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Sample records for polarizable protein force

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. 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...

  8. 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.

  9. 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

  10. 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.

  11. 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)

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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...

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. A force-based protein biochip

    Science.gov (United States)

    Blank, K.; Mai, T.; Gilbert, I.; Schiffmann, S.; Rankl, J.; Zivin, R.; Tackney, C.; Nicolaus, T.; Spinnler, K.; Oesterhelt, F.; Benoit, M.; Clausen-Schaumann, H.; Gaub, H. E.

    2003-09-01

    A parallel assay for the quantification of single-molecule binding forces was developed based on differential unbinding force measurements where ligand-receptor interactions are compared with the unzipping forces of DNA hybrids. Using the DNA zippers as molecular force sensors, the efficient discrimination between specific and nonspecific interactions was demonstrated for small molecules binding to specific receptors, as well as for protein-protein interactions on protein arrays. Finally, an antibody sandwich assay with different capture antibodies on one chip surface and with the detection antibodies linked to a congruent surface via the DNA zippers was used to capture and quantify a recombinant hepatitis C antigen from solution. In this case, the DNA zippers enable not only discrimination between specific and nonspecific binding, but also allow for the local application of detection antibodies, thereby eliminating false-positive results caused by cross-reactive antibodies and nonspecific binding.

  11. 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...

  12. 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)

  13. 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.

  14. 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...

  15. 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 ...

  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. Parallel force assay for protein-protein interactions.

    Science.gov (United States)

    Aschenbrenner, Daniela; Pippig, Diana A; Klamecka, Kamila; Limmer, Katja; Leonhardt, Heinrich; Gaub, Hermann E

    2014-01-01

    Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, namely the bond between different variants of GFP and GFP-binding nanobodies. We present different strategies to adjust the maximum sensitivity window of the assay by influencing the binding strength of the DNA reference duplexes. The binding of the nanobody Enhancer to the different GFP constructs is compared at high sensitivity of the assay. Whereas the binding strength to wild type and enhanced GFP are equal within experimental error, stronger binding to superfolder GFP is observed. This difference in binding strength is attributed to alterations in the amino acids that form contacts according to the crystal structure of the initial wild type GFP-Enhancer complex. Moreover, we outline the potential for large-scale parallelization of the assay.

  18. Parallel force assay for protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Daniela Aschenbrenner

    Full Text Available Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, namely the bond between different variants of GFP and GFP-binding nanobodies. We present different strategies to adjust the maximum sensitivity window of the assay by influencing the binding strength of the DNA reference duplexes. The binding of the nanobody Enhancer to the different GFP constructs is compared at high sensitivity of the assay. Whereas the binding strength to wild type and enhanced GFP are equal within experimental error, stronger binding to superfolder GFP is observed. This difference in binding strength is attributed to alterations in the amino acids that form contacts according to the crystal structure of the initial wild type GFP-Enhancer complex. Moreover, we outline the potential for large-scale parallelization of the assay.

  19. 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.)

  20. 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

  1. 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

  2. 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.)

  3. 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.

  4. 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....

  5. 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...

  6. Ferritin protein imaging and detection by magnetic force microscopy.

    Science.gov (United States)

    Hsieh, Chiung-Wen; Zheng, Bin; Hsieh, Shuchen

    2010-03-14

    Magnetic force microscopy was used to image and detect ferritin proteins and the strength of the magnetic signal is discussed, revealing a large workable lift height between the magnetic tip and the ferritin sample.

  7. Atomic force microscopy and force spectroscopy on the assessment of protein folding and functionality.

    Science.gov (United States)

    Carvalho, Filomena A; Martins, Ivo C; Santos, Nuno C

    2013-03-01

    Atomic force microscopy (AFM) applied to biological systems can, besides generating high-quality and well-resolved images, be employed to study protein folding via AFM-based force spectroscopy. This approach allowed remarkable advances in the measurement of inter- and intramolecular interaction forces with piconewton resolution. The detection of specific interaction forces between molecules based on the AFM sensitivity and the manipulation of individual molecules greatly advanced the understanding of intra-protein and protein-ligand interactions. Apart from the academic interest in the resolution of basic scientific questions, this technique has also key importance on the clarification of several biological questions of immediate biomedical relevance. Force spectroscopy is an especially appropriate technique for "mechanical proteins" that can provide crucial information on single protein molecules and/or domains. Importantly, it also has the potential of combining in a single experiment spatial and kinetic measurements. Here, the main principles of this methodology are described, after which the ability to measure interactions at the single-molecule level is discussed, in the context of relevant protein-folding examples. We intend to demonstrate the potential of AFM-based force spectroscopy in the study of protein folding, especially since this technique is able to circumvent some of the difficulties typically encountered in classical thermal/chemical denaturation studies. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. 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

  9. 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.

  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. Digital force-feedback for protein unfolding experiments using atomic force microscopy

    Science.gov (United States)

    Bippes, Christian A.; Janovjak, Harald; Kedrov, Alexej; Muller, Daniel J.

    2007-01-01

    Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand-receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.

  12. Digital force-feedback for protein unfolding experiments using atomic force microscopy

    International Nuclear Information System (INIS)

    Bippes, Christian A; Janovjak, Harald; Kedrov, Alexej; Muller, Daniel J

    2007-01-01

    Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand-receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA

  13. Compressive Force Spectroscopy: From Living Cells to Single Proteins.

    Science.gov (United States)

    Wang, Jiabin; Liu, Meijun; Shen, Yi; Sun, Jielin; Shao, Zhifeng; Czajkowsky, Daniel Mark

    2018-03-23

    One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these "tensile" force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development.

  14. Protein crystals as scanned probes for recognition atomic force microscopy.

    Science.gov (United States)

    Wickremasinghe, Nissanka S; Hafner, Jason H

    2005-12-01

    Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.

  15. 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.

  16. New force replica exchange method and protein folding pathways probed by force-clamp technique.

    Science.gov (United States)

    Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

    2008-01-28

    We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes

  17. 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....

  18. Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

    Science.gov (United States)

    Hu, Xiaotang; Li, Hongbin

    2014-10-01

    Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  19. Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

    Science.gov (United States)

    Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri I; Lemke, Edward A; Gräter, Frauke

    2015-06-25

    Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

  20. 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

  1. 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 ...

  2. 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.

  3. 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...

  4. 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.

  5. Probabilistic analysis for identifying the driving force of protein folding

    Science.gov (United States)

    Tokunaga, Yoshihiko; Yamamori, Yu; Matubayasi, Nobuyuki

    2018-03-01

    Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.

  6. 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

  7. 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.

  8. Revealing Abrupt and Spontaneous Ruptures of Protein Native Structure under picoNewton Compressive Force Manipulation.

    Science.gov (United States)

    Chowdhury, S Roy; Cao, Jin; He, Yufan; Lu, H Peter

    2018-03-27

    Manipulating protein conformations for exploring protein structure-function relationship has shown great promise. Although protein conformational changes under pulling force manipulation have been extensively studied, protein conformation changes under a compressive force have not been explored quantitatively. The latter is even more biologically significant and relevant in revealing protein functions in living cells associated with protein crowdedness, distribution fluctuations, and cell osmotic stress. Here we report our experimental observations on abrupt ruptures of protein native structures under compressive force, demonstrated and studied by single-molecule AFM-FRET spectroscopic nanoscopy. Our results show that the protein ruptures are abrupt and spontaneous events occurred when the compressive force reaches a threshold of 12-75 pN, a force amplitude accessible from thermal fluctuations in a living cell. The abrupt ruptures are sensitive to local environment, likely a general and important pathway of protein unfolding in living cells.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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....

  14. 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.

  15. 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.)

  16. 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

  17. 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

  18. 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

  19. 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...

  20. 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.

  1. 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

  2. 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...

  3. 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).

  4. 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

  5. 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

  6. 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

  7. 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)

  8. 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)

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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)

  15. 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

  16. 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

  17. 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.

  18. Atomic force microscopy imaging and single molecule recognition force spectroscopy of coat proteins on the surface of Bacillus subtilis spore.

    Science.gov (United States)

    Tang, Jilin; Krajcikova, Daniela; Zhu, Rong; Ebner, Andreas; Cutting, Simon; Gruber, Hermann J; Barak, Imrich; Hinterdorfer, Peter

    2007-01-01

    Coat assembly in Bacillus subtilis serves as a tractable model for the study of the self-assembly process of biological structures and has a significant potential for use in nano-biotechnological applications. In the present study, the morphology of B. subtilis spores was investigated by magnetically driven dynamic force microscopy (MAC mode atomic force microscopy) under physiological conditions. B. subtilis spores appeared as prolate structures, with a length of 0.6-3 microm and a width of about 0.5-2 microm. The spore surface was mainly covered with bump-like structures with diameters ranging from 8 to 70 nm. Besides topographical explorations, single molecule recognition force spectroscopy (SMRFS) was used to characterize the spore coat protein CotA. This protein was specifically recognized by a polyclonal antibody directed against CotA (anti-CotA), the antibody being covalently tethered to the AFM tip via a polyethylene glycol linker. The unbinding force between CotA and anti-CotA was determined as 55 +/- 2 pN. From the high-binding probability of more than 20% in force-distance cycles it is concluded that CotA locates in the outer surface of B. subtilis spores. Copyright (c) 2007 John Wiley & Sons, Ltd.

  19. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

    NARCIS (Netherlands)

    Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.

    2007-01-01

    The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ

  20. 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

  1. 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...

  2. 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)

  3. 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

  4. A Force-Activated Trip Switch Triggers Rapid Dissociation of a Colicin from Its Immunity Protein

    Science.gov (United States)

    Farrance, Oliver E.; Hann, Eleanore; Kaminska, Renata; Housden, Nicholas G.; Derrington, Sasha R.; Kleanthous, Colin; Radford, Sheena E.; Brockwell, David J.

    2013-01-01

    Colicins are protein antibiotics synthesised by Escherichia coli strains to target and kill related bacteria. To prevent host suicide, colicins are inactivated by binding to immunity proteins. Despite their high avidity (Kd≈fM, lifetime ≈4 days), immunity protein release is a pre-requisite of colicin intoxication, which occurs on a timescale of minutes. Here, by measuring the dynamic force spectrum of the dissociation of the DNase domain of colicin E9 (E9) and immunity protein 9 (Im9) complex using an atomic force microscope we show that application of low forces (force-triggered increase in off-rate a trip bond. Using mutational analysis, we elucidate the mechanism of this switch in affinity. We show that the N-terminal region of E9, which has sparse contacts with the hydrophobic core, is linked to an allosteric activator region in E9 (residues 21–30) whose remodelling triggers immunity protein release. Diversion of the force transduction pathway by the introduction of appropriately positioned disulfide bridges yields a force resistant complex with a lifetime identical to that measured by ensemble techniques. A trip switch within E9 is ideal for its function as it allows bipartite complex affinity, whereby the stable colicin:immunity protein complex required for host protection can be readily converted to a kinetically unstable complex whose dissociation is necessary for cellular invasion and competitor death. More generally, the observation of two force phenotypes for the E9:Im9 complex demonstrates that force can re-sculpt the underlying energy landscape, providing new opportunities to modulate biological reactions in vivo; this rationalises the commonly observed discrepancy between off-rates measured by dynamic force spectroscopy and ensemble methods. PMID:23431269

  5. Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins

    Science.gov (United States)

    Dahlke, K.; Sing, C. E.

    2018-02-01

    Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAP-DNA simulation model that incorporates both force- and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems.

  6. Complex oscillatory behaviour in a delayed protein cross talk model with periodic forcing

    International Nuclear Information System (INIS)

    Nikolov, Svetoslav

    2009-01-01

    The purpose of this paper is to examine the effects of periodic forcing on the time delay protein cross talk model behaviour. We assume periodic variation for the plasma membrane permeability. The dynamic behaviour of the system is simulated and bifurcation diagrams are obtained for different parameters. The results show that periodic forcing can very easily give rise to complex dynamics, including a period-doubling cascade, chaos, quasi-periodic oscillating, and periodic windows. Finally, we calculate the maximal Lyapunov exponent in the regions of the parameter space where chaotic motion of delayed protein cross talk model with periodic forcing exists.

  7. Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

    Science.gov (United States)

    Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

    2016-07-28

    The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

  8. Interaction forces between salivary proteins and Streptococcus mutans with and without antigen I/II

    NARCIS (Netherlands)

    Xu, C.P.; Belt-Gritter, van de B.; Dijkstra, R.J.B.; Norde, W.; Mei, van der H.C.; Busscher, H.J.

    2007-01-01

    The antigen I/II family of surface proteins is expressed by oral streptococci, including Streptococcus mutans, and mediates specific binding to, among others, salivary films. The aim of this study was to investigate the interaction forces between salivary proteins and S. mutans with (LT11) and

  9. Quantifying Young's moduli of protein fibrils and particles with bimodal force spectroscopy.

    Science.gov (United States)

    Gilbert, Jay; Charnley, Mirren; Cheng, Christopher; Reynolds, Nicholas P; Jones, Owen G

    2017-10-19

    Force spectroscopy is a means of obtaining mechanical information of individual nanometer-scale structures in composite materials, such as protein assemblies for use in consumer films or gels. As a recently developed force spectroscopy technique, bimodal force spectroscopy relates frequency shifts in cantilevers simultaneously excited at multiple frequencies to the elastic properties of the contacted material, yet its utility for quantitative characterization of biopolymer assemblies has been limited. In this study, a linear correlation between experimental frequency shift and Young's modulus of polymer films was used to calibrate bimodal force spectroscopy and quantify Young's modulus of two protein nanostructures: β-lactoglobulin fibrils and zein nanoparticles. Cross-sectional Young's modulus of protein fibrils was determined to be 1.6 GPa while the modulus of zein nanoparticles was determined as 854 MPa. Parallel measurement of β-lactoglobulin fibril by a competing pulsed-force technique found a higher cross-sectional Young's modulus, highlighting the importance of comparative calibration against known standards in both pulsed and bimodal force spectroscopies. These findings demonstrate a successful procedure for measuring mechanical properties of individual protein assemblies with potential use in biological or packaging applications using bimodal force spectroscopy.

  10. AFM-based force spectroscopy on polystyrene brushes: effect of brush thickness on protein adsorption.

    Science.gov (United States)

    Hentschel, Carsten; Wagner, Hendrik; Smiatek, Jens; Heuer, Andreas; Fuchs, Harald; Zhang, Xi; Studer, Armido; Chi, Lifeng

    2013-02-12

    Herein we present a study on nonspecific binding of proteins at highly dense packed hydrophobic polystyrene brushes. In this context, an atomic force microscopy tip was functionalized with concanavalin A to perform single-molecule force spectroscopy measurements on polystyrene brushes with thicknesses of 10 and 60 nm, respectively. Polystyrene brushes with thickness of 10 nm show an almost two times stronger protein adsorption than brushes with a thickness of 60 nm: 72 pN for the thinner and 38 pN for the thicker layer, which is in qualitative agreement with protein adsorption studies conducted macroscopically by fluorescence microscopy.

  11. Internal force field in proteins seen by divergence entropy

    Science.gov (United States)

    Marchewka, Damian; Banach, Mateusz; Roterman, Irena

    2011-01-01

    The characteristic distribution of non-binding interactions in a protein is described. It establishes that hydrophobic interactions can be characterized by suitable 3D Gauss functions while electrostatic interactions generally follow a random distribution. The implementation of this observation suggests differentiated optimization procedure for these two types of interactions. The electrostatic interaction may follow traditional energy optimization while the criteria for convergence shall measure the accordance with 3-D Gauss function. PMID:21769190

  12. Lipid and protein composition as driving force for multiple sclerosis

    Science.gov (United States)

    Beck, Roy; Shaharabani, Rona

    Physical models and experiments often reduce the number of components aiming to address the fundamental mechanisms. Nevertheless, the inherent heterogeneity is an essential ingredient in the biological context. We present our recent efforts to model and understand the development of multiple sclerosis (MS) from a biophysical perspective. Myelin sheath is a multilamellar complex of various lipids and proteins that surround axons and acts as an insulating layer for proper nerve conduction. In MS the myelin structure is disrupted impairing its function. Previous studies showed that MS is correlated with small lipid composition variation and reduction in the adhesive myelin basic protein. We found that such alterations result in pathological phase transition from a lamellar to inverted hexagonal that involve enhanced local curvature. Similar curvatures are also found in vivo in diseased myelin sheaths. Since the etiology and recovery pathways of MS are currently unclear, these findings delineate novel functional roles to dominant constituents in cytoplasmic myelin sheaths, shed new light on mechanisms disrupting lipid-protein complexes, and suggest new courses for diagnosis and treatment for MS.

  13. Modification of calcite crystal growth by abalone shell proteins: an atomic force microscope study.

    OpenAIRE

    Walters, D A; Smith, B L; Belcher, A M; Paloczi, G T; Stucky, G D; Morse, D E; Hansma, P K

    1997-01-01

    A family of soluble proteins from the shell of Haliotis rufescens was introduced over a growing calcite crystal being scanned in situ by an atomic force microscope (AFM). Atomic step edges on the crystal surface were altered in shape and speed of growth by the proteins. Proteins attached nonuniformly to the surface, indicating different interactions with crystallographically different step edges. The observed changes were consistent with the habit modification induced by this family of protei...

  14. 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

  15. A pairwise residue contact area-based mean force potential for discrimination of native protein structure

    Directory of Open Access Journals (Sweden)

    Pezeshk Hamid

    2010-01-01

    Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

  16. Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

    Science.gov (United States)

    Lee, Kuo Hao; Chen, Jianhan

    2017-06-15

    Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

    OpenAIRE

    Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.

    2005-01-01

    The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

  5. Nanoscale observation of local bound charges of patterned protein arrays by scanning force microscopy

    International Nuclear Information System (INIS)

    Oh, Y J; Jo, W; Kim, S; Park, S; Kim, Y S

    2008-01-01

    A protein patterned surface using micro-contact printing methods has been investigated by scanning force microscopy. Electrostatic force microscopy (EFM) was utilized for imaging the topography and detecting the electrical properties such as the local bound charge distribution of the patterned proteins. It was found that the patterned IgG proteins are arranged down to 1 μm, and the 90 deg. rotation of patterned anti-IgG proteins was successfully undertaken. Through the estimation of the effective areas, it was possible to determine the local bound charges of patterned proteins which have opposite electrostatic force behaviors. Moreover, we studied the binding probability between IgG and anti-IgG in a 1 μm 2 MIMIC system by topographic and electrostatic signals for applicable label-free detections. We showed that the patterned proteins can be used for immunoassay of proteins on the functional substrate, and that they can also be used for bioelectronics device application, indicating distinct advantages with regard to accuracy and a label-free detection

  6. Measuring protein isoelectric points by AFM-based force spectroscopy using trace amounts of sample

    Science.gov (United States)

    Guo, Shifeng; Zhu, Xiaoying; Jańczewski, Dominik; Lee, Serina Siew Chen; He, Tao; Teo, Serena Lay Ming; Vancso, G. Julius

    2016-09-01

    Protein charge at various pH and isoelectric point (pI) values is important in understanding protein function. However, often only trace amounts of unknown proteins are available and pI measurements cannot be obtained using conventional methods. Here, we show a method based on the atomic force microscope (AFM) to determine pI using minute quantities of proteins. The protein of interest is immobilized on AFM colloidal probes and the adhesion force of the protein is measured against a positively and a negatively charged substrate made by layer-by-layer deposition of polyelectrolytes. From the AFM force-distance curves, pI values with an estimated accuracy of ±0.25 were obtained for bovine serum albumin, myoglobin, fibrinogen and ribonuclease A over a range of 4.7-9.8. Using this method, we show that the pI of the ‘footprint’ of the temporary adhesive proteins secreted by the barnacle cyprid larvae of Amphibalanus amphitrite is in the range 9.6-9.7.

  7. Surface force analysis of molecular interfacial interactions of proteins and lipids with polymeric biomaterials

    International Nuclear Information System (INIS)

    Hamilton-Brown, P.; Griesser, H.J.; Meagher, L.

    2001-01-01

    Full text: Adverse biological responses to biomedical devices are often caused by the irreversible accumulation of biological deposits onto the surfaces of devices. Such deposits cause blocking of artificial blood vessels, fibrous encapsulation of soft tissue regenerative devices, 'fouling' of contact lenses, secondary cataracts on intraocular lenses, and other undesirable events that interfere with the intended functions of biomedical devices. The formation of deposits is triggered by an initial stage in which various proteins and lipids rapidly adsorb onto the synthetic material surface; further biological molecules and ultimately cellular entities (e.g., host cells, bacteria) then settle onto the initial adsorbed layer. Hence, to avoid or control the accumulation of biological deposits, molecular understanding is required of the initial adsorption processes. Such adsorption is caused by attractive interfacial forces, which we are characterising by the use of a novel method. In the present study, polymeric thin film coatings, polyethylene oxide (PEO), and polysaccharide coatings have been analysed in terms of their surface forces and the ensuing propensity for protein and lipid adsorption. Interfacial forces are measured using atomic force microscopy (AFM) with a colloid-modified tip in a liquid cell using solutions of physiological pH and ionic strength. The chemical composition and uniformity of the coatings was characterised by X-ray Photon Spectroscopy (XPS). For a polymeric solid coating, repulsive forces have been measured against a silica colloid probe, and the dominant surface force is electrostatic. For the highly hydrated, 'soft' PEO and polysaccharide coatings, on the other hand, steric/entropic forces are also significant and contribute to interfacial interactions with proteins and lipids. In one system we have observed a time dependence of the electrostatic surface potential, which affects interaction with charged proteins. Force measurements were

  8. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  9. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

    Science.gov (United States)

    Xu, Dong; Zhang, Yang

    2012-07-01

    Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

  10. 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

  11. 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)

  12. 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.

  13. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  14. The elastic free energy of a tandem modular protein under force.

    Science.gov (United States)

    Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

    2015-05-01

    Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

  15. A force-based, parallel assay for the quantification of protein-DNA interactions.

    Science.gov (United States)

    Limmer, Katja; Pippig, Diana A; Aschenbrenner, Daniela; Gaub, Hermann E

    2014-01-01

    Analysis of transcription factor binding to DNA sequences is of utmost importance to understand the intricate regulatory mechanisms that underlie gene expression. Several techniques exist that quantify DNA-protein affinity, but they are either very time-consuming or suffer from possible misinterpretation due to complicated algorithms or approximations like many high-throughput techniques. We present a more direct method to quantify DNA-protein interaction in a force-based assay. In contrast to single-molecule force spectroscopy, our technique, the Molecular Force Assay (MFA), parallelizes force measurements so that it can test one or multiple proteins against several DNA sequences in a single experiment. The interaction strength is quantified by comparison to the well-defined rupture stability of different DNA duplexes. As a proof-of-principle, we measured the interaction of the zinc finger construct Zif268/NRE against six different DNA constructs. We could show the specificity of our approach and quantify the strength of the protein-DNA interaction.

  16. A force-based, parallel assay for the quantification of protein-DNA interactions.

    Directory of Open Access Journals (Sweden)

    Katja Limmer

    Full Text Available Analysis of transcription factor binding to DNA sequences is of utmost importance to understand the intricate regulatory mechanisms that underlie gene expression. Several techniques exist that quantify DNA-protein affinity, but they are either very time-consuming or suffer from possible misinterpretation due to complicated algorithms or approximations like many high-throughput techniques. We present a more direct method to quantify DNA-protein interaction in a force-based assay. In contrast to single-molecule force spectroscopy, our technique, the Molecular Force Assay (MFA, parallelizes force measurements so that it can test one or multiple proteins against several DNA sequences in a single experiment. The interaction strength is quantified by comparison to the well-defined rupture stability of different DNA duplexes. As a proof-of-principle, we measured the interaction of the zinc finger construct Zif268/NRE against six different DNA constructs. We could show the specificity of our approach and quantify the strength of the protein-DNA interaction.

  17. 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.

  18. Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy.

    Science.gov (United States)

    Jin, Albert J; Lafer, Eileen M; Peng, Jennifer Q; Smith, Paul D; Nossal, Ralph

    2013-03-01

    Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate. Published by Elsevier Inc.

  19. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    Science.gov (United States)

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  20. Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers.

    Science.gov (United States)

    Sapra, K Tanuj

    2013-01-01

    The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.

  1. 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).

  2. 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.

  3. 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

  4. 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)

  5. High-throughput single-molecule force spectroscopy for membrane proteins

    Science.gov (United States)

    Bosshart, Patrick D.; Casagrande, Fabio; Frederix, Patrick L. T. M.; Ratera, Merce; Bippes, Christian A.; Müller, Daniel J.; Palacin, Manuel; Engel, Andreas; Fotiadis, Dimitrios

    2008-09-01

    Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether ~400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with ~200 (AdiC) and ~400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications.

  6. High-throughput single-molecule force spectroscopy for membrane proteins

    International Nuclear Information System (INIS)

    Bosshart, Patrick D; Casagrande, Fabio; Frederix, Patrick L T M; Engel, Andreas; Fotiadis, Dimitrios; Ratera, Merce; Palacin, Manuel; Bippes, Christian A; Mueller, Daniel J

    2008-01-01

    Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether ∼400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with ∼200 (AdiC) and ∼400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications

  7. High-throughput single-molecule force spectroscopy for membrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bosshart, Patrick D; Casagrande, Fabio; Frederix, Patrick L T M; Engel, Andreas; Fotiadis, Dimitrios [M E Mueller Institute for Structural Biology, Biozentrum of the University of Basel, CH-4056 Basel (Switzerland); Ratera, Merce; Palacin, Manuel [Institute for Research in Biomedicine, Barcelona Science Park, Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona and Centro de Investigacion Biomedica en Red de Enfermedades Raras, E-08028 Barcelona (Spain); Bippes, Christian A; Mueller, Daniel J [BioTechnology Center, Technical University, Tatzberg 47, D-01307 Dresden (Germany)], E-mail: andreas.engel@unibas.ch, E-mail: dimitrios.fotiadis@mci.unibe.ch

    2008-09-24

    Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether {approx}400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with {approx}200 (AdiC) and {approx}400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications.

  8. 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

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Toward the description of electrostatic interactions between globular proteins: potential of mean force in the primitive model.

    Science.gov (United States)

    Dahirel, Vincent; Jardat, Marie; Dufrêche, Jean-François; Turq, Pierre

    2007-09-07

    Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern. Contrarily to Poisson-Boltzmann predictions, attractive, and repulsive direct forces between proteins are not screened similarly. Moreover, it has been shown that the relative orientations of the charge patterns strongly influence salt-mediated interactions. More precisely, for short distances between the proteins, ions enhance the difference of the effective forces between (i) like-charged and oppositely charged proteins, (ii) attractive and repulsive relative orientations of the proteins, which may affect the selectivity of protein/protein recognition. Finally, such results observed with the simplest models are applied to a more elaborate one to demonstrate their generality.

  15. 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.

  16. Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes

    DEFF Research Database (Denmark)

    Lundbæk, Jens August; Collingwood, S.A.; Ingolfsson, H.I.

    2010-01-01

    with collective physical properties (e.g. thickness, intrinsic monolayer curvature or elastic moduli). Studies in physico-chemical model systems have demonstrated that changes in bilayer physical properties can regulate membrane protein function by altering the energetic cost of the bilayer deformation associated...... with a protein conformational change. This type of regulation is well characterized, and its mechanistic elucidation is an interdisciplinary field bordering on physics, chemistry and biology. Changes in lipid composition that alter bilayer physical properties (including cholesterol, polyunsaturated fatty acids...... channels as molecular force probes for studying this mechanism, with a unique ability to discriminate between consequences of changes in monolayer curvature and bilayer elastic moduli....

  17. The Force Exerted by the Membrane Potential During Protein Import into the Mitochondrial Matrix

    Science.gov (United States)

    Shariff, Karim; Ghosal, Sandip; Matouschek, Andreas

    2002-01-01

    The electrostatic force exerted on a targeting sequence by the electrical potential across the inner mitochondrial membrane is calculated and found to vary from 1.4 pN to 2.2 pN (per unit elementary charge) as the radius of the inner membrane pore (assumed aqueous) is varied from 12 to 6.5 Angstroms, its measured range. Since the pore is not very much wider than the distance between water molecules, the full shielding effect of water may not be present; the extreme case of a nonaqueous pore gives a force of 3.1 pN per unit charge, which represents an upper limit. When applied to mitochondrial import experiments on the protein harness, these results imply that a force of 11 plus or minus 4 pN is sufficient to catalyze the unfolding of harness during import. Comparison of these results with unfolding forces measured using atomic force microscopy suggests that the two are not inconsistent.

  18. From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

    Science.gov (United States)

    Forman-Kay, Julie D.; Mittag, Tanja

    2015-01-01

    Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

  19. How well do force fields capture the strength of salt bridges in proteins?

    Directory of Open Access Journals (Sweden)

    Mustapha Carab Ahmed

    2018-06-01

    Full Text Available Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1 to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

  20. 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.)

  1. Measuring the force of single protein molecule detachment from surfaces with AFM.

    Science.gov (United States)

    Tsapikouni, Theodora S; Missirlis, Yannis F

    2010-01-01

    Atomic force microscopy (AFM) was used to measure the non-specific detachment force of single fibrinogen molecules from glass surfaces. The identification of single unbinding events was based on the characteristics of the parabolic curves, recorded during the stretching of protein molecules. Fibrinogen molecules were covalently bound to Si(3)N(4) AFM tips, previously modified with 3-aminopropyl-dimethyl-ethoxysilane, through a homobifunctional poly(ethylene glycol) linker bearing two hydroxysulfosuccinimide esters. The most probable detachment force was found to be 210 pN, when the tip was retracting with a velocity of 1400 nm/s, while the distribution of the detachment distances indicated that the fibrinogen chain can be elongated beyond the length of the physical conformation before detachment. The dependence of the most probable detachment force on the loading rate was examined and the dynamics of fibrinogen binding to the surface were found amenable to the simple expression of the Bell-Evans theory. The theory's expansion, however, by incorporating the concept of the rupture of parallel residue-surface bonds could only describe the detachment of fibrinogen for a small number of such bonds. Finally, the mathematical expression of the Worm-Like Chain model was used to fit the stretching curves before rupture and two interpretations are suggested for the description of the AFM curves with multiple detachment events.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Optimizing atomic force microscopy for characterization of diamond-protein interfaces

    Czech Academy of Sciences Publication Activity Database

    Rezek, Bohuslav; Ukraintsev, Egor; Kromka, Alexander

    2011-01-01

    Roč. 6, Apr. (2011), 337/1-337/10 ISSN 1931-7573 R&D Projects: GA MŠk(CZ) LC06040; GA ČR(CZ) GAP108/11/0794; GA AV ČR KAN400100701; GA MŠk LC510 Institutional research plan: CEZ:AV0Z10100521 Keywords : atomic force microscopy (AFM) * nanocrystalline diamond * oxygen-terminated diamond * hydrogen-terminated diamond * proteins * fetal bovine serum (FBS) Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.726, year: 2011

  9. 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...

  10. 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.

  11. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

    Science.gov (United States)

    Miller, Mark S.; Lay, Wesley K.

    2016-01-01

    Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

  12. Force Spectroscopy of the Plasmodium falciparum Vaccine Candidate Circumsporozoite Protein Suggests a Mechanically Pliable Repeat Region.

    Science.gov (United States)

    Patra, Aditya Prasad; Sharma, Shobhona; Ainavarapu, Sri Rama Koti

    2017-02-10

    The most effective vaccine candidate of malaria is based on the Plasmodium falciparum circumsporozoite protein (CSP), a major surface protein implicated in the structural strength, motility, and immune evasion properties of the infective sporozoites. It is suspected that reversible conformational changes of CSP are required for infection of the mammalian host, but the detailed structure and dynamic properties of CSP remain incompletely understood, limiting our understanding of its function in the infection. Here, we report the structural and mechanical properties of the CSP studied using single-molecule force spectroscopy on several constructs, one including the central region of CSP, which is rich in NANP amino acid repeats (CSP rep ), and a second consisting of a near full-length sequence without the signal and anchor hydrophobic domains (CSP ΔHP ). Our results show that the CSP rep is heterogeneous, with 40% of molecules requiring virtually no mechanical force to unfold (<10 piconewtons (pN)), suggesting that these molecules are mechanically compliant and perhaps act as entropic springs, whereas the remaining 60% are partially structured with low mechanical resistance (∼70 pN). CSP ΔHP having multiple force peaks suggests specifically folded domains, with two major populations possibly indicating the open and collapsed forms. Our findings suggest that the overall low mechanical resistance of the repeat region, exposed on the outer surface of the sporozoites, combined with the flexible full-length conformations of CSP, may provide the sporozoites not only with immune evasion properties, but also with lubricating capacity required during its navigation through the mosquito and vertebrate host tissues. We anticipate that these findings would further assist in the design and development of future malarial vaccines. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. 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

  14. 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)

  15. 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.)

  16. 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

  17. 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)

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor

    Directory of Open Access Journals (Sweden)

    Sandra Posch

    2016-09-01

    Full Text Available We here give information for a deeper understanding of single molecule force spectroscopy (SMFS data through the example of the blood protein von Willebrand factor (VWF. It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK was used for this demonstration. Further, Brownian dynamics (BD simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016 [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor

  4. Molecular shape and binding force of Mycoplasma mobile's leg protein Gli349 revealed by an AFM study

    Energy Technology Data Exchange (ETDEWEB)

    Lesoil, Charles [Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsutacho 4259, Midori-ku, Yokohama 226-8501 (Japan); Nonaka, Takahiro [Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan); Sekiguchi, Hiroshi; Osada, Toshiya [Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsutacho 4259, Midori-ku, Yokohama 226-8501 (Japan); Miyata, Makoto [Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan); Afrin, Rehana [Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsutacho 4259, Midori-ku, Yokohama 226-8501 (Japan); Biofrontier Center, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsutacho 4259, Midori-ku, Yokohama 226-8501 (Japan); Ikai, Atsushi, E-mail: ikai.a.aa@m.titech.ac.jp [Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsutacho 4259, Midori-ku, Yokohama 226-8501 (Japan)

    2010-01-15

    Recent studies of the gliding bacteria Mycoplasma mobile have identified a family of proteins called the Gli family which was considered to be involved in this novel and yet fairly unknown motility system. The 349 kDa protein called Gli349 was successfully isolated and purified from the bacteria, and electron microscopy imaging and antibody experiments led to the hypothesis that it acts as the 'leg' of M. mobile, responsible for attachment to the substrate as well as for gliding motility. However, more precise evidence of the molecular shape and function of this protein was required to asses this theory any further. In this study, an atomic force microscope (AFM) was used both as an imaging and a force measurement device to provide new information about Gli349 and its role in gliding motility. AFM images of the protein were obtained revealing a complex structure with both rigid and flexible parts, consistent with previous electron micrographs of the protein. Single-molecular force spectroscopy experiments were also performed, revealing that Gli349 is able to specifically bind to sialyllactose molecules and withstand unbinding forces around 70 pN. These findings strongly support the idea that Gli349 is the 'leg' protein of M. mobile, responsible for binding and also most probably force generation during gliding motility.

  5. Molecular shape and binding force of Mycoplasma mobile's leg protein Gli349 revealed by an AFM study

    International Nuclear Information System (INIS)

    Lesoil, Charles; Nonaka, Takahiro; Sekiguchi, Hiroshi; Osada, Toshiya; Miyata, Makoto; Afrin, Rehana; Ikai, Atsushi

    2010-01-01

    Recent studies of the gliding bacteria Mycoplasma mobile have identified a family of proteins called the Gli family which was considered to be involved in this novel and yet fairly unknown motility system. The 349 kDa protein called Gli349 was successfully isolated and purified from the bacteria, and electron microscopy imaging and antibody experiments led to the hypothesis that it acts as the 'leg' of M. mobile, responsible for attachment to the substrate as well as for gliding motility. However, more precise evidence of the molecular shape and function of this protein was required to asses this theory any further. In this study, an atomic force microscope (AFM) was used both as an imaging and a force measurement device to provide new information about Gli349 and its role in gliding motility. AFM images of the protein were obtained revealing a complex structure with both rigid and flexible parts, consistent with previous electron micrographs of the protein. Single-molecular force spectroscopy experiments were also performed, revealing that Gli349 is able to specifically bind to sialyllactose molecules and withstand unbinding forces around 70 pN. These findings strongly support the idea that Gli349 is the 'leg' protein of M. mobile, responsible for binding and also most probably force generation during gliding motility.

  6. Potentials of mean force for protein structure prediction vindicated, formalized and generalized.

    Directory of Open Access Journals (Sweden)

    Thomas Hamelryck

    Full Text Available Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge-based potentials based on pairwise distances--so-called "potentials of mean force" (PMFs--have been center stage in the prediction and design of protein structure and the simulation of protein folding. However, the validity, scope and limitations of these potentials are still vigorously debated and disputed, and the optimal choice of the reference state--a necessary component of these potentials--is an unsolved problem. PMFs are loosely justified by analogy to the reversible work theorem in statistical physics, or by a statistical argument based on a likelihood function. Both justifications are insightful but leave many questions unanswered. Here, we show for the first time that PMFs can be seen as approximations to quantities that do have a rigorous probabilistic justification: they naturally arise when probability distributions over different features of proteins need to be combined. We call these quantities "reference ratio distributions" deriving from the application of the "reference ratio method." This new view is not only of theoretical relevance but leads to many insights that are of direct practical use: the reference state is uniquely defined and does not require external physical insights; the approach can be generalized beyond pairwise distances to arbitrary features of protein structure; and it becomes clear for which purposes the use of these quantities is justified. We illustrate these insights with two applications, involving the radius of gyration and hydrogen bonding. In the latter case, we also show how the reference ratio method can be iteratively applied to sculpt an energy funnel. Our results considerably increase the understanding and scope of energy functions derived from known biomolecular structures.

  7. 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...

  8. 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....

  9. 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.

  10. 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

  11. 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.

  12. Importance of anisotropy in detachment rates for force production and cargo transport by a team of motor proteins.

    Science.gov (United States)

    Takshak, Anjneya; Kunwar, Ambarish

    2016-05-01

    Many cellular processes are driven by collective forces generated by a team consisting of multiple molecular motor proteins. One aspect that has received less attention is the detachment rate of molecular motors under mechanical force/load. While detachment rate of kinesin motors measured under backward force increases rapidly for forces beyond stall-force; this scenario is just reversed for non-yeast dynein motors where detachment rate from microtubule decreases, exhibiting a catch-bond type behavior. It has been shown recently that yeast dynein responds anisotropically to applied load, i.e. detachment rates are different under forward and backward pulling. Here, we use computational modeling to show that these anisotropic detachment rates might help yeast dynein motors to improve their collective force generation in the absence of catch-bond behavior. We further show that the travel distance of cargos would be longer if detachment rates are anisotropic. Our results suggest that anisotropic detachment rates could be an alternative strategy for motors to improve the transport properties and force production by the team. © 2016 The Protein Society.

  13. 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.

  14. 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

  15. 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

  16. Atomic force microscopy-based antibody recognition imaging of proteins in the pathological deposits in Pseudoexfoliation Syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Creasey, Rhiannon [School of Chemical and Physical Sciences, Flinders University of SA, GPO Box 2100, Adelaide, SA 5001 (Australia); Sharma, Shiwani [School of Medicine, Ophthalmology, Flinders University of SA, GPO Box 2100, Adelaide, SA 5001 (Australia); Gibson, Christopher T. [School of Chemical and Physical Sciences, Flinders University of SA, GPO Box 2100, Adelaide, SA 5001 (Australia); Craig, Jamie E. [School of Medicine, Ophthalmology, Flinders University of SA, GPO Box 2100, Adelaide, SA 5001 (Australia); Ebner, Andreas [Institute for Biophysics, Johannes Kepler Universitaet Linz, Altenbergerstr. 69, A-4040 Linz (Austria); Becker, Thomas [Nanochemistry Research Institute, Curtin University, GPO Box U1987, Perth, 6845 WA (Australia); Hinterdorfer, Peter [Institute for Biophysics, Johannes Kepler Universitaet Linz, Altenbergerstr. 69, A-4040 Linz (Austria); Voelcker, Nicolas H., E-mail: nico.voelcker@flinders.edu.au [School of Chemical and Physical Sciences, Flinders University of SA, GPO Box 2100, Adelaide, SA 5001 (Australia)

    2011-07-15

    The phenomenon of protein aggregation is of considerable interest to various disciplines, including the field of medicine. A range of disease pathologies are associated with this phenomenon. One of the ocular diseases hallmarked by protein aggregation is the Pseudoexfoliation (PEX) Syndrome. This condition is characterized by the deposition of insoluble proteinaceous material on the anterior human lens capsule. Genomic and proteomic analyses have revealed an association of specific genetic markers and various proteins, respectively, with PEX syndrome. However, the ultrastructure of the protein aggregates is poorly characterized. This study seeks to build capacity to determine the molecular nature of PEX aggregates on human lens capsules in their native state by AFM-based antibody recognition imaging. Lysyl oxidase-Like 1 (LOXL1), a protein identified as a component of PEX aggregates, is detected by an antibody-modified AFM probe. Topographical AFM images and antibody recognition images are obtained using three AFM-based techniques: TREC, phase and force-volume imaging. LOXL1 is found to be present on the lens capsule surface, and is localized around fibrous protein aggregates. Our evaluation shows that TREC imaging is best suited for human tissue imaging and holds significant potential for imaging of human disease tissues in their native state. -- Highlights: {yields} Atomic force microscopy techniques were applied to diseased human tissues. {yields} LOXL1 protein was detected on the small fibers of Pseudoexfoliation deposits. {yields} PicoTREC was the optimum technique for investigating protein aggregates.

  17. 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...

  18. PIEZO channel protein naturally expressed in human breast cancer cell MDA-MB-231 as probed by atomic force microscopy

    Science.gov (United States)

    Weng, Yuanqi; Yan, Fei; Chen, Runkang; Qian, Ming; Ou, Yun; Xie, Shuhong; Zheng, Hairong; Li, Jiangyu

    2018-05-01

    Mechanical stimuli drives many physiological processes through mechanically activated channels, and the recent discovery of PIEZO channel has generated great interests in its mechanotransduction. Many previous researches investigated PIEZO proteins by transcribing them in cells that originally have no response to mechanical stimulation, or by forming PIEZO-combined complexes in vitro, and few studied PIEZO protein's natural characteristics in cells. In this study we show that MDA-MB-231, a malignant cell in human breast cancer cell line, expresses the mechanosensitive behavior of PIEZO in nature without extra treatment, and we report its characteristics in response to localized mechanical stimulation under an atomic force microscope, wherein a correlation between the force magnitude applied and the channel opening probability is observed. The results on PIEZO of MDA-MB-231 can help establish a basis of preventing and controlling of human breast cancer cell via mechanical forces.

  19. Single Molecule Science for Personalized Nanomedicine: Atomic Force Microscopy of Biopolymer-Protein Interactions

    Science.gov (United States)

    Hsueh, Carlin

    Nanotechnology has a unique and relatively untapped utility in the fields of medicine and dentistry at the level of single-biopolymer and -molecule diagnostics. In recent years atomic force microscopy (AFM) has garnered much interest due to its ability to obtain atomic-resolution of molecular structures and probe biophysical behaviors of biopolymers and proteins in a variety of biologically significant environments. The work presented in this thesis focuses on the nanoscale manipulation and observation of biopolymers to develop an innovative technology for personalized medicine while understanding complex biological systems. These studies described here primarily use AFM to observe biopolymer interactions with proteins and its surroundings with unprecedented resolution, providing a better understanding of these systems and interactions at the nanoscale. Transcriptional profiling, the measure of messenger RNA (mRNA) abundance in a single cell, is a powerful technique that detects "behavior" or "symptoms" at the tissue and cellular level. We have sought to develop an alternative approach, using our expertise in AFM and single molecule nanotechnology, to achieve a cost-effective high throughput method for sensitive detection and profiling of subtle changes in transcript abundance. The technique does not require amplification of the mRNA sample because the AFM provides three-dimensional views of molecules with unprecedented resolution, requires minimal sample preparation, and utilizes a simple tagging chemistry on cDNA molecules. AFM images showed collagen polymers in teeth and of Drebrin-A remodeling of filamentous actin structure and mechanics. AFM was used to image collagen on exposed dentine tubules and confirmed tubule occlusion with a desensitizing prophylaxis paste by Colgate-Palmolive. The AFM also superseded other microscopy tools in resolving F-actin helix remodeling and possible cooperative binding by a neuronal actin binding protein---Drebrin-A, an

  20. 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.

  1. 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.

  2. 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

  3. Combination of atomic force microscopy and mass spectrometry for the detection of target protein in the serum samples of children with autism spectrum disorders

    Science.gov (United States)

    Kaysheva, A. L.; Pleshakova, T. O.; Kopylov, A. T.; Shumov, I. D.; Iourov, I. Y.; Vorsanova, S. G.; Yurov, Y. B.; Ziborov, V. S.; Archakov, A. I.; Ivanov, Y. D.

    2017-10-01

    Possibility of detection of target proteins associated with development of autistic disorders in children with use of combined atomic force microscopy and mass spectrometry (AFM/MS) method is demonstrated. The proposed method is based on the combination of affine enrichment of proteins from biological samples and visualization of these proteins by AFM and MS analysis with quantitative detection of target proteins.

  4. 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.

  5. 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.

  6. 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.)

  7. 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.

  8. 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.)

  9. 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

  10. 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.

  11. 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

  12. Improved Parameters for the Martini Coarse-Grained Protein Force Field

    NARCIS (Netherlands)

    de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

    The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. Multiphoton photochemical crosslinking-based fabrication of protein micropatterns with controllable mechanical properties for single cell traction force measurements

    Science.gov (United States)

    Tong, Ming Hui; Huang, Nan; Zhang, Wei; Zhou, Zhuo Long; Ngan, Alfonso Hing Wan; Du, Yanan; Chan, Barbara Pui

    2016-01-01

    Engineering 3D microstructures with predetermined properties is critical for stem cell niche studies. We have developed a multiphoton femtosecond laser-based 3D printing platform, which generates complex protein microstructures in minutes. Here, we used the platform to test a series of fabrication and reagent parameters in precisely controlling the mechanical properties of protein micropillars. Atomic force microscopy was utilized to measure the reduced elastic modulus of the micropillars, and transmission electron microscopy was used to visualize the porosity of the structures. The reduced elastic modulus of the micropillars associated positively and linearly with the scanning power. On the other hand, the porosity and pore size of the micropillars associated inversely and linearly with the scanning power and reagent concentrations. While keeping the elastic modulus constant, the stiffness of the micropillars was controlled by varying their height. Subsequently, the single cell traction forces of rabbit chondrocytes, human dermal fibroblasts, human mesenchymal stem cells, and bovine nucleus pulposus cells (bNPCs) were successfully measured by culturing the cells on micropillar arrays of different stiffness. Our results showed that the traction forces of all groups showed positive relationship with stiffness, and that the chondrocytes and bNPCs generated the highest and lowest traction forces, respectively.

  19. Inhibition of TRAIL-induced apoptosis and forced internalization of TRAIL receptor 1 by adenovirus proteins.

    Science.gov (United States)

    Tollefson, A E; Toth, K; Doronin, K; Kuppuswamy, M; Doronina, O A; Lichtenstein, D L; Hermiston, T W; Smith, C A; Wold, W S

    2001-10-01

    Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) induces apoptosis through two receptors, TRAIL-R1 (also known as death receptor 4) and TRAIL-R2 (also known as death receptor 5), that are members of the TNF receptor superfamily of death domain-containing receptors. We show that human adenovirus type 5 encodes three proteins, named RID (previously named E3-10.4K/14.5K), E3-14.7K, and E1B-19K, that independently inhibit TRAIL-induced apoptosis of infected human cells. This conclusion was derived from studies using wild-type adenovirus, adenovirus replication-competent mutants that lack one or more of the RID, E3-14.7K, and E1B-19K genes, and adenovirus E1-minus replication-defective vectors that express all E3 genes, RID plus E3-14.7K only, RID only, or E3-14.7K only. RID inhibits TRAIL-induced apoptosis when cells are sensitized to TRAIL either by adenovirus infection or treatment with cycloheximide. RID induces the internalization of TRAIL-R1 from the cell surface, as shown by flow cytometry and indirect immunofluorescence for TRAIL-R1. TRAIL-R1 was internalized in distinct vesicles which are very likely to be endosomes and lysosomes. TRAIL-R1 is degraded, as indicated by the disappearance of the TRAIL-R1 immunofluorescence signal. Degradation was inhibited by bafilomycin A1, a drug that prevents acidification of vesicles and the sorting of receptors from late endosomes to lysosomes, implying that degradation occurs in lysosomes. RID was also shown previously to internalize and degrade another death domain receptor, Fas, and to prevent apoptosis through Fas and the TNF receptor. RID was shown previously to force the internalization and degradation of the epidermal growth factor receptor. E1B-19K was shown previously to block apoptosis through Fas, and both E1B-19K and E3-14.7K were found to prevent apoptosis through the TNF receptor. These findings suggest that the receptors for TRAIL, Fas ligand, and TNF play a role in limiting virus

  20. 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)

  1. Molecular recognition of DNA-protein complexes: A straightforward method combining scanning force and fluorescence microscopy

    NARCIS (Netherlands)

    H. Sanchez (Humberto); R. Kanaar (Roland); C. Wyman (Claire)

    2010-01-01

    textabstractCombining scanning force and fluorescent microscopy allows simultaneous identification of labeled biomolecules and analysis of their nanometer level architectural arrangement. Fluorescent polystyrene nano-spheres were used as reliable objects for alignment of optical and topographic

  2. Development and application of a free energy force field for all atom protein folding

    International Nuclear Information System (INIS)

    Verma, A.

    2007-11-01

    Proteins are the workhorses of all cellular life. They constitute the building blocks and the machinery of all cells and typically function in specific three-dimensional conformations into which each protein folds. Currently over one million protein sequences are known, compared to about 40,000 structures deposited in the Protein Data Bank (the world-wide database of protein structures). Reliable theoretical methods for protein structure prediction could help to reduce the gap between sequence and structural databases and elucidate the biological information in structurally unresolved sequences. In this thesis we explore an approach for protein structure prediction and folding that is based on the Anfinsen's hypothesis that most proteins in their native state are in thermodynamic equilibrium with their environment. We have developed a free energy forcefield (PFF02) that locates the native conformation of many proteins from all structural classes at the global minimum of the free-energy model. We have validated the forcefield against a large decoy set (Rosetta). The average root mean square deviation (RMSD) for the lowest energy structure for the 32 proteins of the decoy set was only 2.14 Aa from the experimental conformation. We have successfully implemented and used stochastic optimization methods, such as the basin hopping technique and evolutionary algorithms for all atom protein structure prediction. The evolutionary algorithm performs exceptionally well on large supercomputational architectures, such as BlueGene and MareNostrum. Using the PFF02 forcefield, we were able to fold 13 proteins (12-56 amino acids), which include helix, sheet and mixed secondary structure. On average the predicted structure of these proteins deviated from their experimental conformation by only 2.89 Aa RMSD. (orig.)

  3. Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2.

    Science.gov (United States)

    Lei, Hai; He, Chengzhi; Hu, Chunguang; Li, Jinliang; Hu, Xiaodong; Hu, Xiaotang; Li, Hongbin

    2017-05-22

    Single-molecule force spectroscopy (SMFS) has become a powerful tool in investigating the mechanical unfolding/folding of proteins at the single-molecule level. Polyproteins made of tandem identical repeats have been widely used in atomic force microscopy (AFM)-based SMFS studies, where polyproteins not only serve as fingerprints to identify single-molecule stretching events, but may also improve statistics of data collection. However, the inherent assumption of such experiments is that all the domains in the polyprotein are equivalent and one SMFS trajectory of stretching a polyprotein made of n domains is equivalent to n trajectories of stretching a single domain. Such an assumption has not been validated experimentally. Using a small protein NuG2 and its polyprotein (NuG2) 4 as model systems, here we use optical trapping (OT) to directly validate this assumption. Our results show that OT experiments on NuG2 and (NuG2) 4 lead to identical parameters describing the unfolding and folding kinetics of NuG2, demonstrating that indeed stretching a polyprotein of NuG2 is equivalent to stretching single NuG2 in force spectroscopy experiments and thus validating the use of polyproteins in SMFS experiments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 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

  5. 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

  6. 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

  7. 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....

  8. Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.

    Science.gov (United States)

    Snyder, James A; Abramyan, Tigran; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

    2012-12-01

    Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

  9. 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.

  10. 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

  11. 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

  12. Protein adsorption on tailored substrates: long-range forces and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Bellion, M; Santen, L [Department of Theoretical Physics, Saarland University, 66041 Saarbruecken (Germany); Mantz, H; Haehl, H; Quinn, A; Nagel, A; Gilow, C; Weitenberg, C; Schmitt, Y; Jacobs, K [Department of Experimental Physics, Saarland University, 66041 Saarbruecken (Germany)], E-mail: k.jacobs@physik.uni-saarland.de

    2008-10-08

    Adsorption of proteins onto solid surfaces is an everyday phenomenon that is not yet fully understood. To further the current understanding, we have performed in situ ellipsometry studies to reveal the adsorption kinetics of three different proteins, lysozyme, {alpha}-amylase and bovine serum albumin. As substrates we offer Si wafers with a controlled Si oxide layer thickness and a hydrophilic or hydrophobic surface functionalization, allowing the tailoring of the influence of short- and long-range interactions. Our studies show that not only the surface chemistry determines the properties of an adsorbed protein layer but also the van der Waals contributions of a composite substrate. We compare the experimental findings to results of a colloidal Monte Carlo approach that includes conformational changes of the adsorbed proteins induced by density fluctuations.

  13. 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

  14. Effects of previous protein intake on rectal temperature, blood glucose, plasma thyroid hormone and minerals by laying hens during a forced molt

    International Nuclear Information System (INIS)

    Rodrigues, G.A.; Moraes, V.M.B.; Cherici, I; Furlan, R.L.; Macari, M.

    1991-01-01

    The effects of forced molting on blood glucose, rectal temperature, plasma T4, T3 and minerals were studied in hens previously fed rations with different protein contents (14, 17 and 20% crude protein). Blood samples were obtained from brachial veins for blood glucose, T4 and T3 were measured by radioimmunoassay, and plasma minerals were determined by atomic absorption spectroscopy. Blood glucose and rectal temperature were reduced during fasting regardless of previous protein intake. Pre molting T4 plasma level was higher in laying hens fed higher protein ration, but feed deprivation reduced T 4 and T 3 concentrations irrespective of protein intake, except T 4 level for 14% crude protein fed birds that increased during fasting. The data obtained in this experiment suggest that previous protein intake does not interfere with the metabolic changes during forced molt. (author). 19 refs, 1 fig, 4 tabs

  15. Effects of previous protein intake on rectal temperature, blood glucose, plasma thyroid hormone and minerals by laying hens during a forced molt

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, G A; Moraes, V M.B.; Cherici, I; Furlan, R L; Macari, M [UNESP, Jaboticabal, SP (Brazil). Faculdade de Ciencias Agrarias e Veterinarias

    1991-12-01

    The effects of forced molting on blood glucose, rectal temperature, plasma T4, T3 and minerals were studied in hens previously fed rations with different protein contents (14, 17 and 20% crude protein). Blood samples were obtained from brachial veins for blood glucose, T4 and T3 were measured by radioimmunoassay, and plasma minerals were determined by atomic absorption spectroscopy. Blood glucose and rectal temperature were reduced during fasting regardless of previous protein intake. Pre molting T4 plasma level was higher in laying hens fed higher protein ration, but feed deprivation reduced T{sub 4} and T{sub 3} concentrations irrespective of protein intake, except T{sub 4} level for 14% crude protein fed birds that increased during fasting. The data obtained in this experiment suggest that previous protein intake does not interfere with the metabolic changes during forced molt. (author). 19 refs, 1 fig, 4 tabs.

  16. Micropatterning of bacteria on two-dimensional lattice protein surface observed by atomic force microscopy

    International Nuclear Information System (INIS)

    Oh, Y.J.; Jo, W.; Lim, J.; Park, S.; Kim, Y.S.; Kim, Y.

    2008-01-01

    In this study, we characterized the two-dimensional lattice of bovine serum albumin (BSA) as a chemical and physical barrier against bacterial adhesion, using fluorescence microscopy and atomic force microscopy (AFM). The lattice of BSA on glass surface was fabricated by micro-contact printing (μCP), which is a useful way to pattern a wide range of molecules into microscale features on different types of substrates. The contact-mode AFM measurements showed that the average height of the printed BSA monolayer was 5-6 nm. Escherichia coli adhered rapidly on bare glass slide, while the bacterial adhesion was minimized on the lattices in the range of 1-3 μm 2 . Especially, the bacterial adhesion was completely inhibited on a 1 μm 2 lattice. The results suggest that the anti-adhesion effects are due by the steric repulsion forces exerted by BSA

  17. 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...

  18. 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

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. Probing the molecular forces involved in binding of selected volatile flavour compounds to salt-extracted pea proteins.

    Science.gov (United States)

    Wang, Kun; Arntfield, Susan D

    2016-11-15

    Molecular interactions between heterologous classes of flavour compounds with salt-extracted pea protein isolates (PPIs) were determined using various bond disrupting agents followed by GC/MS analysis. Flavour bound by proteins decreased in the order: dibutyl disulfide>octanal>hexyl acetate>2-octanone=benzaldehyde. Benzaldehyde, 2-octanone and hexyl acetate interacted non-covalently with PPIs, whereas octanal bound PPIs via covalent and non-covalent forces. Dibutyl disulfide reacted with PPIs covalently, as its retention was not diminished by urea and guanidine hydrochloride. Using propylene glycol, H-bonding and ionic interactions were implicated for hexyl acetate, benzaldehyde, and 2-octanone. A protein-destabilising salt (Cl3CCOONa) reduced bindings for 2-octanone, hexyl acetate, and benzaldehyde; however, retention for octanal and dibutyl disulfide increased. Conversely, a protein-stabilising salt (Na2SO4) enhanced retention for benzaldehyde, 2-octanone, hexyl acetate and octanal. Formation of a volatile flavour by-product, 1-butanethiol, from dibutyl disulfide when PPIs were treated with dithiothreitol indicated occurrence of sulfhydryl-disulfide interchange reactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. 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

  5. Performance of repetitive tasks induces decreased grip strength and increased fibrogenic proteins in skeletal muscle: role of force and inflammation.

    Directory of Open Access Journals (Sweden)

    Samir M Abdelmagid

    Full Text Available This study elucidates exposure-response relationships between performance of repetitive tasks, grip strength declines, and fibrogenic-related protein changes in muscles, and their link to inflammation. Specifically, we examined forearm flexor digitorum muscles for changes in connective tissue growth factor (CTGF; a matrix protein associated with fibrosis, collagen type I (Col1; a matrix component, and transforming growth factor beta 1 (TGFB1; an upstream modulator of CTGF and collagen, in rats performing one of two repetitive tasks, with or without anti-inflammatory drugs.To examine the roles of force versus repetition, rats performed either a high repetition negligible force food retrieval task (HRNF, or a high repetition high force handle-pulling task (HRHF, for up to 9 weeks, with results compared to trained only (TR-NF or TR-HF and normal control rats. Grip strength declined with both tasks, with the greatest declines in 9-week HRHF rats. Quantitative PCR (qPCR analyses of HRNF muscles showed increased expression of Col1 in weeks 3-9, and CTGF in weeks 6 and 9. Immunohistochemistry confirmed PCR results, and also showed greater increases of CTGF and collagen matrix in 9-week HRHF rats than 9-week HRNF rats. ELISA, and immunohistochemistry revealed greater increases of TGFB1 in TR-HF and 6-week HRHF, compared to 6-week HRNF rats. To examine the role of inflammation, results from 6-week HRHF rats were compared to rats receiving ibuprofen or anti-TNF-α treatment in HRHF weeks 4-6. Both treatments attenuated HRHF-induced increases in CTGF and fibrosis by 6 weeks of task performance. Ibuprofen attenuated TGFB1 increases and grip strength declines, matching our prior results with anti-TNFα.Performance of highly repetitive tasks was associated with force-dependent declines in grip strength and increased fibrogenic-related proteins in flexor digitorum muscles. These changes were attenuated, at least short-term, by anti-inflammatory treatments.

  6. Potentials of mean force for protein structure prediction vindicated, formalized and generalized

    DEFF Research Database (Denmark)

    Hamelryck, Thomas; Borg, Mikael; Paluszewski, Martin

    2010-01-01

    and the simulation of protein folding. However, the validity, scope and limitations of these potentials are still vigorously debated and disputed, and the optimal choice of the reference state--a necessary component of these potentials--is an unsolved problem. PMFs are loosely justified by analogy to the reversible...

  7. 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 .

  8. 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

  9. 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

  10. Measuring cell viscoelastic properties using a force-spectrometer: influence of protein-cytoplasm interactions.

    Science.gov (United States)

    Canetta, Elisabetta; Duperray, Alain; Leyrat, Anne; Verdier, Claude

    2005-01-01

    Cell adhesive and rheological properties play a very important role in cell transmigration through the endothelial barrier, in particular in the case of inflammation (leukocytes) or cancer metastasis (cancer cells). In order to characterize cell viscoelastic properties, we have designed a force spectrometer (AFM) which can stretch cells thereby allowing measurement of their rheological properties. This custom-made force spectrometer allows two different visualizations, one lateral and one from below. It allows investigation of the effects of rheology involved during cell stretching. To test the ability of our system to characterize such viscoelastic properties, ICAM-1 transfected CHO cells were analyzed. Two forms of ICAM-1 were tested; wild type ICAM-1, which can interact with the cytoskeleton, and a mutant form which lacks the cytoplasmic domain, and is unable to associate with the cytoskeleton. Stretching experiments carried out on these cells show the formation of long filaments. Using a previous model of filament elongation, we could determine the viscoelastic properties of a single cell. As expected, different viscoelastic components were found between the wild type and the mutant, which reveal that the presence of interactions between ICAM-1 and the cytoskeleton increases the stiffness of the cell.

  11. Thickness and morphology of polyelectrolyte coatings on silica surfaces before and after protein exposure studied by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Haselberg, Rob, E-mail: r.haselberg@vu.nl [Biomolecular Analysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (Netherlands); AIMMS Division of BioMolecular Analysis, VU University Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Flesch, Frits M. [Biomolecular Analysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (Netherlands); Boerke, Arjan [Department of Biochemistry and Cell Biology, Utrecht University, Yalelaan 2, 3508 TD Utrecht (Netherlands); Somsen, Govert W. [Biomolecular Analysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (Netherlands); AIMMS Division of BioMolecular Analysis, VU University Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam (Netherlands)

    2013-05-24

    Graphical abstract: -- Highlights: •Atomic force microscopy is used to characterize polyelectrolyte coatings. •Coating procedure leads to nm-thick layers on a silica surface. •Polyelectrolyte coatings effectively prevent protein adsorption. •AFM provides the high resolution to investigate these thin films. •AFM results support earlier findings obtained with capillary electrophoresis. -- Abstract: Analyte–wall interaction is a significant problem in capillary electrophoresis (CE) as it may compromise separation efficiencies and migration time repeatability. In CE, self-assembled polyelectrolyte multilayer films of Polybrene (PB) and dextran sulfate (DS) or poly(vinylsulfonic acid) (PVS) have been used to coat the capillary inner wall and thereby prevent analyte adsorption. In this study, atomic force microscopy (AFM) was employed to investigate the layer thickness and surface morphology of monolayer (PB), bilayer, (PB-DS and PB-PVS), and trilayer (PB-DS-PB and PB-PVS-PB) coatings on glass surfaces. AFM nanoshaving experiments providing height distributions demonstrated that the coating procedures led to average layer thicknesses between 1 nm (PB) and 5 nm (PB-DS-PB), suggesting the individual polyelectrolytes adhere flat on the silica surface. Investigation of the surface morphology of the different coatings by AFM revealed that the PB coating does not completely cover the silica surface, whereas full coverage was observed for the trilayer coatings. The DS-containing coatings appeared on average 1 nm thicker than the corresponding PVS-containing coatings, which could be attributed to the molecular structure of the anionic polymers applied. Upon exposure to the basic protein cytochrome c, AFM measurements showed an increase of the layer thickness for bare (3.1 nm) and PB-DS-coated (4.6 nm) silica, indicating substantial protein adsorption. In contrast, a very small or no increase of the layer thickness was observed for the PB and PB-DS-PB coatings

  12. 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

  13. 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

  14. 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.)

  15. 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}.

  16. 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.

  17. 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.

  18. 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)

  19. Atomic force microscopy recognition of protein A on Staphylococcus aureus cell surfaces by labelling with IgG-Au conjugates.

    Science.gov (United States)

    Tatlybaeva, Elena B; Nikiyan, Hike N; Vasilchenko, Alexey S; Deryabin, Dmitri G

    2013-01-01

    The labelling of functional molecules on the surface of bacterial cells is one way to recognize the bacteria. In this work, we have developed a method for the selective labelling of protein A on the cell surfaces of Staphylococcus aureus by using nanosized immunogold conjugates as cell-surface markers for atomic force microscopy (AFM). The use of 30-nm size Au nanoparticles conjugated with immunoglobulin G (IgG) allowed the visualization, localization and distribution of protein A-IgG complexes on the surface of S. aureus. The selectivity of the labelling method was confirmed in mixtures of S. aureus with Bacillus licheniformis cells, which differed by size and shape and had no IgG receptors on the surface. A preferential binding of the IgG-Au conjugates to S. aureus was obtained. Thus, this novel approach allows the identification of protein A and other IgG receptor-bearing bacteria, which is useful for AFM indication of pathogenic microorganisms in poly-component associations.

  20. Atomic force microscopy recognition of protein A on Staphylococcus aureus cell surfaces by labelling with IgG–Au conjugates

    Directory of Open Access Journals (Sweden)

    Elena B. Tatlybaeva

    2013-11-01

    Full Text Available The labelling of functional molecules on the surface of bacterial cells is one way to recognize the bacteria. In this work, we have developed a method for the selective labelling of protein A on the cell surfaces of Staphylococcus aureus by using nanosized immunogold conjugates as cell-surface markers for atomic force microscopy (AFM. The use of 30-nm size Au nanoparticles conjugated with immunoglobulin G (IgG allowed the visualization, localization and distribution of protein A–IgG complexes on the surface of S. aureus. The selectivity of the labelling method was confirmed in mixtures of S. aureus with Bacillus licheniformis cells, which differed by size and shape and had no IgG receptors on the surface. A preferential binding of the IgG–Au conjugates to S. aureus was obtained. Thus, this novel approach allows the identification of protein A and other IgG receptor-bearing bacteria, which is useful for AFM indication of pathogenic microorganisms in poly-component associations.

  1. Atomic force microscopy recognition of protein A on Staphylococcus aureus cell surfaces by labelling with IgG–Au conjugates

    Science.gov (United States)

    Tatlybaeva, Elena B; Vasilchenko, Alexey S; Deryabin, Dmitri G

    2013-01-01

    Summary The labelling of functional molecules on the surface of bacterial cells is one way to recognize the bacteria. In this work, we have developed a method for the selective labelling of protein A on the cell surfaces of Staphylococcus aureus by using nanosized immunogold conjugates as cell-surface markers for atomic force microscopy (AFM). The use of 30-nm size Au nanoparticles conjugated with immunoglobulin G (IgG) allowed the visualization, localization and distribution of protein A–IgG complexes on the surface of S. aureus. The selectivity of the labelling method was confirmed in mixtures of S. aureus with Bacillus licheniformis cells, which differed by size and shape and had no IgG receptors on the surface. A preferential binding of the IgG–Au conjugates to S. aureus was obtained. Thus, this novel approach allows the identification of protein A and other IgG receptor-bearing bacteria, which is useful for AFM indication of pathogenic microorganisms in poly-component associations. PMID:24367742

  2. 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.

  3. 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

  4. 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)

  5. The role of atomic level steric effects and attractive forces in protein folding.

    Science.gov (United States)

    Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

    2012-02-01

    Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.

  6. 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.

  7. Characterizing interaction forces between actin and proteins of the tropomodulin family reveals the presence of the N-terminal actin-binding site in leiomodin.

    Science.gov (United States)

    Arslan, Baran; Colpan, Mert; Gray, Kevin T; Abu-Lail, Nehal I; Kostyukova, Alla S

    2018-01-15

    Tropomodulin family of proteins includes several isoforms of tropomodulins (Tmod) and leiomodins (Lmod). These proteins can sequester actin monomers or nucleate actin polymerization. Although it is known that their actin-binding properties are isoform-dependent, knowledge on how they vary in strengths of interactions with G-actin is missing. While it is confirmed in many studies that Tmods have two actin-binding sites, information on number and location of actin-binding sites in Lmod2 is controversial. We used atomic force microscopy to study interactions between G-actin and proteins of the tropomodulin family. Unbinding forces between G-actin and Tmod1, Tmod2, Tmod3, or Lmod2 were quantified. Our results indicated that Tmod1 and Tmod3 had unimodal force distributions, Tmod2 had a bimodal distribution and Lmod2 had a trimodal distribution. The number of force distributions correlates with the proteins' abilities to sequester actin or to nucleate actin polymerization. We assigned specific unbinding forces to the individual actin-binding sites of Tmod2 and Lmod2 using mutations that destroy actin-binding sites of Tmod2 and truncated Lmod2. Our results confirm the existence of the N-terminal actin-binding site in Lmod2. Altogether, our data demonstrate how the differences between the number and the strength of actin-binding sites of Tmod or Lmod translate to their functional abilities. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. 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.

  9. 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

  10. 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.).

  11. 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.)

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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...

  19. 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

  20. 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.

  1. 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.

  2. 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)

  3. 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.

  4. 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)

  5. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

    Science.gov (United States)

    2016-01-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  6. 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

  7. 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

  8. Cerebrospinal fluid protein and glucose examinations and tuberculosis:
Will laboratory safety regulations force a change of practice?

    Science.gov (United States)

    Tormey, William P; O'Hagan, Christopher

    2015-01-01

    Cerebrospinal fluid (CSF) protein and glucose examinations are usually performed in chemical pathology departments on autoanalysers. Tuberculosis (TB) is a group 3 biological agent under Directive 2000/54/EC of the European Parliament but in the biochemistry laboratory, no extra precautions are taken in its analysis in possible TB cases. The issue of laboratory practice and safety in the biochemical analyses of CSF specimens, when tuberculosis infection is in question is addressed in the context of ambiguity in the implementation of current national and international health and safety regulations. Additional protective measures for laboratory staff during the analysis of CSF TB samples should force a change in current laboratory practice and become a regulatory issue under ISO 15189. Annual Mantoux skin test or an interferon-γ release assay for TB should be mandatory for relevant staff. This manuscript addresses the issue of biochemistry laboratory practice and safety in the biochemical analyses of CSF specimens when tuberculosis infection is in question in the context of the ambiguity of statutory health and safety regulations.

  9. Modulation of Calcium Oxalate Crystallization by Proteins and Small Molecules Investigated by In Situ Atomic Force Microscopy

    Science.gov (United States)

    Qiu, R.; Orme, C.; Cody, A. M.; Wierzbicki, A.; Hoyer, J.; Nancollas, G.; de Yoreo, J.

    2002-12-01

    Understanding the physical mechanisms by which biological inhibitors control nucleation and growth of inorganic crystals is a major focus of biomineral research. Calcium oxalate monohydrate (COM), which plays a functional role in plant physiology, is also a source of pathogenesis in humans where it causes kidney stone disease. Although a great deal of research has been carried out on the modulation COM by proteins and small molecules, the basic mechanism has not yet been understood. However, because the proteins that play a role in COM growth have been identified and sequenced, COM provides an excellent model system for research into biomineral growth. In this study, in situ atomic force microscopy (AFM) was used to monitor the COM surface under controlled growth conditions both from pure solutions and those doped with citrate and osteopontin (OPN) in order to determine their effects on surface morphology and growth dynamics at the molecular level. As with other solution-grown crystals such as calcite, COM grows on complex dislocation hillocks. In pure solution, while growth on the (010) face is isotropic, hillocks on the (-101) face exhibit anisotropic step kinetics. Steps of [-10-1] and orientation are clearly delineated with the [-10-1] being the fast growing direction. When citrate is added to the solution, both growth rate and morphology are drastically changed on (-101) face, especially along the [-10-1] direction. This results in isotropic disc-shaped hillocks a shape that is then reflected in the macroscopic growth habit. In contrast, no large growth changes were observed on the (010) facet. At the same time, molecular modeling predicts an excellent fit of the citrate ion into the (-101) plane and a poor fit to the (010) face. Here we propose a model that reconciles the step-specific interactions implied by the AFM results with the face-specific predictions of the calculations. Finally, we present the results of doping with aspartic acid as well as OPN, an

  10. 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...

  11. Mechanism underlying bioinertness of self-assembled monolayers of oligo(ethyleneglycol)-terminated alkanethiols on gold: protein adsorption, platelet adhesion, and surface forces.

    Science.gov (United States)

    Hayashi, Tomohiro; Tanaka, Yusaku; Koide, Yuki; Tanaka, Masaru; Hara, Masahiko

    2012-08-07

    The mechanism underlying the bioinertness of the self-assembled monolayers of oligo(ethylene glycol)-terminated alkanethiol (OEG-SAM) was investigated with protein adsorption experiments, platelet adhesion tests, and surface force measurements with an atomic force microscope (AFM). In this work, we performed systematic analysis with SAMs having various terminal groups (-OEG, -OH, -COOH, -NH(2), and -CH(3)). The results of the protein adsorption experiment by the quartz crystal microbalance (QCM) method suggested that having one EG unit and the neutrality of total charges of the terminal groups are essential for protein-resistance. In particular, QCM with energy dissipation analyses indicated that proteins absorb onto the OEG-SAM via a very weak interaction compared with other SAMs. Contrary to the protein resistance, at least three EG units as well as the charge neutrality of the SAM are found to be required for anti-platelet adhesion. When the identical SAMs were formed on both AFM probe and substrate, our force measurements revealed that only the OEG-SAMs possessing more than two EG units showed strong repulsion in the range of 4 to 6 nm. In addition, we found that the SAMs with other terminal groups did not exhibit such repulsion. The repulsion between OEG-SAMs was always observed independent of solution conditions [NaCl concentration (between 0 and 1 M) and pH (between 3 and 11)] and was not observed in solution mixed with ethanol, which disrupts the three-dimensional network of the water molecules. We therefore concluded that the repulsion originated from structured interfacial water molecules. Considering the correlation between the above results, we propose that the layer of the structured interfacial water with a thickness of 2 to 3 nm (half of the range of the repulsion observed in the surface force measurements) plays an important role in deterring proteins and platelets from adsorption or adhesion.

  12. 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...

  13. 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...

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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...

  19. 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

  20. ''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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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 ...

  6. 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

  7. 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

  8. 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.

  9. Myostatin dysfunction impairs force generation in extensor digitorum longus muscle and increases exercise-induced protein efflux from extensor digitorum longus and soleus muscles.

    Science.gov (United States)

    Baltusnikas, Juozas; Kilikevicius, Audrius; Venckunas, Tomas; Fokin, Andrej; Bünger, Lutz; Lionikas, Arimantas; Ratkevicius, Aivaras

    2015-08-01

    Myostatin dysfunction promotes muscle hypertrophy, which can complicate assessment of muscle properties. We examined force generating capacity and creatine kinase (CK) efflux from skeletal muscles of young mice before they reach adult body and muscle size. Isolated soleus (SOL) and extensor digitorum longus (EDL) muscles of Berlin high (BEH) mice with dysfunctional myostatin, i.e., homozygous for inactivating myostatin mutation, and with a wild-type myostatin (BEH+/+) were studied. The muscles of BEH mice showed faster (P myostatin dysfunction leads to impairment in muscle force generating capacity in EDL and increases susceptibility of SOL and EDL to protein loss after exercise.

  10. 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.

  11. 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)

  12. 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.

  13. 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

  14. Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy.

    Science.gov (United States)

    Banerjee, S; Rakshit, T; Sett, S; Mukhopadhyay, R

    2015-10-22

    One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.)

  6. 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

  7. 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.)

  8. 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

  9. Role of calpain in eccentric contraction-induced proteolysis of Ca2+-regulatory proteins and force depression in rat fast-twitch skeletal muscle.

    Science.gov (United States)

    Kanzaki, Keita; Watanabe, Daiki; Kuratani, Mai; Yamada, Takashi; Matsunaga, Satoshi; Wada, Masanobu

    2017-02-01

    The aim of this study was to examine the in vivo effects of eccentric contraction (ECC) on calpain-dependent proteolysis of Ca 2+ -regulatory proteins and force production in fast-twitch skeletal muscles. Rat extensor digitorum longus muscles were exposed to 200 repeated ECC in situ and excised immediately [recovery 0 (REC0)] or 3 days [recovery 3 (REC3)] after cessation of ECC. Calpain inhibitor (CI)-treated rats were intraperitoneally injected with MDL-28170 before ECC and during REC3. Tetanic force was markedly reduced at REC0 and remained reduced at REC3. CI treatment ameliorated the ECC-induced force decline but only at REC3. No evidence was found for proteolysis of dihydropyridine receptor (DHPR), junctophilin (JP)1, JP2, ryanodine receptor (RyR), sarcoplasmic reticulum Ca 2+ -ATPase (SERCA)1a, or junctional face protein-45 at REC0. At REC3, ECC resulted in decreases in DHPR, JP1, JP2, RyR, and SERCA1a. CI treatment prevented the decreases in DHPR, JP1, and JP2, whereas it had little effect on RyR and SERCA1a. These findings suggest that DHPR, JP1, and JP2, but not RyR and SERCA1a, undergo calpain-dependent proteolysis in in vivo muscles subjected to ECC and that impaired function of DHPR and/or JP might cause prolonged force deficits with ECC. NEW & NOTEWORTHY Calpain-dependent proteolysis is one of the contributing factors to muscle damage that occurs with eccentric contraction (ECC). It is unclear, however, whether calpains account for proteolysis of Ca 2+ -regulatory proteins in in vivo muscles subjected to ECC. Here, we provide evidence that dihydropyridine receptor and junctophilin, but not ryanodine receptor and sarcoplasmic reticulum Ca 2+ -ATPase, undergo calpain-dependent proteolysis. Copyright © 2017 the American Physiological Society.

  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. PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

    Science.gov (United States)

    Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

    2004-04-01

    We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

  15. The effect of driving force on intramolecular electron transfer in proteins. Studies on single-site mutated azurins

    DEFF Research Database (Denmark)

    Farver, O; Skov, L K; van de Kamp, M

    1992-01-01

    -6972]. To further investigate the nature of this long-range electron transfer (LRET) proceeding within the protein matrix, we have now investigated it in two azurins where amino acids have been substituted by single-site mutation of the wild-type Pseudomonas aeruginosa azurin. In one mutated protein, a methionine...... the reorganization energy, lambda and electronic coupling factor, beta. The calculated values fit very well with a through-bond LRET mechanism....

  16. 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

  17. NCI-FDA Interagency Oncology Task Force Workshop Provides Guidance for Analytical Validation of Protein-based Multiplex Assays | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    An NCI-FDA Interagency Oncology Task Force (IOTF) Molecular Diagnostics Workshop was held on October 30, 2008 in Cambridge, MA, to discuss requirements for analytical validation of protein-based multiplex technologies in the context of its intended use. This workshop developed through NCI's Clinical Proteomic Technologies for Cancer initiative and the FDA focused on technology-specific analytical validation processes to be addressed prior to use in clinical settings. In making this workshop unique, a case study approach was used to discuss issues related to

  18. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

    Science.gov (United States)

    Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

    2015-02-10

    Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

  19. 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

  20. Electrochemical, atomic force microscopy and infrared reflection absorption spectroscopy studies of pre-formed mussel adhesive protein films on carbon steel for corrosion protection

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Fan, E-mail: fanzhang@kth.se [KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Div. of Surface and Corrosion Science, Drottning Kristinas vaeg.51, SE-100 44 Stockholm (Sweden); Pan, Jinshan [KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Div. of Surface and Corrosion Science, Drottning Kristinas vaeg.51, SE-100 44 Stockholm (Sweden); Claesson, Per Martin [KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Div. of Surface and Corrosion Science, Drottning Kristinas vaeg.51, SE-100 44 Stockholm (Sweden); Institute for Surface Chemistry, P.O. Box 5607, SE-114 86 Stockholm (Sweden); Brinck, Tore [KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Physical Chemistry, Division of Physical Chemistry, Teknikringen 36, SE-10044 Stockholm (Sweden)

    2012-10-01

    Electrochemical measurements, in situ and ex situ atomic force microscopy (AFM) experiments and infrared reflection absorption spectroscopy (IRAS) analysis were performed to investigate the formation and stability as well as corrosion protection properties of mussel adhesive protein (Mefp-1) films on carbon steel, and the influence of cross-linking by NaIO{sub 4} oxidation. The in situ AFM measurements show flake-like adsorbed protein aggregates in the film formed at pH 9. The ex situ AFM images indicate multilayer-like films and that the film becomes more compact and stable in NaCl solution after the cross-linking. The IRAS results reveal the absorption bands of Mefp-1 on carbon steel before and after NaIO{sub 4} induced oxidation of the pre-adsorbed protein. Within a short exposure time, a certain corrosion protection effect was noted for the pre-formed Mefp-1 film in 0.1 M NaCl solution. Cross-linking the pre-adsorbed film by NaIO{sub 4} oxidation significantly enhanced the protection efficiency by up to 80%. - Highlights: Black-Right-Pointing-Pointer Mussel protein was tested as 'green' corrosion protection strategy for steel. Black-Right-Pointing-Pointer At pH 9, the protein adsorbs on carbon steel and forms a multilayer-like film. Black-Right-Pointing-Pointer NaIO{sub 4} leads to structural changes and cross-linking of the protein film. Black-Right-Pointing-Pointer Cross-linking results in a dense and compact film with increased stability. Black-Right-Pointing-Pointer Cross-linking of preformed film significantly enhances the corrosion protection.

  1. 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)

  2. 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.

  3. X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

    Science.gov (United States)

    Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

    2009-02-17

    A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.

  4. 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.

  5. 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

  6. 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...

  7. 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...

  8. 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)

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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].

  15. 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.

  16. 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

  17. 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)

  18. 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.

  19. 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)

  20. Inhibitors Alter the Stochasticity of Regulatory Proteins to Force Cells to Switch to the Other State in the Bistable System.

    Science.gov (United States)

    Jhang, Wun-Sin; Lo, Shih-Chiang; Yeh, Chen-Chao; Shu, Che-Chi

    2017-06-30

    The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins. For a bistable system of a mutually inhibitory network, such a change of noise led to the migration of cells in the bimodal distribution. We proposed that the consumption of regulatory protein caused by the addition of inhibitor is not the only reason for pushing cells to the specific state; the change of the intracellular stochasticity is also the main cause for the redistribution. For the level of the inhibitor capable of driving 99% of cells, if there is no consumption of regulatory protein, 88% of cells were guided to the specific state. It implied that cells were pushed, by the inhibitor, to the specific state due to the change of stochasticity.

  1. Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

    Science.gov (United States)

    Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

    2013-01-01

    In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Nanoscale orientation and lateral organization of chimeric metal-binding green fluorescent protein on lipid membrane determined by epifluorescence and atomic force microscopy

    International Nuclear Information System (INIS)

    Prachayasittikul, Virapong; Isarankura Na Ayudhya, Chartchalerm; Tantimongcolwat, Tanawut; Galla, Hans-Joachim

    2005-01-01

    Epifluorescence microscopy as well as atomic force microscopy was successfully applied to explore the orientation and lateral organization of a group of chimeric green fluorescent proteins (GFPs) on lipid membrane. Incorporation of the chimeric GFP carrying Cd-binding region (His6CdBP4GFP) to the fluid phase of DPPC monolayer resulted in a strong fluorescence intensity at the air-water interface. Meanwhile, non-specific adsorption of the GFP having hexahistidine (His6GFP) led to the perturbation of the protein structure in which very low fluorescence was observed. Specific binding of both of the chimeric GFPs to immobilized zinc ions underneath the metal-chelating lipid membrane was revealed. This specific binding could be reversibly controlled by addition of metal ions or metal chelator. Binding of the chimeric GFPs to the metal-chelating lipid membrane was proven to be the end-on orientation while the side-on adsorption was contrarily noted in the absence of metal ions. Increase of lateral mobility owing to the fluidization effect on the chelating lipid membrane subsequently facilitated crystal formation. All these findings have opened up a potential approach for a specific orientation of immobilization of protein at the membrane interface. This could have accounted for a better opportunity of sensor development

  3. Novel insights into pericarp, protein body globoids of aleurone layer, starchy granules of three cereals gained using atomic force microscopy and environmental scanning electronic microscopy.

    Science.gov (United States)

    Antonini, Elena; Zara, Carolina; Valentini, Laura; Gobbi, Pietro; Ninfali, Paolino; Menotta, Michele

    2018-02-05

    In this study, we applied Environmental Scanning Electron Microscopy-Energy Dispersive Spectroscopy (ESEM-EDS) and Atomic Force Microscopy (AFM) analysis to three different cereal caryopses: barley, oat and einkorn wheat. The morphological structures, chemical elemental composition and surface characteristics of the three cereals were described. Regarding the morphology, barley showed the thickest pericarp, providing a strong barrier digestion and absorption of nutrients. The aleurone layer of each cereal type contained protein body globoids within its cells. Large type-A and small type-B starchy granules were revealed in the endosperm of barley and einkorn wheat, whereas irregular starchy granules were found in oats. The starchy granule elemental composition, detected by ESEM-EDS, was rather homogenous in the three cereals, whereas the pericarp and protein body globoids showed heterogeneity. In the protein body globoids, oats showed higher P and K concentrations than barley and einkorn wheat. Regarding the topographic profiles, detected by AFM, einkorn wheat starchy granules showed a surface profile that differed significantly from that of oats and barley, which were quite similar to one another. The present work provides insights into the morphological and chemical makeup of the three grains shedding light on the higher bio-accessibility of einkorn wheat nutrients compared to barley and oats, providing important suggestions for human nutrition and technological standpoints.

  4. Novel insights into pericarp, protein body globoids of aleurone layer, starchy granules of three cereals gained using atomic force microscopy and environmental scanning electronic microscopy

    Science.gov (United States)

    Antonini, Elena; Zara, Carolina; Valentini, Laura; Gobbi, Pietro; Menotta, Michele

    2018-01-01

    In this study, we applied Environmental Scanning Electron Microscopy-Energy Dispersive Spectroscopy (ESEM-EDS) and Atomic Force Microscopy (AFM) analysis to three different cereal caryopses: barley, oat and einkorn wheat. The morphological structures, chemical elemental composition and surface characteristics of the three cereals were described. Regarding the morphology, barley showed the thickest pericarp, providing a strong barrier to digestion and absorption of nutrients. The aleurone layer of each cereal type contained protein body globoids within its cells. Large type-A and small type-B starchy granules were revealed in the endosperm of barley and einkorn wheat, whereas irregular starchy granules were found in oats. The starchy granule elemental composition, detected by ESEM-EDS, was rather homogenous in the three cereals, whereas the pericarp and protein body globoids showed heterogeneity. In the protein body globoids, oats showed higher P and K concentrations than barley and einkorn wheat. Regarding the topographic profiles, detected by AFM, einkorn wheat starchy granules showed a surface profile that differed significantly from that of oats and barley, which were quite similar to one another. The present work provides insights into the morphological and chemical makeup of the three grains shedding light on the higher bio-accessibility of einkorn wheat nutrients compared to barley and oats, providing important suggestions for human nutrition and technological standpoints. PMID:29569870

  5. 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.

  6. 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.)

  7. 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.

  8. 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

  9. 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)

  10. Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force.

    Science.gov (United States)

    Shimizu, Seishi; Chan, Hue Sun

    2002-12-01

    Free energies of pairwise hydrophobic association are simulated in aqueous solutions of urea at concentrations ranging from 0-8 M. Consistent with the expectation that hydrophobic interactions are weakened by urea, the association of relatively large nonpolar solutes is destabilized by urea. However, the association of two small methane-sized nonpolar solutes in water has the opposite tendency of being slightly strengthened by the addition of urea. Such size effects and the dependence of urea-induced stability changes on the configuration of nonpolar solutes are not predicted by solvent accessible surface area approaches based on energetic parameters derived from bulk-phase solubilities of model compounds. Thus, to understand hydrophobic interactions in proteins, it is not sufficient to rely solely on transfer experiment data that effectively characterize a single nonpolar solute in an aqueous environment but not the solvent-mediated interactions among two or more nonpolar solutes. We find that the m-values for the rate of change of two-methane association free energy with respect to urea concentration is a dramatically nonmonotonic function of the spatial separation between the two methanes, with a distance-dependent profile similar to the corresponding two-methane heat capacity of association in pure water. Our results rationalize the persistence of residual hydrophobic contacts in some proteins at high urea concentrations and explain why the heat capacity signature (DeltaC(P)) of a compact denatured state can be similar to DeltaC(P) values calculated by assuming an open random-coil-like unfolded state. Copyright 2002 Wiley-Liss, Inc.

  11. 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

  12. 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

  13. 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.

  14. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.

    Science.gov (United States)

    Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary

    2018-03-01

    A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.

  15. Investigation of free fatty acid associated recombinant membrane receptor protein expression in HEK293 cells using Raman spectroscopy, calcium imaging, and atomic force microscopy.

    Science.gov (United States)

    Lin, Juqiang; Xu, Han; Wu, Yangzhe; Tang, Mingjie; McEwen, Gerald D; Liu, Pin; Hansen, Dane R; Gilbertson, Timothy A; Zhou, Anhong

    2013-02-05

    G-protein-coupled receptor 120 (GPR120) is a previously orphaned G-protein-coupled receptor that apparently functions as a sensor for dietary fat in the gustatory and digestive systems. In this study, a cDNA sequence encoding a doxycycline (Dox)-inducible mature peptide of GPR120 was inserted into an expression vector and transfected in HEK293 cells. We measured Raman spectra of single HEK293 cells as well as GPR120-expressing HEK293-GPR120 cells at a 48 h period following the additions of Dox at several concentrations. We found that the spectral intensity of HEK293-GPR120 cells is dependent upon the dose of Dox, which correlates with the accumulation of GPR120 protein in the cells. However, the amount of the fatty acid activated changes in intracellular calcium (Ca(2+)) as measured by ratiometric calcium imaging was not correlated with Dox concentration. Principal components analysis (PCA) of Raman spectra reveals that the spectra from different treatments of HEK293-GPR120 cells form distinct, completely separated clusters with the receiver operating characteristic (ROC) area of 1, while those spectra for the HEK293 cells form small overlap clusters with the ROC area of 0.836. It was also found that expression of GPR120 altered the physiochemical and biomechanical properties of the parental cell membrane surface, which was quantitated by atomic force microscopy (AFM). These findings demonstrate that the combination of Raman spectroscopy, calcium imaging, and AFM may provide new tools in noninvasive and quantitative monitoring of membrane receptor expression induced alterations in the biophysical and signaling properties of single living cells.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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)

  1. 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...

  2. 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)

  3. 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.

  4. 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.

  5. 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

  6. 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)

  7. m-Trifluoromethyl-diphenyl Diselenide Regulates Prefrontal Cortical MOR and KOR Protein Levels and Abolishes the Phenotype Induced by Repeated Forced Swim Stress in Mice.

    Science.gov (United States)

    Rosa, Suzan Gonçalves; Pesarico, Ana Paula; Martini, Franciele; Nogueira, Cristina Wayne

    2018-04-05

    The present study aimed to investigate the m-trifluoromethyl-diphenyl diselenide [(m-CF 3 -PhSe) 2 ] effects on prefrontal cortical MOR and KOR protein levels and phenotype induced by repeated forced swim stress (FSS) in mice. Adult Swiss mice were subjected to repeated FSS sessions, and after that, they performed the spontaneous locomotor/exploratory activity, tail suspension, and splash tests. (m-CF 3 -PhSe) 2 (0.1 to 5 mg/kg) was administered to mice 30 min before the first FSS session and 30 min before the subsequent repeated FSS. (m-CF 3 -PhSe) 2 abolished the phenotype induced by repeated FSS in mice. In addition, a single FSS session increased μ but reduced δ-opioid receptor contents, without changing the κ content. Mice subjected to repeated FSS had an increase in the μ content when compared to those of naïve group or subjected to single FSS. Repeated FSS induced an increase of δ-opioid receptor content compared to those mice subjected to single FSS. However, the δ-opioid receptor contents were lower than those found in the naïve group. The mice subjected to repeated FSS showed an increase in the κ-opioid receptor content when compared to that of the naïve mice. (m-CF 3 -PhSe) 2 regulated the protein contents of μ and κ receptors in mice subjected to repeated FSS. These findings demonstrate that (m-CF 3 -PhSe) 2 was effective to abolish the phenotype induced by FSS, which was accompanied by changes in the contents of cortical μ- and κ-opioid receptors.

  8. Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald, E-mail: gerald.mathias@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-03-14

    In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call “Hamiltonian dielectric solvent” (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

  9. 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)

  10. Interaction analysis of chimeric metal-binding green fluorescent protein and artificial solid-supported lipid membrane by quartz crystal microbalance and atomic force microscopy

    International Nuclear Information System (INIS)

    Prachayasittikul, Virapong; Na Ayudhya, Chartchalerm Isarankura; Hilterhaus, Lutz; Hinz, Andreas; Tantimongcolwat, Tanawut; Galla, Hans-Joachim

    2005-01-01

    Non-specific adsorption and specific interaction between a chimeric green fluorescent protein (GFP) carrying metal-binding region and the immobilized zinc ions on artificial solid-supported lipid membranes was investigated using the quartz crystal microbalance technique and the atomic force microscopy (AFM). Supported lipid bilayer, composed of octanethiol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-[N- (5-amino-1-carboxypentyl iminodiacetic acid)succinyl] (NTA-DOGS)-Zn 2+ , was formed on the gold electrode of quartz resonator (5 MHz). Binding of the chimeric GFP to zinc ions resulted in a rapid decrease of resonance frequency. Reversibility of the process was demonstrated via the removal of metal ions by EDTA. Nanoscale structural orientation of the chimeric GFP on the membrane was imaged by AFM. Association constant of the specific binding to metal ions was 2- to 3-fold higher than that of the non-specific adsorption, which was caused by the fluidization effect of the metal-chelating lipid molecules as well as the steric hindrance effect. This infers a possibility for a further development of biofunctionalized membrane. However, maximization is needed in order to attain closer advancement to a membrane-based sensor device

  11. Antidepressant-like effect of fluoxetine may depend on translocator protein activity and pretest session duration in forced swimming test in mice.

    Science.gov (United States)

    Kudryashov, Nikita V; Kalinina, Tatiana S; Shimshirt, Alexander A; Korolev, Anton O; Volkova, Anna V; Voronina, Tatiana A

    2018-06-01

    The antidepressant-like effect of fluoxetine (20 mg/kg i.p.) has been assessed using the forced swimming test (FST) in IRC (CD-1) mice exposed or not to a pretest session of different duration (5 or 20 min). The influence of the mitochondrial translocator protein (TSPO) activity on the antidepressant-like effect of fluoxetine (20 mg/kg i.p.) in the FST was also studied. The antidepressant-like effect of fluoxetine was observed only in mice subjected to a 5-min pretest session 24 h before the FST. The TSPO antagonist PK11195 [1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3-isoquinolinecarboxamide; 1 or 3 mg/kg i.p.] inhibited the antidepressant activity of fluoxetine in the FST. In the present study, fluoxetine or PK11195 was administered for a short duration. We suppose that the functional activity of TSPO may depend on a pretest session and that using this procedure is necessary to detect antidepressant activity of fluoxetine-like drugs.

  12. 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)

  13. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol.

    Science.gov (United States)

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-04-14

    Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Koffas, Telly Stelianos [Univ. of California, Berkeley, CA (United States)

    2004-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and other complementary surface-sensitive techniques have been used to study the surface molecular structure and surface mechanical behavior of biologically-relevant polymer systems. SFG and AFM have emerged as powerful analytical tools to deduce structure/property relationships, in situ, for polymers at air, liquid and solid interfaces. The experiments described in this dissertation have been performed to understand how polymer surface properties are linked to polymer bulk composition, substrate hydrophobicity, changes in the ambient environment (e.g., humidity and temperature), or the adsorption of macromolecules. The correlation of spectroscopic and mechanical data by SFG and AFM can become a powerful methodology to study and engineer materials with tailored surface properties. The overarching theme of this research is the interrogation of systems of increasing structural complexity, which allows us to extend conclusions made on simpler model systems. We begin by systematically describing the surface molecular composition and mechanical properties of polymers, copolymers, and blends having simple linear architectures. Subsequent chapters focus on networked hydrogel materials used as soft contact lenses and the adsorption of protein and surfactant at the polymer/liquid interface. The power of SFG is immediately demonstrated in experiments which identify the chemical parameters that influence the molecular composition and ordering of a polymer chain's side groups at the polymer/air and polymer/liquid interfaces. In general, side groups with increasingly greater hydrophobic character will be more surface active in air. Larger side groups impose steric restrictions, thus they will tend to be more randomly ordered than smaller hydrophobic groups. If exposed to a hydrophilic environment, such as water, the polymer chain will attempt to orient more of its hydrophilic groups to

  7. C-reactive protein as a risk factor for coronary heart disease: a systematic review and meta-analyses for the U.S. Preventive Services Task Force.

    Science.gov (United States)

    Buckley, David I; Fu, Rongwei; Freeman, Michele; Rogers, Kevin; Helfand, Mark

    2009-10-06

    C-reactive protein (CRP) may help to refine global risk assessment for coronary heart disease (CHD), particularly among persons who are at intermediate risk on the basis of traditional risk factors alone. To assist the U.S. Preventive Services Task Force (USPSTF) in determining whether CRP should be incorporated into guidelines for CHD risk assessment. MEDLINE search of English-language articles (1966 to November 2007), supplemented by reference lists of reviews, pertinent studies, editorials, and Web sites and by expert suggestions. Prospective cohort, case-cohort, and nested case-control studies relevant to the independent predictive ability of CRP when used in intermediate-risk persons. Included studies were reviewed according to predefined criteria, and the quality of each study was rated. The validity of the body of evidence and the net benefit or harm of using CRP for CHD risk assessment were evaluated. The combined magnitude of effect was determined by meta-analysis. The body of evidence is of good quality, consistency, and applicability. For good studies that adjusted for all Framingham risk variables, the summary estimate of relative risk for incident CHD was 1.58 (95% CI, 1.37 to 1.83) for CRP levels greater than 3.0 mg/L compared with levels less than 1.0 mg/L. Analyses from 4 large cohorts were consistent in finding evidence that including CRP improves risk stratification among initially intermediate-risk persons. C-reactive protein has desirable test characteristics, and good data exist on the prevalence of elevated CRP levels in intermediate-risk persons. Limited evidence links changes in CRP level to primary prevention of CHD events. Study methods for measuring Framingham risk variables and other covariates varied. Ethnic and racial minority populations were poorly represented in most studies, limiting generalizability. Few studies directly assessed the effect of CRP on risk reclassification in intermediate-risk persons. Strong evidence indicates

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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)

  18. 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.

  19. Atomic Force Microscopy Study of Protein–Protein Interactions in the Cytochrome CYP11A1 (P450scc-Containing Steroid Hydroxylase System

    Directory of Open Access Journals (Sweden)

    Zöllner A

    2011-01-01

    Full Text Available Abstract Atomic force microscopy (AFM and photon correlation spectroscopy (PCS were used for monitoring of the procedure for cytochrome CYP11A1 monomerization in solution without phospholipids. It was shown that the incubation of 100 μM CYP11A1 with 12% Emulgen 913 in 50 mM KP, pH 7.4, for 10 min at T = 22°C leads to dissociation of hemoprotein aggregates to monomers with the monomerization degree of (82 ± 4%. Following the monomerization procedure, CYP11A1 remained functionally active. AFM was employed to detect and visualize the isolated proteins as well as complexes formed between the components of the cytochrome CYP11A1-dependent steroid hydroxylase system. Both Ad and AdR were present in solution as monomers. The typical heights of the monomeric AdR, Ad and CYP11A1 images were measured by AFM and were found to correspond to the sizes 1.6 ± 0.2 nm, 1.0 ± 0.2 nm and 1.8 ± 0.2 nm, respectively. The binary Ad/AdR and AdR/CYP11A1mon complexes with the heights 2.2 ± 0.2 nm and 2.8 ± 0.2 nm, respectively, were registered by use of AFM. The Ad/CYP11A1mon complex formation reaction was kinetically characterized based on optical biosensor data. In addition, the ternary AdR/Ad/CYP11A1 complexes with a typical height of 4 ± 1 nm were AFM registered.

  20. The use of Optical Magnetic Twisting Cytometry and Flourescence Resonance Energy Transfer to quantify force-induced protein dissociation in the nucleus of a living cell

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Yeh-Chuin Poh & Ning Wang ### Abstract Mechanical forces are known to play a significant role in biological processes. These forces can be transmitted to the cell through the cytoskeletal filament network, inducing different biochemical responses within the cytoplasm. Although there have been ample reports showing that cytoplasmic enzymes can be directly activated by a local stress on the cell surface via integrins, there has been no evidence that mechanical forces can direct...

  1. 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.

  2. 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.

  3. 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.

  4. 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…

  5. 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.

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. DelPhiForce web server: electrostatic forces and energy calculations and visualization.

    Science.gov (United States)

    Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

    2017-11-15

    Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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…

  4. 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.

  5. 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.

  6. Non-uniform binding of single-stranded DNA binding proteins to hybrids of single-stranded DNA and single-walled carbon nanotubes observed by atomic force microscopy in air and in liquid

    Energy Technology Data Exchange (ETDEWEB)

    Umemura, Kazuo, E-mail: meicun2006@163.com; Ishizaka, Kei; Nii, Daisuke; Izumi, Katsuki

    2016-12-01

    Highlights: • Conjugates of protein, DNA, and SWNTs were observed by AFM in liquid. • Non-uniform binding of proteins was visualized in liquid. • Thickness of DNA molecules on SWNT surfaces was well characterized in liquid. - Abstract: Using atomic force spectroscopy (AFM), we observed hybrids of single-stranded DNA (ssDNA) and single-walled carbon nanotubes (SWNTs) with or without protein molecules in air and in an aqueous solution. This is the first report of ssDNA–SWNT hybrids with proteins in solution analyzed by AFM. In the absence of protein, the height of the ssDNA–SWNT hybrids was 1.1 ± 0.3 nm and 2.4 ± 0.6 nm in air and liquid, respectively, suggesting that the ssDNA molecules adopted a flexible structure on the SWNT surface. In the presence of single-stranded DNA binding (SSB) proteins, the heights of the hybrids in air and liquid increased to 6.4 ± 3.1 nm and 10.0 ± 4.5 nm, respectively. The AFM images clearly showed binding of the SSB proteins to the ssDNA–SWNT hybrids. The morphology of the SSB–ssDNA–SWNT hybrids was non-uniform, particularly in aqueous solution. The variance of hybrid height was quantitatively estimated by cross-section analysis along the long-axis of each hybrid. The SSB–ssDNA–SWNT hybrids showed much larger variance than the ssDNA–SWNT hybrids.

  7. 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.

  8. Effects of MK-886, a 5-lipoxygenase activating protein (FLAP) inhibitor, and 5-lipoxygenase deficiency on the forced swimming behavior of mice

    Science.gov (United States)

    Uz, Tolga; Dimitrijevic, Nikola; Imbesi, Marta; Manev, Hari; Manev, Radmila

    2008-01-01

    A common biological pathway may contribute to the comorbidity of atherosclerosis and depression. Increased activity of the enzymatic 5-lipoxygenase (5-LOX; 5LO) pathway is a contributing factor in atherosclerosis and a 5-LOX inhibitor, MK-886, is beneficial in animal models of atherosclerosis. In the brain, MK-886 increases phosphorylation of the glutamate receptor subunit GluR1, and the increased phosphorylation of this receptor has been associated with antidepressant treatment. In this work, we evaluated the behavioral effects of MK-886 in an automated assay of mouse forced swimming, which identifies antidepressant activity as increased climbing behavior and/or decreased rest time. Whereas a single injection of MK-886 (3 and 10 mg/kg) did not affect forced swimming behaviors assayed 30 min later, 6 daily injections of 3 mg/kg MK-886 slightly increased climbing and significantly reduced rest time in wild-type mice but not in 5-LOX-deficient mice. A diet delivery of MK-886, 4 μg per 100 mg body-weight per day, required three weeks to affect forced swimming; it increased climbing behavior. Climbing behavior was also increased in naive 5-LOX-deficient mice compared to naive wild-type controls. These results suggest that 5-LOX inhibition and deficiency may be associated with antidepressant activity. Increased climbing in a forced swimming assay is a typical outcome of antidepressants that increase noradrenergic and dopaminergic activity. Interestingly, 5-LOX deficiency and MK-886 treatment have been shown to be capable of increasing the behavioral effects of a noradrenaline/dopamine-potentiating drug, cocaine. Future research is needed to evaluate the clinical relevance of our findings. PMID:18403121

  9. 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.

  10. 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.

  11. Force generation by titin folding.

    Science.gov (United States)

    Mártonfalvi, Zsolt; Bianco, Pasquale; Naftz, Katalin; Ferenczy, György G; Kellermayer, Miklós

    2017-07-01

    Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles. © 2017 The Protein Society.

  12. 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

  13. 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.

  14. 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.

  15. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

    Czech Academy of Sciences Publication Activity Database

    Estarellas, C.; Otyepka, M.; Koča, J.; Banáš, P.; Krepl, Miroslav; Šponer, Jiří

    2015-01-01

    Roč. 1850, č. 5 (2015), s. 1072-1090 ISSN 0304-4165 R&D Projects: GA ČR(CZ) GAP208/12/1878; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : CLASSICAL DRUDE OSCILLATOR * SUGAR-PHOSPHATE BACKBONE * POLARIZABLE FORCE-FIELD Subject RIV: BO - Biophysics Impact factor: 5.083, year: 2015

  16. Driving force behind adsorption-induced protein unfolding: a time-resolved X-ray reflectivity study on lysozyme adsorbed at an air/water interface.

    Science.gov (United States)

    Yano, Yohko F; Uruga, Tomoya; Tanida, Hajime; Toyokawa, Hidenori; Terada, Yasuko; Takagaki, Masafumi; Yamada, Hironari

    2009-01-06

    Time-resolved X-ray reflectivity measurements for lysozyme (LSZ) adsorbed at an air/water interface were performed to study the mechanism of adsorption-induced protein unfolding. The time dependence of the density profile at the air/water interface revealed that the molecular conformation changed significantly during adsorption. Taking into account previous work using Fourier transform infrared (FTIR) spectroscopy, we propose that the LSZ molecules initially adsorbed on the air/water interface have a flat unfolded structure, forming antiparallel beta-sheets as a result of hydrophobic interactions with the gas phase. In contrast, as adsorption continues, a second layer forms in which the molecules have a very loose structure having random coils as a result of hydrophilic interactions with the hydrophilic groups that protrude from the first layer.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Importance of dispersion and electron correlation in ab initio protein folding.

    Science.gov (United States)

    He, Xiao; Fusti-Molnar, Laszlo; Cui, Guanglei; Merz, Kenneth M

    2009-04-16

    Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

  2. 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.

  3. 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.

  4. 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)

  5. 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.

  6. 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.

  7. Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description.

    Science.gov (United States)

    Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

    2014-03-14

    We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by

  8. Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, Sebastian; Mathias, Gerald; Tavan, Paul, E-mail: paul.tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-03-14

    We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ{sub i} of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ{sub i}. A summarizing discussion highlights the achievements of the new theory and of its approximate solution

  9. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob

    2016-01-01

    chemical reference calculations. For the lowest π → π∗ transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity...... (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum...

  10. 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

  11. 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.

  12. 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.)

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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?

  18. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

    Directory of Open Access Journals (Sweden)

    Igor V. Uporov

    2015-09-01

    Full Text Available The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.

  19. 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.

  20. 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.

  1. Phonon forces and cold denaturatio

    DEFF Research Database (Denmark)

    Bohr, Jakob

    2003-01-01

    Protein unfolds upon temperature reduction as Well as upon In increase in temperature, These phenomena are called cold denaturation and hot denaturation, respectively. The contribution from quantum mode forces to denaturation is estimated using a simple phenomenological model describing the molec......Protein unfolds upon temperature reduction as Well as upon In increase in temperature, These phenomena are called cold denaturation and hot denaturation, respectively. The contribution from quantum mode forces to denaturation is estimated using a simple phenomenological model describing...... the molecule Is a continuum. The frequencies of the vibrational modes depend on the molecular dimensionality; hence, the zero-point energies for the folded and the denatured protein are estimated to differ by several electron volts. For a biomolecule such an energy is significant and may contribute to cold...... denaturing. This is consistent with the empirical observation that cold denaturation is exothermic anti hot denaturation endothermic....

  2. 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

  3. 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.

  4. 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](-).

  5. 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)

  6. 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)

  7. 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...

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Towards bridging the gap from molecular forces to the movement of organisms

    DEFF Research Database (Denmark)

    Nielsen, Bjørn Gilbert

    2004-01-01

    Muscles are responsible for generating the forces required for the movement of multicellular organisms. Microscopically, these forces arise as a consequence of motor proteins (myosin) pulling and sliding along actin filaments. Current knowledge states that the molecular forces between actin...

  13. 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

  14. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

    Science.gov (United States)

    Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from

  15. 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.

  16. Mechanics of nonplanar membranes with force-dipole activity

    DEFF Research Database (Denmark)

    Lomholt, Michael Andersen

    2006-01-01

    A study is made of how active membrane proteins can modify the long wavelength mechanics of fluid membranes. The activity of the proteins is modelled as disturbing the protein surroundings through nonlocal force distributions of which a force-dipole distribution is the simplest example. An analytic...... contributions to mechanical properties such as tension and bending moments become apparent. It is also explained how the activity can induce a hydrodynamic attraction between the active proteins in the membrane....

  17. Relationship of serum levels of interleukin 6, interleukin 8, and C-reactive protein with forced expiratory volume in first second in patients with mustard lung and chronic obstructive pulmonary diseases: systematic review and meta-analysis.

    Science.gov (United States)

    Shahriary, Alireza; Panahi, Yunes; Shirali, Saeed; Rahmani, Hossein

    2017-06-01

    The chronic systemic inflammation is a result of releasing inflammatory cytokines from the cells relating to the body immunity system and chronic activation of the innate immunity system. To evaluate the relationship among serum levels of interleukin 6 (IL-6), interleukin 8 (IL-8), C-reactive protein (CRP) with forced expiratory volume in 1 st s (FEV 1 ) in patients with mustard lung (ML) and chronic obstructive pulmonary diseases (COPD). A published literature search was performed through SID, web of science, ISI, Science Direct, Scopus, Medline, and PubMed databases for articles published in English. The correlation coefficient ( r ) and 95% confidence intervals (95% CIs) were calculated using random or fixed effects models. Heterogeneity was assessed using χ 2 and I 2 statistics. In total, 4 published studies were included in the final analysis. Using the random-effect model, meta-analysis showed that the r was -0.052 (95% CI: -0.14-0.049, p = 0.28) at serum level of IL-8, serum levels of CRP and FEV 1 in these results were r = -0.13, p = 0.012, serum levels of tumor necrosis factor (TNF) and FEV 1 levels were r = -0.39, p = 0.03 in the conducted studies on mustard lung patients. The IL-6 serum level was explored in COPD patients. The results of the given studies in these patients are r = -0.006, 95% CI: -0.37-0.15, and p = 0.44. In this meta-analysis, there was evidence that serum levels of CRP and TNF have been significantly increased in chronic obstructive pulmonary diseases compared to the healthy control group, which signifies the presence of systemic inflammation in ML and COPD patients.

  18. 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.

  19. 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.

  20. Near-threshold deuteron photodisintegration: An indirect determination of the Gerasimov-Drell-Hearn sum rule and forward spin polarizability (γ0) for the deuteron at low energies

    International Nuclear Information System (INIS)

    Ahmed, M. W.; Blackston, M. A.; Perdue, B. A.; Tornow, W.; Weller, H. R.; Norum, B.; Sawatzky, B.; Prior, R. M.; Spraker, M. C.

    2008-01-01

    It is shown that a measurement of the analyzing power obtained with linearly polarized γ-rays and an unpolarized target can provide an indirect determination of two physical quantities. These are the Gerasimov-Drell-Hearn (GDH) sum rule integrand for the deuteron and the sum rule integrand for the forward spin polarizability (γ 0 ) near photodisintegration threshold. An analysis of data for the d(γ-vector,n)p reaction and other experiments is presented. A fit to the world data analyzed in this manner gives a GDH integral value of -603±43μb between the photodisintegration threshold and 6 MeV. This result is the first confirmation of the large contribution of the 1 S 0 (M1) transition predicted for the deuteron near photodisintegration threshold. In addition, a sum rule value of 3.75±0.18 fm 4 for γ 0 is obtained between photodisintegration threshold and 6 MeV. This is a first indirect confirmation of the leading-order effective field theory prediction for the forward spin-polarizability of the deuteron