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Sample records for polarizable amoeba force

  1. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    Science.gov (United States)

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-05

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  2. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

    Science.gov (United States)

    Wu, Xiaojing; Clavaguera, Carine; Lagardère, Louis; Piquemal, Jean-Philip; de la Lande, Aurélien

    2018-04-16

    We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H 2 O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.

  3. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

    Science.gov (United States)

    Pande, Vijay S.; Head-Gordon, Teresa; Ponder, Jay W.

    2016-01-01

    A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. The protocol uses an automated procedure, ForceBalance, to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimentally obtained data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The new AMOEBA14 water model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures ranging from 249 K to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to a variety of experimental properties as a function of temperature, including the 2nd virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient and dielectric constant. The viscosity, self-diffusion constant and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2 to 20 water molecules, the AMOEBA14 model yields results similar to the AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model. PMID:25683601

  4. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.; Snow, Christopher D.

    2011-01-01

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full

  5. A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

    Science.gov (United States)

    Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian

    2017-12-01

    We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

  6. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

    Science.gov (United States)

    Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

    2017-03-28

    Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

  7. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

    Science.gov (United States)

    Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip

    2018-01-28

    We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over

  8. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.

    2011-01-24

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.

  9. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and...

  10. Tailored long range forces on polarizable particles by collective scattering of broadband radiation

    International Nuclear Information System (INIS)

    Holzmann, D; Ritsch, H

    2016-01-01

    Collective coherent light scattering by polarizable particles creates surprisingly strong, long range inter-particle forces originating from interference of the light scattered by different particles. While for monochromatic laser beams this interaction decays with the inverse distance, we show here that in general the effective interaction range and geometry can be controlled by the illumination bandwidth and geometry. As generic example we study the modifications inter-particle forces within a 1D chain of atoms trapped in the field of a confined optical nanofiber mode. For two particles we find short range attraction as well as optical binding at multiple distances. The range of stable distances shrinks with increasing light bandwidth and for a very large bandwidth field as e.g. blackbody radiation. We find a strongly attractive potential up to a critical distance beyond which the force gets repulsive. Including multiple scattering can even lead to the appearance of a stable configuration at a large distance. Such broadband scattering forces should be observable contributions in ultra-cold atom interferometers or atomic clocks setups. They could be studied in detail in 1D geometries with ultra-cold atoms trapped along or within an optical nanofiber. Broadband radiation force interactions might also contribute in astrophysical scenarios as illuminated cold dust clouds. (paper)

  11. Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

    Science.gov (United States)

    Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

    2011-01-01

    Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

  12. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

    Science.gov (United States)

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

  13. Simulating the physicochemical properties of borosilicate and lanthanum borosilicate glasses using a polarizable force field

    International Nuclear Information System (INIS)

    Pacaud, Fabien

    2016-01-01

    as result of the nuclear waste vitrification, the knowledge and understanding of the dynamic and structural properties of glasses, including the behavior of radionuclides, is important (in liquid and solid phases). It can influence the glass waste properties, the lifetime of the vitrification process and the amount of radionuclides introduced in the glass matrix. Molecular dynamic simulations have been done to study the influence of the glass matrix composition into the structural and dynamic properties of the glass. a simplified glass, with 3 major oxides of the R7T7 glass such as SiO_2, B_2O_3 and Na_2O, have been used to simulate the R7T7 industrial nuclear glass (a 30 oxides glass). The inclusion of La_2O_3 allows us to simulate the impact of fission products and minor actinides into the properties of the glass matrix. Both systems, the SiO_2-B_2O_3-Na_2O and SiO_2-B_2O_3-Na_2O-La_2O_3, allow us to study the sodium and lanthanum effect on the properties of the glass. During this work, a polarizable force field has been developed to do these simulations. The results obtained at room temperature let us reproduce the experimental results of the structure, the distribution of BIII/BIV and the density. a study has been done on the viscosity and electrical conductivity of the liquid. The distribution BIV/BIII and the influence of the structural changes on the density along with the temperature have also been observed with thermal quenching. The current limits of this approach are also described. (author) [fr

  14. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

    Science.gov (United States)

    Lemkul, Justin A; MacKerell, Alexander D

    2017-05-09

    Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

  15. Atomic polarizabilities

    International Nuclear Information System (INIS)

    Safronova, M. S.; Mitroy, J.; Clark, Charles W.; Kozlov, M. G.

    2015-01-01

    The atomic dipole polarizability governs the first-order response of an atom to an applied electric field. Atomic polarization phenomena impinge upon a number of areas and processes in physics and have been the subject of considerable interest and heightened importance in recent years. In this paper, we will summarize some of the recent applications of atomic polarizability studies. A summary of results for polarizabilities of noble gases, monovalent, and divalent atoms is given. The development of the CI+all-order method that combines configuration interaction and linearized coupled-cluster approaches is discussed

  16. Atomic polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Safronova, M. S. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin NT 0909 (Australia); Clark, Charles W. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, Gaithersburg, Maryland 20899-8410 (United States); Kozlov, M. G. [Petersburg Nuclear Physics Institute, Gatchina 188300 (Russian Federation)

    2015-01-22

    The atomic dipole polarizability governs the first-order response of an atom to an applied electric field. Atomic polarization phenomena impinge upon a number of areas and processes in physics and have been the subject of considerable interest and heightened importance in recent years. In this paper, we will summarize some of the recent applications of atomic polarizability studies. A summary of results for polarizabilities of noble gases, monovalent, and divalent atoms is given. The development of the CI+all-order method that combines configuration interaction and linearized coupled-cluster approaches is discussed.

  17. Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2015-01-01

    In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte so...

  18. Polarizability of DNA Block Copolymer Nanoparticles Observed by Electrostatic Force Microscopy

    NARCIS (Netherlands)

    Sowwan, Mukhles; Faroun, Maryam; Mentovich, Elad; Ibrahim, Imad; Haboush, Shayma; Alemdaroglu, Fikri Emrah; Kwak, Minseok; Richter, Shachar; Herrmann, Andreas

    2010-01-01

    In this study, DNA block copolymer (DBC) micelles with a polystyrene (PS) core and a single-stranded (ss) DNA shell were doped with ferrocene (Fc) molecules. Tapping mode atomic force microscopy (AFM) was used to study the morphology of the doped and undoped block copolymer aggregates. We show that

  19. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

    Science.gov (United States)

    Harger, Matthew; Li, Daniel; Wang, Zhi; Dalby, Kevin; Lagardère, Louis; Piquemal, Jean-Philip; Ponder, Jay; Ren, Pengyu

    2017-09-05

    The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    Science.gov (United States)

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  1. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-01-01

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities

  2. Quantum mechanical determination of atomic polarizabilities of ionic liquids.

    Science.gov (United States)

    Heid, Esther; Szabadi, András; Schröder, Christian

    2018-04-25

    The distribution of a molecule's polarizability to individual atomic sites is inevitable to develop accurate polarizable force fields. We present the direct quantum mechanical calculation of atomic polarizabilities of 27 common ionic liquids. The method is superior to previously published distribution routines based on large databases of the molecular polarizability, and enables the correct description of any ionic liquid and its peculiarities within the quantum mechanical framework.

  3. Structural study of Na2O-B2O3-SiO2 glasses from molecular simulations using a polarizable force field.

    Science.gov (United States)

    Pacaud, Fabien; Delaye, Jean-Marc; Charpentier, Thibault; Cormier, Laurent; Salanne, Mathieu

    2017-10-28

    Sodium borosilicate glasses Na 2 O-B 2 O 3 -SiO 2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO 4 and BO 4 (B IV ) and triangular BO 3 (B III ). One of the salient features of these compounds is the change of the B III /B IV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of B III /B IV with respect to the composition and the temperature.

  4. Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

    Science.gov (United States)

    Savelyev, Alexey; MacKerell, Alexander D.

    2015-01-01

    In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

  5. Electromagnetic polarizabilities of hadrons

    International Nuclear Information System (INIS)

    Friar, J.L.

    1988-01-01

    Electromagnetic polarizabilities of hadrons are reviewed, after a discussion of classical analogues. Differences between relativistic and non-relativistic approaches can lead to conflicts with conventional nuclear physics sum rules and calculational techniques. The nucleon polarizabilities are discussed in the context of the non-relativistic valence quark model, which provides a good qualitative description. The recently measured pion polarizabilities are discussed in the context of chiral symmetry and quark-loop models. 58 refs., 5 figs

  6. Electric dipole polarizability from first principles calculations

    International Nuclear Information System (INIS)

    Miorelli, M.; University of British Columbia, Vancouver, BC; Bacca, S.; University of Manitoba; Barnea, N.

    2016-01-01

    The electric dipole polarizability quantifies the low-energy behavior of the dipole strength and is related to critical observables such as the radii of the proton and neutron distributions. Its computation is challenging because most of the dipole strength lies in the scattering continuum. In our paper we combine integral transforms with the coupled-cluster method and compute the dipole polarizability using bound-state techniques. Furthermore, employing different interactions from chiral effective field theory, we confirm the strong correlation between the dipole polarizability and the charge radius, and study its dependence on three-nucleon forces. Finally, we find good agreement with data for the 4 He, 40 Ca, and 16 O nuclei, and predict the dipole polarizability for the rare nucleus 22 O.

  7. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

    Directory of Open Access Journals (Sweden)

    Raiker Witter

    2015-01-01

    Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

  8. Polarizable Density Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; Steinmann, Casper; Ruud, Kenneth

    2015-01-01

    We present a new QM/QM/MM-based model for calculating molecular properties and excited states of solute-solvent systems. We denote this new approach the polarizable density embedding (PDE) model and it represents an extension of our previously developed polarizable embedding (PE) strategy. The PDE...... model is a focused computational approach in which a core region of the system studied is represented by a quantum-chemical method, whereas the environment is divided into two other regions: an inner and an outer region. Molecules belonging to the inner region are described by their exact densities...

  9. Dynamical polarizability of atoms

    International Nuclear Information System (INIS)

    Mukhopadhyay, G.; Lundqvist, S.

    1980-07-01

    The frequency-dependent polarizability of a closed-shell atom is considered in an RPA type approximation. This is usually done using many-body perturbation theory but can also be recast into the form of equations for the density oscillations as previously shown by the authors. The latter approach is known to lead to a non-hermitian problem because of the structure of the interaction kernel. This note shows that this is also true if using the reaction matrix method. The main result is to derive the expression for the polarizability function taking into account the non-hermitian nature of the problem. (author)

  10. Magnetic polarizability of pion

    Energy Technology Data Exchange (ETDEWEB)

    Luschevskaya, E.V., E-mail: luschevskaya@itep.ru [Institute for Theoretical and Experimental Physics, Bolshaia Cheremushkinskaia 25, 117218 Moscow (Russian Federation); School of Biomedicine, Far Eastern Federal University, 690950 Vladivostok (Russian Federation); Solovjeva, O.E., E-mail: olga.solovjeva@itep.ru [Institute for Theoretical and Experimental Physics, Bolshaia Cheremushkinskaia 25, 117218 Moscow (Russian Federation); Teryaev, O.V., E-mail: teryaev@theor.jinr.ru [Joint Institute for Nuclear Research, Dubna, 141980 (Russian Federation); National Research Nuclear University “MEPhI” (Moscow Engineering Physics Institute), Kashirskoe highway, 31, 115409 Moscow (Russian Federation)

    2016-10-10

    We explore the energy dependence of π mesons off the background Abelian magnetic field on the base of quenched SU(3) lattice gauge theory and calculate the magnetic dipole polarizability of charged and neutral pions for various lattice volumes and lattice spacings. The contribution of the magnetic hyperpolarizability to the neutral pion energy has been also found.

  11. Polarizable Density Embedding

    DEFF Research Database (Denmark)

    Reinholdt, Peter; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    We analyze the performance of the polarizable density embedding (PDE) model-a new multiscale computational approach designed for prediction and rationalization of general molecular properties of large and complex systems. We showcase how the PDE model very effectively handles the use of large...

  12. Spin polarizability of hyperons

    Indian Academy of Sciences (India)

    K B VIJAYA KUMAR. Department of Physics, Mangalore University, Mangalagangothri 574 199, India. E-mail: kbvijayakumar@yahoo.com. DOI: 10.1007/s12043-014-0869-4; ePublication: 4 November 2014. Abstract. We review the recent progress of the theoretical understanding of spin polarizabilities of the hyperon in the ...

  13. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

    Science.gov (United States)

    Narth, Christophe; Lagardère, Louis; Polack, Étienne; Gresh, Nohad; Wang, Qiantao; Bell, David R; Rackers, Joshua A; Ponder, Jay W; Ren, Pengyu Y; Piquemal, Jean-Philip

    2016-02-15

    We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. Copyright © 2016 Wiley Periodicals, Inc.

  14. Polarizability sum rules in QED

    International Nuclear Information System (INIS)

    Llanta, E.; Tarrach, R.

    1978-01-01

    The well founded total photoproduction and the, assumed subtraction free, longitudinal photoproduction polarizability sum rules are checked in QED at the lowest non-trivial order. The first one is shown to hold, whereas the second one turns out to need a subtraction, which makes its usefulness for determining the electromagnetic polarizabilities of the nucleons quite doubtful. (Auth.)

  15. Static polarizabilities of dielectric nanoclusters

    International Nuclear Information System (INIS)

    Kim, Hye-Young; Sofo, Jorge O.; Cole, Milton W.; Velegol, Darrell; Mukhopadhyay, Gautam

    2005-01-01

    A cluster consisting of many atoms or molecules may be considered, in some circumstances, to be a single large molecule with a well-defined polarizability. Once the polarizability of such a cluster is known, one can evaluate certain properties--e.g. the cluster's van der Waals interactions, using expressions derived for atoms or molecules. In the present work, we evaluate the static polarizability of a cluster using a microscopic method that is exact within the linear and dipolar approximations. Numerical examples are presented for various shapes and sizes of clusters composed of identical atoms, where the term 'atom' actually refers to a generic constituent, which could be any polarizable entity. The results for the clusters' polarizabilities are compared with those obtained by assuming simple additivity of the constituents' atomic polarizabilities; in many cases, the difference is large, demonstrating the inadequacy of the additivity approximation. Comparison is made (for symmetrical geometries) with results obtained from continuum models of the polarizability. Also, the surface effects due to the nonuniform local field near a surface or edge are shown to be significant

  16. Parity nonconservation and nuclear polarizabilities

    International Nuclear Information System (INIS)

    Haxton, W.

    1990-01-01

    The hadronic weak interaction contributes to parity nonconserving observables in semileptonic interactions. Weak nuclear polarizabilities are frequently important in such interactions. Some of the interesting physics is illustrated by 18 F, a nucleus that provides an important constraint on the neutral weak hadronic current. One observable where the nuclear polarizability is expected to dominate is the nuclear anapole moment. The long-range pion contribution to this weak radiative correction is explored for both nucleons and nuclei. Similar polarizabilities that arise for time-reversal-odd hadronic interactions that conserve or violate parity are discussed in connection with atomic electric dipole moments. 20 refs., 4 figs

  17. Pion electromagnetic polarizabilities and quarks

    International Nuclear Information System (INIS)

    Llanta, E.; Tarrach, R.

    1980-01-01

    The electric and magnetic polarizabilities of the neutral and charged pion are calculated in a coloured quark field theory at the one-loop level. The theory has as free parameter the quark mass but our results do not depend on it. We have found that the electric polarizabilities are αsub(π+-) = -0.04 α/m 3 sub(π), αsub(π 0 ) = -0.4 α/m 3 sub(π). These values are compared with calculations in other models and some comments are made about the polarizability sum rules. (orig.)

  18. Pion polarizabilities measurement at COMPASS

    CERN Document Server

    Guskov, Alexey

    2008-01-01

    The electromagnetic structure of pions is probed in $\\pi^{−}+(A,Z) \\rightarrow\\pi^{−}+(A,Z)+\\gamma$ Compton scattering in inverse kinematics (Primakoff reaction) and described by the electric ($\\bar{\\alpha_{\\pi}}$) and the magnetic ($\\bar{\\beta_{\\pi}}$) polarizabilities that depend on the rigidity of pion’s internal structure as a composite particle. Values for pion polarizabilities can be extracted from the comparison of the differential cross section for scattering of pointlike pions with the measured cross section. The pion polarizability measurement was performed with a $\\pi^{-}$ beam of 190 GeV. The high beam intensity, the good spectrometer resolution, the high rate capability, the high acceptance and the possibility to use pion and muon beams, unique to the COMPASS experiment, provide the tools to measure precisely the pion polarizabilities in the Primakoff reaction.

  19. Molecular Properties through Polarizable Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2011-01-01

    We review the theory related to the calculation of electric and magnetic molecular properties through polarizable embedding. In particular, we derive the expressions for the response functions up to the level of cubic response within the density functional theory-based polarizable embedding (PE......-DFT) formalism. In addition, we discuss some illustrative applications related to the calculation of nuclear magnetic resonance parameters, nonlinear optical properties, and electronic excited states in solution....

  20. Pion polarizabilities measurement at COMPASS

    CERN Document Server

    Guskov, Alexey

    2008-01-01

    The electromagnetic structure of pions is probed in $\\pi^{−} + (A,Z)\\rightarrow\\pi^{−} + (A,Z) +\\gamma$ Compton scattering in inverse kinematics (Primakoff reaction) and described by the electric $(\\bar{\\alpha_{\\pi}})$ and the magnetic $(\\bar{\\beta_{\\pi}})$ polarizabilities that depend on the rigidity of pion’s internal structure as a composite particle. Values for pion polarizabilities can be extracted from the comparison of the differential cross section for scattering of pointlike pions with the measured cross section. The pion polarizability measurement was performed with $a \\pi^{−}$ beam of 190 GeV. The high beam intensity, the good spectrometer resolution, the high rate capability, the high acceptance and the possibility to use pion and muon beams, unique to the COMPASS experiment, provide the tools to measure precisely the pion polarizabilities in the Primakoff reaction. The preliminary result for pion polarizabilities under the assumption of $\\bar{\\alpha_{\\pi}} + \\bar{\\beta_{\\pi}} =$ 0 is $\\ba...

  1. Double-polarizating scanning radiometer

    International Nuclear Information System (INIS)

    Mishev, D.N.; Nazyrski, T.G.

    1986-01-01

    The double-polarizating single-channel scanning radiometer comprises the following serial connected parts: a scanning double-polarizating aerial, a block for polarization separation, a radiometer receiver, an analog-to-digit converter and an information flow forming block. The low frequency input of the radiometer receiver is connected with a control block, which is also connected with a first bus of a microprocessor, the second bus of which is connected with the A-D converter. The control input of the scanning double-polarizating aerial is connected with the first microprocessor bus. The control inputs of the block for polarization separation are linked by an electronic switch with the output of the forming block, the input of which is connected to the first input of the control block. The control inputs of the block for polarization separation are connected with the second and the third input of the information flow forming block. 2 cls

  2. Gravitational polarizability of black holes

    International Nuclear Information System (INIS)

    Damour, Thibault; Lecian, Orchidea Maria

    2009-01-01

    The gravitational polarizability properties of black holes are compared and contrasted with their electromagnetic polarizability properties. The 'shape' or 'height' multipolar Love numbers h l of a black hole are defined and computed. They are then compared to their electromagnetic analogs h l EM . The Love numbers h l give the height of the lth multipolar 'tidal bulge' raised on the horizon of a black hole by faraway masses. We also discuss the shape of the tidal bulge raised by a test-mass m, in the limit where m gets very close to the horizon.

  3. Polarizability effects on the structure and dynamics of ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Cavalcante, Ary de Oliveira, E-mail: arycavalcante@ufam.edu.br [Institute of Chemistry, University of Campinas – UNICAMP, Cx. P. 6154, Campinas, SP 13084-862 (Brazil); Departamento de Química, Universidade Federal do Amazonas, Av. Rodrigo Octávio, 6200, Coroado, Manaus, AM (Brazil); Ribeiro, Mauro C. C. [Laboratório de Espectroscopia Molecular, Instituto de Química, Universidade de São Paulo, São Paulo, SP C.P. 26077, 05513 970 São Paulo, SP (Brazil); Skaf, Munir S. [Institute of Chemistry, University of Campinas – UNICAMP, Cx. P. 6154, Campinas, SP 13084-862 (Brazil)

    2014-04-14

    Polarization effects on the structure and dynamics of ionic liquids are investigated using molecular dynamics simulations. Four different ionic liquids were simulated, formed by the anions Cl{sup −} and PF{sub 6}{sup −}, treated as single fixed charge sites, and the 1-n-alkyl-3-methylimidazolium cations (1-ethyl and 1-butyl-), which are polarizable. The partial charge fluctuation of the cations is provided by the electronegativity equalization model (EEM) and a complete parameter set for the cations electronegativity (χ) and hardness (J) is presented. Results obtained from a non-polarizable model for the cations are also reported for comparison. Relative to the fixed charged model, the equilibrium structure of the first solvation shell around the imidazolium cations shows that inclusion of EEM polarization forces brings cations closer to each other and that anions are preferentially distributed above and below the plane of the imidazolium ring. The polarizable model yields faster translational and reorientational dynamics than the fixed charges model in the rotational-diffusion regime. In this sense, the polarizable model dynamics is in better agreement with the experimental data.

  4. Time reversal violating nuclear polarizability and atomic electric dipole moment

    International Nuclear Information System (INIS)

    Ginges, J.S.M.; Flambaum, V.V.; Mititelu, G.

    2000-01-01

    Full text: We propose a nuclear mechanism which can induce an atomic electric dipole moment (EDM). The interaction of external electric E and magnetic H fields with nuclear electric and magnetic dipole moments, d and ,u, gives rise to an energy shift, U= -β ik E i H k , where β ik is the nuclear polarizability. Parity and time invariance violating (P,T-odd) nuclear forces generate a mixed P,T-odd nuclear polarizability, whereψ 0 and ψ n are P,T-odd perturbed ground and excited nuclear states, respectively. In the case of a heavy spherical nucleus with a single unpaired nucleon, the perturbed wavefunctions are U = -β ik E i H k , where ξis a constant proportional to the strength of the nuclear P,T-odd interaction, σ is the nuclear spin operator, and ψ n is an unperturbed wavefunction. There are both scalar and tensor contributions to the nuclear P,T-odd polarizability. An atomic EDM is induced by the interaction of the fields of an unpaired electron in an atom with the P,T-odd perturbed atomic nucleus. An estimate for the value of this EDM has been made. The measurements of atomic EDMs can provide information about P,T-odd nuclear forces and test models of CP-violation

  5. Computational analysis of electronic polarizabilities in Thomas ...

    African Journals Online (AJOL)

    The electric polarizability,α, of a molecule is a measure of its ability to respond to an electric field and acquire an electric dipole moment, μ. The electric polarizability, α has been calculated for several ions and atoms by obtaining the perturbation of wave functions by an external field from a numerical solution of differential ...

  6. Microscopic evaluation of the nuclear dipole polarizability

    Energy Technology Data Exchange (ETDEWEB)

    Lipparini, E; Orlandini, G; Stringari, S; Traini, M [Trento Univ. (Italy). Dept. di Matematica e Fisica

    1977-12-01

    The dipole polarizability sum rule has been evaluated by means of a restricted Hartree-Fock approach. The method leads to a simple and analytical expression for the dipole polarizability. Explicit calculations have been performed in /sup 16/O and /sup 40/Ca with different types of interaction.

  7. Excited States in Solution through Polarizable Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus; Aidas, Kestutis; Kongsted, Jacob

    2010-01-01

    mechanical calculation. The polarizable embedding potential is described by an atomistic representation including terms up to localized octupoles and anisotropic polarizabilities. It is generally applicable to any quantum chemical description but is here implemented for the case of Kohn−Sham density...

  8. Vibrational polarizabilities of hydrogen-bonded water

    International Nuclear Information System (INIS)

    Torii, Hajime

    2013-01-01

    Highlights: ► Vibrational polarizabilities of hydrogen-bonded water are analyzed theoretically. ► Total vibrational polarizability is (at least) comparable to the electronic one. ► Molecular translations contribute to the vibrational polarizability below 300 cm −1 . ► Intermolecular charge fluxes along H bonds are induced by molecular translations. ► The results are discussed in relation to the observed dielectric properties. - Abstract: The vibrational polarizabilities and the related molecular properties of hydrogen-bonded water are analyzed theoretically, taking the case of (water) 30 clusters as an example case. It is shown that some off-diagonal dipole derivatives are large for the translations of incompletely hydrogen-bonded molecules, and this is reasonably explained by the scheme of intermolecular charge fluxes induced along hydrogen bonds. In total, because of these intermolecular charge fluxes, molecular translations give rise to the vibrational polarizability of 2.8–3.3 a 0 3 per molecule, which is as large as about 40% of the electronic polarizability, mainly in the frequency region below 300 cm −1 . Adding the contributions of the molecular rotations (librations) and the translation–rotation cross term, the total polarizability (electronic + vibrational) at ∼100 cm −1 is slightly larger than the double of that at >4000 cm −1 . The relation of these results to some observed time- and frequency-dependent dielectric properties of liquid water is briefly discussed

  9. Shining light on polarizable dark particles

    Energy Technology Data Exchange (ETDEWEB)

    Fichet, Sylvain [ICTP South American Institute for Fundamental Research, Instituto de Fisica Teorica, Sao Paulo State University,Rua Dr. Bento Teobaldo Ferraz 271, Bloco 2, Barra Funda (Brazil)

    2017-04-14

    We investigate the possibilities of searching for a self-conjugate polarizable particle in the self-interactions of light. We first observe that polarizability can arise either from the exchange of mediator states or as a consequence of the inner structure of the particle. To exemplify this second possibility we calculate the polarizability of a neutral bosonic open string, and find it is described only by dimension-8 operators. Focussing on the spin-0 case, we calculate the light-by-light scattering amplitudes induced by the dimension-6 and 8 polarizability operators. Performing a simulation of exclusive diphoton production with proton tagging at the LHC, we find that the imprint of the polarizable dark particle can be potentially detected at 5σ significance for mass and cutoff reaching values above the TeV scale, for √s=13 TeV and 300 fb{sup −1} of integrated luminosity. If the polarizable dark particle is stable, it can be a dark matter candidate, in which case we argue this exclusive diphoton search may complement the existing LHC searches for polarizable dark matter.

  10. Engineering an artificial amoeba propelled by nanoparticle-triggered actin polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Yi Jinsoo; Schmidt, Jacob; Chien Aichi; Montemagno, Carlo D [Department of Bioengineering, University of California Los Angeles, 420 Westwood Plaza, 7523 Boelter Hall, Los Angeles, CA 90095-1600 (United States)], E-mail: montemcd@ucmail.uc.edu

    2009-02-25

    We have engineered an amoeba system combining nanofabricated inorganic materials with biological components, capable of propelling itself via actin polymerization. The nanofabricated materials have a mechanism similar to the locomotion of the Listeria monocytogenes, food poisoning bacteria. The propulsive force generation utilizes nanoparticles made from nickel and gold functionalized with the Listeria monocytogenes transmembrane protein, ActA. These Listeria-mimic nanoparticles were in concert with actin, actin binding proteins, ATP (adenosine triphosphate) and encapsulated within a lipid vesicle. This system is an artificial cell, such as a vesicle, where artificial nanobacteria and actin polymerization machinery are used in driving force generators inside the cell. The assembled structure was observed to crawl on a glass surface analogously to an amoeba, with the speed of the movement dependent on the amount of actin monomers and ATP present.

  11. Infection and Proliferation of Giant Viruses in Amoeba Cells.

    Science.gov (United States)

    Takemura, Masaharu

    2016-01-01

    Acanthamoeba polyphaga mimivirus, the first discovered giant virus with genome size and particle size much larger than previously discovered viruses, possesses several genes for translation and CRISPER Cas system-like defense mechanism against virophages, which co-infect amoeba cells with the giant virus and which inhibit giant virus proliferation. Mimiviruses infect amoeba cells by phagocytosis and release their DNA into amoeba cytoplasm through their stargate structure. After infection, giant virion factories (VFs) form in amoeba cytoplasm, followed by DNA replication and particle formation at peripheral regions of VF. Marseilleviruses, the smallest giant viruses, infect amoeba cells by phagocytosis or endocytosis, form larger VF than Mimivirus's VF in amoeba cytoplasm, and replicate their particles. Pandoraviruses found in 2013 have the largest genome size and particle size among all viruses ever found. Pandoraviruses infect amoeba cells by phagocytosis and release their DNA into amoeba cytoplasm through their mouth-like apical pores. The proliferation of Pandoraviruses occurs along with nucleus disruption. New virions form at the periphery of the region formerly occupied by the amoeba cell nucleus.

  12. Amoeba: a distributed operating system for the 1990s

    NARCIS (Netherlands)

    Mullender, Sape J.; van Rossum, Guido; Tanenbaum, Andrew S.; van Renesse, Robbert; van Staveren, Hans

    A description is given of the Amoeba distributed operating system, which appears to users as a centralized system but has the speed, fault tolerance, security safeguards, and flexibility required for the 1990s. The Amoeba software is based on objects. Objects are managed by server processes and

  13. Culture growth of testate amoebae under different silicon concentrations.

    Science.gov (United States)

    Wanner, Manfred; Seidl-Lampa, Barbara; Höhn, Axel; Puppe, Daniel; Meisterfeld, Ralf; Sommer, Michael

    2016-10-01

    Testate amoebae with self-secreted siliceous shell platelets ("idiosomes") play an important role in terrestrial silicon (Si) cycles. In this context, Si-dependent culture growth dynamics of idiosomic testate amoebae are of interest. Clonal cultures of idiosomic testate amoebae were analyzed under three different Si concentrations: low (50μmolL -1 ), moderate/site-specific (150μmolL -1 ) and high Si supply (500μmolL -1 ). Food (Saccharomyces cerevisiae) was provided in surplus. (i) Shell size of four different clones of idiosomic testate amoebae either decreased (Trinema galeata, Euglypha filifera cf.), increased (E. rotunda cf.), or did not change (E. rotunda) under the lowest Si concentration (50μmolSiL -1 ). (ii) Culture growth of idiosomic Euglypha rotunda was dependent on Si concentration. The more Si available in the culture medium, the earlier the entry into exponential growth phase. (iii) Culture growth of idiosomic Euglypha rotunda was dependent on origin of inoculum. Amoebae previously cultured under a moderate Si concentration revealed highest sustainability in consecutive cultures. Amoebae derived from cultures with high Si concentrations showed rapid culture growth which finished early in consecutive cultures. (iv) Si (diluted in the culture medium) was absorbed by amoebae and fixed in the amoeba shells resulting in decreased Si concentrations. Copyright © 2016 Elsevier GmbH. All rights reserved.

  14. Amoeba: A Distributed Operating System for the 1990s

    NARCIS (Netherlands)

    Mullender, S.J.; van Rossum, G.; Tanenbaum, A.S.; van Renesse, R.; van Staveren, H.

    1990-01-01

    A description is given of the Amoeba distributed operating system, which appears to users as a centralized system but has the speed, fault tolerance, security safeguards, and flexibility required for the 1990s. The Amoeba software is based on objects. Objects are managed by server processes and

  15. Static electric dipole polarizabilities of tri- and tetravalent U, Np, and Pu ions.

    Science.gov (United States)

    Parmar, Payal; Peterson, Kirk A; Clark, Aurora E

    2013-11-21

    High-quality static electric dipole polarizabilities have been determined for the ground states of the hard-sphere cations of U, Np, and Pu in the III and IV oxidation states. The polarizabilities have been calculated using the numerical finite field technique in a four-component relativistic framework. Methods including Fock-space coupled cluster (FSCC) and Kramers-restricted configuration interaction (KRCI) have been performed in order to account for electron correlation effects. Comparisons between polarizabilities calculated using Dirac-Hartree-Fock (DHF), FSCC, and KRCI methods have been made using both triple- and quadruple-ζ basis sets for U(4+). In addition to the ground state, this study also reports the polarizability data for the first two excited states of U(3+/4+), Np(3+/4+), and Pu(3+/4+) ions at different levels of theory. The values reported in this work are the most accurate to date calculations for the dipole polarizabilities of the hard-sphere tri- and tetravalent actinide ions and may serve as reference values, aiding in the calculation of various electronic and response properties (for example, intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications.

  16. Transferability of polarizable models for ion-water electrostatic interaction

    International Nuclear Information System (INIS)

    Masia, Marco

    2009-01-01

    Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li + - water and Cl - -water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

  17. Charged pions polarizability measurement at COMPASS

    CERN Document Server

    Guskov, A

    2010-01-01

    The pion electromagnetic structure can be probed in $\\pi^{−}+(A,Z)\\rightarrow\\pi^{-}+(A,Z)+\\gamma$ Compton scattering in inverse kinematics (Primakoff reaction) and described by the electric $(\\alpha_{\\pi})$ and the magnetic $(\\beta_{\\pi})$ polarizabilities that depend on the rigidity of pion’s internal structure as a composite particle. Values for pion polarizabilities can be extracted from the comparison of the differential cross section for scattering of point-like pions with the measured cross section. The opportunity to measure pion polarizability via the Primakoff reaction at the COMPASS experiment was studied with $a$ $\\pi^{-}$ beam of 190 GeV during pilot run 2004. The obtained results were used for preparation of the new data taking which was performed in 2009.

  18. Hadron polarizability data analysis: GoAT

    Energy Technology Data Exchange (ETDEWEB)

    Stegen, H., E-mail: hkstegen@mta.ca; Hornidge, D. [Mount Allison University, Sackville (Canada); Collicott, C. [Dalhousie University, Halifax (Canada); Martel, P. [Mount Allison University, Sackville (Canada); Johannes Gutenberg University, Mainz (Germany); Ott, P. [Johannes Gutenberg University, Mainz (Germany)

    2015-12-31

    The A2 Collaboration at the Institute for Nuclear Physics in Mainz, Germany, is working towards determining the polarizabilities of hadrons from nonperturbative quantum chromodynamics through Compton scattering experiments at low energies. The asymmetry observables are directly related to the scalar and spin polarizabilities of the hadrons. Online analysis software, which will give real-time feedback on asymmetries, efficiencies, energies, and angle distributions, has been developed. The new software is a big improvement over the existing online code and will greatly develop the quality of the acquired data.

  19. Hadron polarizability data analysis: GoAT

    Science.gov (United States)

    Stegen, H.; Collicott, C.; Hornidge, D.; Martel, P.; Ott, P.

    2015-12-01

    The A2 Collaboration at the Institute for Nuclear Physics in Mainz, Germany, is working towards determining the polarizabilities of hadrons from nonperturbative quantum chromodynamics through Compton scattering experiments at low energies. The asymmetry observables are directly related to the scalar and spin polarizabilities of the hadrons. Online analysis software, which will give real-time feedback on asymmetries, efficiencies, energies, and angle distributions, has been developed. The new software is a big improvement over the existing online code and will greatly develop the quality of the acquired data.

  20. On the polarizability dyadics of electrically small, convex objects

    Science.gov (United States)

    Lakhtakia, Akhlesh

    1993-11-01

    This communication on the polarizability dyadics of electrically small objects of convex shapes has been prompted by a recent paper published by Sihvola and Lindell on the polarizability dyadic of an electrically gyrotropic sphere. A mini-review of recent work on polarizability dyadics is appended.

  1. Pion polarizability in a chiral quark model

    International Nuclear Information System (INIS)

    Ebert, D.; Volkov, M.K.

    1981-01-01

    The pion polarizability is calculated in a chiral meson-quark model at the one-loop level. The results are in complete agreement with earlier ones obtained within a chiral meson-baryon theory. A critical discussion of a recent paper by Llanta and Tarrach is given. (orig.)

  2. Pion polarizability in a chiral quark model

    International Nuclear Information System (INIS)

    Volkov, M.K.; Ehbert, D.

    1980-01-01

    The pion polarizability is calculated in a chiral meson-quark model at the one-loop level. The results are in complete agreement with earlier ones obtained within a chiral meson-baryon theory. A critical discussion of a recent paper by Lanta and Tarrach is given. The results of the paper give evidence to the nonlinear chiral Lagrangian favour

  3. Pion polarizability in a chiral quark model

    International Nuclear Information System (INIS)

    Volkov, M.K.; Ehbert, D.

    1981-01-01

    The pion polarizability is calculated in a chiral meson- quark model at the one-loop level. The results are in complete agreement with earlier ones obtained within a chiral meson-baryon theory. A critical discussion of a recent paper by Llanta and Tarrach is given [ru

  4. Pion polarizability in a chiral quark model

    International Nuclear Information System (INIS)

    Volkov, M.K.; Ebert, D.

    1981-01-01

    It is shown that the pion polarizability calculated in a chiral model with quark loops agrees exactly with the analogous quantity found in a chiral meson-baryon model. The results of a paper by Llanta and Tarrach are discussed critically

  5. The polarizable embedding coupled cluster method

    DEFF Research Database (Denmark)

    Sneskov, Kristian; Schwabe, Tobias; Kongsted, Jacob

    2011-01-01

    We formulate a new combined quantum mechanics/molecular mechanics (QM/MM) method based on a self-consistent polarizable embedding (PE) scheme. For the description of the QM region, we apply the popular coupled cluster (CC) method detailing the inclusion of electrostatic and polarization effects...

  6. Hadron electric polarizability from lattice QCD

    Science.gov (United States)

    Alexandru, Andrei

    2017-09-01

    Electromagnetic polarizabilities are important parameters for hadron structure, describing the response of the charge and current distributions inside the hadron to an external electromagnetic field. For most hadrons these quantities are poorly constrained experimentally since they can only be measured indirectly. Lattice QCD can be used to compute these quantities directly in terms of quark and gluons degrees of freedom, using the background field method. We present results for the neutron electric polarizability for two different quark masses, light enough to connect to chiral perturbation theory. These are currently the lightest quark masses used in polarizability studies. For each pion mass we compute the polarizability at four different volumes and perform an infinite volume extrapolation. We also discuss the effect of turning on the coupling between the background field and the sea quarks. A.A. is supported in part by the National Science Foundation CAREER Grant PHY-1151648 and by U.S. DOE Grant No. DE-FG02-95ER40907.

  7. The axial polarizability of nucleons and nuclei

    International Nuclear Information System (INIS)

    Ericson, M.; Figureau, A.

    1981-02-01

    The part of the static nuclear axial polarizability arising from the nucleonic excitations is derived from the low energy expansion of the πN amplitude. It is shown that the contribution of the Δ intermediate state, though dominant, does not saturate the nucleonic response. A similar effect, though more pronounced, is known to occur for the magnetic susceptibility

  8. Polarizable Density Embedding Coupled Cluster Method

    DEFF Research Database (Denmark)

    Hršak, Dalibor; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2018-01-01

    by an embedding potential consisting of a set of fragment densities obtained from calculations on isolated fragments with a quantum-chemistry method such as Hartree-Fock (HF) or Kohn-Sham density functional theory (KS-DFT) and dressed with a set of atom-centered anisotropic dipole-dipole polarizabilities...

  9. K$_{-}$ and K$_{-}$ polarizability from kaonic atoms

    CERN Document Server

    Backenstoss, Gerhard; Bergström, I; Bunaciu, T; Egger, J; Hagelberg, R; Hultberg, S; Koch, H; Lynen, Y; Ritter, H G; Schwitter, A; Tauscher, L

    1973-01-01

    The K/sup -/ mass was determined from kaonic atomic X-rays from Au and Ba to be 493.691+or-0.040 MeV. An upper limit for the polarizability of the K/sup -/ was found to be 0.020 fm/sup 3/ at 90% confidence. (18 refs).

  10. Polarizability tensor and Kramers-Heisenberg induction

    NARCIS (Netherlands)

    Wijers, Christianus M.J.

    2004-01-01

    A general expression for the semiclassical, nonrelativistic linear polarizability of an arbitrary volume element V has been derived in the long wavelength approximation. The derivation starts from the expectation value of the dipole strength, as in the original Kramers-Heisenberg paper about optical

  11. Dinamical polarizability of highly excited hydrogen-like states

    International Nuclear Information System (INIS)

    Delone, N.B.; Krajnov, V.P.

    1982-01-01

    Analytic expressions are derived for the dynamic polarizability of highly excited hydrogen-like atomic states. It is shown that in the composite matrix element which determines the dynamic polarizability there is a strong compensation of the terms as a result of which the resulting magnitude of the dynamic polarizability is quasiclasically small compared to the individual terms of the composite matrix. It is concluded that the resonance behaviour of the dynamic polarizability of highly excited states differs significantly from the resonance behaviour of the polarizability for the ground and low-lying atomic states. The static limit and high-frequency limit of on electromagnetic field are considered

  12. Static dipole polarizabilities of Scn (n ≤ 15) clusters

    International Nuclear Information System (INIS)

    Xi-Bo, Li; Jiang-Shan, Luo; Wei-Dong, Wu; Yong-Jian, Tang; Hong-Yan, Wang; Yun-Dong, Guo

    2009-01-01

    The static dipole polarizabilities of scandium clusters with up to 15 atoms are determined by using the numerically finite field method in the framework of density functional theory. The electronic effects on the polarizabilities are investigated for the scandium clusters. We examine a large highest occupied molecular orbital — the lowest occupied molecular orbital (HOMO–LUMO) gap of a scandium cluster usually corresponds to a large dipole moment. The static polarizability per atom decreases slowly and exhibits local minimum with increasing cluster size. The polarizability anisotropy and the ratio of mean static polarizability to the HOMO–LUMO gap can also reflect the cluster stability. The polarizability of the scandium cluster is partially related to the HOMO–LUMO gap and is also dependent on geometrical characteristics. A strong correlation between the polarizability and ionization energy is observed. (atomic and molecular physics)

  13. Collision-induced polarizabilities of inert gas atoms

    International Nuclear Information System (INIS)

    Clarke, K.L.; Madden, P.A.; Buckingham, A.D.

    1978-01-01

    The use of polarizability densities to calculate collision-induced polarizabilities is investigated. One method for computing polarizabilities of inert gas diatoms employs atomic polarizability densities from finite-field Hartree-Fock calculations, together with classical equations for the polarization of dielectrics. It is shown that this model gives inaccurate values for both the local fields and the local response to non-uniform fields. An alternative method incorporating the same physical effects is used to compute the pair polarizabilities to first order in the interatomic interaction. To first order the pair contribution to the trace of the polarizability is negative at short range. The calculated anisotropy does not differ significantly from the DID value, whereas the polarizability density calculation gives a substantial reduction in the anisotropy. (author)

  14. Buse_Francisella and free-living amoebae data sets

    Data.gov (United States)

    U.S. Environmental Protection Agency — Co-infection data in the form of colony forming units and amoeba cell counts. This dataset is associated with the following publication: Buse , H., F. Schaefer, and...

  15. An electronic implementation of amoeba anticipation

    Science.gov (United States)

    Ziegler, Martin; Ochs, Karlheinz; Hansen, Mirko; Kohlstedt, Hermann

    2014-02-01

    In nature, the capability of memorizing environmental changes and recalling past events can be observed in unicellular organisms like amoebas. Pershin and Di Ventra have shown that such learning behavior can be mimicked in a simple memristive circuit model consisting of an LC (inductance capacitance) contour and a memristive device. Here, we implement this model experimentally by using an Ag/TiO2- x /Al memristive device. A theoretical analysis of the circuit is used to gain insight into the functionality of this model and to give advice for the circuit implementation. In this respect, the transfer function, resonant frequency, and damping behavior for a varying resistance of the memristive device are discussed in detail.

  16. Review: Occurrence of the pathogenic amoeba Naegleria fowleri in groundwater

    Science.gov (United States)

    Bright, Kelly R.; Gerba, Charles P.

    2017-06-01

    Naegleria fowleri is a thermophilic free-living amoeba found worldwide in soils and warm freshwater. It is the causative agent of primary amebic meningoencephalitis, a nearly always fatal disease afflicting mainly children and young adults. Humans are exposed to the organism via swimming, bathing, or other recreational activity during which water is forcefully inhaled into the upper nasal passages. Although many studies have looked at the occurrence of N. fowleri in surface waters, limited information is available regarding its occurrence in groundwater and geothermally heated natural waters such as hot springs. This paper reviews the current literature related to the occurrence of N. fowleri in these waters and the methods employed for its detection. Case reports of potential groundwater exposures are also included. Despite increased interest in N. fowleri in recent years due to well-publicized cases linked to drinking water, many questions still remain unanswered. For instance, why the organism persists in some water sources and not in others is not well understood. The role of biofilms in groundwater wells and plumbing in individual buildings, and the potential for warming due to climate change to expand the occurrence of the organism into new regions, are still unclear. Additional research is needed to address these questions in order to better understand the ecology of N. fowleri and the conditions that result in greater risks to bathers.

  17. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    Energy Technology Data Exchange (ETDEWEB)

    Zope, Rajendra R., E-mail: rzope@utep.edu; Baruah, Tunna [Department of Physics, The University of Texas at El Paso, El Paso, Texas 79958 (United States); Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79958 (United States); Bhusal, Shusil; Basurto, Luis [Department of Physics, The University of Texas at El Paso, El Paso, Texas 79958 (United States); Jackson, Koblar [Physics Department and Science of Advanced Materials Ph.D. Program, Central Michigan University, Mt. Pleasant, Michigan 48859 (United States)

    2015-08-28

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C{sub 60}@C{sub 240} and C{sub 60}@C{sub 180} onions shows that, compared to the polarizability of isolated C{sub 60} fullerene, the encapsulation of the C{sub 60} in C{sub 240} and C{sub 180} fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C{sub 60} in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  18. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    International Nuclear Information System (INIS)

    Zope, Rajendra R.; Baruah, Tunna; Bhusal, Shusil; Basurto, Luis; Jackson, Koblar

    2015-01-01

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C 60 @C 240 and C 60 @C 180 onions shows that, compared to the polarizability of isolated C 60 fullerene, the encapsulation of the C 60 in C 240 and C 180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C 60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability

  19. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    Science.gov (United States)

    Zope, Rajendra R.; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

    2015-08-01

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  20. Polarizabilities of the beryllium clock transition

    International Nuclear Information System (INIS)

    Mitroy, J.

    2010-01-01

    The polarizabilities of the three lowest states of the beryllium atom are determined from a large basis configuration interaction calculation. The polarizabilities of the 2s 2 1 S e ground state (37.73a 0 3 ) and the 2s2p 3 P 0 o metastable state (39.04a 0 3 ) are found to be very similar in size and magnitude. This leads to an anomalously small blackbody radiation shift at 300 K of -0.018(4) Hz for the 2s 2 1 S e -2s2p 3 P 0 o clock transition. Magic wavelengths for simultaneous trapping of the ground and metastable states are also computed.

  1. Atomic polarizability in negative-ion photodetachment

    International Nuclear Information System (INIS)

    Watanabe, S.; Greene, C.H.

    1980-01-01

    The influence of a strong atomic polarizability on photodetachment processes is isolated. In a model study of K - photodetachment near the 4p/sub 1/2/, 4p/sub 3/2/ levels of K, the polarizability (α/sub 4p/ approx. = 600a 3 0 ) is shown to cause a striking energy dependence of the parameters which determine the cross section. This study extends the effective range theory of O'Malley, Spruch, and Rosenberg to a broader energy range and to multichannel systems. An appendix provides a derivation of the polarization potential (and correction terms) starting from the electron-atom close-coupling equations, showing some new features

  2. Polarizability of a crystal with impurities

    International Nuclear Information System (INIS)

    Goettig, S.

    1985-09-01

    The expression for the complex frequency- and wavevector-dependent longitudinal electronic polarizability due to the presence of a weak static disorder (e.g. impurities) in a crystal with an arbitrary band structure is derived. The quantum kinetic equation in the self-consistent-field approximation is solved, expanding the one-particle density operator in powers of the screened static imperfection field and a weak perturbing electric field. The polarizability is determined by the induced electronic charge density quadratic in the imperfection field and linear in the perturbing field, averaged over the statistical distribution of imperfections. The obtained expression, which accounts properly for the collective effects in the electronic plasma, takes also into account the polar coupling of the plasma with longitudinal optical phonons. The conductivity in the optical limit (q-vector→O) is calculated, and the correspondence with one-band effective-mass approximation is established. (author)

  3. Phase coexistence properties of polarizable Stockmayer fluids

    International Nuclear Information System (INIS)

    Kiyohara, K.; Gubbins, K.E.; Panagiotopoulos, A.Z.

    1997-01-01

    We report the phase coexistence properties of polarizable Stockmayer fluids of reduced permanent dipoles |m 0 * |= 1.0 and 2.0 and reduced polarizabilities α * = 0.00, 0.03, and 0.06, calculated by a series of grand canonical Monte Carlo simulations with the histogram reweighting method. In the histogram reweighting method, the distributions of density and energy calculated in Grand Canonical Monte Carlo simulations are stored in histograms and analyzed to construct the grand canonical partition function of the system. All thermodynamic properties are calculated from the grand partition function. The results are compared with Wertheim close-quote s renormalization perturbation theory. Deviations between theory and simulation results for the coexistence envelope are near 2% for the lower dipole moment and 10% for the higher dipole moment we studied. copyright 1997 American Institute of Physics

  4. On the dynamic polarizability of atoms

    International Nuclear Information System (INIS)

    Nuroh, K.; Zaremba, E.

    1989-04-01

    The positive frequency dependent polarizability of atoms is discussed in terms of the particle-hole polarization propagator. It is considered in the simplest approximation defined by the Bethe-Salpeter equation which includes a subset of particle-hole interactions to all orders in the Coulomb potential. Its solution is used to show the relationship between different formulations of atomic photoabsorption via the effective dipole matrix element (Fermi's 'golden rule'), the TDLDA and the reaction matrix. (author). 21 refs, 7 figs

  5. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

    Science.gov (United States)

    Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W

    2011-10-11

    An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

  6. Electrode redox reactions with polarizable molecules

    Science.gov (United States)

    Matyushov, Dmitry V.

    2018-04-01

    A theory of redox reactions involving electron transfer between a metal electrode and a polarizable molecule in solution is formulated. Both the existence of molecular polarizability and its ability to change due to electron transfer distinguish this problem from classical theories of interfacial electrochemistry. When the polarizability is different between the oxidized and reduced states, the statistics of thermal fluctuations driving the reactant over the activation barrier becomes non-Gaussian. The problem of electron transfer is formulated as crossing of two non-parabolic free energy surfaces. An analytical solution for these free energy surfaces is provided and the activation barrier of electrode electron transfer is given in terms of two reorganization energies corresponding to the oxidized and reduced states of the molecule in solution. The new non-Gaussian theory is, therefore, based on two theory parameters in contrast to one-parameter Marcus formulation for electrode reactions. The theory, which is consistent with the Nernst equation, predicts asymmetry between the cathodic and anodic branches of the electrode current. They show different slopes at small electrode overpotentials and become curved at larger overpotentials. However, the curvature of the Tafel plot is reduced compared to the Marcus-Hush model and approaches the empirical Butler-Volmer form with different transfer coefficients for the anodic and cathodic currents.

  7. Measurement of molecular polarizability on Rayleigh light scattering

    International Nuclear Information System (INIS)

    Nerushev, O.A.; Novopashin, S.A.

    1994-01-01

    The installation for measuring the polarizability of atoms and molecules on Rayleigh light scattering is described. The measurements in gases with the known polarizability are used for a calibration. Test measurements are carried out on nitrogen, argon, carbon dioxide, vapours of water and acetone. The results of measurements are compared with the table data. The technique is used for measuring the polarizability of fullerene molecules. 6 refs., 2 figs

  8. Dielectric constant of atomic fluids with variable polarizability

    OpenAIRE

    Alder, B. J.; Beers, J. C.; Strauss, H. L.; Weis, J. J.

    1980-01-01

    The Clausius-Mossotti function for the dielectric constant is expanded in terms of single atom and pair polarizabilities, leading to contributions that depend on both the trace and the anisotropy of the pair-polarizability tensor. The short-range contribution of the anisotropic part to the pair polarizabilities has previously been obtained empirically from light scattering experiments, whereas the trace contribution is now empirically determined by comparison to dielectric experiments. For he...

  9. Casimir friction between polarizable particle and half-space with radiation damping at zero temperature

    International Nuclear Information System (INIS)

    Høye, J S; I Brevik; Milton, K A

    2015-01-01

    Casimir friction between a polarizable particle and a semi-infinite space is a delicate physical phenomenon, as it concerns the interaction between a microscopic quantum particle and a semi-infinite reservoir. Not unexpectedly, results obtained in the past about the friction force obtained via different routes are sometimes, at least apparently, wildly different from each other. Recently, we considered the Casimir friction force for two dielectric semi-infinite plates moving parallel to each other Høye and Brevik (2014 Eur. Phys. J. D 68 61), and managed to get essential agreement with results obtained by Pendry (1997 J. Phys.: Condens. Matter 9 10301), Volokitin and Persson (2007 Rev. Mod. Phys. 79 1291), and Barton (2011 New J. Phys. 13 043023; 2011 J. Phys.: Condens. Matter 23 335004). Our method was based upon use of the Kubo formalism. In the present paper we focus on the interaction between a polarizable particle and a dielectric half-space again, and calculate the friction force using the same basic method as before. The new ingredient in the present analysis is that we take into account radiative damping, and derive the modifications thereof. Some comparisons are also made with works from others. Essential agreement with the results of Intravaia, Behunin, and Dalvit can also be achieved using the modification of the atomic polarizability by the metallic plate. (paper)

  10. Integral-functional representation of mass operator of quasiparticles interacting with polarizational phonons at T = 0 K

    International Nuclear Information System (INIS)

    Tkach, M.V.

    2002-01-01

    The integral-functional representation of mass operator of spinless quasiparticles interacting with polarizational phonons at T = 0 K is obtained for the first time. This representation is equivalent to the infinite branched integral fraction. It does not depend on the binding force and effectively takes into account the many phonon processes

  11. Palaeoecology of testate amoebae in a tropical peatland.

    Science.gov (United States)

    Swindles, Graeme T; Lamentowicz, Mariusz; Reczuga, Monika; Galloway, Jennifer M

    2016-09-01

    We present the first detailed analysis of subfossil testate amoebae from a tropical peatland. Testate amoebae were analysed in a 4-m peat core from western Amazonia (Peru) and a transfer function developed from the site was applied to reconstruct changes in water table over the past ca. 8,000 years. Testate amoebae were in very low abundance in the core, especially in the lower 125cm, due to a combination of poor preservation and obscuration by other organic matter. A modified preparation method enabled at least 50 testate amoebae to be counted in each core sample. The most abundant taxa preserved include Centropyxis aculeata, Hyalosphenia subflava, Phryganella acropodia and Trigonopyxis arcula. Centropyxis aculeata, an unambiguous wet indicator, is variably present and indicates several phases of near-surface water table. Our work shows that even degraded, low-abundance assemblages of testate amoebae can provide useful information regarding the long-term ecohydrological developmental history of tropical peatlands. Copyright © 2015 Elsevier GmbH. All rights reserved.

  12. Pion polarizability in nonlocal quark model

    International Nuclear Information System (INIS)

    Efimov, G.V.; Okhlopkova, V.A.

    1978-01-01

    The γγ→ππ amplitude was calculated in nonlocal quark model in the fourth order on the perturbation theory. The coefficients of electric[a) and magnetic polarizability (β) determined are equal in magnitude and opposite in sign αsub(π+-)=βsub(π+-)=+0.014α/msub(π)sup(3), αsub(πsup(0))=-βsub(πsup(0))=-0.07α/msub(π)sup(3). The results have been compared with calculations in other models

  13. Polarizability properties of bianisotropic spheres with noncomplete magnetoelectric dyadics

    Science.gov (United States)

    Sihvola, A. H.

    1994-02-01

    The polarizability expressions for bianisotropic scatterers are often complicated expressions of the material parameters. The communication treats the question how the dyadic inversion operations needed in the expressions can be carried out in a well-behaving way. Also, the particular polarizabilities of biaxial chiral spheres are studied in detail.

  14. Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide

    DEFF Research Database (Denmark)

    Kjær, Hanna; Nielsen, Monia R.; Pagola, Gabriel I.

    2012-01-01

    In this paper we present the so far most extended investigation of the calculation of the coupling constant polarizability of a molecule. The components of the coupling constant polarizability are derivatives of the NMR indirect nuclear spin-spin coupling constant with respect to an external elec...

  15. An averaged polarizable potential for multiscale modeling in phospholipid membranes

    DEFF Research Database (Denmark)

    Witzke, Sarah; List, Nanna Holmgaard; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl...

  16. Parasitic amoebae found in water bodies of Ukraine.

    Science.gov (United States)

    Patsyuk, Marina

    2017-12-01

    Two parasitic amoebian species are found in mollusks of the water bodies of Ukraine. Vahlkampfia sp. is found in hepatopankreas of Unio conus Spengler, 1793, and Acanthamoeba sp. is observed in mantle cavity of Viviparus viviparus Linnaeus, 1758. For these protist species, the mollusks are shown to be intermediate hosts where amoebae feed and reproduce. An experimental infection with Vahlkampfia sp. and Acanthamoeba sp. was not successful, no pathological changes in mollusks were observed. These amoebae are successfully cultured in fresh water and agar medium, hence we can safely consider them free-living. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Measurement of the charged-pion polarizability.

    Science.gov (United States)

    Adolph, C; Akhunzyanov, R; Alexeev, M G; Alexeev, G D; Amoroso, A; Andrieux, V; Anosov, V; Austregesilo, A; Badełek, B; Balestra, F; Barth, J; Baum, G; Beck, R; Bedfer, Y; Berlin, A; Bernhard, J; Bicker, K; Bieling, J; Birsa, R; Bisplinghoff, J; Bodlak, M; Boer, M; Bordalo, P; Bradamante, F; Braun, C; Bressan, A; Büchele, M; Burtin, E; Capozza, L; Chiosso, M; Chung, S U; Cicuttin, A; Colantoni, M; Crespo, M L; Curiel, Q; Dalla Torre, S; Dasgupta, S S; Dasgupta, S; Denisov, O Yu; Dinkelbach, A M; Donskov, S V; Doshita, N; Duic, V; Dünnweber, W; Dziewiecki, M; Efremov, A; Elia, C; Eversheim, P D; Eyrich, W; Faessler, M; Ferrero, A; Filin, A; Finger, M; Finger, M; Fischer, H; Franco, C; du Fresne von Hohenesche, N; Friedrich, J M; Frolov, V; Gautheron, F; Gavrichtchouk, O P; Gerassimov, S; Geyer, R; Gnesi, I; Gobbo, B; Goertz, S; Gorzellik, M; Grabmüller, S; Grasso, A; Grube, B; Grussenmeyer, T; Guskov, A; Guthörl, T; Haas, F; von Harrach, D; Hahne, D; Hashimoto, R; Heinsius, F H; Herrmann, F; Hinterberger, F; Höppner, Ch; Horikawa, N; d'Hose, N; Huber, S; Ishimoto, S; Ivanov, A; Ivanshin, Yu; Iwata, T; Jahn, R; Jary, V; Jasinski, P; Jörg, P; Joosten, R; Kabuss, E; Ketzer, B; Khaustov, G V; Khokhlov, Yu A; Kisselev, Yu; Klein, F; Klimaszewski, K; Koivuniemi, J H; Kolosov, V N; Kondo, K; Königsmann, K; Konorov, I; Konstantinov, V F; Kotzinian, A M; Kouznetsov, O; Krämer, M; Kroumchtein, Z V; Kuchinski, N; Kuhn, R; Kunne, F; Kurek, K; Kurjata, R P; Lednev, A A; Lehmann, A; Levillain, M; Levorato, S; Lichtenstadt, J; Maggiora, A; Magnon, A; Makke, N; Mallot, G K; Marchand, C; Martin, A; Marzec, J; Matousek, J; Matsuda, H; Matsuda, T; Meshcheryakov, G; Meyer, W; Michigami, T; Mikhailov, Yu V; Miyachi, Y; Moinester, M A; Nagaytsev, A; Nagel, T; Nerling, F; Neubert, S; Neyret, D; Nikolaenko, V I; Novy, J; Nowak, W-D; Nunes, A S; Olshevsky, A G; Orlov, I; Ostrick, M; Panknin, R; Panzieri, D; Parsamyan, B; Paul, S; Peshekhonov, D; Platchkov, S; Pochodzalla, J; Polyakov, V A; Pretz, J; Quaresma, M; Quintans, C; Ramos, S; Regali, C; Reicherz, G; Rocco, E; Rossiyskaya, N S; Ryabchikov, D I; Rychter, A; Samoylenko, V D; Sandacz, A; Sarkar, S; Savin, I A; Sbrizzai, G; Schiavon, P; Schill, C; Schlüter, T; Schmidt, K; Schmieden, H; Schönning, K; Schopferer, S; Schott, M; Shevchenko, O Yu; Silva, L; Sinha, L; Sirtl, S; Slunecka, M; Sosio, S; Sozzi, F; Srnka, A; Steiger, L; Stolarski, M; Sulc, M; Sulej, R; Suzuki, H; Szabelski, A; Szameitat, T; Sznajder, P; Takekawa, S; ter Wolbeek, J; Tessaro, S; Tessarotto, F; Thibaud, F; Uhl, S; Uman, I; Virius, M; Wang, L; Weisrock, T; Wilfert, M; Windmolders, R; Wollny, H; Zaremba, K; Zavertyaev, M; Zemlyanichkina, E; Ziembicki, M; Zink, A

    2015-02-13

    The COMPASS collaboration at CERN has investigated pion Compton scattering, π(-)γ→π(-)γ, at center-of-mass energy below 3.5 pion masses. The process is embedded in the reaction π(-)Ni→π(-)γNi, which is initiated by 190 GeV pions impinging on a nickel target. The exchange of quasireal photons is selected by isolating the sharp Coulomb peak observed at smallest momentum transfers, Q(2)<0.0015  (GeV/c)(2). From a sample of 63,000 events, the pion electric polarizability is determined to be α(π)=(2.0±0.6(stat)±0.7(syst))×10(-4)  fm(3) under the assumption α(π)=-β(π), which relates the electric and magnetic dipole polarizabilities. It is the most precise measurement of this fundamental low-energy parameter of strong interaction that has been addressed since long by various methods with conflicting outcomes. While this result is in tension with previous dedicated measurements, it is found in agreement with the expectation from chiral perturbation theory. An additional measurement replacing pions by muons, for which the cross-section behavior is unambiguously known, was performed for an independent estimate of the systematic uncertainty.

  18. Model-independent effects of Δ excitation in nucleon polarizabilities

    International Nuclear Information System (INIS)

    Pascalutsa, Vladimir; Phillips, Daniel R.

    2003-01-01

    Model-independent effects of Δ(1232) excitation on nucleon polarizabilities are computed in a Lorentz-invariant fashion. We find a large effect of relative order (M Δ -M)/M in some of the spin polarizabilities, with the backward spin polarizability receiving the largest contribution. Similar subleading effects are found to be important in the fourth-order spin-independent polarizabilities α Eν , α E2 , β Mν , and β M2 . Combining our results with those for the model-independent effects of pion loops we obtain predictions for spin and fourth-order polarizabilities which compare favorably with the results of a recent dispersion-relation analysis of data

  19. Molecular Polarizability of Sc and C (Fullerene and Graphite Clusters

    Directory of Open Access Journals (Sweden)

    Francisco Torrens

    2001-05-01

    Full Text Available A method (POLAR for the calculation of the molecular polarizability is presented. It uses the interacting induced dipoles polarization model. As an example, the method is applied to Scn and Cn (fullerene and one-shell graphite model clusters. On varying the number of atoms, the clusters show numbers indicative of particularly polarizable structures. The are compared with reference calculations (PAPID. In general, the Scn calculated (POLAR and Cn computed (POLAR and PAPID are less polarizable than what is inferred from the bulk. However, the Scn calculated (PAPID are more polarizable than what is inferred. Moreover, previous theoretical work yielded the same trend for Sin, Gen and GanAsm small clusters. The high polarizability of the Scn clusters (PAPID is attributed to arise from dangling bonds at the surface of the cluster.

  20. Hyperfine-mediated static polarizabilities of monovalent atoms and ions

    International Nuclear Information System (INIS)

    Dzuba, V. A.; Flambaum, V. V.; Beloy, K.; Derevianko, A.

    2010-01-01

    We apply relativistic many-body methods to compute static differential polarizabilities for transitions inside the ground-state hyperfine manifolds of monovalent atoms and ions. Knowledge of this transition polarizability is required in a number of high-precision experiments, such as microwave atomic clocks and searches for CP-violating permanent electric dipole moments. While the traditional polarizability arises in the second order of interaction with the externally applied electric field, the differential polarizability involves an additional contribution from the hyperfine interaction of atomic electrons with nuclear moments. We derive formulas for the scalar and tensor polarizabilities including contributions from magnetic dipole and electric quadrupole hyperfine interactions. Numerical results are presented for Al, Rb, Cs, Yb + , Hg + , and Fr.

  1. Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbours.

    Science.gov (United States)

    Thomas, Vincent; Greub, Gilbert

    2010-01-01

    Free-living amoebae serve as hosts for a variety of amoebae-resisting microorganisms, including giant viruses and certain bacteria. The latter include symbiotic bacteria as well as bacteria exhibiting a pathogenic phenotype towards amoebae. Amoebae-resisting bacteria have been shown to be widespread in water and to use the amoebae as a reservoir, a replication niche, a protective armour as well as a training ground to select virulence traits allowing survival in the face of microbicidal effects of macrophages, the first line of defense against invading pathogens. More importantly, amoebae play a significant role as a melting pot for genetic exchanges. These ecological and evolutionary roles of amoebae might also be at play for giant viruses and knowledge derived from the study of amoebae-resisting bacteria is useful for the study and understanding of interactions between amoebae and giant viruses. This is especially important since some genes have spread in all domains of life and the exponential availability of eukaryotic genomes and metagenomic sequences will allow researchers to explore these genetic exchanges in a more comprehensive way, thus completely changing our perception of the evolutionary history of organisms. Thus, a large part of this review is dedicated to report current known gene exchanges between the different amoebae-resisting organisms and between amoebae and the internalized bacteria. Copyright 2010 S. Karger AG, Basel.

  2. The Evolution of a distributed operating system (Amoeba)

    NARCIS (Netherlands)

    van Renesse, Robbert; Tanenbaum, Andrew S.; Mullender, Sape J.

    1989-01-01

    AMOEBA is a research project to build a true distributed operating system using the object model. Under the COST11-ter MANDIS project this work was extended to cover wide-area networks. Besides describing the system, this paper discusses the successive versions in the implementation of its model,

  3. Checklist, diversity and distribution of testate amoebae in Chile.

    Science.gov (United States)

    Fernández, Leonardo D; Lara, Enrique; Mitchell, Edward A D

    2015-10-01

    Bringing together more than 170 years of data, this study represents the first attempt to construct a species checklist and analyze the diversity and distribution of testate amoebae in Chile, a country that encompasses the southwestern region of South America, countless islands and part of the Antarctic. In Chile, known diversity includes 416 testate amoeba taxa (64 genera, 352 infrageneric taxa), 24 of which are here reported for the first time. Species-accumulation plots show that in Chile, the number of testate amoeba species reported has been continually increasing since the mid-19th century without leveling off. Testate amoebae have been recorded in 37 different habitats, though they are more diverse in peatlands and rainforest soils. Only 11% of species are widespread in continental Chile, while the remaining 89% of the species exhibit medium or short latitudinal distribution ranges. Also, species composition of insular Chile and the Chilean Antarctic territory is a depauperated subset of that found in continental Chile. Nearly, the 10% of the species reported here are endemic to Chile and many of them are distributed only within the so-called Chilean biodiversity hotspot (ca. 25° S-47° S). These findings are here thoroughly discussed in a biogeographical and evolutionary context. Copyright © 2015 Elsevier GmbH. All rights reserved.

  4. Counting Legionella cells within single amoeba host cells

    Science.gov (United States)

    Here we present the first attempt to quantify L. pneumophila cell numbers within individual amoebae hosts that may be released into engineered water systems. The maximum numbers of culturable L. pneumophila cells grown within Acanthamoeba polyphaga and Naegleria fowleri were 134...

  5. The genome of the social amoeba Dictyostelium discoideum

    DEFF Research Database (Denmark)

    Eichinger, L; Pachebat, J A; Glöckner, G

    2005-01-01

    The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins,...

  6. Advances in the knowledge of amphizoic amoebae infecting fish

    Czech Academy of Sciences Publication Activity Database

    Dyková, Iva; Lom, Jiří

    2004-01-01

    Roč. 51, 2/3 (2004), s. 81-97 ISSN 0015-5683 R&D Projects: GA AV ČR IAA6022202 Institutional research plan: CEZ:AV0Z6022909 Keywords : amphizoic amoebae * fish hosts * review Subject RIV: EA - Cell Biology Impact factor: 0.837, year: 2004

  7. Density and polarizability of liquid 4He

    International Nuclear Information System (INIS)

    Kempin'ski, V.; Zhuk, T.; Stankovski, Ya.; Sitarzh, S.

    1988-01-01

    The temperature changes in the density of liquid helium are measured in the temperature range of 1.63 to 4.2 K.; Unlike the conventional pycnometric technique, the changes in the hydrostatic displacement of the liquid were determined. The cirrectness of the method chosen and the appropriate equipment for its realization are substantiated. The results obtained are in good agreement with those of other authors. On the basis of temperature measurements of the dependence of density ρ and permittivity ε, the dependence of polarizability A of liquid 4 He on temperature and density was calculated. The results obtained show an alternating character of the dependences A(T) and A(ρ). These dependences are found to correlate

  8. Accelerating GW calculations with optimal polarizability basis

    Energy Technology Data Exchange (ETDEWEB)

    Umari, P.; Stenuit, G. [CNR-IOM DEMOCRITOS Theory Elettra Group, Basovizza (Trieste) (Italy); Qian, X.; Marzari, N. [Department of Materials Science and Engineering, MIT, Cambridge, MA (United States); Giacomazzi, L.; Baroni, S. [CNR-IOM DEMOCRITOS Theory Elettra Group, Basovizza (Trieste) (Italy); SISSA - Scuola Internazionale Superiore di Studi Avanzati, Trieste (Italy)

    2011-03-15

    We present a method for accelerating GW quasi-particle (QP) calculations. This is achieved through the introduction of optimal basis sets for representing polarizability matrices. First the real-space products of Wannier like orbitals are constructed and then optimal basis sets are obtained through singular value decomposition. Our method is validated by calculating the vertical ionization energies of the benzene molecule and the band structure of crystalline silicon. Its potentialities are illustrated by calculating the QP spectrum of a model structure of vitreous silica. Finally, we apply our method for studying the electronic structure properties of a model of quasi-stoichiometric amorphous silicon nitride and of its point defects. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Electronic Energy Transfer in Polarizable Heterogeneous Environments

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Kongsted, Jacob

    2015-01-01

    such couplings provide important insight into the strength of interaction between photo-active pigments in protein-pigment complexes. Recently, attention has been payed to how the environment modifies or even controls the electronic couplings. To enable such theoretical predictions, a fully polarizable embedding......-order multipole moments. We use this extended model to systematically examine three different ways of obtaining EET couplings in a heterogeneous medium ranging from use of the exact transition density to a point-dipole approximation. Several interesting observations are made including that explicit use...... of transition densities in the calculation of the electronic couplings - also when including the explicit environment contribution - can be replaced by a much simpler transition point charge description without comprising the quality of the model predictions....

  10. Bounds on complex polarizabilities and a new perspective on scattering by a lossy inclusion

    Science.gov (United States)

    Milton, Graeme W.

    2017-09-01

    Here, we obtain explicit formulas for bounds on the complex electrical polarizability at a given frequency of an inclusion with known volume that follow directly from the quasistatic bounds of Bergman and Milton on the effective complex dielectric constant of a two-phase medium. We also describe how analogous bounds on the orientationally averaged bulk and shear polarizabilities at a given frequency can be obtained from bounds on the effective complex bulk and shear moduli of a two-phase medium obtained by Milton, Gibiansky, and Berryman, using the quasistatic variational principles of Cherkaev and Gibiansky. We also show how the polarizability problem and the acoustic scattering problem can both be reformulated in an abstract setting as "Y problems." In the acoustic scattering context, to avoid explicit introduction of the Sommerfeld radiation condition, we introduce auxiliary fields at infinity and an appropriate "constitutive law" there, which forces the Sommerfeld radiation condition to hold. As a consequence, we obtain minimization variational principles for acoustic scattering that can be used to obtain bounds on the complex backwards scattering amplitude. Some explicit elementary bounds are given.

  11. Dielectric constant of atomic fluids with variable polarizability.

    Science.gov (United States)

    Alder, B J; Beers, J C; Strauss, H L; Weis, J J

    1980-06-01

    The Clausius-Mossotti function for the dielectric constant is expanded in terms of single atom and pair polarizabilities, leading to contributions that depend on both the trace and the anisotropy of the pair-polarizability tensor. The short-range contribution of the anisotropic part to the pair polarizabilities has previously been obtained empirically from light scattering experiments, whereas the trace contribution is now empirically determined by comparison to dielectric experiments. For helium, the short-range trace part agrees well with electronic structure calculations, whereas for argon qualitative agreement is achieved.

  12. Surveillance of parasitic Legionella in surface waters by using immunomagnetic separation and amoebae enrichment.

    Science.gov (United States)

    Hsu, Tsui-Kang; Wu, Shu-Fen; Hsu, Bing-Mu; Kao, Po-Min; Tao, Chi-Wei; Shen, Shu-Min; Ji, Wen-Tsai; Huang, Wen-Chien; Fan, Cheng-Wei

    2015-01-01

    Free-living amoebae (FLA) are potential reservoirs of Legionella in aquatic environments. However, the parasitic relationship between various Legionella and amoebae remains unclear. In this study, surface water samples were gathered from two rivers for evaluating parasitic Legionella. Warmer water temperature is critical to the existence of Legionella. This result suggests that amoebae may be helpful in maintaining Legionella in natural environments because warmer temperatures could enhance parasitisation of Legionella in amoebae. We next used immunomagnetic separation (IMS) to identify extracellular Legionella and remove most free Legionella before detecting the parasitic ones in selectively enriched amoebae. Legionella pneumophila was detected in all the approaches, confirming that the pathogen is a facultative amoebae parasite. By contrast, two obligate amoebae parasites, Legionella-like amoebal pathogens (LLAPs) 8 and 9, were detected only in enriched amoebae. However, several uncultured Legionella were detected only in the extracellular samples. Because the presence of potential hosts, namely Vermamoeba vermiformis, Acanthamoeba spp. and Naegleria gruberi, was confirmed in the samples that contained intracellular Legionella, uncultured Legionella may survive independently of amoebae. Immunomagnetic separation and amoebae enrichment may have referential value for detecting parasitic Legionella in surface waters.

  13. Polarizabilities and hyperpolarizabilities of the alkali metal atoms

    Energy Technology Data Exchange (ETDEWEB)

    Fuentealba, P. (Chile Univ., Santiago (Chile). Departamento de Fisica and Centro de Mecanica Cuantica Aplicada (CMCA)); Reyes, O. (Chile Univ., Santiago (Chile). Dept. de Fisica)

    1993-08-14

    The electric static dipole polarizability [alpha], quadrupole polarizability C, dipole-quadrupole polarizability B, and the second dipole hyperpolarizability [gamma] have been calculated for the alkali metal atoms in the ground state. The results are based on a pseudopotential which is able to incorporate the very important core-valence correlation effect through a core polarization potential, and, in an empirical way, the main relativistic effects. The calculated properties compare very well with more elaborated calculations for the Li atom, excepting the second hyperpolarizability [gamma]. For the other atoms, there is neither theoretical nor experimental information about most of the higher polarizabilities. Hence, the results of this paper should be seen as a first attempt to give a complete account of the series expansion of the interaction energy of an alkali metal atom and a static electric field. (author).

  14. The polarizability of diatomic helium. Ph.D. Thesis

    Science.gov (United States)

    Fortune, P. J.

    1974-01-01

    The calculation of the electric dipole polarizability tensor of the He 2 dimer is described, and the results are used in the computation of several dielectric and optical properties of helium gas, at both high (322 K) and low (4 K) temperatures. The properties considered are the second dielectric virial coefficient, the second Kerr virial coefficient, and the depolarization ratio of the integrated intensities for the Raman scattering experiments. The thesis consists of five parts: the polarizability and various properties are defined; the calculation of the polarizability in the long-range region in terms of a quantum mechanical multipole expansion is described; the calculation of the He2 polarizability in the overlap region via coupled Hartree-Fock perturbation theory is described; the calculation of the quantum pair distribution function for both the He-3 and He-4 isotopes at 4 K is discussed; and the calculated values of the properties of helium gas are given.

  15. Contributions of polarizabilities to four basis polarizations of electromagnetic media

    International Nuclear Information System (INIS)

    Bukina, E.N.; Dubovik, V.M.

    1999-01-01

    All contributions to four basis polarizations of an arbitrary electromagnetic medium at the expense of mixed polarizabilities up to fourth rank tensors are presented. Some concrete examples are considered

  16. Polarizabilities and hyperpolarizabilities of the alkali metal atoms

    International Nuclear Information System (INIS)

    Fuentealba, P.; Reyes, O.

    1993-01-01

    The electric static dipole polarizability α, quadrupole polarizability C, dipole-quadrupole polarizability B, and the second dipole hyperpolarizability γ have been calculated for the alkali metal atoms in the ground state. The results are based on a pseudopotential which is able to incorporate the very important core-valence correlation effect through a core polarization potential, and, in an empirical way, the main relativistic effects. The calculated properties compare very well with more elaborated calculations for the Li atom, excepting the second hyperpolarizability γ. For the other atoms, there is neither theoretical nor experimental information about most of the higher polarizabilities. Hence, the results of this paper should be seen as a first attempt to give a complete account of the series expansion of the interaction energy of an alkali metal atom and a static electric field. (author)

  17. Dynamic polarizabilities for the low lying states of Ca+

    International Nuclear Information System (INIS)

    Tang, Yong-Bo; Shi, Ting-Yun; Qiao, Hao-Xue; Mitroy, J

    2014-01-01

    The dynamic polarizabilities of the 4s, 3d and 4p states of Ca + are calculated using a relativistic structure model. The wavelengths at which the Stark shifts between different pairs of transitions are zero are calculated. Experimental determination of the magic wavelengths could prove useful in developing better atomic structure models and in particular lead to improved values of the polarizabilities for the Ca + (3d) states

  18. Black-Body Radiation Correction to the Polarizability of Helium

    OpenAIRE

    Puchalski, M.; Jentschura, U. D.; Mohr, P. J.

    2011-01-01

    The correction to the polarizability of helium due to black-body radiation is calculated near room temperature. A precise theoretical determination of the black-body radiation correction to the polarizability of helium is essential for dielectric gas thermometry and for the determination of the Boltzmann constant. We find that the correction, for not too high temperature, is roughly proportional to a modified hyperpolarizability (two-color hyperpolarizability), which is different from the ord...

  19. Effect of core polarizability on photoionization cross-section calculations.

    Science.gov (United States)

    Kirkpatrick, R. C.

    1972-01-01

    Demonstration of the importance of core polarizability in a case where cancellation is only moderate, with suggestion of an improvement to the scaled Thomas-Fermi (STF) wave functions of Stewart and Rotenberg (1965). The inclusion of dipole polarizability of the core for argon is shown to substantially improve the agreement between the theoretical and experimental photoionization cross sections for the ground-state configuration.

  20. Electric dipole polarizability: from few- to many-body systems

    Directory of Open Access Journals (Sweden)

    Miorelli Mirko

    2016-01-01

    Full Text Available We review the Lorentz integral transform coupled-cluster method for the calculation of the electric dipole polarizability. We benchmark our results with exact hyperspherical harmonics calculations for 4He and then we move to a heavier nucleus studying 16O. We observe that the implemented chiral nucleon-nucleon interaction at next-to-next-to-next-to-leading order underestimates the electric dipole polarizability.

  1. Raman spectroscopic study on the excystation process in a single unicellular organism amoeba (Acanthamoeba polyphaga)

    Science.gov (United States)

    Lin, Yu-Chung; Perevedentseva, Elena; Cheng, Chia-Liang

    2015-05-01

    An in vivo Raman spectroscopic study of amoeba (Acanthamoeba polyphaga) is presented. The changes of the spectra during the amoeba cyst activation and excystation are analyzed. The spectra show the changes of the relative intensities of bands corresponding to protein, lipid, and carotenoid components during cyst activation. The presence of carotenoids in the amoeba is observed via characteristic Raman bands. These signals in the Raman spectra are intense in cysts but decrease in intensity with cyst activation and exhibit a correlation with the life cycle of amoeba. This work demonstrates the feasibility of using Raman spectroscopy for the detection of single amoeba microorganisms in vivo and for the analysis of the amoeba life activity. The information obtained may have implications for the estimation of epidemiological situations and for the diagnostics and prognosis of the development of amoebic inflammations.

  2. Density Functional Studies of Molecular Polarizabilities. 7. Anthracene and Phenanthrene

    Directory of Open Access Journals (Sweden)

    Humberto J. Soscun Machado

    2000-03-01

    Full Text Available We report accurate Ab Initio studies of the static dipole polarizabilities of anthracene and phenanthrene. Geometries were optimized at the HF/6-311G(3d,2p level of theory. Dipole polarizabilities were calculated at the HF/6-311++G(3d,2p and BLYP/6-311++G(3d,2p levels of theory, using HF/6-311G(3d,2p geometries. The calculated dipole polarizabilities for anthracene are compared with experiment. Inclusion of electron correlation using the BLYP procedure increases the L and M components of the dipole polarizability, but not the perpendicular (N component. Examination of corresponding BLYP results for the polyacene series benzene, naphthalene and anthracene shows that the normal component of the dipole polarizability scales linearly with the number of benzene ring units, with an increment of 20.8 au. The medium component also scales linearly with an increment of 42.8 atomic units. The long component does not scale linearly. Semi-emiprical AM1 calculations are also given for comparison; the normal component of the dipole polarizability tensor is poorly represented by such calculations.

  3. Kin discrimination increases with genetic distance in a social amoeba.

    Science.gov (United States)

    Ostrowski, Elizabeth A; Katoh, Mariko; Shaulsky, Gad; Queller, David C; Strassmann, Joan E

    2008-11-25

    In the social amoeba Dictyostelium discoideum, thousands of cells aggregate upon starvation to form a multicellular fruiting body, and approximately 20% of them die to form a stalk that benefits the others. The aggregative nature of multicellular development makes the cells vulnerable to exploitation by cheaters, and the potential for cheating is indeed high. Cells might avoid being victimized if they can discriminate among individuals and avoid those that are genetically different. We tested how widely social amoebae cooperate by mixing isolates from different localities that cover most of their natural range. We show here that different isolates partially exclude one another during aggregation, and there is a positive relationship between the extent of this exclusion and the genetic distance between strains. Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals, suggesting the existence of a mechanism that discerns the degree of genetic similarity between individuals in this social microorganism.

  4. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

    Science.gov (United States)

    Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

    2015-07-15

    Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

  5. Repulsive Casimir-Polder forces from cosmic strings

    International Nuclear Information System (INIS)

    Saharian, A.A.; Kotanjyan, A.S.

    2011-01-01

    We investigate the Casimir-Polder force acting on a polarizable microparticle in the geometry of a straight cosmic string. In order to develop this analysis we evaluate the electromagnetic field Green tensor on the imaginary frequency axis. The expression for the Casimir-Polder force is derived in the general case of anisotropic polarizability. In dependence on the eigenvalues for the polarizability tensor and of the orientation of its principal axes, the Casimir-Polder force can be either repulsive or attractive. Moreover, there are situations where the force changes the sign with separation. We show that for an isotropic polarizability tensor the force is always repulsive. At large separations between the microparticle and the string, the force varies inversely with the fifth power of the distance. In the non-retarded regime, corresponding to separations smaller than the relevant transition wavelengths, the force decays with the inverse fourth power of the distance. In the case of anisotropic polarizability, the dependence of the Casimir-Polder potential on the orientation of the polarizability tensor principal axes also leads to a moment of force acting on the particle. (orig.)

  6. Analytic behavior of the QED polarizability function at finite temperature

    International Nuclear Information System (INIS)

    Bernal, A.; Perez, A.

    2012-01-01

    We revisit the analytical properties of the static quasi-photon polarizability function for an electron gas at finite temperature, in connection with the existence of Friedel oscillations in the potential created by an impurity. In contrast with the zero temperature case, where the polarizability is an analytical function, except for the two branch cuts which are responsible for Friedel oscillations, at finite temperature the corresponding function is non analytical, in spite of becoming continuous everywhere on the complex plane. This effect produces, as a result, the survival of the oscillatory behavior of the potential. We calculate the potential at large distances, and relate the calculation to the non-analytical properties of the polarizability.

  7. Polarizability tensor invariants of H2, HD, and D2

    Science.gov (United States)

    Raj, Ankit; Hamaguchi, Hiro-o.; Witek, Henryk A.

    2018-03-01

    We report an exhaustive compilation of wavelength-dependent matrix elements over the mean polarizability (α ¯ ) and polarizability anisotropy (γ) operators for the rovibrational states of the H2, HD, and D2 molecules together with an accompanying computer program for their evaluation. The matrix elements can be readily evaluated using the provided codes for rovibrational states with J = 0-15 and v = 0-4 and for any laser wavelengths in the interval 182.25-1320.6 nm corresponding to popular, commercially available lasers. The presented results substantially extend the scope of the data available in the literature, both in respect of the rovibrational transitions analyzed and the range of covered laser frequencies. The presented detailed tabulation of accurate polarizability tensor invariants is essential for successful realization of our main long-term goal: developing a universal standard for determining absolute Raman cross sections and absolute Raman intensities in experimental Rayleigh and Raman scattering studies of molecules.

  8. The possibility for a pion polarizability measurement at COMPASS

    CERN Document Server

    Guskov, A

    2010-01-01

    The pion electromagnetic structure can be probed in $\\pi^{−}+(A,Z)\\rightarrow\\pi^{-}+(A,Z) + \\gamma$ Compton scattering in inverse kinematics (Primakoff reaction) and described by the electric $(\\alpha_{\\pi})$ and the magnetic $(\\beta_{\\pi})$ polarizabilities that depend on the rigidity of pion’s internal structure as a composite particle. Values for pion polarizabilities can be extracted from the comparison of the differential cross section for scattering of point-like pions with the measured cross section. The opportunity to measure pion polarizability via the Primakoff reaction at the COMPASS experiment was studied with a $\\pi^{−}$ beam of 190 GeV. The obtained results are used for preparation of the new measurement.

  9. Polarizability of Fluid Droplets and the Kerr Effect on Microemulsions

    CERN Document Server

    Lisy, V

    2001-01-01

    Spheroidal fluid droplets immersed in another fluid and thermally fluctuating in the shape are considered. The polarizability of the droplet is evaluated up to the second order in the fluctuation amplitudes. The correlation functions of the polarizability tensor components are found and used to describe the polarized and depolarized scattering of light, and the Kerr effect on microemulsions. By comparison of the theoretical results with the Kerr constant measurements from the literature, we estimate the bending rigidity of the surfactant monolayer that separates the oil and water phases in droplet microemulsions.

  10. Open-ended response theory with polarizable embedding

    DEFF Research Database (Denmark)

    Steindal, Arnfinn Hykkerud; Beerepoot, Maarten T P; Ringholm, Magnus

    2016-01-01

    We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state......-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins. In addition, environmental effects on multiphoton absorption (MPA...

  11. Compton scattering, meson exchange, and the polarizabilities of bound nucleons

    International Nuclear Information System (INIS)

    Feldman, G.; Mellendorf, K.E.; Eisenstein, R.A.; Federspiel, F.J.; Garino, G.; Igarashi, R.; Kolb, N.R.; Lucas, M.A.; MacGibbon, B.E.; Mize, W.K.; Nathan, A.M.; Pywell, R.E.; Wells, D.P.

    1996-01-01

    Elastic photon scattering cross sections on 16 O have been measured in the energy range 27 endash 108 MeV. These data are inconsistent with a conventional interpretation in which the electric and magnetic polarizabilities of the bound nucleon are unchanged from the free values and the meson-exchange seagull amplitude is taken in the zero-energy limit. Agreement with the data can be achieved by invoking either strongly modified polarizabilities or a substantial energy dependence to the meson-exchange seagull amplitude. It is argued that these seemingly different explanations are experimentally indistinguishable and probably physically equivalent. copyright 1996 The American Physical Society

  12. Blackbody-radiation correction to the polarizability of helium

    International Nuclear Information System (INIS)

    Puchalski, M.; Jentschura, U. D.; Mohr, P. J.

    2011-01-01

    The correction to the polarizability of helium due to blackbody radiation is calculated near room temperature. A precise theoretical determination of the blackbody radiation correction to the polarizability of helium is essential for dielectric gas thermometry and for the determination of the Boltzmann constant. We find that the correction, for not too high temperature, is roughly proportional to a modified hyperpolarizability (two-color hyperpolarizability), which is different from the ordinary hyperpolarizability of helium. Our explicit calculations provide a definite numerical result for the effect and indicate that the effect of blackbody radiation can be excluded as a limiting factor for dielectric gas thermometry using helium or argon.

  13. One-Photon Absorption Properties from a Hybrid Polarizable Density Embedding/Complex Polarization Propagator Approach for Polarizable Solutions

    DEFF Research Database (Denmark)

    Hršak, Dalibor; Nørby, Morten Steen; Coriani, Sonia

    2018-01-01

    We present a formulation of the polarizable density embedding (PDE) method in combination with the complex polarization propagator (CPP) method for the calculation of absorption spectra of molecules in solutions. The method is particularly useful for the calculation of near-edge X-ray absorption...... fine structure (NEXAFS) spectra. We compare the performance of PDE-CPP with the previously formulated polarizable embedding (PE)-CPP model for the calculation of the NEXAFS spectra of adenine, formamide, glycine, and adenosine triphosphate (ATP) in water at the carbon and nitrogen K-edges, as well...

  14. Partial Molar Volume of Methanol in Water: Effect of Polarizability

    Czech Academy of Sciences Publication Activity Database

    Moučka, F.; Nezbeda, Ivo

    2009-01-01

    Roč. 74, č. 4 (2009), s. 559-563 ISSN 0010-0765 R&D Projects: GA AV ČR IAA400720802 Institutional research plan: CEZ:AV0Z40720504 Keywords : water–methanol mixtures * partial molar volume * polarizability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.856, year: 2009

  15. Theory and applications of atomic and ionic polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Mitroy, J [School of Engineering, Charles Darwin University, Darwin NT 0909 (Australia); Safronova, M S [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Clark, Charles W, E-mail: jxm107@rsphysse.anu.edu.a, E-mail: msafrono@udel.ed, E-mail: charles.clark@nist.go [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, Gaithersburg, MD 20899-8410 (United States)

    2010-10-28

    Atomic polarization phenomena impinge upon a number of areas and processes in physics. The dielectric constant and refractive index of any gas are examples of macroscopic properties that are largely determined by the dipole polarizability. When it comes to microscopic phenomena, the existence of alkaline-earth anions and the recently discovered ability of positrons to bind to many atoms are predominantly due to the polarization interaction. An imperfect knowledge of atomic polarizabilities is presently looming as the largest source of uncertainty in the new generation of optical frequency standards. Accurate polarizabilities for the group I and II atoms and ions of the periodic table have recently become available by a variety of techniques. These include refined many-body perturbation theory and coupled-cluster calculations sometimes combined with precise experimental data for selected transitions, microwave spectroscopy of Rydberg atoms and ions, refractive index measurements in microwave cavities, ab initio calculations of atomic structures using explicitly correlated wavefunctions, interferometry with atom beams and velocity changes of laser cooled atoms induced by an electric field. This review examines existing theoretical methods of determining atomic and ionic polarizabilities, and discusses their relevance to various applications with particular emphasis on cold-atom physics and the metrology of atomic frequency standards. (topical review)

  16. Hyperon polarizabilities in the bound-state soliton model

    International Nuclear Information System (INIS)

    Gobbi, C.; Scoccola, N.N.

    1996-01-01

    A detailed calculation of electric and magnetic static polarizabilities of octet hyperons is presented in the framework of the bound-state soliton model. Both seagull and dispersive contributions are considered, and the results are compared with different model predictions. (orig.)

  17. Molecular polarizabilities and susceptibilities from Frost-model wavefunctions

    International Nuclear Information System (INIS)

    Amos, A.T.; Yoffe, J.A.

    1975-01-01

    Average polarizabilities and susceptibilities of a number of molecules are computed from Frost-model wavefunctions using a form of symmetry-adapted double perturbation theory. The anisotropy of α and chi is found for a few molecules using the elliptical Gaussian form of the Frost model. The results obtained are in reasonable agreement with experiment and other calculated values

  18. Theory and applications of atomic and ionic polarizabilities

    International Nuclear Information System (INIS)

    Mitroy, J; Safronova, M S; Clark, Charles W

    2010-01-01

    Atomic polarization phenomena impinge upon a number of areas and processes in physics. The dielectric constant and refractive index of any gas are examples of macroscopic properties that are largely determined by the dipole polarizability. When it comes to microscopic phenomena, the existence of alkaline-earth anions and the recently discovered ability of positrons to bind to many atoms are predominantly due to the polarization interaction. An imperfect knowledge of atomic polarizabilities is presently looming as the largest source of uncertainty in the new generation of optical frequency standards. Accurate polarizabilities for the group I and II atoms and ions of the periodic table have recently become available by a variety of techniques. These include refined many-body perturbation theory and coupled-cluster calculations sometimes combined with precise experimental data for selected transitions, microwave spectroscopy of Rydberg atoms and ions, refractive index measurements in microwave cavities, ab initio calculations of atomic structures using explicitly correlated wavefunctions, interferometry with atom beams and velocity changes of laser cooled atoms induced by an electric field. This review examines existing theoretical methods of determining atomic and ionic polarizabilities, and discusses their relevance to various applications with particular emphasis on cold-atom physics and the metrology of atomic frequency standards. (topical review)

  19. Polarizability and Aqueous Solvation of the Sulfate Dianion

    Czech Academy of Sciences Publication Activity Database

    Jungwirth, Pavel; Curtis, J. E.; Tobias, D. J.

    2003-01-01

    Roč. 367, - (2003), s. 704-710 ISSN 0009-2614 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : polarizability * aqueous solvation * dianion Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.438, year: 2003

  20. Electro-optical parameters of bond polarizability model for aluminosilicates.

    Science.gov (United States)

    Smirnov, Konstantin S; Bougeard, Daniel; Tandon, Poonam

    2006-04-06

    Electro-optical parameters (EOPs) of bond polarizability model (BPM) for aluminosilicate structures were derived from quantum-chemical DFT calculations of molecular models. The tensor of molecular polarizability and the derivatives of the tensor with respect to the bond length are well reproduced with the BPM, and the EOPs obtained are in a fair agreement with available experimental data. The parameters derived were found to be transferable to larger molecules. This finding suggests that the procedure used can be applied to systems with partially ionic chemical bonds. The transferability of the parameters to periodic systems was tested in molecular dynamics simulation of the polarized Raman spectra of alpha-quartz. It appeared that the molecular Si-O bond EOPs failed to reproduce the intensity of peaks in the spectra. This limitation is due to large values of the longitudinal components of the bond polarizability and its derivative found in the molecular calculations as compared to those obtained from periodic DFT calculations of crystalline silica polymorphs by Umari et al. (Phys. Rev. B 2001, 63, 094305). It is supposed that the electric field of the solid is responsible for the difference of the parameters. Nevertheless, the EOPs obtained can be used as an initial set of parameters for calculations of polarizability related characteristics of relevant systems in the framework of BPM.

  1. Communication: A simplified coupled-cluster Lagrangian for polarizable embedding.

    Science.gov (United States)

    Krause, Katharina; Klopper, Wim

    2016-01-28

    A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.

  2. Communication: A simplified coupled-cluster Lagrangian for polarizable embedding

    International Nuclear Information System (INIS)

    Krause, Katharina; Klopper, Wim

    2016-01-01

    A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian

  3. Substituent effects of the alkyl groups: Polarity vs. polarizability

    Czech Academy of Sciences Publication Activity Database

    Exner, Otto; Böhm, S.

    -, č. 17 (2007), s. 2870-2876 ISSN 1434-193X Institutional research plan: CEZ:AV0Z40550506 Keywords : density functional calculations * hyperconjugation * inductive effect * polarizability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.914, year: 2007

  4. Detection and Identification of Free-living Amoeba from Environmental Water in Taiwan by PCR Method

    Science.gov (United States)

    Tsai, H. F.; Hsu, B. M.; Huang, K. H.; She, C. Y.; Kao, P. M.; Shen, S. M.; Tseng, S. F.; Chen, J. S.

    2012-04-01

    Acanthamoeba, Naegleria, Balamuthia and Hartmannella all belong to free-living amoebae that are present ubiquitously in the environment including water, soil, and air. Free-living amoebae are parasites which can infect humans and can lead to serious illness and even death. The aim of this study is to investigate the presence of free-living amoebae in aquatic environment in Taiwan, and to compare the differences between Acanthamoeba and Naegleria in diverse cultivation methods and conditions. In this study, we used molecular method by PCR amplification with specific primers to analyze the occurrence of free-living amoebae. We collected 176 samples from environmental water including drinking water treatment plants, stream water, and hot spring recreational areas in Taiwan. Based on the results of PCR, 43 water samples (24.4%) were detected positive for free-living amoebae. The most common Acanthamoeba genotype isolated from samples including T2, T4, T5, T12, and T15. N. australiensis and N. lovaniensis were also identified by molecular biology techniques. Furthermore, we found that both Acanthamoeba and Naegleria can be cultured by PYG in 30° C, but not all free-living amoebae can be isolated and enriched by using storage-cultivation method. Because of the widespread presence of Acanthamoeba and Naegleria in aquatic environments, the water quality and safety of aquatic environments should be more conscious in Taiwan and worldwide. Keywords: free-living amoebae; Acanthamoeba; Naegleria; Balamuthia; Hartmannella; PCR

  5. Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

    2017-09-01

    We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

  6. Contrasting species-environment relationships in communities of testate amoebae, bryophytes and vascular plants along the fen-bog gradient.

    Science.gov (United States)

    Lamentowicz, Mariusz; Lamentowicz, Lukasz; van der Knaap, Willem O; Gabka, Maciej; Mitchell, Edward A D

    2010-04-01

    We studied the vegetation, testate amoebae and abiotic variables (depth of the water table, pH, electrical conductivity, Ca and Mg concentrations of water extracted from mosses) along the bog to extremely rich fen gradient in sub-alpine peatlands of the Upper Engadine (Swiss Alps). Testate amoeba diversity was correlated to that of mosses but not of vascular plants. Diversity peaked in rich fen for testate amoebae and in extremely rich fen for mosses, while for testate amoebae and mosses it was lowest in bog but for vascular plants in extremely rich fen. Multiple factor and redundancy analyses (RDA) revealed a stronger correlation of testate amoebae than of vegetation to water table and hydrochemical variables and relatively strong correlation between testate amoeba and moss community data. In RDA, hydrochemical variables explained a higher proportion of the testate amoeba and moss data than water table depth. Abiotic variables explained a higher percentage of the species data for testate amoebae (30.3% or 19.5% for binary data) than for mosses (13.4%) and vascular plants (10%). These results show that (1) vascular plant, moss and testate amoeba communities respond differently to ecological gradients in peatlands and (2) testate amoebae are more strongly related than vascular plants to the abiotic factors at the mire surface. These differences are related to vertical trophic gradients and associated niche differentiation.

  7. Amoebae and other protozoa in material samples from moisture-damaged buildings

    International Nuclear Information System (INIS)

    Yli-Pirilae, T.; Kusnetsov, Jaana; Haatainen, Susanna; Haenninen, Marja; Jalava, Pasi; Reiman, Marjut; Seuri, Markku; Hirvonen, Maija-Riitta; Nevalainen, Aino

    2004-01-01

    Mold growth in buildings has been shown to be associated with adverse health effects. The fungal and bacterial growth on moistened building materials has been studied, but little attention has been paid to the other organisms spawning in the damaged materials. We examined moist building materials for protozoa, concentrating on amoebae. Material samples (n=124) from moisture-damaged buildings were analyzed for amoebae, fungi, and bacteria. Amoebae were detected in 22% of the samples, and they were found to favor cooccurrence with bacteria and the fungi Acremonium spp., Aspergillus versicolor, Chaetomium spp., and Trichoderma spp. In addition, 11 seriously damaged samples were screened for other protozoa. Ciliates and flagellates were found in almost every sample analyzed. Amoebae are known to host pathogenic bacteria, such as chlamydiae, legionellae, and mycobacteria and they may have a role in the complex of exposure that contributes to the health effects associated with moisture damage in buildings

  8. Occurrence of Infected Free-Living Amoebae in Cooling Towers of Southern Brazil.

    Science.gov (United States)

    Soares, Scheila S; Souza, Thamires K; Berté, Francisco K; Cantarelli, Vlademir V; Rott, Marilise B

    2017-12-01

    This study determined the occurrence of potentially pathogenic free-living amoebae (FLA) and bacteria associated with amoebae in air-conditioning cooling towers in southern Brazil. Water samples were collected from 36 cooling systems from air-conditioning in the state of Rio Grande do Sul, Brazil. The organisms were identified using polymerase chain reaction (PCR) and sequencing automated. The results showed that these aquatic environments, with variable temperature, are potential "hot spots" for emerging human pathogens like free-living amoebae and bacteria associated. In total, 92% of the cooling-tower samples analyzed were positive for FLA, and Acanthamoeba was the dominant genus by culture and PCR. Amoebal isolates revealed intracellular bacteria in 39.3% of them and all were confirmed as members of the genus Pseudomonas. The results obtained show the important role of cooling towers as a source of amoebae-associated pathogens.

  9. Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes.

    Science.gov (United States)

    Colson, Philippe; La Scola, Bernard; Raoult, Didier

    2017-09-29

    Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.

  10. A polarizable embedding DFT study of one-photon absorption in fluorescent proteins

    DEFF Research Database (Denmark)

    Beerepoot, Maarten; Steindal, Arnfinn H.; Kongsted, Jacob

    2013-01-01

    mutants (BFP, eGFP, YFP and eCFP). The observed trends in excitation energies among the FPs are reproduced by our approach when performing calculations directly on the crystal structures or when using structures extracted from a molecular dynamics simulations. However, in the former case, QM/MM geometry......A theoretical study of the one-photon absorption of five fluorescent proteins (FPs) is presented. The absorption properties are calculated using a polarizable embedding approach combined with density functional theory (PE-DFT) on the wild-type green fluorescent protein (wtGFP) and several of its...... optimization of the chromophores within a frozen protein environment is needed in order to reproduce the experimental trends. Explicit account of polarization in the force field is not needed to yield the correct trend between the different FPs, but is necessary for reproducing the experimentally observed red...

  11. Evaluating the use of testate amoebae for palaeohydrological reconstruction in permafrost peatlands

    OpenAIRE

    Swindles, Graeme T.; Amesbury, Matthew J.; Turner, T. Edward; Carrivick, Jonathan L.; Woulds, Clare; Raby, Cassandra; Mullan, Donal; Roland, Thomas P.; Galloway, Jennifer M.; Parry, Lauren; Kokfelt, Ulla; Garneau, Michelle; Charman, Dan J.; Holden, Joseph

    2015-01-01

    The melting of high-latitude permafrost peatlands is a major concern due to a potential positive feedback on global climate change. We examine the ecology of testate amoebae in permafrost peatlands, based on sites in Sweden (~ 200 km north of the Arctic Circle). Multivariate statistical analysis confirms that water-table depth and moisture content are the dominant controls on the distribution of testate amoebae, corroborating the results from studies in mid-latitude peatlands. We present a ne...

  12. Measurement of the charged pion polarizability at COMPASS

    International Nuclear Information System (INIS)

    Nagel, Thiemo Christian Ingo

    2012-01-01

    The reaction π - +Z→π - +γ+Z in which a photon is produced by a beam pion scattering off a quasi-real photon of the Coulomb field of the target nucleus is identified experimentally by the tiny magnitude of the momentum transfer to the nucleus. This process gives access to the charged pion polarizabilities α π and β π whose experimental determination constitutes an important test of Chiral Perturbation Theory. In this work, the pion polarizability is obtained as α π =(1.9±0.7 stat. ±0.8 syst. ) x 10 -4 fm 3 from data taken with 190 GeV/c hadron beam provided by SPS to the COMPASS experiment at CERN in November 2009 and under the assumption of α π +β π =0.

  13. Dynamic polarizability of a complex atom in strong laser fields

    International Nuclear Information System (INIS)

    Rapoport, L.P.; Klinskikh, A.F.; Mordvinov, V.V.

    1997-01-01

    An asymptotic expansion of the dynamic polarizability of a complex atom in a strong circularly polarized light field is found for the case of high frequencies. The self-consistent approximation of the Hartree-Fock type for the ''atom+field'' system is developed, within the framework of which a numerical calculation of the dynamic polarizability of Ne, Kr, and Ar atoms in a strong radiation field is performed. The strong field effect is shown to manifest itself not only in a change of the energy spectrum and the character of behavior of the wave functions of atomic electrons, but also in a modification of the one-electron self-consistent potential for the atom in the field

  14. Measurement of the charged pion polarizability at COMPASS

    Energy Technology Data Exchange (ETDEWEB)

    Nagel, Thiemo Christian Ingo

    2012-09-26

    The reaction {pi}{sup -}+Z{yields}{pi}{sup -}+{gamma}+Z in which a photon is produced by a beam pion scattering off a quasi-real photon of the Coulomb field of the target nucleus is identified experimentally by the tiny magnitude of the momentum transfer to the nucleus. This process gives access to the charged pion polarizabilities {alpha}{sub {pi}} and {beta}{sub {pi}} whose experimental determination constitutes an important test of Chiral Perturbation Theory. In this work, the pion polarizability is obtained as {alpha}{sub {pi}}=(1.9{+-}0.7{sub stat.}{+-}0.8{sub syst.}) x 10{sup -4} fm{sup 3} from data taken with 190 GeV/c hadron beam provided by SPS to the COMPASS experiment at CERN in November 2009 and under the assumption of {alpha}{sub {pi}}+{beta}{sub {pi}}=0.

  15. Myosin-II sets the optimal response time scale of chemotactic amoeba

    Science.gov (United States)

    Hsu, Hsin-Fang; Westendorf, Christian; Tarantola, Marco; Bodenschatz, Eberhard; Beta, Carsten

    2014-03-01

    The response dynamics of the actin cytoskeleton to external chemical stimuli plays a fundamental role in numerous cellular functions. One of the key players that governs the dynamics of the actin network is the motor protein myosin-II. Here we investigate the role of myosin-II in the response of the actin system to external stimuli. We used a microfluidic device in combination with a photoactivatable chemoattractant to apply stimuli to individual cells with high temporal resolution. We directly compare the actin dynamics in Dictyostelium discodelium wild type (WT) cells to a knockout mutant that is deficient in myosin-II (MNL). Similar to the WT a small population of MNL cells showed self-sustained oscillations even in absence of external stimuli. The actin response of MNL cells to a short pulse of chemoattractant resembles WT during the first 15 sec but is significantly delayed afterward. The amplitude of the dominant peak in the power spectrum from the response time series of MNL cells to periodic stimuli with varying period showed a clear resonance peak at a forcing period of 36 sec, which is significantly delayed as compared to the resonance at 20 sec found for the WT. This shift indicates an important role of myosin-II in setting the response time scale of motile amoeba. Institute of Physics und Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.

  16. Amoeba-related health risk in drinking water systems: could monitoring of amoebae be a complementary approach to current quality control strategies?

    Science.gov (United States)

    Codony, Francesc; Pérez, Leonardo Martín; Adrados, Bárbara; Agustí, Gemma; Fittipaldi, Mariana; Morató, Jordi

    2012-01-01

    Culture-based methods for fecal indicator microorganisms are the standard protocol to assess potential health risk from drinking water systems. However, these traditional fecal indicators are inappropriate surrogates for disinfection-resistant fecal pathogens and the indigenous pathogens that grow in drinking water systems. There is now a range of molecular-based methods, such as quantitative PCR, which allow detection of a variety of pathogens and alternative indicators. Hence, in addition to targeting total Escherichia coli (i.e., dead and alive) for the detection of fecal pollution, various amoebae may be suitable to indicate the potential presence of pathogenic amoeba-resisting microorganisms, such as Legionellae. Therefore, monitoring amoeba levels by quantitative PCR could be a useful tool for directly and indirectly evaluating health risk and could also be a complementary approach to current microbial quality control strategies for drinking water systems.

  17. Detecting Stealth Dark Matter Directly through Electromagnetic Polarizability.

    Science.gov (United States)

    Appelquist, T; Berkowitz, E; Brower, R C; Buchoff, M I; Fleming, G T; Jin, X-Y; Kiskis, J; Kribs, G D; Neil, E T; Osborn, J C; Rebbi, C; Rinaldi, E; Schaich, D; Schroeder, C; Syritsyn, S; Vranas, P; Weinberg, E; Witzel, O

    2015-10-23

    We calculate the spin-independent scattering cross section for direct detection that results from the electromagnetic polarizability of a composite scalar "stealth baryon" dark matter candidate, arising from a dark SU(4) confining gauge theory-"stealth dark matter." In the nonrelativistic limit, electromagnetic polarizability proceeds through a dimension-7 interaction leading to a very small scattering cross section for dark matter with weak-scale masses. This represents a lower bound on the scattering cross section for composite dark matter theories with electromagnetically charged constituents. We carry out lattice calculations of the polarizability for the lightest "baryon" states in SU(3) and SU(4) gauge theories using the background field method on quenched configurations. We find the polarizabilities of SU(3) and SU(4) to be comparable (within about 50%) normalized to the stealth baryon mass, which is suggestive for extensions to larger SU(N) groups. The resulting scattering cross sections with a xenon target are shown to be potentially detectable in the dark matter mass range of about 200-700 GeV, where the lower bound is from the existing LUX constraint while the upper bound is the coherent neutrino background. Significant uncertainties in the cross section remain due to the more complicated interaction of the polarizablity operator with nuclear structure; however, the steep dependence on the dark matter mass, 1/m(B)(6), suggests the observable dark matter mass range is not appreciably modified. We briefly highlight collider searches for the mesons in the theory as well as the indirect astrophysical effects that may also provide excellent probes of stealth dark matter.

  18. Electric field enhanced hydrogen storage on polarizable materials substrates

    Science.gov (United States)

    Zhou, J.; Wang, Q.; Sun, Q.; Jena, P.; Chen, X. S.

    2010-01-01

    Using density functional theory, we show that an applied electric field can substantially improve the hydrogen storage properties of polarizable substrates. This new concept is demonstrated by adsorbing a layer of hydrogen molecules on a number of nanomaterials. When one layer of H2 molecules is adsorbed on a BN sheet, the binding energy per H2 molecule increases from 0.03 eV/H2 in the field-free case to 0.14 eV/H2 in the presence of an electric field of 0.045 a.u. The corresponding gravimetric density of 7.5 wt% is consistent with the 6 wt% system target set by Department of Energy for 2010. The strength of the electric field can be reduced if the substrate is more polarizable. For example, a hydrogen adsorption energy of 0.14 eV/H2 can be achieved by applying an electric field of 0.03 a.u. on an AlN substrate, 0.006 a.u. on a silsesquioxane molecule, and 0.007 a.u. on a silsesquioxane sheet. Thus, application of an electric field to a polarizable substrate provides a novel way to store hydrogen; once the applied electric field is removed, the stored H2 molecules can be easily released, thus making storage reversible with fast kinetics. In addition, we show that materials with rich low-coordinated nonmetal anions are highly polarizable and can serve as a guide in the design of new hydrogen storage materials. PMID:20133647

  19. Experimental Constraints on Polarizability Corrections to Hydrogen Hyperfine Structure

    International Nuclear Information System (INIS)

    Nazaryan, Vahagn; Carlson, Carl E.; Griffioen, Keith A.

    2006-01-01

    We present a state-of-the-art evaluation of the polarizability corrections--the inelastic nucleon corrections--to the hydrogen ground-state hyperfine splitting using analytic fits to the most recent data. We find a value Δ pol =1.3±0.3 ppm. This is 1-2 ppm smaller than the value of Δ pol deduced using hyperfine splitting data and elastic nucleon corrections obtained from modern form factor fits

  20. Diversity and community ecology of forest epiphyte testate amoebae from European Russia.

    Science.gov (United States)

    Payne, Richard J; Belyakova, Olga; Mazei, Yuri

    2015-10-01

    Testate amoebae are an abundant group of microorganisms which make a significant contribution to the diversity of protist life. Most of the world's potential habitats for testate amoebae have been barely studied and when such places are investigated they frequently reveal novel communities and species. Here we consider the testate amoeba communities associated with boreal forest epiphytes (mosses and lichens); an environment which we argue has been under-researched. We present a dataset of 165 samples from four regions of western Russia and analyse these data in relation to micro-habitat position and selected environmental data. The testate amoebae of epiphytes are abundant but dominated by ubiquitous species. We show that there are trends toward a lower species richness and test concentration with greater elevation on the trunk and in lichens compared to mosses. There are considerable differences in community composition between sampling regions. Of all measured environmental variables only moisture content showed a significant relationship with testate amoeba community structure. Our data highlight how little is known about testate amoeba communities of this habitat and call for greater research efforts, particularly in less-studied regions and biomes. Copyright © 2015 Elsevier GmbH. All rights reserved.

  1. Behavioural differentiation induced by environmental variation when crossing a toxic zone in an amoeba

    International Nuclear Information System (INIS)

    Kunita, Itsuki; Kuroda, Shigeru; Nakagaki, Toshiyuki; Ueda, Kei-Ichi; Akita, Dai

    2017-01-01

    Organisms choose from among various courses of action in response to a wide variety of environmental conditions and the mechanism by which various behaviours are induced is an open question. Interesting behaviour was recently reported: that a unicellular organism of slime mold Physarum polycephalum known as an amoeba had multiple responses (crossing, returning, etc) when the amoeba encounters a zone with toxic levels of quinine, even under carefully controlled conditions. We here examined this elegant example in more detail to obtain insight into behavioural differentiation. We found that the statistical distribution of passage times across a quinine zone switch from unimodal to bimodal (with peaks corresponding to fast crossing and no crossing) when a periodic light stimulation to modulate a biorhythm in amoeba is applied homogeneously across the space, even under the same level of chemical stimuli. Based on a mathematical model for cell movement in amoeba, we successfully reproduced the stimulation-induced differentiation, which was observed experimentally. These dynamics may be explained by a saddle structure around a canard solution. Our results imply that the differentiation of behavioural types in amoeba is modified step-by-step via the compounding of stimulation inputs. The complex behaviour like the differentiation in amoeba may provide a basis for understanding the mechanism of behaviour selection in higher animals from an ethological perspective. (paper)

  2. Behavioural differentiation induced by environmental variation when crossing a toxic zone in an amoeba

    Science.gov (United States)

    Kunita, Itsuki; Ueda, Kei-Ichi; Akita, Dai; Kuroda, Shigeru; Nakagaki, Toshiyuki

    2017-09-01

    Organisms choose from among various courses of action in response to a wide variety of environmental conditions and the mechanism by which various behaviours are induced is an open question. Interesting behaviour was recently reported: that a unicellular organism of slime mold Physarum polycephalum known as an amoeba had multiple responses (crossing, returning, etc) when the amoeba encounters a zone with toxic levels of quinine, even under carefully controlled conditions. We here examined this elegant example in more detail to obtain insight into behavioural differentiation. We found that the statistical distribution of passage times across a quinine zone switch from unimodal to bimodal (with peaks corresponding to fast crossing and no crossing) when a periodic light stimulation to modulate a biorhythm in amoeba is applied homogeneously across the space, even under the same level of chemical stimuli. Based on a mathematical model for cell movement in amoeba, we successfully reproduced the stimulation-induced differentiation, which was observed experimentally. These dynamics may be explained by a saddle structure around a canard solution. Our results imply that the differentiation of behavioural types in amoeba is modified step-by-step via the compounding of stimulation inputs. The complex behaviour like the differentiation in amoeba may provide a basis for understanding the mechanism of behaviour selection in higher animals from an ethological perspective.

  3. A study of nucleo-cytoplasmic large DNA viruses: detection and characterization of viruses in environmental amoeba

    OpenAIRE

    Fugas, Mariana Costa

    2012-01-01

    Tese de mestrado. Biologia (Biologia Molecular e Genética). Universidade de Lisboa, Faculdade de Ciências, 2012 Amoeba associated microorganisms (ARMs) are bacteria or viruses that share a symbiotic relationship with amoebas. Many ARMs are associated with human diseases and it has been reported the acquisition of resistance inside their host. These facts highlight the importance of finding and characterizing ARMs in a public health’s perspective. In the present work, amoebas from environme...

  4. Dynamic dipole polarizabilities of the Li atom and the Be+ ion

    International Nuclear Information System (INIS)

    Tang Liyan; Yan Zongchao; Shi Tingyun; Mitroy, J.

    2010-01-01

    The dynamic dipole polarizabilities for Li atoms and Be + ions in the 2 2 S and 2 2 P states are calculated using the variational method with a Hylleraas basis. The present polarizabilities represent the definitive values in the nonrelativistic limit. Corrections due to relativistic effects are also estimated. Analytic representations of the polarizabilities for frequency ranges encompassing the n=3 excitations are presented. The recommended polarizabilities for 7 Li and 9 Be + are 164.11±0.03 a 0 3 and 24.489±0.004 a 0 3 , respectively.

  5. Physical Principles of Development of the State Standard of Biological Cell Polarizability

    Science.gov (United States)

    Shuvalov, G. V.; Generalov, K. V.; Generalov, V. M.; Kruchinina, M. V.; Koptev, E. S.; Minin, O. V.; Minin, I. V.

    2018-03-01

    A new state standard of biological cell polarizability based on micron-size latex particles has been developed. As a standard material, it is suggested to use polystyrene. Values of the polarizability calculated for erythrocytes and values of the polarizability of micron-size spherical latex particles measured with measuring-computing complexes agree within the limits of satisfactory relative error. The Standard allows one the unit of polarizability measurements [m3] to be assigned to cells and erythrocytes for the needs of medicine.

  6. Chiral model predictions for electromagnetic polarizabilities of the nucleon: A 'consumer report'

    International Nuclear Information System (INIS)

    Broniowski, W.

    1992-01-01

    This contribution has two parts: (1) The author critically discusses predictions for the electromagnetic polarizabilities of the nucleon obtained in two different approaches: (a) hedgehog models (HM), such as Skyrmions, chiral quark models, hybrid bags, NJL etc., and (b) chiral perturbation theory (χPT). (2) The author shows new results obtained in HM: N c -counting of polarizabilities, splitting of the neutron and proton polarizabilities (he argues that α n > α p in models with pionic clouds), relevance of dispersive terms in the magnetic polarizability β, important role of the Δ resonance in pionic loops, and the effects of non-minimal substitution terms in the effective lagrangian. 3 refs

  7. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

    Energy Technology Data Exchange (ETDEWEB)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2016-03-21

    The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

  8. Calculations of polarizabilities and hyperpolarizabilities for the Be+ ion

    International Nuclear Information System (INIS)

    Tang Liyan; Zhang Junyi; Mitroy, J.; Yan Zongchao; Shi Tingyun; Babb, James F.

    2009-01-01

    The polarizabilities and hyperpolarizabilities of the Be + ion in the 2 2 S state and the 2 2 P state are determined. Calculations are performed using two independent methods: (i) variationally determined wave functions using Hylleraas basis set expansions and (ii) single electron calculations utilizing a frozen-core Hamiltonian. The first few parameters in the long-range interaction potential between a Be + ion and a H, He, or Li atom, and the leading parameters of the effective potential for the high-L Rydberg states of beryllium were also computed. All the values reported are the results of calculations close to convergence. Comparisons are made with published results where available.

  9. Detection and identification of free-living amoeba from aquatic environment in Taiwan

    Science.gov (United States)

    Jiun Tzeng, Kai; Che Tung, Min; Hsu, Bing Mu; Tsai, Hsiu Feng; Huang, Po Hsiang; Hao Huang, Kuan; Kao, Po Min; Shen, Shu Min; Chen, Jung Sheng

    2013-04-01

    Free-living amoebae including Acanthamoeba, Naegleria, Balamuthia and Hartmannella are widely distributed in water, soil, and air. They can infect humans and can lead to serious illness even death. The aim of this study is to investigate the presence of free-living amoebae from aquatic environment in Taiwan, and to compare the differences between Acanthamoeba and Naegleria in different cultivation methods and conditions. In this study, we used molecular method with specific primers by Polymerase Chain Reaction (PCR) to amplify and to analyze the occurrence of free-living amoebae in aquatic environment. We collected 92 samples from environmental water in Taiwan. The results show that 33 water samples (35.9%) and 11 water samples (12.0%) were detected positive for Acanthamoeba and Naegleria, respectively. Furthermore, both Acanthamoeba and Naegleria can be cultured by PYG in 30° C, but not all free-living amoebae can be enriched and isolated by using storage-cultivation method. Due to the presence of Acanthamoeba and Naegleria in aquatic environment, the water quality monitoring should be more conscious. Keywords: free-living amoebae; Acanthamoeba; Naegleria; Balamuthia; Hartmannella; PCR

  10. Origin and diversity of testate amoebae shell composition: Example of Bullinularia indica living in Sphagnum capillifolium.

    Science.gov (United States)

    Delaine, Maxence; Bernard, Nadine; Gilbert, Daniel; Recourt, Philippe; Armynot du Châtelet, Eric

    2017-06-01

    Testate amoebae are free-living shelled protists that build a wide range of shells with various sizes, shapes, and compositions. Recent studies showed that xenosomic testate amoebae shells could be indicators of atmospheric particulate matter (PM) deposition. However, no study has yet been conducted to assess the intra-specific mineral, organic, and biologic grain diversity of a single xenosomic species in a natural undisturbed environment. This study aims at providing new information about grain selection to develop the potential use of xenosomic testate amoebae shells as bioindicators of the multiple-origin mineral/organic diversity of their proximal environment. To fulfil these objectives, we analysed the shell content of 38 Bullinularia indica individuals, a single xenosomic testate amoeba species living in Sphagnum capillifolium, by scanning electron microscope (SEM) coupled with X-ray spectroscopy. The shells exhibited high diversities of mineral, organic, and biomineral grains, which confirms their capability to recycle xenosomes. Mineral grain diversity and size of B. indica matched those of the atmospheric natural mineral PM deposited in the peatbog. Calculation of grain size sorting revealed a discrete selection of grains agglutinated by B. indica. These results are a first step towards understanding the mechanisms of particle selection by xenosomic testate amoebae in natural conditions. Copyright © 2017 Elsevier GmbH. All rights reserved.

  11. Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria.

    Science.gov (United States)

    DiSalvo, Susanne; Haselkorn, Tamara S; Bashir, Usman; Jimenez, Daniela; Brock, Debra A; Queller, David C; Strassmann, Joan E

    2015-09-08

    Symbiotic associations can allow an organism to acquire novel traits by accessing the genetic repertoire of its partner. In the Dictyostelium discoideum farming symbiosis, certain amoebas (termed "farmers") stably associate with bacterial partners. Farmers can suffer a reproductive cost but also gain beneficial capabilities, such as carriage of bacterial food (proto-farming) and defense against competitors. Farming status previously has been attributed to amoeba genotype, but the role of bacterial partners in its induction has not been examined. Here, we explore the role of bacterial associates in the initiation, maintenance, and phenotypic effects of the farming symbiosis. We demonstrate that two clades of farmer-associated Burkholderia isolates colonize D. discoideum nonfarmers and infectiously endow them with farmer-like characteristics, indicating that Burkholderia symbionts are a major driver of the farming phenomenon. Under food-rich conditions, Burkholderia-colonized amoebas produce fewer spores than uncolonized counterparts, with the severity of this reduction being dependent on the Burkholderia colonizer. However, the induction of food carriage by Burkholderia colonization may be considered a conditionally adaptive trait because it can confer an advantage to the amoeba host when grown in food-limiting conditions. We observed Burkholderia inside and outside colonized D. discoideum spores after fruiting body formation; this observation, together with the ability of Burkholderia to colonize new amoebas, suggests a mixed mode of symbiont transmission. These results change our understanding of the D. discoideum farming symbiosis by establishing that the bacterial partner, Burkholderia, is an important causative agent of the farming phenomenon.

  12. Electric and magnetic polarizabilities of hadrons via elastic Compton scattering at KAON

    International Nuclear Information System (INIS)

    Moinester, M.A.; Blecher, M.

    1990-08-01

    The study of dynamic properties of hadrons presents a challenge. Among the most basic of these are the electric and magnetic polarizabilities describing the electromagnetic structure of hadrons. They characterize the induced transient dipole moments of hadrons in an external electromagnetic field. During gamma-hadron Compton scattering the lowest order scattering is determined by the charge and magnetic moment. The next order scattering is determined by the induced dipole moments. The dipole polarizabilities probe the rigidity of the internal structure of baryons and mesons, the dipole moments being induced by the rearrangement of the hadron constituents driven by the presence of the electric and magnetic fields of the photon during scattering. A sophisticated understanding of hadrons within the framework of QCD will be tested, in part, by the prediction of these quantities. For the light charged pion, chiral symmetry leads to a precise prediction for the polarizabilities. For the heavier charged kaon, chiral perturbation theory can be applied to predict the polarizabilities. For these cases, the experimental polarizabilities subject the underlying chiral symmetry and chiral perturbation techniques of QCD to new and serious tests. Here the physics of electromagnetic polarizabilities is first described, followed by a review of previous experimental and theoretical polarizability results for the proton, neutron, pion, and kaon. A brief description is then given of how polarizabilities for these hadrons can be studied at the proposed TRIUMF KAON facility. (36 refs., 4 figs.)

  13. Electric polarizability of pions in the semirelativistic quark model; Ehlektricheskaya polyarizuemost' pionov v polurelyativistskoj kvarkovoj modeli

    Energy Technology Data Exchange (ETDEWEB)

    Maksimenko, N V [Gomel& #x27; skij Gosudarstvennyj Univ. im. F.Skoriny, Gomel (Belarus); Kuchin, S M [Filial Bryanskogo Gosudarstvennogo Univ. im. akademika I.G.Petrovskogo, Novozybkov (Russian Federation)

    2012-07-01

    In the paper the calculation is performed of the generalized and static polarizability of charged pions, which are considered as a relativistic system of two point spinor quarks with the linear interaction potential. The question of the relationship between static electricity and generalized polarizabilities of pions in the framework of this approach is studied.

  14. Do the seagull terms really survive for the electric polarizability of the nucleon?

    International Nuclear Information System (INIS)

    Saito, S.

    1998-01-01

    The seagull terms for the electric polarizability of the nucleon are shown indeed to vanish, if one introduces fluctuations around the Skyrmion configuration, and the origin of the electric polarizability cannot after all be attributed to the seagull terms in the Skyrme model. (orig.)

  15. The electric double layer at high surface potentials: The influence of excess ion polarizability

    NARCIS (Netherlands)

    Hatlo, M. M.; van Roij, R.H.H.G.; Lue, L.

    2012-01-01

    By including the excess ion polarizability into the Poisson-Boltzmann theory, we show that the decrease in differential capacitance with voltage, observed for metal electrodes above a threshold potential, can be understood in terms of thickening of the double layer due to ion-induced polarizability

  16. Effective electric and magnetic polarizabilities of pointlike spin-1/2 particles

    OpenAIRE

    Silenko, A. J.

    2014-01-01

    Effective electric and magnetic polarizabilities of pointlike spin-1/2 particles possesing an anomalous magnetic moment are calculated with the transformation of an initial Hamiltonian to the Foldy-Wouthuysen representation. Polarizabilities of spin-1/2 and spin-1 particles are compared.

  17. Lithium photoionization cross-section and dynamic polarizability using square integrable basis sets and correlated wave functions

    International Nuclear Information System (INIS)

    Hollauer, E.; Nascimento, M.A.C.

    1985-01-01

    The photoionization cross-section and dynamic polarizability for lithium atom are calculated using a discrete basis set to represent both the bound and the continuum-states of the atom, to construct an approximation to the dynamic polarizability. From the imaginary part of the complex dynamic polarizability one extracts the photoionization cross-section and from its real part the dynamic polarizability. The results are in good agreement with the experiments and other more elaborate calculations (Author) [pt

  18. Late Holocene palaeohydrological changes in a Sphagnum peat bog from NW Romania based on testate amoebae

    Directory of Open Access Journals (Sweden)

    Andrei-Cosmin Diaconu

    2016-04-01

    Full Text Available This paper investigates the possibility of reconstructing the palaeohydrological changes in an active Sphagnum peat bog from north-western Romania using testate amoebae fauna and organic matter content determined by loss on ignition (LOI. In total 28 taxa of testate amoebae were identified of which 11 were frequent enough to present a remarkable ecological significance. Based on the relative abundance of these taxa nine zones were identified, crossing from very wet to dry climate conditions. The wet periods identified are characterized by taxa like Centropyxis cassis, Amphitrema flavum and Hyalosphenia papilio, while in the dry periods Difflugia pulex and Nebela militaris thrive. We showed that combining qualitative information regarding hydrological preferences with the quantitative percentage data from the fossil record it is possible to obtain information regarding major surface moisture changes from the peat bog surface. Furthermore we identified a link between distribution of testate amoebae assemblages, organic matter variation and minerogenic material.

  19. [Nitrogen input altered testate amoebae community in peatland of Sanjiang Plain, Northeast China].

    Science.gov (United States)

    Song, Li-hong; Yan, Xiu-min; Wang, Ke-hong; Zhu, Xiao-yan; Wu, Dong-hu

    2015-02-01

    In the present study, an in situ control experiment was carried out to explore the response of testate amoebae to exogenous nitrogen addition in peatland of Sanjiang Plain. The results showed that nitrogen addition increased the biomass of testate amoebae at lower levels (6 g N · m(-2)), while decreased it at higher levels (> 12 g N · m(-2)). At genus level, nitrogen addition significantly increased the biomass of Arcella and Phryganella, decreased the biomass of Euglypha. Only lower nitrogen addition significantly increased the biomass of Centropyxis. At species level, nitrogen addition significantly decreased the biomass of Euglypha rotunda, while the biomass of either Centropyxis cassis or Phryganella acropodia was increased by a lower nitrogen addition treatment. This study suggested that the response of peatland testate amoebae to nitrogen addition was species specific, which could potentially be used as an indicator for the environment of peatlands.

  20. Amoeba Management System Transformation in the Light of Organisational Change Literature

    Directory of Open Access Journals (Sweden)

    Urban Wieslaw

    2017-03-01

    Full Text Available The object of this study is the system of amoebas founded originally in Japanese Kyocera. The study aims to identify milestones of the transformation in a company organisational system to the Amoeba Management System (AMS. The study takes a conceptual research approach. It starts from the analysis of available sources on the AMS, identifies the most challenging points of this system, and afterwards, based on organisational change literature, formulates the main steps of transformation towards AMS. The following milestones of AMS implementation emerge from organisational change theories: (1 the preparation for AMS, (2 the change of organisational structure, (3 the design and introduction of a new accounting system, (4 the introduction of inner prices between amoebas, and (5 the transformation of the organisational culture. At the end of the study, the most important issues for future research are listed.

  1. Excitations in opal photonic crystals infiltrated with polarizable media

    Science.gov (United States)

    Eradat, Nayer; Sivachenko, A. Y.; Raikh, Mikhail E.; Vardeny, Z. Valy; Zakhidov, Anvar A.; Li, S.; Baughman, Ray H.

    2002-12-01

    Photonic crystals (PC) are a class of artificial structures with a periodic dielectric function. PCs can be a laboratory for testing fundamental processes involving interactions of radiation with matter in novel conditions. We have studied the optical properties of opal PCs that are infiltrated with highly polarizable media such as j-aggregates of cyanine dyes. Opals are self-assembled structures of silica spheres. We report our studies on clarifying the relationship between a polaritonic gap and a photonic stop band (Bragg gap) when they resonantly coexist in the same structure. Infiltration of opal with polarizable molecules combines the polaritonic and Bragg diffractive effects. Both effects exist independently when the Bragg (at ω = ωB) and polaritonic (ω = ωT) resonances are well separated in frequency. A completely different situation occurs when ωT ~ωB. Such a condition was achieved in opals that were infiltrated with J-aggregates of cyanine dyes that have large Rabi frequency. Our measurements show some dramatic changes in the shape of the reflectivity plateaus, which are due to the interplay between the photonic band gap and the polaritonic gap. The experimental results on reflectivity and its dependence on the light propagation angle and concentration of the cyanie dyes are in agreement with the theoretical calculations.

  2. Measurement of the proton scalar polarizabilities at MAMI

    Energy Technology Data Exchange (ETDEWEB)

    Mornacchi, Edoardo [Institut fuer Kernphysik, Universitaet Mainz (Germany); Collaboration: A2-Collaboration

    2016-07-01

    The electric (α{sub E{sub 1}}) and magnetic (β{sub M1}) scalar polarizabilities are fundamental properties related to the internal structure of the nucleon. They play a crucial role not only in our understanding of the nucleon, but also in other areas such as atomic physics, where they provide e.g. corrections to the Lamb Shift. In order to determine the scalar polarizabilities of the proton, the beam asymmetry Σ{sub 3} was measured, for the first time for the Compton scattering, below the pion photoproduction threshold. The measurement was performed at the MAMI accelerator facility in Mainz. The linearly polarized primary photons impinged on a liquid hydrogen target and the outgoing particles were detected in a nearly 4π detector setup, composed by Crystall Ball and TAPS calorimeters. In this talk the results on the Compton scattering beam asymmetry Σ{sub 3} and their influence on the extraction of α{sub E{sub 1}} and β{sub M1} are discussed.

  3. Polarizability of KC60: Evidence for Potassium Skating on the C60 Surface

    Science.gov (United States)

    Rayane, D.; Antoine, R.; Dugourd, Ph.; Benichou, E.; Allouche, A. R.; Aubert-Frécon, M.; Broyer, M.

    2000-02-01

    We present the first measurement of the polarizability and the permanent dipole moment of isolated KC60 molecules by molecular beam deflection technique. We have obtained a value of 2506+/-250 Å3 for the polarizability at room temperature. The addition of a potassium atom enhances by more than a factor of 20 the polarizability of a pure C60 molecule. This very high polarizability and the lack of observed permanent dipole show that the apparent polarizability of KC60 is induced by the free skating of the potassium atom on the C60 surface, resulting in a statistical orientation of the dipole. The results are interpreted with a simple model similar to the Langevin theory for paramagnetic systems.

  4. Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

    Science.gov (United States)

    Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

    2004-10-01

    Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

  5. Average electronegativity, electronic polarizability and optical basicity of lanthanide oxides for different coordination numbers

    International Nuclear Information System (INIS)

    Zhao Xinyu; Wang Xiaoli; Lin Hai; Wang Zhiqiang

    2008-01-01

    On the basis of new electronegativity values, electronic polarizability and optical basicity of lanthanide oxides are calculated from the concept of average electronegativity given by Asokamani and Manjula. The estimated values are in close agreement with our previous conclusion. Particularly, we attempt to obtain new data of electronic polarizability and optical basicity of lanthanide sesquioxides for different coordination numbers (6-12). The present investigation suggests that both electronic polarizability and optical basicity increase gradually with increasing coordination number. We also looked for another double peak effect, that is, electronic polarizability and optical basicity of trivalent lanthanide oxides show a gradual decrease and then an abrupt increase at the Europia and Ytterbia. Furthermore, close correlations are investigated among average electronegativity, optical basicity, electronic polarizability and coordination number in this paper

  6. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

    Science.gov (United States)

    Bryce, Richard A

    2011-04-01

    The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

  7. [The role of the floodplain gradient in structuring of testate amoebae communities in the Ilych River].

    Science.gov (United States)

    Mazeĭ, Iu A; Malysheva, E A; Lapteva, E M; Komarov, A A; Taskaeva, A A

    2012-01-01

    Forty-two testate amoebae taxa were identified in alluvial soils of floodplain islands in the Ilych River. Among the pedo- and eurybionts, there were aquatic rhizopods. Along the floodplain transect (willow --> meadow --> deciduous forest --> coniferous forest), the testate amoebae community changed directly. There are spatially homogeneous (low beta-diversity) testacean communities but species rich on the local level (high alpha-diversity) within forests. Within willows and meadows, communities are characterized by low alpha-diversity and high heterogeneity that leads to high gamma-diversity.

  8. Long Range Forces between Atomic Impurities in Liquid Helium

    International Nuclear Information System (INIS)

    Dupont-Roc, J.

    2002-01-01

    Van der Waals or Casimir interaction between neutral quantum objects in their ground state is known to be universally attractive. This is not necessarily so when these objects are embedded in a polarizable medium. We show that atomic impurities in liquid helium may indeed realize repulsive forces, and even Van der Waals and Casimir forces with different signs. (author)

  9. Model Hamiltonian Calculations of the Nonlinear Polarizabilities of Conjugated Molecules.

    Science.gov (United States)

    Risser, Steven Michael

    This dissertation advances the theoretical knowledge of the nonlinear polarizabilities of conjugated molecules. The unifying feature of these molecules is an extended delocalized pi electron structure. The pi electrons dominate the electronic properties of the molecules, allowing prediction of molecular properties based on the treatment of just the pi electrons. Two separate pi electron Hamiltonians are used in the research. The principal Hamiltonian used is the non-interacting single-particle Huckel Hamiltonian, which replaces the Coulomb interaction among the pi electrons with a mean field interaction. The simplification allows for exact solution of the Hamiltonian for large molecules. The second Hamiltonian used for this research is the interacting multi-particle Pariser-Parr-Pople (PPP) Hamiltonian, which retains explicit Coulomb interactions. This limits exact solutions to molecules containing at most eight electrons. The molecular properties being investigated are the linear polarizability, and the second and third order hyperpolarizabilities. The hyperpolarizabilities determine the nonlinear optical response of materials. These molecular parameters are determined by two independent approaches. The results from the Huckel Hamiltonian are obtained through first, second and third order perturbation theory. The results from the PPP Hamiltonian are obtained by including the applied field directly in the Hamiltonian and determining the ground state energy at a series of field strengths. By fitting the energy to a polynomial in field strength, the polarizability and hyperpolarizabilities are determined. The Huckel Hamiltonian is used to calculate the third order hyperpolarizability of polyenes. These calculations were the first to show the average hyperpolarizability of the polyenes to be positive, and also to show the saturation of the hyperpolarizability. Comparison of these Huckel results to those from the PPP Hamiltonian shows the lack of explicit Coulomb

  10. Amoebae as potential environmental hosts for Mycobacterium ulcerans and other mycobacteria, but doubtful actors in Buruli ulcer epidemiology.

    Directory of Open Access Journals (Sweden)

    Sophie Gryseels

    Full Text Available The reservoir and mode of transmission of Mycobacterium ulcerans, the causative agent of Buruli ulcer, remain unknown. Ecological, genetic and epidemiological information nonetheless suggests that M. ulcerans may reside in aquatic protozoa.We experimentally infected Acanthamoeba polyphaga with M. ulcerans and found that the bacilli were phagocytised, not digested and remained viable for the duration of the experiment. Furthermore, we collected 13 water, 90 biofilm and 45 detritus samples in both Buruli ulcer endemic and non-endemic communities in Ghana, from which we cultivated amoeboid protozoa and mycobacteria. M. ulcerans was not isolated, but other mycobacteria were as frequently isolated from intracellular as from extracellular sources, suggesting that they commonly infect amoebae in nature. We screened the samples as well as the amoeba cultures for the M. ulcerans markers IS2404, IS2606 and KR-B. IS2404 was detected in 2% of the environmental samples and in 4% of the amoeba cultures. The IS2404 positive amoeba cultures included up to 5 different protozoan species, and originated both from Buruli ulcer endemic and non-endemic communities.This is the first report of experimental infection of amoebae with M. ulcerans and of the detection of the marker IS2404 in amoeba cultures isolated from the environment. We conclude that amoeba are potential natural hosts for M. ulcerans, yet remain sceptical about their implication in the transmission of M. ulcerans to humans and their importance in the epidemiology of Buruli ulcer.

  11. Dielectric constant of polarizable, nonpolar fluids and suspensions

    International Nuclear Information System (INIS)

    Cichocki, B.; Felderhof, B.U.

    1988-01-01

    We study the dielectric constant of a polarizable, nonpolar fluid or suspension of spherical particles by use of a renormalized cluster expansion.The particles may have induced multipole moments of any order. We show that the Clausius-Mossotti formula results from a virtual overlap contribution. The corrections to the Clausius-Mossotti formula are expressed with the aid of a cluster expansion. The integrands of the cluster integrals are expressed in terms of two-body nodal connectors which incorporate all reflections between a pair of particles. We study the two- and three-body cluster integrals in some detail and show how these are related to the dielectric virial expansion and to the first term of the Kirkwood-Yvon expansion

  12. Dynamic polarizabilities and Rydberg states of the argon isoelectronic sequence

    International Nuclear Information System (INIS)

    Ghosh, T.K.; Das, A.K.; Castro, M.; Canuto, S.; Mukherjee, P.K.

    1993-01-01

    Dynamic dipole polarizabilities α d (ω) have been calculated within and beyond the normal-dispersion region for the isoelectronic members of argon up to Mn 7+ using time-dependent coupled Hartree-Fock theory. Excitation energies, oscillator strengths, and quantum-defect values have been estimated for the dipole-allowed transitions 3p 6 1 Se→3p 5 ( 2 P)ns 1 Po (n=4,...,7) and 3p 6 1 Se→3p 5 ( 2 P)nd 1 Po (n=3,...,7). Analytic representations of the singly excited Rydberg orbitals have been obtained. The results compare favorably with the existing theoretical and experimental data. The oscillator strengths show an interesting trend of variation along the isoelectronic sequence

  13. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach

    DEFF Research Database (Denmark)

    Nørby, Morten S; Olsen, Jógvan Magnus Haugaard; Steinmann, Casper

    2017-01-01

    We present a systematic investigation of the key components needed to model single chromophore electronic circular dichroism (ECD) within the polarizable embedding (PE) approach. By relying on accurate forms of the embedding potential, where especially the inclusion of local field effects...... are in focus, we show that qualitative agreement between rotatory strength parameters calculated by full quantum mechanical calculations and the more efficient embedding calculations can be obtained. An important aspect in the computation of reliable absorption parameters is the need for conformational...... sampling. We show that a significant number of snapshots are needed to avoid artifacts in the calculated electronic circular dichroism parameters due to insufficient configurational sampling, thus highlighting the efficiency of the PE model....

  14. Seasonal changes in Sphagnum peatland testate amoeba communities along a hydrological gradient.

    Science.gov (United States)

    Marcisz, Katarzyna; Lamentowicz, Lukasz; Słowińska, Sandra; Słowiński, Michał; Muszak, Witold; Lamentowicz, Mariusz

    2014-10-01

    Testate amoebae are an abundant and functionally important group of protists in peatlands, but little is known about the seasonal patterns of their communities. We investigated the relationships between testate amoeba diversity and community structure and water table depth and light conditions (shading vs. insolation) in a Sphagnum peatland in Northern Poland (Linje mire) in spring and summer 2010. We monitored the water table at five sites across the peatland and collected Sphagnum samples in lawn and hummock micro-sites around each piezometer, in spring (3 May) and mid-summer (6 August) 2010. Water table differed significantly between micro-sites and seasons (Kruskal-Wallis test, p=0.001). The community structure of testate amoebae differed significantly between spring and summer in both hummock and lawn micro-sites. We recorded a small, but significant drop in Shannon diversity, between spring and summer (1.76 vs. 1.72). Strongest correlations were found between testate amoeba communities and water table lowering and light conditions. The relative abundance of mixotrophic species Hyalosphenia papilio, Archerella flavum and of Euglypha ciliata was higher in the summer. Copyright © 2014 Elsevier GmbH. All rights reserved.

  15. Evaluating the use of testate amoebae for palaeohydrological reconstruction in permafrost peatlands

    DEFF Research Database (Denmark)

    Swindles, Graeme T.; Amesbury, Matthew J.; Turner, T. Edward

    2015-01-01

    The melting of high-latitude permafrost peatlands is a major concern due to a potential positive feedback on global climate change. We examine the ecology of testate amoebae in permafrost peatlands, based on sites in Sweden (similar to 200 km north of the Arctic Circle). Multivariate statistical ...

  16. Mimivirus: leading the way in the discovery of giant viruses of amoebae.

    Science.gov (United States)

    Colson, Philippe; La Scola, Bernard; Levasseur, Anthony; Caetano-Anollés, Gustavo; Raoult, Didier

    2017-04-01

    The accidental discovery of the giant virus of amoeba - Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) - in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.

  17. Exposure to synthetic greywater inhibits amoebae encystation and alters expression of Legionella pneumophila virulence genes

    Science.gov (United States)

    Water conservation efforts have focused on greywater (GW) usage, especially for applications that do not require potable water quality. However, there is a need to better understand environmental pathogens and their free-living amoebae (FLA) hosts within GW. Using synthetic gre...

  18. Presence of rotavirus and free-living amoebae in the water supplies of Karachi, Pakistan

    Science.gov (United States)

    Yousuf, Farzana Abubakar; Siddiqui, Ruqaiyyah; Khan, Naveed Ahmed

    2017-01-01

    ABSTRACT Rotavirus and pathogenic free-living amoebae are causative agents of important health problems, especially for developing countries like Pakistan where the population has limited access to clean water supplies. Here, we evaluated the prevalence of rotavirus and free-living amoebae (Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri) in drinking water supplies of Karachi, Pakistan. Six water filtration plants that supply drinking water to the population of Karachi were investigated. Additionally, drinking water samples from households were analyzed for the presence of rotavirus and free-living amoebae. Rotavirus was present in 35% of the water samples collected from water filtration plants; however, domestic tap water samples had a prevalence of only 5%. Out of 20 water samples from filtration plants, 13 (65%) were positive for Acanthamoeba spp., and one (5%) was positive for B. mandrillaris. Out of 20 drinking water samples collected from different areas of Karachi, 35% were positive for Acanthamoeba spp. Rotavirus was detected in 5% of the drinking water samples tested. Overall, these findings showed for the first time the presence of rotavirus, in addition to pathogenic free-living amoebae in drinking water supplies of Karachi that could be an important public health risk for the affected population. PMID:28591260

  19. Presence of rotavirus and free-living amoebae in the water supplies of Karachi, Pakistan

    Directory of Open Access Journals (Sweden)

    Farzana Abubakar Yousuf

    Full Text Available ABSTRACT Rotavirus and pathogenic free-living amoebae are causative agents of important health problems, especially for developing countries like Pakistan where the population has limited access to clean water supplies. Here, we evaluated the prevalence of rotavirus and free-living amoebae (Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri in drinking water supplies of Karachi, Pakistan. Six water filtration plants that supply drinking water to the population of Karachi were investigated. Additionally, drinking water samples from households were analyzed for the presence of rotavirus and free-living amoebae. Rotavirus was present in 35% of the water samples collected from water filtration plants; however, domestic tap water samples had a prevalence of only 5%. Out of 20 water samples from filtration plants, 13 (65% were positive for Acanthamoeba spp., and one (5% was positive for B. mandrillaris. Out of 20 drinking water samples collected from different areas of Karachi, 35% were positive for Acanthamoeba spp. Rotavirus was detected in 5% of the drinking water samples tested. Overall, these findings showed for the first time the presence of rotavirus, in addition to pathogenic free-living amoebae in drinking water supplies of Karachi that could be an important public health risk for the affected population.

  20. Quadrulella texcalense sp nov from a Mexican desert: An unexpected new environment for hyalospheniid testate amoebae

    Czech Academy of Sciences Publication Activity Database

    Perez-Juarez, H.; Serrano-Vazquez, A.; Kosakyan, Anush; Mitchell, E.A.D.; Rivera Aguilar, V. M.; Lahr, D. J. G.; Hernandez Moreno, M. M.; Macías Cuellar, H.; Eguiarte, L. E.; Lara, E.

    2017-01-01

    Roč. 61, 17 July (2017), s. 253-264 ISSN 0932-4739 Institutional support: RVO:60077344 Keywords : Adaptation * Biological soil crust desert * Protist * Tehuacain-Cuicatlain Biosphere Reserve * Testate amoebae Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 2.581, year: 2016

  1. Long-Term Hydrological Reconstruction From a Beaver Meadow Using Testate Amoebae

    Science.gov (United States)

    Von Ness, K.; Loisel, J.; Karran, D. J.; Westbrook, C.; Kohlmeyer, C.

    2016-12-01

    Beaver ponds contribute up to 0.8 Tg/yr of atmospheric methane (CH4) globally (Whitfield et al., 2014) and were found to be the largest CH4 emitters among all the wetland types in boreal environments (Roulet et al., 1992). However, the sources and underlying mechanisms of carbon emission and sequestration in beaver ponds requires further elucidation. Here we present the historical development of a beaver meadow located in the Sibbald Research Wetland in the Rocky Mountains of Kananaskis Provincial Park, Alberta, Canada. We use a combination of testate amoebae, plant macrofossils, and other geochemical proxies to provide high-resolution reconstructions along three peat cores extracted in hydrologically distinct portions of the meadow. To our knowledge, this is the first attempt at reconstructing long-term hydrological conditions in these systems. Testate amoebae (Protozoa: Rhizopoda) are single-celled organisms that inhabit moist substrates and produce a decay-resistant test. As each taxon generally occupies a discrete ecological niche related to soil moisture and pH, testate amoebae are good indicators of past and ongoing hydrological change. Preliminary analysis of testate amoebae assemblages downcore suggests that this proxy is suitable to reconstruct hydrological changes in meadows, with wetter and drier communities being in good agreement with wetter and drier plant macrofossil assemblages. The nitrogen isotopic signature of peat samples (ongoing) will be used as a proxy for changes in nutrient input; it could become a proxy for past beaver activity.

  2. Theoretical studies of the global minima and polarizabilities of small lithium clusters

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Hanshi; Zhao, Ya-Fan; Hammond, Jeffrey R.; Bylaska, Eric J.; Apra, Edoardo; van Dam, Hubertus JJ; Li, Jun; Govind, Niranjan; Kowalski, Karol

    2016-01-16

    Lithium clusters Lin (n=1-20) have been investigated with density functional theory (DFT) and coupled—cluster (CC) methods. The global-minimum structures are located via an improved basin---hopping algorithm and the lowest energy Lin isomers are confirmed with DFT geometry optimizations, CCSD(T) energy calculations, and by comparing simulated and experimental polarizabilities. The tetrahedral Li4 structure is found to be the basic building block of lithium clusters Lin (n=6-20). Simulated polarizabilities, including thermal effects at room temperature, are in good agreement with measured isotropic polarizabilities.

  3. Relativity, nuclear polarizability, and screening in sub-Coulomb elastic scattering

    International Nuclear Information System (INIS)

    Lynch, W.G.; Tsang, M.B.; Bhang, H.C.; Cramer, J.G.; Puigh, R.J.

    Elastic scattering of p-shell nuclear projectiles from 208 Pb has been examined for deviations from Rutherford scattering. Four effects can be important: atomic screening, vacuum polarization, nuclear polarizability and a relativistic effect of dynamical origin. The presence of atomic screening, nuclear polarizability and the relativistic effect was observed thus constituting the first measurement of this relativistic effect using complex nuclei and the first measurement of this relativistic effect using complex nuclei and the first measurement of nuclear polarizability in an external Coulomb field

  4. Static and dynamic polarizabilities of Na- within a variationally stable coupled-channel hyperspherical method

    International Nuclear Information System (INIS)

    Masili, Mauro; Groote, J.J. de

    2004-01-01

    Using a model potential representation combined with a variationally stable method, we present a precise calculation of the electric dipole polarizabilities of the sodium negative ion (Na - ). The effective two-electron eigensolutions for Na - are obtained from a hyperspherical coupled-channel calculation. This approach allows efficient error control and insight into the system's properties through one-dimensional potential curves. Our result of 1018.3 a.u. for the static dipole polarizability is in agreement with previous calculations and supports our results for the dynamic polarizability, which has scarcely been investigated hitherto

  5. Seasonal abundances of naked amoebae in biofilms on shells of zebra mussels (Dreissena polymorpha) with comparative data from rock scrapings.

    Science.gov (United States)

    Bischoff, Paul J; Wetmore, Scott

    2009-01-01

    In North America, zebra mussels (Dreissena polymorpha) are notoriously known as invasive species. The abundance of naked amoebae sampled from the shells of zebra mussels was compared with abundances from rock scrapings at approximately monthly intervals for 1 year. The sites were 2 km apart along the same shoreline. No significant difference in abundance of naked amoebae (F = 1.44; P amoebae in winter, followed by peaks in early spring. The percent encysted increased from a low of 1% in the summer to 80% in early winter.

  6. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    International Nuclear Information System (INIS)

    Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.

    2015-01-01

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties

  7. Correlated, Static and Dynamic Polarizabilities of Small Molecules. Comparison of Four "Black Box" Methods

    DEFF Research Database (Denmark)

    Dalskov, Erik K.; Sauer, Stephan P. A.

    1998-01-01

    Molecular static and dynamic polarizabilities for thirteen small molecules have been calculated using four "black box" ab initio methods, the random phase approximation, RPA, the second-order polarization propagator approximation, SOPPA, the second-order polarization propagator approximation...

  8. Conduction of molecular electronic devices: Qualitative insights through atom-atom polarizabilities

    International Nuclear Information System (INIS)

    Stuyver, T.; Fias, S.; De Proft, F.; Geerlings, P.; Fowler, P. W.

    2015-01-01

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability

  9. Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations

    DEFF Research Database (Denmark)

    Schwabe, Tobias; Olsen, Magnus; Sneskov, Kristian

    2011-01-01

    The polarizable embedding (PE) approach, which combines quantum mechanics (QM) and molecular mechanics (MM), is applied to predict solvatochromic effects on excitation energies of several representative molecules in aqueous, methanol, acetonitrile, and carbon tetrachloride solutions. Good agreement...

  10. Conduction of molecular electronic devices: Qualitative insights through atom-atom polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Stuyver, T.; Fias, S., E-mail: sfias@vub.ac.be; De Proft, F.; Geerlings, P. [ALGC, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel (Belgium); Fowler, P. W. [Department of Chemistry, University of Sheffield, Sheffield S3 7HF (United Kingdom)

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  11. Conduction of molecular electronic devices: qualitative insights through atom-atom polarizabilities.

    Science.gov (United States)

    Stuyver, T; Fias, S; De Proft, F; Fowler, P W; Geerlings, P

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  12. Metal-organic materials (MOMs) for adsorption of polarizable gases and methods of using MOMs

    Science.gov (United States)

    Zaworotko, Michael; Mohamed, Mona H.; Elsaidi, Sameh

    2017-06-14

    Embodiments of the present disclosure provide for multi-component metal-organic materials (MOMs), systems including the MOM, systems for separating components in a gas, methods of separating polarizable gases from a gas mixture, and the like.

  13. Charged ion source with a polarizable probe and with a cyclotron electronic resonance

    International Nuclear Information System (INIS)

    Briand, P.

    1992-01-01

    This invention is about ion sources with a polarizable probe able to produce, from neutral atoms, highly charged ions. This source is composed of an hyperfrequency cavity, production means of an axial magnetic field in the cavity, production means of a multipolar radial magnetic field in this cavity, a high frequency inlet, gas input in the cavity, ion extraction means and a polarizable probe in tension to improve gas ionization

  14. Enhanced polarizability of aromatic molecules placed in the vicinity of silver clusters

    International Nuclear Information System (INIS)

    Mayer, A; Schatz, G C

    2009-01-01

    We use a charge-dipole interaction model to study the polarizability of aromatic molecules that are placed between two silver clusters. In particular we examine the enhancement in polarizability induced by the clusters at plasmon-like resonant frequencies of the cluster-molecule-cluster system. The model used for these simulations relies on representation of the atoms by both a net electric charge and a dipole. By relating the time variation of the atomic charges to the currents that flow through the bonds of the structures considered, a least-action principle can be formulated that enables the atomic charges and dipoles to be determined. We consider benzene, naphthalene and anthracene for this study, comparing the polarizability of these aromatic molecules when placed in the middle between two Ag 120 clusters, with their polarizability as isolated molecules. We find that the polarizability of these molecules is enhanced by the clusters, and this increases the electromagnetic coupling between the two clusters. This results in significant red-shifting (by up to 0.8 eV) of the lowest energy optical transition in the cluster-molecule-cluster system compared to plasmon-like excitation in the cluster-cluster system. The resulting resonant polarizability enhancement leads to an electromagnetic enhancement in surface-enhanced Raman scattering of over 10 6 .

  15. Analytical transition-matrix treatment of electric multipole polarizabilities of hydrogen-like atoms

    International Nuclear Information System (INIS)

    Kharchenko, V.F.

    2015-01-01

    The direct transition-matrix approach to the description of the electric polarization of the quantum bound system of particles is used to determine the electric multipole polarizabilities of the hydrogen-like atoms. It is shown that in the case of the bound system formed by the Coulomb interaction the corresponding inhomogeneous integral equation determining an off-shell scattering function, which consistently describes virtual multiple scattering, can be solved exactly analytically for all electric multipole polarizabilities. Our method allows to reproduce the known Dalgarno–Lewis formula for electric multipole polarizabilities of the hydrogen atom in the ground state and can also be applied to determine the polarizability of the atom in excited bound states. - Highlights: • A new description for electric polarization of hydrogen-like atoms. • Expression for multipole polarizabilities in terms of off-shell scattering functions. • Derivation of integral equation determining the off-shell scattering function. • Rigorous analytic solving the integral equations both for ground and excited states. • Study of contributions of virtual multiple scattering to electric polarizabilities

  16. Influence of Gaussian white noise on the frequency-dependent linear polarizability of doped quantum dot

    International Nuclear Information System (INIS)

    Ganguly, Jayanta; Ghosh, Manas

    2014-01-01

    Highlights: • Linear polarizability of quantum dot has been studied. • Quantum dot is doped with a repulsive impurity. • The polarizabilities are frequency-dependent. • Influence of Gaussian white noise has been monitored. • Noise exploited is of additive and multiplicative nature. - Abstract: We investigate the profiles of diagonal components of frequency-dependent linear (α xx and α yy ) optical response of repulsive impurity doped quantum dots. The dopant impurity potential chosen assumes Gaussian form. The study principally puts emphasis on investigating the role of noise on the polarizability components. In view of this we have exploited Gaussian white noise containing additive and multiplicative characteristics (in Stratonovich sense). The frequency-dependent polarizabilities are studied by exposing the doped dot to a periodically oscillating external electric field of given intensity. The oscillation frequency, confinement potentials, dopant location, and above all, the noise characteristics tune the linear polarizability components in a subtle manner. Whereas the additive noise fails to have any impact on the polarizabilities, the multiplicative noise influences them delicately and gives rise to additional interesting features

  17. Evidence of test detachment in Astrorhiza limicola and two consequential synonyms: Amoeba gigantea and Megamoebomyxa argillobia (Foraminiferida)

    DEFF Research Database (Denmark)

    Cedhagen, Tomas; Tendal, Ole S.

    1989-01-01

    Laboratory observations and experiments demonstrate that the naked rhizopods Amoeba gigantea SANDAHL, 1857 and Megamoebomyxa argillo~ia NYHOLM, 1950, and the foraminifers Astrorhiza arenifera STSCHEDRlNA, 1946, A. sabulifera STSCHEDRINA, 1946 and A. arctlca STSCHEDRINA, 1958 are synonyms of Astro......Laboratory observations and experiments demonstrate that the naked rhizopods Amoeba gigantea SANDAHL, 1857 and Megamoebomyxa argillo~ia NYHOLM, 1950, and the foraminifers Astrorhiza arenifera STSCHEDRlNA, 1946, A. sabulifera STSCHEDRINA, 1946 and A. arctlca STSCHEDRINA, 1958 are synonyms...

  18. Detection and identification of free-living amoeba from aquatic environment in different seasons in Taiwan

    Science.gov (United States)

    Tzeng, K.; Hsu, B.; Tsai, H.; Huang, P.; Tsai, J.; Kao, P.; Huang, K.; Chen, J.

    2013-12-01

    Free-living amoeba includes Acanthamoeba and Naegleria, which are widely distributed in water and soil. Human infection with free-living amoeba leads to serious illness, even lethal. For example, central nervous system infection will cause amoebic meningoencephalitis, and infections will cause amoebic keratitis. The presence of free-living amoeba in environment water can be used as a water quality indicator in ecosystem assessment. In Taiwan, reservoirs are indispensable because of the water source are limited by the steep terrain and the short river flow. Therefore, we need to pay more attention in the quality control of reservoirs water. The aims of this study are to investigate the presence of free-living amoeba in Taiwan reservoirs, and to compare the differences among seasons. At last, the identification and genotyping of Acanthamoeba and Naegleria are investigated. In this study, we use polymerase chain reaction with specific primers to analyze the presence of free-living amoeba in aquatic environment. We collected total 60 samples from reservoirs in Taiwan. The water samples are divided into two parts for both direct concentration method and culture method. The results show the different detection rates among seasons. For Acanthamoeba, the detection rates were 28.3% (17 of 60 water samples), 21.7% (13 of 60 water samples) and 8.3% (5 of 60 water samples) in autumn, winter and spring, respectively. For Naegleria, the detection rates were 6.7% (4 of 60 water samples), 0% (0 of 60 water samples) and 0% (0 of 60 water samples) were detected positive in autumn, winter and spring, respectively. Sequence analysis showed that the major genotypes in Acanthamoeba were T3, T4, T10 and T11 in autumn, T2, T4 and T10 in winter, T4 in spring. Due to the presences of Acanthamoeba and Naegleria in reservoirs, we should pay more attention in water quality monitoring to prevent the potential risks of diseases. Keywords: free-living amoeba, Acanthamoeba, Naegleria, polymerase

  19. Platyamoeba pseudovannellida n. sp., a naked amoeba with wide salt tolerance isolated from the Salton Sea, California.

    Science.gov (United States)

    Hauer, G; Rogerson, A; Anderson, O R

    2001-01-01

    A new species of naked amoeba, Platyamoeba pseudovannellida n.sp., is described on the basis of light microscopic and fine structural features. The amoeba was isolated from the Salton Sea, California, from water at a salinity of ca. 44%. Locomotive amoebae occasionally had a spatulate outline and floating cells had radiating pseudopodia, sometimes with pointed tips. Both these features are reminiscent of the genus Vannella. However, the surface coat (glycocalyx) as revealed by TEM indicates that this is a species of Platyamoeba. Although salinity was not used as a diagnostic feature, this species was found to have remarkable tolerance to fluctuating salinity levels, even when changes were rapid. Amoebae survived over the range 0 per thousand to 150 per thousand salt and grew within the range 0 per thousand to 138 per thousand salt. The generation time of cells averaged 29 h and was not markedly affected by salt concentration. This is longer than expected for an amoeba of this size and suggests a high energetic cost of coping with salinity changes. The morphology of cells changed with increasing salinity: at 0 per thousand cells were flattened and active and at the other extreme (138 per thousand) amoebae were wrinkled and domed and cell movement was very slow. At the ultrastructural level, the cytoplasm of cells grown at high salinity (98 per thousand was considerably denser than that of cells reared at 0 per thousand.

  20. Spin Sum Rules and Polarizabilities: Results from Jefferson Lab

    International Nuclear Information System (INIS)

    Jian-Ping Chen

    2006-01-01

    The nucleon spin structure has been an active, exciting and intriguing subject of interest for the last three decades. Recent experimental data on nucleon spin structure at low to intermediate momentum transfers provide new information in the confinement regime and the transition region from the confinement regime to the asymptotic freedom regime. New insight is gained by exploring moments of spin structure functions and their corresponding sum rules (i.e. the generalized Gerasimov-Drell-Hearn, Burkhardt-Cottingham and Bjorken). The Burkhardt-Cottingham sum rule is verified to good accuracy. The spin structure moments data are compared with Chiral Perturbation Theory calculations at low momentum transfers. It is found that chiral perturbation calculations agree reasonably well with the first moment of the spin structure function g 1 at momentum transfer of 0.05 to 0.1 GeV 2 but fail to reproduce the neutron data in the case of the generalized polarizability (delta) LT (the (delta) LT puzzle). New data have been taken on the neutron ( 3 He), the proton and the deuteron at very low Q 2 down to 0.02 GeV 2 . They will provide benchmark tests of Chiral dynamics in the kinematic region where the Chiral Perturbation theory is expected to work

  1. Determination of lifetimes and nonadiabatic correlations from measured dipole polarizabilities

    International Nuclear Information System (INIS)

    Curtis, Lorenzo J

    2007-01-01

    In atomic systems for which the total oscillator strength of excitations from the ground state is dominated by the transition to the lowest resonance level, the f-sum rule provides a bracketing inequality connecting the lifetime τ of that level to the dipole polarizability α d . This relationship has been used previously to deduce α d from τ. It is shown here that improved spectroscopic accuracies now permit this procedure to be inverted, with τ deduced from a value for α d obtained spectroscopically using the core polarization model. A similar quantitative relationship exists connecting the nonadiabatic correlation factor β to τ, and thus also to α d . The method is applied to a recent measurement of α d for Kr 6+ to obtain the values τ(4s4p 1 P 1 ) 0.096 ± 0.003 ns and β(Kr 6+ ) = 1.71 ± 0.03a 5 0 . It is shown that the use of this method to make precision lifetime determinations for a small number of ions in an isoelectronic sequence permits the exploitation of observed semiempirical regularities to specify the lifetimes of all ions in that sequence

  2. Electronic Polarizability and the Effective Pair Potentials of Water

    Science.gov (United States)

    Leontyev, I. V.; Stuchebrukhov, A. A.

    2014-01-01

    Employing the continuum dielectric model for electronic polarizability, we have developed a new consistent procedure for parameterization of the effective nonpolarizable potential of liquid water. The model explains the striking difference between the value of water dipole moment μ~3D reported in recent ab initio and experimental studies with the value μeff~2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the consistency of the parameterization scheme can be achieved if the magnitude of the effective dipole of water is understood as a scaled value μeff=μ∕εel, where εel =1.78 is the electronic (high-frequency) dielectric constant of water, and a new electronic polarization energy term, missing in the previous theories, is included. The new term is evaluated by using Kirkwood - Onsager theory. The new scheme is fully consistent with experimental data on enthalpy of vaporization, density, diffusion coefficient, and static dielectric constant. The new theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes. PMID:25383062

  3. Generalized polarizabilities of the nucleon in baryon chiral perturbation theory

    Energy Technology Data Exchange (ETDEWEB)

    Lensky, Vadim [Johannes Gutenberg Universitaet Mainz, Institut fuer Kernphysik, Cluster of Excellence PRISMA, Mainz (Germany); Institute for Theoretical and Experimental Physics, Moscow (Russian Federation); National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow (Russian Federation); Pascalutsa, Vladimir; Vanderhaeghen, Marc [Johannes Gutenberg Universitaet Mainz, Institut fuer Kernphysik, Cluster of Excellence PRISMA, Mainz (Germany)

    2017-02-15

    The nucleon generalized polarizabilities (GPs), probed in virtual Compton scattering (VCS), describe the spatial distribution of the polarization density in a nucleon. They are accessed experimentally via the process of electron-proton bremsstrahlung (ep → epγ) at electron-beam facilities, such as MIT-Bates, CEBAF (Jefferson Lab), and MAMI (Mainz). We present the calculation of the nucleon GPs and VCS observables at next-to-leading order in baryon chiral perturbation theory (BχPT), and confront the results with the empirical information. At this order our results are predictions, in the sense that all the parameters are well known from elsewhere. Within the relatively large uncertainties of our calculation we find good agreement with the experimental observations of VCS and the empirical extractions of the GPs. We find large discrepancies with previous chiral calculations - all done in heavy-baryon χPT (HBχPT) - and discuss the differences between BχPT and HBχPT responsible for these discrepancies. (orig.)

  4. The muon anomalous magnetic moment and the pion polarizability

    Energy Technology Data Exchange (ETDEWEB)

    Engel, Kevin T. [University of Maryland, College Park, MD 20742 (United States); Ramsey-Musolf, Michael J. [Physics Department, University of Massachusetts Amherst, Amherst, MA 01003 (United States); Kellogg Radiation Laboratory, California Institute of Technology, Pasadena, CA 91125 (United States)

    2014-11-10

    We compute the charged pion loop contribution to the muon anomalous magnetic moment a{sub μ}, taking into account the previously omitted effect of the charged pion polarizability, (α{sub 1}−β{sub 1}){sub π{sup +}}. We evaluate this contribution using two different models that are consistent with the requirements of chiral symmetry in the low-momentum regime and perturbative quantum chromodynamics in the asymptotic region. The result may increase the disagreement between the present experimental value for a{sub μ} and the theoretical, Standard Model prediction by as much as ∼60×10{sup −11}, depending on the value of (α{sub 1}−β{sub 1}){sub π{sup +}} and the choice of the model. The planned determination of (α{sub 1}−β{sub 1}){sub π{sup +}} at Jefferson Laboratory will eliminate the dominant parametric error, leaving a theoretical model uncertainty commensurate with the error expected from planned Fermilab measurement of a{sub μ}.

  5. Dipole polarizability of neutron rich nuclei and the symmetry energy

    Energy Technology Data Exchange (ETDEWEB)

    Horvat, Andrea; Johansen, Jacob; Miki, Kenjiro; Schindler, Fabia; Schrock, Philipp [IKP, TU Darmstadt (Germany); Aumann, Thomas [IKP, TU Darmstadt (Germany); GSI, Darmstadt (Germany); Boretzky, Konstanze [GSI, Darmstadt (Germany); Collaboration: R3B-Collaboration

    2015-07-01

    As a part of a systematic investigation of the dipole response of stable up to very neutron rich tin isotopes, nuclear and electromagnetic excitation of {sup 124}Sn-{sup 134}Sn has been investigated at relativistic energies in inverse kinematics induced by carbon and lead targets at the LAND-R3B setup at GSI in Darmstadt. The electric dipole response and the nuclear reaction cross section, total and charge-changing, are obtained from the kinematically complete determination of momenta of all particles on an event by event basis. The dipole polarizability is extracted from the Coulomb excitation interaction channel, in order to make use of relevant correlations of this observable with nuclear matter properties such as the symmetry energy at saturation density (J) and it's slope (L). The systematics of the low-lying ''pygmy'' dipole strength, the giant dipole resonance (GDR) and the neutron skin thickness are determined with respect to increasing isospin asymmetry. This talk also discusses the correlations and sensitivities of these variables and observables obtained within the framework of nuclear energy density functional theory.

  6. New experimental method for investigation of the nucleon polarizabilities

    International Nuclear Information System (INIS)

    Yevetska, O.; Watzlawik, S.; Ahrens, J.; Alkhazov, G.D.; Chizhov, V.P.; Maev, E.M.; Neumann-Cosel, P. von; Orischin, E.M.; Petrov, G.E.; Porte, J.-M.; Richter, A.; Sarantsev, V.V.; Schrieder, G.; Smirenin, Yu.V.

    2010-01-01

    At the continuous wave (cw) Superconducting Darmstadt Electron Linear Accelerator S-DALINAC, a new method has been developed for the determination of the electric (α-bar) and magnetic (β-bar) polarizabilities of the proton and the deuteron. For that purpose the energy and angular dependence of the differential cross-section for elastic γp and γd scattering of bremsstrahlung photons in the energy range between 20 and 100 MeV is measured by detecting the recoiling proton (deuteron) in coincidence with the scattered bremsstrahlung photon. α-bar and β-bar are then found by means of a best fit to a theoretical description of the scattering cross-section with these quantities as open parameters. The experimental setup consists of a bremsstrahlung photon facility, two specially designed high pressure hydrogen (deuterium) ionization chambers which serve as targets and detectors of the recoil proton (deuteron), NaI gamma spectrometers and several additional detectors for beam diagnostics and normalization. The whole setup was tested using bremsstrahlung photon beams with endpoint energies of 60 and 79.3 MeV. The results of the test experiments show that future high-statistics measurements are feasible.

  7. El Naschie's structures in the electrodynamics of polarizable media

    International Nuclear Information System (INIS)

    Agop, M.; Merches, I.; Enache, V.

    2005-01-01

    Using the concept of 'combined field', an electrodynamics of polarizable media on a fractal space-time is constructed. In this context, using the scale relativity theory, the permanent electric moment, the induced electric moment, the vacuum fluctuations, the paraelectrics, the diaelectrics, the electric Zeeman-type effect, the electric Einstein-de Haas-type effect, the electric Aharonov-Bohm-type effect, the superconductors in the 'combined field', the double layers as coherent structures, the magnetic Aharonov-Casher-type effect, are analyzed. Correspondence with the ε (∞) space-time is accomplished either by admitting an anomal electric Zeeman-type effect, or through a fractal string as in the case of a superconductor in 'combined field', or, by phase coherence of the electron-ion pairs from the electric double layers (El Naschie's coherence). Moreover, the electric double layer or multiple layer may be considered as two-dimensional projections of the same El Naschie's fractal strings (higher-dimensional strings in ε (∞) space-time)

  8. Variational principles for the static electric and magnetic polarizabilities of anisotropic media with perfect electric conductor inclusions

    International Nuclear Information System (INIS)

    Sjoeberg, Daniel

    2009-01-01

    We present four variational principles for the electric and magnetic polarizabilities for a structure consisting of anisotropic media with perfect electric conductor (PEC) inclusions. From these principles, we derive monotonicity results and upper and lower bounds on the electric and magnetic polarizabilities. When computing the polarizabilities numerically, the bounds can be used as error bounds. The variational principles demonstrate important differences between electrostatics and magnetostatics when PEC bodies are present.

  9. Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model.

    Science.gov (United States)

    Bauer, Brad A; Patel, Sandeep

    2009-08-28

    We present an extension of the TIP4P-QDP model, TIP4P-QDP-LJ, that is designed to couple changes in repulsive and dispersive nonbond interactions to changes in polarizability. Polarizability is intimately related to the dispersion component of classical force field models of interactions, and we explore the effect of incorporating this connection explicitly on properties along the liquid-vapor coexistence curve of pure water. Parametrized to reproduce condensed-phase liquid water properties at 298 K, the TIP4P-QDP-LJ model predicts density, enthalpy of vaporization, self-diffusion constant, and the dielectric constant at ambient conditions to about the same accuracy as TIP4P-QDP but shows remarkable improvement in reproducing the liquid-vapor coexistence curve. TIP4P-QDP-LJ predicts critical constants of T(c)=623 K, rho(c)=0.351 g/cm(3), and P(c)=250.9 atm, which are in good agreement with experimental values of T(c)=647.1 K, rho(c)=0.322 g/cm(3), and P(c)=218 atm, respectively. Applying a scaling factor correction (obtained by fitting the experimental vapor-liquid equilibrium data to the law of rectilinear diameters using a three-term Wegner expansion) the model predicts critical constants (T(c)=631 K and rho(c)=0.308 g/cm(3)). Dependence of enthalpy of vaporization, self-diffusion constant, surface tension, and dielectric constant on temperature are shown to reproduce experimental trends. We also explore the interfacial potential drop across the liquid-vapor interface for the temperatures studied. The interfacial potential demonstrates little temperature dependence at lower temperatures (300-450 K) and significantly enhanced (exponential) dependence at elevated temperatures. Terms arising from the decomposition of the interfacial potential into dipole and quadrupole contributions are shown to monotonically approach zero as the temperature approaches the critical temperature. Results of this study suggest that self-consistently treating the coupling of phase

  10. Ecology of Testate Amoebae in the Komořany Ponds in the Vltava Basin

    Czech Academy of Sciences Publication Activity Database

    Burdíková, Zuzana; Čapek, Martin; Švindrych, Zdeněk; Gryndler, M.; Kubínová, Lucie; Holcová, K.

    2012-01-01

    Roč. 64, č. 1 (2012), s. 117-130 ISSN 0095-3628 R&D Projects: GA MŠk(CZ) LC06063; GA ČR(CZ) GAP108/11/0794 Institutional research plan: CEZ:AV0Z50110509 Keywords : ecology * freshwater ecosystem * testate amoebae * seasonal variability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.277, year: 2012

  11. Interactions Between Testate Amoebae and Saprotrophic Microfungi in a Scots Pine Litter Microcosm

    Czech Academy of Sciences Publication Activity Database

    Vohník, Martin; Burdíková, Zuzana; Vyhnal, Aleš; Koukol, O.

    2011-01-01

    Roč. 61, č. 3 (2011), s. 660-668 ISSN 0095-3628 R&D Projects: GA ČR GP206/09/P340; GA ČR(CZ) GD204/09/H084 Institutional research plan: CEZ:AV0Z50110509; CEZ:AV0Z60050516 Keywords : testate amoebae * saprotrophic fungi * litter Subject RIV: EF - Botanics Impact factor: 2.912, year: 2011

  12. Brain-Eating Amoebae: Predilection Sites in the Brain and Disease Outcome

    OpenAIRE

    Ong, Timothy Yu Yee; Khan, Naveed Ahmed; Siddiqui, Ruqaiyyah

    2017-01-01

    Acanthamoeba spp. and Balamuthia mandrillaris are causative agents of granulomatous amoebic encephalitis (GAE), while Naegleria fowleri causes primary amoebic meningoencephalitis (PAM). PAM is an acute infection that lasts a few days, while GAE is a chronic to subacute infection that can last up to several months. Here, we present a literature review of 86 case reports from 1968 to 2016, in order to explore the affinity of these amoebae for particular sites of the brain, diagnostic modalities...

  13. Environmental Free-Living Amoebae Isolated from Soil in Khon Kaen, Thailand, Antagonize Burkholderia pseudomallei.

    Directory of Open Access Journals (Sweden)

    Parumon Noinarin

    Full Text Available Presence of Burkholderia pseudomallei in soil and water is correlated with endemicity of melioidosis in Southeast Asia and northern Australia. Several biological and physico-chemical factors have been shown to influence persistence of B. pseudomallei in the environment of endemic areas. This study was the first to evaluate the interaction of B. pseudomallei with soil amoebae isolated from B. pseudomallei-positive soil site in Khon Kaen, Thailand. Four species of amoebae, Paravahlkampfia ustiana, Acanthamoeba sp., Naegleria pagei, and isolate A-ST39-E1, were isolated, cultured and identified based on morphology, movement and 18S rRNA gene sequence. Co-cultivation combined with a kanamycin-protection assay of B. pseudomallei with these amoebae at MOI 20 at 30°C were evaluated during 0-6 h using the plate count technique on Ashdown's agar. The fate of intracellular B. pseudomallei in these amoebae was also monitored by confocal laser scanning microscopy (CLSM observation of the CellTracker™ Orange-B. pseudomallei stained cells. The results demonstrated the ability of P. ustiana, Acanthamoeba sp. and isolate A-ST39-E1 to graze B. pseudomallei. However, the number of internalized B. pseudomallei substantially decreased and the bacterial cells disappeared during the observation period, suggesting they had been digested. We found that B. pseudomallei promoted the growth of Acanthamoeba sp. and isolate A-ST39-E1 in co-cultures at MOI 100 at 30°C, 24 h. These findings indicated that P. ustiana, Acanthamoeba sp. and isolate A-ST39-E1 may prey upon B. pseudomallei rather than representing potential environmental reservoirs in which the bacteria can persist.

  14. Response of testate amoebae to a late Holocene ecosystem shift in an Amazonian peatland.

    Science.gov (United States)

    Swindles, Graeme T; Kelly, Thomas J; Roucoux, Katherine H; Lawson, Ian T

    2018-03-15

    To date there have only been two studies using testate amoebae as palaeoecological indicators in tropical peatlands. Here we present a new ∼500-year testate amoeba record from San Jorge, a domed peatland in Peruvian Amazonia, which has a well-constrained vegetation history based on pollen analysis. We observe a major shift from Hyalosphenia subflava to Cryptodifflugia oviformis-dominated communities at ∼50 cm depth (c. AD 1760), which suggests a change to drier conditions in the peatland. The application of a statistical transfer function also suggests a deepening of the water table at this time. The transition in the microbial assemblage occurs at a time when pollen and geochemical data indicate drier conditions (reduced influence of river flooding), leading to an ecosystem switch to more ombrotrophic-like conditions in the peatland. Our work illustrates the potential of testate amoebae as important tools in tropical peatland palaeoecology, and the power of multiproxy approaches for understanding the long-term development of tropical peatlands. Copyright © 2018 Elsevier GmbH. All rights reserved.

  15. What is the optimum sample size for the study of peatland testate amoeba assemblages?

    Science.gov (United States)

    Mazei, Yuri A; Tsyganov, Andrey N; Esaulov, Anton S; Tychkov, Alexander Yu; Payne, Richard J

    2017-10-01

    Testate amoebae are widely used in ecological and palaeoecological studies of peatlands, particularly as indicators of surface wetness. To ensure data are robust and comparable it is important to consider methodological factors which may affect results. One significant question which has not been directly addressed in previous studies is how sample size (expressed here as number of Sphagnum stems) affects data quality. In three contrasting locations in a Russian peatland we extracted samples of differing size, analysed testate amoebae and calculated a number of widely-used indices: species richness, Simpson diversity, compositional dissimilarity from the largest sample and transfer function predictions of water table depth. We found that there was a trend for larger samples to contain more species across the range of commonly-used sample sizes in ecological studies. Smaller samples sometimes failed to produce counts of testate amoebae often considered minimally adequate. It seems likely that analyses based on samples of different sizes may not produce consistent data. Decisions about sample size need to reflect trade-offs between logistics, data quality, spatial resolution and the disturbance involved in sample extraction. For most common ecological applications we suggest that samples of more than eight Sphagnum stems are likely to be desirable. Copyright © 2017 Elsevier GmbH. All rights reserved.

  16. Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae.

    Science.gov (United States)

    Aguilar, María; Lado, Carlos

    2012-08-01

    Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds-protosteloid amoebae-in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an 'everything is everywhere' scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale.

  17. Pathogenic waterborne free-living amoebae: An update from selected Southeast Asian countries

    Science.gov (United States)

    Abdul Majid, Mohamad Azlan; Mahboob, Tooba; Mong, Brandon G. J.; Jaturas, Narong; Richard, Reena Leeba; Tian-Chye, Tan; Phimphila, Anusorn; Mahaphonh, Panomphanh; Aye, Kyaw Nyein; Aung, Wai Lynn; Chuah, Joon; Ziegler, Alan D.; Yasiri, Atipat; Sawangjaroen, Nongyao; Lim, Yvonne A. L.; Nissapatorn, Veeranoot

    2017-01-01

    Data on the distribution of free-living amoebae is still lacking especially in Southeast Asian region. The aquatic environment revealed a high occurrence of free-living amoebae (FLA) due to its suitable condition and availability of food source, which subsequently causes infection to humans. A total of 94 water samples consisted of both treated and untreated from Laos (31), Myanmar (42), and Singapore (21) were investigated for the presence of pathogenic FLA. Each water sample was filtered and cultured onto non-nutrient agar seeded with live suspension of Escherichia coli and incubated at room temperature. Morphological identification was conducted for both trophozoites and cysts via microscopic stains (Giemsa and immunofluorescence). The presence of Naegleria-like structures was the most frequently encountered in both treated and untreated water samples, followed by Acanthamoeba-like and Vermamoeba-like features. To identify the pathogenic isolates, species-specific primer sets were applied for molecular identification of Acanthamoeba, Naegleria, and Vermamoeba. The pathogenic species of Acanthamoeba lenticulata and A. triangularis were detected from untreated water samples, while Vermamoeba vermiformis was found in both treated and untreated water samples. Our results suggested that poor water quality as well as inadequate maintenance and treatment might be the cause of this alarming problem since chlorine disinfection is ineffective in eradicating these amoebas in treated water samples. Regular monitoring and examination of water qualities are necessary in order to control the growth, hence, further preventing the widespread of FLA infections among the public. PMID:28212409

  18. Real-time PCR systems targeting giant viruses of amoebae and their virophages.

    Science.gov (United States)

    Ngounga, Tatsiana; Pagnier, Isabelle; Reteno, Dorine-Gaelle Ikanga; Raoult, Didier; La Scola, Bernard; Colson, Philippe

    2013-01-01

    Giant viruses that infect amoebae, including mimiviruses and marseilleviruses, were first described in 2003. Virophages were subsequently described that infect mimiviruses. Culture isolation with Acanthamoeba spp. and metagenomic studies have shown that these giant viruses are common inhabitants of our biosphere and have enabled the recent detection of these viruses in human samples. However, the genomes of these viruses display substantial genetic diversity, making it a challenge to examine their presence in environmental and clinical samples using conventional and real-time PCR. We designed and evaluated the performance of PCR systems capable of detecting all currently isolated mimiviruses, marseilleviruses and virophages to assess their prevalence in various samples. Our real-time PCR assays accurately detected all or most of the members of the currently delineated lineages of giant viruses infecting acanthamoebae as well as the mimivirus virophages, and enabled accurate classification of the mimiviruses of amoebae in lineages A, B or C. We were able to detect four new mimiviruses directly from environmental samples and correctly classified these viruses within mimivirus lineage C. This was subsequently confirmed by culture on amoebae followed by partial Sanger sequencing. PCR systems such as those implemented here may contribute to an improved understanding of the prevalence of mimiviruses, their virophages and marseilleviruses in humans.

  19. Potential influence of birds on soil testate amoebae in the Arctic

    Science.gov (United States)

    Mazei, Yuri A.; Lebedeva, Natalia V.; Taskaeva, Anastasia A.; Ivanovsky, Alexander A.; Chernyshov, Viktor A.; Tsyganov, Andrey N.; Payne, Richard J.

    2018-06-01

    Birds can be an important agent of environmental change in High Arctic ecosystems, particularly due to the role of seabirds as a vector transferring nutrients from the marine to terrestrial realms. The soils of bird nesting sites are known to host distinct plant communities but the consequences of bird modification for microorganisms are much less clear. Our focus here is testate amoebae: a widely-distributed group of protists with significant roles in many aspects of ecosystem functioning. We compared the testate amoeba assemblages of a site on Spitsbergen (Svalbard archipelago) affected by nesting birds, with nearby control sites. We found differences in assemblage between sites, typified by reduced relative abundance of Phryganella acropodia and Centropyxis aerophila in bird-modified soils. These changes may reflect a reduced availability of fungal food sources. We found no evidence for differences in assemblage diversity or test concentration between bird-modified and control soils. Our dataset is small but results provide the first evidence for the potential effect of bird modification of soils on testate amoebae in the Arctic. Results show only limited similarity to experimental studies of nutrient addition, implying that response mechanisms may be more complicated than simply additional nutrient supply.

  20. [CHROMATIN ORGANIZATION IN CELL CYCLE OF AMOEBA PROTEUS ACCORDING TO OPTICAL TOMOGRAPHY DATA].

    Science.gov (United States)

    Demin, S Yu; Berdieva, M A; Podlipaeva, Yu I; Yudin, A L; Goodkov, A V

    2015-01-01

    For the first time the nuclear cycle of large freshwater amoeba Amoeba proteus was studied by the method of optical tomography. The nuclei were fixed in situ in the cells of synchronized culture, stained by DAPI and examined by confocal laser scanning microscope. 3D-images of intranuclear chromatin were studied in details at different stages of nuclear cycle. The obtained data, together with literary ones allow represent the dynamics of structural organization of the nucleus in Amoeba proteus cell cycle in a new fashion. It was concluded that in this species the two-stage interphase takes place, as well as mitosis of peculiar type which does not correspond to any known type of mitosis according to classification existing now. It is presumed that in the course of nuclear cycle the chromosomes and/or their fragments are amplified, this presumption being in a good correspondence with the data about nuclear DNA hyperreplication in the cell cycle of A. proteus. As a result of chromosomes amplification their number may vary at different stages of cell cycle, and it allows to explain the contradictory data concerning the exact number of chromosomes in this species. The elimination of extra-DNA occurs mainly at the stage between prophase and prometaphase. We presume the majority of chromosomes, or may be even all of them to be referred to cholocentric type according to their behaviour during the mitosis.

  1. Many body effects in the van der Waals force

    International Nuclear Information System (INIS)

    Perez, P.; Claro, F.

    1985-08-01

    A classical model of fluctuating dipoles is proposed for the evaluation of many-body effects in the van der Waals force between neutral polarizable particles. The method is applied to solid xenon giving the correct low temperature stable structure, unlike the usual two-body potential result. (author)

  2. The potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum peatlands.

    Science.gov (United States)

    Sullivan, Maura E; Booth, Robert K

    2011-07-01

    Testate amoebae are a group of moisture-sensitive, shell-producing protozoa that have been widely used as indicators of changes in mean water-table depth within oligotrophic peatlands. However, short-term environmental variability (i.e., sub-annual) also probably influences community composition. The objective of this study was to assess the potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum-dominated peatlands. Testate amoebae and environmental conditions, including hourly measurements of relative humidity within the upper centimeter of the peatland surface, were examined throughout the 2008 growing season at 72 microsites within 11 peatlands of Pennsylvania and Wisconsin, USA. Relationships among testate amoeba communities, vegetation, depth to water table, pH, and an index of short-term environmental variability (EVI), were examined using nonmetric multidimensional scaling and correlation analysis. Results suggest that EVI influences testate amoeba communities, with some taxa more abundant under highly variable conditions (e.g., Arcella discoides, Difflugia pulex, and Hyalosphenia subflava) and others more abundant when environmental conditions at the peatland surface were relatively stable (e.g., Archerella flavum and Bullinularia indica). The magnitude of environmental variability experienced at the peatland surface appears to be primarily controlled by vegetation composition and density. In particular, sites with dense Sphagnum cover had lower EVI values than sites with loose-growing Sphagnum or vegetation dominated by vascular plants and/or non-Sphagnum bryophytes. Our results suggest that more environmental information may be inferred from testate amoebae than previously recognized. Knowledge of relationships between testate amoebae and short-term environmental variability should lead to more detailed and refined environmental inferences.

  3. Correlation among electronegativity, cation polarizability, optical basicity and single bond strength of simple oxides

    Energy Technology Data Exchange (ETDEWEB)

    Dimitrov, Vesselin, E-mail: vesselin@uctm.edu [Department of Silicate Technology, University of Chemical Technology and Metallurgy, 8, Kl. Ohridski Blvd., Sofia 1756 (Bulgaria); Komatsu, Takayuki, E-mail: komatsu@mst.nagaokaut.ac.jp [Department of Materials Science and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka 940-2188 (Japan)

    2012-12-15

    A suitable relationship between free-cation polarizability and electronegativity of elements in different valence states and with the most common coordination numbers has been searched on the basis of the similarity in physical nature of both quantities. In general, the cation polarizability increases with decreasing element electronegativity. A systematic periodic change in the polarizability against the electronegativity has been observed in the isoelectronic series. It has been found that generally the optical basicity increases and the single bond strength of simple oxides decreases with decreasing the electronegativity. The observed trends have been discussed on the basis of electron donation ability of the oxide ions and type of chemical bonding in simple oxides. - Graphical abstract: This figure shows the single bond strength of simple oxides as a function of element electronegativity. A remarkable correlation exists between these independently obtained quantities. High values of electronegativity correspond to high values of single bond strength and vice versa. It is obvious that the observed trend in this figure is closely related to the type of chemical bonding in corresponding oxide. Highlights: Black-Right-Pointing-Pointer A suitable relationship between free-cation polarizability and electronegativity of elements was searched. Black-Right-Pointing-Pointer The cation polarizability increases with decreasing element electronegativity. Black-Right-Pointing-Pointer The single bond strength of simple oxides decreases with decreasing the electronegativity. Black-Right-Pointing-Pointer The observed trends were discussed on the basis of type of chemical bonding in simple oxides.

  4. Investigation of Compton effect on π-meson and charged pion polarizability

    International Nuclear Information System (INIS)

    Antipov, Yu.M.; Batarin, V.A.; Bezzubov, V.A.

    1986-01-01

    The results of an experiment aimed at the study of the 40 GeV/c pion radiative scattering on nuclei at small momentum transfers are presented. Compton effect on the pion was investigated and the charged pion polarizability was measured. The pion Compton-effect cross section dependence on the incident photon energy ω' 1 (rest pion frame) was measured in the 100 - 600 MeV range. The polarizability of charged pion from the analysis of Compton-effect events has been found to be β π =-α π =(-6.9 ± 1.4 stat. ± 1.2 syst. )x10 -43 cm 3 and the sun of pion electrical α π and magnetic β π polarizability has been estimated to be in agreement with theoretical predictions: α π +β π ≅ 0

  5. Some measurements of H/D polarizability isotope effects using differential refractometry

    Energy Technology Data Exchange (ETDEWEB)

    Foster Smith, M; Van Hook, W A [Tennessee Univ., Knoxville (USA). Dept. of Chemistry

    1989-05-01

    Refractive index differences between the H and D isomers of some common molecules in the liquid phase were measured between 404.7 and 690.0 nm. The data are combined with information on molar volume isotope effects to yield values for H/D isotope effects on the static polarizability, the vibrational contribution to the static and frequency dependent parts of the polarizability, and the H/D isotope effect on the second moment of the electronic charge distribution. The present results suffice to demonstrate the practicability of this technique to measure the components of the polarizability listed above. However for accurate resolution of the vibrational and second moment contributions, refractive index data of still greater precision will be required. (orig.).

  6. Some measurements of H/D polarizability isotope effects using differential refractometry

    International Nuclear Information System (INIS)

    Foster Smith, M.; Van Hook, W.A.

    1989-01-01

    Refractive index differences between the H and D isomers of some common molecules in the liquid phase were measured between 404.7 and 690.0 nm. The data are combined with information on molar volume isotope effects to yield values for H/D isotope effects on the static polarizability, the vibrational contribution to the static and frequency dependent parts of the polarizability, and the H/D isotope effect on the second moment of the electronic charge distribution. The present results suffice to demonstrate the practicability of this technique to measure the components of the polarizability listed above. However for accurate resolution of the vibrational and second moment contributions, refractive index data of still greater precision will be required. (orig.)

  7. Maximum hardness and minimum polarizability principles through lattice energies of ionic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Kaya, Savaş, E-mail: savaskaya@cumhuriyet.edu.tr [Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas 58140 (Turkey); Kaya, Cemal, E-mail: kaya@cumhuriyet.edu.tr [Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas 58140 (Turkey); Islam, Nazmul, E-mail: nazmul.islam786@gmail.com [Theoretical and Computational Chemistry Research Laboratory, Department of Basic Science and Humanities/Chemistry Techno Global-Balurghat, Balurghat, D. Dinajpur 733103 (India)

    2016-03-15

    The maximum hardness (MHP) and minimum polarizability (MPP) principles have been analyzed using the relationship among the lattice energies of ionic compounds with their electronegativities, chemical hardnesses and electrophilicities. Lattice energy, electronegativity, chemical hardness and electrophilicity values of ionic compounds considered in the present study have been calculated using new equations derived by some of the authors in recent years. For 4 simple reactions, the changes of the hardness (Δη), polarizability (Δα) and electrophilicity index (Δω) were calculated. It is shown that the maximum hardness principle is obeyed by all chemical reactions but minimum polarizability principles and minimum electrophilicity principle are not valid for all reactions. We also proposed simple methods to compute the percentage of ionic characters and inter nuclear distances of ionic compounds. Comparative studies with experimental sets of data reveal that the proposed methods of computation of the percentage of ionic characters and inter nuclear distances of ionic compounds are valid.

  8. Maximum hardness and minimum polarizability principles through lattice energies of ionic compounds

    International Nuclear Information System (INIS)

    Kaya, Savaş; Kaya, Cemal; Islam, Nazmul

    2016-01-01

    The maximum hardness (MHP) and minimum polarizability (MPP) principles have been analyzed using the relationship among the lattice energies of ionic compounds with their electronegativities, chemical hardnesses and electrophilicities. Lattice energy, electronegativity, chemical hardness and electrophilicity values of ionic compounds considered in the present study have been calculated using new equations derived by some of the authors in recent years. For 4 simple reactions, the changes of the hardness (Δη), polarizability (Δα) and electrophilicity index (Δω) were calculated. It is shown that the maximum hardness principle is obeyed by all chemical reactions but minimum polarizability principles and minimum electrophilicity principle are not valid for all reactions. We also proposed simple methods to compute the percentage of ionic characters and inter nuclear distances of ionic compounds. Comparative studies with experimental sets of data reveal that the proposed methods of computation of the percentage of ionic characters and inter nuclear distances of ionic compounds are valid.

  9. Polarizabilities of Ba and Ba2: Comparison of molecular beam experiments with relativistic quantum chemistry

    International Nuclear Information System (INIS)

    Schaefer, Sascha; Mehring, Max; Schaefer, Rolf; Schwerdtfeger, Peter

    2007-01-01

    The dielectric response to an inhomogeneous electric field has been investigated for Ba and Ba 2 within a molecular beam experiment. The ratio of the polarizabilities per atom of Ba 2 and Ba is determined to be 1.30±0.13. The experimental result is compared to a high level ab initio quantum chemical coupled cluster calculation with an energy-consistent scalar relativistic small-core pseudopotential for Ba. For the barium atom a polarizability of 40.82 A 3 is obtained and the isotropic value of the polarizability calculated for Ba 2 is 97.88 A 3 , which is in good agreement with the experimental results, demonstrating that a quantitative understanding of the interaction between two closed-shell heavy element metal atoms has been achieved

  10. Comparison of self-consistent calculations of the static polarizability of atoms and molecules

    International Nuclear Information System (INIS)

    Moullet, I.; Martins, J.L.

    1990-01-01

    The static dipole polarizabilities and other ground-state properties of H, H 2 , He, Na, and Na 2 are calculated using five different self-consistent schemes: Hartree--Fock, local spin density approximation, Hartree--Fock plus local density correlation, self-interaction-corrected local spin density approximation, and Hartree--Fock plus self-interaction-corrected local density correlation. The inclusion of the self-interaction corrected local spin density approximation in the Hartree--Fock method improves dramatically the calculated dissociation energies of molecules but has a small effect on the calculated polarizabilities. Correcting the local spin density calculations for self-interaction effects improves the calculated polarizability in the cases where the local spin density results are mediocre, and has only a small effect in the cases where the local spin density values are in reasonable agreement with experiment

  11. Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model

    DEFF Research Database (Denmark)

    Hrsak, Dalibor; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2017-01-01

    Embedding techniques in combination with response theory represent a successful approach to calculate molecular properties and excited states in large molecular systems such as solutions and proteins. Recently, the polarizable embedding model has been extended by introducing explicit electronic...... densities of the molecules in the nearest environment, resulting in the polarizable density embedding (PDE) model. This improvement provides a better description of the intermolecular interactions at short distances. However, the electronic densities of the environment molecules are calculated in isolation...... interaction energies calculated on the basis of full quantum-mechanical calculations. The obtained optimal factors are used in PDE calculations of various ground- and excited-state properties of molecules embedded in solvents described as polarizable environments. © 2017 Wiley Periodicals, Inc....

  12. Effect of substituents on polarizability and hyperpolarizability values of benzimidazole metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Praveen, P. A.; Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in [Crystal Growth and Thin films Laboratory, Department of Physics, Bharathidasan University, Tiruchirappalli - 620 024, Tamilnadu (India)

    2016-05-23

    In this report, the polarizability and first and second order hyperpolarizability values of bis benzimidazole Zn(II)-2R and bis benzimidazole Cd(II)-2R complexes, with different electron donating moieties R (R= Cl, Br, I, Acetate) were calculated using time dependent Hartree-Fock (TDHF) formalism embedded in MOPAC2012 package. Further the role of substituents on polarizability and hyperpolarizability values is investigated for the first time by analyzing the frontier molecular orbitals of the complexes with respect to the electronegativity of the substituents. It is found that the increase in electronegativity of the substituents correspondingly increases the energy gap of the molecules, which in turn reduces the polarizability values of both Zn and Cd benzimidazole complexes. Similarly, increase in electronegativity reduces the electric quadrupole moments of both the metal complexes, which in turn reduces the hyperpolarizability values.

  13. Dipole polarizability and neutron skin in {sup 68}Ni

    Energy Technology Data Exchange (ETDEWEB)

    Rossi, Dominic [GSI Darmstadt (Germany); Univ. Mainz (Germany); NSCL, MSU (United States); Aumann, Thomas [TU Darmstadt (Germany); Boretzky, Konstanze [GSI Darmstadt (Germany); Collaboration: R3B-Collaboration

    2014-07-01

    The symmetry energy term E{sub sym} of the nuclear equation-of-state describes fundamental phenomena both in nuclear physics and in astrophysics. The electric dipole (E1) response of nuclei as a function of the isospin asymmetry is driven by E{sub sym} and in particular by its density dependence. Studies of the Pygmy Dipole Resonance (PDR) in exotic nuclei have been used to constrain E{sub sym} or the neutron skin thickness ΔR{sub n,p}. The electric dipole polarizability α{sub D}, being very sensitive to the low-lying E1 strength, is correlated to ΔR{sub n,p} in a robust and only moderately less model-dependent manner [PRC 81, 051303 (2010)]. Recently, for the stable nucleus, 208Pb the neutron skin thickness was extracted from the measured αD. Here, a first experimental determination of α{sub D} in an unstable nucleus and the derivation of its ΔR{sub n,p} will be reported. Coulomb excitation in inverse kinematics at the R3B-LAND setup at GSI allows for the investigation of the dipole strength distribution in the neutron-rich {sup 68}Ni covering the pygmy (PDR) and giant dipole resonance (GDR). The E1 strength distribution in the neutron-rich {sup 68}Ni covering the pygmy (PDR) and giant dipole resonance (GDR) s investigated using the R3B-LAND setup at GSI. From the E1 strength distribution in {sup 68}Ni measured using the R3B-LAND setup at GSI, the resonance parameters for the observed PDR at 9.55(17) MeV and the giant dipole resonance at 17.1(2) MeV are determined. In combination with results from Wieland et al. [PRL 102, 092502 (2009)] an unexpectedly large direct photon-decay branching ratio of 7(2) is observed for the PDR. The measured α{sub D} of 3.40(23) fm{sup 3} is compared to relativistic RPA calculations yielding ΔR{sub n,p} of 0.17(2) fm for {sup 68}Ni.

  14. A comparison of density functional theory and coupled cluster methods for the calculation of electric dipole polarizability gradients of methane

    DEFF Research Database (Denmark)

    Paidarová, Ivana; Sauer, Stephan P. A.

    2012-01-01

    We have compared the performance of density functional theory (DFT) using five different exchange-correlation functionals with four coupled cluster theory based wave function methods in the calculation of geometrical derivatives of the polarizability tensor of methane. The polarizability gradient...

  15. Static electric dipole polarizabilities of An5+/6+ and AnO2+/2+ (An = U, Np, and Pu) ions

    International Nuclear Information System (INIS)

    Parmar, Payal; Peterson, Kirk A.; Clark, Aurora E.

    2014-01-01

    The parallel components of static electric dipole polarizabilities have been calculated for the lowest lying spin-orbit states of the penta- and hexavalent oxidation states of the actinides (An) U, Np, and Pu, in both their atomic and molecular diyl ion forms (An 5+/6+ and AnO 2 +/2+ ) using the numerical finite-field technique within a four-component relativistic framework. The four-component Dirac-Hartree-Fock method formed the reference for MP2 and CCSD(T) calculations, while multireference Fock space coupled-cluster (FSCC), intermediate Hamiltonian Fock space coupled-cluster (IH-FSCC) and Kramers restricted configuration interaction (KRCI) methods were used to incorporate additional electron correlation. It is observed that electron correlation has significant (∼5 a.u. 3 ) impact upon the parallel component of the polarizabilities of the diyls. To the best of our knowledge, these quantities have not been previously reported and they can serve as reference values in the determination of various electronic and response properties (for example intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications. The highest quality numbers for the parallel components (α zz ) of the polarizability for the lowest Ω levels corresponding to the ground electronic states are (in a.u. 3 ) 44.15 and 41.17 for UO 2 + and UO 2 2+ , respectively, 45.64 and 41.42 for NpO 2 + and NpO 2 2+ , respectively, and 47.15 for the PuO 2 + ion

  16. Static electric dipole polarizabilities of An{sup 5+/6+} and AnO{sub 2}{sup +/2+} (An = U, Np, and Pu) ions

    Energy Technology Data Exchange (ETDEWEB)

    Parmar, Payal, E-mail: payal.parmar@wsu.edu, E-mail: kipeters@wsu.edu, E-mail: auclark@wsu.edu; Peterson, Kirk A., E-mail: payal.parmar@wsu.edu, E-mail: kipeters@wsu.edu, E-mail: auclark@wsu.edu [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States); Clark, Aurora E., E-mail: payal.parmar@wsu.edu, E-mail: kipeters@wsu.edu, E-mail: auclark@wsu.edu [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States); Material Science and Engineering Program, Washington State University, Pullman, Washington 99164 (United States)

    2014-12-21

    The parallel components of static electric dipole polarizabilities have been calculated for the lowest lying spin-orbit states of the penta- and hexavalent oxidation states of the actinides (An) U, Np, and Pu, in both their atomic and molecular diyl ion forms (An{sup 5+/6+} and AnO{sub 2}{sup +/2+}) using the numerical finite-field technique within a four-component relativistic framework. The four-component Dirac-Hartree-Fock method formed the reference for MP2 and CCSD(T) calculations, while multireference Fock space coupled-cluster (FSCC), intermediate Hamiltonian Fock space coupled-cluster (IH-FSCC) and Kramers restricted configuration interaction (KRCI) methods were used to incorporate additional electron correlation. It is observed that electron correlation has significant (∼5 a.u.{sup 3}) impact upon the parallel component of the polarizabilities of the diyls. To the best of our knowledge, these quantities have not been previously reported and they can serve as reference values in the determination of various electronic and response properties (for example intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications. The highest quality numbers for the parallel components (α{sub zz}) of the polarizability for the lowest Ω levels corresponding to the ground electronic states are (in a.u.{sup 3}) 44.15 and 41.17 for UO{sub 2}{sup +} and UO{sub 2}{sup 2+}, respectively, 45.64 and 41.42 for NpO{sub 2}{sup +} and NpO{sub 2}{sup 2+}, respectively, and 47.15 for the PuO{sub 2}{sup +} ion.

  17. Static electric dipole polarizabilities of An(5+/6+) and AnO2 (+/2+) (An = U, Np, and Pu) ions.

    Science.gov (United States)

    Parmar, Payal; Peterson, Kirk A; Clark, Aurora E

    2014-12-21

    The parallel components of static electric dipole polarizabilities have been calculated for the lowest lying spin-orbit states of the penta- and hexavalent oxidation states of the actinides (An) U, Np, and Pu, in both their atomic and molecular diyl ion forms (An(5+/6+) and AnO2 (+/2+)) using the numerical finite-field technique within a four-component relativistic framework. The four-component Dirac-Hartree-Fock method formed the reference for MP2 and CCSD(T) calculations, while multireference Fock space coupled-cluster (FSCC), intermediate Hamiltonian Fock space coupled-cluster (IH-FSCC) and Kramers restricted configuration interaction (KRCI) methods were used to incorporate additional electron correlation. It is observed that electron correlation has significant (∼5 a.u.(3)) impact upon the parallel component of the polarizabilities of the diyls. To the best of our knowledge, these quantities have not been previously reported and they can serve as reference values in the determination of various electronic and response properties (for example intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications. The highest quality numbers for the parallel components (αzz) of the polarizability for the lowest Ω levels corresponding to the ground electronic states are (in a.u.(3)) 44.15 and 41.17 for UO2 (+) and UO2 (2+), respectively, 45.64 and 41.42 for NpO2 (+) and NpO2 (2+), respectively, and 47.15 for the PuO2 (+) ion.

  18. Raman polarizabilities of the ν2, ν5 bands of CD3Cl

    International Nuclear Information System (INIS)

    Escribano, R.; Hernandez, M.G.; Mejias, M.; Brodersen, S.

    1985-01-01

    The Raman spectrum of the Coriolis interacting ν 2 , ν 5 bands of CD 3 Cl was recorded with a resolution of ca 0.6 cm -1 . Using the vibrational-rotational parameters of Yamada and Hirota, a computer simulation of the Raman contour was performed, yielding relative values of Raman polarizability derivatives for these bands. By comparison with the absolute intensity measurement of Orza et al., absolute values of the Raman polarizabilities were obtained. The sign of the Raman intensity perturbation was found to be negative. (author)

  19. Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

    Science.gov (United States)

    Nagata, Yuki

    2010-02-01

    A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

  20. Effect of impurities on the two-dimensional electron gas polarizability

    International Nuclear Information System (INIS)

    Nkoma, J.S.

    1980-06-01

    The polarizability for a two-dimensional electron gas is calculated in the presence of impurities by a Green function formalism. This leads to a system with finite mean free path due to electrons scattering off impurities. The calculated polarizability is found to be strongly dependent on the mean free path. The main feature is the suppression of the sharp corner at wave vector 2ksub(F) for finite mean free paths, and the pure metal result is recovered for the infinite mean free path. A possible application of the results to the transport properties of semiconductor inversion layers is discussed. (author)

  1. Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface.

    Science.gov (United States)

    Bauer, Brad A; Warren, G Lee; Patel, Sandeep

    2009-02-10

    We discuss a new classical water force field that explicitly accounts for differences in polarizability between liquid and vapor phases. The TIP4P-QDP (4-point transferable intermolecular potential with charge dependent-polarizability) force field is a modification of the original TIP4P-FQ fluctuating charge water force field of Rick et al.(1) that self-consistently adjusts its atomic hardness parameters via a scaling function dependent on the M-site charge. The electronegativity (χ) parameters are also scaled in order to reproduce condensed-phase dipole moments of comparable magnitude to TIP4P-FQ. TIP4P-QDP is parameterized to reproduce experimental gas-phase and select condensed-phase properties. The TIP4P-QDP water model possesses a gas phase polarizability of 1.40 Å(3) and gas-phase dipole moment of 1.85 Debye, in excellent agreement with experiment and high-level ab initio predictions. The liquid density of TIP4P-QDP is 0.9954(±0.0002) g/cm(3) at 298 K and 1 atmosphere, and the enthalpy of vaporization is 10.55(±0.12) kcal/mol. Other condensed-phase properties such as the isobaric heat capacity, isothermal compressibility, and diffusion constant are also calculated within reasonable accuracy of experiment and consistent with predictions of other current state-of-the-art water force fields. The average molecular dipole moment of TIP4P-QDP in the condensed phase is 2.641(±0.001) Debye, approximately 0.02 Debye higher than TIP4P-FQ and within the range of values currently surmised for the bulk liquid. The dielectric constant, ε = 85.8 ± 1.0, is 10% higher than experiment. This is reasoned to be due to the increase in the condensed phase dipole moment over TIP4P-FQ, which estimates ε remarkably well. Radial distribution functions for TIP4P-QDP and TIP4P-FQ show similar features, with TIP4P-QDP showing slightly reduced peak heights and subtle shifts towards larger distance interactions. Since the greatest effects of the phase-dependent polarizability are

  2. Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface

    Science.gov (United States)

    Bauer, Brad A.; Warren, G. Lee; Patel, Sandeep

    2012-01-01

    We discuss a new classical water force field that explicitly accounts for differences in polarizability between liquid and vapor phases. The TIP4P-QDP (4-point transferable intermolecular potential with charge dependent-polarizability) force field is a modification of the original TIP4P-FQ fluctuating charge water force field of Rick et al.1 that self-consistently adjusts its atomic hardness parameters via a scaling function dependent on the M-site charge. The electronegativity (χ) parameters are also scaled in order to reproduce condensed-phase dipole moments of comparable magnitude to TIP4P-FQ. TIP4P-QDP is parameterized to reproduce experimental gas-phase and select condensed-phase properties. The TIP4P-QDP water model possesses a gas phase polarizability of 1.40 Å3 and gas-phase dipole moment of 1.85 Debye, in excellent agreement with experiment and high-level ab initio predictions. The liquid density of TIP4P-QDP is 0.9954(±0.0002) g/cm3 at 298 K and 1 atmosphere, and the enthalpy of vaporization is 10.55(±0.12) kcal/mol. Other condensed-phase properties such as the isobaric heat capacity, isothermal compressibility, and diffusion constant are also calculated within reasonable accuracy of experiment and consistent with predictions of other current state-of-the-art water force fields. The average molecular dipole moment of TIP4P-QDP in the condensed phase is 2.641(±0.001) Debye, approximately 0.02 Debye higher than TIP4P-FQ and within the range of values currently surmised for the bulk liquid. The dielectric constant, ε = 85.8 ± 1.0, is 10% higher than experiment. This is reasoned to be due to the increase in the condensed phase dipole moment over TIP4P-FQ, which estimates ε remarkably well. Radial distribution functions for TIP4P-QDP and TIP4P-FQ show similar features, with TIP4P-QDP showing slightly reduced peak heights and subtle shifts towards larger distance interactions. Since the greatest effects of the phase-dependent polarizability are

  3. Control of Branchionus sp. and Amoeba sp. in cultures of Arthrospira sp. Control de Branchionus sp. y Amoeba sp. en cultivos de Arthrospira sp.

    Directory of Open Access Journals (Sweden)

    Carlos Méndez

    2012-09-01

    Full Text Available Cultivation of cyanobacterium Arthrospira sp. has been developed in many countries for the production of proteins, pigments and other compounds. Outdoor mass cultures are often affected by biological contamination, drastically reducing productivity as far as bringing death. This study evaluates the control of Branchionus sp. and Amoeba sp. with two chemical compounds: urea (U and ammonium bicarbonate (AB, in laboratory conditions and outdoor mass culture of Arthrospira sp. The lethal concentration 100 (LC100 at 24 h for Branchionus sp. and Amoeba sp. determined was of 60-80 mg L-1 (U and 100-150 mg L-1 (AB. The average effective inhibition concentration for 50% of the population (IC50 in Arthrospira sp., after 72 h, was 80 mg L-1 (U and 150 mg L-1 (AB. The application of doses of 60 mg L-1 (U or 100 mg L-1 (AB in the outdoor mass culture of this contaminated microalga, completely inhibited grazing and did not affect the growth of Arthrospira sp. but rather promoted rapid recovery of algal density at levels prior to infestation. These compounds provided an economical and effective control of predators in cultures of Arthrospira sp.El cultivo de la cianobacteria Arthrospira sp. ha sido desarrollado en muchos países para la obtención de proteínas, pigmentos y otros compuestos. Cultivo que a nivel industrial se ve afectado frecuentemente por contaminación biológica, reduciendo drásticamente la productividad hasta causar la muerte. Este estudio evalúa el control de Branchionus sp. y de Amoeba sp. con dos compuestos químicos, la urea (U y bicarbonato de amonio (AB en cultivos de Arthrospira sp. La concentración letal 100 (LC100 determinada a las 24 h para Branchionus sp. y Amoeba sp. fue de 60-80 mg L-1 (U y 100-150 mg L-1 (AB. La concentración media de inhibición efectiva, después de 72 h, para el 50% de la población (IC50 en Arthrospira fue de 80 mg L-1 (U y 150 mg L-1 (AB. La aplicación de dosis de 60 mg L-1 (U ó 100 mg L-1 (AB en

  4. Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

    OpenAIRE

    Lemkul, Justin A.; Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Base flipping in DNA is an important process involved in genomic repair and epigenetic control of gene expression. The driving forces for these processes are not fully understood, especially in the context of the underlying dynamics of the DNA and solvent effects. We studied double-stranded DNA oligomers that have been previously characterized by imino proton exchange NMR using both additive and polarizable force fields. Our results highlight the importance of induced polarization on the base...

  5. Testate amoebae communities sensitive to surface moisture conditions in Patagonian peatlands

    Science.gov (United States)

    Loisel, J.; Booth, R.; Charman, D.; van Bellen, S.; Yu, Z.

    2017-12-01

    Here we examine moss surface samples that were collected during three field campaigns (2005, 2010, 2014) across southern Patagonian peatlands to assess the potential use of testate amoebae and 13C isotope data as proxy indicators of soil moisture. These proxies have been widely tested across North America, but their use as paleoecological tools remains sparse in the southern hemisphere. Samples were collected along a hydrological gradient spanning a range of water table depth from 0cm in wet hollows to over 85cm in dry hummocks. Moss moisture content was measured in the field. Over 25 taxa were identified, with many of them not found in North America. Ordinations indicate statistically significant and dominant effects of soil moisture and water table depth on testate assemblages, though interestingly 13C is even more strongly correlated with testates amoebae than direct soil conditions. It is possible that moss 13C signature constitutes a compound indicator that represents seasonal soil moisture better than opportunistic sampling during field campaigns. There is no significant effect of year or site across the dataset. In addition to providing a training set that translates testate amoebae moisture tolerance range into water tabel depth for Patagonian peatlands, we also compare our results with those from the North American training set to show that, despite 'novel' Patagonian taxa, the robustness of international training sets is probably sufficient to quantify most changes in soil moisture from any site around the world. We also identify key indicator species that are shown to be of universal value in peat-based hydrological reconstructions.

  6. Brain-Eating Amoebae: Predilection Sites in the Brain and Disease Outcome

    Science.gov (United States)

    Ong, Timothy Yu Yee; Siddiqui, Ruqaiyyah

    2017-01-01

    ABSTRACT Acanthamoeba spp. and Balamuthia mandrillaris are causative agents of granulomatous amoebic encephalitis (GAE), while Naegleria fowleri causes primary amoebic meningoencephalitis (PAM). PAM is an acute infection that lasts a few days, while GAE is a chronic to subacute infection that can last up to several months. Here, we present a literature review of 86 case reports from 1968 to 2016, in order to explore the affinity of these amoebae for particular sites of the brain, diagnostic modalities, treatment options, and disease outcomes in a comparative manner. PMID:28404683

  7. A quantum-mechanical perspective on linear response theory within polarizable embedding

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Norman, Patrick; Kongsted, Jacob

    2017-01-01

    We present a derivation of linear response theory within polarizable embedding starting from a rigorous quantum-mechanical treatment of a composite system. To this aim, two different subsystem decompositions (symmetric and nonsymmetric) of the linear response function are introduced and the pole...

  8. Impact of graphene on the polarizability of a neighbour nanoparticle: A dyadic green's function study

    DEFF Research Database (Denmark)

    Amorim, B.; Dias Gonçalves, Paulo André; Vasilevskiy, M. I.

    2017-01-01

    We discuss the renormalization of the polarizability of a nanoparticle in the presence of either: (1) a continuous graphene sheet; or (2) a plasmonic graphene grating, taking into account retardation effects. Our analysis demonstrates that the excitation of surface plasmon polaritons in graphene...

  9. Finite-volume and partial quenching effects in the magnetic polarizability of the neutron

    Science.gov (United States)

    Hall, J. M. M.; Leinweber, D. B.; Young, R. D.

    2014-03-01

    There has been much progress in the experimental measurement of the electric and magnetic polarizabilities of the nucleon. Similarly, lattice QCD simulations have recently produced dynamical QCD results for the magnetic polarizability of the neutron approaching the chiral regime. In order to compare the lattice simulations with experiment, calculation of partial quenching and finite-volume effects is required prior to an extrapolation in quark mass to the physical point. These dependencies are described using chiral effective field theory. Corrections to the partial quenching effects associated with the sea-quark-loop electric charges are estimated by modeling corrections to the pion cloud. These are compared to the uncorrected lattice results. In addition, the behavior of the finite-volume corrections as a function of pion mass is explored. Box sizes of approximately 7 fm are required to achieve a result within 5% of the infinite-volume result at the physical pion mass. A variety of extrapolations are shown at different box sizes, providing a benchmark to guide future lattice QCD calculations of the magnetic polarizabilities. A relatively precise value for the physical magnetic polarizability of the neutron is presented, βn=1.93(11)stat(11)sys×10-4 fm3, which is in agreement with current experimental results.

  10. Finite volume effects on the electric polarizability of neutral hadrons in lattice QCD

    Science.gov (United States)

    Lujan, M.; Alexandru, A.; Freeman, W.; Lee, F. X.

    2016-10-01

    We study the finite volume effects on the electric polarizability for the neutron, neutral pion, and neutral kaon using eight dynamically generated two-flavor nHYP-clover ensembles at two different pion masses: 306(1) and 227(2) MeV. An infinite volume extrapolation is performed for each hadron at both pion masses. For the neutral kaon, finite volume effects are relatively mild. The dependence on the quark mass is also mild, and a reliable chiral extrapolation can be performed along with the infinite volume extrapolation. Our result is αK0 phys=0.356 (74 )(46 )×10-4 fm3 . In contrast, for neutron, the electric polarizability depends strongly on the volume. After removing the finite volume corrections, our neutron polarizability results are in good agreement with chiral perturbation theory. For the connected part of the neutral pion polarizability, the negative trend persists, and it is not due to finite volume effects but likely sea quark charging effects.

  11. Electric dipole, polarizability and structure of cesium chloride clusters with one-excess electron

    International Nuclear Information System (INIS)

    Jraij, A.; Allouche, A.R.; Rabilloud, F.; Korek, M.; Aubert-Frecon, M.; Rayane, D.; Compagnon, I.; Antoine, R.; Broyer, M.; Dugourd, Ph.

    2006-01-01

    The measurement of the electric dipole of gas phase one-excess electron Cs n Cl n-1 clusters is reported together with a theoretical ab initio prediction of stable structures, dipole moments and electronic polarizabilities for these species in their ground state. Results are in agreement with NaCl cubic structures

  12. Polarizability of the Nitrate Anion and Its Solvation at the Air/Water Interface

    Czech Academy of Sciences Publication Activity Database

    Salvador, P.; Curtis, J. E.; Tobias, D. J.; Jungwirth, Pavel

    2003-01-01

    Roč. 5, - (2003), s. 3752-3757 ISSN 1463-9076 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : polarizability * nitrate anion * air/water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.959, year: 2003

  13. Calculation of dipole polarizability derivatives of adamantane and their use in electron scattering computations

    DEFF Research Database (Denmark)

    Sauer, Stephan P. A.; Paidarová, Ivana; Čársky, Petr

    2016-01-01

    In this paper we present calculations of the static polarizability and its derivatives for the adamantane molecule carried out at the density functional theory level using the B3LYP exchange correlation functional and Sadlej’s polarized valence triple zeta basis set. It is shown...

  14. Optical basicity and electronic polarizability of zinc borotellurite glass doped La3+ ions

    Directory of Open Access Journals (Sweden)

    M.K. Halimah

    Full Text Available Zinc borotellurite glasses doped with lanthanum oxide were successfully prepared through melt-quenching technique. The amorphous nature of the glass system was validated by the presence of a broad hump in the XRD result. The refractive index of the prepared glass samples was calculated by using the equation proposed by Dimitrov and Sakka. The theoretical value of molar refraction, electronic polarizability, oxide ion polarizability and metallization criterion were calculated by using Lorentz-Lorenz equation. Meanwhile, expression proposed by Duffy and Ingram for the theoretical value of optical basicity of multi-component glasses were applied to obtain energy band gap based optical basicity and refractive index based optical basicity. The optical basicity of prepared glasses decreased with the increasing concentration of lanthanum oxide. Metallization criterion on the basis of refractive index showed an increasing trend while energy band gap based metallization criterion showed a decreasing trend. The small metallization criterion values of the glass samples represent that the width of the conduction band becomes larger which increase the tendency for metallization of the glasses. The results obtained indicates that the fabricated glasses have high potential to be applied on optical limiting devices in photonic field. Keywords: Borotellurite glasses, Refractive index, Electronic polarizability, Oxide ion polarizability, Optical basicity, Metallization criterion

  15. ''Atomic'' Bremsstrahlung or polarizational radiation in collision of many-electron ions

    International Nuclear Information System (INIS)

    Amusia, M.Ya.; Solov'yov, A.V.

    1991-01-01

    In this work the so-called ''Atomic'' bremsstrahlung (AB) or polarizational radiation, created in collisions of atoms or ions, is discussed. This kind of radiation arises due to the polarization of the electron shell of colliding particles. It is created by the structured projectiles and targets if the constituents are electrically charged. 6 refs, 2 figs

  16. A calculation of internal kinetic energy and polarizability of compressed argon from the statistical atom model

    NARCIS (Netherlands)

    Seldam, C.A. ten; Groot, S.R. de

    1952-01-01

    From Jensen's and Gombás' modification of the statistical Thomas-Fermi atom model, a theory for compressed atoms is developed by changing the boundary conditions. Internal kinetic energy and polarizability of argon are calculated as functions of pressure. At 1000 atm. an internal kinetic energy of

  17. Collision-induced absorption intensity redistribution and the atomic pair polarizabilities

    International Nuclear Information System (INIS)

    Bulanin, M. O.

    1997-01-01

    A modified relation between the trace polarizability of a diatom and the S(-2) dipole sum is proposed that accounts for the effect of atomic collisions on the dipole oscillator strength distribution. Contribution to the collision-induced trace due to redistribution in the ionization continuum of Ar is evaluated and is found to be significant

  18. Electron polarizability of crystalline solids in quantizing magnetic fields and topological gap numbers

    Czech Academy of Sciences Publication Activity Database

    Středa, Pavel; Jonckheere, T.; Martin, T.

    2008-01-01

    Roč. 100, - (2008), 146804/1-146804/4 ISSN 0031-9007 R&D Projects: GA ČR GA202/05/0365 Institutional research plan: CEZ:AV0Z10100521 Keywords : electron polarizability * quantum Hall effect * topological numbers Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.180, year: 2008

  19. A thermodynamic derivation of equations for dielectric-relaxation phenomena in anisotropic polarizable media

    NARCIS (Netherlands)

    Ciancio, V.; Kluitenberg, G.A.

    1990-01-01

    Using the general methods of non-equilibrium thermodynamics, a theory for anisotropic polarizable media in which dielectric relaxation phenomena occur is developed. Assuming that ii microscopic phenomena give rise to dielectric relaxation, the contributions of these phenomena to the macroscopic

  20. A model with charges and polarizability for CS2 in an ionic liquid

    Indian Academy of Sciences (India)

    RUTH M LYNDEN-BELL

    the static electrostatic distribution in the CS2 molecule with 7 charged sites and anisotropic polarizability on the carbon site and isotropic .... the charges modified to reproduce the molecular quad- ... face at 1.5 times the van der Waals radii from the nuclei ..... shows the probability distribution of induced dipoles on the C site ...

  1. On the theory of electric double layer with explicit account of a polarizable co-solvent

    Energy Technology Data Exchange (ETDEWEB)

    Budkov, Yu. A., E-mail: urabudkov@rambler.ru [Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo (Russian Federation); Department of Applied Mathematics, National Research University Higher School of Economics, Moscow (Russian Federation); Kolesnikov, A. L. [Institut für Nichtklassische Chemie e.V., Universität Leipzig, Leipzig (Germany); Kiselev, M. G. [Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo (Russian Federation)

    2016-05-14

    We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On

  2. On the theory of electric double layer with explicit account of a polarizable co-solvent

    International Nuclear Information System (INIS)

    Budkov, Yu. A.; Kolesnikov, A. L.; Kiselev, M. G.

    2016-01-01

    We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On

  3. Size-scaling behaviour of the electronic polarizability of one-dimensional interacting systems

    Science.gov (United States)

    Chiappe, G.; Louis, E.; Vergés, J. A.

    2018-05-01

    Electronic polarizability of finite chains is accurately calculated from the total energy variation of the system produced by small but finite static electric fields applied along the chain direction. Normalized polarizability, that is, polarizability divided by chain length, diverges as the second power of length for metallic systems but approaches a constant value for insulating systems. This behaviour provides a very convenient way to characterize the wave-function malleability of finite systems as it avoids the need of attaching infinite contacts to the chain ends. Hubbard model calculations at half filling show that the method works for a small U  =  1 interaction value that corresponds to a really small spectral gap of 0.005 (hopping t  =  ‑1 is assumed). Once successfully checked, the method has been applied to the long-range hopping model of Gebhard and Ruckenstein showing 1/r hopping decay (Gebhard and Ruckenstein 1992 Phys. Rev. Lett. 68 244; Gebhard et al 1994 Phys. Rev. B 49 10926). Metallicity for U values below the reported metal-insulator transition is obtained but the surprise comes for U values larger than the critical one (when a gap appears in the spectral density of states) because a steady increase of the normalized polarizability with size is obtained. This critical size-scaling behaviour can be understood as corresponding to a molecule which polarizability is unbounded. We have checked that a real transfer of charge from one chain end to the opposite occurs as a response to very small electric fields in spite of the existence of a large gap of the order of U for one-particle excitations. Finally, ab initio quantum chemistry calculations of realistic poly-acetylene chains prove that the occurrence of such critical behaviour in real systems is unlikely.

  4. The effective χ parameter in polarizable polymeric systems: One-loop perturbation theory and field-theoretic simulations.

    Science.gov (United States)

    Grzetic, Douglas J; Delaney, Kris T; Fredrickson, Glenn H

    2018-05-28

    We derive the effective Flory-Huggins parameter in polarizable polymeric systems, within a recently introduced polarizable field theory framework. The incorporation of bead polarizabilities in the model self-consistently embeds dielectric response, as well as van der Waals interactions. The latter generate a χ parameter (denoted χ̃) between any two species with polarizability contrast. Using one-loop perturbation theory, we compute corrections to the structure factor Sk and the dielectric function ϵ^(k) for a polarizable binary homopolymer blend in the one-phase region of the phase diagram. The electrostatic corrections to S(k) can be entirely accounted for by a renormalization of the excluded volume parameter B into three van der Waals-corrected parameters B AA , B AB , and B BB , which then determine χ̃. The one-loop theory not only enables the quantitative prediction of χ̃ but also provides useful insight into the dependence of χ̃ on the electrostatic environment (for example, its sensitivity to electrostatic screening). The unapproximated polarizable field theory is amenable to direct simulation via complex Langevin sampling, which we employ here to test the validity of the one-loop results. From simulations of S(k) and ϵ^(k) for a system of polarizable homopolymers, we find that the one-loop theory is best suited to high concentrations, where it performs very well. Finally, we measure χ̃N in simulations of a polarizable diblock copolymer melt and obtain excellent agreement with the one-loop theory. These constitute the first fully fluctuating simulations conducted within the polarizable field theory framework.

  5. Old lineages in a new ecosystem: diversification of arcellinid amoebae (Amoebozoa and peatland mosses.

    Directory of Open Access Journals (Sweden)

    Omar Fiz-Palacios

    Full Text Available Arcellinid testate amoebae (Amoebozoa form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5-20 Myr ago. Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr. Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands.

  6. Two distinct sensing pathways allow recognition of Klebsiella pneumoniae by Dictyostelium amoebae.

    Science.gov (United States)

    Lima, Wanessa C; Balestrino, Damien; Forestier, Christiane; Cosson, Pierre

    2014-03-01

    Recognition of bacteria by metazoans is mediated by receptors that recognize different types of microorganisms and elicit specific cellular responses. The soil amoebae Dictyostelium discoideum feeds upon a variable mixture of environmental bacteria, and it is expected to recognize and adapt to various food sources. To date, however, no bacteria-sensing mechanisms have been described. In this study, we isolated a Dictyostelium mutant (fspA KO) unable to grow in the presence of non-capsulated Klebsiella pneumoniae bacteria, but growing as efficiently as wild-type cells in the presence of other bacteria, such as Bacillus subtilis. fspA KO cells were also unable to respond to K. pneumoniae and more specifically to bacterially secreted folate in a chemokinetic assay, while they responded readily to B. subtilis. Remarkably, both WT and fspA KO cells were able to grow in the presence of capsulated LM21 K. pneumoniae, and responded to purified capsule, indicating that capsule recognition may represent an alternative, FspA-independent mechanism for K. pneumoniae sensing. When LM21 capsule synthesis genes were deleted, growth and chemokinetic response were lost for fspA KO cells, but not for WT cells. Altogether, these results indicate that Dictyostelium amoebae use specific recognition mechanisms to respond to different K. pneumoniae elements. © 2013 John Wiley & Sons Ltd.

  7. Preferential feeding in Naegleria fowleri; intracellular bacteria isolated from amoebae in operational drinking water distribution systems.

    Science.gov (United States)

    Miller, Haylea C; Morgan, Matthew J; Walsh, Tom; Wylie, Jason T; Kaksonen, Anna H; Puzon, Geoffrey J

    2018-05-06

    The amoeba Naegleria fowleri is the causative agent of the highly fatal disease, primary amoebic meningoencephalitis, and estimated to cause 16 deaths per year in the United States alone. Colonisation of drinking water distribution systems (DWDSs) by the N. fowleri is a significant public health issue. Understanding the factors which enable this pathogen to colonise and thrive in DWDSs is critical for proper management. The microbial ecology within DWDSs may influence the ability of N. fowleri to colonise DWDSs by facilitating the availability of an appropriate food source. Using biofilm samples obtained from operational DWDSs, 16S rRNA amplicon metabarcoding was combined with genus-specific PCR and Sanger sequencing of intracellular associated bacteria from isolated amoeba and their parental biofilms to identify Meiothermus chliarophilus as a potential food source for N. fowleri. Meiothermus was confirmed as a food source for N. fowleri following successful serial culturing of axenic N. fowleri with M. chliarophilus or M. ruber as the sole food source. The ability to identify environmental and ecological conditions favourable to N. fowleri colonisation, including the detection of appropriate food sources such as Meiothermus, could provide water utilities with a predictive tool for managing N. fowleri colonisation within the DWDS. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Evidence of parasexual activity in "asexual amoebae" Cochliopodium spp. (Amoebozoa): extensive cellular and nuclear fusion.

    Science.gov (United States)

    Tekle, Yonas I; Anderson, O Roger; Lecky, Ariel F

    2014-09-01

    The majority of microbial eukaryotes have long been considered asexual, though new evidence indicates sex, or sexual-like (parasexual) behaviors that deviate from the usual union of two gametes, among other variant aspects. Over a dozen amoebozoans are implicated to have sexual stages. However, the exact mechanism by which sex occurs in these lineages remains elusive. This is mainly due to the diverse quality and cryptic nature of their life cycle. In this study we present evidence of some previously unreported aspects of the life cycle of an amoeba, Cochliopodium, that undergoes unusual intraspecific interactions using light microscopy and immunocytochemistry. Similar to other amoebozoans, Cochliopodium, is considered asexual with no published reports of sex or parasexuality. We also investigated environmental conditions that govern the observed intraspecific interactions. Both light microscopic and immunocytochemistry evidence demonstrates Cochliopodium undergoes cellular fusion (plasmogamy) and nuclear fusion (karyogamy). Large plasmodia eventually undergo karyogamy and contain large fused, polyploid, nuclei. These are observed to fragment, subsequently, by karyotomy (nuclear fission) and cytoplasmic fission to yield uninucleated amoebae. This process could lead to a non-meiotic, parasexual exchange of chromosomes in Cochliopodium. These findings strongly suggest that Cochliopodium is involved in parasexual activity and should no longer be considered strictly asexual. Copyright © 2014 Elsevier GmbH. All rights reserved.

  9. Polarization effects in molecular mechanical force fields

    Energy Technology Data Exchange (ETDEWEB)

    Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

    2009-08-19

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

  10. Effective oscillator strength distributions of spherically symmetric atoms for calculating polarizabilities and long-range atom–atom interactions

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jun, E-mail: phyjiang@yeah.net [Key Laboratory of Atomic and Molecular Physics and Functional Materials of Gansu Province, College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070 (China); School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Cheng, Yongjun, E-mail: cyj83mail@gmail.com [School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin 150080 (China); Bromley, M.W.J., E-mail: brom@physics.uq.edu.au [School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland 4075 (Australia)

    2015-01-15

    Effective oscillator strength distributions are systematically generated and tabulated for the alkali atoms, the alkaline-earth atoms, the alkaline-earth ions, the rare gases and some miscellaneous atoms. These effective distributions are used to compute the dipole, quadrupole and octupole static polarizabilities, and are then applied to the calculation of the dynamic polarizabilities at imaginary frequencies. These polarizabilities can be used to determine the long-range C{sub 6}, C{sub 8} and C{sub 10} atom–atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations.

  11. Effective oscillator strength distributions of spherically symmetric atoms for calculating polarizabilities and long-range atom–atom interactions

    International Nuclear Information System (INIS)

    Jiang, Jun; Mitroy, J.; Cheng, Yongjun; Bromley, M.W.J.

    2015-01-01

    Effective oscillator strength distributions are systematically generated and tabulated for the alkali atoms, the alkaline-earth atoms, the alkaline-earth ions, the rare gases and some miscellaneous atoms. These effective distributions are used to compute the dipole, quadrupole and octupole static polarizabilities, and are then applied to the calculation of the dynamic polarizabilities at imaginary frequencies. These polarizabilities can be used to determine the long-range C 6 , C 8 and C 10 atom–atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations

  12. Differential growth of Legionella pneumophila strains within a range of amoebae at various temperatures associated with in-premise plumbing

    Science.gov (United States)

    The potential effect of in-premise plumbing temperatures (24, 32, 37 and 41 °C) on the growth of five different L. pneumophila strains within free-living amoebae (Acanthamoeba polyphaga, Hartmannella vermiformis and Naegleria fowleri) was examined. Compared to controls only fed E...

  13. Contrasting diversity of testate amoebae communities in Sphagnum and brown-moss dominated patches in relation to shell counts.

    Science.gov (United States)

    Lizoňová, Zuzana; Horsák, Michal

    2017-04-01

    Ecological studies of peatland testate amoebae are generally based on totals of 150 individuals per sample. However, the suitability of this standard has never been assessed for alkaline habitats such as spring fens. We explored the differences in testate amoeba diversity between Sphagnum and brown-moss microhabitats at a mire site with a highly diversified moss layer which reflects the small-scale heterogeneity in groundwater chemistry. Relationships between sampling efficiency and sample completeness were explored using individual-based species accumulation curves and the effort required to gain an extra species was assessed. Testate amoeba diversity differed substantially between microhabitats, with brown mosses hosting on average twice as many species and requiring greater shell totals to reach comparable sample analysis efficiency as for Sphagnum. Thus, for samples from alkaline conditions an increase in shell totals would be required and even an overall doubling up to 300 individuals might be considered for reliable community description. Our small-scale data are likely not robust enough to provide an ultimate solution for the optimization of shell totals. However, the results proved that testate amoebae communities from acidic and alkaline environments differ sharply in both species richness and composition and they might call for different methodological approaches. Copyright © 2017 Elsevier GmbH. All rights reserved.

  14. SSU rRNA reveals a sequential increase in shell complexity among the euglyphid testate amoebae (Rhizaria: Euglyphida)

    DEFF Research Database (Denmark)

    Lara, Enrique; Heger, Thierry J; Mitchell, Edward A D

    2007-01-01

    The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a stu...

  15. A free-living amoeba with unusual pattern of mitochondrial structure isolated from Atlantic salmon, Salmo salar L

    Czech Academy of Sciences Publication Activity Database

    Dyková, Iva; Veverková, Marie; Fiala, Ivan; Macháčková, Blanka

    2002-01-01

    Roč. 41, - (2002), s. 415-419 ISSN 0065-1583 R&D Projects: GA AV ČR IAA6022202 Institutional research plan: CEZ:AV0Z6022909 Keywords : free-living amoeba * mitochondrial cristae * Salmo salar Subject RIV: EA - Cell Biology Impact factor: 0.446, year: 2002

  16. Effect of UV irradiation (253.7 nm) on free Legionella and Legionella associated with its amoebae hosts.

    Science.gov (United States)

    Cervero-Aragó, Sílvia; Sommer, Regina; Araujo, Rosa M

    2014-12-15

    Water systems are the primary reservoir for Legionella spp., where the bacteria live in association with other microorganisms, such as free-living amoebae. A wide range of disinfection treatments have been studied to control and prevent Legionella colonization but few of them were performed considering its relation with protozoa. In this study, the effectiveness of UV irradiation (253.7 nm) using low-pressure lamps was investigated as a disinfection method for Legionella and amoebae under controlled laboratory conditions. UV treatments were applied to 5 strains of Legionella spp., 4 strains of free-living amoeba of the genera Acanthamoeba and Vermamoeba, treating separately trophozoites and cysts, and to two different co-cultures of Legionella pneumophila with the Acanthamoeba strains. No significant differences in the UV inactivation behavior were observed among Legionella strains tested which were 3 logs reduced for fluences around 45 J/m(2). UV irradiation was less effective against free-living amoebae; which in some cases required up to 990 J/m(2) to obtain the same population reduction. UV treatment was more effective against trophozoites compared to cysts; moreover, inactivation patterns were clearly different between the genus Acanthamoeba and Vermamoeba. For the first time data about Vermamoeba vermiformis UV inactivation has been reported in a study. Finally, the results showed that the association of L. pneumophila with free-living amoebae decreases the effectiveness of UV irradiation against the bacteria in a range of 1.5-2 fold. That fact demonstrates that the relations established between different microorganisms in the water systems can modify the effectiveness of the UV treatments applied. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Exploring the Dipole Polarizability of $^{11}$Li at REX-ISOLDE

    CERN Multimedia

    2002-01-01

    Dipole polarizability refers to the effect of the excitation to negative parity states through the electric dipole interaction. In nuclear physics dipole polarizability has not yet played a major role. For nuclei close to the drip lines where the separation energies of neutrons (or protons) are small, a substantial part of the dipole strength function occurs at low excitation energies. We here propose to investigate this effect by measuring elastic scattering at energies close to the Coulomb barrier. REX-ISOLDE together with the new improved yields of $^{11}$Li provides the ideal setting for this experiment. We ask for a total of 24 shifts with proton beam plus 3 shifts of stable beam from a Ta-foil target.

  18. Induced-Charge Enhancement of the Diffusion Potential in Membranes with Polarizable Nanopores.

    Science.gov (United States)

    Ryzhkov, I I; Lebedev, D V; Solodovnichenko, V S; Shiverskiy, A V; Simunin, M M

    2017-12-01

    When a charged membrane separates two salt solutions of different concentrations, a potential difference appears due to interfacial Donnan equilibrium and the diffusion junction. Here, we report a new mechanism for the generation of a membrane potential in polarizable conductive membranes via an induced surface charge. It results from an electric field generated by the diffusion of ions with different mobilities. For uncharged membranes, this effect strongly enhances the diffusion potential and makes it highly sensitive to the ion mobilities ratio, electrolyte concentration, and pore size. Theoretical predictions on the basis of the space-charge model extended to polarizable nanopores fully agree with experimental measurements in KCl and NaCl aqueous solutions.

  19. Lanczos-driven coupled-cluster damped linear response theory for molecules in polarizable environments

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Coriani, Sonia; Kongsted, Jacob

    2014-01-01

    are specifically motivated by a twofold aim: (i) computation of core excitations in realistic surroundings and (ii) examination of the effect of the differential response of the environment upon excitation solely related to the CC multipliers (herein denoted the J matrix) in computations of excitation energies......We present an extension of a previously reported implementation of a Lanczos-driven coupled-cluster (CC) damped linear response approach to molecules in condensed phases, where the effects of a surrounding environment are incorporated by means of the polarizable embedding formalism. We...... and transition moments of polarizable-embedded molecules. Numerical calculations demonstrate that the differential polarization of the environment due to the first-order CC multipliers provides only minor contributions to the solvatochromic shift for all transitions considered. We thus complement previous works...

  20. Spin-orbit coupling and the static polarizability of single-wall carbon nanotubes

    International Nuclear Information System (INIS)

    Diniz, Ginetom S.; Ulloa, Sergio E.

    2014-01-01

    We calculate the static longitudinal polarizability of single-wall carbon tubes in the long wavelength limit taking into account spin-orbit effects. We use a four-orbital orthogonal tight-binding formalism to describe the electronic states and the random phase approximation to calculate the dielectric function. We study the role of both the Rashba as well as the intrinsic spin-orbit interactions on the longitudinal dielectric response, i.e., when the probing electric field is parallel to the nanotube axis. The spin-orbit interaction modifies the nanotube electronic band dispersions, which may especially result in a small gap opening in otherwise metallic tubes. The bandgap size and state features, the result of competition between Rashba and intrinsic spin-orbit interactions, result in drastic changes in the longitudinal static polarizability of the system. We discuss results for different nanotube types and the dependence on nanotube radius and spin-orbit couplings.

  1. Spin-orbit coupling and the static polarizability of single-wall carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Diniz, Ginetom S., E-mail: ginetom@gmail.com; Ulloa, Sergio E. [Department of Physics and Astronomy and Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701-2979 (United States)

    2014-07-14

    We calculate the static longitudinal polarizability of single-wall carbon tubes in the long wavelength limit taking into account spin-orbit effects. We use a four-orbital orthogonal tight-binding formalism to describe the electronic states and the random phase approximation to calculate the dielectric function. We study the role of both the Rashba as well as the intrinsic spin-orbit interactions on the longitudinal dielectric response, i.e., when the probing electric field is parallel to the nanotube axis. The spin-orbit interaction modifies the nanotube electronic band dispersions, which may especially result in a small gap opening in otherwise metallic tubes. The bandgap size and state features, the result of competition between Rashba and intrinsic spin-orbit interactions, result in drastic changes in the longitudinal static polarizability of the system. We discuss results for different nanotube types and the dependence on nanotube radius and spin-orbit couplings.

  2. Coupled cluster calculations for static and dynamic polarizabilities of C60

    Science.gov (United States)

    Kowalski, Karol; Hammond, Jeff R.; de Jong, Wibe A.; Sadlej, Andrzej J.

    2008-12-01

    New theoretical predictions for the static and frequency dependent polarizabilities of C60 are reported. Using the linear response coupled cluster approach with singles and doubles and a basis set especially designed to treat the molecular properties in external electric field, we obtained 82.20 and 83.62 Å3 for static and dynamic (λ =1064 nm) polarizabilities. These numbers are in a good agreement with experimentally inferred data of 76.5±8 and 79±4 Å3 [R. Antoine et al., J. Chem. Phys.110, 9771 (1999); A. Ballard et al., J. Chem. Phys.113, 5732 (2000)]. The reported results were obtained with the highest wave function-based level of theory ever applied to the C60 system.

  3. Magnetic polarizabilities of light mesons in SU(3 lattice gauge theory

    Directory of Open Access Journals (Sweden)

    E.V. Luschevskaya

    2015-09-01

    Full Text Available We investigate the ground state energies of neutral pseudoscalar and vector meson in SU(3 lattice gauge theory in the strong abelian magnetic field. The energy of ρ0 meson with zero spin projection sz=0 on the axis of the external magnetic field decreases, while the energies with non-zero spins sz=−1 and +1 increase with the field. The energy of π0 meson decreases as a function of the magnetic field. We calculate the magnetic polarizabilities of pseudoscalar and vector mesons for lattice volume 184. For ρ0 with spin |sz|=1 and π0 meson the polarizabilities in the continuum limit have been evaluated. We do not observe any evidence in favour of tachyonic mode existence.

  4. Method of the reduced-added Green function in the calculation of atomic polarizabilities

    International Nuclear Information System (INIS)

    Chernov, V.E.; Dorofeev, D.L.; Kretinin, I.Yu.; Zon, B.A.

    2005-01-01

    The Green function in the quantum defect theory provides an exact account for high-excited and continuum electronic states. We modify it by taking into account the ground and low-excited states using their wave functions calculated ab initio. As an application, we present a simple and efficient semianalytical method for the calculation of atomic electric frequency-dependent scalar dipole polarizability, for both real and imaginary frequencies. The polarizabilities calculated for some atoms (Li, Na, K, Be, Mg, Ca, Si, P, S, O, Al, Ge, C, N, F, He, Ne, Ar, Kr, and Xe) are compared with existing methods of computational quantum chemistry and with experiments; good accuracy of the proposed method is demonstrated

  5. Polarizability of Kr6+ from high-L Kr5+ fine-structure measurements

    International Nuclear Information System (INIS)

    Lundeen, S. R.; Fehrenbach, C. W.

    2007-01-01

    The transition between n=55 and n=109 Rydberg levels of Kr 5+ has been studied at high resolution using the resonant excitation stark ionization spectroscopy method. Resolved excitation of L=6, 7, 8, and 9 levels in n=55 lead to a determination of the fine-structure energies of these levels. Interpreted with the long-range polarization model, this leads to a measurement of the dipole polarizabilities of Zn-like Kr 6+ , α d =2.69(4)a 0 3 . Obtaining a value of the quadrupole polarizability from the data will require additional theoretical input. Factors contributing to the signal and noise levels in measurements of this type are discussed

  6. Quasi-free Compton scattering and the polarizabilities of the neutron

    International Nuclear Information System (INIS)

    Kossert, K.; Camen, M.; Wissmann, F.; Schumacher, M.; Seitz, B.; Ahrens, J.; Arends, H.J.; Beck, R.; Caselotti, G.; Jahn, O.; Jennewein, P.; Olmos de Leon, V.; Annand, J.R.M.; McGeorge, J.C.; Rosner, G.; Grabmayr, P.; Natter, A.; Levchuk, M.I.; L'vov, A.I.; Petrun'kin, V.A.; Smend, F.; Thomas, A.; Weihofen, W.; Zapadtka, F.

    2003-01-01

    Differential cross-sections for quasi-free Compton scattering from the proton and neutron bound in the deuteron have been measured using the Glasgow/Mainz photon tagging spectrometer at the Mainz MAMI accelerator together with the Mainz 48cm diameter x 64cm NaI(Tl) photon detector and the Goettingen SENECA recoil detector. The data cover photon energies ranging from 200MeV to 400MeV at θ LAB γ =136.2 . Liquid deuterium and hydrogen targets allowed direct comparison of free and quasi-free scattering from the proton. The neutron detection efficiency of the SENECA detector was measured via the reaction p(γ,π + n). The ''free'' proton Compton scattering cross-sections extracted from the bound proton data are in reasonable agreement with those for the free proton which gives confidence in the method to extract the differential cross-section for free scattering from quasi-free data. Differential cross-sections on the free neutron have been extracted and the difference of the electromagnetic polarizabilities of the neutron has been determined to be α n -β n =9.8±3.6(stat) +2.1 -1.1 (syst)±2.2(model) in units of 10 -4 fm 3 . In combination with the polarizability sum α n +β n =15.2±0.5 deduced from photoabsorption data, the neutron electric and magnetic polarizabilities, α n =12.5±1.8(stat) + 1 .1 -0.6 (syst)±1.1(model) and β n =2.7±1.8(stat) +0.6 -1.1 (syst)±1.1(model) are obtained. The backward spin polarizability of the neutron was determined to be γ (n) π =(58.6±4.0) x 10 -4 fm 4 . (orig.)

  7. Natural Fe3O4 nanoparticles embedded zinc–tellurite glasses: Polarizability and optical properties

    International Nuclear Information System (INIS)

    Widanarto, W.; Sahar, M.R.; Ghoshal, S.K.; Arifin, R.; Rohani, M.S.; Hamzah, K.; Jandra, M.

    2013-01-01

    Modifying the optical behavior of zinc–tellurite glass by embedding magnetic nanoparticles has implication in nanophotonics. A series of zinc–tellurite glasses containing natural Fe 3 O 4 nanoparticles with composition (80 − x)TeO 2 ·xFe 3 O 4 ·20ZnO (0 ≤ x ≤ 2) in mol% are synthesized by melt quenching method and their optical properties are investigated using FTIR and UV–vis–NIR spectroscopies. Lorentz–Lorenz relations are exploited to determine the refractive index, molar refraction and electronic polarizability. The sharp absorption peaks of FTIR spectra show a shift from 667 cm −1 to 671 cm −1 in the presence of nanoparticles that increase the non-bridging oxygen, confirmed by the intensity change of the TeO 3 peak at 752 cm −1 . A new peak around 461 cm −1 is also observed which is attributed to the band characteristic of covalent Fe–O linkages. A decrease in the Urbach energy as much as 0.122 eV and the optical energy band gap with the increase of Fe 3 O 4 concentration (0.5–1.0 mol%) is evidenced. Electronic polarizability of the glasses increases with increasing Fe 3 O 4 nanoparticles concentration up to 1 mol%. Interestingly, the polarizability tends to decrease with the further increase of Fe 3 O 4 concentration at 2 mol%. The role of magnetic nanoparticles in influencing the structural and optical behavior are examined and understood. - Highlights: ► Incorporation of natural Fe 3 O 4 nanoparticles into the zinc–tellurite glass. ► Influence of magnetic nanoparticles in modifying structure and optical properties. ► Enhancement of refraction index and change in electronic polarizability

  8. Nucleon electric polarizability in soliton models and the role of the seagull terms

    International Nuclear Information System (INIS)

    Scoccola, N.N.; Cohen, T.D.

    1996-01-01

    The full Hamiltonian of the soliton models contains no electric seagull terms. Here it is shown that if one restricts the fields to the collective subspace then electric seagull terms are induced in the effective Hamiltonian. These effective seagull contributions are consistent with gauge invariance. They also reproduce the leading non-analytic behavior of a large N c chiral perturbation theory calculation of the electric polarizability. (orig.)

  9. Calculation of dipole polarizability derivatives of adamantane and their use in electron scattering computations

    Czech Academy of Sciences Publication Activity Database

    Sauer, S. P. A.; Paidarová, Ivana; Čársky, Petr; Čurík, Roman

    2016-01-01

    Roč. 70, č. 5 (2016), č. článku 105. ISSN 1434-6060 R&D Projects: GA MŠk LD14088 Grant - others:COST(XE) CM1301 Institutional support: RVO:61388955 Keywords : DENSITY-FUNCTIONAL- THEORY * COUPLED-CLUSTER CALCULATIONS * FREQUENCY-DEPENDENT POLARIZABILITIES Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.288, year: 2016

  10. Many-body calculations of molecular electric polarizabilities in asymptotically complete basis sets

    Science.gov (United States)

    Monten, Ruben; Hajgató, Balázs; Deleuze, Michael S.

    2011-10-01

    The static dipole polarizabilities of Ne, CO, N2, F2, HF, H2O, HCN, and C2H2 (acetylene) have been determined close to the Full-CI limit along with an asymptotically complete basis set (CBS), according to the principles of a Focal Point Analysis. For this purpose the results of Finite Field calculations up to the level of Coupled Cluster theory including Single, Double, Triple, Quadruple and perturbative Pentuple excitations [CCSDTQ(P)] were used, in conjunction with suited extrapolations of energies obtained using augmented and doubly-augmented Dunning's correlation consistent polarized valence basis sets of improving quality. The polarizability characteristics of C2H4 (ethylene) and C2H6 (ethane) have been determined on the same grounds at the CCSDTQ level in the CBS limit. Comparison is made with results obtained using lower levels in electronic correlation, or taking into account the relaxation of the molecular structure due to an adiabatic polarization process. Vibrational corrections to electronic polarizabilities have been empirically estimated according to Born-Oppenheimer Molecular Dynamical simulations employing Density Functional Theory. Confrontation with experiment ultimately indicates relative accuracies of the order of 1 to 2%.

  11. Communication: Polarizable polymer chain under external electric field in a dilute polymer solution.

    Science.gov (United States)

    Budkov, Yu A; Kolesnikov, A L; Kiselev, M G

    2015-11-28

    We study the conformational behavior of polarizable polymer chain under an external homogeneous electric field within the Flory type self-consistent field theory. We consider the influence of electric field on the polymer coil as well as on the polymer globule. We show that when the polymer chain conformation is a coil, application of external electric field leads to its additional swelling. However, when the polymer conformation is a globule, a sufficiently strong field can induce a globule-coil transition. We show that such "field-induced" globule-coil transition at the sufficiently small monomer polarizabilities goes quite smoothly. On the contrary, when the monomer polarizability exceeds a certain threshold value, the globule-coil transition occurs as a dramatic expansion in the regime of first-order phase transition. The developed theoretical model can be applied to predicting polymer globule density change under external electric field in order to provide more efficient processes of polymer functionalization, such as sorption, dyeing, and chemical modification.

  12. The determination of accurate dipole polarizabilities alpha and gamma for the noble gases

    Science.gov (United States)

    Rice, Julia E.; Taylor, Peter R.; Lee, Timothy J.; Almloef, Jan

    1989-01-01

    The static dipole polarizabilities alpha and gamma for the noble gases helium through xenon were determined using large flexible one-particle basis sets in conjunction with high-level treatments of electron correlation. The electron correlation methods include single and double excitation coupled-cluster theory (CCSD), an extension of CCSD that includes a perturbational estimate of connected triple excitations, CCSD(T), and second order perturbation theory (MP2). The computed alpha and gamma values are estimated to be accurate to within a few percent. Agreement with experimental data for the static hyperpolarizability gamma is good for neon and xenon, but for argon and krypton the differences are larger than the combined theoretical and experimental uncertainties. Based on our calculations, we suggest that the experimental value of gamma for argon is too low; adjusting this value would bring the experimental value of gamma for krypton into better agreement with our computed result. The MP2 values for the polarizabilities of neon, argon, krypton and zenon are in reasonabe agreement with the CCSD and CCSD(T) values, suggesting that this less expensive method may be useful in studies of polarizabilities for larger systems.

  13. Electroabsorption spectra of carotenoid isomers: Conformational modulation of polarizability vs. induced dipole moments

    International Nuclear Information System (INIS)

    Krawczyk, Stanislaw; Jazurek, Beata; Luchowski, Rafal; Wiacek, Dariusz

    2006-01-01

    Electroabsorption spectra of all-trans, 13-cis and 15-cis isomers of carotenoids violaxanthin and β-carotene frozen in organic solvents were analysed in terms of changes in permanent dipole moment, Δμ, and in the linear polarizability, Δα, on electronic excitation. The spectral range investigated covered the two carotenoid absorption bands in the VIS and UV, known to originate from differently oriented transition dipole moments. In contrast with the collinearity of the apparent Δμ with Δα in the lowest-energy allowed (VIS) transition 1A g - ->1B u + , the axis of the largest polarizability change in the UV transition 1A g - ->1A g + (''cis band'') was found to make a large angle with the transition moment, while the direction of Δμ appears to be much closer to it. These data support the view that Δμ's inferred from electrochromic spectra of carotenoids are apparent and are not induced by the local matrix field in the solvent cavity, but merely result from conformational modulation of molecular polarizability

  14. Bioaccumulation of pathogenic bacteria and amoeba by zebra mussels and their presence in watercourses.

    Science.gov (United States)

    Mosteo, R; Goñi, P; Miguel, N; Abadías, J; Valero, P; Ormad, M P

    2016-01-01

    Dreissena polymorpha (the zebra mussel) has been invading freshwater bodies in Europe since the beginning of the nineteenth century. Filter-feeding organisms can accumulate and concentrate both chemical and biological contaminants in their tissues. Therefore, zebra mussels are recognized as indicators of freshwater quality. In this work, the capacity of the zebra mussel to accumulate human pathogenic bacteria and protozoa has been evaluated and the sanitary risk associated with their presence in surface water has also been assessed. The results show a good correlation between the pathogenic bacteria concentration in zebra mussels and in watercourses. Zebra mussels could therefore be used as an indicator of biological contamination. The bacteria (Escherichia coli, Enterococcus spp., Pseudomonas spp., and Salmonella spp.) and parasites (Cryptosporidium oocysts and free-living amoebae) detected in these mussels reflect a potential sanitary risk in water.

  15. Spontaneous emergence of large-scale cell cycle synchronization in amoeba colonies

    International Nuclear Information System (INIS)

    Segota, Igor; Boulet, Laurent; Franck, David; Franck, Carl

    2014-01-01

    Unicellular eukaryotic amoebae Dictyostelium discoideum are generally believed to grow in their vegetative state as single cells until starvation, when their collective aspect emerges and they differentiate to form a multicellular slime mold. While major efforts continue to be aimed at their starvation-induced social aspect, our understanding of population dynamics and cell cycle in the vegetative growth phase has remained incomplete. Here we show that cell populations grown on a substrate spontaneously synchronize their cell cycles within several hours. These collective population-wide cell cycle oscillations span millimeter length scales and can be completely suppressed by washing away putative cell-secreted signals, implying signaling by means of a diffusible growth factor or mitogen. These observations give strong evidence for collective proliferation behavior in the vegetative state. (paper)

  16. Amoeba-like self-oscillating polymeric fluids with autonomous sol-gel transition.

    Science.gov (United States)

    Onoda, Michika; Ueki, Takeshi; Tamate, Ryota; Shibayama, Mitsuhiro; Yoshida, Ryo

    2017-07-13

    In the field of polymer science, many kinds of polymeric material systems that show a sol-gel transition have been created. However, most systems are unidirectional stimuli-responsive systems that require physical signals such as a change in temperature. Here, we report on the design of a block copolymer solution that undergoes autonomous and periodic sol-gel transition under constant conditions without any on-off switching through external stimuli. The amplitude of this self-oscillation of the viscosity is about 2,000 mPa s. We also demonstrate an intermittent forward motion of a droplet of the polymer solution synchronized with the autonomous sol-gel transition. This polymer solution bears the potential to become the base for a type of slime-like soft robot that can transform its shape kaleidoscopically and move autonomously, which is associated with the living amoeba that moves forward by a repeated sol-gel transition.

  17. Giants among larges: how gigantism impacts giant virus entry into amoebae.

    Science.gov (United States)

    Rodrigues, Rodrigo Araújo Lima; Abrahão, Jônatas Santos; Drumond, Betânia Paiva; Kroon, Erna Geessien

    2016-06-01

    The proposed order Megavirales comprises the nucleocytoplasmic large DNA viruses (NCLDV), infecting a wide range of hosts. Over time, they co-evolved with different host cells, developing various strategies to penetrate them. Mimiviruses and other giant viruses enter cells through phagocytosis, while Marseillevirus and other large viruses explore endocytosis and macropinocytosis. These differing strategies might reflect the evolution of those viruses. Various scenarios have been proposed for the origin and evolution of these viruses, presenting one of the most enigmatic issues to surround these microorganisms. In this context, we believe that giant viruses evolved independently by massive gene/size gain, exploring the phagocytic pathway of entry into amoebas. In response to gigantism, hosts developed mechanisms to evade these parasites. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Reaching an entrepreneurial management system of amoebas. A qualitative insight into the European experiences

    Directory of Open Access Journals (Sweden)

    Urban Wiesław

    2016-03-01

    Full Text Available The aim of the study is an assessment of the Amoeba Management System (AMS introduction advancements in some European companies. The study takes the practically focused research approach. The approaches, achievements and phases whilst introducing the AMS principles by companies are observed and critically assessed. First insight into the challenges of AMS introduction is taken basing on critical study of the literature output. The scientific studies and managerial publications are taken into consideration. The empirical part of the study is based on the qualitative approach. A multiple case study methodology is employed. The research objects are three companies, one of them operates in Sweden, the next two in Poland. Each of them have different experiences in AMS implementation, they also manifest different management styles and habits. The study demonstrates that AMS is a very prospective management methodology which can support companies in employees commitment during their journey towards operational excellence. The analysis results show different motivations for AMS introduction as well as different development paths, these are harmonized with different management styles in companies and culture occurring in countries. The study is particularly valuable because this is one of the first empirical investigations of AMS implementation in European companies. In the field of theory the study proposes the four level scale for amoebas system maturity. This scale allows to classify companies following AMS principles and, at the same time, this scale is also the kind of path of AMS implementation. The study points out basic tools for companies which support AMS implementation. These tools are already known in management literature, but experience of investigated companies shows that they are fundamental for successful AMS implementation.

  19. Check-list of microscopic protosteloid amoebae from the Southwest of Europe

    Directory of Open Access Journals (Sweden)

    Aguilar, María

    2012-12-01

    Full Text Available A biodiversity survey for protosteloid amoebae was carried out in Spain, Portugal and France between 2005 and 2010. Samples were collected from three different microhabitats – aerial litter, ground litter, and bark of living plants – in a total of 97 localities. As result 26 to 28 species out of the 33 species of microscopic protosteloid amoebae described to date were recorded. An annotated list that comprises all available data about these organisms from this part of the world, a key to the species, comments on the morphology of the sporocarps and the trophic stages is presented. Photomicrographs of the fruiting bodies of most species, and distribution maps are also included.

    Se ha realizado un estudio de la biodiversidad de las amebas protos - teloides en España, Portugal y Francia entre 2005 y 2010. Las muestras se recolectaron en tres microhábitats diferentes –hojarasca aérea, hojarasca del suelo y corteza de plantas vivas– en un total de 97 localidades. Como resultado se encontraron entre 26 y 28 especies de las 33 especies de amebas protosteloides microscópicas descritas. Se presenta una lista comentada que contiene todos los datos disponibles sobre estos organismos en esta parte del mundo, una clave de las especies y comentarios sobre la morfología de los esporocarpos y de los estados tróficos. También se incluyen fotomicrografías de los cuerpos fructíferos de la mayoría de las especies y mapas de distribución.

  20. Holocene environmental changes in southern Kamchatka, Far Eastern Russia, inferred from a pollen and testate amoebae peat succession record

    Science.gov (United States)

    Klimaschewski, A.; Barnekow, L.; Bennett, K. D.; Andreev, A. A.; Andrén, E.; Bobrov, A. A.; Hammarlund, D.

    2015-11-01

    High resolution palaeoenvironmental records in Far-Eastern Russia are rare, and the Kamchatka Peninsula is among the least studied areas of the region. This paper describes a record spanning the last ca. 11,000 yr, obtained from a bog in the southern part of Kamchatka. The radiocarbon dated core was analysed for pollen, testate amoebae, charcoal and loss-on-ignition (LOI). The vegetation during the early Holocene was dominated by grasses (Poaceae), birch (Betula) and heath (Ericaceae p. p.). Around 10,300 cal yr BP there was a substantial change in the vegetation cover to shrub alder (Alnus viridis s.l.) stands with sedges and ferns (Polypodiophyta) as well as herbs such as meadow rue (Thalictrum) in the understory. In the surroundings of Utka peatlands started to form. The variations in the vegetation cover were most probably caused by climatic changes. At the beginning of sediment accumulation, before 10,300 cal yr BP, the composition of the vegetation points to cooler summers and/or decreased annual precipitation. Around 10,300 cal yr BP, changes in vegetation occurred due to rising temperatures and/or changed water regimes. Increased abundancies of dry indicating testate amoebae after 9100 cal yr BP point to intermediate to dry soil conditions. Between 8600 and 7700 cal yr BP tree alder (Alnus incana) was widely spread at the site which probably indicates optimal environmental conditions. The tephra layer at 381-384.5 cm (ca. 8500 cal yr BP) produces a strong impact on the testate amoebae assemblages. At 7700 cal yr BP there was a sudden drop of A. incana in the local vegetation. From this time on, A. incana and also A. viridis decrease continuously whereas Betula gradually increases. The upper part of the sequence (after 6300 cal yr BP) shows higher abundancies of meadowsweet (Filipendula) and sweet gale (Myrica) pollen. After 6300 cal yr BP, changes in testate amoebae demonstrate variable soil moisture conditions at the site. Between 3700 and 1800 cal yr BP

  1. Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

    Science.gov (United States)

    Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

    2015-01-01

    Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

  2. Fabricating off-diagonal components of frequency-dependent linear and nonlinear polarizabilities of doped quantum dots by Gaussian white noise

    International Nuclear Information System (INIS)

    Saha, Surajit; Ganguly, Jayanta; Ghosh, Manas

    2015-01-01

    We make a rigorous exploration of the profiles of off-diagonal components of frequency-dependent linear (α xy , α yx ), first nonlinear (β xyy , β yxx ), and second nonlinear (γ xxyy , γ yyxx ) polarizabilities of quantum dots driven by Gaussian white noise. The quantum dot is doped with repulsive Gaussian impurity. Noise has been applied additively and multiplicatively to the system. An external oscillatory electric field has also been applied to the system. Gradual variations of external frequency, dopant location, and noise strength give rise to interesting features of polarizability components. The observations reveal intricate interplay between noise strength and dopant location which designs the polarizability profiles. Moreover, the mode of application of noise also modulates the polarizability components. Interestingly, in case of additive noise the noise strength has no role on polarizabilities whereas multiplicative noise invites greater delicacy in them. The said interplay provides a rather involved framework to attain stable, enhanced, and often maximized output of linear and nonlinear polarizabilities. - Highlights: • Linear and nonlinear polarizabilities of quantum dot are studied. • The polarizability components are off-diagonal and frequency-dependent. • Quantum dot is doped with a repulsive impurity. • Doped system is subject to Gaussian white noise. • Mode of noise application affects polarizabilities

  3. Distribution of Legionella pneumophila bacteria and Naegleria and Hartmannella amoebae in thermal saline baths used in balneotherapy.

    Science.gov (United States)

    Zbikowska, Elżbieta; Walczak, Maciej; Krawiec, Arkadiusz

    2013-01-01

    The present study was aimed at investigating the coexistence and interactions between free living amoebae of Naegleria and Hartmannella genera and pathogenic Legionella pneumophila bacteria in thermal saline baths used in balneotherapy in central Poland. Water samples were collected from November 2010 to May 2011 at intervals longer than 1 month. The microorganisms were detected with the use of a very sensitive fluorescence in situ hybridisation method. In addition, the morphology of the amoebae was studied. Despite relatively high salinity level, ranging from 1.5 to 5.0 %, L. pneumophila were found in all investigated baths, although their number never exceeded 10(6) cells dm(-3). Hartmannella were not detected, while Naegleria fowleri were found in one bath. The observation that N. fowleri and L. pneumophila may coexist in thermal saline baths is the first observation emphasising potential threat from these microorganisms in balneotherapy.

  4. Growth regulation of Legionella Pneumophila in biofilms and amoebae; Wachstumsregulation von Legionella Pneumophila in Biofilmen und Amoeben

    Energy Technology Data Exchange (ETDEWEB)

    Hilbi, H.

    2006-07-01

    This final report for the Swiss Federal Office of Energy (SFOE) presents the results of studies made on the regulation of the growth of Legionella Pneumophila bacteria in biofilms and amoebae. In a first project, the formation of biofilms by Legionella Pneumophila bacteria was analysed in static and dynamic systems using a complex growth medium. Under static and dynamic clinical and environmental conditions, the adherence of the biofilms on polystyrene tissue was studied. This was also examined under dynamic flow conditions. In a second part of the project, the regulation of growth of Legionella Pneumophila in amoebae was examined in that changes were made to the genome of the bacteria. The importance of the work for the de-activation of Legionella Pneumophila bacteria in biofilms is noted in the conclusions of the report.

  5. Growth-supporting activity for Legionella pneumophila in tap water cultures and implication of hartmannellid amoebae as growth factors.

    Science.gov (United States)

    Wadowsky, R M; Butler, L J; Cook, M K; Verma, S M; Paul, M A; Fields, B S; Keleti, G; Sykora, J L; Yee, R B

    1988-11-01

    Photosynthetic cyanobacteria, heterotrophic bacteria, free-living amoebae, and ciliated protozoa may support growth of Legionella pneumophila. Studies were done with two tap water cultures (WS1 and WS2) containing L. pneumophila and associated microbiota to characterize growth-supporting activity and assess the relative importance of the microbiota in supporting multiplication of L. pneumophila. The water cultures were incubated in the dark at 35 degrees C. The growth-supporting factor(s) was separated from each culture by filtration through 1-micron-pore-size membrane filters. The retentate was then suspended in sterile tap water. Multiplication of L. pneumophila occurred when both the retentate suspension and the filtrate from either culture were inoculated into sterile tap water. L. pneumophila did not multiply in tap water inoculated with only the filtrate, even though filtration did not reduce the concentration of L. pneumophila or heterotrophic bacteria in either culture. Growth-supporting activity of the retentate suspension from WS1 was inactivated at 60 degrees C but unaffected at 0, 25, and 45 degrees C after 30-min incubations. Filtration experiments indicated that the growth-supporting factor(s) in WS1 was 2 to 5 micron in diameter. Ciliated protozoa were not detected in either culture. Hartmannellid amoebae were conclusively demonstrated in WS2 but not in WS1. L. pneumophila multiplied in tap water inoculated with the amoebae (10(3)/ml) and the 1-micron filtrate of WS2. No multiplication occurred in tap water inoculated with the filtrate only. Growth-supporting activity for L. pneumophila may be present in plumbing systems; hartmannellid amoebae appear to be important determinants of multiplication of L. pneumophila in some tap water cultures.

  6. The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems

    Science.gov (United States)

    Bosak, Tanja; Lara, Enrique; Mitchell, Edward A.D.

    2015-01-01

    The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si. PMID:26734499

  7. An analysis of hereditary increase in frequency of cell mortality induced by external factors (Experiments on nuclear transplantation in amoebae)

    International Nuclear Information System (INIS)

    Bychkovskaya, I.B.; Ochinskaya, G.K.; Yudin, A.L.; AN SSSR, Leningrad. Inst. Tsitologii)

    1980-01-01

    By using nuclear transplantations in Amoeba proteus a study was made of a peculiar heritable effect, a stable increase in the frequency of cell mortality incuced by comparatively low doses of x radiation (50 Gy) or slight heating (29 0 C during 6 to 7 h). This effect differs qualitatively from the known radiation effects (reproductive death, lethal sectoring) by its being non-specific for radiation. In addition, the effect is saltatory appearing in 100% of the treated cells and the extent of its expression is not dependent on the dose of an inducing factor (at supra-threshold doses) and the period of time after treatment. It was found that (1) the hereditary changes in amoebae, unlike those resulting in reproductive death, are transmitted during intercellular transplantations both by the nucleus and cytoplasm of an altered cell; (2) the transfer of the character under test is accomplished by means of a certiin factor capable of shuttling between the nucleus and cytoplasm, (3) the effect is not necessarily a consequence of primary injury of nuclear structures and it may be induced by treatment of the cytoplasm of an enucleated cell renucleated then by the nucleus of a normal amoeba. In this respect, the effect under test differs also from the known types of hereditary post-radiation lethal effects which are commonly suggested to involve primary injury of the nucleus. Possible mechanisms of genetic control over the character tested are discussed. (author)

  8. Potentially pathogenic free-living amoebae in some flood-affected areas during 2011 Chiang Mai flood.

    Science.gov (United States)

    Wannasan, Anchalee; Uparanukraw, Pichart; Songsangchun, Apichart; Morakote, Nimit

    2013-01-01

    The survey was carried out to investigate the presence of potentially pathogenic free-living amoebae (FLA) during flood in Chiang Mai, Thailand in 2011. From different crisis flood areas, seven water samples were collected and tested for the presence of amoebae using culture and molecular methods. By monoxenic culture, FLA were detected from all samples at 37 °C incubation. The FLA growing at 37 °C were morphologically identified as Acanthamoeba spp., Naegleria spp. and some unidentified amoebae. Only three samples (42.8%), defined as thermotolerant FLA, continued to grow at 42 °C. By molecular methods, two non-thermotolerant FlA were shown to have 99% identity to Acanthamoeba sp. and 98% identity to Hartmannella vermiformis while the two thermotolerant FLA were identified as Echinamoeba exundans (100% identity) and Hartmannella sp. (99% identity). This first report of the occurrence of FLA in water during the flood disaster will provide information to the public to be aware of potentially pathogenic FLA.

  9. Pathogenic free-living amoebae in a closed-loop power plant; risk assessment and risk management

    International Nuclear Information System (INIS)

    Cabanes, P.; Pernin, P.

    1998-01-01

    Since 1980, the water used for cooling in French power plants has been tested for pathogenic amoebae, especially Naegleria fowleri, the causative agent of Primary Amoebic Meningoencephalitis (PAM), a rapid fatal disease of the central nervous system. The replacement of brass condensers by stainless steel condensers resulted in increased Naegleria fowleri development, to a density of as much as 3000 l -1 in the Dampierre power plant cooling water. Downstream from Dampierre, the maximum detected density of this amoeba during the summer of 1995 was 80 l -1 , at low river flow. The replacement of a second condenser in 1996 at the same power plant was expected to double the amoebae concentration in the river. The hypothetical PAM risk for swimmers was then predicted to be 10 -4 per swim. To reduce the risk continuous chlorination of the closed-loop cooling system was implemented at a free residual chlorine level in the range of 0.3-0.5 mg.l -1 . Naegleria fowleri concentrations decreased immediately and thereafter remained under 4 l -1 . Total residual chlorine and chlorinated organic compounds were also monitored in the evaluation of the environmental impact of this preventive action. (authors)

  10. Coupled influence of noise and damped propagation of impurity on linear and nonlinear polarizabilities of doped quantum dots

    International Nuclear Information System (INIS)

    Ganguly, Jayanta; Ghosh, Manas

    2015-01-01

    Highlights: • Linear and nonlinear polarizabilities of quantum dot are studied. • Quantum dot is doped with a repulsive impurity. • Doped system is subject to Gaussian white noise. • Dopant migrates under damped condition. • Noise-damping coupling affects polarizabilities. - Abstract: We investigate the profiles of diagonal components of static and frequency-dependent linear, first, and second nonlinear polarizabilities of repulsive impurity doped quantum dot. We have considered propagation of dopant within an environment that damps the motion. Simultaneous presence of noise inherent to the system has also been considered. The dopant has a Gaussian potential and noise considered is a Gaussian white noise. The doped system is exposed to an external electric field which could be static or time-dependent. Noise undergoes direct coupling with damping and the noise-damping coupling strength appears to be a crucial parameter that designs the profiles of polarizability components. This happens because the coupling strength modulates the dispersive and asymmetric character of the system. The frequency of external field brings about additional features in the profiles of polarizability components. The present investigation highlights some useful features in the optical properties of doped quantum dots

  11. Atom interferometry experiments with lithium. Accurate measurement of the electric polarizability

    International Nuclear Information System (INIS)

    Miffre, A.

    2005-06-01

    Atom interferometers are very sensitive tools to make precise measurements of physical quantities. This study presents a measurement of the static electric polarizability of lithium by atom interferometry. Our result, α = (24.33 ± 0.16)*10 -30 m 3 , improves by a factor 3 the most accurate measurements of this quantity. This work describes the tuning and the operation of a Mach-Zehnder atom interferometer in detail. The two interfering arms are separated by the elastic diffraction of the atomic wave by a laser standing wave, almost resonant with the first resonance transition of lithium atom. A set of experimental techniques, often complicated to implement, is necessary to build the experimental set-up. After a detailed study of the atom source (a supersonic beam of lithium seeded in argon), we present our experimental atom signals which exhibit a very high fringe visibility, up to 84.5 % for first order diffraction. A wide variety of signals has been observed by diffraction of the bosonic isotope at higher diffraction orders and by diffraction of the fermionic less abundant isotope. The quality of these signals is then used to do very accurate phase measurements. A first experiment investigates how the atom interferometer signals are modified by a magnetic field gradient. An absolute measurement of lithium atom electric polarizability is then achieved by applying a static electric field on one of the two interfering arms, separated by only 90 micrometers. The construction of such a capacitor, its alignment in the experimental set-up and its operation are fully detailed.We obtain a very accurate phase measurement of the induced Lo Surdo - Stark phase shift (0.07 % precision). For this first measurement, the final uncertainty on the electric polarizability of lithium is only 0.66 %, and is dominated by the uncertainty on the atom beam mean velocity, so that a further reduction of the uncertainty can be expected. (author)

  12. Polarizabilities and hyperpolarizabilities for the atoms Al, Si, P, S, Cl, and Ar: Coupled cluster calculations.

    Science.gov (United States)

    Lupinetti, Concetta; Thakkar, Ajit J

    2005-01-22

    Accurate static dipole polarizabilities and hyperpolarizabilities are calculated for the ground states of the Al, Si, P, S, Cl, and Ar atoms. The finite-field computations use energies obtained with various ab initio methods including Moller-Plesset perturbation theory and the coupled cluster approach. Excellent agreement with experiment is found for argon. The experimental alpha for Al is likely to be in error. Only limited comparisons are possible for the other atoms because hyperpolarizabilities have not been reported previously for most of these atoms. Our recommended values of the mean dipole polarizability (in the order Al-Ar) are alpha/e(2)a(0) (2)E(h) (-1)=57.74, 37.17, 24.93, 19.37, 14.57, and 11.085 with an error estimate of +/-0.5%. The recommended values of the mean second dipole hyperpolarizability (in the order Al-Ar) are gamma/e(4)a(0) (4)E(h) (-3)=2.02 x 10(5), 4.31 x 10(4), 1.14 x 10(4), 6.51 x 10(3), 2.73 x 10(3), and 1.18 x 10(3) with an error estimate of +/-2%. Our recommended polarizability anisotropy values are Deltaalpha/e(2)a(0) (2)E(h) (-1)=-25.60, 8.41, -3.63, and 1.71 for Al, Si, S, and Cl respectively, with an error estimate of +/-1%. The recommended hyperpolarizability anisotropies are Deltagamma/e(4)a(0) (4)E(h) (-3)=-3.88 x 10(5), 4.16 x 10(4), -7.00 x 10(3), and 1.65 x 10(3) for Al, Si, S, and Cl, respectively, with an error estimate of +/-4%. (c) 2005 American Institute of Physics.

  13. Simulations of Coulomb systems confined by polarizable surfaces using periodic Green functions.

    Science.gov (United States)

    Dos Santos, Alexandre P; Girotto, Matheus; Levin, Yan

    2017-11-14

    We present an efficient approach for simulating Coulomb systems confined by planar polarizable surfaces. The method is based on the solution of the Poisson equation using periodic Green functions. It is shown that the electrostatic energy arising from the surface polarization can be decoupled from the energy due to the direct Coulomb interaction between the ions. This allows us to combine an efficient Ewald summation method, or any other fast method for summing over the replicas, with the polarization contribution calculated using Green function techniques. We apply the method to calculate density profiles of ions confined between the charged dielectric and metal surfaces.

  14. Role of polarizability in the 3H(d,n)4He reaction

    International Nuclear Information System (INIS)

    Belyaev, V.B.; Kuzmichev, V.E.; Peresypkin, V.V.; Zepalova, M.L.

    1987-01-01

    The influence is investigated of the deuteron electric dipole polarizability on the cross section, astrophysical S-factor, and the yield of helium nuclei in the 3 H(d,n) 4 He reaction in the region of extremely low energies. Prediction is made of the existence of narrow maximum in the cross section at energies of an incident triton lower that 10 keV produced by the action of an attractive polarization potential in the d 3 H system. The growth of the cross section of d 3 H reaction increases the yield of 4 He nuclei at temperatures lower than keV

  15. Dynamical polarizability of graphene irradiated by circularly polarized ac electric fields

    DEFF Research Database (Denmark)

    Busl, Maria; Platero, Gloria; Jauho, Antti-Pekka

    2012-01-01

    We examine the low-energy physics of graphene in the presence of a circularly polarized electric field in the terahertz regime. Specifically, we derive a general expression for the dynamical polarizability of graphene irradiated by an ac electric field. Several approximations are developed...... that allow one to develop a semianalytical theory for the weak-field regime. The ac field changes qualitatively the single- and many-electron excitations of graphene: Undoped samples may exhibit collective excitations (in contrast to the equilibrium situation), and the properties of the excitations in doped...

  16. Ion Transfer Voltammetry Associated with Two Polarizable Interfaces Within Water and Moderately Hydrophobic Ionic Liquid Systems

    DEFF Research Database (Denmark)

    Gan, Shiyu; Zhou, Min; Zhang, Jingdong

    2013-01-01

    An electrochemical system composed of two polarizable interfaces (the metallic electrode|water and water|ionic liquid interfaces), namely two‐polarized‐interface (TPI) technique, has been proposed to explore the ion transfer processes between water and moderately hydrophobic ionic liquids (W...... to an extremely narrow polarized potential window (ppw) caused by these moderately hydrophobic ionic components. In this article, we show that TPI technique has virtually eliminated the ppw limitation based on a controlling step of concentration polarization at the electrode|water interface. With the aid...

  17. Relativistic Quadrupole Polarizability for the Ground State of Hydrogen-Like Ions

    International Nuclear Information System (INIS)

    Zhang Yong-Hu; Zhang Xian-Zhou; Tang Li-Yan; Shi Ting-Yun; Mitroy Jim

    2012-01-01

    The static quadrupole polarizabilities for hydrogen-like ions from Z = 1 to Z = 100 in the 1S 1/2 ground state are calculated to high precision by solving the Dirac equation using the B-spline Galerkin method. The results are consistent with the expression of Kaneko [J. Phys. B 10 (1977) 3347] at low Z. The quadrupole oscillator strength sum Σ n f (2) gn is computed to be zero to a very high degree of precision. (atomic and molecular physics)

  18. Performance test of multicomponent quantum mechanical calculation with polarizable continuum model for proton chemical shift.

    Science.gov (United States)

    Kanematsu, Yusuke; Tachikawa, Masanori

    2015-05-21

    Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

  19. Validation of PM6 & PM7 semiempirical methods on polarizability calculations

    Science.gov (United States)

    Praveen, P. A.; Babu, R. Ramesh; Ramamurthi, K.

    2015-06-01

    Modern semiempirical methods such as PM6 and PM7 are often used to explore the electronic structure dependent properties of molecules. In this work we report the evaluation of PM6 and PM7 methods towards linear and nonlinear optical polarizability calculations for different molecules and solid nanoclusters. The results are compared with reported experimental results as well as theoretical results from other high level theories for the same systems. It is found that both methods produce accurate results for small molecules and the accuracy increases with the increase in asymmetry of the medium sized organic molecules and accuracy reduces for solid nanoclusters.

  20. Frequency dependent polarizabilities for the ground state of H2, HD, and D2

    International Nuclear Information System (INIS)

    Rychlewski, J.

    1983-01-01

    A variation-perturbation method has been employed to calculate the dynamic dipole polarizability for the ground state of the hydrogen molecule. The explicit correlated electronic wave functions were used. The averaged values of α(#betta#) and #betta#(#betta#) for several vibration-rotation states of HD and D 2 are presented. Similar values for H 2 have also been calculated and were used to test the efficiency of the method and the validity of the assumption applied in the present calculation. The agreement of the present theoretical results with the existing experimental data is found to be satisfactory

  1. Electronic structure and static dipole polarizability of C60-C240

    International Nuclear Information System (INIS)

    Zope, Rajendra R

    2008-01-01

    The electronic structure of C 60 -C 240 and its first-order response to a static electric field is studied by an all-electron density functional theory calculation using large polarized Gaussian basis sets. Our results show that the outer C 240 shell almost completely shields the inner C 60 as inferred from the practically identical values of dipole polarizability of the C 60 -C 240 onion (449 A 3 ) and that of the isolated C 240 fullerene (441 A 3 ). The C 60 -C 240 is thus a near-perfect Faraday cage

  2. Polarizability of Helium, Neon, and Argon: New Perspectives for Gas Metrology

    Science.gov (United States)

    Gaiser, Christof; Fellmuth, Bernd

    2018-03-01

    With dielectric-constant gas thermometry, the molar polarizability of helium, neon, and argon has been determined with relative standard uncertainties of about 2 parts per million. A series of isotherms measured with the three noble gases and two different experimental setups led to this unprecedented level of uncertainty. These data are crucial for scientists in the field of gas metrology, working on pressure and temperature standards. Furthermore, with the new benchmark values for neon and argon, theoretical calculations, today about 3 orders of magnitude larger in uncertainty, can be checked and improved.

  3. Sensitivity of the electric dipole polarizability to the neutron skin thickness in {sup 208}Pb

    Energy Technology Data Exchange (ETDEWEB)

    Roca-Maza, X.; Agrawal, B. K.; Colo, G.; Nazarewicz, W.; Paar, N.; Piekarewicz, J.; Reinhard, P.-G.; Vretenar, D. [INFN, sezione di Milano, via Celoria 16, I-20133 Milano (Italy); Saha Institute of Nuclear Physics, Kolkata 700064 (India); Dipartimento di Fisica, Universita degli Studi di Milano and INFN, Sezione di Milano, 20133 Milano (Italy); Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States) and Institute of Theoretical Physics, University of Warsaw, Hoza 69, PL-00-681 Warsaw (Poland); Physics Department, Faculty of Science, University of Zagreb, Zagreb (Croatia); Department of Physics, Florida State University, Tallahassee, FL 32306 (United States); Institut fuer Theoretische Physik II, Universitaet Erlangen-Nuernberg, Staudtstrasse 7, D-91058 Erlangen (Germany); Physics Department, Faculty of Science, University of Zagreb, Zagreb (Croatia)

    2012-10-20

    The static dipole polarizability, {alpha}{sub D}, in {sup 208}Pb has been recently measured with highresolution via proton inelastic scattering at the Research Center for Nuclear Physics (RCNP) [1]. This observable is thought to be intimately connected with the neutron skin thickness, r{sub skin}, of the same nucleus and, more fundamentally, it is believed to be associated with the density dependence of the nuclear symmetry energy. The impact of r{sub skin} on {alpha}{sub D} in {sup 208}Pb is investigated and discussed on the basis of a large and representative set of relativistic and non-relativistic nuclear energy density functionals (EDF) [2].

  4. Validation of PM6 & PM7 semiempirical methods on polarizability calculations

    Energy Technology Data Exchange (ETDEWEB)

    Praveen, P. A.; Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in [Crystal Growth and Thin film Laboratory, Department of Physics, Bharathidasan University, Tiruchirappalli-620024, Tamilnadu (India); Ramamurthi, K. [Department of Physics and Nanotechnology, Faculty of Engineering and Technology, SRM University, Kattankulathur – 603 203, Tamil Nadu (India)

    2015-06-24

    Modern semiempirical methods such as PM6 and PM7 are often used to explore the electronic structure dependent properties of molecules. In this work we report the evaluation of PM6 and PM7 methods towards linear and nonlinear optical polarizability calculations for different molecules and solid nanoclusters. The results are compared with reported experimental results as well as theoretical results from other high level theories for the same systems. It is found that both methods produce accurate results for small molecules and the accuracy increases with the increase in asymmetry of the medium sized organic molecules and accuracy reduces for solid nanoclusters.

  5. Validation of PM6 & PM7 semiempirical methods on polarizability calculations

    International Nuclear Information System (INIS)

    Praveen, P. A.; Babu, R. Ramesh; Ramamurthi, K.

    2015-01-01

    Modern semiempirical methods such as PM6 and PM7 are often used to explore the electronic structure dependent properties of molecules. In this work we report the evaluation of PM6 and PM7 methods towards linear and nonlinear optical polarizability calculations for different molecules and solid nanoclusters. The results are compared with reported experimental results as well as theoretical results from other high level theories for the same systems. It is found that both methods produce accurate results for small molecules and the accuracy increases with the increase in asymmetry of the medium sized organic molecules and accuracy reduces for solid nanoclusters

  6. Self-consistent nonlinearly polarizable shell-model dynamics for ferroelectric materials

    International Nuclear Information System (INIS)

    Mkam Tchouobiap, S.E.; Kofane, T.C.; Ngabireng, C.M.

    2002-11-01

    We investigate the dynamical properties of the polarizable shellmodel with a symmetric double Morse-type electron-ion interaction in one ionic species. A variational calculation based on the Self-Consistent Einstein Model (SCEM) shows that a theoretical ferroelectric (FE) transition temperature can be derive which demonstrates the presence of a first-order phase transition for the potassium selenate (K 2 SeO 4 ) crystal around Tc 91.5 K. Comparison of the model calculation with the experimental critical temperature yields satisfactory agreement. (author)

  7. Influence of Gaussian white noise on the frequency-dependent first nonlinear polarizability of doped quantum dot

    Energy Technology Data Exchange (ETDEWEB)

    Ganguly, Jayanta [Department of Chemistry, Brahmankhanda Basapara High School, Basapara, Birbhum 731215, West Bengal (India); Ghosh, Manas, E-mail: pcmg77@rediffmail.com [Department of Chemistry, Physical Chemistry Section, Visva Bharati University, Santiniketan, Birbhum 731 235, West Bengal (India)

    2014-05-07

    We investigate the profiles of diagonal components of frequency-dependent first nonlinear (β{sub xxx} and β{sub yyy}) optical response of repulsive impurity doped quantum dots. We have assumed a Gaussian function to represent the dopant impurity potential. This study primarily addresses the role of noise on the polarizability components. We have invoked Gaussian white noise consisting of additive and multiplicative characteristics (in Stratonovich sense). The doped system has been subjected to an oscillating electric field of given intensity, and the frequency-dependent first nonlinear polarizabilities are computed. The noise characteristics are manifested in an interesting way in the nonlinear polarizability components. In case of additive noise, the noise strength remains practically ineffective in influencing the optical responses. The situation completely changes with the replacement of additive noise by its multiplicative analog. The replacement enhances the nonlinear optical response dramatically and also causes their maximization at some typical value of noise strength that depends on oscillation frequency.

  8. Electric dipole moments and polarizabilities of small Bi{sub n} (n = 2-24, 40, 80) clusters

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Song; Yuan, Hong Kuan; Chen, Hong; Wu, Bo [School of Physical Science and Technology, Southwest University, Chongqing 400715 (China); Kuang, An Long [School of Physical Science and Technology, Southwest University, Chongqing 400715 (China); School of Physical Science and Technology, Suzhou University, Suzhou 215006 (China)

    2012-01-15

    The electric dipole moments (EDMs) and polarizabilities of small Bi{sub n} (n = 2-24, 40, 80) clusters are investigated by the finite field method within density functional theory (DFT). The results show that both dipole moments and polarizabilities have even-odd oscillation behaviors, and they strongly depend on geometrical structures and electronic structures. High symmetry structure prohibits the occurrence of EDMs on Bi clusters. The increasing polarizabilities of Bi clusters are attributed to the inherent novel chain-like geometrical evolution, which is significantly different from the characters observed in metal clusters or semiconductor clusters. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Unveiling exceptional Baltic bog ecohydrology, autogenic succession and climate change during the last 2000 years in CE Europe using replicate cores, multi-proxy data and functional traits of testate amoebae

    Science.gov (United States)

    Gałka, Mariusz; Tobolski, Kazimierz; Lamentowicz, Łukasz; Ersek, Vasile; Jassey, Vincent E. J.; van der Knaap, Willem O.; Lamentowicz, Mariusz

    2017-01-01

    We present the results of high-resolution, multi-proxy palaeoecological investigations of two parallel peat cores from the Baltic raised bog Mechacz Wielki in NE Poland. We aim to evaluate the role of regional climate and autogenic processes of the raised bog itself in driving the vegetation and hydrology dynamics. Based on partly synchronous changes in Sphagnum communities in the two study cores we suggest that extrinsic factors (climate) played an important role as a driver in mire development during the bog stage (500-2012 CE). Using a testate amoebae transfer function, we found exceptionally stable hydrological conditions during the last 2000 years with a relatively high water table and lack of local fire events that allowed for rapid peat accumulation (2.75 mm/year) in the bog. Further, the strong correlation between pH and community-weighted mean of testate amoeba traits suggests that other variables than water-table depth play a role in driving microbial properties under stable hydrological conditions. There is a difference in hydrological dynamics in bogs between NW and NE Poland until ca 1500 CE, after which the water table reconstructions show more similarities. Our results illustrate how various functional traits relate to different environmental variables in a range of trophic and hydrological scenarios on long time scales. Moreover, our data suggest a common regional climatic forcing in Mechacz Wielki, Gązwa and Kontolanrahka. Though it may still be too early to attempt a regional summary of wetness change in the southern Baltic region, this study is a next step to better understand the long-term peatland palaeohydrology in NE Europe.

  10. Flourish or flush: effects of simulated extreme rainfall events on Sphagnum-dwelling testate amoebae in a subarctic bog (Abisko, Sweden).

    Science.gov (United States)

    Tsyganov, Andrey N; Keuper, Frida; Aerts, Rien; Beyens, Louis

    2013-01-01

    Extreme precipitation events are recognised as important drivers of ecosystem responses to climate change and can considerably affect high-latitude ombrotrophic bogs. Therefore, understanding the relationships between increased rainfall and the biotic components of these ecosystems is necessary for an estimation of climate change impacts. We studied overall effects of increased magnitude, intensity and frequency of rainfall on assemblages of Sphagnum-dwelling testate amoebae in a field climate manipulation experiment located in a relatively dry subarctic bog (Abisko, Sweden). The effects of the treatment were estimated using abundance, species diversity and structure of living and empty shell assemblages of testate amoebae in living and decaying layers of Sphagnum. Our results show that increased rainfall reduced the mean abundance and species richness of living testate amoebae. Besides, the treatment affected species structure of both living and empty shell assemblages, reducing proportions of hydrophilous species. The effects are counterintuitive as increased precipitation-related substrate moisture was expected to have opposite effects on testate amoeba assemblages in relatively dry biotopes. Therefore, we conclude that other rainfall-related factors such as increased infiltration rates and frequency of environmental disturbances can also affect testate amoeba assemblages in Sphagnum and that hydrophilous species are particularly sensitive to variation in these environmental variables.

  11. Hydroecology of Amazonian lacustrine Arcellinida (testate amoebae): A case study from Lake Quistococha, Peru.

    Science.gov (United States)

    Patterson, R Timothy; Huckerby, Gail; Kelly, Thomas J; Swindles, Graeme T; Nasser, Nawaf A

    2015-10-01

    Organic rich sediments were obtained from seven core tops taken in Lake Quistococha, near the city of Iquitos in the Peruvian Amazon. Subsamples from 0 to 4cm depth in each core were analyzed under dissecting light microscopy to carry out the first investigation of Arcellinida (testate lobose amoebae) from a lacustrine environment in this ecologically important region. The fauna was characterized by a low diversity, low abundance community dominated by centropyxids. This fauna is similar to 'stressed' assemblages reported from temperate latitudes, except that test concentrations were two orders of magnitude lower than typical in temperate lakes. Principle arcellinidan stressors in Lake Quistococha likely include the low pH 4 conditions in the lake, and a general lack of suitable minerogenic material to construct tests in the organic rich lake substrate. The low pH conditions are the result of runoff and seepage of water high in dissolved organic carbon from the adjacent similarly low pH 4 terrestrial peatland. The dearth of minerogenic material is the result of the lake being isolated from riverine input for the past ∼2000 years, even during flooding events. Other limiting factors contributing to depressed arcellinidan populations may include nutrient supply, predation pressure, competition, and post-mortem taphonomic factors. Copyright © 2015 Elsevier GmbH. All rights reserved.

  12. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms

    Directory of Open Access Journals (Sweden)

    Claire eBertelli

    2012-08-01

    Full Text Available Based on Darwin’s concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host’s factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms.

  13. Quadrulella texcalense sp. nov. from a Mexican desert: An unexpected new environment for hyalospheniid testate amoebae.

    Science.gov (United States)

    Pérez-Juárez, Horacio; Serrano-Vázquez, Angélica; Kosakyan, Anush; Mitchell, Edward A D; Rivera Aguilar, Víctor M; Lahr, Daniel J G; Hernández Moreno, Mayra M; Cuellar, Humberto Macías; Eguiarte, Luis E; Lara, Enrique

    2017-10-01

    Quadrulella (Amoebozoa, Arcellinida, Hyalospheniidae) is a genus of testate amoebae with unmistakable morphology, which secretes characteristic square plates to reinforce the test. They are mainly known from fens and freshwater habitats and have never been documented in deserts. We describe a new species, Quadrulella texcalense, from biological soil crusts in the intertropical desert of Tehuacán (state of Puebla, Mexico). Quadrulella texcalense occurred only at altitudes between 2140 and 2221m.a.s.l., together with the bryophyte genera Pseudocrossidium, Weissia, Bryum, Didymodon, Neohyophyla and Aloina. The soil was extremely dry (moisture of 1.97-2.6%), which contrasts sharply with previous reports for the Quadrulella genus. Single cell mitochondrial cytochrome oxidase I (COI) barcoding of thirteen isolated cells showed an important morphological variability despite having all the same COI barcode sequence. Quadrulella texcalense was placed in a tree containing other Hyalsopheniidae, including a newly barcoded South African species, Q. elegans. Q. texcalense unambiguously branched within genus Quadrulella in a compact clade but with a long branch, suggesting accelerated evolution due to a transition towards a new environment and/or under-sampling. Copyright © 2017 Elsevier GmbH. All rights reserved.

  14. Influence of climate and geography on the occurrence of Legionella and amoebae in composting facilities.

    Science.gov (United States)

    Conza, Lisa; Casati Pagani, Simona; Gaia, Valeria

    2014-11-24

    The incidence of Legionnaires' disease (LD) in southern Switzerland is three times higher than in northern Switzerland. Climatic and geographic factors may be potential causes for this difference.We studied the prevalence of Legionella and free-living amoebae (FLA) in compost and bioaerosol in two Swiss regions to understand the role of climate and geography in the transmission of LD. We also tried to investigate whether or not compost storage duration would influence the composition of Legionella and FLA communities. A larger proportion of compost heaps in facilities from southern Switzerland harbor more diverse Legionella compared to the north (P=0.0146). FLA were isolated from composts in northern facilities at slightly higher rates (88.2% vs. 69.2%) and at lower rates from bioaerosols (6.3% vs. 13%) than in southern Switzerland. The diversity of FLA was higher in northern than in southern Switzerland (80% vs. 65%). A general decrease in the presence and variety of species was observed with decreasing compost storage time length. A discriminant model showed that values of vapour pressure, relative humidity and temperature distinguish the two regions, which were also characterised by different contamination rates by FLA and Legionella. The duration of outdoor storage may favour contamination of the compost by Legionella, and may increase the number and isolation of Legionella naturally occurring in compost. The climate in the south seems to favour higher Legionella contamination of compost heaps: this could explain the higher incidence of LD in southern Switzerland.

  15. The rate and effects of spontaneous mutation on fitness traits in the social amoeba, Dictyostelium discoideum.

    Science.gov (United States)

    Hall, David W; Fox, Sara; Kuzdzal-Fick, Jennie J; Strassmann, Joan E; Queller, David C

    2013-07-08

    We performed a mutation accumulation (MA) experiment in the social amoeba Dictyostelium discoideum to estimate the rate and distribution of effects of spontaneous mutations affecting eight putative fitness traits. We found that the per-generation mutation rate for most fitness components is 0.0019 mutations per haploid genome per generation or larger. This rate is an order of magnitude higher than estimates for fitness components in the unicellular eukaryote Saccharomyces cerevisiae, even though the base-pair substitution rate is two orders of magnitude lower. The high rate of fitness-altering mutations observed in this species may be partially explained by a large mutational target relative to S. cerevisiae. Fitness-altering mutations also may occur primarily at simple sequence repeats, which are common throughout the genome, including in coding regions, and may represent a target that is particularly likely to give fitness effects upon mutation. The majority of mutations had deleterious effects on fitness, but there was evidence for a substantial fraction, up to 40%, being beneficial for some of the putative fitness traits. Competitive ability within the multicellular slug appears to be under weak directional selection, perhaps reflecting the fact that slugs are sometimes, but not often, comprised of multiple clones in nature. Evidence for pleiotropy among fitness components across MA lines was absent, suggesting that mutations tend to act on single fitness components.

  16. On a relationship between molecular polarizability and partial molar volume in water.

    Science.gov (United States)

    Ratkova, Ekaterina L; Fedorov, Maxim V

    2011-12-28

    We reveal a universal relationship between molecular polarizability (a single-molecule property) and partial molar volume in water that is an ensemble property characterizing solute-solvent systems. Since both of these quantities are of the key importance to describe solvation behavior of dissolved molecular species in aqueous solutions, the obtained relationship should have a high impact in chemistry, pharmaceutical, and life sciences as well as in environments. We demonstrated that the obtained relationship between the partial molar volume in water and the molecular polarizability has in general a non-homogeneous character. We performed a detailed analysis of this relationship on a set of ~200 organic molecules from various chemical classes and revealed its fine well-organized structure. We found that this structure strongly depends on the chemical nature of the solutes and can be rationalized in terms of specific solute-solvent interactions. Efficiency and universality of the proposed approach was demonstrated on an external test set containing several dozens of polyfunctional and druglike molecules.

  17. Nucleon polarizabilities from deuteron Compton scattering within a Green's function hybrid approach

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrandt, R.P.; Hemmert, T.R. [Technische Universitaet Muenchen, Institut fuer Theoretische Physik (T39), Physik-Department, Garching (Germany); Griesshammer, H.W. [Technische Universitaet Muenchen, Institut fuer Theoretische Physik (T39), Physik-Department, Garching (Germany); Universitaet Erlangen-Nuernberg, Institut fuer Theoretische Physik III, Naturwissenschaftliche Fakultaet I, Erlangen (Germany); The George Washington University, Center for Nuclear Studies, Department of Physics, Washington DC (United States)

    2010-10-15

    We examine elastic Compton scattering from the deuteron for photon energies ranging from zero to 100MeV, using state-of-the-art deuteron wave functions and NN potentials. Nucleon-nucleon rescattering between emission and absorption of the two photons is treated by Green's functions in order to ensure gauge invariance and the correct Thomson limit. With this Green's function hybrid approach, we fulfill the low-energy theorem of deuteron Compton scattering and there is no significant dependence on the deuteron wave function used. Concerning the nucleon structure, we use the chiral effective field theory with explicit {delta} (1232) degrees of freedom within the small-scale expansion up to leading-one-loop order. Agreement with available data is good at all energies. Our 2-parameter fit to all elastic {gamma} d data leads to values for the static isoscalar dipole polarizabilities which are in excellent agreement with the isoscalar Baldin sum rule. Taking this value as additional input, we find {alpha}{sub E}{sup s} = (11.3{+-}0.7(stat){+-}0.6(Baldin){+-}1(theory)){sup .}10{sup -4} fm{sup 3} and {beta}{sub M}{sup s} = (3.2{+-}0.7(stat){+-}0.6(Baldin){+-}1(theory)){sup .}10{sup -4} fm{sup 3} and conclude by comparison to the proton numbers that neutron and proton polarizabilities are the same within rather small errors. (orig.)

  18. Band gap and polarizability of boro-tellurite glass: Influence of erbium ions

    Science.gov (United States)

    Said Mahraz, Zahra Ashur; Sahar, M. R.; Ghoshal, S. K.

    2014-08-01

    Understanding the influence of rare earth ions in improving the structural and optical properties of inorganic glasses are the key issues. Er3+-doped zinc boro-tellurite glasses with composition 30B2O3-10ZnO-(60-x) TeO2-xEr2O3 are prepared (x = 0, 0.5, 1, 1.5 and 2 mol%) using melt quenching technique. The physical and optical characterizations are measured by density and UV-Vis-IR absorption spectroscopy. The color of the glass changed from light yellow to deep pink due to the introduction of Er3+ ions. The maximum density is found to be ∼4.73 g cm-3 for 1 mol% of Er3+ doping. The variations in the polarizability (6.7-6.8 cm3) and the molar volume (27.987-28.827 cm3 mol-1) with dopant concentration are ascribed to the formation of non-bridging oxygen. This observation is consistent with the alteration of number of bonds per unit volume. The direct and indirect optical band gaps are increased while the phonon cut-off wavelength and Urbach energy decreased with the increase of erbium content. A high density and wide transparency range in VIS-IR area are achieved. Our results on high refractive index (∼2.416) and polarizability suggest that these glasses are potential for photonics, solid state lasers and communications devices.

  19. Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

    International Nuclear Information System (INIS)

    Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz

    2005-01-01

    Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP

  20. Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems.

    Science.gov (United States)

    Steindal, Arnfinn Hykkerud; Beerepoot, Maarten T P; Ringholm, Magnus; List, Nanna Holmgaard; Ruud, Kenneth; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard

    2016-10-12

    We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins. In addition, environmental effects on multiphoton absorption (MPA) properties can be studied by evaluating single residues of the response functions. The PE approach includes mutual polarization effects between the quantum and classical parts of the system through induced dipoles that are determined self-consistently with respect to the electronic density. The applicability of our approach is demonstrated by calculating MPA strengths up to four-photon absorption for the green fluorescent protein. We show how the size of the quantum region, as well as the treatment of the border between the quantum and classical regions, is crucial in order to obtain reliable MPA predictions.

  1. Effects of polarons on static polarizabilities and second order hyperpolarizabilities of conjugated polymers

    International Nuclear Information System (INIS)

    Wang Ya-Dong; Meng Yan; Di Bing; Wang Shu-Ling; An Zhong

    2010-01-01

    According to the one-dimensional tight-binding Su—Schrieffer—Heeger model, we have investigated the effects of charged polarons on the static polarizability, α xx , and the second order hyperpolarizabilities, γ xxxx , of conjugated polymers. Our results are consistent qualitatively with previous ab initio and semi-empirical calculations. The origin of the universal growth is discussed using a local-view formalism that is based on the local atomic charge derivatives. Furthermore, combining the Su-Schrieffer-Heeger model and the extended Hubbard model, we have investigated systematically the effects of electron-electron interactions on α xx and γ xxxx of charged polymer chains. For a fixed value of the nearest-neighbour interaction V, the values of α xx and γ xxxx increase as the on-site Coulomb interaction U increases for U c and decrease with U for U > U c , where U c is a critical value of U at which the static polarizability or the second order hyperpolarizability reaches a maximal value of α max or γ max . It is found that the effect of the e-e interaction on the value of α xx is dependent on the ratio between U and V for either a short or a long charged polymer. Whereas, that effect on the value of γ xxxx is sensitive both to the ratio of U to V and to the size of the molecule. (rapid communication)

  2. Ecology of testate amoebae in an Amazonian peatland and development of a transfer function for palaeohydrological reconstruction.

    Science.gov (United States)

    Swindles, Graeme T; Reczuga, Monika; Lamentowicz, Mariusz; Raby, Cassandra L; Turner, T Edward; Charman, Dan J; Gallego-Sala, Angela; Valderrama, Elvis; Williams, Christopher; Draper, Frederick; Honorio Coronado, Euridice N; Roucoux, Katherine H; Baker, Tim; Mullan, Donal J

    2014-08-01

    Tropical peatlands represent globally important carbon sinks with a unique biodiversity and are currently threatened by climate change and human activities. It is now imperative that proxy methods are developed to understand the ecohydrological dynamics of these systems and for testing peatland development models. Testate amoebae have been used as environmental indicators in ecological and palaeoecological studies of peatlands, primarily in ombrotrophic Sphagnum-dominated peatlands in the mid- and high-latitudes. We present the first ecological analysis of testate amoebae in a tropical peatland, a nutrient-poor domed bog in western (Peruvian) Amazonia. Litter samples were collected from different hydrological microforms (hummock to pool) along a transect from the edge to the interior of the peatland. We recorded 47 taxa from 21 genera. The most common taxa are Cryptodifflugia oviformis, Euglypha rotunda type, Phryganella acropodia, Pseudodifflugia fulva type and Trinema lineare. One species found only in the southern hemisphere, Argynnia spicata, is present. Arcella spp., Centropyxis aculeata and Lesqueresia spiralis are indicators of pools containing standing water. Canonical correspondence analysis and non-metric multidimensional scaling illustrate that water table depth is a significant control on the distribution of testate amoebae, similar to the results from mid- and high-latitude peatlands. A transfer function model for water table based on weighted averaging partial least-squares (WAPLS) regression is presented and performs well under cross-validation (r(2)(apparent)= 0.76, RMSE = 4.29; r(2)(jack)= 0.68, RMSEP =5.18). The transfer function was applied to a 1-m peat core, and sample-specific reconstruction errors were generated using bootstrapping. The reconstruction generally suggests near-surface water tables over the last 3,000 years, with a shift to drier conditions at c. cal. 1218-1273 AD.

  3. Lowest-order corrections to the RPA polarizability and GW self-energy of a semiconducting wire

    NARCIS (Netherlands)

    Groot, de H.J.; Ummels, R.T.M.; Bobbert, P.A.; van Haeringen, W.

    1996-01-01

    We present the results of the addition of lowest-order vertex and self-consistency corrections to the RPA polarizability and the GW self-energy for a semiconducting wire. It is found that, when starting from a local density approximation zeroth-order Green function and systematically including these

  4. Electron scattering in dense atomic and molecular gases: An empirical correlation of polarizability and electron scattering length

    International Nuclear Information System (INIS)

    Rupnik, K.; Asaf, U.; McGlynn, S.P.

    1990-01-01

    A linear correlation exists between the electron scattering length, as measured by a pressure shift method, and the polarizabilities for He, Ne, Ar, Kr, and Xe gases. The correlative algorithm has excellent predictive capability for the electron scattering lengths of mixtures of rare gases, simple molecular gases such as H 2 and N 2 and even complex molecular entities such as methane, CH 4

  5. Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap.

    Science.gov (United States)

    Gan, Lin; Camacho-Alanis, Fernanda; Ros, Alexandra

    2015-12-15

    DNA nanoassemblies, such as DNA origamis, hold promise in biosensing, drug delivery, nanoelectronic circuits, and biological computing, which require suitable methods for migration and precision positioning. Insulator-based dielectrophoresis (iDEP) has been demonstrated as a powerful migration and trapping tool for μm- and nm-sized colloids as well as DNA origamis. However, little is known about the polarizability of origami species, which is responsible for their dielectrophoretic migration. Here, we report the experimentally determined polarizabilities of the six-helix bundle origami (6HxB) and triangle origami by measuring the migration times through a potential landscape exhibiting dielectrophoretic barriers. The resulting migration times correlate to the depth of the dielectrophoretic potential barrier and the escape characteristics of the origami according to an adapted Kramer's rate model, allowing their polarizabilities to be determined. We found that the 6HxB polarizability is larger than that of the triangle origami, which correlates with the variations in charge density of both origamis. Further, we discuss the orientation of both origami species in the dielectrophoretic trap and discuss the influence of diffusion during the escape process. Our study provides detailed insight into the factors contributing to the migration through dielectrophoretic potential landscapes, which can be exploited for applications with DNA and other nanoassemblies based on dielectrophoresis.

  6. Arcellacea (testate amoebae) as bio-indicators of road salt contamination in lakes.

    Science.gov (United States)

    Roe, Helen M; Patterson, R Timothy

    2014-08-01

    Winter deicing operations occur extensively in mid- to high-latitude metropolitan regions around the world and result in a significant reduction in road accidents. Deicing salts can, however, pose a major threat to water quality and aquatic organisms. In this paper, we examine the utility of Arcellacea (testate amoebae) for monitoring lakes that have become contaminated by winter deicing salts, particularly sodium chloride. We analysed 50 sediment samples and salt-related water property variables (chloride concentrations; conductivity) from 15 lakes in the Greater Toronto Area and adjacent areas of southern Ontario, Canada. The sampled lakes included lakes in proximity to major highways and suburban roads and control lakes in forested settings away from road influences. Samples from the most contaminated lakes, with chloride concentrations in excess of 400 mg/l and conductivities of >800 μS/cm, were dominated by species typically found in brackish and/or inhospitable lake environments and by lower faunal diversities (lowest Shannon diversity index values) than samples with lower readings. Q-R-mode cluster analysis and detrended correspondence analysis (DCA) resulted in the recognition of four assemblage groupings. These reflect varying levels of salt contamination in the study lakes, along with other local influences, including nutrient loading. The response to nutrients can, however, be isolated if the planktic eutrophic indicator species Cucurbitella tricuspis is removed from the counts. The findings show that the group has considerable potential for biomonitoring in salt-contaminated lakes, and their presence in lake sediment cores may provide significant insights into long-term benthic community health, which is integral for remedial efforts.

  7. Presence of Legionella and Free-Living Amoebae in Composts and Bioaerosols from Composting Facilities

    Science.gov (United States)

    Conza, Lisa; Pagani, Simona Casati; Gaia, Valeria

    2013-01-01

    Several species of Legionella cause Legionnaires’ disease (LD). Infection may occur through inhalation of Legionella or amoebal vesicles. The reservoirs of Legionella are water, soil, potting soil and compost. Some species of free-living amoebae (FLA) that are naturally present in water and soil were described as hosts for Legionella. This study aimed to understand whether or not the composting facilities could be sources of community-acquired Legionella infections after development of bioaerosols containing Legionella or FLA. We looked for the presence of Legionella (by co-culture) and FLA (by culture) in composts and bioaerosols collected at four composting facilities located in southern Switzerland. We investigated the association between the presence of Legionella and compost and air parameters and presence of FLA. Legionella spp. (including L. pneumophila) were detected in 69.3% (61/88) of the composts and FLA (mainly Acanthamoeba, Vermamoeba, Naegleria and Stenamoeba) in 92.0% (81/88). L. pneumophila and L. bozemanii were most frequently isolated. FLA as potential host for Legionella spp. were isolated from 40.9% (36/88) of the composts in all facilities. In Legionella-positive samples the temperature of compost was significantly lower (P = 0.012) than in Legionella-negative samples. Of 47 bioaerosol samples, 19.1% (9/47) were positive for FLA and 10.6% (5/47) for L. pneumophila. Composts (62.8%) were positive for Legionella and FLA contemporaneously, but both microorganisms were never detected simultaneously in bioaerosols. Compost can release bioaerosol containing FLA or Legionella and could represent a source of infection of community-acquired Legionella infections for workers and nearby residents. PMID:23844174

  8. Lamarckian evolution of the giant Mimivirus in allopatric laboratory culture on amoebae.

    Science.gov (United States)

    Colson, Philippe; Raoult, Didier

    2012-01-01

    Acanthamoeba polyphaga Mimivirus has been subcultured 150 times on germ-free amoebae. This allopatric niche is very different from that found in the natural environment, where the virus is in competition with many other organisms. In this experiment, substantial gene variability and loss occurred concurrently with the emergence of phenotypically different viruses. We sought to quantify the respective roles of Lamarckian and Darwinian evolution during this experiment. We postulated that the Mimivirus genes that were down-regulated at the beginning of the allopatric laboratory culture and inactivated after 150 passages experienced Lamarckian evolution because phenotypic modifications preceded genotypic modifications, whereas we considered that genes that were highly transcribed in the new niche but were later inactivated obeyed Darwinian rules. We used the total transcript abundances and sequences described for the genes of Mimivirus at the beginning of its laboratory life and after 150 passages in allopatric culture on Acanthamoeba spp. We found a statistically significant positive correlation between the level of gene expression at the beginning of the culture and gene inactivation during the 150 passages. In particular, the mean transcript abundance at baseline was significantly lower for inactivated genes than for unchanged genes (165 ± 589 vs. 470 ± 1,625; p allopatric laboratory culture if they were encoded by variable genes than if they were encoded by conserved genes (9 vs. 15%; p = 0.062). Finally, Lamarckian evolution represented the evolutionary process encountered by 63% of the inactivated genes. Such observations may be explained by the lower level of DNA repair of useless genes.

  9. Presence of Legionella and free-living Amoebae in composts and bioaerosols from composting facilities.

    Directory of Open Access Journals (Sweden)

    Lisa Conza

    Full Text Available Several species of Legionella cause Legionnaires' disease (LD. Infection may occur through inhalation of Legionella or amoebal vesicles. The reservoirs of Legionella are water, soil, potting soil and compost. Some species of free-living amoebae (FLA that are naturally present in water and soil were described as hosts for Legionella. This study aimed to understand whether or not the composting facilities could be sources of community-acquired Legionella infections after development of bioaerosols containing Legionella or FLA. We looked for the presence of Legionella (by co-culture and FLA (by culture in composts and bioaerosols collected at four composting facilities located in southern Switzerland. We investigated the association between the presence of Legionella and compost and air parameters and presence of FLA. Legionella spp. (including L. pneumophila were detected in 69.3% (61/88 of the composts and FLA (mainly Acanthamoeba, Vermamoeba, Naegleria and Stenamoeba in 92.0% (81/88. L. pneumophila and L. bozemanii were most frequently isolated. FLA as potential host for Legionella spp. were isolated from 40.9% (36/88 of the composts in all facilities. In Legionella-positive samples the temperature of compost was significantly lower (P = 0.012 than in Legionella-negative samples. Of 47 bioaerosol samples, 19.1% (9/47 were positive for FLA and 10.6% (5/47 for L. pneumophila. Composts (62.8% were positive for Legionella and FLA contemporaneously, but both microorganisms were never detected simultaneously in bioaerosols. Compost can release bioaerosol containing FLA or Legionella and could represent a source of infection of community-acquired Legionella infections for workers and nearby residents.

  10. New predictions for generalized spin polarizabilities from heavy baryon chiral perturbation theory

    International Nuclear Information System (INIS)

    Chung-Wen Kao; Barbara Pasquini; Marc Vanderhaeghen

    2004-01-01

    We extract the next-to-next-to-leading order results for spin-flip generalized polarizabilities (GPs) of the nucleon from the spin-dependent amplitudes for virtual Compton scattering (VCS) at Ο(p 4 ) in heavy baryon chiral perturbation theory. At this order, no unknown low energy constants enter the theory, allowing us to make absolute predictions for all spin-flip GPs. Furthermore, by using constraint equations between the GPs due to nucleon crossing combined with charge conjugation symmetry of the VCS amplitudes, we get a next-to-next-to-next-to-leading order prediction for one of the GPs. We provide estimates for forthcoming double polarization experiments which allow to access these spin-flip GPs of the nucleon

  11. A Polarizable and Transferable PHAST CO 2 Potential for Materials Simulation

    KAUST Repository

    Mullen, Ashley L.

    2013-12-10

    Reliable PHAST (Potentials with High Accuracy Speed and Transferability) intermolecular potential energy functions for CO2 have been developed from first principles for use in heterogeneous systems, including one with explicit polarization. The intermolecular potentials have been expressed in a transferable form and parametrized from nearly exact electronic structure calculations. Models with and without explicit many-body polarization effects, known to be important in simulation of interfacial processes, are constructed. The models have been validated on pressure-density isotherms of bulk CO 2 and adsorption in three metal-organic framework (MOF) materials. The present models appear to offer advantages over high quality fluid/liquid state potentials in describing CO2 interactions in interfacial environments where sorbates adopt orientations not commonly explored in bulk fluids. Thus, the nonpolar CO2-PHAST and polarizable CO 2-PHAST* potentials are recommended for materials/interfacial simulations. © 2013 American Chemical Society.

  12. First Determination of Generalized Polarizabilities of the Proton by a Virtual Compton Scattering Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Roche, J. [CEA Saclay, DSM/DAPNIA/SPhN, 91191 Gif-sur-Yvette Cedex, (France); Friedrich, J. M. [Institut fuer Kernphysik, Universitaet Mainz, 55099 Mainz, (Germany); Lhuillier, D. [CEA Saclay, DSM/DAPNIA/SPhN, 91191 Gif-sur-Yvette Cedex, (France); Bartsch, P. [Institut fuer Kernphysik, Universitaet Mainz, 55099 Mainz, (Germany); Baumann, D. [Institut fuer Kernphysik, Universitaet Mainz, 55099 Mainz, (Germany); Berthot, J. [LPC de Clermont-Fd, IN2P3-CNRS, Universite Blaise Pascal, 63177 Aubiere Cedex, (France); Bertin, P. Y. [LPC de Clermont-Fd, IN2P3-CNRS, Universite Blaise Pascal, 63177 Aubiere Cedex, (France); Breton, V. [LPC de Clermont-Fd, IN2P3-CNRS, Universite Blaise Pascal, 63177 Aubiere Cedex, (France); Boeglin, W. U. [Institut fuer Kernphysik, Universitaet Mainz, 55099 Mainz, (Germany); Boehm, R. [Institut fuer Kernphysik, Universitaet Mainz, 55099 Mainz, (Germany)] (and others)

    2000-07-24

    Absolute differential cross sections for the reaction ep{yields}ep{gamma} have been measured at a four-momentum transfer with virtuality Q{sup 2}=0.33 GeV{sup 2} and polarization {epsilon}=0.62 in the range 33.6 to 111.5 MeV/c for the momentum of the outgoing photon in the photon-proton center of mass frame. The experiment has been performed with the high-resolution spectrometers at the Mainz Microtron MAMI. From the photon angular distributions, two structure functions which are a linear combination of the generalized polarizabilities have been determined for the first time. (c) 2000 The American Physical Society.

  13. Polarizable Embedded RI-CC2 Method for Two-Photon Absorption Calculations

    DEFF Research Database (Denmark)

    Hršak, Dalibor; Khah, Alireza Marefat; Christiansen, Ove

    2015-01-01

    We present a novel polarizable embedded resolution-of-identity coupled cluster singles and approximate doubles (PERI-CC2) method for calculation of two-photon absorption (TPA) spectra of large molecular systems. The method was benchmarked for three types of systems: a water-solvated molecule...... of formamide, a uracil molecule in aqueous solution, and a set of mutants of the channelrhodopsin (ChR) protein. The first test case shows that the PERI-CC2 method is in excellent agreement with the PE-CC2 method and in good agreement with the PE-CCSD method. The uracil test case indicates that the effects...... of hydrogen bonding on the TPA of a chromophore with the nearest environment is well-described with the PERI-CC2 method. Finally, the ChR calculation shows that the PERI-CC2 method is well-suited and efficient for calculations on proteins with medium-sized chromophores....

  14. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

    DEFF Research Database (Denmark)

    Hedegård, Erik D.; Olsen, Jógvan Magnus Haugaard; Knecht, Stefan

    2015-01-01

    . To demonstrate the capabilities of PE-MC-srDFT, we also investigated the retinylidene Schiff base chromophore embedded in the channelrhodopsin protein. While using a much more compact reference wave function in terms of active space, our PE-MC-srDFT approach yields excitation energies comparable in quality......We present here the coupling of a polarizable embedding (PE) model to the recently developed multiconfiguration short-range density functional theory method (MC-srDFT), which can treat multiconfigurational systems with a simultaneous account for dynamical and static correlation effects. PE......-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory...

  15. Electronic structure and static dipole polarizability of C{sub 60}-C{sub 240}

    Energy Technology Data Exchange (ETDEWEB)

    Zope, Rajendra R [Department of Physics, University of Texas at El Paso, El Paso, TX 79958 (United States)

    2008-04-28

    The electronic structure of C{sub 60}-C{sub 240} and its first-order response to a static electric field is studied by an all-electron density functional theory calculation using large polarized Gaussian basis sets. Our results show that the outer C{sub 240} shell almost completely shields the inner C{sub 60} as inferred from the practically identical values of dipole polarizability of the C{sub 60}-C{sub 240} onion (449 A{sup 3}) and that of the isolated C{sub 240} fullerene (441 A{sup 3}). The C{sub 60}-C{sub 240} is thus a near-perfect Faraday cage.

  16. Basis set convergence on static electric dipole polarizability calculations of alkali-metal clusters

    International Nuclear Information System (INIS)

    Souza, Fabio A. L. de; Jorge, Francisco E.

    2013-01-01

    A hierarchical sequence of all-electron segmented contracted basis sets of double, triple and quadruple zeta valence qualities plus polarization functions augmented with diffuse functions for the atoms from H to Ar was constructed. A systematic study of basis sets required to obtain reliable and accurate values of static dipole polarizabilities of lithium and sodium clusters (n = 2, 4, 6 and 8) at their optimized equilibrium geometries is reported. Three methods are examined: Hartree-Fock (HF), second-order Moeller-Plesset perturbation theory (MP2), and density functional theory (DFT). By direct calculations or by fitting the directly calculated values through one extrapolation scheme, estimates of the HF, MP2 and DFT complete basis set limits were obtained. Comparison with experimental and theoretical data reported previously in the literature is done (author)

  17. The Electromagnetic Zero-Point Field and the Flat Polarizable Vacuum Representation

    CERN Document Server

    Desiato, J T

    2003-01-01

    There are several interpretations of the Polarizable Vacuum (PV). One is the variable speed of light (VSL) approach, that has been shown to be isomorphic to General Relativity (GR) within experimental limits. However, another interpretation is representative of flat geometry, in which intervals of time and distance are measured in local inertial reference frames where the speed of light remains constant. The Flat PV approach leads to variable impedance transformations, governed by the spectral energy content of the Quantum Vacuum’s Electromagnetic (EM) Zero-Point Field (ZPF). The EM ZPF consists of photons. An unlimited number of photons may occupy the same quantum state at an arbitrary set of coordinates. Therefore, the spectral energy of the ZPF may be varied smoothly, represented by a superposition of EM waves with a large number of photons per cubic wavelength. Utilizing the Flat PV representation, a family of frequency dependent solutions of Poisson’s equation are derived, that may be applied as tool...

  18. Basis set convergence on static electric dipole polarizability calculations of alkali-metal clusters

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Fabio A. L. de; Jorge, Francisco E., E-mail: jorge@cce.ufes.br [Departamento de Fisica, Universidade Federal do Espirito Santo, 29060-900 Vitoria-ES (Brazil)

    2013-07-15

    A hierarchical sequence of all-electron segmented contracted basis sets of double, triple and quadruple zeta valence qualities plus polarization functions augmented with diffuse functions for the atoms from H to Ar was constructed. A systematic study of basis sets required to obtain reliable and accurate values of static dipole polarizabilities of lithium and sodium clusters (n = 2, 4, 6 and 8) at their optimized equilibrium geometries is reported. Three methods are examined: Hartree-Fock (HF), second-order Moeller-Plesset perturbation theory (MP2), and density functional theory (DFT). By direct calculations or by fitting the directly calculated values through one extrapolation scheme, estimates of the HF, MP2 and DFT complete basis set limits were obtained. Comparison with experimental and theoretical data reported previously in the literature is done (author)

  19. Electric Dipole Polarizability of ^{48}Ca and Implications for the Neutron Skin.

    Science.gov (United States)

    Birkhan, J; Miorelli, M; Bacca, S; Bassauer, S; Bertulani, C A; Hagen, G; Matsubara, H; von Neumann-Cosel, P; Papenbrock, T; Pietralla, N; Ponomarev, V Yu; Richter, A; Schwenk, A; Tamii, A

    2017-06-23

    The electric dipole strength distribution in ^{48}Ca between 5 and 25 MeV has been determined at RCNP, Osaka from proton inelastic scattering experiments at forward angles. Combined with photoabsorption data at higher excitation energy, this enables the first extraction of the electric dipole polarizability α_{D}(^{48}Ca)=2.07(22)  fm^{3}. Remarkably, the dipole response of ^{48}Ca is found to be very similar to that of ^{40}Ca, consistent with a small neutron skin in ^{48}Ca. The experimental results are in good agreement with ab initio calculations based on chiral effective field theory interactions and with state-of-the-art density-functional calculations, implying a neutron skin in ^{48}Ca of 0.14-0.20 fm.

  20. Exploratory conformational study of (+)-catechin. Modeling of the polarizability and electric dipole moment.

    Science.gov (United States)

    Bentz, Erika N; Pomilio, Alicia B; Lobayan, Rosana M

    2014-12-01

    The extension of the study of the conformational space of the structure of (+)-catechin at the B3LYP/6-31G(d,p) level of theory is presented in this paper. (+)-Catechin belongs to the family of the flavan-3-ols, which is one of the five largest phenolic groups widely distributed in nature, and whose biological activity and pharmaceutical utility are related to the antioxidant activity due to their ability to scavenge free radicals. The effects of free rotation around all C-O bonds of the OH substituents at different rings are taken into account, obtaining as the most stable conformer, one that had not been previously reported. One hundred seven structures, and a study of the effects of charge delocalization and stereoelectronic effects at the B3LYP/6-311++G(d,p) level are reported by natural bond orbital analysis, streamlining the order of these structures. For further analysis of the structural and molecular properties of this compound in a biological environment, the calculation of polarizabilities, and the study of the electric dipole moment are performed considering the whole conformational space described. The results are analyzed in terms of accumulated knowledge for (4α → 6″, 2α → O → 1″)-phenylflavans and (+)-catechin in previous works, enriching the study of both types of structures, and taking into account the importance of considering the whole conformational space in modeling both the polarizability and the electric dipole moment, also proposing to define a descriptive subspace of only 16 conformers.

  1. Chemical Potentials, Activity Coefficients, and Solubility in Aqueous NaCl Solutions: Prediction by Polarizable Force Fields.

    Czech Academy of Sciences Publication Activity Database

    Moučka, F.; Nezbeda, Ivo; Smith, W.R.

    2016-01-01

    Roč. 11, č. 4 (2016), s. 1756-1764 ISSN 1549-9618 Grant - others:NSERC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : monte-carlo simulations * molecular-dynamic simulations * free-energy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.245, year: 2016

  2. The reconstruction of late Holocene depth-to-water-table based on testate amoebae in an eastern Australian mire

    Science.gov (United States)

    Zheng, X.; Money, S.; Hope, G.

    2017-12-01

    There are relatively few quantitative palaeo-hydrological records available in eastern Australia, and those that are available, for example from dendroclimatology and the reconstruction of lake level, are often relatively short or have a relatively coarse temporal resolution (e.g. Wilkins et al. 2013; Palmer et al. 2015). Testate amoebae, a widely used hydrological proxy in the Northern Hemisphere, were used here to reconstruct depth to water table (DWT) at Snowy Flat, which is a Sphagnum-Richea-Empodismahigh altitude (1618 m asl) shrub bog in the Australian Capital Territory, Australia. Testate amoebae were quantified in a Snowy Flat core representing 4,200 cal Y BP and the community composition was used to reconstruct DWT based on our recently established transfer functions. Results from three different types of transfer functions (Fig. 1) consistently show there was a decreasing DWT (wetter) period centred on about 3350 cal Y BP, a trend towards increased dryness from about 3300 to 2200 cal Y BP and a distinctly drier period 850 to 700 cal Y BP which was immediately followed by a wetter period from 700 to 500 cal Y BP. We discuss these episodes and trends in relation to the drivers of climatic variability in this region and in particular, by comparing our results with other south-eastern Australia records, comment on the history of the southern annular mode.

  3. Folic acid is a potent chemoattractant of free-living amoebae in a new and amazing species of protist, Vahlkampfia sp.

    Science.gov (United States)

    Maeda, Yasuo; Mayanagi, Taira; Amagai, Aiko

    2009-03-01

    Folic acid (folate; vitamin Bc) is well recognized as essential for the proper metabolism of the essential amino acid methionine as well as for the synthesis of adenine and thymine. A folate deficiency has been Implicated in a wide variety of disorders from Alzheimer's disease to depression and neural tube defects. In the cellular slime molds, including Dictyostelium, vegetative growth-phase cells are known to chemotactically move toward folate that is secreted by bacterial food sources such as Escherichia coli. Intracellular folate signal transductlon, including G proteins, Ca(2+)channels, and the PIP3 pathway, has been reported in D. discoideum. To our surprise, the genuine chemoattractant(s) of free-living protozoan amoebae have remained to be determined, possibly because of lack of a pertinent method for assaying chemotaxis. We recently isolated a primitive free-living amoeba from the soil of Costa Rica and identified it as a new species of the genus Vahlkampfia belonging to Subclass Gymnamoebia, which includes Entamoeba and Acanthamoeba. The amoebae can grow and multiply quite rapidly, engulfing nearby bacteria such as E. coli. Importantly, we have demonstrated here using a quite simple but finely designed chemotaxis assay that the Vahlkampfia amoebae exhibit chemotaxis toward higher folate concentrations. Riboflavin and cyanocobalamin were also found to serve as positive chemoattractants. Among these chemoattractants, folate is of particular importance because its function seems to be evolutionarily conserved as a potent chemoattractant of amoeboid cells in a wide range of organisms as well as in the Protista and cellular slime molds.

  4. Amoebae of the genera Vannella Bovee, 1965 and Platyamoeba Page, 1969 isolated from fish and their phylogeny inferred from SSU rRNA gene and ITS sequences

    Czech Academy of Sciences Publication Activity Database

    Dyková, Iva; Boháčová, Lenka; Fiala, Ivan; Macháčková, Blanka; Pecková, Hana; Dvořáková, Helena

    2005-01-01

    Roč. 41, č. 3 (2005), s. 219-230 ISSN 0932-4739 R&D Projects: GA AV ČR IAA6022202 Institutional research plan: CEZ:AV0Z60220518 Keywords : fish-isolated amoebae * Vannella * Platyamoeba Subject RIV: EA - Cell Biology Impact factor: 1.253, year: 2005

  5. Subatomic forces

    International Nuclear Information System (INIS)

    Sutton, C.

    1989-01-01

    Inside the atom, particles interact through two forces which are never felt in the everyday world. But they may hold the key to the Universe. These ideas on subatomic forces are discussed with respect to the strong force, the electromagnetic force and the electroweak force. (author)

  6. Loss of Cln3 impacts protein secretion in the social amoeba Dictyostelium.

    Science.gov (United States)

    Huber, Robert J

    2017-07-01

    Neuronal ceroid lipofuscinosis (NCL), also referred to as Batten disease, is the most common form of childhood neurodegeneration. Mutations in CLN3 cause the most prevalent subtype of the disease, which manifests during early childhood and is currently untreatable. The precise function of the CLN3 protein is still not known, which has inhibited the development of targeted therapies. In the social amoeba Dictyostelium discoideum, loss of the CLN3 homolog, Cln3, reduces adhesion during early development, which delays streaming and aggregation. The results of the present study indicate that this phenotype may be at least partly due to aberrant protein secretion in cln3 - cells. It is well-established that Cln3 localizes primarily to the contractile vacuole (CV) system in Dictyostelium, and to a lesser extent, compartments of the endocytic pathway. Intriguingly, the CV system has been linked to the secretion of proteins that do not contain a signal peptide for secretion (i.e., unconventional protein secretion). Proteins that do contain a signal peptide are secreted via a conventional mechanism involving the endoplasmic reticulum, transport through the Golgi, and secretion via vesicle release. In this study, Cln3 was observed to co-localize with the Golgi marker wheat germ agglutinin suggesting that Cln3 participates in both secretion mechanisms. Chimeras of wild-type (WT) and cln3 - cells displayed delayed streaming and aggregation, and interestingly, cln3 - cells starved in conditioned media (CM) harvested from starving WT cells showed near normal timing of streaming and aggregation suggesting aberrant protein secretion in Cln3-deficient cells. Based on these observations, LC-MS/MS was used to reveal the protein content of CM from starved cells (mass spectrometry data are available via ProteomeXchange with identifier PXD004897). A total of 450 proteins were detected in WT and cln3 - CM, of which 3 were absent in cln3 - CM. Moreover, 12 proteins that were present in

  7. Repulsive Casimir and Casimir–Polder forces

    International Nuclear Information System (INIS)

    Milton, Kimball A; Abalo, E K; Parashar, Prachi; Pourtolami, Nima; Brevik, Iver; Ellingsen, Simen Å

    2012-01-01

    Casimir and Casimir–Polder repulsions have been known for more than 50 years. The general ‘Lifshitz’ configuration of parallel semi-infinite dielectric slabs permits repulsion if they are separated by a dielectric fluid that has a value of permittivity that is intermediate between those of the dielectric slabs. This was indirectly confirmed in the 1970s, and more directly by Capasso’s group recently. It has also been known for many years that electrically and magnetically polarizable bodies can experience a repulsive quantum vacuum force. More amenable to practical application are situations where repulsion could be achieved between ordinary conducting and dielectric bodies in vacuum. The status of the field of Casimir repulsion with emphasis on some recent developments will be surveyed. Here, stress will be placed on analytic developments, especially on Casimir–Polder (CP) interactions between anisotropically polarizable atoms, and CP interactions between anisotropic atoms and bodies that also exhibit anisotropy, either because of anisotropic constituents, or because of geometry. Repulsion occurs for wedge-shaped and cylindrical conductors, provided the geometry is sufficiently asymmetric, that is, either the wedge is sufficiently sharp or the atom is sufficiently far from the cylinder. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical in honour of Stuart Dowker’s 75th birthday devoted to ‘Applications of zeta functions and other spectral functions in mathematics and physics’. (review)

  8. Dispersion forces and small-angle neutron scattering from liquid noble metals

    International Nuclear Information System (INIS)

    March, N.H.

    1988-01-01

    Maggs and Ashcroft [Phys. Rev. letts., 59,113 (1987)] have re-opened the question of the analogy between the cohesion of a molecular crystal, in which dispersion forces play a major role, and that in a metal crystal with polarizable ion cores. It is pointed out that small-angle neutron scattering from liquid noble metals could be used to test their predictions. (author)

  9. 4fn-15d centroid shift in lanthanides and relation with anion polarizability, covalency, and cation electronegativity

    International Nuclear Information System (INIS)

    Dorenbos, P.; Andriessen, J.; Eijk, C.W.E. van

    2003-01-01

    Data collected on the centroid shift of the 5d-configuration of Ce 3+ in oxide and fluoride compounds were recently analyzed with a model involving the correlated motion between 5d-electron and ligand electrons. The correlation effects are proportional to the polarizability of the anion ligands and it leads, like covalency, to lowering of the 5d-orbital energies. By means of ab initio Hartree-Fock-LCAO calculations including configuration interaction the contribution from covalency and correlated motion to the centroid shift are determined separately for Ce 3+ in various compounds. It will be shown that in fluoride compounds, covalency provides an insignificant contribution. In oxides, polarizability appears to be of comparable importance as covalency

  10. On the calculation and interpretation of covalency in the intensity parameters of 4f–4f transitions in Eu{sup 3+} complexes based on the chemical bond overlap polarizability

    Energy Technology Data Exchange (ETDEWEB)

    Moura, Renaldo T., E-mail: renaldotmjr@gmail.com; Carneiro Neto, Albano N.; Longo, Ricardo L.; Malta, Oscar L.

    2016-02-15

    The concepts of chemical bond overlap polarizability (α{sub OP}) and of specific ionic valence (υ) were used to characterize the Eu{sup 3+}–ligating atom bonds in complexes. The underlying chemical bond properties, namely, bond distance, overlap integral, force constant, and the energy excitation, were successfully calculated for the Eu{sup 3+}–ligating atom diatomic-like species under the influence of the molecular environment. The quantities α{sub OP} and υ were used to reshape and reinterpret the expressions of the forced electric dipole (FED) and the dynamic coupling (DC) mechanisms responsible for the intensity parameters of 4f–4f transitions. These parameters were calculated with this new approach for a series of Eu{sup 3+} complexes: [EuL{sub 3}L′] with L=AIND, BIND, TTA, BTFA, FOD, ABSe, ABSeCl, DPM and L′=(H{sub 2}O){sub 2}, NO{sub 3}, DPbpy, DBSO, TPPO, Phen, for which the experimental intensity parameters and some E{sub 00} (={sup 5}D{sub 0}→{sup 7}F{sub 0}) energies are available. Comparisons between the theoretical and experimental results suggest that this new methodology is reliable and an important step toward an approach to calculate the 4f–4f intensities free of adjustable parameters, which has been accomplished for complexes without aquo ligand. - Highlights: • New methodology to calculate intensity parameters of f–f transitions. • Inclusion of overlap polarizability (covalency) on dynamic coupling mechanism. • Analytical calculation of the charge factors in the ligand field Hamiltonian. • Step towards a parameter-free computational method for f–f intensities. • Interpretation and quantification of the intensity parameters in terms of covalency.

  11. Assessing the high frequency behavior of non-polarizable electrodes for spectral induced polarization measurements

    Science.gov (United States)

    Abdulsamad, Feras; Florsch, Nicolas; Schmutz, Myriam; Camerlynck, Christian

    2016-12-01

    During the last decades, the usage of spectral induced polarization (SIP) measurements in hydrogeology and detecting environmental problems has been extensively increased. However, the physical mechanisms which are responsible for the induced polarization response over the usual frequency range (typically 1 mHz to 10-20 kHz) require better understanding. The phase shift observed at high frequencies is sometimes attributed to the so-called Maxwell-Wagner polarization which takes place when charges cross an interface. However, SIP measurements of tap water show a phase shift at frequencies higher than 1 kHz, where no Maxwell-Wagner polarization may occur. In this paper, we enlighten the possible origin of this phase shift and deduce its likely relationship with the types of the measuring electrodes. SIP Laboratory measurements of tap water using different types of measuring electrodes (polarizable and non-polarizable electrodes) are carried out to detect the origin of the phase shift at high frequencies and the influence of the measuring electrodes types on the observed complex resistivity. Sodium chloride is used to change the conductivity of the medium in order to quantify the solution conductivity role. The results of these measurements are clearly showing the impact of the measuring electrodes type on the measured phase spectrum while the influence on the amplitude spectrum is negligible. The phenomenon appearing on the phase spectrum at high frequency (> 1 kHz) whatever the electrode type is, the phase shows an increase compared to the theoretical response, and the discrepancy (at least in absolute value) increases with frequency, but it is less severe when medium conductivity is larger. Additionally, the frequency corner is shifted upward in frequency. The dependence of this phenomenon on the conductivity and the measuring electrodes type (electrode-electrolyte interface) seems to be due to some dielectric effects (as an electrical double layer of small

  12. Deuteron polarizability and S-wave π+d scattering at energies below 1 keV

    International Nuclear Information System (INIS)

    Pupyshev, V.V.

    1987-01-01

    The influence of deuteron polarizability on the S-wave π + d-scattering in a low-energy limit is explored in the framework of the variable phase method. It is shown that the nonoscillating part of the S-wave cross section of π + d-scattering has a deep and sharp minimum in the energy region ∼ 0.4 keV

  13. Relativistic coupled-cluster calculations of 20Ne, 40Ar, 84Kr, and 129Xe: Correlation energies and dipole polarizabilities

    International Nuclear Information System (INIS)

    Mani, B. K.; Angom, D.; Latha, K. V. P.

    2009-01-01

    We have carried out a detailed and systematic study of the correlation energies of inert gas atoms Ne, Ar, Kr, and Xe using relativistic many-body perturbation theory and relativistic coupled-cluster theory. In the relativistic coupled-cluster calculations, we implement perturbative triples and include these in the correlation energy calculations. We then calculate the dipole polarizability of the ground states using perturbed coupled-cluster theory.

  14. High Precision Measurement of the Neutron Polarizabilities via Compton Scattering on Deuterium at HI γS

    Science.gov (United States)

    Sikora, Mark

    2016-09-01

    The electric (αn) and magnetic (βn) polarizabilities of the neutron are fundamental properties arising from its internal structure which describe the nucleon's response to applied electromagnetic fields. Precise measurements of the polarizabilities provide crucial constraints on models of Quantum Chromodynamics (QCD) in the low energy regime such as Chiral Effective Field Theories as well as emerging ab initio calculations from lattice-QCD. These values also contribute the most uncertainty to theoretical determinations of the proton-neutron mass difference. Historically, the experimental challenges to measuring αn and βn have been due to the difficulty in obtaining suitable targets and sufficiently intense beams, leading to significant statistical uncertainties. To address these issues, a program of Compton scattering experiments on the deuteron is underway at the High Intensity Gamma Source (HI γS) at Duke University with the aim of providing the world's most precise measurement of αn and βn. We report measurements of the Compton scattering differential cross section obtained at incident photon energies of 65 and 85 MeV and discuss the sensitivity of these data to the polarizabilities.

  15. High Precision Measurement of the Neutron Polarizabilities via Compton Scattering on Deuterium at Eγ=65 MeV

    Science.gov (United States)

    Sikora, Mark; Compton@HIGS Team

    2017-01-01

    The electric (αn) and magnetic (βn) polarizabilities of the neutron are fundamental properties arising from its internal structure which describe the nucleon's response to applied electromagnetic fields. Precise measurements of the polarizabilities provide crucial constraints on models of Quantum Chromodynamics (QCD) in the low energy regime such as Chiral Effective Field Theories as well as emerging ab initio calculations from lattice-QCD. These values also contribute the most uncertainty to theoretical determinations of the proton-neutron mass difference. Historically, the experimental challenges to measuring αn and βn have been due to the difficulty in obtaining suitable targets and sufficiently intense beams, leading to significant statistical uncertainties. To address these issues, a program of Compton scattering experiments on the deuteron is underway at the High Intensity Gamma Source (HI γS) at Duke University with the aim of providing the world's most precise measurement of αn and βn. We report measurements of the Compton scattering differential cross section obtained at an incident photon energy of 65 MeV and discuss the sensitivity of these data to the polarizabilities.

  16. Effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field

    International Nuclear Information System (INIS)

    Chen Jianxin; Cui Xiaomei; Huang Bomin; Wu Hongchun; Zhuo Shuangmu

    2006-01-01

    In the rotation equation of the angle θ between the molecular axis and the laser polarization direction, the dependence of laser-induced polarizability on the molecular internuclear distance R is considered. The effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field is investigated with 20 and 100 fs laser pulses for N 2 molecules and with 60 and 100 fs laser pulses for Br 2 molecules at intensities of 5x10 14 W cm -2 and 5x10 15 W cm -2 . This effect exists and only occurs during the dissociative process after the molecule is ionized. It enhances the degrees of molecular dynamic alignment and is more significant in reorienting the angular distributions of molecules towards the laser polarization direction in the conditions of high laser intensity and short pulse length. Compared with the N 2 molecule, the effect of the R dependence of laser-induced polarizability on molecular dynamic alignment for Br 2 is stronger. The reasons are presented and discussed

  17. Polarizability and binding energy of a shallow donor in spherical quantum dot-quantum well (QD-QW)

    Science.gov (United States)

    Rahmani, K.; Chrafih, Y.; M’Zred, S.; Janati, S.; Zorkani, I.; Jorio, A.; Mmadi, A.

    2018-03-01

    The polarizability and the binding energy is estimated for a shallow donor confined to move in inhomogeneous quantum dots (CdS/HgS/CdS). In this work, the Hass variational method within the effective mass approximation in used in the case of an infinitely deep well. The polarizability and the binding energy depend on the inner and the outer radius of the QDQW, also it depends strongly on the donor position. It’s found that the stark effect is more important when the impurity is located at the center of the (QDQW) and becomes less important when the donor moves toward the extremities of the spherical layer. When the electric field increases, the binding energy and the polarizability decreases. Its effects is more pronounced when the impurity is placed on the center of the spherical layer and decrease when the donor move toward extremities of this spherical layer. We have demonstrated the existence of a critical value {≤ft( {{{{R_1}} \\over {{R_2}}}} \\right)cri} which can be used to distinguish the tree dimension confinement from the spherical surface confinement and it’s may be important for the nanofabrication techniques.

  18. Electric dipole strength and dipole polarizability in 48Ca within a fully self-consistent second random–phase approximation

    Directory of Open Access Journals (Sweden)

    D. Gambacurta

    2018-02-01

    Full Text Available The second random–phase–approximation model corrected by a subtraction procedure designed to cure double counting, instabilities, and ultraviolet divergences, is employed for the first time to analyze the dipole strength and polarizability in 48Ca. All the terms of the residual interaction are included, leading to a fully self-consistent scheme. Results are illustrated with two Skyrme parametrizations, SGII and SLy4. Those obtained with the SGII interaction are particularly satisfactory. In this case, the low-lying strength below the neutron threshold is well reproduced and the giant dipole resonance is described in a very satisfactory way especially in its spreading and fragmentation. Spreading and fragmentation are produced in a natural way within such a theoretical model by the coupling of 1 particle-1 hole and 2 particle-2 hole configurations. Owing to this feature, we may provide for the electric polarizability as a function of the excitation energy a curve with a similar slope around the centroid energy of the giant resonance compared to the corresponding experimental results. This represents a considerable improvement with respect to previous theoretical predictions obtained with the random–phase approximation or with several ab-initio models. In such cases, the spreading width of the excitation cannot be reproduced and the polarizability as a function of the excitation energy displays a stiff increase around the predicted centroid energy of the giant resonance.

  19. Electric dipole strength and dipole polarizability in 48Ca within a fully self-consistent second random-phase approximation

    Science.gov (United States)

    Gambacurta, D.; Grasso, M.; Vasseur, O.

    2018-02-01

    The second random-phase-approximation model corrected by a subtraction procedure designed to cure double counting, instabilities, and ultraviolet divergences, is employed for the first time to analyze the dipole strength and polarizability in 48Ca. All the terms of the residual interaction are included, leading to a fully self-consistent scheme. Results are illustrated with two Skyrme parametrizations, SGII and SLy4. Those obtained with the SGII interaction are particularly satisfactory. In this case, the low-lying strength below the neutron threshold is well reproduced and the giant dipole resonance is described in a very satisfactory way especially in its spreading and fragmentation. Spreading and fragmentation are produced in a natural way within such a theoretical model by the coupling of 1 particle-1 hole and 2 particle-2 hole configurations. Owing to this feature, we may provide for the electric polarizability as a function of the excitation energy a curve with a similar slope around the centroid energy of the giant resonance compared to the corresponding experimental results. This represents a considerable improvement with respect to previous theoretical predictions obtained with the random-phase approximation or with several ab-initio models. In such cases, the spreading width of the excitation cannot be reproduced and the polarizability as a function of the excitation energy displays a stiff increase around the predicted centroid energy of the giant resonance.

  20. The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions

    Science.gov (United States)

    Nguyen, Mary; Rick, Steven W.

    2018-06-01

    The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.

  1. On different types of hereditable changes in the viability of Amoeba protens cells x-irradiated with varying doses

    International Nuclear Information System (INIS)

    Bychkovskaya, I.B.; Ochinskaya, G.K.; Erokhina, G.M.

    1976-01-01

    Qualitatively different types of cells lethality have been observed in the posterity of amoebae irradiated with doses ranging from 0.5 to 40 kR and from 60 to 120 kR. At doses of 0.5 to 40 kR, a certain part of cells in a population dies, and the effect is characterized by stability and independency of a radiation dose, hereditable radiation damage of all the cells in the population, and by the fact that it might be caused not only by a derect action of radiation but also by a preirradiated culture medium. Higher doses (60 to 120 kR) cause a more drastic but sell stable effect. Depending on a dose value, a varying percentage of cells has shown the effect not being caused by the action of the preirradiated medium. The data obtained indicate that there are different mechanisms of hereditable radiation damages to cells caused by varying radiation doses

  2. Hartree-Fock limit values of multipole moments, polarizabilities, and hyperpolarizabilities for atoms and diatomic molecules

    Science.gov (United States)

    Kobus, Jacek

    2015-02-01

    Recently it has been demonstrated that the finite difference Hartree-Fock method can be used to deliver highly accurate values of electric multipole moments together with polarizabilities αz z,Az ,z z , and hyperpolarizabilities βz z z, γz z z,Bz z ,z z , for the ground states of various atomic and diatomic systems. Since these results can be regarded as de facto Hartree-Fock limit values their quality is of the utmost importance. This paper reexamines the use of the finite field method to calculate these electric properties, discusses its accuracy, and presents an updated list of the properties for the following atoms and diatomic molecules: H-, He, Li, Li+,Li2 +,Li-,Be2 + , Be, B+,C2 + , Ne, Mg2 +, Mg, Al+,Si2 + , Ar, K+,Ca2 +,Rb+,Sr2 +,Zr4 +,He2 , Be2,N2,F2,O2 , HeNe, LiH2 +, LiCl, LiBr, BH, CO, FH, NaCl, and KF. The potential energy curves and the dependence of the electric properties on the internuclear distance is also studied for He2,LiH+,Be2 , and HeNe systems.

  3. On the importance of excited state dynamic response electron correlation in polarizable embedding methods.

    Science.gov (United States)

    Eriksen, Janus J; Sauer, Stephan P A; Mikkelsen, Kurt V; Jensen, Hans J Aa; Kongsted, Jacob

    2012-09-30

    We investigate the effect of including a dynamic reaction field at the lowest possible ab inito wave function level of theory, namely the Hartree-Fock (HF) self-consistent field level within the polarizable embedding (PE) formalism. We formulate HF based PE within the linear response theory picture leading to the PE-random-phase approximation (PE-RPA) and bridge the expressions to a second-order polarization propagator approximation (SOPPA) frame such that dynamic reaction field contributions are included at the RPA level in addition to the static response described at the SOPPA level but with HF induced dipole moments. We conduct calculations on para-nitro-aniline and para-nitro-phenolate using said model in addition to dynamic PE-RPA and PE-CAM-B3LYP. We compare the results to recently published PE-CCSD data and demonstrate how the cost effective SOPPA-based model successfully recovers a great portion of the inherent PE-RPA error when the observable is the solvatochromic shift. We furthermore demonstrate that whenever the change in density resulting from the ground state-excited state electronic transition in the solute is not associated with a significant change in the electric field, dynamic response contributions formulated at the HF level of theory manage to capture the majority of the system response originating from derivative densities. Copyright © 2012 Wiley Periodicals, Inc.

  4. The cavity electromagnetic field within the polarizable continuum model of solvation

    Energy Technology Data Exchange (ETDEWEB)

    Pipolo, Silvio, E-mail: silvio.pipolo@nano.cnr.it [Center S3, CNR Institute of Nanoscience, Modena (Italy); Department of Physics, University of Modena and Reggio Emilia, Modena (Italy); Corni, Stefano, E-mail: stefano.corni@nano.cnr.it [Center S3, CNR Institute of Nanoscience, Modena (Italy); Cammi, Roberto, E-mail: roberto.cammi@unipr.it [Department of Chemistry, Università degli studi di Parma, Parma (Italy)

    2014-04-28

    Cavity field effects can be defined as the consequences of the solvent polarization induced by the probing electromagnetic field upon spectroscopies of molecules in solution, and enter in the definitions of solute response properties. The polarizable continuum model of solvation (PCM) has been extended in the past years to address the cavity-field issue through the definition of an effective dipole moment that couples to the external electromagnetic field. We present here a rigorous derivation of such cavity-field treatment within the PCM starting from the general radiation-matter Hamiltonian within inhomogeneous dielectrics and recasting the interaction term to a dipolar form within the long wavelength approximation. To this aim we generalize the Göppert-Mayer and Power-Zienau-Woolley gauge transformations, usually applied in vacuo, to the case of a cavity vector potential. Our derivation also allows extending the cavity-field correction in the long-wavelength limit to the velocity gauge through the definition of an effective linear momentum operator. Furthermore, this work sets the basis for the general PCM treatment of the electromagnetic cavity field, capable to describe the radiation-matter interaction in dielectric media beyond the long-wavelength limit, providing also a tool to investigate spectroscopic properties of more complex systems such as molecules close to large nanoparticles.

  5. Deuterium isotope effects on the dipole moment and polarizability of HCl and NH3

    International Nuclear Information System (INIS)

    Scher, C.; Ravid, B.; Halevi, E.A.

    1982-01-01

    A previously described adaptation of the conventional Debye procedure for the direct determination of small dipole moment and polarizability differences between two polar gases is applied to the isotopic pairs DCl-HCl and ND 3 -NH 3 . The dipole moment difference obtained for the first isotopic pair, by using the Debye-Van Vleck equation for electric susceptibility, μ(DCl) - μ(HCl) = 0.005 5 +/- 0.0002 D, is consistent with published spectroscopically determined values of μ 00 (DCl) and μ 00 (HCl), while that obtained by using the classical Debye equation is not. For the second pair, use of the Debye-Van Vleck equation, along with a correction for thermal population of vibrationally excited levels, is shown to be essential and yields μ(ND) 3 - μ(NH 3 ) = +0.013 5 +/- 0.001 D and α(ND 3 ) - α(NH 3 ) = -(2.2 +/- 1.7) x 10 -26 cm 3

  6. Electronic polarizability of light crude oil from optical and dielectric studies

    Science.gov (United States)

    George, A. K.; Singh, R. N.

    2017-07-01

    In the present paper we report the temperature dependence of density, refractive indices and dielectric constant of three samples of crude oils. The API gravity number estimated from the temperature dependent density studies revealed that the three samples fall in the category of light oil. The measured data of refractive index and the density are used to evaluate the polarizability of these fluids. Molar refractive index and the molar volume are evaluated through Lorentz-Lorenz equation. The function of the refractive index, FRI , divided by the mass density ρ, is a constant approximately equal to one-third and is invariant with temperature for all the samples. The measured values of the dielectric constant decrease linearly with increasing temperature for all the samples. The dielectric constant estimated from the refractive index measurements using Lorentz-Lorentz equation agrees well with the measured values. The results are promising since all the three measured properties complement each other and offer a simple and reliable method for estimating crude oil properties, in the absence of sufficient data.

  7. Solvation of actinide salts in water using a polarizable continuum model.

    Science.gov (United States)

    Kumar, Narendra; Seminario, Jorge M

    2015-01-29

    In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

  8. Sum rules across the unpolarized Compton processes involving generalized polarizabilities and moments of nucleon structure functions

    Science.gov (United States)

    Lensky, Vadim; Hagelstein, Franziska; Pascalutsa, Vladimir; Vanderhaeghen, Marc

    2018-04-01

    We derive two new sum rules for the unpolarized doubly virtual Compton scattering process on a nucleon, which establish novel low-Q2 relations involving the nucleon's generalized polarizabilities and moments of the nucleon's unpolarized structure functions F1(x ,Q2) and F2(x ,Q2). These relations facilitate the determination of some structure constants which can only be accessed in off-forward doubly virtual Compton scattering, not experimentally accessible at present. We perform an empirical determination for the proton and compare our results with a next-to-leading-order chiral perturbation theory prediction. We also show how these relations may be useful for a model-independent determination of the low-Q2 subtraction function in the Compton amplitude, which enters the two-photon-exchange contribution to the Lamb shift of (muonic) hydrogen. An explicit calculation of the Δ (1232 )-resonance contribution to the muonic-hydrogen 2 P -2 S Lamb shift yields -1 ±1 μ eV , confirming the previously conjectured smallness of this effect.

  9. The memory effect of a pentacene field-effect transistor with a polarizable gate dielectric

    Science.gov (United States)

    Unni, K. N. N.; de Bettignies, Remi; Dabos-Seignon, Sylvie; Nunzi, Jean-Michel

    2004-06-01

    The nonvolatile transistor memory element is an interesting topic in organic electronics. In this case a memory cell consists of only one device where the stored information is written as a gate insulator polarization by a gate voltage pulse and read by the channel conductance control with channel voltage pulse without destruction of the stored information. Therefore such transistor could be the base of non-volatile non-destructively readable computer memory of extremely high density. Also devices with polarizable gate dielectrics can function more effectively in certain circuits. The effective threshold voltage Vt can be brought very close to zero, for applications where the available gate voltage is limited. Resonant and adaptive circuits can be tuned insitu by polarizing the gates. Poly(vinylidene fluoride), PVDF and its copolymer with trifluoroethylene P(VDF-TrFE) are among the best known and most widely used ferroelectric polymers. In this manuscript, we report new results of an organic FET, fabricated with pentacene as the active material and P(VDF-TrFE) as the gate insulator. Application of a writing voltage of -50 V for short duration results in significant change in the threshold voltage and remarkable increase in the drain current. The memory effect is retained over a period of 20 hours.

  10. Measurement of pion polarizability and chiral anomaly in Primakoff reactions at COMPASS

    Energy Technology Data Exchange (ETDEWEB)

    Nagel, Thiemo; Friedrich, Jan Michael; Gerassimov, Sergei; Grabmueller, Stefanie; Haas, Florian; Ketzer, Bernhard; Konorov, Igor; Kuhn, Roland; Neubert, Sebastian; Paul, Stephan; Weitzel, Quirin [TU Muenchen, Physik-Department E18 (Germany); Dinkelbach, Anna-Maria [Prueftechnik Alignment Systems, Ismaning (Germany)

    2008-07-01

    In a pilot run in 2004, the COMPASS experiment at CERN observed the scattering of negative pions of 190 GeV/c off various nuclear targets, measuring soft processes. Primakoff reactions, i.e. interactions between the beam particle and a quasi-real photon from the Coulomb field of the nucleus, are used to study the physics of strong interaction at small momentum transfer. The inverse Compton scattering reaction {pi}{sup -}+Z{yields}{pi}{sup -}+{gamma}+Z gives access to the polarizabilities anti {alpha}{sub {pi}} and anti {beta}{sub {pi}} of the beam pion, which may be used to test chiral pertubation theory. Under the assumption of anti {alpha}{sub {pi}}+ anti {beta}{sub {pi}}=0 a preliminary result has been extracted which is in agreement with calculations of {chi}PT. The {pi}{sup 0} production reaction {pi}{sup -}+Z{yields}{pi}{sup -}+{pi}{sup 0}+Z permits determination of the F{sup 3{pi}} coupling constant of the {gamma}{yields}3{pi} vertex, a measurement crucial for the confirmation of the chiral anomaly hypothesis. Here, the current status of analysis will be shown.

  11. Effect of dipole polarizability on positron binding by strongly polar molecules

    International Nuclear Information System (INIS)

    Gribakin, G F; Swann, A R

    2015-01-01

    A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron–positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including the polarization potential via perturbation theory and non-perturbatively. The perturbative model makes reliable predictions of binding energies for a range of polar organic molecules and hydrogen cyanide. The model also agrees with the linear dependence of the binding energies on the polarizability inferred from the experimental data (Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203). The effective core radii, however, remain unphysically small for most molecules. Treating molecular polarization non-perturbatively leads to physically meaningful core radii for all of the molecules studied and enables even more accurate predictions of binding energies to be made for nearly all of the molecules considered. (paper)

  12. Exploration of dynamic dipole polarizability of impurity doped quantum dots in presence of noise

    Science.gov (United States)

    Ghosh, Anuja; Bera, Aindrila; Saha, Surajit; Arif, Sk. Md.; Ghosh, Manas

    2018-02-01

    Present study strives to perform a rigorous exploration of dynamic dipole polarizability (DDP) of GaAs quantum dot (QD) containing dopant with special reference to influence of Gaussian white noise. Several physical quantities have been varied over a range to observe the modulations of the DDP profiles. Aforesaid physical quantities include magnetic field, confinement potential, dopant location, dopant potential, noise strength, aluminium concentration (only for Alx Ga1 - x As alloy QD), position-dependent effective mass (PDEM), position-dependent dielectric screening function (PDDSF), anisotropy, hydrostatic pressure (HP) and temperature. The DDP profiles reveal noticeable characteristics governed by the particular physical quantity involved, presence/absence of noise, the manner (additive/multiplicative) noise is applied to the system and the incoming photon frequency. As a general observation we have found that additive noise causing greater deviation of the DDP profile from noise-free state than its multiplicative neighbor. The study highlights viable means of harnessing DDP of doped QD under the governance of noise by appropriate adjustment of several relevant factors. The study merits importance in the light of technological applications of QD-based devices where noise appears as an integral component.

  13. Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

    Energy Technology Data Exchange (ETDEWEB)

    Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de [Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg (Germany); Kibies, Patrick; Frach, Roland; Kast, Stefan M., E-mail: stefan.kast@tu-dortmund.de [Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund (Germany); Imoto, Sho, E-mail: sho.imoto@theochem.rub.de; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany); Suladze, Saba; Winter, Roland [Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund (Germany)

    2016-04-14

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  14. Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

    Science.gov (United States)

    Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M

    2016-04-14

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  15. Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

    International Nuclear Information System (INIS)

    Hölzl, Christoph; Horinek, Dominik; Kibies, Patrick; Frach, Roland; Kast, Stefan M.; Imoto, Sho; Marx, Dominik; Suladze, Saba; Winter, Roland

    2016-01-01

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  16. Labor Force

    Science.gov (United States)

    Occupational Outlook Quarterly, 2012

    2012-01-01

    The labor force is the number of people ages 16 or older who are either working or looking for work. It does not include active-duty military personnel or the institutionalized population, such as prison inmates. Determining the size of the labor force is a way of determining how big the economy can get. The size of the labor force depends on two…

  17. An introductory study using impedance spectroscopy technique with polarizable microelectrode for amino acids characterization

    Science.gov (United States)

    Chin, K. B.; Chi, I.; Pasalic, J.; Huang, C.-K.; Barge, Laura M.

    2018-04-01

    Portable, low power, yet ultra-sensitive life detection instrumentations are vital to future astrobiology flight programs at NASA. In this study, initial attempts to characterize amino acids in an aqueous environment by electrochemical impedance spectroscopy (EIS) using polarizable (blocking) electrodes in order to establish a means of detection via their electrical properties. Seven amino acids were chosen due to their scientific importance in demonstrating sensitivity levels in the range of part per billion concentration. Albeit more challenging in real systems of analyst mixtures, we found individual amino acids in aqueous environment do exhibit some degree of chemical and physical uniqueness to warrant characterization by EIS. The polar amino acids (Asp, Glu, and His) exhibited higher electrochemical activity than the non-polar amino acids (Ala, Gly, Val, and Leu). The non-polar amino acids (Gly and Ala) also exhibited unique electrical properties which appeared to be more dependent on physical characteristics such as molecular weight and structure. At concentrations above 1 mM where the amino acids play a more dominant transport role within the water, the conductivity was found to be more sensitive to concentrations. At lower concentrations activity with water. As revealed by equivalent circuit modeling, the relaxation times showed a 1-2 order of magnitude difference between polar and non-polar amino acids. The pseudo-capacitance from EIS measurements on sample mixtures containing salt water and individual amino acids revealed the possibility for improvement in amino acid selectivity using gold nanoporous surface enhanced electrodes. This work establishes important methodologies for characterizing amino acids using EIS combined with microscale electrodes, supporting the case for instrumentation development for life detection and origin of life programs.

  18. Changes in Structure and Functioning of Protist (Testate Amoebae Communities Due to Conversion of Lowland Rainforest into Rubber and Oil Palm Plantations.

    Directory of Open Access Journals (Sweden)

    Valentyna Krashevska

    Full Text Available Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and functionally important protists in litter and soil. Living testate amoebae species richness, density and biomass were all lower in replacement land uses than in rainforest, with the impact being more pronounced in litter than in soil. Similar abundances of species of high and low trophic level in rainforest suggest that trophic interactions are more balanced, with a high number of functionally redundant species, than in rubber and oil palm. In contrast, plantations had a low density of high trophic level species indicating losses of functions. This was particularly so in oil palm plantations. In addition, the relative density of species with siliceous shells was >50% lower in the litter layer of oil palm and rubber compared to rainforest and jungle rubber. This difference suggests that rainforest conversion changes biogenic silicon pools and increases silicon losses. Overall, the lower species richness, density and biomass in plantations than in rainforest, and the changes in the functional composition of the testate amoebae community, indicate detrimental effects of rainforest conversion on the structure and functioning of microbial food webs.

  19. Changes in Structure and Functioning of Protist (Testate Amoebae) Communities Due to Conversion of Lowland Rainforest into Rubber and Oil Palm Plantations.

    Science.gov (United States)

    Krashevska, Valentyna; Klarner, Bernhard; Widyastuti, Rahayu; Maraun, Mark; Scheu, Stefan

    2016-01-01

    Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and functionally important protists in litter and soil. Living testate amoebae species richness, density and biomass were all lower in replacement land uses than in rainforest, with the impact being more pronounced in litter than in soil. Similar abundances of species of high and low trophic level in rainforest suggest that trophic interactions are more balanced, with a high number of functionally redundant species, than in rubber and oil palm. In contrast, plantations had a low density of high trophic level species indicating losses of functions. This was particularly so in oil palm plantations. In addition, the relative density of species with siliceous shells was >50% lower in the litter layer of oil palm and rubber compared to rainforest and jungle rubber. This difference suggests that rainforest conversion changes biogenic silicon pools and increases silicon losses. Overall, the lower species richness, density and biomass in plantations than in rainforest, and the changes in the functional composition of the testate amoebae community, indicate detrimental effects of rainforest conversion on the structure and functioning of microbial food webs.

  20. First Record of Potentially Pathogenic Amoeba Vermamoeba vermiformis (Lobosea: Gymnamoebia Isolated from a Freshwater of Dokdo Island in the East Sea, Korea

    Directory of Open Access Journals (Sweden)

    Jong Soo Park

    2016-01-01

    Full Text Available Vermamoeba vermiformis is a very important free-living amoeba for human health in association with Legionnaires’ disease and keratitis. This interesting amoeba was firstly isolated from a freshwater of Dokdo (island, which was historically used for drinking water. Trophozoites and cyst forms of V. vermiformis strain MG1 are very similar to previous reported species. Trophozoites of V. vermiformis strain MG1 showed cylindrical shape with prominent anterior hyaline region. The average ratio of length and width was about 6.5. Typically, cysts of the strain MG1 showed a spherical or slightly ovoidal shape with smooth wall, and lacked cyst pores. Some cysts had crenulatewalled ectocyst, which was separated from endocyst wall. Further, 18S rRNA gene sequence of V. vermiformis strain MG1 showed very high similarity to other V. vermiformis species (99.4%-99.9% identity. Molecular phylogenetic analysis based on 18S rRNA gene sequences clearly confirmed that the isolate was one strain of V. vermiformis with maximum bootstrap value (maximum likelihood: 100% and Bayesian posterior probability of 1. Thus, the freshwater of Dokdo in Korea could harbor potentially pathogenic amoeba that may cause diseases in humans.

  1. Dispersion Forces

    CERN Document Server

    Buhmann, Stefan Yoshi

    2012-01-01

    In this book, a modern unified theory of dispersion forces on atoms and bodies is presented which covers a broad range of advanced aspects and scenarios. Macroscopic quantum electrodynamics is shown to provide a powerful framework for dispersion forces which allows for discussing general properties like their non-additivity and the relation between microscopic and macroscopic interactions. It is demonstrated how the general results can be used to obtain dispersion forces on atoms in the presence of bodies of various shapes and materials. Starting with a brief recapitulation of volume I, this volume II deals especially with bodies of irregular shapes, universal scaling laws, dynamical forces on excited atoms, enhanced forces in cavity quantum electrodynamics, non-equilibrium forces in thermal environments and quantum friction. The book gives both the specialist and those new to the field a thorough overview over recent results in the field. It provides a toolbox for studying dispersion forces in various contex...

  2. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

    Energy Technology Data Exchange (ETDEWEB)

    Orimoto, Yuuichi, E-mail: orimoto.yuuichi.888@m.kyushu-u.ac.jp [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Aoki, Yuriko [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012 (Japan)

    2016-07-14

    An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

  3. Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse

    Directory of Open Access Journals (Sweden)

    A. Leonov

    2014-11-01

    Full Text Available The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron–electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 1012 photons pulse−1 (focusing on a spot size of ∼1 µm. This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm−2. The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm−2.

  4. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

    International Nuclear Information System (INIS)

    Orimoto, Yuuichi; Aoki, Yuriko

    2016-01-01

    An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

  5. Natural Fe{sub 3}O{sub 4} nanoparticles embedded zinc–tellurite glasses: Polarizability and optical properties

    Energy Technology Data Exchange (ETDEWEB)

    Widanarto, W. [Physics Study Program, Jenderal Soedirman University, Jl. Dr. Soeparno 61, Purwokerto 53123 (Indonesia); Sahar, M.R., E-mail: rahimsahar@utm.my [Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Skudai 81310 (Malaysia); Ghoshal, S.K.; Arifin, R.; Rohani, M.S.; Hamzah, K. [Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Skudai 81310 (Malaysia); Jandra, M. [FTI, University Teknologi Malaysia, Johor Bahru, Skudai 81310 (Malaysia)

    2013-02-15

    Modifying the optical behavior of zinc–tellurite glass by embedding magnetic nanoparticles has implication in nanophotonics. A series of zinc–tellurite glasses containing natural Fe{sub 3}O{sub 4} nanoparticles with composition (80 − x)TeO{sub 2}·xFe{sub 3}O{sub 4}·20ZnO (0 ≤ x ≤ 2) in mol% are synthesized by melt quenching method and their optical properties are investigated using FTIR and UV–vis–NIR spectroscopies. Lorentz–Lorenz relations are exploited to determine the refractive index, molar refraction and electronic polarizability. The sharp absorption peaks of FTIR spectra show a shift from 667 cm{sup −1} to 671 cm{sup −1} in the presence of nanoparticles that increase the non-bridging oxygen, confirmed by the intensity change of the TeO{sub 3} peak at 752 cm{sup −1}. A new peak around 461 cm{sup −1} is also observed which is attributed to the band characteristic of covalent Fe–O linkages. A decrease in the Urbach energy as much as 0.122 eV and the optical energy band gap with the increase of Fe{sub 3}O{sub 4} concentration (0.5–1.0 mol%) is evidenced. Electronic polarizability of the glasses increases with increasing Fe{sub 3}O{sub 4} nanoparticles concentration up to 1 mol%. Interestingly, the polarizability tends to decrease with the further increase of Fe{sub 3}O{sub 4} concentration at 2 mol%. The role of magnetic nanoparticles in influencing the structural and optical behavior are examined and understood. - Highlights: ► Incorporation of natural Fe{sub 3}O{sub 4} nanoparticles into the zinc–tellurite glass. ► Influence of magnetic nanoparticles in modifying structure and optical properties. ► Enhancement of refraction index and change in electronic polarizability.

  6. Molecular dynamics of polarizable point dipole models for molten NaI. Comparison with first principles simulations

    Directory of Open Access Journals (Sweden)

    Trullàs J.

    2011-05-01

    Full Text Available Molecular dynamics simulations of molten NaI at 995 K have been carried out using polarizable ion models based on rigid ion pair potentials to which the anion induced dipole polarization is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and deformation short-range damping interactions that oppose the electrically induced dipole moments. The structure and self-diffusion results are compared with those obtained by Galamba and Costa Cabral using first principles Hellmann-Feynman molecular dynamics simulations and using classical molecular dynamics of a shell model which allows only the iodide polarization

  7. Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model.

    Science.gov (United States)

    Boulanger, Eliot; Thiel, Walter

    2012-11-13

    Accurate quantum mechanical/molecular mechanical (QM/MM) treatments should account for MM polarization and properly include long-range electrostatic interactions. We report on a development that covers both these aspects. Our approach combines the classical Drude oscillator (DO) model for the electronic polarizability of the MM atoms with the generalized solvent boundary Potential (GSBP) and the solvated macromolecule boundary potential (SMBP). These boundary potentials (BP) are designed to capture the long-range effects of the outer region of a large system on its interior. They employ a finite difference approximation to the Poisson-Boltzmann equation for computing electrostatic interactions and take into account outer-region bulk solvent through a polarizable dielectric continuum (PDC). This approach thus leads to fully polarizable three-layer QM/MM-DO/BP methods. As the mutual responses of each of the subsystems have to be taken into account, we propose efficient schemes to converge the polarization of each layer simultaneously. For molecular dynamics (MD) simulations using GSBP, this is achieved by considering the MM polarizable model as a dynamical degree of freedom, and hence contributions from the boundary potential can be evaluated for a frozen state of polarization at every time step. For geometry optimizations using SMBP, we propose a dual self-consistent field approach for relaxing the Drude oscillators to their ideal positions and converging the QM wave function with the proper boundary potential. The chosen coupling schemes are evaluated with a test system consisting of a glycine molecule in a water ball. Both boundary potentials are capable of properly reproducing the gradients at the inner-region atoms and the Drude oscillators. We show that the effect of the Drude oscillators must be included in all terms of the boundary potentials to obtain accurate results and that the use of a high dielectric constant for the PDC does not lead to a polarization

  8. Isolamento de amebas de vida livre potencialmente patogênicas em poeira de hospitais Isolation of potencially pathogenic free-living amoebas in hospital dust

    Directory of Open Access Journals (Sweden)

    Maria Aparecida da Silva

    2003-04-01

    Full Text Available OBJETIVO: Observar a ocorrência de amebas de vida livre dos gêneros Acanthamoeba e Naegleria em amostras de poeira coletadas em hospitais. MÉTODOS: Foram coletadas 132 amostras de poeira em dois hospitais do município de Presidente Prudente, São Paulo. Os locais da coleta foram: Unidade de Terapia Intensiva, Centro Cirúrgico, Isolamento de Moléstias Infecciosas, Berçário, Emergência e Cozinha. As amostras foram semeadas em três meios de cultura: meio de ágar não nutriente com Escherichia coli, meio de ágar infusão de soja e microcultivo em meio de Pavlova modificado por Giazzi. As amebas isoladas foram identificadas segundo critérios morfológicos. RESULTADOS: O índice geral de positividade para amebas de vida livre, potencialmente patogênicas, dos gêneros Acanthamoeba e Naegleria, foi de 45,5%, sendo positivas 41,6% das amostras de poeira coletadas no hospital universitário e 50% no hospital estadual. Obtiveram-se 45,5% de positividade do gênero Acanthamoeba e 3,8% para amebas do gênero Naegleria. CONCLUSÕES: As amebas de vida livre, potencialmente patogênicas, estavam presentes em todos os ambientes estudados dos dois hospitais, sendo que as espécies do gênero Acanthamoeba foram as isoladas com maior freqüência.OBJECTIVE: To evaluate the occurrence of free-living amoebas of the genera Acanthamoeba and Naegleria is dust samples colleted in two hospitals. METHODS: One-hundred and thirty-two dust samples were collected in two hospitals in Brazil. Hospital collection sites were the following: intensive care unit, operation rooms, nursery, kitchen, emergency and infectious diseases isolation room . The isolation of the amoebas was performed in three culture media: non-nutrient agar inoculated with Escherichia coli, soy agar, and microculture in Giazzi-modified Pavlova's medium. The amoebas were identified according to morphological criteria. RESULTS: Amoebas of the genera Acanthamoeba and Naegleria were found in 45.5% of

  9. Relativistic many-body calculation of energies, transition rates, lifetimes, and multipole polarizabilities in Cs-like La iii

    Science.gov (United States)

    Safronova, U. I.; Safronova, M. S.

    2014-05-01

    Excitation energies of the [Xe]nd (n =5-9), [Xe]ns (n =6-10), [Xe]np (n =6-9), [Xe]nf (n =4-8), and [Xe]ng (n =5-8) states in La iii, where [Xe] = 1s22s22p63s23p63d104s24p64d105s25p6, are evaluated. Electric dipole matrix elements for the allowed transitions between the low-lying [Xe]nd, [Xe]ns, [Xe]np, [Xe]nf, and [Xe]ng states in the La iii ion are calculated using the high-precision relativistic all-order method where all single, double, and partial triple excitations of the Dirac-Fock wave functions are included to all orders of perturbation theory. Recommended values are provided for a large number of electric dipole matrix elements, oscillator strengths, transition rates, and lifetimes. Scalar and tensor polarizabilities of the states listed above are evaluated. The uncertainties of the recommended values are estimated. Electric quadrupole and magnetic dipole matrix elements are calculated to determine lifetimes of the 5d5/2 and 6s metastable levels. The ground-state E1, E2, and E3 static polarizabilities are calculated. This work provides recommended values critically evaluated for their accuracy for a number of La iii atomic properties for use in planning and analysis of various experiments as well as theoretical modeling.

  10. Infrared optical constants, dielectric constants, molar polarizabilities, transition moments, dipole moment derivatives and Raman spectrum of liquid cyclohexane

    Science.gov (United States)

    Keefe, C. Dale; Pickup, Janet E.

    2009-06-01

    Previous studies have been done in this laboratory focusing on the optical properties of several liquid aromatic and aliphatic hydrocarbons in the infrared. The current study reports the infrared and absorption Raman spectra of liquid cyclohexane. Infrared spectra were recorded at 25 °C over a wavenumber range of 7400-490 cm -1. Infrared measurements were taken using transmission cells with pathlengths ranging from 3 to 5000 μm. Raman spectra were recorded between 3700 and 100 cm -1 at 25 °C using a 180° reflection geometry. Ab initio calculations of the vibrational wavenumbers at the B3LYP/6311G level of theory were performed and used to help assign the observed IR and Raman spectra. Extensive assignments of the fundamentals and binary combinations observed in the infrared imaginary molar polarizability spectrum are reported. The imaginary molar polarizability spectrum was curve fitted to separate the intensity from the various transitions and used to determine the transition moments and magnitudes of the derivatives of the dipole moment with respect to the normal coordinates for the fundamentals.

  11. Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

    Energy Technology Data Exchange (ETDEWEB)

    List, Nanna Holmgaard, E-mail: nhl@sdu.dk; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob [Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark (Denmark); Beerepoot, Maarten T. P.; Gao, Bin; Ruud, Kenneth [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø–The Arctic University of Norway, N-9037 Tromsø (Norway); Olsen, Jógvan Magnus Haugaard [Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark (Denmark); Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland)

    2015-01-21

    We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn–Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange–repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.

  12. Calculations on the Nonlinear Second—Order Optical Polarizabilities for Series of Donor—C60 Molecules

    Institute of Scientific and Technical Information of China (English)

    刘孝娟; 封继康; 任爱民

    2003-01-01

    The equilibrium geometries and UV-visible spectra of a series of donor-C60 molecules were obtained by means of the AM1 and INDO/CI method,on the basis of accurate geometric and electronic structures.The nonlinear second-order optical polarizabilities were calculated using the method INDO/SDCI combined with the Sum-Over-States(SOS) expression.The calculatedβ(λ=1.34μm) values are 28.81,48.56,57.33,66.99,70.85,85.84,and 142.14(×10-30 esu) for the molecules A,B,C,D,E,F and G,respectively.The frontier orbitals were plot for the representative molecules in order to exhibit the intramolecular charge transfer.The results indicate the introduction of thienylethylene can enhance the NLO response and the dimethylaniline-substituted dithienyl-ethylene-C60 (molecule G) possesses the largest NLO second-order optical polarizability.The large β values can be attributed to the charge transfer between the substituents and C60,as well as within the three-dimensional conjugated sphere of C60.

  13. Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole

    Directory of Open Access Journals (Sweden)

    Mohammad Firoz Khan

    2016-12-01

    Full Text Available Ab initio calculations were carried out to study the geometry, solvation free energy, dipole moment, molecular electrostatic potential (MESP, Mulliken and Natural charge distribution, polarizability, hyperpolarizability, Natural Bond Orbital (NBO energetic and different molecular properties like global reactivity descriptors (chemical hardness, softness, chemical potential, electronegativity, electrophilicity index of 2-methylimidazole. B3LYP/6-31G(d,p level of theory was used to optimize the structure both in the gas phase and in solution. The solvation free energy, dipole moment and molecular properties were calculated by applying the Solvation Model on Density (SMD in four solvent systems, namely water, dimethylsulfoxide (DMSO, n-octanol and chloroform. The computed bond distances, bond angles and dihedral angles of 2-methylimidazole agreed reasonably well with the experimental data except for C(2-N(1, C(4-C(5 and N(1-H(7 bond lengths and N(1-C(5-C(4 bond angle. The solvation free energy, dipole moment, polarizability, first order hyperpolarizability, chemical potential, electronegativity and electrophilicity index of 2-methylimidazole increased on going from non-polar to polar solvents. Chemical hardness also increased with increasing polarity of the solvent and the opposite relation was found in the case of softness. These results provide better understanding of the stability and reactivity of 2-methylimidazole in different solvent systems.

  14. To semi-centenary anniversary of discovering the Schwinger scattering and starting the first works on neutron polarizability

    International Nuclear Information System (INIS)

    Alexandrov, Yu.A.

    2006-01-01

    The theory of neutron Schwinger scattering was proposed and developed by Schwinger in 1948, but despite multiple efforts, the experimental discovery of this phenomenon was made eight years later. Currently, Schwinger scattering should be accounted for in many precise neutron experiments, for example, while studying the electromagnetic interaction of neutrons with nuclei. By means of Schwinger scattering it is possible to measure the degree of polarization of the initial beam even at particle energies of 1 GeV order. The concept of neutron polarizability was introduced as additional natural phenomenon indicating the nucleon space structure after the first Hofstadter's experiments (1953-1954). The neutron polarizability was detected in a small-angle neutron scattering experiment in 1957. However, the serious contradiction between the results obtained in megaelectronvolt and kiloelectronvolt neutron energy ranges was explained only in 2001. It is also shown that existent small-angle neutron experiments at megaelectronvolt energy by heavy nuclei do not confirm the idea of (n+3)-dimensional gravity

  15. Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

    International Nuclear Information System (INIS)

    List, Nanna Holmgaard; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob; Beerepoot, Maarten T. P.; Gao, Bin; Ruud, Kenneth; Olsen, Jógvan Magnus Haugaard

    2015-01-01

    We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn–Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange–repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters

  16. Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response

    Science.gov (United States)

    Caricato, Marco

    2018-04-01

    We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

  17. Impact of two hot and dry summers on the community structure and functional diversity of testate amoebae in an artificial bog, illustrating their use as bioindicators of peatland health

    Directory of Open Access Journals (Sweden)

    I. Koenig

    2018-04-01

    Full Text Available Ongoing climate warming threatens the survival of bogs at the warm/dry limit of their distribution (e.g. in central Europe, and jeopardises the restoration of damaged bogs even more. Because vegetation changes can be slow, early indicators of hydrological change such as testate amoebae are useful. We used testate amoeba community structure and community weighted mean of functional traits to monitor the impact of two very hot and dry summers on a small (around 100 m2 artificial peatland constructed in the botanic garden of Neuchâtel, Switzerland. We collected analogous samples in a naturally regenerating cutover peatland at 1000 m a.s.l. in the Jura Mountains as a reference. The comparison of living and dead assemblages in the botanic garden showed an increased representation of smaller testate amoeba taxa (Corythion dubium, small Euglypha sp. with a small pseudostome (indicative of dry conditions and a loss of mixotrophy in 2015, followed by a weaker further shift in 2016. Nevertheless, the testate amoeba community structure in 2016 still indicated a dry Sphagnum bog. Testate amoeba analysis allows rapid assessment of peatland health and/or restoration success. The comparison of living and dead assemblages makes it possible to observe changes within a season in a single sampling campaign.

  18. Sphagnum-dwelling testate amoebae in subarctic bogs are more sensitive to soil warming in the growing season than in winter: the results of eight-year field climate manipulations.

    Science.gov (United States)

    Tsyganov, Andrey N; Aerts, Rien; Nijs, Ivan; Cornelissen, Johannes H C; Beyens, Louis

    2012-05-01

    Sphagnum-dwelling testate amoebae are widely used in paleoclimate reconstructions as a proxy for climate-induced changes in bogs. However, the sensitivity of proxies to seasonal climate components is an important issue when interpreting proxy records. Here, we studied the effects of summer warming, winter snow addition solely and winter snow addition together with spring warming on testate amoeba assemblages after eight years of experimental field climate manipulations. All manipulations were accomplished using open top chambers in a dry blanket bog located in the sub-Arctic (Abisko, Sweden). We estimated sensitivity of abundance, diversity and assemblage structure of living and empty shell assemblages of testate amoebae in the living and decaying layers of Sphagnum. Our results show that, in a sub-arctic climate, testate amoebae are more sensitive to climate changes in the growing season than in winter. Summer warming reduced species richness and shifted assemblage composition towards predominance of xerophilous species for the living and empty shell assemblages in both layers. The higher soil temperatures during the growing season also decreased abundance of empty shells in both layers hinting at a possible increase in their decomposition rates. Thus, although possible effects of climate changes on preservation of empty shells should always be taken into account, species diversity and structure of testate amoeba assemblages in dry subarctic bogs are sensitive proxies for climatic changes during the growing season. Copyright © 2011 Elsevier GmbH. All rights reserved.

  19. Detection of viable Helicobacter pylori inside free-living amoebae in wastewater and drinking water samples from Eastern Spain.

    Science.gov (United States)

    Moreno-Mesonero, Laura; Moreno, Yolanda; Alonso, José Luis; Ferrús, M Antonia

    2017-10-01

    Helicobacter pylori is one of the most concerning emerging waterborne pathogens. It has been suggested that it could survive in water inside free-living amoebae (FLA), but nobody has studied this relationship in the environment yet. Thus, we aimed to detect viable H. pylori cells from inside FLA in water samples. Sixty-nine wastewater and 31 drinking water samples were collected. FLA were purified and identified by PCR and sequencing. For exclusively detecting H. pylori inside FLA, samples were exposed to sodium hypochlorite and assayed by specific PMA-qPCR, DVC-FISH and culture. FLA were detected in 38.7% of drinking water and 79.7% of wastewater samples, even after disinfection. In wastewater, Acanthamoeba spp. and members of the family Vahlkampfiidae were identified. In drinking water, Acanthamoeba spp. and Echinamoeba and/or Vermamoeba were present. In 39 (58.2%) FLA-positive samples, H. pylori was detected by PMA-qPCR. After DVC-FISH, 21 (31.3%) samples harboured viable H. pylori internalized cells. H. pylori was cultured from 10 wastewater samples. To our knowledge, this is the first report that demonstrates that H. pylori can survive inside FLA in drinking water and wastewater, strongly supporting the hypothesis that FLA could play an important role in the transmission of H. pylori to humans. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. The TOM Complex of Amoebozoans: the Cases of the Amoeba Acanthamoeba castellanii and the Slime Mold Dictyostelium discoideum.

    Science.gov (United States)

    Wojtkowska, Małgorzata; Buczek, Dorota; Stobienia, Olgierd; Karachitos, Andonis; Antoniewicz, Monika; Slocinska, Małgorzata; Makałowski, Wojciech; Kmita, Hanna

    2015-07-01

    Protein import into mitochondria requires a wide variety of proteins, forming complexes in both mitochondrial membranes. The TOM complex (translocase of the outer membrane) is responsible for decoding of targeting signals, translocation of imported proteins across or into the outer membrane, and their subsequent sorting. Thus the TOM complex is regarded as the main gate into mitochondria for imported proteins. Available data indicate that mitochondria of representative organisms from across the major phylogenetic lineages of eukaryotes differ in subunit organization of the TOM complex. The subunit organization of the TOM complex in the Amoebozoa is still elusive, so we decided to investigate its organization in the soil amoeba Acanthamoeba castellanii and the slime mold Dictyostelium discoideum. They represent two major subclades of the Amoebozoa: the Lobosa and Conosa, respectively. Our results confirm the presence of Tom70, Tom40 and Tom7 in the A. castellanii and D. discoideum TOM complex, while the presence of Tom22 and Tom20 is less supported. Interestingly, the Tom proteins display the highest similarity to Opisthokonta cognate proteins, with the exception of Tom40. Thus representatives of two major subclades of the Amoebozoa appear to be similar in organization of the TOM complex, despite differences in their lifestyle. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.

  1. Response of forest soil euglyphid testate amoebae (Rhizaria: Cercozoa) to pig cadavers assessed by high-throughput sequencing.

    Science.gov (United States)

    Seppey, Christophe V W; Fournier, Bertrand; Szelecz, Ildikò; Singer, David; Mitchell, Edward A D; Lara, Enrique

    2016-03-01

    Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro-environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.

  2. Systematic Analysis of γ-Aminobutyric Acid (GABA) Metabolism and Function in the Social Amoeba Dictyostelium discoideum*

    Science.gov (United States)

    Wu, Yuantai; Janetopoulos, Chris

    2013-01-01

    While GABA has been suggested to regulate spore encapsulation in the social amoeba Dictyostelium discoideum, the metabolic profile and other potential functions of GABA during development remain unclear. In this study, we investigated the homeostasis of GABA metabolism by disrupting genes related to GABA metabolism and signaling. Extracellular levels of GABA are tightly regulated during early development, and GABA is generated by the glutamate decarboxylase, GadB, during growth and in early development. However, overexpression of the prespore-specific homologue, GadA, in the presence of GadB reduces production of extracellular GABA. Perturbation of extracellular GABA levels delays the process of aggregation. Cytosolic GABA is degraded by the GABA transaminase, GabT, in the mitochondria. Disruption of a putative vesicular GABA transporter (vGAT) homologue DdvGAT reduces secreted GABA. We identified the GABAB receptor-like family member GrlB as the major GABA receptor during early development, and either disruption or overexpression of GrlB delays aggregation. This delay is likely the result of an abolished pre-starvation response and late expression of several “early” developmental genes. Distinct genes are employed for GABA generation during sporulation. During sporulation, GadA alone is required for generating GABA and DdvGAT is likely responsible for GABA secretion. GrlE but not GrlB is the GABA receptor during late development. PMID:23548898

  3. Environmental factors shaping cultured free-living amoebae and their associated bacterial community within drinking water network.

    Science.gov (United States)

    Delafont, Vincent; Bouchon, Didier; Héchard, Yann; Moulin, Laurent

    2016-09-01

    Free-living amoebae (FLA) constitute an important part of eukaryotic populations colonising drinking water networks. However, little is known about the factors influencing their ecology in such environments. Because of their status as reservoir of potentially pathogenic bacteria, understanding environmental factors impacting FLA populations and their associated bacterial community is crucial. Through sampling of a large drinking water network, the diversity of cultivable FLA and their bacterial community were investigated by an amplicon sequencing approach, and their correlation with physicochemical parameters was studied. While FLA ubiquitously colonised the water network all year long, significant changes in population composition were observed. These changes were partially explained by several environmental parameters, namely water origin, temperature, pH and chlorine concentration. The characterisation of FLA associated bacterial community reflected a diverse but rather stable consortium composed of nearly 1400 OTUs. The definition of a core community highlighted the predominance of only few genera, majorly dominated by Pseudomonas and Stenotrophomonas. Co-occurrence analysis also showed significant patterns of FLA-bacteria association, and allowed uncovering potentially new FLA - bacteria interactions. From our knowledge, this study is the first that combines a large sampling scheme with high-throughput identification of FLA together with associated bacteria, along with their influencing environmental parameters. Our results demonstrate the importance of physicochemical parameters in the ecology of FLA and their bacterial community in water networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Different forces

    CERN Multimedia

    1982-01-01

    The different forces, together with a pictorial analogy of how the exchange of particles works. The table lists the relative strength of the couplings, the quanta associated with the force fields and the bodies or phenomena in which they have a dominant role.

  5. Labor Force

    Science.gov (United States)

    Occupational Outlook Quarterly, 2010

    2010-01-01

    The labor force is the number of people aged 16 or older who are either working or looking for work. It does not include active-duty military personnel or institutionalized people, such as prison inmates. Quantifying this total supply of labor is a way of determining how big the economy can get. Labor force participation rates vary significantly…

  6. Numerical study of the lateral resolution in electrostatic force microscopy for dielectric samples

    International Nuclear Information System (INIS)

    Riedel, C; AlegrIa, A; Colmenero, J; Schwartz, G A; Saenz, J J

    2011-01-01

    We present a study of the lateral resolution in electrostatic force microscopy for dielectric samples in both force and gradient modes. Whereas previous studies have reported expressions for metallic surfaces having potential heterogeneities (Kelvin probe force microscopy), in this work we take into account the presence of a dielectric medium. We introduce a definition of the lateral resolution based on the force due to a test particle being either a point charge or a polarizable particle on the dielectric surface. The behaviour has been studied over a wide range of typical experimental parameters: tip-sample distance (1-20) nm, sample thickness (0-5) μm and dielectric constant (1-20), using the numerical simulation of the equivalent charge method. For potential heterogeneities on metallic surfaces expressions are in agreement with the bibliography. The lateral resolution of samples having a dielectric constant of more than 10 tends to metallic behaviour. We found a characteristic thickness of 100 nm, above which the lateral resolution measured on the dielectric surface is close to that of an infinite medium. As previously reported, the lateral resolution is better in the gradient mode than in the force mode. Finally, we showed that for the same experimental conditions, the lateral resolution is better for a polarizable particle than for a charge, i.e. dielectric heterogeneities should always look 'sharper' (better resolved) than inhomogeneous charge distributions. This fact should be taken into account when interpreting images of heterogeneous samples.

  7. Numerical study of the lateral resolution in electrostatic force microscopy for dielectric samples

    Energy Technology Data Exchange (ETDEWEB)

    Riedel, C; AlegrIa, A; Colmenero, J [Departamento de Fisica de Materiales UPV/EHU, Facultad de Quimica, Apartado 1072, 20080 San Sebastian (Spain); Schwartz, G A [Centro de Fisica de Materiales CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastian (Spain); Saenz, J J, E-mail: riedel@ies.univ-montp2.fr [Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastian (Spain)

    2011-07-15

    We present a study of the lateral resolution in electrostatic force microscopy for dielectric samples in both force and gradient modes. Whereas previous studies have reported expressions for metallic surfaces having potential heterogeneities (Kelvin probe force microscopy), in this work we take into account the presence of a dielectric medium. We introduce a definition of the lateral resolution based on the force due to a test particle being either a point charge or a polarizable particle on the dielectric surface. The behaviour has been studied over a wide range of typical experimental parameters: tip-sample distance (1-20) nm, sample thickness (0-5) {mu}m and dielectric constant (1-20), using the numerical simulation of the equivalent charge method. For potential heterogeneities on metallic surfaces expressions are in agreement with the bibliography. The lateral resolution of samples having a dielectric constant of more than 10 tends to metallic behaviour. We found a characteristic thickness of 100 nm, above which the lateral resolution measured on the dielectric surface is close to that of an infinite medium. As previously reported, the lateral resolution is better in the gradient mode than in the force mode. Finally, we showed that for the same experimental conditions, the lateral resolution is better for a polarizable particle than for a charge, i.e. dielectric heterogeneities should always look 'sharper' (better resolved) than inhomogeneous charge distributions. This fact should be taken into account when interpreting images of heterogeneous samples.

  8. Novel parallel plate condenser for single particle electrostatic force measurements in atomic force microscope

    KAUST Repository

    Kwek, Jin Wang

    2011-07-01

    A combination of small parallel plate condenser with Indium Tin Oxide (ITO) glass slides as electrodes and an atomic force microscope (AFM) is used to characterize the electrostatic behavior of single glass bead microparticles (105-150 μm) glued to the AFM cantilever. This novel setup allows measurements of the electrostatic forces acting on a particle in an applied electrical field to be performed in ambient air conditions. By varying the position of the microparticle between the electrodes and the strength of the applied electric field, the relative contributions of the particle net charge, induced and image charges were investigated. When the microparticle is positioned in the middle of the electrodes, the force acting on the microparticle was linear with the applied electric field and proportional to the microparticle net charge. At distances close to the bottom electrode, the force follows a parabolic relationship with the applied electric field reflecting the contributions of induced and image charges. The method can be used for the rapid evaluation of the charging and polarizability properties of the microparticle as well as an alternative to the conventional Faraday\\'s pail technique. © 2011 Elsevier B.V.

  9. Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.

    Science.gov (United States)

    Quillin, M L; Breyer, W A; Griswold, I J; Matthews, B W

    2000-09-29

    To investigate the relative importance of size and polarizability in ligand binding within proteins, we have determined the crystal structures of pseudo wild-type and cavity-containing mutant phage T4 lysozymes in the presence of argon, krypton, and xenon. These proteins provide a representative sample of predominantly apolar cavities of varying size and shape. Even though the volumes of these cavities range up to the equivalent of five xenon atoms, the noble gases bind preferentially at highly localized sites that appear to be defined by constrictions in the walls of the cavities, coupled with the relatively large radii of the noble gases. The cavities within pseudo wild-type and L121A lysozymes each bind only a single atom of noble gas, while the cavities within mutants L133A and F153A have two independent binding sites, and the L99A cavity has three interacting sites. The binding of noble gases within two double mutants was studied to characterize the additivity of binding at such sites. In general, when a cavity in a protein is created by a "large-to-small" substitution, the surrounding residues relax somewhat to reduce the volume of the cavity. The binding of xenon and, to a lesser degree, krypton and argon, tend to expand the volume of the cavity and to return it closer to what it would have been had no relaxation occurred. In nearly all cases, the extent of binding of the noble gases follows the trend xenon>krypton>argon. Pressure titrations of the L99A mutant have confirmed that the crystallographic occupancies accurately reflect fractional saturation of the binding sites. The trend in noble gas affinity can be understood in terms of the effects of size and polarizability on the intermolecular potential. The plasticity of the protein matrix permits repulsion due to increased ligand size to be more than compensated for by attraction due to increased ligand polarizability. These results have implications for the mechanism of general anesthesia, the migration

  10. Influence of permittivity on gradient force exerted on Mie spheres.

    Science.gov (United States)

    Chen, Jun; Li, Kaikai; Li, Xiao

    2018-04-01

    In optical trapping, whether a particle could be stably trapped into the focus region greatly depends on the strength of the gradient force. Individual theoretical study on gradient force exerted on a Mie particle is rare because the mathematical separation of the gradient force and the scattering force in the Mie regime is difficult. Based on the recent forces separation work by Du et al. [Sci. Rep.7, 18042 (2017)SRCEC32045-232210.1038/s41598-017-17874-1], we investigate the influence of permittivity (an important macroscopic physical quantity) on the gradient force exerted on a Mie particle by cooperating numerical calculation using fast Fourier transform and analytical analysis using multipole expansion. It is revealed that gradient forces exerted on small spheres are mainly determined by the electric dipole moment except for certain permittivity with which the real part of polarizability of the electric dipole approaches zero, and gradient forces exerted on larger spheres are complex because of the superposition of the multipole moments. The classification of permittivity corresponding to different varying tendencies of gradient forces exerted on small spheres or larger Mie particles are illustrated. Absorption of particles favors the trapping of small spheres by gradient force, while it is bad for the trapping of larger particles. Moreover, the absolute values of the maximal gradient forces exerted on larger Mie particles decline greatly versus the varied imaginary part of permittivity. This work provides elaborate investigation on the different varying tendencies of gradient forces versus permittivity, which favors more accurate and free optical trapping.

  11. Ubiquiter circovirus sequences raise challenges in laboratory diagnosis: the case of honey bee and bee mite, reptiles, and free living amoebae.

    Science.gov (United States)

    Marton, Szilvia; Ihász, Katalin; Lengyel, György; Farkas, Szilvia L; Dán, Ádám; Paulus, Petra; Bányai, Krisztián; Fehér, Enikő

    2015-03-01

    Circoviruses of pigs and birds are established pathogens, however, the exact role of other, recently described circoviruses and circovirus-like viruses remains to be elucidated. The aim of this study was the detection of circoviruses in neglected host species, including honey bees, exotic reptiles and free-living amoebae by widely used broad-spectrum polymerase chain reaction (PCR) assays specific for the replication initiation protein coding gene of these viruses. The majority of sequences obtained from honey bees were highly similar to canine and porcine circoviruses, or, were distantly related to dragonfly cycloviruses. Other rep sequences detected in some honey bees, reptiles and amoebae showed similarities to various rep sequences deposited in the GenBank. Back-to-back PCR primers designed for the amplification of whole viral genomes failed to work that suggested the existence of integrated rep-like elements in many samples. Rolling circle amplification and exonuclease treatment confirmed the absence of small circular DNA genomes in the specimens analysed. In case of honey bees Varroa mite DNA contamination might be a source of the identified endogenous rep-like elements. The reptile and amoebae rep-like sequences were nearly identical with each other and with sequences detected in chimpanzee feces raising the possibility that detection of novel or unusual rep-like elements in some host species might originate from the microbial community of the host. Our results indicate that attention is needed when broad-spectrum rep gene specific polymerase chain reaction is chosen for laboratory diagnosis of circovirus infections.

  12. Acetate and succinate production in amoebae, helminths, diplomonads, trichomonads and trypanosomatids: common and diverse metabolic strategies used by parasitic lower eukaryotes.

    Science.gov (United States)

    Bringaud, F; Ebikeme, C; Boshart, M

    2010-08-01

    Parasites that often grow anaerobically in their hosts have adopted a fermentative strategy relying on the production of partially oxidized end products, including lactate, glycerol, ethanol, succinate and acetate. This review focuses on recent progress in understanding acetate production in protist parasites, such as amoebae, diplomonads, trichomonads, trypanosomatids and in the metazoan parasites helminths, as well as the succinate production pathway(s) present in some of them. We also describe the unconventional organisation of the tricarboxylic acid cycle associated with the fermentative strategy adopted by the procyclic trypanosomes, which may resemble the probable structure of the primordial TCA cycle in prokaryotes.

  13. Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum.

    Directory of Open Access Journals (Sweden)

    Gerda Saxer

    Full Text Available Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9, with a Poisson confidence interval of 4.1×10(-9 - 9.5×10(-9, per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10(-11, with a Poisson confidence interval ranging from 7.4×10(-13 to 1.6×10(-10, is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.

  14. Amoeba-inspired Tug-of-War algorithms for exploration-exploitation dilemma in extended Bandit Problem.

    Science.gov (United States)

    Aono, Masashi; Kim, Song-Ju; Hara, Masahiko; Munakata, Toshinori

    2014-03-01

    The true slime mold Physarum polycephalum, a single-celled amoeboid organism, is capable of efficiently allocating a constant amount of intracellular resource to its pseudopod-like branches that best fit the environment where dynamic light stimuli are applied. Inspired by the resource allocation process, the authors formulated a concurrent search algorithm, called the Tug-of-War (TOW) model, for maximizing the profit in the multi-armed Bandit Problem (BP). A player (gambler) of the BP should decide as quickly and accurately as possible which slot machine to invest in out of the N machines and faces an "exploration-exploitation dilemma." The dilemma is a trade-off between the speed and accuracy of the decision making that are conflicted objectives. The TOW model maintains a constant intracellular resource volume while collecting environmental information by concurrently expanding and shrinking its branches. The conservation law entails a nonlocal correlation among the branches, i.e., volume increment in one branch is immediately compensated by volume decrement(s) in the other branch(es). Owing to this nonlocal correlation, the TOW model can efficiently manage the dilemma. In this study, we extend the TOW model to apply it to a stretched variant of BP, the Extended Bandit Problem (EBP), which is a problem of selecting the best M-tuple of the N machines. We demonstrate that the extended TOW model exhibits better performances for 2-tuple-3-machine and 2-tuple-4-machine instances of EBP compared with the extended versions of well-known algorithms for BP, the ϵ-Greedy and SoftMax algorithms, particularly in terms of its short-term decision-making capability that is essential for the survival of the amoeba in a hostile environment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  15. Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

    Energy Technology Data Exchange (ETDEWEB)

    Duchemin, Ivan, E-mail: ivan.duchemin@cea.fr [INAC, SP2M/L-Sim, CEA/UJF Cedex 09, 38054 Grenoble (France); Jacquemin, Denis [Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3 (France); Institut Universitaire de France, 1 rue Descartes, 75005 Paris Cedex 5 (France); Blase, Xavier [CNRS, Inst. NÉEL, F-38000 Grenoble (France); Univ. Grenoble Alpes, Inst. NÉEL, F-38000 Grenoble (France)

    2016-04-28

    We have implemented the polarizable continuum model within the framework of the many-body Green’s function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.

  16. Nuclear forces

    International Nuclear Information System (INIS)

    Holinde, K.

    1990-01-01

    In this paper the present status of the meson theory of nuclear forces is reviewed. After some introductory remarks about the relevance of the meson exchange concept in the era of QCD and the empirical features of the NN interaction, the exciting history of nuclear forces is briefly outlined. In the main part, the author gives the basic physical ideas and sketch the derivation of the one-boson-exchange model of the nuclear force, in the Feynman approach. Secondly we describe, in a qualitative way, various necessary extensions, leading to the Bonn model of the N interaction. Finally, points to some interesting pen questions connected with the extended quark structure of the hadrons, which are topics of current research activity

  17. The Alexandria library, a quantum-chemical database of molecular properties for force field development.

    Science.gov (United States)

    Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

    2018-04-10

    Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

  18. The Alexandria library, a quantum-chemical database of molecular properties for force field development

    Science.gov (United States)

    Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

    2018-04-01

    Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

  19. Testate amoebae analysis in the peat deposits of the swamp Dolgon’koye in the south of Western Siberia and peatland paleohydrology for last 3100 years

    Science.gov (United States)

    Kurina, Irina V.; Blyakharchuk, Tatiana A.

    2018-03-01

    Our research is devoted to paleohydrological reconstruction in the swamp located in the river valley on the piedmont of the Altai Mountains in the south of Western Siberia. The reconstruction was carried out based on rhizopod analysis for the last 3100 cal yr. A large amount of different testate amoebae was found in the peat. Total 64 testate amoebae taxa were recorded in the peat core with the most abundant being: Trinema lineare, Centropyxis aculeata, C. aerophila, Euglypha rotunda, Cryptodifflugia sp. Decrease of surface wetness in the swamp are observed 2280, 2140, 1900–600 cal yr BP and increase – in 2700, 2500–1900, 230–215 cal yr BP. The results of our reconstruction of the swamp paleohydrology agrees well with the paleoclimatic data obtained earlier for the central area of the south of Western Siberia Plain. It indicates a high sensitivity of the swamp to climatic changes in the Holocene. The rhizopod analysis proved to be very effective when used for paleohydrology reconstruction in minerotrophic peat.

  20. MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.

    Science.gov (United States)

    Avesson, Lotta; Reimegård, Johan; Wagner, E Gerhart H; Söderbom, Fredrik

    2012-10-01

    The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.

  1. The scaled-charge additive force field for amino acid based ionic liquids

    DEFF Research Database (Denmark)

    Fileti, E. E.; Chaban, V. V.

    2014-01-01

    Ionic liquids (ILs) constitute an emerging research field. New ILs involve more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non-polarizable force field (FF) for the eight AAILs...... comprising 1-ethyl-3-methylimidazolium cation and amino acid anions. The anions were obtained via deprotonation of carboxyl group. Specific cation-anion non-covalent interactions were taken into account by computing electrostatic potential for ion pairs. The van der Waals interactions were adopted from...

  2. Sphagnum-dwelling testate amoebae in subarctic bogs are more sensitive to soil warming in the growing season than in winter: the results of eight-year field climate manipulations.

    NARCIS (Netherlands)

    Tsyganov, A.N.; Aerts, R.; Nijs, I.; Cornelissen, J.H.C.; Beyens, L.

    2012-01-01

    Sphagnum-dwelling testate amoebae are widely used in paleoclimate reconstructions as a proxy for climate-induced changes in bogs. However, the sensitivity of proxies to seasonal climate components is an important issue when interpreting proxy records. Here, we studied the effects of summer warming,

  3. Response of sphagnum peatland testate amoebae to a 1-year transplantation experiment along an artificial hydrological gradient.

    Science.gov (United States)

    Marcisz, Katarzyna; Fournier, Bertrand; Gilbert, Daniel; Lamentowicz, Mariusz; Mitchell, Edward A D

    2014-05-01

    Peatland testate amoebae (TA) are well-established bioindicators for depth to water table (DWT), but effects of hydrological changes on TA communities have never been tested experimentally. We tested this in a field experiment by placing Sphagnum carpets (15 cm diameter) collected in hummock, lawn and pool microsites (origin) at three local conditions (dry, moist and wet) using trenches dug in a peatland. One series of samples was seeded with microorganism extract from all microsites. TA community were analysed at T0: 8-2008, T1: 5-2009 and T2: 8-2009. We analysed the data using conditional inference trees, principal response curves (PRC) and DWT inferred from TA communities using a transfer function used for paleoecological reconstruction. Density declined from T0 to T1 and then increased sharply by T2. Species richness, Simpson diversity and Simpson evenness were lower at T2 than at T0 and T1. Seeded communities had higher species richness in pool samples at T0. Pool samples tended to have higher density, lower species richness, Simpson diversity and Simpson Evenness than hummock and/or lawn samples until T1. In the PRC, the effect of origin was significant at T0 and T1, but the effect faded away by T2. Seeding effect was strongest at T1 and lowest vanished by T2. Local condition effect was strong but not in line with the wetness gradient at T1 but started to reflect it by T2. Likewise, TA-inferred DWT started to match the experimental conditions by T2, but more so in hummock and lawn samples than in pool samples. This study confirmed that TA responds to hydrological changes over a 1-year period. However, sensitivity of TA to hydrological fluctuations, and thus the accuracy of inferred DWT changes, was habitat specific, pool TA communities being least responsive to environmental changes. Lawns and hummocks may be thus better suited than pools for paleoecological reconstructions. This, however, contrasts with the higher prediction error and species' tolerance for

  4. Ab initio potential energy surface, electric-dipole moment, polarizability tensor, and theoretical rovibrational spectra in the electronic ground state of {sup 14}NH{sub 3}{sup +}

    Energy Technology Data Exchange (ETDEWEB)

    Yurchenko, Sergei N. [Technische Universitaet Dresden, Institut fuer Physikalische Chemie und Elektrochemie, D-01062 Dresden (Germany); Thiel, Walter [Max-Planck-Institut fuer Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Muelheim an der Ruhr (Germany); Carvajal, Miguel [Departamento de Fisica Aplicada, Facultad de Ciencias Experimentales, Avenida de las Fuerzas Armadas s/n, Universidad de Huelva, E-21071 Huelva (Spain); Jensen, Per [Theoretische Chemie, Bergische Universitaet, D-42097 Wuppertal (Germany)], E-mail: jensen@uni-wuppertal.de

    2008-05-04

    We report the calculation of a six-dimensional CCSD(T)/aug-cc-pVQZ potential energy surface for the electronic ground state of NH{sub 3}{sup +} together with the corresponding CCSD(T)/aug-cc-pVTZ dipole moment and polarizability surface of {sup 14}NH{sub 3}{sup +}. These electronic properties have been computed on a large grid of molecular geometries. A number of newly calculated band centers are presented along with the associated electric-dipole transition moments. We further report the first calculation of vibrational matrix elements of the polarizability tensor components for {sup 14}NH{sub 3}{sup +}; these matrix elements determine the intensities of Raman transitions. In addition, the rovibrational absorption spectra of the {nu}{sub 2}, {nu}{sub 3}, {nu}{sub 4}, 2{nu}{sub 2}-{nu}{sub 2}, and {nu}{sub 2}+{nu}{sub 3}-{nu}{sub 2} bands have been simulated.

  5. Application of discrete solvent reaction field model with self-consistent atomic charges and atomic polarizabilities to calculate the χ(1) and χ(2) of organic molecular crystals

    Science.gov (United States)

    Lu, Shih-I.

    2018-01-01

    We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.

  6. Dipole polarizability of 2 3S1 and 2 1S0 metastable helium measured by the electric deflection time-of-flight method

    International Nuclear Information System (INIS)

    Crosby, D.A.; Zorn, J.C.

    1977-01-01

    The static dipole polarizability of helium atoms in the metastable 2 3 S 1 and 2 1 S 0 states has been determined by measuring the deflection of a beam of excited helium atoms that is caused by an inhomogeneous electric field of known properties. The necessary velocity distribution information is obtained from time-of-flight measurements, and a resonance quenching technique made it possible to distinguish the singlet and triplet components of the beam. The results, α(2 3 S 1 ) = (44.6 +- 3) x 10 -24 cm 3 and α(2 1 S 0 ) = (108 +- 13) x 10 -24 cm 3 , agree with the theoretical value that has been used to calibrate earlier polarizability measurements of the alkali metals and the heavier noble gases

  7. Dipole moment and polarizability of impurity doped quantum dots under anisotropy, spatially-varying effective mass and dielectric screening function: Interplay with noise

    Science.gov (United States)

    Ghosh, Anuja; Ghosh, Manas

    2018-01-01

    Present work explores the profiles of polarizability (αp) and electric dipole moment (μ) of impurity doped GaAs quantum dot (QD) under the aegis of spatially-varying effective mass, spatially-varying dielectric constant and anisotropy of the system. Presence of noise has also been invoked to examine how its intervention further tunes αp and μ. Noise term maintains a Gaussian white feature and it has been incorporated to the system through two different roadways; additive and multiplicative. The various facets of influence of spatially-varying effective mass, spatially-varying dielectric constant and anisotropy on αp and μ depend quite delicately on presence/absence of noise and also on the mode through which noise has been administered. The outcomes of the study manifest viable routes to harness the dipole moment and polarizability of doped QD system through the interplay between noise, anisotropy and variable effective mass and dielectric constant of the system.

  8. Calculations of electric dipole moments and static dipole polarizabilities based on the two-component normalized elimination of the small component method

    Science.gov (United States)

    Yoshizawa, Terutaka; Zou, Wenli; Cremer, Dieter

    2016-11-01

    The analytical energy gradient and Hessian of the two-component Normalized Elimination of the Small Component (2c-NESC) method with regard to the components of the electric field are derived and used to calculate spin-orbit coupling (SOC) corrected dipole moments and dipole polarizabilities of molecules, which contain elements with high atomic number. Calculated 2c-NESC dipole moments and isotropic polarizabilities agree well with the corresponding four-component-Dirac Hartree-Fock or density functional theory values. SOC corrections for the electrical properties are in general small, but become relevant for the accurate prediction of these properties when the molecules in question contain sixth and/or seventh period elements (e.g., the SO effect for At2 is about 10% of the 2c-NESC polarizability). The 2c-NESC changes in the electric molecular properties are rationalized in terms of spin-orbit splitting and SOC-induced mixing of frontier orbitals with the same j = l + s quantum numbers.

  9. Simultaneous effects of hydrostatic pressure and electric field on impurity binding energy and polarizability in coupled InAs/GaAs quantum wires

    International Nuclear Information System (INIS)

    Tangarife, E.; Duque, C.A.

    2011-01-01

    This work is concerned with the theoretical study of the combined effects of applied electric field and hydrostatic pressure on the binding energy and impurity polarizability of a donor impurity in laterally coupled double InAs/GaAs quantum-well wires. Calculations have been made in the effective mass and parabolic band approximations and using a variational method. The results are reported for different configurations of wire and barriers widths, impurity position, and electric field and hydrostatic pressure strengths. Our results show that for symmetrical structures the binding energy is an even function of the impurity position along the growth direction of the structure. Also, we found that for hydrostatic pressure strength up to 38 kbar, the binding energy increases linearly with hydrostatic pressure, while for larger values of hydrostatic pressure the binding energy has a non-linear behavior. Finally, we found that the hydrostatic pressure can increase the coupling between the two parallel quantum-well wires. -- Research highlights: → Binding energy for donor impurity in coupled wires strongly depends on the confinement potential. → Polarizability for donor impurity in coupled wires strongly depends on the confinement potential. → Binding energy strongly depends on the direction of the applied electric field. → Polarizability strongly depends on the direction of the applied electric field. → The coupling between the two parallel wires increases with the hydrostatic pressure.

  10. Correlation corrections to the Hartree-Fock perturbation theory of atomic and molecular properties. Dipole polarizabilities of He, Be and Ne

    International Nuclear Information System (INIS)

    Sadlej, A.J.

    1980-01-01

    The problem of the most efficient perturbation calculation of the correlation contributions to atomic and molecular properties is discussed. The method which is based on the coupled Hartree-Fock (CHF) perturbation theory appears to be the most promising one. The CHF-based perturbation theory of correlation effects is applied to the calculation of the second-order correlation contributions to the electric dipole polarizabilities of He, Be and Ne. The numerical approach employed in this paper consists in computing first the electric-field-dependent SCF functions. Then, the field dependent second-order correlation energy is calculated. The electric dipole polarizabilities, accurate through the second-order in correlation, are obtained via the numerical differentiation of the field-dependent energies with respect to the external electric field strength. In order to avoid the use of very large basis sets the so-called electric-field-variant (EFV) orbitals are employed in the present study. The CHF results obtained in this paper are of the same accuracy as the best literature data. In addition of the second-order correlation correction the final values of the electric dipole polarizability differ from the accurate or experimental results by less than a few per cent. (author)

  11. Calculations of electric dipole moments and static dipole polarizabilities based on the two-component normalized elimination of the small component method.

    Science.gov (United States)

    Yoshizawa, Terutaka; Zou, Wenli; Cremer, Dieter

    2016-11-14

    The analytical energy gradient and Hessian of the two-component Normalized Elimination of the Small Component (2c-NESC) method with regard to the components of the electric field are derived and used to calculate spin-orbit coupling (SOC) corrected dipole moments and dipole polarizabilities of molecules, which contain elements with high atomic number. Calculated 2c-NESC dipole moments and isotropic polarizabilities agree well with the corresponding four-component-Dirac Hartree-Fock or density functional theory values. SOC corrections for the electrical properties are in general small, but become relevant for the accurate prediction of these properties when the molecules in question contain sixth and/or seventh period elements (e.g., the SO effect for At 2 is about 10% of the 2c-NESC polarizability). The 2c-NESC changes in the electric molecular properties are rationalized in terms of spin-orbit splitting and SOC-induced mixing of frontier orbitals with the same j = l + s quantum numbers.

  12. Higher-Order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models.

    Science.gov (United States)

    Albaugh, Alex; Head-Gordon, Teresa; Niklasson, Anders M N

    2018-02-13

    Generalized extended Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) methods provide a framework for fast iteration-free simulations of models that normally require expensive electronic ground state optimizations prior to the force evaluations at every time step. XLBOMD uses dynamically driven auxiliary degrees of freedom that fluctuate about a variationally optimized ground state of an approximate "shadow" potential which approximates the true reference potential. While the requirements for such shadow potentials are well understood, constructing such potentials in practice has previously been ad hoc, and in this work, we present a systematic development of XLBOMD shadow potentials that match the reference potential to any order. We also introduce a framework for combining friction-like dissipation for the auxiliary degrees of freedom with general-order integration, a combination that was not previously possible. These developments are demonstrated with a simple fluctuating charge model and point induced dipole polarization models.

  13. [i]Legionella spp[/i]., amoebae and not-fermenting Gram negative bacteria in an Italian university hospital water system

    Directory of Open Access Journals (Sweden)

    Pasqualina Laganà

    2014-09-01

    Full Text Available [b]Introduction. [/b]In hospital and other health care facilities, contamination of water systems by potentially infectious microorganisms, such as bacteria, viruses and protozoa, is a source of nosocomial infections, which may originate fromcolonization of water pipes, cooling towers, spa pools, taps, showers and water supplies. [b]Objective. [/b]The study focuses on the occurrence of [i]Legionella spp.[/i], free-living amoebae and non-fermenting Gram-negative microorganisms in a University hospital water system located in the town of Messina (Sicily, Italy, which had never been examined previously. Materials and Methods. From January 2008 – March 2009, hot tap water samples were collected from 10 wards.[i] Legionella spp[/i]. recovered on selective culture medium were identified by microagglutination latex test; free-living amoebae were cultured using [i]Escherichia coli [/i]as a food source. Non-fermenting Gram negative microorganisms were identified by API 20 NE strips. [b]Results.[/b] [i]Legionella spp.[/i] were found in 33.33% of the samples. [i]L. pneumophila[/i] serogroup 1 was recovered from the Laboratory Diagnostic and Anaesthesia-Neurology Wards, with a peak of 3.5 × 10[sup]4[/sup] cfu/L in May 2008. [i]L. pneumophila[/i] serogroups 2–14 were found in the Othorhinolaryngology, Pathologic Anatomy, Paediatrics and Surgery Wards, and peaked (4 × 10[sup]4[/sup] cfu/L in April 2008. Pseudomonadaceae and Hyphomycetes were also detected. Legionella spp. were recovered from samples positive for non-pathogenic amoebae [i]Hartmannella spp[/i]. [b]Conclusion.[/b] This first study of a Messina hospital water system suggested potential health risks related to the detection of [i]Hartmannella spp[/i]., as reservoirs for[i] Legionella spp.[/i], and Pseudomonas aeruginosa, a Gram negative non-fermenting bacterium frequently causing nosocomial pneumonia. The urgent need for monitoring programmes and prevention measures to ensure hospital water

  14. Species richness of testate amoebae in different environments from the upper Paraná river floodplain (PR/MS - doi: 10.4025/actascibiolsci.v33i3.7261 Species richness of testate amoebae in different environments from the upper Paraná river floodplain (PR/MS - doi: 10.4025/actascibiolsci.v33i3.7261

    Directory of Open Access Journals (Sweden)

    Fábio Amodêo Lansac-Tôha

    2011-07-01

    Full Text Available This study evaluated the species richness of testate amoebae in the plankton from different environments of the upper Paraná river floodplain. Samplings were performed at subsurface of pelagic region from twelve environments using motorized pump and plankton net (68 µm, during four hydrological periods. We identified 67 taxa, distributed in seven families and Arcellidae, Difflugiidae and Centropyxidae were the most representative families. Higher values of species richness were observed in the lakes (connected and isolated during the flood pulses. Centropyxis aculeata, Difflugia gramem and D. pseudogramem were frequent throughout the study period. Seasonal variability of species in the channels and isolated lakes was evidenced by beta diversity. Besides that, in the rivers, extreme changes in species composition were verified during the high-water period. Our results highlight the importance of the present study to improve the knowledge about the diversity and geographic distribution of these organisms in Brazil and emphasize the importance of current flow in the displacement of testate amoebae from their preferred habitats, marginal vegetation and sediment.This study evaluated the species richness of testate amoebae in the plankton from different environments of the upper Paraná river floodplain. Samplings were performed at subsurface of pelagic region from twelve environments using motorized pump and plankton net (68 µm, during four hydrological periods. We identified 67 taxa, distributed in seven families and Arcellidae, Difflugiidae and Centropyxidae were the most representative families. Higher values of species richness were observed in the lakes (connected and isolated during the flood pulses. Centropyxis aculeata, Difflugia gramem and D. pseudogramem were frequent throughout the study period. Seasonal variability of species in the channels and isolated lakes was evidenced by beta diversity. Besides that, in the rivers, extreme

  15. Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

    International Nuclear Information System (INIS)

    You, Zhi-Qiang; Herbert, John M.; Mewes, Jan-Michael; Dreuw, Andreas

    2015-01-01

    The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents

  16. Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

    Energy Technology Data Exchange (ETDEWEB)

    You, Zhi-Qiang; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States); Mewes, Jan-Michael; Dreuw, Andreas [Interdisciplinary Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg (Germany)

    2015-11-28

    The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.

  17. Dipole polarizabilities and van der Waals coefficients for small molecular systems, from the atomic study to the crystal one

    International Nuclear Information System (INIS)

    Begue, D.

    1999-01-01

    Many criteria have been used to translate correctly the dynamical vectors of the electric properties: taking into account many spectroscopic states, the gauge and the quasi-spectral series to determine the analytical equation of the one order function. This approach is applied to two iso-electronic systems: CO and BF. The TDGI method allows to access the systems properties in their fundamental state and in their excited states. This work is illustrated by the beryllium atom study for the five first spectroscopic states. A theoretical study, based on the perturbations method, is presented for the determination of the interaction energy between two distant atoms. The formalism giving the general expression of the matrix elements of the dispersion energy needed to the Van der Waals, has been developed. Three examples illustrate this work: Be 2 , BeLi and K 2 . For this last one, the correlations between the calculation and the experimental observations are presented. Some theoretical results on the static and dynamic properties of beryllium clusters (Be N with N=2,3 and 4). The developed approach allowed to show the variations laws of polarizability with the cluster size and to show the asymptotical behavior of the property. (A.L.B.)

  18. Electronic polarizability, optical basicity and interaction parameter for Nd2O3 doped lithium-zinc-phosphate glasses

    Science.gov (United States)

    Algradee, M. A.; Sultan, M.; Samir, O. M.; Alwany, A. Elwhab B.

    2017-08-01

    The Nd3+-doped lithium-zinc-phosphate glasses were prepared by means of conventional melt quenching method. X-ray diffraction results confirmed the glassy nature of the studied glasses. The physical parameters such as the density, molar volume, ion concentration, polaron radius, inter-ionic distance, field strength and oxygen packing density were calculated using different formulae. The transmittance and reflectance spectra of glasses were recorded in the wavelength range 190-1200 nm. The values of optical band gap and Urbach energy were determined based on Mott-Davis model. The refractive indices for the studied glasses were evaluated from optical band gap values using different methods. The average electronic polarizability of the oxide ions, optical basicity and an interaction parameter were investigated from the calculated values of the refractive index and the optical band gap for the studied glasses. The variations in the different physical and optical properties of glasses with Nd2O3 content were discussed in terms of different parameters such as non-bridging oxygen and different concentrations of Nd cation in glass system.

  19. Relativistic coupled-cluster-theory analysis of energies, hyperfine-structure constants, and dipole polarizabilities of Cd+

    Science.gov (United States)

    Li, Cheng-Bin; Yu, Yan-Mei; Sahoo, B. K.

    2018-02-01

    Roles of electron correlation effects in the determination of attachment energies, magnetic-dipole hyperfine-structure constants, and electric-dipole (E 1 ) matrix elements of the low-lying states in the singly charged cadmium ion (Cd+) have been analyzed. We employ the singles and doubles approximated relativistic coupled-cluster (RCC) method to calculate these properties. Intermediate results from the Dirac-Hartree-Fock approximation,the second-order many-body perturbation theory, and considering only the linear terms of the RCC method are given to demonstrate propagation of electron correlation effects in this ion. Contributions from important RCC terms are also given to highlight the importance of various correlation effects in the evaluation of these properties. At the end, we also determine E 1 polarizabilities (αE 1) of the ground and 5 p 2P1 /2 ;3 /2 states of Cd+ in the ab initio approach. We estimate them again by replacing some of the E 1 matrix elements and energies from the measurements to reduce their uncertainties so that they can be used in the high-precision experiments of this ion.

  20. Intensity-modulated polarizabilities and magic trapping of alkali-metal and divalent atoms in infrared optical lattices

    Science.gov (United States)

    Topcu, Turker; Derevianko, Andrei

    2014-05-01

    Long range interactions between neutral Rydberg atoms has emerged as a potential means for implementing quantum logical gates. These experiments utilize hyperfine manifold of ground state atoms to act as a qubit basis, while exploiting the Rydberg blockade mechanism to mediate conditional quantum logic. The necessity for overcoming several sources of decoherence makes magic wavelength trapping in optical lattices an indispensable tool for gate experiments. The common wisdom is that atoms in Rydberg states see trapping potentials that are essentially that of a free electron, and can only be trapped at laser intensity minima. We show that although the polarizability of a Rydberg state is always negative, the optical potential can be both attractive or repulsive at long wavelengths (up to ~104 nm). This opens up the possibility of magic trapping Rydberg states with ground state atoms in optical lattices, thereby eliminating the necessity to turn off trapping fields during gate operations. Because the wavelengths are near the CO2 laser band, the photon scattering and the ensuing motional heating is also reduced compared to conventional traps near low lying resonances, alleviating an important source of decoherence. This work was supported by the National Science Foundation (NSF) Grant No. PHY-1212482.

  1. Coriolis Force

    Science.gov (United States)

    Marciuc, Daly; Solschi, Viorel

    2017-04-01

    Understanding the Coriolis effect is essential for explaining the movement of air masses and ocean currents. The lesson we propose aims to familiarize students with the manifestation of the Coriolis effect. Students are guided to build, using the GeoGebra software, a simulation of the motion of a body, related to a rotating reference system. The mathematical expression of the Coriolis force is deduced, for particular cases, and the Foucault's pendulum is presented and explained. Students have the opportunity to deepen the subject, by developing materials related to topics such as: • Global Wind Pattern • Ocean Currents • Coriolis Effect in Long Range Shooting • Finding the latitude with a Foucault Pendulum

  2. Invisible force

    International Nuclear Information System (INIS)

    Panek, Richard

    2010-01-01

    Astronomers have compiled evidence that what we always thought of as the actual universe- all the planets, stars, galaxies and matter in space -represents a mere 4% of what's out there. The rest is dark: 23% is called dark matter, 73% dark energy. Scientists have ideas about what dark matter is, but hardly any understanding about dark energy. This has led to rethinking traditional physics and cosmology. Assuming the existence of dark matter and that the law of gravitation is universal, two teams of astrophysicists, from Lawrence Berkeley National Laboratory and the Australian National University, analysed the universe's growth and to their surprise both concluded that the universe expansion is not slowing but speeding up. If the dominant force of evolution isn't gravity what is it?

  3. An evolutionarily significant unicellular strategy in response to starvation stress in Dictyostelium social amoebae [v1; ref status: indexed, http://f1000r.es/3hg

    Directory of Open Access Journals (Sweden)

    Darja Dubravcic

    2014-06-01

    Full Text Available The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation and constitutes a model of choice in microbial cooperation studies. Aggregates of up to 106 cells form fruiting bodies containing two cell types: (i dormant spores (~80% that can persist for months in the absence of nutrients, and (ii dead stalk cells (~20% that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus regulate population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. D. discoideum thus constitutes a model system lying at the intersection of microbial cooperation and bet hedging, defining a new

  4. Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.

    Science.gov (United States)

    Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola; Licari, Daniele; Monti, Susanna; Prampolini, Giacomo

    2013-03-21

    The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.

  5. Generating a stationary infinite range tractor force via a multimode optical fibre

    Science.gov (United States)

    Ebongue, C. A.; Holzmann, D.; Ostermann, S.; Ritsch, H.

    2017-06-01

    Optical fibres confine and guide light almost unattenuated and thus convey light forces to polarizable nano-particles over very long distances. Radiation pressure forces arise from scattering of guided photons into free space while gradient forces are based on coherent scattering between different fibre modes or propagation directions. Interestingly, even scattering between co-propagating modes induces longitudinal forces as the transverse confinement of the light modes creates mode dependent longitudinal wave-vectors and photon momenta. We generalize a proven scattering matrix based approach to calculate single as well as inter-particle forces to include several forward and backward propagating modes. We show that an injection of the higher order mode only in a two mode fibre will induce a stationary tractor force against the injection direction, when the mode coupling to the lower order mode dominates against backscattering and free space losses. Generically this arises for non-absorbing particles at the centre of a waveguide. The model also gives improved predictions for inter-particle forces in evanescent nanofibre fields as experimentally observed recently. Surprisingly strong tractor forces can also act on whole optically bound arrays.

  6. Quantum mechanical methods for calculation of force constants

    International Nuclear Information System (INIS)

    Mullally, D.J.

    1985-01-01

    The focus of this thesis is upon the calculation of force constants; i.e., the second derivatives of the potential energy with respect to nuclear displacements. This information is useful for the calculation of molecular vibrational modes and frequencies. In addition, it may be used for the location and characterization of equilibrium and transition state geometries. The methods presented may also be applied to the calculation of electric polarizabilities and infrared and Raman vibrational intensities. Two approaches to this problem are studied and evaluated: finite difference methods and analytical techniques. The most suitable method depends on the type and level of theory used to calculate the electronic wave function. Double point displacement finite differencing is often required for accurate calculation of the force constant matrix. These calculations require energy and gradient calculations on both sides of the geometry of interest. In order to speed up these calculations, a novel method is presented that uses geometry dependent information about the wavefunction. A detailed derivation for the analytical evaluation of force constants with a complete active space multiconfiguration self consistent field wave function is presented

  7. Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

    Science.gov (United States)

    Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

    1998-08-01

    A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

  8. Empirical parameters for solvent acidity, basicity, dipolarity, and polarizability of the ionic liquids [BMIM][BF4] and [BMIM][PF6].

    Science.gov (United States)

    del Valle, J C; García Blanco, F; Catalán, J

    2015-04-02

    The empirical solvent scales for polarizability (SP), dipolarity (SdP), acidity (SA), and basicity (SB) have been successfully used to interpret the solvatochromism of compounds dissolved in organic solvents and their solvent mixtures. Providing that the published solvatochromic parameters for the ionic liquids 1-(1-butyl)-3-methylimidazolium tetrafluoroborate, [BMIM][BF4] and 1-(1-butyl)-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], are excessively widespread, their SP, SdP, SA, and SB values are measured herein at temperatures from 293 to 353 K. Four key points are emphasized herein: (i) the origin of the solvatochromic solvent scales--the gas phase, that is the absence of any medium perturbation--; (ii) the separation of the polarizability and dipolarity effects; (iii) the simplification of the probing process in order to obtain the solvatochromic parameters; and (iv) the SP, SdP, SA, and SB solvent scales can probe the polarizability, dipolarity, acidity, and basicity of ionic liquids as well as of organic solvents and water-organic solvent mixtures. From the multiparameter approach using the four pure solvent scales one can draw the conclusion that (a) the solvent influence of [BMIM][BF4] parallels that of formamide at 293 K, both of them miscible with water; (b) [BMIM][PF6] shows a set of solvatochromic parameters similar to that of chloroacetonitrile, both of them water insoluble; and (c) that the corresponding solvent acidity and basicity of the ionic liquids can be explained to a great extent from the cation species by comparing the empirical parameters of [BMIM](+) with those of the solvent 1-methylimidazole. The insolubility of [BMIM][PF6] in water as compared to [BMIM][BF4] is tentatively connected to some extent to the larger molar volume of the anion [PF6](-), and to the difference in basicity of [PF6](-) and [BF4](-).

  9. Atom interferometry experiments with lithium. Accurate measurement of the electric polarizability; Experiences d'interferometrie atomique avec le lithium. Mesure de precision de la polarisabilite electrique

    Energy Technology Data Exchange (ETDEWEB)

    Miffre, A

    2005-06-15

    Atom interferometers are very sensitive tools to make precise measurements of physical quantities. This study presents a measurement of the static electric polarizability of lithium by atom interferometry. Our result, {alpha} = (24.33 {+-} 0.16)*10{sup -30} m{sup 3}, improves by a factor 3 the most accurate measurements of this quantity. This work describes the tuning and the operation of a Mach-Zehnder atom interferometer in detail. The two interfering arms are separated by the elastic diffraction of the atomic wave by a laser standing wave, almost resonant with the first resonance transition of lithium atom. A set of experimental techniques, often complicated to implement, is necessary to build the experimental set-up. After a detailed study of the atom source (a supersonic beam of lithium seeded in argon), we present our experimental atom signals which exhibit a very high fringe visibility, up to 84.5 % for first order diffraction. A wide variety of signals has been observed by diffraction of the bosonic isotope at higher diffraction orders and by diffraction of the fermionic less abundant isotope. The quality of these signals is then used to do very accurate phase measurements. A first experiment investigates how the atom interferometer signals are modified by a magnetic field gradient. An absolute measurement of lithium atom electric polarizability is then achieved by applying a static electric field on one of the two interfering arms, separated by only 90 micrometers. The construction of such a capacitor, its alignment in the experimental set-up and its operation are fully detailed.We obtain a very accurate phase measurement of the induced Lo Surdo - Stark phase shift (0.07 % precision). For this first measurement, the final uncertainty on the electric polarizability of lithium is only 0.66 %, and is dominated by the uncertainty on the atom beam mean velocity, so that a further reduction of the uncertainty can be expected. (author)

  10. Atom interferometry experiments with lithium. Accurate measurement of the electric polarizability; Experiences d'interferometrie atomique avec le lithium. Mesure de precision de la polarisabilite electrique

    Energy Technology Data Exchange (ETDEWEB)

    Miffre, A

    2005-06-15

    Atom interferometers are very sensitive tools to make precise measurements of physical quantities. This study presents a measurement of the static electric polarizability of lithium by atom interferometry. Our result, {alpha} = (24.33 {+-} 0.16)*10{sup -30} m{sup 3}, improves by a factor 3 the most accurate measurements of this quantity. This work describes the tuning and the operation of a Mach-Zehnder atom interferometer in detail. The two interfering arms are separated by the elastic diffraction of the atomic wave by a laser standing wave, almost resonant with the first resonance transition of lithium atom. A set of experimental techniques, often complicated to implement, is necessary to build the experimental set-up. After a detailed study of the atom source (a supersonic beam of lithium seeded in argon), we present our experimental atom signals which exhibit a very high fringe visibility, up to 84.5 % for first order diffraction. A wide variety of signals has been observed by diffraction of the bosonic isotope at higher diffraction orders and by diffraction of the fermionic less abundant isotope. The quality of these signals is then used to do very accurate phase measurements. A first experiment investigates how the atom interferometer signals are modified by a magnetic field gradient. An absolute measurement of lithium atom electric polarizability is then achieved by applying a static electric field on one of the two interfering arms, separated by only 90 micrometers. The construction of such a capacitor, its alignment in the experimental set-up and its operation are fully detailed.We obtain a very accurate phase measurement of the induced Lo Surdo - Stark phase shift (0.07 % precision). For this first measurement, the final uncertainty on the electric polarizability of lithium is only 0.66 %, and is dominated by the uncertainty on the atom beam mean velocity, so that a further reduction of the uncertainty can be expected. (author)

  11. Virtual Compton scattering and the generalized polarizabilities of the proton at Q²=0.92 and 1.76 GeV²

    OpenAIRE

    Fonvieille, H; Laveissiere, G; Degrande, N; Jaminion, S; Jutier, C; Todor, L; Di Salvo, R; Van Hoorebeke, Luc; Alexa, LC; Anderson, BD; Aniol, KA; Arundell, K; Audit, G; Auerbach, L; Baker, FT

    2012-01-01

    Virtual Compton scattering (VCS) on the proton has been studied at the Jefferson Laboratory using the exclusive photon electroproduction reaction ep -> ep gamma. This paper gives a detailed account of the analysis which has led to the determination of the structure functions P-LL - P-TT/epsilon and P-LT and the electric and magnetic generalized polarizabilities (GPs) alpha(E) (Q(2)) and beta(M) (Q(2)) at values of the four-momentum transfer squared Q(2) = 0.92 and 1.76 GeV2. These data, toget...

  12. The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

    International Nuclear Information System (INIS)

    Alcaraz, Olga; Trullàs, Joaquim; Tahara, Shuta; Kawakita, Yukinobu; Takeda, Shin’ichi

    2016-01-01

    The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å −1 related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

  13. The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

    Energy Technology Data Exchange (ETDEWEB)

    Alcaraz, Olga; Trullàs, Joaquim, E-mail: quim.trullas@upc.edu [Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord UPC B4-B5, 08034 Barcelona (Spain); Tahara, Shuta [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, Okinawa 903-0213 (Japan); Kawakita, Yukinobu [J-PARC Center, Japan Atomic Energy Agency (JAEA), Ibaraki 319-1195 (Japan); Takeda, Shin’ichi [Department of Physics, Faculty of Sciences, Kyushu University, Fukuoka 819-0395 (Japan)

    2016-09-07

    The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å{sup −1} related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

  14. Electrostatic force microscopy: imaging DNA and protein polarizations one by one

    International Nuclear Information System (INIS)

    Mikamo-Satoh, Eriko; Yamada, Fumihiko; Takagi, Akihiko; Matsumoto, Takuya; Kawai, Tomoji

    2009-01-01

    We present electrostatic force microscopy images of double-stranded DNA and transcription complex on an insulating mica substrate obtained with molecular resolution using a frequency-mode noncontact atomic force microscope. The electrostatic potential images show that both DNA and transcription complexes are polarized with an upward dipole moment. Potential differences of these molecules from the mica substrate enabled us to estimate dipole moments of isolated DNA and transcription complex in zero external field to be 0.027 D/base and 0.16 D/molecule, respectively. Scanning capacitance microscopy demonstrates characteristic contrast inversion between DNA and transcription complex images, indicating the difference in electric polarizability of these molecules. These findings indicate that the electrostatic properties of individual biological molecules can be imaged on an insulator substrate while retaining complex formation.

  15. 12th Air Force > Home

    Science.gov (United States)

    Force AOR Travel Info News prevnext Slide show 76,410 pounds of food delivered to Haiti 12th Air Force the French Air Force, Colombian Air Force, Pakistan Air Force, Belgian Air Force, Brazilian Air Force

  16. Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

    Science.gov (United States)

    Riniker, Sereina

    2018-03-26

    In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

  17. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: bimetallic binding site and structured waters.

    Science.gov (United States)

    Gresh, Nohad; El Hage, Krystel; Perahia, David; Piquemal, Jean-Philip; Berthomieu, Catherine; Berthomieu, Dorothée

    2014-11-05

    The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn-superoxide dismutase (SOD) has been inferred from high-resolution X-ray crystallography. Long-duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second-generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn-SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short-duration MD simulations of 296 waters solvating Cu/Zn-SOD. Six representative geometries are selected and energy-minimized. Single-point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest-energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments

  18. Novel parallel plate condenser for single particle electrostatic force measurements in atomic force microscope

    KAUST Repository

    Kwek, Jin Wang; Vakarelski, Ivan Uriev; Ng, Waikiong; Heng, Jerry; Tan, Reginald

    2011-01-01

    and image charges. The method can be used for the rapid evaluation of the charging and polarizability properties of the microparticle as well as an alternative to the conventional Faraday's pail technique. © 2011 Elsevier B.V.

  19. Quantum mechanical study of pre-dissociation enhancement of linear and nonlinear polarizabilities of (TeO2)(n) oligomers as a key to understanding the remarkable dielectric properties of TeO2 glasses.

    Science.gov (United States)

    Smirnov, Mikhail; Mirgorodsky, Andrei; Masson, Olivier; Thomas, Philippe

    2012-09-20

    The effects of intermolecular interactions of TeO(2) molecules in the (TeO(2))(n) oligomers on the polarizability (α) and second hyperpolarizability (γ) are investigated by the use of a density functional method. A significant intermolecular distance dependence of both quantities is observed. The huge dissociation-induced polarizability enhancement is analyzed in terms of the molecular orbital evolution. It is shown that the obtained results can provide a new look at the microscopic origin of the extraordinary dielectric properties of TeO(2) glass.

  20. Size dependence of the polarizability and Haynes rule for an exciton bound to an ionized donor in a single spherical quantum dot

    Energy Technology Data Exchange (ETDEWEB)

    Feddi, E., E-mail: e.feddi@um5s.net.ma; Zouitine, A. [Université Mohamed V Souissi, Ecole Normale Supérieure de l' Enseignement Technique (ENSET), Rabat (Morocco); Oukerroum, A.; Zazoui, M. [Laboratory of Condensed Matter, Faculty of Sciences and Techniques, University of Hassan II-Mohammedia, B.P. 146, 20800 Mohammedia (Morocco); Dujardin, F. [LCP-A2MC, Université de Lorraine, ICPM, 1 Bd Arago, 57070 Metz (France); Assaid, E. [Laboratoire d' Électronique et Optique des Nanostructures de Semiconducteurs, Faculté des Sciences, B. P. 20, El Jadida (Morocco)

    2015-02-14

    We study the effect of an external electric field on an exciton bound to an ionized donor (D{sup +}, X) confined in a spherical quantum dot using a perturbative-variational method where the wave function and energy are developed in series of powers of the electric field strength. After testing this new approach in the determination of the band gap for some semiconductor materials, we generalize it to the case of (D{sup +}, X) in the presence of the electric field and for several materials ZnO, PbSe, and InAs, with significant values of the mass ratio. Three interesting results can be deduced: First, we show that the present method allows to determine the ground state energy in the presence of a weak electric field in a simple way (E = E{sub 0} − αf{sup 2}) using the energy without electric field E{sub 0} and the polarizability α. The second point is that our theoretical predictions show that the polarizability of (D{sup +}, X) varies proportionally to R{sup 3.5} and follows an ordering α{sub D{sup 0}}<α{sub X}<α{sub (D{sup +},X)}. The last point to highlight is that the Haynes rule remains valid even in the presence of a weak electric field.