2/6-311++G(3d,3p) calculations and +/-0.05 D and 51.2 km mol(-1) when compared with the experimental values. Charge (C), charge flux (CF), and dipole flux (DF) contributions are reported for all the normal vibrations of these molecules. A large negative correlation coefficient of -0.83 is calculated between the charge flux and dipole flux contributions and indicates that electronic charge transfer from one side of the molecule to the other during vibrations is accompanied by a relaxation effect with electron density polarization in the opposite direction. The characteristic substituent effect that has been observed for experimental infrared intensity parameters and core electron ionization energies has been applied to the CCFDF/QTAIM parameters of F2CO, Cl2CO, F2CS, and Cl2CS. The individual atomic charge, atomic charge flux, and atomic dipole flux contributions are seen to obey the characteristic substituent effect equation just as accurately as the total dipole moment derivative. The CH, CF, and CCl stretching normal modes of these molecules are shown to have characteristic sets of charge, charge flux, and dipole flux contributions.

  9. EDITORIAL: Selected papers from the 16th Workshop on MHD Stability Control: Optimizing and Understanding the Role of Coils for Mode Control Selected papers from the 16th Workshop on MHD Stability Control: Optimizing and Understanding the Role of Coils for Mode Control

    NASA Astrophysics Data System (ADS)

    La Haye, Rob

    2012-09-01

    The Magnetohydrodynamic (MHD) Control Workshop with the theme 'Optimizing and Understanding the Role of Coils for Mode Control' was held at General Atomics (20-22 November 2011) following the 2011 APS-DPP Annual Meeting in Salt Lake City, Utah (14-18 November). This was the 16th in the annual series and was organized jointly by Columbia University, General Atomics, Princeton Plasma Physics Laboratory, and the University of Wisconsin-Madison. Program committee participation included representatives from the EU and Japan along with other US laboratory and university institutions. This workshop highlighted the role of applied non-axisymmetric magnetic fields from both internal and external coils for control of MHD stability to achieve high performance fusion plasmas. The application of 3D magnetic field offers control of important elements of equilibrium, stability, and transport. The use of active 3D fields to stabilize global instabilities and to correct magnetic field errors is an established tool for achieving high beta configurations. 3D fields also affect transport and plasma momentum, and are shown to be important for the control of edge localized modes (ELMs), resistive wall modes, and optimized stellarator configurations. The format was similar to previous workshops, including 13 invited talks, 21 contributed talks, and this year there were 2 panel discussions ('Error Field Correction' led by Andrew Cole of Columbia University and 'Application of Coils in General' led by Richard Buttery of General Atomics). Ted Strait of General Atomics also gave a summary of the International Tokamak Physics Activity (ITPA) MHD meeting in Padua, a group for which he is now the leader. In this special section of Plasma Physics and Controlled Fusion (PPCF) is a sample of the presentations at the workshop, which have been subject to the normal refereeing procedures of the journal. They include a review (A Boozer) and an invited talk (R Fitzpatrick) on error fields, an invited

  10. Establishing and storing of deterministic quantum entanglement among three distant atomic ensembles.

    PubMed

    Yan, Zhihui; Wu, Liang; Jia, Xiaojun; Liu, Yanhong; Deng, Ruijie; Li, Shujing; Wang, Hai; Xie, Changde; Peng, Kunchi

    2017-09-28

    It is crucial for the physical realization of quantum information networks to first establish entanglement among multiple space-separated quantum memories and then, at a user-controlled moment, to transfer the stored entanglement to quantum channels for distribution and conveyance of information. Here we present an experimental demonstration on generation, storage, and transfer of deterministic quantum entanglement among three spatially separated atomic ensembles. The off-line prepared multipartite entanglement of optical modes is mapped into three distant atomic ensembles to establish entanglement of atomic spin waves via electromagnetically induced transparency light-matter interaction. Then the stored atomic entanglement is transferred into a tripartite quadrature entangled state of light, which is space-separated and can be dynamically allocated to three quantum channels for conveying quantum information. The existence of entanglement among three released optical modes verifies that the system has the capacity to preserve multipartite entanglement. The presented protocol can be directly extended to larger quantum networks with more nodes.Continuous-variable encoding is a promising approach for quantum information and communication networks. Here, the authors show how to map entanglement from three spatial optical modes to three separated atomic samples via electromagnetically induced transparency, releasing it later on demand.

  11. Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

    NASA Astrophysics Data System (ADS)

    Blum, Volker

    This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

  12. Mode control in photonic crystal surface emitting lasers (PCSELs) through in-plane feedback (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Taylor, Richard J. E.; Li, Guangrui; Ivanov, Pavlo; Childs, David T. D.; Stevens, Ben J.; Babazadeh, Nasser; Ignatova, Olesya; Hogg, Richard A.

    2017-02-01

    All-semiconductor photonic crystal surface-emitting lasers (PCSELs) operating in CW mode at room temperature and coherently coupled arrays of these lasers are reviewed. These PCSELs are grown via MOVPE on GaAs substrates and include QW active elements and GaAs/InGaP photonic crystal (PC) layer situated above this active zone. Atoms of triangular shapes have been shown to increase optical power from the PCSEL but are also shown to result in a competition between lasing modes. Simulation shows that the energy splitting of lasing modes is smaller for triangular atoms, than for circles making high power single-mode devices difficult to achieve. In this work we experimentally investigate the effect of lateral optical feedback introduced by a facet cleave along one or two perpendicular PCSEL edges. This cleavage plane is misaligned to the PC resulting in a periodic variation of facet phase along the side of the device. Results confirm that a single cleave selects the lowest threshold 2D lasing mode, resulting in a 20% reduction in threshold current and favours single-mode emission. The addition of a second cleave at right-angles to the first has no significant effect upon threshold current. The virgin device is shown to have a symmetric far-field (1 degree) whilst a single cleave produces a 1 degree divergence perpendicular to cleave and 5 degree parallel to cleave. The second orthogonal cleave results in the far field becoming symmetric again but with a divergence angle of 1 degree indicating that single-mode lasing is supported over a wider area.

  13. On Kinetic Slow Modes, Fluid Slow Modes, and Pressure-balanced Structures in the Solar Wind

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Verscharen, Daniel; Chen, Christopher H. K.; Wicks, Robert T., E-mail: daniel.verscharen@unh.edu, E-mail: christopher.chen@imperial.ac.uk, E-mail: r.wicks@ucl.ac.uk

    Observations in the solar wind suggest that the compressive component of inertial-range solar-wind turbulence is dominated by slow modes. The low collisionality of the solar wind allows for nonthermal features to survive, which suggests the requirement of a kinetic plasma description. The least-damped kinetic slow mode is associated with the ion-acoustic (IA) wave and a nonpropagating (NP) mode. We derive analytical expressions for the IA-wave dispersion relation in an anisotropic plasma in the framework of gyrokinetics and then compare them to fully kinetic numerical calculations, results from two-fluid theory, and magnetohydrodynamics (MHD). This comparison shows major discrepancies in the predictedmore » wave phase speeds from MHD and kinetic theory at moderate to high β . MHD and kinetic theory also dictate that all plasma normal modes exhibit a unique signature in terms of their polarization. We quantify the relative amplitude of fluctuations in the three lowest particle velocity moments associated with IA and NP modes in the gyrokinetic limit and compare these predictions with MHD results and in situ observations of the solar-wind turbulence. The agreement between the observations of the wave polarization and our MHD predictions is better than the kinetic predictions, which suggests that the plasma behaves more like a fluid in the solar wind than expected.« less

  14. Local phase space and edge modes for diffeomorphism-invariant theories

    NASA Astrophysics Data System (ADS)

    Speranza, Antony J.

    2018-02-01

    We discuss an approach to characterizing local degrees of freedom of a subregion in diffeomorphism-invariant theories using the extended phase space of Donnelly and Freidel [36]. Such a characterization is important for defining local observables and entanglement entropy in gravitational theories. Traditional phase space constructions for subregions are not invariant with respect to diffeomorphisms that act at the boundary. The extended phase space remedies this problem by introducing edge mode fields at the boundary whose transformations under diffeomorphisms render the extended symplectic structure fully gauge invariant. In this work, we present a general construction for the edge mode symplectic structure. We show that the new fields satisfy a surface symmetry algebra generated by the Noether charges associated with the edge mode fields. For surface-preserving symmetries, the algebra is universal for all diffeomorphism-invariant theories, comprised of diffeomorphisms of the boundary, SL(2, ℝ) transformations of the normal plane, and, in some cases, normal shearing transformations. We also show that if boundary conditions are chosen such that surface translations are symmetries, the algebra acquires a central extension.

  15. Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains.

    PubMed

    Sabater, Carlos; Untiedt, Carlos; van Ruitenbeek, Jan M

    2015-01-01

    This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a 'Berry force'. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.

  16. Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

    PubMed Central

    Sabater, Carlos; Untiedt, Carlos

    2015-01-01

    Summary This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose. PMID:26734525

  17. Optical beams with embedded vortices: building blocks for atom optics and quantum information

    NASA Astrophysics Data System (ADS)

    Chattrapiban, N.; Arakelyan, I.; Mitra, S.; Hill, W. T., III

    2006-05-01

    Laser beams with embedded vortices, Bessel or Laguerre-Gaussian modes, provide a unique opportunity for creating elements for atom optics, entangling photons and, potentially, mediating novel quantum interconnects between photons and matter. High-order Bessel modes, for example, contain intensity voids and propagate nearly diffraction-free for tens of meters. These vortices can be exploited to produce dark channels oriented longitudinally (hollow beams) or transversely to the laser propagation direction. Such channels are ideal for generating networks or circuits to guide and manipulate cold neutral atoms, an essential requirement for realizing future applications associated with atom interferometry, atom lithography and even some neutral atom-based quantum computing architectures. Recently, we divided a thermal cloud of neutral atoms moving within a blue-detuned beam into two clouds with two different momenta by crossing two hollow beams. In this presentation, we will describe these results and discuss the prospects for extending the process to coherent ensembles of matter.

  18. Use of Atomic Oxygen for the Determination of Document Alteration

    NASA Technical Reports Server (NTRS)

    Banks, Bruce A.; Klubnik, Larisa M.

    2003-01-01

    Atomic oxygen, which normally is found only the near Earth space environment, causes oxidation and erosion of polymers on spacecraft. The development of technology to prevent this degradation has required NASA to develop ground laboratory facilities that generate atomic oxygen. Atomic oxygen has also been found to be able to oxidize most types of ink from a variety of types of pens. The use of atomic oxygen to identify alteration of documents has been investigated and is reported. Results of testing indicates that for many types of ink, pen, and paper, identification of document alteration of pen and ink numbers and evidence of alteration can be made visible by exposing the questionable writing to atomic oxygen. Atomic oxygen provides discrimination because different inks may oxidize at different rates, the amount of time between delayed alteration may add to ink thickness at crossings, and the end of pen strokes tend to have much thicker ink deposits than the rest of the character. Examples and techniques of using atomic oxygen to identify document alteration indicate that the technology can, in many but not all cases, provide discrimination between original and altered documents.

  19. Heat conduction in double-walled carbon nanotubes with intertube additional carbon atoms.

    PubMed

    Cui, Liu; Feng, Yanhui; Tan, Peng; Zhang, Xinxin

    2015-07-07

    Heat conduction of double-walled carbon nanotubes (DWCNTs) with intertube additional carbon atoms was investigated for the first time using a molecular dynamics method. By analyzing the phonon vibrational density of states (VDOS), we revealed that the intertube additional atoms weak the heat conduction along the tube axis. Moreover, the phonon participation ratio (PR) demonstrates that the heat transfer in DWCNTs is dominated by low frequency modes. The added atoms cause the mode weight factor (MWF) of the outer tube to decrease and that of the inner tube to increase, which implies a lower thermal conductivity. The effects of temperature, tube length, and the number and distribution of added atoms were studied. Furthermore, an orthogonal array testing strategy was designed to identify the most important structural factor. It is indicated that the tendencies of thermal conductivity of DWCNTs with added atoms change with temperature and length are similar to bare ones. In addition, thermal conductivity decreases with the increasing number of added atoms, more evidently for atom addition concentrated at some cross-sections rather than uniform addition along the tube length. Simultaneously, the number of added atoms at each cross-section has a considerably more remarkable impact, compared to the tube length and the density of chosen cross-sections to add atoms.

  20. Intensity modulated operating mode of the rotating gamma system.

    PubMed

    Sengupta, Bishwambhar; Gulyas, Laszlo; Medlin, Donald; Koroknai, Tibor; Takacs, David; Filep, Gyorgy; Panko, Peter; Godo, Bence; Hollo, Tamas; Zheng, Xiao Ran; Fedorcsak, Imre; Dobai, Jozsef; Bognar, Laszlo; Takacs, Endre

    2018-05-01

    The purpose of this work was to explore two novel operation modalities of the rotating gamma systems (RGS) that could expand its clinical application to lesions in close proximity to critical organs at risk (OAR). The approach taken in this study consists of two components. First, a Geant4-based Monte Carlo (MC) simulation toolkit is used to model the dosimetric properties of the RGS Vertex 360™ for the normal, intensity modulated radiosurgery (IMRS), and speed modulated radiosurgery (SMRS) operation modalities. Second, the RGS Vertex 360™ at the Rotating Gamma Institute in Debrecen, Hungary is used to collect experimental data for the normal and IMRS operation modes. An ion chamber is used to record measurements of the absolute dose. The dose profiles are measured using Gafchromic EBT3 films positioned within a spherical water equivalent phantom. A strong dosimetric agreement between the measured and simulated dose profiles and penumbra was found for both the normal and IMRS operation modes for all collimator sizes (4, 8, 14, and 18 mm diameter). The simulated falloff and maximum dose regions agree better with the experimental results for the 4 and 8 mm diameter collimators. Although the falloff regions align well in the 14 and 18 mm collimators, the maximum dose regions have a larger difference. For the IMRS operation mode, the simulated and experimental dose distributions are ellipsoidal, where the short axis aligns with the blocked angles. Similarly, the simulated dose distributions for the SMRS operation mode also adopt an ellipsoidal shape, where the short axis aligns with the angles where the orbital speed is highest. For both modalities, the dose distribution is highly constrained with a sharper penumbra along the short axes. Dose modulation of the RGS can be achieved with the IMRS and SMRS modes. By providing a highly constrained dose distribution with a sharp penumbra, both modes could be clinically applicable for the treatment of lesions in close

  1. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  2. Ultrafast Pulse Sequencing for Fast Projective Measurements of Atomic Hyperfine Qubits

    NASA Astrophysics Data System (ADS)

    Ip, Michael; Ransford, Anthony; Campbell, Wesley

    2015-05-01

    Projective readout of quantum information stored in atomic hyperfine structure typically uses state-dependent CW laser-induced fluorescence. This method requires an often sophisticated imaging system to spatially filter out the background CW laser light. We present an alternative approach that instead uses simple pulse sequences from a mode-locked laser to affect the same state-dependent excitations in less than 1 ns. The resulting atomic fluorescence occurs in the dark, allowing the placement of non-imaging detectors right next to the atom to improve the qubit state detection efficiency and speed. We also discuss methods of Doppler cooling with mode-locked lasers for trapped ions, where the creation of the necessary UV light is often difficult with CW lasers.

  3. Raman intensity and vibrational modes of armchair CNTs

    NASA Astrophysics Data System (ADS)

    Hur, Jaewoong; Stuart, Steven J.

    2017-07-01

    Raman intensity changes and frequency patterns have been studied using the various armchair (n, n) to understand the variations of bond polarizability, in regard to changing diameters, lengths, and the number of atoms in the (n, n). The Raman intensity trends of the (n, n) are validated by those of Cn isomers. For frequency trends, similar frequency patterns and frequency inward shifts for the (n, n) are characterized. Also, VDOS trends of the (n, n) expressing Raman modes are interpreted. The decomposition of vibrational modes in the (n, n) into radial, longitudinal, and tangential mode is beneficially used to recognize the distinct characteristics of vibrational modes.

  4. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

    PubMed

    Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

    2016-02-23

    The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in

  5. Arrays of strongly coupled atoms in a one-dimensional waveguide

    NASA Astrophysics Data System (ADS)

    Ruostekoski, Janne; Javanainen, Juha

    2017-09-01

    We study the cooperative optical coupling between regularly spaced atoms in a one-dimensional waveguide using decompositions to subradiant and super-radiant collective excitation eigenmodes, direct numerical solutions, and analytical transfer-matrix methods. We illustrate how the spectrum of transmitted light through the waveguide, including the emergence of narrow Fano resonances, can be understood by the resonance features of the eigenmodes. We describe a method based on super-radiant and subradiant modes to engineer the optical response of the waveguide and to store light. The stopping of light is obtained by transferring an atomic excitation to a subradiant collective mode with the zero radiative resonance linewidth by controlling the level shift of an atom in the waveguide. Moreover, we obtain an exact analytic solution for the transmitted light through the waveguide for the case of a regular lattice of atoms and provide a simple description of how the light transmission may present large resonance shifts when the lattice spacing is close, but not exactly equal, to half of the wavelength of the light. Experimental imperfections such as fluctuations of the positions of the atoms and loss of light from the waveguide are easily quantified in the numerical simulations, which produce the natural result that the optical response of the atomic array tends toward the response of a gas with random atomic positions.

  6. All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding

    NASA Astrophysics Data System (ADS)

    Wang, Fang; Orioli, Simone; Ianeselli, Alan; Spagnolli, Giovanni; a Beccara, Silvio; Gershenson, Anne; Faccioli, Pietro; Wintrode, Patrick L.

    2018-05-01

    Protein misfolding is implicated in many diseases, including the serpinopathies. For the canonical inhibitory serpin {\\alpha}1-antitrypsin (A1AT), mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes leading to liver disease. Using all-atom simulations based on the recently developed Bias Functional algorithm we elucidate how wild-type A1AT folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, while the relatively benign S mutant shows late stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.

  7. All-optical spinor Bose-Einstein condensation and the spinor dynamics-driven atom laser

    NASA Astrophysics Data System (ADS)

    Lundblad, Nathan Eric

    Optical trapping as a viable means of exploring the physics of ultracold dilute atomic gases has revealed a new spectrum of physical phenomena. In particular, macroscopic and sudden occupation of the ground state below a critical temperature---a phenomenon known as Bose-Einstein condensation---has become an even richer system for the study of quantum mechanics, ultracold collisions, and many-body physics in general. Optical trapping liberates the spin degree of the BEC, making the order parameter vectorial ('spinor BEC'), as opposed to the scalar order of traditional magnetically trapped condensates. The work described within is divided into two main efforts. The first encompasses the all-optical creation of a Bose-Einstein condensate in rubidium vapor. An all-optical path to spinor BEC (as opposed to transfer to an optical trap from a magnetic trap condensate) was desired both for the simplicity of the experimental setup and also for the potential gains in speed of creation; evaporative cooling, the only known path to dilute-gas condensation, works only as efficiently as the rate of elastic collisions in the gas, a rate that starts out much higher in optical traps. The first all-optical BEC was formed elsewhere in 2001; the years following saw many groups worldwide seeking to create their own version. Our own all-optical spinor BEC, made with a single-beam dipole trap formed by a focused CO2 laser, is described here, with particular attention paid to trap loading, measurement of trap parameters, and the use of a novel 780 nm high-power laser system. The second part describes initial experiments performed with the nascent condensate. The spinor properties of the condensate are documented, and a measurement is made of the density-dependent rate of spin mixing in the condensate. In addition, we demonstrate a novel dual-beam atom laser formed by outcoupling oppositely polarized components of the condensate, whose populations have been coherently evolved through spin

  8. Spectrally tailored supercontinuum generation from single-mode-fiber amplifiers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hao, Qiang; Guo, Zhengru; Zhang, Qingshan

    Spectral filtering of an all-normal-dispersion Yb-doped fiber laser was demonstrated effective for broadband supercontinuum generation in the picosecond time region. The picosecond pump pulses were tailored in spectrum with 1 nm band-pass filter installed between two single-mode fiber amplifiers. By tuning the spectral filter around 1028 nm, four-wave mixing was initiated in a photonic crystal fiber spliced with single-mode fiber, as manifested by the simultaneous generation of Stokes wave at 1076 nm and anti-Stokes wave at 984 nm. Four-wave mixing took place in cascade with the influence of stimulated Raman scattering and eventually extended the output spectrum more than 900 nm of 10 dB bandwidth.more » This technique allows smooth octave supercontinuum generation by using simple single-mode fiber amplifiers rather than complicated multistage large-mode-area fiber amplifiers.« less

  9. Simultaneously exciting two atoms with photon-mediated Raman interactions

    NASA Astrophysics Data System (ADS)

    Zhao, Peng; Tan, Xinsheng; Yu, Haifeng; Zhu, Shi-Liang; Yu, Yang

    2017-06-01

    We propose an approach to simultaneously excite two atoms by using a cavity-assisted Raman process in combination with a cavity-photon-mediated interaction. The system consists of a two-level atom and a Λ -type or V -type three-level atom, which are coupled together with a cavity mode. Having derived the effective Hamiltonian, we find that under certain circumstances a single photon can simultaneously excite two atoms. In addition, multiple photons and even a classical field can also simultaneously excite two atoms. As an example, we show a scheme to realize our proposal in a circuit QED setup, which is artificial atoms coupled with a cavity. The dynamics and the quantum-statistical properties of the process are investigated with experimentally feasible parameters.

  10. Mode detuning in systems of weakly coupled oscillators

    NASA Astrophysics Data System (ADS)

    Spencer, Ross L.; Robertson, Richard D.

    2001-11-01

    A system of weakly magnetically coupled oscillating blades is studied experimentally, computationally, and theoretically. It is found that when the uncoupled natural frequencies of the blades are nearly equal, the normal modes produced by the coupling are almost impossible to find experimentally if the random variation level in the system parameters is on the order of (or larger than) the relative differences between mode frequencies. But if the uncoupled natural frequencies are made to vary (detuned) in a smooth way such that the total relative spread in natural frequency exceeds the random variations, normal modes are rather easy to find. And if the detuned uncoupled frequencies of the system are parabolically distributed, the modes are found to be shaped like Hermite functions.

  11. Hamilton's principle and normal mode coupling in an aspherical planet with a fluid core

    NASA Astrophysics Data System (ADS)

    Al-Attar, David; Crawford, Ophelia; Valentine, Andrew P.; Trampert, Jeannot

    2018-04-01

    We apply Hamilton's principle to obtain the exact equations of motion for an elastic planet that is rotating, self-gravitating, and comprises both fluid and solid regions. This variational problem is complicated by the occurrence of tangential slip at fluid-solid boundaries, but we show how this can be accommodated both directly and using the method of Lagrange multipliers. A novelty of our approach is that the planet's motion is described relative to an arbitrary reference configuration, with this generality offering advantages for numerical calculations. In particular, aspherical topography on the free surface or internal boundaries of the planet's equilibrium configuration can be converted exactly into effective volumetric heterogeneities within a geometrically spherical reference body by applying a suitable particle relabelling transformation. The theory is then specialised to consider the linearised motion of a planet about a steadily rotating equilibrium configuration, with these results having applications to normal mode coupling calculations used within studies of long period seismology, tidal deformation, and related fields. In particular, we explain how our new theory will, for the first time, allow aspherical boundary topography to be incorporated exactly within such coupling calculations.

  12. Tunable zero-line modes via magnetic field in bilayer graphene

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Qiao, Zhenhua

    Zero-line modes appear in bilayer graphene at the internal boundary between two opposite vertical electrostatic confinements. These one-dimensional modes are metallic along the boundary and exhibit quantized conductance in the absence of inter-valley scattering. However, experimental results show that the conductance is around 0.5 e2/h rather than quantized. This observation can be explained from our numerical results, which suggest that the scattering between zero-line mode and bound states and the presence of atomic scale disorders that provide inter-valley scattering can effectively reduce the conductance to about 0.5 e2/h. We further find that out-of-plane magnetic field can strongly suppress these scattering mechanisms and gives rise to nearly quantized conductance. On one hand, the presence of magnetic field makes bound states become Landau levels, which reduces the scattering between zero-line mode and bound states. On the other hand, the wave function distributions of oppositely propagating zero-line modes at different valleys are spatially separated, which can strongly suppress the inter-valley scattering. Specifically speaking, the conductance can be increased to 3.2 e2/h at 8 T even when the atomic Anderson type disorders are considered.

  13. A Transportable Gravity Gradiometer Based on Atom Interferometry

    NASA Technical Reports Server (NTRS)

    Yu, Nan; Thompson, Robert J.; Kellogg, James R.; Aveline, David C.; Maleki, Lute; Kohel, James M.

    2010-01-01

    A transportable atom interferometer-based gravity gradiometer has been developed at JPL to carry out measurements of Earth's gravity field at ever finer spatial resolutions, and to facilitate high-resolution monitoring of temporal variations in the gravity field from ground- and flight-based platforms. Existing satellite-based gravity missions such as CHAMP and GRACE measure the gravity field via precise monitoring of the motion of the satellites; i.e. the satellites themselves function as test masses. JPL's quantum gravity gradiometer employs a quantum phase measurement technique, similar to that employed in atomic clocks, made possible by recent advances in laser cooling and manipulation of atoms. This measurement technique is based on atomwave interferometry, and individual laser-cooled atoms are used as drag-free test masses. The quantum gravity gradiometer employs two identical atom interferometers as precision accelerometers to measure the difference in gravitational acceleration between two points (Figure 1). By using the same lasers for the manipulation of atoms in both interferometers, the accelerometers have a common reference frame and non-inertial accelerations are effectively rejected as common mode noise in the differential measurement of the gravity gradient. As a result, the dual atom interferometer-based gravity gradiometer allows gravity measurements on a moving platform, while achieving the same long-term stability of the best atomic clocks. In the laboratory-based prototype (Figure 2), the cesium atoms used in each atom interferometer are initially collected and cooled in two separate magneto-optic traps (MOTs). Each MOT, consisting of three orthogonal pairs of counter-propagating laser beams centered on a quadrupole magnetic field, collects up to 10(exp 9) atoms. These atoms are then launched vertically as in an atom fountain by switching off the magnetic field and introducing a slight frequency shift between pairs of lasers to create a moving

  14. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

    PubMed Central

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-01-01

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic–inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios. PMID:27876797

  15. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-11-01

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

  16. Examining the origins of the hydration force between lipid bilayers using all-atom simulations.

    PubMed

    Gentilcore, Anastasia N; Michaud-Agrawal, Naveen; Crozier, Paul S; Stevens, Mark J; Woolf, Thomas B

    2010-05-01

    Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

  17. Evaluation of left ventricular performance during supine exercise by transoesophageal M-mode echocardiography in normal subjects.

    PubMed Central

    Matsumoto, M; Hanrath, P; Kremer, P; Tams, C; Langenstein, B A; Schlüter, M; Weiter, R; Bleifeld, W

    1982-01-01

    In order to evaluate left ventricular function during dynamic exercise transoesophageal M-mode recordings of the left ventricle were carried out with a newly developed transducer gastroscope system. Twelve healthy subjects performed a graded supine bicycle exercise test. Stable and good quality images of the left ventricle at rest and during exercise at different steps up to a maximum workload of 100 watts were obtained in all patients. Isotonic maximum exercise resulted in a significant increase in fractional shortening of the left ventricle, peak shortening rate, and peak lengthening rate of the left ventricular minor axis. Left ventricular end-diastolic dimension decreased significantly. With increasing workload the pressure rate product increased significantly. It is concluded that transoesophageal M-mode echocardiography is a useful method of evaluating left ventricular performance during dynamic exercise. Images PMID:7082515

  18. New On-Orbit Sensitivity Calibrationfor All STIS Echelle Modes

    NASA Astrophysics Data System (ADS)

    Aloisi, Alessandra; Bohlin, Ralph; Quijano, Jessica Kim

    2007-01-01

    On-orbit sensitivities for the 32 medium- and high-resolution STIS echelle secondarymodes were determined for the rst time using observations of the fundamental DAwhite dwarf standard star G191-B2B. Revised on-orbit sensitivities for the 12 mediumandhigh-resolution echelle prime modes based on observations of the same standardstar are also presented. We review the procedures and assumptions used to derive theadopted throughputs and implement them into the pipeline.

  19. Application of normal mode theory to seismic source and structure problems: Seismic investigations of upper mantle lateral heterogeneity. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Okal, E. A.

    1978-01-01

    The theory of the normal modes of the earth is investigated and used to build synthetic seismograms in order to solve source and structural problems. A study is made of the physical properties of spheroidal modes leading to a rational classification. Two problems addressed are the observability of deep isotropic seismic sources and the investigation of the physical properties of the earth in the neighborhood of the Core-Mantle boundary, using SH waves diffracted at the core's surface. Data sets of seismic body and surface waves are used in a search for possible deep lateral heterogeneities in the mantle. In both cases, it is found that seismic data do not require structural differences between oceans and continents to extend deeper than 250 km. In general, differences between oceans and continents are found to be on the same order of magnitude as the intrinsic lateral heterogeneity in the oceanic plate brought about by the aging of the oceanic lithosphere.

  20. Polarizing Ytterbium-Doped all-Solid Photonic Bandgap Fiber with 1150 micrometers2 Effective Mode Area

    DTIC Science & Technology

    2015-02-11

    RESPONSIBLE PERSON 19b. TELEPHONE NUMBER Liang Dong Fanting Kong,, Guancheng Gu,, Thomas W. Hawkins ,, Joshua Parsons, Maxwell Jones,, Christopher...Dunn,, Monica T. Kalichevsky-Dong,, Benjamin Pulford,, Iyad Dajani,, Kunimasa Saitoh,, Stephen P. Palese,, Eric Cheung,, Liang Dong c. THIS PAGE The...ytterbium-doped all-solid photonic bandgap fiber with ~1150µm2 effective mode area Fanting Kong,1,* Guancheng Gu,1 Thomas W. Hawkins ,1 Joshua Parsons

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