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Sample records for polarizable protein force

  1. 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.

  2. Quantum Gravitational Force Between Polarizable Objects

    Science.gov (United States)

    Ford, L. H.; Hertzberg, Mark P.; Karouby, J.

    2016-04-01

    Since general relativity is a consistent low energy effective field theory, it is possible to compute quantum corrections to classical forces. Here we compute a quantum correction to the gravitational potential between a pair of polarizable objects. We study two distant bodies and compute a quantum force from their induced quadrupole moments due to two-graviton exchange. The effect is in close analogy to the Casimir-Polder and London-van der Waals forces between a pair of atoms from their induced dipole moments due to two photon exchange. The new effect is computed from the shift in vacuum energy of metric fluctuations due to the polarizability of the objects. We compute the potential energy at arbitrary distances compared to the wavelengths in the system, including the far and near regimes. In the far distance, or retarded, regime, the potential energy takes on a particularly simple form: V (r )=-3987 ℏc G2α1 Sα2 S/(4 π r11) , where α1 S , α2 S are the static gravitational quadrupole polarizabilities of each object. We provide estimates of this effect.

  3. Accounting for electronic polarization in non-polarizable force fields.

    Science.gov (United States)

    Leontyev, Igor; Stuchebrukhov, Alexei

    2011-02-21

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole μ∼ 3D reported in recent ab initio and experimental studies with the value μ(eff)∼ 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value μ(eff) = μ/√ε(el), where ε(el) = 1.78 is the electronic (high-frequency) dielectric constant of water. This simple 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.

  4. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ONAB INITIOTARGET DATA.

    Science.gov (United States)

    Huang, Lei; Roux, Benoît

    2013-08-13

    Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out.

  5. A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

    Science.gov (United States)

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

    2017-12-31

    In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.

  6. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

    Science.gov (United States)

    Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

    2017-04-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars ( d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  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

    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...... shift from vacuum to protein. This is the first computational study of a range of fluorescent proteins using a polarizable embedding potential....... 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. 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.

  9. Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.

    Science.gov (United States)

    Lin, Fang-Yu; MacKerell, Alexander D

    2018-02-13

    The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.

  10. Solvation structure and dynamics of Ni{sup 2+}(aq) from a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Mareš, Jiří, E-mail: jiri.mares@oulu.fi; Vaara, Juha

    2014-10-31

    Highlights: • We parameterize the Ni{sup 2+} ion within the AMOEBA polarizable forcefield. • Besides vdW parameters, we fit also polarizability, Thole damping and charge. • We use an empirical adjustment to account for the transition into condensed phase. • Very good structural and dynamical properties of Ni{sup 2+}(aq) are demonstrated. - Abstract: An aqueous solution of Ni{sup 2+} has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni{sup 2+}(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni{sup 2+} ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H{sub 2}O){sub 6}]{sup 2+} complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni{sup 2+}(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

  11. 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.

  12. Polarizable water model for the coarse-grained MARTINI force field.

    Directory of Open Access Journals (Sweden)

    Semen O Yesylevskyy

    2010-06-01

    Full Text Available Coarse-grained (CG simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.

  13. 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)

  14. 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 2 O 3 and Na 2 O, have been used to simulate the R7T7 industrial nuclear glass (a 30 oxides glass). The inclusion of La 2 O 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 2 O 3 -Na 2 O and SiO 2 -B 2 O 3 -Na 2 O-La 2 O 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

  15. Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atom-centered charge, extra-point and polarizable force fields.

    Science.gov (United States)

    Baucom, Jason; Transue, Thomas; Fuentes-Cabrera, Miguel; Krahn, Joseph; Darden, Thomas; Sagui, Celeste

    2004-03-01

    Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)2 were used to study the relationship between DNA sequence and structure. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field and an ``extra-point" force field (with additional charges on extra-nuclear sites). It is found that in crystal environment all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force fields, however, outperforms the other two, pointing out to the need of the inclusion of polarization for accurate descriptions of DNA.

  16. Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Weimin; Niu, Haitao; Lin, Tong; Wang, Xungai; Kong, Lingxue [Institute for Frontier Materials, Deakin University, Waurn Ponds VIC 3216 (Australia)

    2014-01-28

    The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform external electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.

  17. Two studies of colloidal interactions: electric polarizability and protein crystallization. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fraden, Seth; Hu, Yue

    2001-08-06

    (I)Electric polarizability. During this grant period, the focus was on five topics concerning electric field effects on colloids. The first topic focuses on electric interactions between charged colloids in the absence of external fields, and the remaining four deal with colloids in the presence of external fields. The topics are (1) calculation of the effect of confinement on the pair-potential between like-charged colloids, (2) experimental determination of the interparticle potential under the conditions of dielectric polarization, (3) measurement of the evolution of structure of ER fluids, (4) synthesis of novel colloids designed for ER studies, and (5) computer modeling of polarization of surface charge. (II) Protein crystallization. Studies of the phase behavior of mixtures of proteins and polymers were initiated. The motivation was to test recent theories that suggested that optimal conditions for protein crystallization could be obtained using such mixtures. Combined light scattering measurements of the virial coefficients and determination of the phase diagram of protein/polymer mixtures revealed that the theoretical picture needs to be substantially modified.

  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. 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.

  1. Evaluating excited state atomic polarizabilities of chromophores.

    Science.gov (United States)

    Heid, Esther; Hunt, Patricia A; Schröder, Christian

    2018-03-28

    Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered.

  2. 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

  3. 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

  4. 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

    2017-10-01

    Sodium borosilicate glasses Na2O-B2O3-SiO2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO4 and BO4 (BIV) and triangular BO3 (BIII). One of the salient features of these compounds is the change of the BIII/BIV 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 BIII/BIV with respect to the composition and the temperature.

  5. Electromagnetic polarizabilities of hadrons

    International Nuclear Information System (INIS)

    Friar, J.L.

    1988-01-01

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

  6. Excited States in Solution through Polarizable Embedding

    DEFF Research Database (Denmark)

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

    2010-01-01

    We present theory and implementation of an advanced quantum mechanics/molecular mechanics (QM/MM) approach using a fully self-consistent polarizable embedding (PE) scheme. It is a polarizable layered model designed for effective yet accurate inclusion of an anisotropic medium in a quantum...... a nonequilibrium formulation of the environmental response. In our formulation of polarizable embedding we explicitly take into account the full self-consistent many-body environmental response from both ground and excited states. The PE-DFT method can be applied to any molecular system, e.g., proteins...

  7. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.

    Science.gov (United States)

    Lin, Zhixiong; Bachmann, Stephan J; van Gunsteren, Wilfred F

    2015-03-07

    Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

  8. QM/MM based fitting of atomic polarizabilities for use in condensed-phase biomolecular simulation

    NARCIS (Netherlands)

    Vosmeer, C.R.; Rustenburg, A.S.; Rice, J.E.; Horn, H.W.; Swope, W.C.; Geerke, D.P.

    2012-01-01

    Accounting for electronic polarization effects in biomolecular simulation (by using a polarizable force field) can increase the accuracy of simulation results. However, the use of gas-phase estimates of atomic polarizabilities α

  9. Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model.

    Science.gov (United States)

    Woo Kim, Hyun; Rhee, Young Min

    2012-07-30

    Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. Copyright © 2012 Wiley Periodicals, Inc.

  10. 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

    is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural...

  11. Hydrophobic-hydrophilic forces in protein folding.

    Science.gov (United States)

    Durell, Stewart R; Ben-Naim, Arieh

    2017-08-01

    The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as well as from interactions with the solvent (solvent-induced forces). We present a statistical-mechanical formalism that describes both these direct and indirect, solvent-induced thermodynamic forces on groups of the protein. We focus on 2 kinds of protein groups, commonly referred to as hydrophobic and hydrophilic. Analysis of this result leads to the conclusion that the forces on hydrophilic groups are in general stronger than on hydrophobic groups. This is then tested and verified by a series of molecular dynamics simulations, examining both hydrophobic alkanes of different sizes and hydrophilic moieties represented by polar-neutral hydroxyl groups. The magnitude of the force on assemblies of hydrophilic groups is dependent on their relative orientation: with 2 to 4 times larger forces on groups that are able to form one or more direct hydrogen bonds. © 2017 Wiley Periodicals, Inc.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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......-called PE-CCSDR(3) model. Finally, we utilize the presented method in the description of a full protein by investigating the shift of the intense electronic excitation energy of the photoactive yellow protein due to the surrounding amino acids....

  17. 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....

  18. Radiation damping of a polarizable particle

    Science.gov (United States)

    Novotny, Lukas

    2017-09-01

    A polarizable body moving in an external electromagnetic field will slow down. This effect is referred to as radiation damping and is analogous to Doppler cooling in atomic physics. Using the principles of special relativity we derive an expression for the radiation damping force and find that it solely depends on the scattered power. The cooling of the particle's center-of-mass motion is balanced by heating due to radiation pressure shot noise, giving rise to an equilibrium that depends on the ratio of the field's frequency and the particle's mass. While damping is of relativistic nature, heating has its roots in quantum mechanics.

  19. 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...

  20. Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

    Science.gov (United States)

    Soteras, Ignacio; Curutchet, Carles; Bidon-Chanal, Axel; Dehez, François; Ángyán, János G; Orozco, Modesto; Chipot, Christophe; Luque, F Javier

    2007-11-01

    The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.

  1. Thole's interacting polarizability model in computational chemistry practice

    NARCIS (Netherlands)

    deVries, AH; vanDuijnen, PT; Zijlstra, RWJ; Swart, M

    Thole's interacting polarizability model to calculate molecular polarizabilities from interacting atomic polarizabilities is reviewed and its major applications in computational chemistry are illustrated. The applications include prediction of molecular polarizabilities, use in classical expressions

  2. Gravitational polarizability of black holes

    International Nuclear Information System (INIS)

    Damour, Thibault; Lecian, Orchidea Maria

    2009-01-01

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

  3. Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Cossio, Pilar; Hummer, Gerhard; Szabo, Attila

    2016-08-23

    Ductile materials can absorb spikes in mechanical force, whereas brittle ones fail catastrophically. Here we develop a theory to quantify the kinetic ductility of single molecules from force spectroscopy experiments, relating force-spike resistance to the differential responses of the intact protein and the unfolding transition state to an applied mechanical force. We introduce a class of unistable one-dimensional potential surfaces that encompass previous models as special cases and continuously cover the entire range from ductile to brittle. Compact analytic expressions for force-dependent rates and rupture-force distributions allow us to analyze force-clamp and force-ramp pulling experiments. We find that the force-transmitting protein domains of filamin and titin are kinetically ductile when pulled from their two termini, making them resistant to force spikes. For the mechanostable muscle protein titin, a highly ductile model reconciles data over 10 orders of magnitude in force loading rate from experiment and simulation. Copyright © 2016 Biophysical Society. All rights reserved.

  4. Variation of the electronic dipole polarizability on the reaction path.

    Science.gov (United States)

    Jędrzejewski, Mateusz; Ordon, Piotr; Komorowski, Ludwik

    2013-10-01

    The reaction force and the electronic flux, first proposed by Toro-Labbé et al. (J Phys Chem A 103:4398, 1999) have been expressed by the existing conceptual DFT apparatus. The critical points (extremes) of the chemical potential, global hardness and softness have been identified by means of the existing and computable energy derivatives: the Hellman-Feynman force, nuclear reactivity and nuclear stiffness. Specific role of atoms at the reaction center has been unveiled by indicating an alternative method of calculation of the reaction force and the reaction electronic flux. The electron dipole polarizability on the IRC has been analyzed for the model reaction HF + CO→HCOF. The electron polarizability determined on the IRC α e (ξ) was found to be reasonably parallel to the global softness curve S(ξ). The softest state on the IRC (not TS) coincides with zero electronic flux.

  5. Nonlinearly Additive Forces in Multivalent Ligand Binding to a Single Protein Revealed with Force Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ratto, T V; Rudd, R E; Langry, K C; Balhorn, R L; McElfresh, M W

    2005-07-15

    We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between ConcanavalinA (ConA) and {alpha}-D-mannose, but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 66, and 85 pN, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and non-specific binding. We analyze the binding configuration (i.e. serial versus parallel connections) through fitting the polymer stretching data with modified Worm-Like Chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.

  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. 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

  9. 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.

  10. Pion Polarizability Status Report (2017)

    OpenAIRE

    Moinester, Murray

    2017-01-01

    The electric ${\\alpha}_{\\pi}$ and magnetic $\\beta_{\\pi}$ charged pion Compton polarizabilities are of fundamental interest in the low-energy sector of quantum chromodynamics (QCD).They are directly linked to the phenomenon of spontaneously broken chiral symmetry within QCD and to the dynamics of the pion-photon interaction.The combination (${\\alpha}_{\\pi}-\\beta_{\\pi}$) was measured by:(1) CERN COMPASS via radiative pion Primakoff scattering (Bremsstrahlung) in the nuclear Coulomb field, ${\\pi...

  11. 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....

  12. Nanoscale adhesion forces between enamel pellicle proteins and hydroxyapatite.

    Science.gov (United States)

    Vukosavljevic, D; Hutter, J L; Helmerhorst, E J; Xiao, Y; Custodio, W; Zaidan, F C; Oppenheim, F G; Siqueira, W L

    2014-05-01

    The acquired enamel pellicle (AEP) is important for minimizing the abrasion caused by parafunctional conditions as they occur, for instance, during bruxism. It is a remarkable feature of the AEP that a protein/peptide film can provide enough protection in normofunction to prevent teeth from abrasion and wear. Despite its obvious critical role in the protection of tooth surfaces, the essential adhesion features of AEP proteins on the enamel surface are poorly characterized. The objective of this study was to measure the adhesion force between histatin 5, a primary AEP component, and hydroxyapatite (HA) surfaces. Both biotinylated histatin 5 and biotinylated human serum albumin were allowed to adsorb to streptavidin-coated silica microspheres attached to atomic force microscope (AFM) cantilevers. A multimode AFM with a Nanoscope IIIa controller was used to measure the adhesion force between protein-functionalized silica microspheres attached to cantilever tips and the HA surface. The imaging was performed in tapping mode with a Si3N4 AFM cantilever, while the adhesion forces were measured in AFM contact mode. A collection of force-distance curves (~3,000/replicate) was obtained to generate histograms from which the adhesion forces between histatin 5 or albumin and the HA surface were measured. We found that histatin 5 exhibited stronger adhesion forces (90% >1.830 nN) to the HA surface than did albumin (90% > 0.282 nN). This study presents an objective approach to adhesion force measurements between histatin 5 and HA, and provides the experimental basis for measuring the same parameters for other AEP constituents. Such knowledge will help in the design of synthetic proteins and peptides with preventive and therapeutic benefits for tooth enamel.

  13. Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field

    Science.gov (United States)

    Jing, Zhifeng; Qi, Rui; Liu, Chengwen; Ren, Pengyu

    2017-10-01

    The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

  14. 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

  15. 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 ...

  16. Sampling Protein Form and Function with the Atomic Force Microscope

    NARCIS (Netherlands)

    Baclayon, Marian; Roos, Wouter H.; Wuite, Gijs J. L.

    To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e. g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe

  17. RNA force field with accuracy comparable to state-of-the-art protein force fields.

    Science.gov (United States)

    Tan, Dazhi; Piana, Stefano; Dirks, Robert M; Shaw, David E

    2018-02-13

    Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models ("force fields") available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, we introduce an extensive revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures. We evaluate these revised parameters through long-timescale MD simulations of a set of RNA molecules that covers a wide range of structural complexity, including single-stranded RNAs, RNA duplexes, RNA hairpins, and riboswitches. The structural and thermodynamic properties measured in these simulations exhibited dramatically improved agreement with experimentally determined values. Based on the comparisons we performed, this RNA force field appears to achieve a level of accuracy comparable to that of state-of-the-art protein force fields, thus significantly advancing the utility of MD simulation as a tool for elucidating the structural dynamics and function of RNA molecules and RNA-containing biological assemblies. Copyright © 2018 the Author(s). Published by PNAS.

  18. Classification of Simple Oxides: A Polarizability Approach

    Science.gov (United States)

    Dimitrov, Vesselin; Komatsu, Takayuki

    2002-01-01

    A simple oxide classification has been proposed on the basis of correlation between electronic polarizabilities of the ions and their binding energies determined by XPS. Three groups of oxides have been considered taking into account the values obtained on refractive-index- or energy-gap-based oxide ion polarizability, cation polarizability, optical basicity, O 1s binding energy, metal (or nonmetal) binding energy, and Yamashita-Kurosawa's interaction parameter of the oxides. The group of semicovalent predominantly acidic oxides includes BeO, B2O3, P2O5, SiO2, Al2O3, GeO2, and Ga2O3 with low oxide ion polarizability, high O 1s binding energy, low cation polarizability, high metal (or nonmetal) outermost binding energy, comparatively low optical basicity, and strong interionic interaction, leading to the formation of strong covalent bonds. Some main group oxides so-called ionic or basic such as CaO, In2O3, SnO2, and TeO2 and most transition metal oxides show relatively high oxide ion polarizability, O 1s binding energy in a very narrow medium range, high cation polarizability, and low metal (or nonmetal) binding energy. Their optical basicity varies in a narrow range and it is close to that of CaO. The group of very ionic or very basic oxides includes CdO, SrO, and BaO as well as PbO, Sb2O3, and Bi2O3, which possess very high oxide ion polarizability, low O 1s binding energy, very high cation polarizability, and very low metal (or nonmetal) binding energy. Their optical basicity is higher than that of CaO and the interionic interaction is very weak, giving rise to the formation of very ionic chemical bonds.

  19. Force microscopy imaging of individual protein molecules with sub-pico Newton force sensitivity.

    Science.gov (United States)

    Patil, Shivprasad; Martinez, Nicolas F; Lozano, Jose R; Garcia, Ricardo

    2007-01-01

    The capability of atomic force microscopes (AFM) to generate atomic or nanoscale resolution images of surfaces has deeply transformed the study of materials. However, high resolution imaging of biological systems has proved more difficult than obtaining atomic resolution images of crystalline surfaces. In many cases, the forces exerted by the tip on the molecules (1-10 nN) either displace them laterally or break the noncovalent bonds that hold the biomolecules together. Here, we apply a force microscope concept based on the simultaneous excitation of the first two flexural modes of the cantilever. The coupling of the modes generated by the tip-molecule forces enables imaging under the application of forces ( approximately 35 pN) which are smaller than those needed to break noncovalent bonds. With this instrument we have resolved the intramolecular structure of antibodies in monomer and pentameric forms. Furthermore, the instrument has a force sensitivity of 0.2 pN which enables the identification of compositional changes along the protein fragments. Copyright (c) 2007 John Wiley & Sons, Ltd.

  20. Single Protein Molecule Mapping with Magnetic Atomic Force Microscopy

    Science.gov (United States)

    Moskalenko, Andriy V.; Yarova, Polina L.; Gordeev, Sergey N.; Smirnov, Sergey V.

    2010-01-01

    Abstract Understanding the structural organization and distribution of proteins in biological cells is of fundamental importance in biomedical research. The use of conventional fluorescent microscopy for this purpose is limited due to its relatively low spatial resolution compared to the size of a single protein molecule. Atomic force microscopy (AFM), on the other hand, allows one to achieve single-protein resolution by scanning the cell surface using a specialized ligand-coated AFM tip. However, because this method relies on short-range interactions, it is limited to the detection of binding sites that are directly accessible to the AFM tip. We developed a method based on magnetic (long-range) interactions and applied it to investigate the structural organization and distribution of endothelin receptors on the surface of smooth muscle cells. Endothelin receptors were labeled with 50-nm superparamagnetic microbeads and then imaged with magnetic AFM. Considering its high spatial resolution and ability to “see” magnetically labeled proteins at a distance of up to 150 nm, this approach may become an important tool for investigating the dynamics of individual proteins both on the cell membrane and in the submembrane space. PMID:20141762

  1. Molecular dynamics simulations of nonpolarizable inorganic salt solution interfaces: NaCl, NaBr, and NaI in transferable intermolecular potential 4-point with charge dependent polarizability (TIP4P-QDP) water

    Science.gov (United States)

    Bauer, Brad A.; Patel, Sandeep

    2010-01-01

    We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water [B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 (2009)]; this water model accommodates increased solvent polarizability (relative to the condensed phase) in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration (TI) and appropriate energy corrections. Density profiles of Cl-, Br-, and I- exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions (independent of their interactions with solvent), we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase {1.31 Å3 for TIP4P-QDP versus 1.1 Å3 (TIP4P-FQ) and 0.87 Å3 (POL3) [Ponder and Case, Adv. Protein Chem. 66, 27 (2003)]} based on ab initio

  2. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation.

    Science.gov (United States)

    Caprasecca, Stefano; Jurinovich, Sandro; Viani, Lucas; Curutchet, Carles; Mennucci, Benedetta

    2014-04-08

    We present the mathematical derivation and the computational implementation of the analytical geometry derivatives for a polarizable QM/MM model (QM/MMPol). In the adopted QM/MMPol model, the focused part is treated at QM level of theory, while the remaining part (the environment) is described classically as a set of fixed charges and induced dipoles. The implementation is performed within the ONIOM procedure, resulting in a polarizable embedding scheme, which can be applied to solvated and embedded systems and combined with different polarizable force fields available in the literature. Two test cases characterized by strong hydrogen-bond and dipole-dipole interactions, respectively, are used to validate the method with respect to the nonpolarizable one. Finally, an application to geometry optimization of the chromophore of Rhodopsin is presented to investigate the impact of including mutual polarization between the QM and the classical parts in conjugated systems.

  3. 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.

  4. Measurement of the pion polarizabilities at COMPASS

    CERN Document Server

    Guskov, A V

    2006-01-01

    The electromagnetic structure of pions is probed in $\\pi\\gamma$ Compton scattering in inverse kinematics (Primakoff effect) and described by the electric ($\\alpha_{\\pi}$) and 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 theoretically predicted (under approximation of unstructured pion) cross section of Primakoff scattering and the measured cross section. The high beam intensity, good spectrometer resolution, the high rate capability, the high acceptance and possibility to use pion and muon beams, that are unique to the COMPASS experiment provide the tools to measure precisely the pion polarizabilities in the $\\pi^{-} + (A,Z)\\rightarrow\\pi^{-} + (A,Z) + \\gamma$ Primakoff reaction. This cross section is related to the cross section of Compton scattering on pion. A precise tracking system, electromagnetic and hadron calorimeters provide good conditions for...

  5. 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......). In the PDE-CC method, the smaller, but chemically important core region is described with a high-level CC method. The environment surrounding the core region can be separated into two levels of description: an inner and an outer region. The effect of the inner region on the core region is described......We present the theory and implementation of the polarizable density embedding (PDE) model in combination with coupled cluster (CC) theory (PDE-CC). This model has been implemented in the Dalton quantum chemistry program by adapting the CC code to the polarizable embedding library (PElib...

  6. 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.

  7. Parallelization of the polarizable embedding scheme for higher-order response functions

    Science.gov (United States)

    Hykkerud Steindal, Arnfinn; Magnus Haugaard Olsen, Jógvan; Frediani, Luca; Kongsted, Jacob; Ruud, Kenneth

    2012-10-01

    We present a parallel implementation of the Polarizable Embedding (PE) method, an advanced quantum mechanics/molecular mechanics (QM/MM) approach, for Hartree-Fock (PE-HF) and density functional theory (PE-DFT). The parallelization includes calculations of energies and linear, quadratic, and cubic response functions. The couplings to the QM system due to the polarizable embedding potential have been implemented using a master/slave approach. The implementation shows good scaling behaviour, demonstrated through calculations on a small (a water molecule in a bulk of water molecules) and a larger system (Green Fluorescent Protein (GFP)).

  8. 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).

  9. 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

  10. Analyzing Forced Unfolding of Protein Tandems by Ordered Variates, 2: Dependent Unfolding Times

    Science.gov (United States)

    Bura, E.; Klimov, D. K.; Barsegov, V.

    2008-01-01

    Statistical analyses of forced unfolding data for protein tandems, i.e., unfolding forces (force-ramp) and unfolding times (force-clamp), used in single-molecule dynamic force spectroscopy rely on the assumption that the unfolding transitions of individual protein domains are independent (uncorrelated) and characterized, respectively, by identically distributed unfolding forces and unfolding times. In our previous work, we showed that in the experimentally accessible piconewton force range, this assumption, which holds at a lower constant force, may break at an elevated force level, i.e., the unfolding transitions may become correlated when force is increased. In this work, we develop much needed statistical tests for assessing the independence of the unobserved forced unfolding times for individual protein domains in the tandem and equality of their parent distributions, which are based solely on the observed ordered unfolding times. The use and performance of these tests are illustrated through the analysis of unfolding times for computer models of protein tandems. The proposed tests can be used in force-clamp atomic force microscopy experiments to obtain accurate information on protein forced unfolding and to probe data on the presence of interdomain interactions. The order statistics-based formalism is extended to cover the analysis of correlated unfolding transitions. The use of order statistics leads naturally to the development of new kinetic models, which describe the probabilities of ordered unfolding transitions rather than the populations of chemical species. PMID:18065466

  11. Enhancement of polarizabilities of cylinders with cylinder-slab resonances.

    Science.gov (United States)

    Xiao, Meng; Huang, Xueqin; Liu, H; Chan, C T

    2015-02-02

    If an object is very small in size compared with the wavelength of light, it does not scatter light efficiently. It is hence difficult to detect a very small object with light. We show using analytic theory as well as full wave numerical calculation that the effective polarizability of a small cylinder can be greatly enhanced by coupling it with a superlens type metamaterial slab. This kind of enhancement is not due to the individual resonance effect of the metamaterial slab, nor due to that of the object, but is caused by a collective resonant mode between the cylinder and the slab. We show that this type of particle-slab resonance which makes a small two-dimensional object much "brighter" is actually closely related to the reverse effect known in the literature as "cloaking by anomalous resonance" which can make a small cylinder undetectable. We also show that the enhancement of polarizability can lead to strongly enhanced electromagnetic forces that can be attractive or repulsive, depending on the material properties of the cylinder.

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

    Science.gov (United States)

    Laury, Marie L; Wang, Lee-Ping; Pande, Vijay S; Head-Gordon, Teresa; Ponder, Jay W

    2015-07-23

    A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental 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 AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second 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 2-20 water molecules, the AMOEBA14 model yields results similar to 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.

  13. 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.

  14. Characterization of Hepatitis C Virus Core Protein Dimerization by Atomic Force Microscopy.

    Science.gov (United States)

    Li, Wenhui; Kou, Xiaolong; Xu, Jiachao; Zhou, Wei; Zhao, Rong; Zhang, Zhen; Fang, Xiaohong

    2018-03-14

    Dimerization of core protein is a crucial step in the formation of the hepatitis C virus (HCV) nucleocapsid, and inhibition of dimer formation is regarded as an attractive approach to design anti-HCV drugs. In this work, we developed the atomic force microscopy based single molecular force spectroscopy (AFM-SMFS) method for the characterization of core protein dimerization with the advantages of small amount of sample consumption and no need of labeling. Interaction force of the core protein with its antibody or aptamer was analyzed to investigate its stoichiometry and binding property. The two specific binding forces were detected due to the probing of dimeric and monomeric core protein, respectively. Moreover, the binding property of protein dimer was different from the monomer. Our work offers a new approach to study the dimerization of core protein, as well as other proteins, and to screen the HCV candidate inhibitors.

  15. Axial polarizability and weak currents in nuclei

    International Nuclear Information System (INIS)

    Ericson, M.

    1977-01-01

    The weak interaction nucleonic coupling constants in nuclei are modified by the presence of the neighbouring nucleons. One type of modification is due to the virtual excitation of the isobars through meson exchange. The influence of the isobars is described by means of the nuclear axial polarizability coefficient. This polarizability is known; it is linked to the p-wave πN scattering volume. A relation is derived between the axial nuclear current and the pion field which incorporates the polarizability effects. This relation has an electromagnetic analogue. It is then possible to derive the axial and pseudoscalar coupling constants from a knowledge of the pion field. This field in turn obeys a Klein-Gordon equation which has to include the isobaric excitations. The propagation of the pion field is similar to that of an electromagnetic wave in a dielectric medium. The strong interaction coupling constant is shown to be renormalized in nuclei by the effect of the various types of correlations. (author)

  16. A Biochemical Study of Noncovalent Forces in Proteins Using Phycocyanin from Spirulina

    Science.gov (United States)

    Heller, Barbara A.; Gindt, Yvonne M.

    2000-11-01

    Protein tertiary structure is maintained by noncovalent forces. These forces are disrupted by simple environmental changes (increasing temperature, pH, or adding denaturants) but are not always simple to observe. This experiment, suitable for all levels of undergraduate biochemistry laboratories, uses absorption spectroscopy to monitor the denaturation of a pigmented protein. The protein, phycocyanin, contains a covalently attached pigment whose visible spectrum is sensitive to changes in protein environment. The experiment can be done in one or two 3-hour lab periods. The first session isolates the protein from cyanobacteria capsules and the second session studies the denaturation of the protein.

  17. 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

  18. 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

  19. Radiative corrections for pion polarizability experiments

    International Nuclear Information System (INIS)

    Akhundov, A.A.; Gerzon, S.; Kananov, S.; Moinester, M.A.

    1994-08-01

    We use the semi-analytical program RCFORGV to evaluate radiative corrections to one-photon radiative emission in the high-energy scattering of pions in the Coulomb field of a nucleus with atomic number Z. It is shown that radiative corrections can simulate a pion polarizability effect. The average effect is α rc π =-β rc π =(0.20±0.05) x 10 -43 cm 3 , for pion energies 40-600 GeV. We also study the range of applicability of the equivalent photon approximation in describing one-photon radiative emission. (author). 21 refs, 6 figs, 1 tab

  20. Relativistic corrections to molecular dynamic dipole polarizabilities

    DEFF Research Database (Denmark)

    Kirpekar, Sheela; Oddershede, Jens; Jensen, Hans Jørgen Aagaard

    1995-01-01

    in the correlated calculations, as has also been observed for other properties. For SnH4 the correlation contribution and the pure relativistic correction are of the same order of magnitude, whereas for PbH 4 the relativistic correction becomes more important than the correlation contribution. We report estimated...... Cauchy moments, obtained from fitting the dispersion of the calculated corrections as a function of ω2. The frequency dependence of the nonrelativistic polarizability is most pronounced at the correlated level, mainly due to lower excitation energies in the multiconfigurational calculations than those...

  1. 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.

  2. 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...

  3. 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

  4. Force

    CERN Document Server

    Graybill, George

    2007-01-01

    Forces are at work all around us. Discover what a force is, and different kinds of forces that work on contact and at a distance. We use simple language and vocabulary to make this invisible world easy for students to ""see"" and understand. Examine how forces ""add up"" to create the total force on an object, and reinforce concepts and extend learning with sample problems.

  5. 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.

  6. 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.

  7. The MARTINI coarse-grained force field : Extension to proteins

    NARCIS (Netherlands)

    Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier; Larson, Ronald G.; Tieleman, D. Peter; Marrink, Siewert-Jan

    Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on

  8. Ion specific protein assembly and hydrophobic surface forces

    Czech Academy of Sciences Publication Activity Database

    Lund, Mikael; Jungwirth, Pavel; Woodward, C. E.

    2008-01-01

    Roč. 100, č. 25 (2008), 258105/1-258105/4 ISSN 0031-9007 R&D Projects: GA MŠk LC512; GA ČR GA203/07/1006 Institutional research plan: CEZ:AV0Z40550506 Keywords : lysozyme * water * protein association Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.180, year: 2008

  9. Evolution of the potential energy landscape with static pulling force for two model proteins.

    Science.gov (United States)

    Wales, David J; Head-Gordon, Teresa

    2012-07-26

    The energy landscape is analyzed for off-lattice bead models of protein L and protein G as a function of a static pulling force. Two different pairs of attachment points (pulling directions) are compared in each case, namely, residues 1/56 and 10/32. For the terminal residue pulling direction 1/56, the distinct global minimum structures are all extended, aside from the compact geometry that correlates with zero force. The helical turns finally disappear at the highest pulling forces considered. For the 10/32 pulling direction, the changes are more complicated, with a variety of competing arrangements for beads outside the region where the force is directly applied. These alternatives produce frustrated energy landscapes, with low-lying minima separated by high barriers. The calculated folding pathways in the absence of force are in good agreement with previous work. The N-terminal hairpin folds first for protein L and the C-terminal hairpin for protein G, which exhibits an intermediate. However, for a relatively low static force, where the global minimum retains its structure, the folding mechanisms change, sometimes dramatically, depending on the protein and the attachment points. The scaling relations predicted by catastrophe theory are found to hold in the limit of short path lengths.

  10. Analyzing Forced Unfolding of Protein Tandems by Ordered Variates, 1: Independent Unfolding Times

    Science.gov (United States)

    Bura, E.; Klimov, D. K.; Barsegov, V.

    2007-01-01

    Most of the mechanically active proteins are organized into tandems of identical repeats, (D)N, or heterogeneous tandems, D1–D2–…–DN. In current atomic force microscopy experiments, conformational transitions of protein tandems can be accessed by employing constant stretching force f (force-clamp) and by analyzing the recorded unfolding times of individual domains. Analysis of unfolding data for homogeneous tandems relies on the assumption that unfolding times are independent and identically distributed, and involves inference of the (parent) probability density of unfolding times from the histogram of the combined unfolding times. This procedure cannot be used to describe tandems characterized by interdomain interactions, or heteregoneous tandems. In this article, we introduce an alternative approach that is based on recognizing that the observed data are ordered, i.e., first, second, third, etc., unfolding times. The approach is exemplified through the analysis of unfolding times for a computer model of the homogeneous and heterogeneous tandems, subjected to constant force. We show that, in the experimentally accessible range of stretching forces, the independent and identically distributed assumption may not hold. Specifically, the uncorrelated unfolding transitions of individual domains at lower force may become correlated (dependent) at elevated force levels. The proposed formalism can be used in atomic force microscopy experiments to infer the unfolding time distributions of individual domains from experimental histograms of ordered unfolding times, and it can be extended to analyzing protein tandems that exhibit interdomain interactions. PMID:17496033

  11. Direct observation of bunching of elementary steps on protein crystals under forced flow conditions

    Directory of Open Access Journals (Sweden)

    Gen Sazaki

    2015-07-01

    Full Text Available Bunching of elementary steps by solution flow is still not yet clarified for protein crystals. Hence, in this study, we observed elementary steps on crystal surfaces of model protein hen egg-white lysozyme (HEWL under forced flow conditions, by our advanced optical microscopy. We found that in the case of a HEWL solution of 99.99% purity, forced flow changed bunched steps into elementary ones (debunching on tetragonal HEWL crystals. In contrast, in the case of a HEWL solution of 98.5% purity, forced flow significantly induced bunching of elementary steps. These results indicate that in the case of HEWL crystals, the mass transfer of impurities is more significantly enhanced by forced solution flow than that of solute HEWL molecules. We also showed that forced flow induced the incorporation of microcrystals into a mother crystal and the subsequent formation of screw dislocations and spiral growth hillocks.

  12. 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

  13. 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.

  14. Electrostatic assembly of protein lysozyme on DNA visualized by atomic force microscopy

    International Nuclear Information System (INIS)

    Yang Tao; Wei Gang; Li Zhuang

    2007-01-01

    In the present work, atomic force microscopy (AFM) has been used to study the assembly of protein lysozyme on DNA molecule. Based on the electrostatic interaction, the positively charged lysozyme can easily bind onto the negatively charged DNA molecule surface. The protein molecules appear as globular objects on the DNA scaffold, which are distinguishable in the AFM images. At the same time, lysozyme molecules can be assembled onto DNA as dense or sporadic pattern by varying the protein concentration. This work may provide fundamental aspects for building protein nanostructures and studying of DNA-protein interaction

  15. 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.

  16. Interfacial Structural Transition in Hydration Shells of a Polarizable Solute.

    Science.gov (United States)

    Dinpajooh, Mohammadhasan; Matyushov, Dmitry V

    2015-05-22

    Electrostatics of polar solvation is typically described by harmonic free energy functionals. Polarizability contributes a negative polarization term that can make the harmonic free energy negative. The harmonic truncation fails in this regime. Simulations of polarizable ideal dipoles in water show that water's susceptibility passes through a maximum in the range of polarizabilities zeroing the harmonic term out. The microscopic origin of the nonmonotonic behavior is an interfacial structural transition involving the density collapse of the first hydration layer and enhanced number of dangling OH bonds.

  17. 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

  18. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  19. 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).

  20. 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

  1. 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.

  2. Colloid-probe AFM studies of the interaction forces of proteins adsorbed on colloidal crystals.

    Science.gov (United States)

    Singh, Gurvinder; Bremmell, Kristen E; Griesser, Hans J; Kingshott, Peter

    2015-04-28

    In recent years, colloid-probe AFM has been used to measure the direct interaction forces between colloidal particles of different size or surface functionality in aqueous media, as one can study different forces in symmerical systems (i.e., sphere-sphere geometry). The present study investigates the interaction between protein coatings on colloid probes and hydrophilic surfaces decorated with hexagonally close packed single particle layers that are either uncoated or coated with proteins. Controlled solvent evaporation from aqueous suspensions of colloidal particles (coated with or without lysozyme and albumin) produces single layers of close-packed colloidal crystals over large areas on a solid support. The measurements have been carried out in an aqueous medium at different salt concentrations and pH values. The results show changes in the interaction forces as the surface charge of the unmodified or modified particles, and ionic strength or pH of the solution is altered. At high ionic strength or pH, electrostatic interactions are screened, and a strong repulsive force at short separation below 5 nm dominates, suggesting structural changes in the absorbed protein layer on the particles. We also study the force of adhesion, which decreases with an increment in the salt concentration, and the interaction between two different proteins indicating a repulsive interaction on approach and adhesion on retraction.

  3. Protein-DNA docking with a coarse-grained force field

    Directory of Open Access Journals (Sweden)

    Setny Piotr

    2012-09-01

    Full Text Available Abstract Background Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming an increasingly important tool in the field of macromolecular assemblies, complementing particularly demanding protein-nucleic acids X ray crystallography and providing means for the refinement and integration of low resolution data coming from rapidly advancing methods such as cryoelectron microscopy. Results We present a new coarse-grained force field suitable for protein-DNA docking. The force field is an extension of previously developed parameter sets for protein-RNA and protein-protein interactions. The docking is based on potential energy minimization in translational and orientational degrees of freedom of the binding partners. It allows for fast and efficient systematic search for native-like complex geometry without any prior knowledge regarding binding site location. Conclusions We find that the force field gives very good results for bound docking. The quality of predictions in the case of unbound docking varies, depending on the level of structural deviation from bound geometries. We analyze the role of specific protein-DNA interactions on force field performance, both with respect to complex structure prediction, and the reproduction of experimental binding affinities. We find that such direct, specific interactions only partially contribute to protein-DNA recognition, indicating an important role of shape complementarity and sequence-dependent DNA internal energy, in line with the concept of indirect protein-DNA readout mechanism.

  4. High-resolution atomic force microscopy and spectroscopy of native membrane proteins

    Science.gov (United States)

    Bippes, Christian A.; Muller, Daniel J.

    2011-08-01

    Membranes confining cells and cellular compartments are essential for life. Membrane proteins are molecular machines that equip cell membranes with highly sophisticated functionality. Examples of such functions are signaling, ion pumping, energy conversion, molecular transport, specific ligand binding, cell adhesion and protein trafficking. However, it is not well understood how most membrane proteins work and how the living cell regulates their function. We review how atomic force microscopy (AFM) can be applied for structural and functional investigations of native membrane proteins. High-resolution time-lapse AFM imaging records membrane proteins at work, their oligomeric state and their dynamic assembly. The AFM stylus resembles a multifunctional toolbox that allows the measurement of several chemical and physical parameters at the nanoscale. In the single-molecule force spectroscopy (SMFS) mode, AFM quantifies and localizes interactions in membrane proteins that stabilize their folding and modulate their functional state. Dynamic SMFS discloses fascinating insights into the free energy landscape of membrane proteins. Single-cell force spectroscopy quantifies the interactions of live cells with their environment to single-receptor resolution. In the future, technological progress in AFM-based approaches will enable us to study the physical nature of biological interactions in more detail and decipher how cells control basic processes.

  5. On the use of pseudostates to calculate molecular polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Marc; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower St, London WC1E 6BT (United Kingdom)

    2010-02-28

    The polarizability of a molecule is an intrinsic property which is important for a large variety of problems. However, determining reliable values for these polarizabilities is not straightforward: for instance the standard sum over states formulation of the problem does not converge because of the need to include not only many excited states but also to allow for contributions from the continuum. Here a formulation of this technique is given which uses pseudostates to allow for physical and continuum states otherwise omitted from the expansion. The pseudostates are represented by even-tempered expansions of Gaussian-type orbitals at the molecular centre-of-mass. The method is tested for LiH, Li{sub 2}, water and CO molecules. For LiH and CO, calculations for the polarizability of low-lying excited states are presented including that for the A {sup 3}PI state of CO, whose polarizability appears not to have been previously determined. It is suggested that the use of pseudostates provides a straightforward method of calculating static polarizabilities of molecules in both ground and excited electronic states. The extension of the method to the calculation of dynamic polarizabilities is discussed.

  6. Effect of the deuteron anisotropy: longitudinal and transverse components of the electric dipole polarizability

    International Nuclear Information System (INIS)

    Kharchenko, A.V.

    1997-01-01

    The anisotropy effect of the electric polarization (stretching) of the deuteron in the Coulomb field, caused by the tensor character of the nuclear force, is investigated. The values of the longitudinal (with the major axis, or the spin of the deuteron, directed along the electric field), and transverse components of the deuteron electric dipole polarizability that correspond to the low-energy n-p data, are predicted to be α parallel =0.669 fm 3 and α perpendicular to =0.555 fm 3 (the potential YYm). The values of the major and minor semi-axes of the deuteron are calculated. (orig.)

  7. Effects of long-range electrostatic forces on simulated protein folding kinetics.

    Science.gov (United States)

    Robertson, Alex; Luttmann, Edgar; Pande, Vijay S

    2008-04-15

    Molecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle-mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics. We quantitatively compare different methods by a correlation of quantitative measures of protein folding kinetics. The results of these comparisons show that for protein folding kinetics, the RF algorithm can quantitatively reproduce the kinetics of the more costly PME algorithm. These results not only assist the selection of appropriate algorithms for future simulations, but also give insight on the role that long-range electrostatic forces have in protein folding. (c) 2007 Wiley Periodicals, Inc.

  8. Influence of self-consistent screening and polarizability contractions on interlayer sliding behavior of hexagonal boron nitride

    Science.gov (United States)

    Gong, Wenbin; Zhang, Wei; Wang, Chengbin; Yao, Yagang; Lu, Weibang

    2017-11-01

    The interlayer sliding behaviors of hexagonal boron nitride (h -BN) were investigated via a density functional theory approach with dispersion interaction included. It was found that the self-consistent screening effect (SCS) and the polarizability contractions had significant influences on London dispersion forces, which are responsible for not only the stacking modes but also for the sliding behaviors of h -BN. In consideration of the ionic characteristics of h -BN, surprisingly, the calculated dispersion force was found to dominate the electrostatic interaction along a minimum-energy sliding pathway and make a pronounced contribution (˜35 %) to the barrier during the constrained sliding. This study demonstrates that the SCS and polarizability contractions play important roles in the sliding behaviors of h -BN and that the long-range dispersion interaction should be carefully treated, even in systems with ionic characteristics.

  9. Event horizons in the Polarizable Vacuum Model

    CERN Document Server

    Desiato, J T

    2003-01-01

    The Polarizable Vacuum (PV) Model representation of General Relativity (GR) is used to show that an in-falling particle of matter will reach the central mass object in a finite amount of proper time, as measured along the world line of the particle, when using the PV Metric. It is shown that the in-falling particle passes through an event horizon, analogous to that found in the Schwarzschild solution of GR. Once it passes through this horizon, any light signal emitted outward by the in-falling particle will be moving slower than the in-falling particle, due to the reduced speed of light in this region. Therefore the signal can never escape this horizon. However, the light emitted by a stationary object below the horizon is exponentially red-shifted and can escape along the null geodesics, as was originally predicted by the PV Model. A static, non-rotating charge distribution is added to the central mass and the PV equivalent to the Reissner-Nordstrom metric is derived. It is illustrated that the dipole moment...

  10. Direct Visualization of Dynamic Protein-DNA Interactions with a Dedicated Atomic Force Microscope

    NARCIS (Netherlands)

    van Noort, S.J.T.; van der Werf, Kees; Eker, Andre P.M.; Wyman, Claire; de Grooth, B.G.; van Hulst, N.F.; Greve, Jan

    1998-01-01

    Photolyase DNA interactions and the annealing of restriction fragment ends are directly visualized with the atomic force microscope (AFM). To be able to interact with proteins, DNA must be loosely bound to the surface. When MgCl2 is used to immobilize DNA to mica, DNA is attached to the surface at

  11. 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.

  12. 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

  13. 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.

  14. Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein.

    Science.gov (United States)

    Jagannathan, Bharat; Elms, Phillip J; Bustamante, Carlos; Marqusee, Susan

    2012-10-30

    Many biological processes generate force, and proteins have evolved to resist and respond to tension along different force axes. Single-molecule force spectroscopy allows for molecular insight into the behavior of proteins under force and the mechanism of protein folding in general. Here, we have used src SH3 to investigate the effect of different pulling axes under the low-force regime afforded by an optical trap. We find that this small cooperatively folded protein shows an anisotropic response to force; the protein is more mechanically resistant to force applied along a longitudinal axis compared to force applied perpendicular to the terminal β strand. In the longitudinal axis, we observe an unusual biphasic behavior revealing a force-induced switch in the unfolding mechanism suggesting the existence of two parallel unfolding pathways. A site-specific variant can selectively affect one of these pathways. Thus, even this simple two-state protein demonstrates a complex mechanical unfolding trajectory, accessing multiple unfolding pathways under the low-force regime of the optical trap; the specific unfolding pathway depends on the perturbation axis and the applied force.

  15. 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.

  16. 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.

  17. Polarizable Embedding Based on Multiconfigurational Methods: Current Developments and the Road Ahead

    DEFF Research Database (Denmark)

    Hedegård, Erik D.; Jensen, H. J. A.; Kongsted, J.

    2014-01-01

    This perspective gives a brief overview of recent developments within the polarizable embedding (PE) method - a multiscale approach developed over the last years. In particular, we are concerned with a recent coupling of the PE method to a multiconfiguration self-consistent field (MCSCF) code......-srDFT). A short discussion of CAS active spaces is also given. A few sample results using a retinal chromophore surrounded by a protein environment illustrate both the importance of the choice of active space and the importance of dynamical correlation. (C) 2014 Wiley Periodicals, Inc....

  18. 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.

  19. 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

  20. Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.

    Science.gov (United States)

    Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong

    2011-03-31

    In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1-2 (bonded) and 1-3 (separated by two bonds) interactions are turned off, 1-4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 Å(3). When the short-range 1-2, 1-3, and full 1-4 terms are taken into account (set D models), the APE ranges from 1.30 to 1.58% for the three Thole models, whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å(3) for the three Thole models, compared with 0.446 Å(3) for the Applequist model. Further assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy.

  1. 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.

  2. Dipole (hyper)polarizabilities of neutral silver clusters

    Science.gov (United States)

    Jorge, Francisco E.; de Macedo, Luiz G. M.

    2016-12-01

    At the Douglas-Kroll-Hess (DKH) level, the B3PW91 functional along with the all-electron relativistic basis sets of valence triple and quadruple zeta qualities are used to determine the structure, stability, and electronic properties of the small silver clusters (Agn, n ⩽ 7). The results presented in this study are in good agreement with the experimental data and theoretical values obtained at a higher level of theory from the literature. Static polarizability and hyperpolarizability are also reported. It is verified that the mean dipole polarizability per atom exhibits an odd-even oscillation and that the polarizability anisotropy is directly related to the cluster shape. In this article, the first study of hyperpolarizabilities of small silver clusters is presented. Except for the monomer, the second hyperpolarizabilities of the silver clusters are significantly larger than those of the copper clusters. Project supported by CNPq, CAPES, and FAPES (Brazilian Agencies).

  3. Direct visualization of ligand-protein interactions using atomic force microscopy

    OpenAIRE

    Neish, Calum S; Martin, Ian L; Henderson, Robert M; Edwardson, J Michael

    2002-01-01

    Streptavidin is a 60-kDa tetramer which binds four molecules of biotin with extremely high affinity (KA∼1014 M−1). We have used atomic force microscopy (AFM) to visualize this ligand-protein interaction directly.Biotin was tagged with a short (152-basepair; 50-nm) DNA rod and incubated with streptavidin. The resulting complexes were then imaged by AFM. The molecular volume of streptavidin calculated from the dimensions of the protein particles (105±3 nm3) was in close agreement with the value...

  4. Forced protein unfolding leads to highly elastic and tough protein hydrogels

    Science.gov (United States)

    Fang, Jie; Mehlich, Alexander; Koga, Nobuyasu; Huang, Jiqing; Koga, Rie; Gao, Xiaoye; Hu, Chunguang; Jin, Chi; Rief, Matthias; Kast, Juergen; Baker, David; Li, Hongbin

    2013-12-01

    Protein-based hydrogels usually do not exhibit high stretchability or toughness, significantly limiting the scope of their potential biomedical applications. Here we report the engineering of a chemically cross-linked, highly elastic and tough protein hydrogel using a mechanically extremely labile, de novo-designed protein that assumes the classical ferredoxin-like fold structure. Due to the low mechanical stability of the ferredoxin-like fold structure, swelling of hydrogels causes a significant fraction of the folded domains to unfold. Subsequent collapse and aggregation of unfolded ferredoxin-like domains leads to intertwining of physically and chemically cross-linked networks, entailing hydrogels with unusual physical and mechanical properties: a negative swelling ratio, high stretchability and toughness. These hydrogels can withstand an average strain of 450% before breaking and show massive energy dissipation. Upon relaxation, refolding of the ferredoxin-like domains enables the hydrogel to recover its massive hysteresis. This novel biomaterial may expand the scope of hydrogel applications in tissue engineering.

  5. 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...

  6. 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.

  7. Gaussian-Charge Polarizable and Nonpolarizable Models for CO2.

    Science.gov (United States)

    Jiang, Hao; Moultos, Othonas A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2016-02-11

    A polarizable intermolecular potential model using three classical Drude oscillators on the atomic sites has been developed for CO2. The model is rigid with bond lengths and molecular geometries set to their experimental values. Electrostatic interactions are represented by three Gaussian charges connected to the molecular frame by harmonic springs. Nonelectrostatic interactions are represented by the Buckingham exponential-6 potential, with potential parameters optimized to vapor-liquid equilibria (VLE) data. A nonpolarizable CO2 model that shares the other ingredients of the polarizable model was also developed and optimized to VLE data. Gibbs ensemble Monte Carlo and molecular dynamics simulations were used to evaluate the two models with respect to a variety of thermodynamic and transport properties, including the enthalpy of vaporization, second virial coefficient, density in the one-phase fluid region, isobaric and isochoric heat capacities, radial distribution functions, self-diffusion coefficient, and shear viscosity. Excellent agreement between model predictions and experimental data was found for all properties studied. The polarizable and nonpolarizable models provide a similar representation of CO2 properties, which indicates that the properties of pure CO2 fluid are not strongly affected by polarization. The polarizable model, which has an order of magnitude higher computational cost than the nonpolarizable model, will likely be useful for the study of a mixture of CO2 and polar components for which polarization is important.

  8. 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

  9. Neutron polarizability. Possibilities of its determination in neutron experiments

    CERN Document Server

    Aleksandrov, Y A

    2001-01-01

    The history of question of neutron polarizability is discussed. Most of the neutron physical experiments conducted at neutron energies below 14 MeV to discover the electric polarizability of the neutron are reviewed.The existence of additional scattering after all known long range-related phenomena are taken into account are emphasized. In the keV neutron energy region, the effect of neutron polarizability on the angular distribution of scattering (over a wide range of angles) and the energy behavior of the total cross section of neutron interaction is studied. Finally, in the region of low energies (below 1 keV) the focus is on the influence of polarizability on the energy dependence of total neutron cross sections. It is emphasized that measurements at energies below several hundreds keV have not given any positive results yet due to the smallness of the experimental effect. Possible existence of an additional potential of neutron scattering on nuclei with a longer range than that of the usual nuclear poten...

  10. 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)

  11. 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

  12. 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)

  13. Calculations of the thermal conductivities of ionic materials by simulation with polarizable interaction potentials.

    Science.gov (United States)

    Ohtori, Norikazu; Salanne, Mathieu; Madden, Paul A

    2009-03-14

    Expressions for the energy current of a system of charged, polarizable ions in periodic boundary conditions are developed in order to allow the thermal conductivity in such a system to be calculated by computer simulation using the Green-Kubo method. Dipole polarizable potentials for LiCl, NaCl, and KCl are obtained on a first-principles basis by "force matching" to the results of ab initio calculations on suitable condensed-phase ionic configurations. Simulation results for the thermal conductivity, and also other transport coefficients, for the melts are compared with experimental data and with results obtained with other interaction potentials. The agreement with experiment is almost quantitative, especially for NaCl and KCl, indicating that these methodologies, perhaps with more sophisticated forms for the potential, can be used to predict thermal conductivities for melts for which experimental determination is very difficult. It is demonstrated that the polarization effects have an important effect on the energy current and are crucial to a predictive scheme for the thermal conductivity.

  14. 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.

  15. Protein Viability on Au Nanoparticles during an Electrospray and Electrostatic-Force-Directed Assembly Process

    Directory of Open Access Journals (Sweden)

    Shun Mao

    2010-01-01

    Full Text Available We study the protein viability on Au nanoparticles during an electrospray and electrostatic-force-directed assembly process, through which Au nanoparticle-antibody conjugates are assembled onto the surface of carbon nanotubes (CNTs to fabricate carbon nanotube field-effect transistor (CNTFET biosensors. Enzyme-linked immunosorbent assay (ELISA and field-effect transistor (FET measurements have been used to investigate the antibody activity after the nanoparticle assembly. Upon the introduction of matching antigens, the colored reaction from the ELISA and the change in the electrical characteristic of the CNTFET device confirm that the antibody activity is preserved during the assembly process.

  16. 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

  17. 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...

  18. Nuclear dipole polarizability from mean-field modeling constrained by chiral effective field theory

    Science.gov (United States)

    Zhang, Zhen; Lim, Yeunhwan; Holt, Jeremy W.; Ko, Che Ming

    2018-02-01

    We construct a new Skyrme interaction Skχm* by fitting the equation of state and nucleon effective masses in asymmetric nuclear matter from chiral two- and three-body forces as well as the binding energies of finite nuclei. Employing this interaction to study the electric dipole polarizabilities of 48Ca, 68Ni, 120Sn, and 208Pb in the random-phase approximation, we find that the theoretical predictions are in good agreement with experimentally measured values without additional fine tuning of the Skyrme interaction, thus confirming the usefulness of the new Skyrme interaction in studying the properties of nuclei. We further use this interaction to study the neutron skin thicknesses of 48Ca and 208Pb, and they are found to be consistent with the experimental data.

  19. 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.

  20. 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.

  1. Polarizability of deformed nuclei and energy shifts in muonic atoms

    International Nuclear Information System (INIS)

    Nali, P.F.; Quarati, P.

    1980-01-01

    The polarizability and nuclear-polarization energy shifts of nuclei composed of closed shells plus valence nucleons in muonic atoms have been calculated: the harmonic-oscillator results of the El polarizability and the energy shifts have been corrected by means of a perturbative approach, which takes into account the effects introduced by the deformation Nilsson potential. Furthermore, to take into account the core polarization effect, different harmonic-oscillator parameters for the core and the valence nucleons have been assumed. The energy shifts of a sequence of states occupied by the muon during its atomic electromagnetic cascade for the nuclei 17 O and 17 F, 41 Ca and 41 Sc have been calculated. (author)

  2. 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

  3. Polarizability of π-mesons in the quark confinement model

    International Nuclear Information System (INIS)

    Avakyan, E.Z.; Avakyan, S.L.; Efimov, G.V.; Ivanov, M.A.

    1988-01-01

    The electric α π and magnetic β π polarizabilities are calculated in the Quark Confinement Model (QCM). The diagrams with vector, scalar and axial intermediate states are taken into account. It is found that intermediate scalar mesons give an essential contribution to electric and magnetic polarizabilities of pions. The following values for α π and β π are obtained: α π ± =4.06x10 -43 cm 3 ; β π ± =-3.84x10 -43 ; α π 0 =-0.18x10 -43 cm 3 ; β π 0 =1.92x10 -43 cm 3 . The widths of strong (α 0 (980) → πη, f 0 (975) → ππ, ε(730) → ππ) and radiative (α 0 (980), f 0 (980), ε(730) → γγ) decays are calculated. The results are obtained to be in satisfactory agreement with expermental data

  4. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu [Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Wang, Lee-Ping; Pande, Vijay S. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  5. 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.

  6. 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

  7. Real and virtual Compton scattering: The nucleon polarizabilities

    International Nuclear Information System (INIS)

    Downie, E.J.; Fonvieille, H.

    2011-01-01

    We give an overview of low-energy Compton scattering γ (*) p → γp with a real or virtual incoming photon. These processes allow the investigation of one of the fundamental properties of the nucleon, i.e. how its internal structure deforms under an applied static electromagnetic field. Our knowledge of nucleon polarizabilities and their generalization to non-zero four-momentum transfer will be reviewed, including the presently ongoing experiments and future perspectives. (authors)

  8. 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...

  9. Density Functional Studies of Molecular Polarizabilities. 10. Fulvenes and Fulvalenes

    Directory of Open Access Journals (Sweden)

    Humberto J. Soscún Machado

    2000-09-01

    Full Text Available We report accurate Ab Initio Hartree Fock (HF and Density Functional Theory (DFT studies of the static dipole polarizabilities and first hyperpolarizabilities of the [n] fulvene and the [n,m] fulvalene series of molecules (with n, m = 3,5,7. Calculations are also reported for the parent cycloalkenes: cyclopropene, cyclopentadiene and cycloheptatriene (1-3 respectively. Geometries were optimized at the HF/6-311G(3d,2p level of theory. All the fulvenes (4-6 and the smaller fulvalenes (7, 9 and 10 are found to be planar. Pentaheptafulvalene (11 is slightly non-planar whilst heptafulvalene (12 has a folded C2h structure. Calculated C-C bond lengths are consistently smaller than the experimental values. Dipole polarizabilities and non-zero hyperpolarizabilities 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. Dipole polarizabilities correlate well with those given on the basis of atom additivity. Molecules (8, (9 and (11 show very large dipole hyperpolarizabilities.

  10. 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.

  11. The Ice-Vapor Interface and the Melting Point of Ice I-h for the Polarizable POL3 Water Model

    Czech Academy of Sciences Publication Activity Database

    Muchová, E.; Gladich, Ivan; Picaud, S.; Hoang, P. N. M.; Roeselová, Martina

    2011-01-01

    Roč. 115, č. 23 (2011), s. 5973-5982 ISSN 1089-5639 R&D Projects: GA ČR(CZ) GAP208/10/1724; GA MŠk LC512; GA MŠk MEB020919; GA MŠk MEB020715 Institutional research plan: CEZ:AV0Z40550506 Keywords : polarizable water force field * ice surface * melting point * ice slab Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.946, year: 2011

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    Science.gov (United States)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

    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.

  17. Surface field of forces and protein adsorption behavior of poly(hydroxyethylmethacrylate) films deposited from plasma.

    Science.gov (United States)

    Morra, M; Cassinelli, C

    1995-01-01

    Polymeric films were deposited from hydroxyethylmethacrylate (HEMA) plasma on non-woven poly(butyleneterephtalate) (PBT) filter materials. To test the effect of deposition conditions on surface properties, film were deposited using a constant monomer flow rate and a discharge power ranging from 40-100 W. Surface composition and surface energetics were evaluated by Electron Spectroscopy for Chemical Analysis (ESCA) and contact angle measurement, respectively. Albumin (Alb) and fibrinogen (Fg) adsorption from single protein solutions to the plasma-coated filters was measured. Results illustrate the marked effects of the deposition condition on the surface composition, the surface field of forces, and the protein adsorption behavior. The latter is modeled by the application of the Good-van Oss-Chaudhury theory of Lewis acid-base contribution to interfacial energetics. Materials endowed with widely different properties are obtained from the same monomer and different deposition conditions, a result that must be taken into account both in the production step, to assure constant quality, and in the development of specifically tailored materials.

  18. Life in extreme environments: single molecule force spectroscopy as a tool to explore proteins from extremophilic organisms.

    Science.gov (United States)

    Tych, Katarzyna M; Hoffmann, Toni; Batchelor, Matthew; Hughes, Megan L; Kendrick, Katherine E; Walsh, Danielle L; Wilson, Michael; Brockwell, David J; Dougan, Lorna

    2015-04-01

    Extremophiles are organisms which survive and thrive in extreme environments. The proteins from extremophilic single-celled organisms have received considerable attention as they are structurally stable and functionally active under extreme physical and chemical conditions. In this short article, we provide an introduction to extremophiles, the structural adaptations of proteins from extremophilic organisms and the exploitation of these proteins in industrial applications. We provide a review of recent developments which have utilized single molecule force spectroscopy to mechanically manipulate proteins from extremophilic organisms and the information which has been gained about their stability, flexibility and underlying energy landscapes.

  19. 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.

  20. Forces and Kinetics of the Bacillus subtilis Spore Coat Proteins CotY and CotX Binding to CotE Inspected by Single Molecule Force Spectroscopy.

    Science.gov (United States)

    Liu, Huiqing; Krajcikova, Daniela; Wang, Nan; Zhang, Zhe; Wang, Hongda; Barak, Imrich; Tang, Jilin

    2016-02-18

    Spores are uniquely stable cell types that are produced when bacteria encounter nutrient limitations. Spores are encased in a complex multilayered coat, which provides protection against environmental insults. The spore coat of Bacillus subtilis is composed of around 70 individual proteins that are organized into four distinct layers. Here we explored how morphogenetic protein CotE guides formation of the outermost layer of the coat, the crust, around the forespore by focusing on three proteins: CotE, CotY, and CotX. Single molecule force spectroscopy (SMFS) was used to investigate the interactions among CotE, CotY, and CotX at the single-molecule level. Direct interactions among these three proteins were observed. Additionally, the dissociation kinetics was also studied by measuring the unbinding forces of the complexes at different loading rates. A series of kinetic data of these complexes were acquired. It was found that the interaction of CotE and CotY was stronger than that of CotE and CotX.

  1. 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......) 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...

  2. Polarizability expressions for predicting resonances in plasmonic and Mie scatterers

    Science.gov (United States)

    Colom, Rémi; Devilez, Alexis; Enoch, Stefan; Stout, Brian; Bonod, Nicolas

    2017-06-01

    Polarizability expressions are commonly used in optics and photonics to model light scattering by small particles. Models based on Taylor series of the scattering coefficients of the particles fail to predict the morphologic resonances hosted by dielectric particles. Here we propose to use the factorization of the special functions appearing in the expression of the Mie scattering coefficients to derive pointlike models. These models can be applied to reproduce both Mie resonances of dielectric particles and plasmonic resonances of metallic particles. They provide simple but robust tools to predict accurately the electric and magnetic Mie resonances in dielectric particles.

  3. On the magnetic polarizability tensor of US coinage

    Science.gov (United States)

    Davidson, John L.; Abdel-Rehim, Omar A.; Hu, Peipei; Marsh, Liam A.; O’Toole, Michael D.; Peyton, Anthony J.

    2018-03-01

    The magnetic dipole polarizability tensor of a metallic object gives unique information about the size, shape and electromagnetic properties of the object. In this paper, we present a novel method of coin characterization based on the spectroscopic response of the absolute tensor. The experimental measurements are validated using a combination of tests with a small set of bespoke coin surrogates and simulated data. The method is applied to an uncirculated set of US coins. Measured and simulated spectroscopic tensor responses of the coins show significant differences between different coin denominations. The presented results are encouraging as they strongly demonstrate the ability to characterize coins using an absolute tensor approach.

  4. 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.

  5. Pion and kaon polarizabilities in the quark confinement model

    International Nuclear Information System (INIS)

    Ivanov, M.A.; Mizutani, T.

    1992-01-01

    The quark confinement model (QCM) which is based on quark confinement and the composite nature of hadrons, is applied to the study of electromagnetic polarizabilities of the π and K mesons. The Compton scattering amplitude for pseudoscalar meson in the QCM obtains contributions from the following processes (or diagrams): (1) the photon scattering by a point charge, (2) diagrams which involve only one quark loop, (3) the scalar, vector, and axial meson exchanges. The presence of quark loops in QCM diagrams introduces nontrivial momentum dependences which do not exist in the effective Lagrangian scheme with only meson degrees of freedom

  6. Weak-field Hall effect and static polarizability of Bloch electrons

    Czech Academy of Sciences Publication Activity Database

    Středa, Pavel; Jonckheere, T.

    2009-01-01

    Roč. 79, č. 11 (2009), 115115/1-115115/8 ISSN 1098-0121 R&D Projects: GA ČR GA202/08/0551 Institutional research plan: CEZ:AV0Z10100521 Keywords : Hall effect * magnetization * Bloch electrons electron polarizability * electron polarizability Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.475, year: 2009

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

    NARCIS (Netherlands)

    Hatlo, M. M.|info:eu-repo/dai/nl/412640678; van Roij, R.H.H.G.|info:eu-repo/dai/nl/152978984; 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

  8. Polarizability and alignment of dielectric nanoparticles in an external electric field: Bowls, dumbbells, and cuboids

    NARCIS (Netherlands)

    Kwaadgras, B.W.; Verdult, M.; Dijkstra, M.; van Roij, R.H.H.G.

    2011-01-01

    We employ the coupled dipole method to calculate the polarizability tensor of various anisotropic dielectric clusters of polarizable atoms, such as cuboid-, bowl-, and dumbbell-shaped nanoparticles. Starting from a Hamiltonian of a many-atom system, we investigate how this tensor depends on the size

  9. Statistical field theory description of inhomogeneous polarizable soft matter.

    Science.gov (United States)

    Martin, Jonathan M; Li, Wei; Delaney, Kris T; Fredrickson, Glenn H

    2016-10-21

    We present a new molecularly informed statistical field theory model of inhomogeneous polarizable soft matter. The model is based on fluid elements, referred to as beads, that can carry a net monopole of charge at their center of mass and a fixed or induced dipole through a Drude-type distributed charge approach. The beads are thus polarizable and naturally manifest attractive van der Waals interactions. Beyond electrostatic interactions, beads can be given soft repulsions to sustain fluid phases at arbitrary densities. Beads of different types can be mixed or linked into polymers with arbitrary chain models and sequences of charged and uncharged beads. By such an approach, it is possible to construct models suitable for describing a vast range of soft-matter systems including electrolyte and polyelectrolyte solutions, ionic liquids, polymerized ionic liquids, polymer blends, ionomers, and block copolymers, among others. These bead models can be constructed in virtually any ensemble and converted to complex-valued statistical field theories by Hubbard-Stratonovich transforms. One of the fields entering the resulting theories is a fluctuating electrostatic potential; other fields are necessary to decouple non-electrostatic interactions. We elucidate the structure of these field theories, their consistency with macroscopic electrostatic theory in the absence and presence of external electric fields, and the way in which they embed van der Waals interactions and non-uniform dielectric properties. Their suitability as a framework for computational studies of heterogeneous soft matter systems using field-theoretic simulation techniques is discussed.

  10. Toward mechanical manipulations of cell membranes and membrane proteins using an atomic force microscope: an invited review.

    Science.gov (United States)

    Ikai, Atsushi; Afrin, Rehana

    2003-01-01

    Recent advances in the use of the atomic force microscope (AFM) for manipulating cell membranes and membrane proteins are reviewed. Early pioneering work on measurements of the magnitude of the force required to create indentations with defined depth on their surfaces and to separate interacting pairs of avidin-biotin, antigen-antibody, and complementary DNA pairs formed the basis of this field. The method has subsequently been applied to map the presence of cell surface receptors and polysaccharides on live cell membranes by force measurement, with promising results. Attempts to extract phospholipids and proteins from lipid bilayers and live cell surfaces have been reported, providing a new tool for the manipulation of cellular activities and biochemical analysis at the single-cell level. An increasing awareness of the effect of the pulling speed (nm/s or microm/s), or more accurately, the force loading rate (pN/s or nN/s) on the magnitude of the rupture force, has led researchers to construct energy diagrams of rupture events based on the parameters available from such studies. Information on such nature of the interplay of force and loading rate is vital for nanomanipulation of living cells and cell membranes. Some relevant work for membrane manipulation using other methods is also reviewed in relation to AFM-based methodology.

  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. Polarizability and alignment of dielectric nanoparticles in an external electric field: bowls, dumbbells, and cuboids.

    Science.gov (United States)

    Kwaadgras, Bas W; Verdult, Maarten; Dijkstra, Marjolein; van Roij, René

    2011-10-07

    We employ the coupled dipole method to calculate the polarizability tensor of various anisotropic dielectric clusters of polarizable atoms, such as cuboid-, bowl-, and dumbbell-shaped nanoparticles. Starting from a Hamiltonian of a many-atom system, we investigate how this tensor depends on the size and shape of the cluster. We use the polarizability tensor to calculate the energy difference associated with turning a nanocluster from its least to its most favorable orientation in a homogeneous static electric field, and we determine the cluster dimension for which this energy difference exceeds the thermal energy such that particle alignment by the field is possible. Finally, we study in detail the (local) polarizability of a cubic-shaped cluster and present results indicating that, when retardation is ignored, a bulk polarizability cannot be reached by scaling up the system. © 2011 American Institute of Physics

  13. Viewing dynamic interactions of proteins and a model lipid membrane with atomic force microscopy.

    Science.gov (United States)

    Quinn, Anthony S; Rand, Jacob H; Wu, Xiao-Xuan; Taatjes, Douglas J

    2013-01-01

    The information covered in this chapter will present a model homogenous membrane preparation technique and dynamic imaging procedure that can be successfully applied to more than one type of lipid study and atomic force microscope (AFM) instrument setup. The basic procedural steps have been used with an Asylum Research MFP-3D BIO and the Bruker (formerly, Veeco) BioScope. The AFM imaging protocol has been supplemented by procedures (not to be presented in this chapter) of ellipsometry, standardized western blotting, and dot-blots to verify appropriate purity and activity of all experimental molecular components; excellent purity and activity level of the lipids, proteins, and drug(s) greatly influence the success of imaging experiments in the scanning probe microscopy field. The major goal of the chapter is to provide detailed procedures for sample preparation and operation of the Asylum Research MFP-3D BIO AFM. In addition, one should be cognizant that our comprehensive description in the use of the MFP-3D BIO's functions for successful image acquisitions and analyses is greatly enhanced by Asylum Research's (AR's) accompanying extensive manual(s), technical notes, and AR's users forum. Ultimately, the stepwise protocol and information will allow novice personnel to begin acquiring quality images for processing and analysis with minimal supervision.

  14. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field

    Science.gov (United States)

    Nielsen, Jakob T.; Eghbalnia, Hamid R.; Nielsen, Niels Chr.

    2011-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field. PMID:22293396

  15. 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.

  16. Simulations of impulsive laser scattering of biological protein assemblies: Application to M13 bacteriophage

    Science.gov (United States)

    Dykeman, Eric C.; Benson, Daryn; Tsen, K.-T.; Sankey, Otto F.

    2009-10-01

    We develop a theoretical framework, based on a bond-polarizability model, for simulating the impulsive force experienced on a protein or an assembly of proteins from a pulsed light source by coupling the laser electric field to an atomic distortion. The mechanism is impulsive stimulated Raman scattering (ISRS) where mechanical distortions produce variation in the electronic polarization through atomic displacements similar to vibrational Raman scattering. The magnitude of the impulsive force is determined from the empirical two-body bond-polarizability model and the intensity of the incident light. We apply the method to the M13 bacteriophage protein capsid system by performing several classical molecular-dynamics simulations that include the additional impulsive laser scattering force at various light intensities and pulse widths. The results of the molecular-dynamics simulations are then qualitatively interpreted with a simple harmonic oscillator model driven by ISRS. The intensity of light required to produce damage to the capsid in the simulations was found to be far higher than what was found in recent pulsed laser scattering experiments of M13 phage, suggesting that the observed inactivation of viruses with ultrashort laser pulses involves processes and/or mechanisms not taken into account in the present simulations.

  17. Polarizability extraction of complementary metamaterial elements in waveguides for aperture modeling

    Science.gov (United States)

    Pulido-Mancera, Laura; Bowen, Patrick T.; Imani, Mohammadreza F.; Kundtz, Nathan; Smith, David

    2017-12-01

    We consider the design and modeling of metasurfaces that couple energy from guided waves to propagating wave fronts. To this purpose, we develop a comprehensive, multiscale dipolar interpretation for large arrays of complementary metamaterial elements embedded in a waveguide structure. Within this modeling technique, the detailed electromagnetic response of each metamaterial element is replaced by a polarizable dipole, described by means of an effective polarizability. In this paper, we present two methods to extract this effective polarizability. The first method invokes surface equivalence principles, averaging over the effective surface currents and charges induced in the element's surface in order to obtain the effective dipole moments, from which the effective polarizability can be inferred. The second method is based in the coupled-mode theory, from which a direct relationship between the effective polarizability and the amplitude coefficients of the scattered waves can be deduced. We demonstrate these methods on several variants of waveguide-fed metasurface elements (both one- and two-dimensional waveguides), finding excellent agreement between the two, as well as with the analytical expressions derived for circular and elliptical irises. With the effective polarizabilities of the metamaterial elements accurately determined, the radiated fields generated by a waveguide-fed metasurface can be found self-consistently by including the interactions between polarizable dipoles. The dipole description provides an effective perspective and computational framework for engineering metasurface structures such as holograms, lenses, and beam-forming arrays, among others.

  18. Multipolar Polarizabilities and Hyperpolarizabilities in the Sr Optical Lattice Clock

    Science.gov (United States)

    Porsev, S. G.; Safronova, M. S.; Safronova, U. I.; Kozlov, M. G.

    2018-02-01

    We address the problem of the lattice Stark shifts in the Sr clock caused by the multipolar M 1 and E 2 atom-field interactions and by the term nonlinear in lattice intensity and determined by the hyperpolarizability. We develop an approach to calculate hyperpolarizabilities for atoms and ions based on a solution of the inhomogeneous equation which allows us to effectively and accurately carry out complete summations over intermediate states. We apply our method to the calculation of the hyperpolarizabilities for the clock states in Sr. We also carry out an accurate calculation of the multipolar polarizabilities for these states at the magic frequency. Understanding these Stark shifts in optical lattice clocks is crucial for further improvement of the clock accuracy.

  19. 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.

  20. 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

  1. 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

  2. Age-related Differences in Dystrophin: Impact on Force Transfer Proteins, Membrane Integrity, and Neuromuscular Junction Stability.

    Science.gov (United States)

    Hughes, David C; Marcotte, George R; Marshall, Andrea G; West, Daniel W D; Baehr, Leslie M; Wallace, Marita A; Saleh, Perrie M; Bodine, Sue C; Baar, Keith

    2017-05-01

    The loss of muscle strength with age has been studied from the perspective of a decline in muscle mass and neuromuscular junction (NMJ) stability. A third potential factor is force transmission. The purpose of this study was to determine the changes in the force transfer apparatus within aging muscle and the impact on membrane integrity and NMJ stability. We measured an age-related loss of dystrophin protein that was greatest in the flexor muscles. The loss of dystrophin protein occurred despite a twofold increase in dystrophin mRNA. Importantly, this disparity could be explained by the four- to fivefold upregulation of the dystromir miR-31. To compensate for the loss of dystrophin protein, aged muscle contained increased α-sarcoglycan, syntrophin, sarcospan, laminin, β1-integrin, desmuslin, and the Z-line proteins α-actinin and desmin. In spite of the adaptive increase in other force transfer proteins, over the 48 hours following lengthening contractions, the old muscles showed more signs of impaired membrane integrity (fourfold increase in immunoglobulin G-positive fibers and 70% greater dysferlin mRNA) and NMJ instability (14- to 96-fold increases in Runx1, AchRδ, and myogenin mRNA). Overall, these data suggest that age-dependent alterations in dystrophin leave the muscle membrane and NMJ more susceptible to contraction-induced damage even before changes in muscle mass are obvious. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. The electric polarizability of a particle bound by a one-dimensional ionic crystal

    International Nuclear Information System (INIS)

    Balderas, Daniel; González, Gabriel

    2013-01-01

    We consider the problem of a particle confined to a one-dimensional ionic crystal of finite length modeled by repulsive and attractive delta functions and subject to the application of an external constant electric field. Exact expressions for the electric polarizability of the system via the Dalgarno–Lewis technique are obtained in second order perturbation theory. The study uncovers the behavior of the electric polarizability as a function of the number of ions in the system. (paper)

  8. 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.)

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

    Energy Technology Data Exchange (ETDEWEB)

    Ganguly, Jayanta [Department of Chemistry, Brahmankhanda Basapara High School, Basapara, Birbhum 731 215, 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)

    2014-06-25

    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{sub xx} and α{sub 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. 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

  11. 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

  12. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

    International Nuclear Information System (INIS)

    Hedegård, Erik Donovan; Olsen, Jógvan Magnus Haugaard; Knecht, Stefan; Kongsted, Jacob; Jensen, Hans Jørgen Aagaard

    2015-01-01

    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, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linear response have been implemented in a development version of DALTON. To benchmark the PE-MC-srDFT approach against the literature data, we have investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies. 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 to CASSCF/CASPT2 benchmarks

  13. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

    Science.gov (United States)

    Hedegârd, Erik Donovan; Olsen, Jógvan Magnus Haugaard; Knecht, Stefan; Kongsted, Jacob; Jensen, Hans Jørgen Aagaard

    2015-03-01

    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, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linear response have been implemented in a development version of Dalton. To benchmark the PE-MC-srDFT approach against the literature data, we have investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies. 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 to CASSCF/CASPT2 benchmarks.

  14. Stark effect, polarizability, and electroabsorption in silicon nanocrystals

    Science.gov (United States)

    Bulutay, Ceyhun; Kulakci, Mustafa; Turan, Raşit

    2010-03-01

    Demonstrating the quantum-confined Stark effect (QCSE) in silicon nanocrystals (NCs) embedded in oxide has been rather elusive, unlike the other materials. Here, the recent experimental data from ion-implanted Si NCs is unambiguously explained within the context of QCSE using an atomistic pseudopotential theory. This further reveals that the majority of the Stark shift comes from the valence states which undergo a level crossing that leads to a nonmonotonic radiative recombination behavior with respect to the applied field. The polarizability of embedded Si NCs including the excitonic effects is extracted over a diameter range of 2.5-6.5 nm, which displays a cubic scaling, α=cDNC3 , with c=2.436×10-11C/(Vm) , where DNC is the NC diameter. Finally, based on intraband electroabsorption analysis, it is predicted that p -doped Si NCs will show substantial voltage tunability, whereas n -doped samples should be almost insensitive. Given the fact that bulk silicon lacks the linear electro-optic effect as being a centrosymmetric crystal, this may offer a viable alternative for electrical modulation using p -doped Si NCs.

  15. Shear rheology of mixed protein adsorption layers vs their structure studied by surface force measurements.

    Science.gov (United States)

    Danov, Krassimir D; Kralchevsky, Peter A; Radulova, Gergana M; Basheva, Elka S; Stoyanov, Simeon D; Pelan, Eddie G

    2015-08-01

    The hydrophobins are proteins that form the most rigid adsorption layers at liquid interfaces in comparison with all other investigated proteins. The mixing of hydrophobin HFBII with other conventional proteins is expected to reduce the surface shear elasticity and viscosity, E(sh) and η(sh), proportional to the fraction of the conventional protein. However, the experiments show that the effect of mixing can be rather different depending on the nature of the additive. If the additive is a globular protein, like β-lactoglobulin and ovalbumin, the surface rigidity is preserved, and even enhanced. The experiments with separate foam films indicate that this is due to the formation of a bilayer structure at the air/water interface. The more hydrophobic HFBII forms the upper layer adjacent to the air phase, whereas the conventional globular protein forms the lower layer that faces the water phase. Thus, the elastic network formed by the adsorbed hydrophobin remains intact, and even reinforced by the adjacent layer of globular protein. In contrast, the addition of the disordered protein β-casein leads to softening of the HFBII adsorption layer. Similar (an even stronger) effect is produced by the nonionic surfactant Tween 20. This can be explained with the penetration of the hydrophobic tails of β-casein and Tween 20 between the HFBII molecules at the interface, which breaks the integrity of the hydrophobin interfacial elastic network. The analyzed experimental data for the surface shear rheology of various protein adsorption layers comply with a viscoelastic thixotropic model, which allows one to determine E(sh) and η(sh) from the measured storage and loss moduli, G' and G″. The results could contribute for quantitative characterization and deeper understanding of the factors that control the surface rigidity of protein adsorption layers with potential application for the creation of stable foams and emulsions with fine bubbles or droplets. Copyright © 2014

  16. Hierarchical Networks of Casein Proteins: An Elasticity Study Based on Atomic Force Microscopy

    NARCIS (Netherlands)

    Uricanu, V.I.; Duits, Michael H.G.; Mellema, J.

    2004-01-01

    2D- and 3D-atomic force microscopy (AFM) experiments were performed on single casein micelles (CM) in native state, submerged in liquid, using a home-built AFM instrument. The micelles were immobilized via carbodiimide chemistry to a self-assembled monolayer supported on gold-coated slides. Off-line

  17. 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.

  18. 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.

  19. Spin polarizabilities and characteristics of spin-one hadrons related to parity nonconservation in the Duffin-Kemmer-Petiau formalism

    International Nuclear Information System (INIS)

    Vakulina, E.V.; Maksimenko, N.V.

    2017-01-01

    Using the relativistic-invariant effective tensor representation of the Lagrangians of the two-photon interaction with hadrons within the Duffin-Kemmer-Petiau formalism, the spin polarizabilities of the spin 1 particles that are characteristic of spin 1/2 hadrons have been determined. Along with this, new spin polarizabilities of spin 1 particles have been determined, that are related to the presence of the tensor polarizabilities.

  20. Application of atomic force microscopy to protein anatomy:. Imaging of supramolecular structures of self-assemblies formed from synthetic peptides

    Science.gov (United States)

    Shibata-Seki, T.; Masai, J.; Ogawa, Y.; Sato, K.; Yanagawa, H.

    This paper reports morphological studies of structures of self-assemblies from synthetic peptide fragments with the use of atomic force microscope (AFM) and transmission electron microscope (TEM). Two systems of synthetic peptides have been examined: one is peptides from barnase (a ribonuclease) and the other is those from tau protein (Alzheimer's disease-related protein). The AFM observation was carried out by using a commercially available AFM operated in the tapping mode in air. The general appearance in shape and size of the peptide assemblies in AFM images was essentially similar to that in TEM images, except that the AFM images provide us with fruitful three-dimensional information about the assemblies. For assemblies from barnase peptides, possible formation processes of the supramolecular structures from the corresponding peptide fragment have been proposed on the basis of the AFM images.

  1. Kinesin-8 is a low-force motor protein with a weakly bound slip state.

    Science.gov (United States)

    Jannasch, Anita; Bormuth, Volker; Storch, Marko; Howard, Jonathon; Schäffer, Erik

    2013-06-04

    During the cell cycle, kinesin-8s control the length of microtubules by interacting with their plus ends. To reach these ends, the motors have to be able to take many steps without dissociating. However, the underlying mechanism for this high processivity and how stepping is affected by force are unclear. Here, we tracked the motion of yeast (Kip3) and human (Kif18A) kinesin-8s with high precision under varying loads using optical tweezers. Surprisingly, both kinesin-8 motors were much weaker compared with other kinesins. Furthermore, we discovered a force-induced stick-slip motion: the motor frequently slipped, recovered from this state, and then resumed normal stepping motility without detaching from the microtubule. The low forces are consistent with kinesin-8s being regulators of microtubule dynamics rather than cargo transporters. The weakly bound slip state, reminiscent of a molecular safety leash, may be an adaptation for high processivity. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. 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

  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. 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.

  5. High-precision measurements and theoretical calculations of indium excited-state polarizabilities

    Science.gov (United States)

    Vilas, N. B.; Wang, B.-Y.; Rupasinghe, P. M.; Maser, D. L.; Safronova, M. S.; Safronova, U. I.; Majumder, P. K.

    2018-02-01

    We report measurements of the scalar and tensor static polarizabilities of the 115In7 p1 /2 and 7 p3 /2 excited states using two-step diode laser spectroscopy in an atomic beam. These scalar polarizabilities are one to two orders of magnitude larger than for lower-lying indium states due to the close proximity of the 7 p and 6 d states. For the scalar polarizabilities, we find values (in atomic units) of 1.811 (4 ) ×105a03 and 2.876 (6 ) ×105a03 for the 7 p1 /2 and 7 p3 /2 states, respectively. We determine the tensor polarizability component of the 7 p3 /2 state to be -1.43 (18 ) ×104a03 . These measurements set high-precision benchmarks of the transition properties for highly excited states in trivalent atomic systems. We also present ab initio calculations of these quantities and other In polarizabilities using two high-precision relativistic methods to make a global comparison of the accuracies of the two approaches. The precision of the experiment is sufficient to differentiate between the two theoretical methods as well as to allow precise determination of the indium 7 p -6 d matrix elements. The results obtained in this paper are applicable to other heavier and more complicated systems, and provide much needed guidance for the development of even more precise theoretical approaches.

  6. Polarizable crystals in apocrine sweat gland tumors: A series of 3 cases.

    Science.gov (United States)

    Johnson, Gina; Gardner, Jerad M; Shalin, Sara C

    2017-08-01

    Polarizable calcium oxalate (CaOx) crystals have been well documented in breast biopsies, generally associated with benign apocrine metaplasia. In contrast, polarizable crystals are only rarely reported in skin adnexal neoplasms. We report 3 different cases of sweat gland tumors with polarizable crystals morphologically suggestive of CaOx: 1 apocrine hidrocystoma and 2 tubular apocrine adenomas. The histologic features were examined in 3 cases. Clinical presentation summary included 2 males and 1 female, ages 53 to 74 years, with lesions located on the left cheek, inferior vertex scalp and the left eyebrow. All 3 cases showed polarizable, geometric, plate-like and fractured, colorless crystals within the lumens of the neoplasm. Of note, these crystals were seen only on the toluidine blue-stained section of Case #1, but were not present on the corresponding permanent section. We hypothesize that polarizable crystals may be present in sweat gland neoplasms more often than previously documented, but that they may often dissolve with routine processing, accounting for their rare visibility. We highlight this rare finding, and suggest that it may be underreported. We only noted this finding in benign apocrine tumors; further investigation would be necessary to determine whether these crystals are also seen in other cutaneous adnexal neoplasms. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. MDVRY: a polarizable classical molecular dynamics package for biomolecules

    Science.gov (United States)

    Souaille, M.; Loirat, H.; Borgis, D.; Gaigeot, M. P.

    2009-02-01

    The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a 'Car-Parrinello' dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water. Program summaryProgram title: MDVRY Catalogue identifier: AEBY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 39 156 No. of bytes in distributed program, including test data, etc.: 277 197 Distribution format: tar.bz2 Programming language: C Computer: Linux machines with FFTW Fourier Transform package installed Operating system: Linux machines, SUSE & RedHat distributions Classification: 3, 16.13, 23 External routines: FFTW ( http://www.fftw.org/) Nature of problem: Molecular Dynamics Software package. Solution method: Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are

  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. 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...... 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...... 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...

  10. Protein Crystal Growth Under Forced Solution Flow: Experimental Setup and General Response of Lysozyme

    Science.gov (United States)

    Vekilov, P. G.; Rosenberger, F.

    1998-01-01

    We have experimentally studied the effects of solution flow on the growth kinetics of the protein lysozyme. To this end, we have expanded our interferometry setup by a novel crystallization cell and solution recirculation system. This combination permits monitoring of interface morphology and kinetics with a depth resolution of 200 A at bulk flow rates of up to 2000 micron/s. Particular attention was paid to the prevention of protein denaturation that is often associated with the pumping of protein solutions. We found that at bulk flow rates it less than 250 microns/s the average growth rate and step velocity, R(sub avg) and upsilon(sub avg) increase with increasing it. This can be quantitatively understood in terms of the enhanced, convective solute supply to the interface. With high-purity solutions, it u greater than 250 microns/s lead to growth deceleration, and, at low supersaturations sigma, to growth cessation. When solutions containing approx. 1% of other protein impurities were used, growth deceleration occurred at any u greater than 0 and cessation in the low sigma experiments was reached at about half the it causing cessation with pure solution. The flow-induced changes in R(sub avg) and upsilon(sub avg) including growth cessation, were reversible and reproducible, independent of the direction of the u-changes and solution purity. Hence, we attribute the deceleration to the convection-enhanced supply of impurities to the interface, which at higher flow rates overpowers the effects of enhanced interfacial solute concentration. Most importantly, we found that convective transport leads to a significant reduction in kinetics fluctuations, in agreement with our earlier expectations for the lysozyme system. This supports our hypothesis that these long-term fluctuations represent an intrinsic response feature of the coupled bulk transport-interfacial kinetics system in the mixed growth control regime.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-23

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

  13. 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

  14. Polarizable Water Model for the Coarse-Grained MARTINI Force Field

    NARCIS (Netherlands)

    Yesylevskyy, Semen O.; Schafer, Lars V.; Sengupta, Durba; Marrink, Siewert J.

    Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent,

  15. A Fractionally Ionic Approach to Polarizability and van der Waals Many-Body Dispersion Calculations.

    Science.gov (United States)

    Gould, Tim; Lebègue, Sébastien; Ángyán, János G; Bučko, Tomáš

    2016-12-13

    By explicitly including fractionally ionic contributions to the polarizability of a many-component system, we are able to significantly improve on previous atom-wise many-body van der Waals approaches with essentially no extra numerical cost. For nonionic systems, our method is comparable in accuracy to existing approaches. However, it offers substantial improvements in ionic solids, e.g., producing better polarizabilities by over 65% in some cases. It has particular benefits for two-dimensional transition metal dichalcogenides and interactions of H 2 with modified coronenes, ionic systems of nanotechnological interest. It thus offers an efficient improvement on existing approaches, valid for a wide range of systems.

  16. 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

  17. 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.

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

    Indian Academy of Sciences (India)

    The environment of a solute molecule in an ionic liquid is likely to have large fluctuating electrostatic fields, and so the electrostatic properties of such a solute including its charge distribution and its polarizability may make a difference to both its static and dynamic properties. We have developed a new model forthe static ...

  19. Bulkiness versus anisotropy: The optimal shape of polarizable Brownian nanoparticles for alignment in electric fields

    NARCIS (Netherlands)

    Kwaadgras, B.W.; Dijkstra, M.; van Roij, R.H.H.G.

    2012-01-01

    Self-assembly and alignment of anisotropic colloidal particles are important processes that can be influenced by external electric fields. However, dielectric nanoparticles are generally hard to align this way because of their small size and low polarizability. In this work, we employ the coupled

  20. The Dynamic Electric Polarizability of a Particle Bound by a Double Delta Potential

    Science.gov (United States)

    Maize, M. A.; Smetanka, J. J.

    2008-01-01

    In this paper we derive an expression for the dynamic electric polarizability of a particle bound by a double delta potential for frequencies below and above the absolute value of the particle's ground state energy. The derived expression will be used to study some of the fundamental features of the system and its representation of real systems.…

  1. 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

  2. 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

  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. Transcendental-function representation of Stark-modified hydrogenic states and atomic dipole polarizability

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, A.; Talukdar, B. [Department of Physics, Visva-Bharati University, Santiniketan (India); Banerji, G. [Mathematics Department, BU, Burdwan (India); Roy, U. [Theoretical Physics Department, IACS, Calcutta (India)

    1998-01-30

    A differential equation approach to the perturbation theoretic correction for excited hydrogenic states is introduced. The radial equations for the problem are solved in terms of known transcendental functions and the method to determine the complete primitive is discussed. The constructed perturbative correction to the wavefunction is adapted to evaluate the dipole polarizability of hydrogenic atoms. (author)

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

    Indian Academy of Sciences (India)

    RUTH M LYNDEN-BELL

    : CS2(C) and ring C1; red-dashed: CS2(S) and ring C1: .... The red curve shows the probability distribution of induced dipoles on the C site (which is purely axial as the polarizability is axial). The values of the C site dipole follow a Gaussian.

  6. 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...

  7. Quadrupole polarizabilities of the pion in the Nambu-Jona-Lasinio model

    International Nuclear Information System (INIS)

    Hiller, B.; Broniowski, W.; Osipov, A.A.; Blin, A.H.

    2009-01-01

    The electromagnetic dipole and quadrupole polarizabilities of the neutral and charged pions are calculated in the Nambu-Jona-Lasinio model. Our results agree with the recent experimental analysis of these quantities based on dispersion sum rules. Comparison is made with the results from the chiral perturbation theory.

  8. 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|mIL)...

  9. The static polarizability and second hyperpolarizability of fullerenes and carbon nanotubes

    NARCIS (Netherlands)

    Jensen, L; Astrand, PO; Mikkelsen, KV

    2004-01-01

    Utilizing a point-dipole interaction model, we present an investigation of the static polarizability and second hyperpolarizability of fullerenes and carbon nanotubes by varying their structure. The following effects are investigated: (1) the length dependence of the components of the static

  10. ''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

  11. 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

    produces a large enhancement of the real and imaginary parts of the renormalized polarizability. We show that the imaginary part can be changed by a factor of up to 100 relative to its value in the absence of graphene. We also show that the resonance in the case of the grating is narrower than...

  12. 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

  13. 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...

  14. 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

    that the polarizability tensor is necessary to correct long-range behavior of DFT functionals used in electron-molecule scattering calculations. The impact of such a long-range correction is demonstrated on elastic and vibrationally inelastic electron collisions with adamantane, a molecule representing a large polyatomic...

  15. 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

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

    Science.gov (United States)

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

    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

  17. 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.

  18. 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

  19. 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.

  20. Detection of hepatitis C virus core protein in serum by atomic force microscopy combined with mass spectrometry.

    Science.gov (United States)

    Ivanov, Yuri D; Kaysheva, Anna L; Frantsuzov, Pavel A; Pleshakova, Tatyana O; Krohin, Nikolay V; Izotov, Alexander A; Shumov, Ivan D; Uchaikin, Vasiliy F; Konev, Vladimir A; Ziborov, Vadim S; Archakov, Alexander I

    2015-01-01

    A method for detection and identification of core antigen of hepatitis C virus (HCVcoreAg)-containing particles in the serum was proposed, with due account taken of the interactions of proteotypic peptides with Na(+), K(+), and Cl(-) ions. The method is based on a combination of reversible biospecific atomic force microscopy (AFM)-fishing and mass spectrometry (MS). AFM-fishing enables concentration, detection, and counting of protein complexes captured on the AFM chip surface, with their subsequent MS identification. Biospecific AFM-fishing of HCVcoreAg-containing particles from serum samples was carried out using AFM chips with immobilized antibodies against HCVcoreAg (HCVcoreAgim). Formation of complexes between anti-HCVcoreAgim and HCVcoreAg-containing particles on the AFM chip surface during the fishing process was demonstrated. These complexes were registered and counted by AFM. Further MS analysis allowed reliable identification of HCVcoreAg within the complexes formed on the AFM chip surface. It was shown that MS data processing, with account taken of the interactions between HCVcoreAg peptides and Na(+), K(+) cations, and Cl(-) anions, allows an increase in the number of peptides identified.

  1. The 2ν{sub 3} Raman overtone of sulfur hexafluoride: Absolute spectra, pressure effects, and polarizability properties

    Energy Technology Data Exchange (ETDEWEB)

    Chrysos, M., E-mail: michel.chrysos@univ-angers.fr; Rachet, F.; Kremer, D. [LUNAM Université, Université d’Angers, CNRS UMR 6200, Laboratoire MOLTECH-Anjou, 2 Bd Lavoisier, 49045 Angers (France)

    2014-03-28

    Of the six normal vibrations of SF{sub 6}, ν{sub 3} has a key role in the mechanisms of radiative forcing. This vibration, though inactive in Raman, shows up through the transition 2ν{sub 3} allowing for a complementary view on the asymmetric stretch of the molecule. Here, we look back into this topic, which has already caught some interest in the past but with some points been left out. We make a systematic incoherent-light-scattering analysis of the overtone with the use of different gas pressures and polarization orientations for the incident beam. Absolute-scale isotropic and anisotropic spectra are reported along with natural and pressure-induced widths and shifts, and other spectral features such as the peaks corresponding to the (experimentally indistinguishable) interfering channels E{sub g} and F{sub 2g} hitherto seen solely as two-photon IR-absorption features. We make the first-ever prediction of the SF{sub 6} polarizability second derivative with respect to the ν{sub 3}-mode coordinate and we develop a heuristic argument to explain why the superposition of the three degenerate stretching motions that are related to the ν{sub 3} mode cannot but generate a polarized Raman band.

  2. 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

  3. 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.

  4. 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.

  5. Isotensor Axial Polarizability and Lattice QCD Input for Nuclear Double-β Decay Phenomenology

    Science.gov (United States)

    Shanahan, Phiala E.; Tiburzi, Brian C.; Wagman, Michael L.; Winter, Frank; Chang, Emmanuel; Davoudi, Zohreh; Detmold, William; Orginos, Kostas; Savage, Martin J.; Nplqcd Collaboration

    2017-08-01

    The potential importance of short-distance nuclear effects in double-β decay is assessed using a lattice QCD calculation of the n n →p p transition and effective field theory methods. At the unphysical quark masses used in the numerical computation, these effects, encoded in the isotensor axial polarizability, are found to be of similar magnitude to the nuclear modification of the single axial current, which phenomenologically is the quenching of the axial charge used in nuclear many-body calculations. This finding suggests that nuclear models for neutrinoful and neutrinoless double-β decays should incorporate this previously neglected contribution if they are to provide reliable guidance for next-generation neutrinoless double-β decay searches. The prospects of constraining the isotensor axial polarizabilities of nuclei using lattice QCD input into nuclear many-body calculations are discussed.

  6. 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

  7. 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

  8. 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

  9. Polarizational stopping power of heavy-ion diclusters in two-dimensional electron liquids

    International Nuclear Information System (INIS)

    Ballester, D.; Fuentes, A. M.; Tkachenko, I. M.

    2007-01-01

    The in-plane polarizational stopping power of heavy-ion diclusters in a two-dimensional strongly coupled electron liquid is studied. Analytical expressions for the stopping power of both fast and slow projectiles are derived. To go beyond the random-phase approximation we make use of the inverse dielectric function obtained by means of the method of moments and some recent analytical expressions for the static local-field correction factor

  10. Effect of Level Broadening on the Polarizability in a Two-Dimensional System

    Science.gov (United States)

    Ando, Tsuneya

    1982-10-01

    The Lindhard polarizability is calculated in a two-dimensional system in the self-consistent Born approximation by assuming short-range scatterers. The known singularity at q{=}2kF, where kF is the Fermi wave vector, is shown to be rounded off in the presence of impurities. The effect is similar to that of nonzero temperatures in contrast to the result of Nkoma [J. Phys. C 14 (1981) 1685].

  11. Measurements of double-polarized compton scattering asymmetries and extraction of the proton spin polarizabilities.

    Science.gov (United States)

    Martel, P P; Miskimen, R; Aguar-Bartolome, P; Ahrens, J; Akondi, C S; Annand, J R M; Arends, H J; Barnes, W; Beck, R; Bernstein, A; Borisov, N; Braghieri, A; Briscoe, W J; Cherepnya, S; Collicott, C; Costanza, S; Denig, A; Dieterle, M; Downie, E J; Fil'kov, L V; Garni, S; Glazier, D I; Gradl, W; Gurevich, G; Hall Barrientos, P; Hamilton, D; Hornidge, D; Howdle, D; Huber, G M; Jude, T C; Kaeser, A; Kashevarov, V L; Keshelashvili, I; Kondratiev, R; Korolija, M; Krusche, B; Lazarev, A; Lisin, V; Livingston, K; MacGregor, I J D; Mancell, J; Manley, D M; Meyer, W; Middleton, D G; Mushkarenkov, A; Nefkens, B M K; Neganov, A; Nikolaev, A; Oberle, M; Ortega Spina, H; Ostrick, M; Ott, P; Otte, P B; Oussena, B; Pedroni, P; Polonski, A; Polyansky, V; Prakhov, S; Rajabi, A; Reicherz, G; Rostomyan, T; Sarty, A; Schrauf, S; Schumann, S; Sikora, M H; Starostin, A; Steffen, O; Strakovsky, I I; Strub, T; Supek, I; Thiel, M; Tiator, L; Thomas, A; Unverzagt, M; Usov, Y; Watts, D P; Witthauer, L; Werthmüller, D; Wolfes, M

    2015-03-20

    The spin polarizabilities of the nucleon describe how the spin of the nucleon responds to an incident polarized photon. The most model-independent way to extract the nucleon spin polarizabilities is through polarized Compton scattering. Double-polarized Compton scattering asymmetries on the proton were measured in the Δ(1232) region using circularly polarized incident photons and a transversely polarized proton target at the Mainz Microtron. Fits to asymmetry data were performed using a dispersion model calculation and a baryon chiral perturbation theory calculation, and a separation of all four proton spin polarizabilities in the multipole basis was achieved. The analysis based on a dispersion model calculation yields γ(E1E1)=-3.5±1.2, γ(M1M1)=3.16±0.85, γ(E1M2)=-0.7±1.2, and γ(M1E2)=1.99±0.29, in units of 10(-4)  fm(4).

  12. Relativistic many-body calculation of energies, lifetimes, hyperfine constants, and polarizabilities in 7Li

    International Nuclear Information System (INIS)

    Johnson, W. R.; Safronova, U. I.; Derevianko, A.; Safronova, M. S.

    2008-01-01

    The excitation energies of ns, np, nd, and nf (n≤6) states in neutral lithium are evaluated within the framework of relativistic many-body theory. First-, second-, third-, and all-order Coulomb energies and first- and second-order Breit corrections to energies are calculated. All-order calculations of reduced matrix elements, oscillator strengths, transition rates, and lifetimes are given for levels up to n=4. Electric-dipole (2s-np), electric-quadrupole (2s-nd), and electric-octupole (2s-nf), matrix elements are evaluated to obtain the corresponding ground-state multipole polarizabilities using the sum-over-states approach. Scalar and tensor polarizabilities for the 2p 1/2 and 2p 3/2 states are also calculated. Magnetic-dipole hyperfine constants A are determined for low-lying levels up to n=4. The quadratic Stark shift for the (F=2 M=0)↔(F=1 M=0) ground-state hyperfine transition is found to be -0.0582 Hz/(kV/cm) 2 , in slight disagreement with the experimental value -0.061±0.002 Hz/(kV/cm) 2 . Matrix elements used in evaluating polarizabilities, hyperfine constants, and the quadratic Stark shift are obtained using the all-order method

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

  14. The multi-configuration self-consistent field method within a polarizable embedded framework

    Science.gov (United States)

    Hedegârd, Erik Donovan; List, Nanna H.; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob

    2013-07-01

    We present a detailed derivation of Multi-Configuration Self-Consistent Field (MCSCF) optimization and linear response equations within the polarizable embedding scheme: PE-MCSCF. The MCSCF model enables a proper description of multiconfigurational effects in reaction paths, spin systems, excited states, and other properties which cannot be described adequately with current implementations of polarizable embedding in density functional or coupled cluster theories. In the PE-MCSCF scheme the environment surrounding the central quantum mechanical system is represented by distributed multipole moments and anisotropic dipole-dipole polarizabilities. The PE-MCSCF model has been implemented in DALTON. As a preliminary application, the low lying valence states of acetone and uracil in water has been calculated using Complete Active Space Self-Consistent Field (CASSCF) wave functions. The dynamics of the water environment have been simulated using a series of snapshots generated from classical Molecular Dynamics. The calculated shifts from gas-phase to water display between good and excellent correlation with experiment and previous calculations. As an illustration of another area of potential applications we present calculations of electronic transitions in the transition metal complex, [Fe(NO)(CN)5]2 - in a micro-solvated environment. This system is highly multiconfigurational and the influence of solvation is significant.

  15. Measuring the dynamic polarizability of tungsten atom via electrical wire explosion in vacuum

    Science.gov (United States)

    Shi, Huantong; Zou, Xiaobing; Wang, Xinxin

    2018-02-01

    Electrical explosion of wire provides a practical approach to the experimental measurement of dynamic polarizability of metal atoms with high melting and boiling temperatures. With the help of insulation coating, a section of tungsten wire was transformed to the plasma state while the near electrode region was partially vaporized, which enabled us to locate the "neutral-region" (consisting of gaseous atoms) in the Mach-Zehnder interferogram. In this paper, the polarizability of the tungsten atom at 532 nm was reconstructed based on a technique previously used for the same purpose, and the basic preconditions of the measurement were verified in detail, including the existence of the neutral region, conservation of linear density of tungsten during wire expansion, and neglect of the vaporized insulation coating. The typical imaging time varied from 80 ns to as late as 200 ns and the reconstructed polarizability of the tungsten atom was 16 ± 1 Å3, which showed good statistical consistency and was also in good agreement with the previous results.

  16. 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

  17. Detection of hepatitis C virus core protein in serum by atomic force microscopy combined with mass spectrometry

    Directory of Open Access Journals (Sweden)

    Ivanov YD

    2015-02-01

    Full Text Available Yuri D Ivanov,1 Anna L Kaysheva,1,2 Pavel A Frantsuzov,1 Tatyana O Pleshakova,1 Nikolay V Krohin,1 Alexander A Izotov,1 Ivan D Shumov,1 Vasiliy F Uchaikin,1 Vladimir A Konev,1 Vadim S Ziborov,1 Alexander I Archakov11Institute of Biomedical Chemistry, 2PostgenTech Ltd, Moscow, RussiaAbstract: A method for detection and identification of core antigen of hepatitis C virus (HCVcoreAg-containing particles in the serum was proposed, with due account taken of the interactions of proteotypic peptides with Na+, K+, and Cl- ions. The method is based on a combination of reversible biospecific atomic force microscopy (AFM-fishing and mass spectrometry (MS. AFM-fishing enables concentration, detection, and counting of protein complexes captured on the AFM chip surface, with their subsequent MS identification. Biospecific AFM-fishing of HCVcoreAg-containing particles from serum samples was carried out using AFM chips with immobilized antibodies against HCVcoreAg (HCVcoreAgim. Formation of complexes between anti-HCVcoreAgim and HCVcoreAg-containing particles on the AFM chip surface during the fishing process was demonstrated. These complexes were registered and counted by AFM. Further MS analysis allowed reliable identification of HCVcoreAg within the complexes formed on the AFM chip surface. It was shown that MS data processing, with account taken of the interactions between HCVcoreAg peptides and Na+, K+ cations, and Cl- anions, allows an increase in the number of peptides identified.Keywords: hepatitis C virus, molecular detector, biospecific fishing

  18. 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 < 0.01) twitch and tetanus contraction times compared with BEH+/+ mice, but only EDL displayed lower (P < 0.05) specific force. SOL and EDL of age-matched but not younger BEH mice showed greater exercise-induced CK efflux compared with BEH+/+ mice. In summary, myostatin dysfunction leads to impairment in muscle force generating capacity in EDL and increases susceptibility of SOL and EDL to protein loss after exercise.

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

    Energy Technology Data Exchange (ETDEWEB)

    Saha, Surajit [Department of Chemistry, Bishnupur Ramananda College, Bishnupur, Bankura 722122, West Bengal (India); 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)

    2015-07-15

    We make a rigorous exploration of the profiles of off-diagonal components of frequency-dependent linear (α{sub xy}, α{sub yx}), first nonlinear (β{sub xyy}, β{sub yxx}), and second nonlinear (γ{sub xxyy}, γ{sub 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.

  20. 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.

  1. 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.

  2. Statistical theory of polarizable target compound impregnation into a polymer coil under the influence of an electric field.

    Science.gov (United States)

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

    2017-06-21

    The paper presents a theoretical approach for describing the influence of an electric field on the conformation of an electrically neutral dielectric polymer chain dissolved in a dielectric solvent with an admixture of a target compound. Each monomer and each molecule of the target compound carries positive excess polarizability and the solvent is described as a continuous dielectric medium. The model is based on the Flory-type mean-field theory. We demonstrate non-monotonic dependences of the expansion factor and the concentration of the target compound on the strength of the electric field and molecular polarizability. Namely, the target compound concentration in the internal polymer volume as a function of electric field strength has pronounced maxima if the molecules are polarizable. In addition, the expansion factor of the non-polarizable polymer chain can be controlled by the electric field. The dependences of the expansion factor and target compound concentration on the monomer polarizability exhibit minima and intersection points. The intersection points correspond to the equality of dielectric permittivities in the bulk solution and in the internal polymer volume.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ganguly, Jayanta [Department of Chemistry, Brahmankhanda Basapara High School, Basapara, Birbhum 731 215, 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)

    2015-02-02

    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.

  4. 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)

  5. Electromagnetic Scattering of Finite and Infinite 3D Lattices in Polarizable Backgrounds

    International Nuclear Information System (INIS)

    Gallinet, Benjamin; Martin, Olivier J. F.

    2009-01-01

    A novel method is elaborated for the electromagnetic scattering from periodical arrays of scatterers embedded in a polarizable background. A dyadic periodic Green's function is introduced to calculate the scattered electric field in a lattice of dielectric or metallic objects. The method exhibits strong advantages: discretization and computation of the field are restricted to the volume of the scatterers in the unit cell, open and periodic boundary conditions for the electric field are included in the Green's tensor, and finally both near and far-fields physics are directly revealed, without any additional computational effort. Promising applications include the design of periodic structures such as frequency-selective surfaces, photonic crystals and metamaterials.

  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. Molecular response functions for the polarizable continuum model physical basis and quantum mechanical formalism

    CERN Document Server

    Cammi, Roberto

    2013-01-01

    This Brief presents the main aspects of the response functions theory (RFT) for molecular solutes described within the framework of the Polarizable Continuum Model (PCM). PCM is a solvation model for a Quantum Mechanical molecular system in which the solvent is represented as a continuum distribution of matter. Particular attention is devoted to the description of the basic features of the PCM model, and to the problems characterizing the study of the response function theory for molecules in solution with respect to the analogous theory on isolated molecules.

  8. Blackbody radiation shift, multipole polarizabilities, oscillator strengths, lifetimes, hyperfine constants, and excitation energies in Ca+

    International Nuclear Information System (INIS)

    Safronova, M. S.; Safronova, U. I.

    2011-01-01

    A systematic study of Ca + atomic properties is carried out using a 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. Reduced matrix elements, oscillator strengths, transition rates, and lifetimes are determined for the levels up to n=7. Recommended values and estimates of their uncertainties are provided for a large number of electric-dipole transitions. Electric-dipole scalar polarizabilities for the 5s, 6s, 7s, 8s, 4p j , 5p j , 3d j , and 4d j states and tensor polarizabilities for the 4p 3/2 , 5p 3/2 , 3d j , and 4d j states in Ca + are calculated. Methods are developed to accurately treat the contributions from highly excited states, resulting in significant (factor of 3) improvement in the accuracy of the 3d 5/2 static polarizability value, 31.8(3)a 0 3 , in comparison with the previous calculation [Arora et al., Phys. Rev. A 76, 064501 (2007).]. The blackbody radiation shift of the 4s-3d 5/2 clock transition in Ca + is calculated to be 0.381(4) Hz at room temperature, T=300 K. Electric-quadrupole 4s-nd and electric-octupole 4s-nf matrix elements are calculated to obtain the ground-state multipole E2 and E3 static polarizabilities. Excitation energies of the ns, np, nd, nf, and ng states with n≤ 7 in are evaluated and compared with experiment. Recommended values are provided for the 7p 1/2 , 7p 3/2 , 8p 1/2 , and 8p 3/2 removal energies for which experimental measurements are not available. The hyperfine constants A are determined for the low-lying levels up to n=7. The quadratic Stark effect on hyperfine structure levels of 43 Ca + ground state is investigated. These calculations provide recommended values critically evaluated for their accuracy for a number of Ca + atomic properties for use in planning and analysis of various experiments as well as theoretical modeling.

  9. 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

    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...... by confirming numerically the validity of the routinely invoked neglect of the J matrix contribution as well as motivating future use of the approximation that offers a reduction of the dimensionality of the eigenvalue problem. Preliminary applications to K-edge absorption of liquid water and aqueous acrolein...

  10. 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)

  11. 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

    with coupled cluster singles and doubles amplitudes, SOPPA(CCSD), and the coupled cluster singles and doubles linear response function method, CCSDLR. The frequency dependence of the polarizabilities is given in terms of the dipole oscillator strength sum rules or Cauchy moments S(-4) and S(-6). Two basis sets...... were employed, Sadlej's medium size polarized basis set and Dunning's correlation consistent basis set of triple- quality augmented by two diffuse functions of each angular momentum (daug-cc-pVTZ). The results are compared to other theoretical results as well as to experimental values for the static...

  12. 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)

  13. Domain nucleation in the contact layer at an interface of water and a polarizable substrate

    Science.gov (United States)

    Shevkunov, S. V.

    2013-10-01

    The growth of a molecular water film on the basic plane of a silver iodide monocrystal is studied through computer simulation. Decomposition into domains with spontaneous polarization is observed in the contact layer of the film at the interface with the substrate. The formation of domains is found to be sharply enhanced on a model substrate with the double polarizability of iodine ions; heteropolarization interactions caused by the formation of domain structures increase the film's coupling with the substrate. It is demonstrated that the vapor pressure needed for molecular film growth is reduced appreciably via heteropolarization interactions.

  14. 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.

  15. Surface aggregation of urinary proteins and aspartic acid-rich peptides on the faces of calcium oxalate monohydrate investigated by in situ force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, M L; Qiu, S R; Hoyer, J R; Casey, W H; Nancollas, G H; De Yoreo, J J

    2008-05-28

    The growth of calcium oxalate monohydrate in the presence of Tamm-Horsfall protein (THP), osteopontin (OPN), and the 27-residue synthetic peptides (DDDS){sub 6}DDD and (DDDG){sub 6}DDD [where D = aspartic acid and X = S (serine) or G (glycine)] was investigated via in situ atomic force microscopy (AFM). The results show that these three growth modulators create extensive deposits on the crystal faces. Depending on the modulator and crystal face, these deposits can occur as discrete aggregates, filamentary structures, or uniform coatings. These proteinaceous films can lead to either the inhibition or increase of the step speeds (with respect to the impurity-free system) depending on a range of factors that include peptide or protein concentration, supersaturation and ionic strength. While THP and the linear peptides act, respectively, to exclusively increase and inhibit growth on the (-101) face, both exhibit dual functionality on the (010) face, inhibiting growth at low supersaturation or high modulator concentration and accelerating growth at high supersaturation or low modulator concentration. Based on analyses of growth morphologies and dependencies of step speeds on supersaturation and protein or peptide concentration, we argue for a picture of growth modulation that accounts for the observations in terms of the strength of binding to the surfaces and steps and the interplay of electrostatic and solvent-induced forces at crystal surface.

  16. Cortical forces and CDC-42 control clustering of PAR proteins for Caenorhabditis elegans embryonic polarization.

    Science.gov (United States)

    Wang, Shyi-Chyi; Low, Tricia Yu Feng; Nishimura, Yukako; Gole, Laurent; Yu, Weimiao; Motegi, Fumio

    2017-08-01

    Cell polarization enables zygotes to acquire spatial asymmetry, which in turn patterns cellular and tissue axes during development. Local modification in the actomyosin cytoskeleton mediates spatial segregation of partitioning-defective (PAR) proteins at the cortex, but how mechanical changes in the cytoskeleton are transmitted to PAR proteins remains elusive. Here we uncover a role of actomyosin contractility in the remodelling of PAR proteins through cortical clustering. During embryonic polarization in Caenorhabditis elegans, actomyosin contractility and the resultant cortical tension stimulate clustering of PAR-3 at the cortex. Clustering of atypical protein kinase C (aPKC) is supported by PAR-3 clusters and is antagonized by activation of CDC-42. Cortical clustering is associated with retardation of PAR protein exchange at the cortex and with effective entrainment of advective cortical flows. Our findings delineate how cytoskeleton contractility couples the cortical clustering and long-range displacement of PAR proteins during polarization. The principles described here would apply to other pattern formation processes that rely on local modification of cortical actomyosin and PAR proteins.

  17. 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.

  18. The concept of apparent polarizability for calculating the extinction of electromagnetic radiation by porous aerosol particles

    Science.gov (United States)

    Haspel, C.; Adler, G.

    2017-04-01

    In the current study, the electromagnetic properties of porous aerosol particles are calculated in two ways. In the first, a porous target input file is generated by carving out voids in an otherwise homogeneous particle, and the discrete dipole approximation (DDA) is used to compute the extinction efficiency of the particle assuming that the voids are near vacuum dielectrics and assuming random particle orientation. In the second, an effective medium approximation (EMA) style approach is employed in which an apparent polarizability of the voids is defined based on the well-known solution to the problem in classical electrostatics of a spherical cavity within a dielectric. It is found that for porous particles with smaller overall diameter with respect to the wavelength of incident radiation, describing the voids as near vacuum dielectrics within the DDA sufficiently reproduces measured values of extinction efficiency, whereas for porous particles with moderate to larger overall diameters with respect to the wavelength of the radiation, the apparent polarizability EMA approach better reproduces the measured values of extinction efficiency.

  19. 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.

  20. Enhancement of molecular polarizabilities by the push-pull mechanism: A DFT study of substituted hexatriene

    Energy Technology Data Exchange (ETDEWEB)

    Labidi, N.S., E-mail: labidi2006@univ-usto.d [Department of chemistry, Faculty of sciences, University of the Sciences and Technology of Oran (U.S.T.O.MB), BP-1505 Oran El-M' naouer, 31000 (Algeria); Djebaili, A. [Faculte des Sciences, Universite de Batna, 05000 (Algeria)

    2010-05-25

    The static polarizabilities {alpha} for a series of substituted hexatriene molecules of the NO{sub 2}-(CH=CH){sub 3}-D and NO{sub 2}-(CH=CH){sub 3}-A types (D, A = N(Me){sub 2}, Br, OCH{sub 3},CH{sub 3}, NH{sub 2}, Cl, OH, F, COCN, C{sub 2}H, COF, NO, CHO, CN, CF{sub 3}) have been computed using DFT method at B3LYP/6-311 G(d,p) level of theory. Our results allowed to sort out the considered {Pi}-donor and {Pi}-acceptor substituents by decreasing static isotropic {alpha} value. An excellent agreement between the DFT and PM6 results, they give a correlation coefficient of 0.97. Miller QSAR-quality polarizability calculations give a correlation coefficient of 0.99 when compared with B3LYP/6-311G(d,p) values. Empirical models based on molecular volumes give unrealistic values for <{alpha}> but these values correlate well 0.97 with B3LYP/6-311G(d,p) results.

  1. Electrochemical characteristics of ideal polarizable interfaces with limited number of charge carriers.

    Science.gov (United States)

    Přibyl, Michal; Slouka, Zdeněk

    2015-11-01

    Recent progress in material chemistry and surface engineering has led to emergence of new electrode materials with unique physical and electrochemical properties. Here, we introduce a physical model describing charging of ideal polarizable electrode-electrolyte interface where the electrode is characterized by a limited capacity to store charge. The analytical model treats the electrode and electrolyte phases as independent nonlinear capacitors that are eventually coupled through the condition of equality of the total stored electrical charge opposite in sign. Gouy-Chapman and condensed layer theories applied to a general 1:n valent electrolyte are used to predict dependencies of differential capacitance of the electrolyte phase and surface concentration of the electrical charge on the applied potential. The model of the nonlinear capacitor for the electrode phase is described by a theory of electron donors and acceptors present in conductive solids as a result of thermal fluctuations. Both the differential capacitance and the surface concentration of the electrical charge in the electrode are evaluated as functions of the applied potential and related to the capacity of the electrode phase to accumulate charge and its ability to form electron donors and acceptors. The knowledge of capacitive properties of both phases allows to predict electrochemical characteristics of ideal polarizable interfaces, e.g., current responses in linear sweep voltammetry. The coupled model also shows significant potential drops in the electrode comparable to those in the electrolyte phase for materials with low charge carrier concentrations.

  2. Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system

    Science.gov (United States)

    Amano, Ken-ich; Oshima, Hiraku; Kinoshita, Masahiro

    2011-11-01

    Insertion of a large solute into an even larger vessel comprising biopolymers followed by release of the same solute from it is one of the important functions sustaining life. As a typical example, an unfolded protein is inserted into a chaperonin from bulk aqueous solution, a cochaperonin acting as a lid is attached to the chaperonin rim and the protein folds into its native structure within the closed cavity, the cochaperonin is detached after the folding is finished, and the folded protein is released back to the bulk solution. On the basis of the experimental observations manifesting that the basic aspects of the protein flux through the chaperonin system is independent of the chaperonin, cochaperonin, and protein species, we adopt a simple model system with which we can cover the whole cycle of the protein flux. We calculate the spatial distribution of the solvent-mediated potential of mean force (PMF) between a spherical solute and a cylindrical vessel or vessel/lid complex. The calculation is performed using the three-dimensional integral equation theory, and the PMF is decomposed into energetic and entropic components. We argue that an unfolded protein with a larger excluded volume (EV) and weak hydrophobicity is entropically inserted into the chaperonin cavity and constrained within a small space almost in its center. The switch from insertion to release is achieved by decreasing the EV and turning the protein surface hydrophilic in the folding process. For this release, in which the energetic component is a requisite, the feature that the chaperonin inner surface in the absence of the cochaperonin is not hydrophilic plays essential roles. On the other hand, the inner surface of the chaperonin/cochaperonin complex is hydrophilic, and the protein is energetically repelled from it: The protein remains constrained within the small space mentioned above without contacting the inner surface for correct folding. The structural and inner-surface properties of the

  3. 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.

  4. 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.

  5. Three days of intermittent stretching after muscle disuse alters the proteins involved in force transmission in muscle fibers in weanling rats.

    Science.gov (United States)

    Gianelo, M C S; Polizzelo, J C; Chesca, D; Mattiello-Sverzut, A C

    2016-02-01

    The aim of this study was to determine the effects of intermittent passive manual stretching on various proteins involved in force transmission in skeletal muscle. Female Wistar weanling rats were randomly assigned to 5 groups: 2 control groups containing 21- and 30-day-old rats that received neither immobilization nor stretching, and 3 test groups that received 1) passive stretching over 3 days, 2) immobilization for 7 days and then passive stretching over 3 days, or 3) immobilization for 7 days. Maximal plantar flexion in the right hind limb was imposed, and the stretching protocol of 10 repetitions of 30 s stretches was applied. The soleus muscles were harvested and processed for HE and picrosirius staining; immunohistochemical analysis of collagen types I, III, IV, desmin, and vimentin; and immunofluorescence labeling of dystrophin and CD68. The numbers of desmin- and vimentin-positive cells were significantly decreased compared with those in the control following immobilization, regardless of whether stretching was applied (Pstretching protocol was applied. In conclusion, the largest changes in response to stretching were observed in muscles that had been previously immobilized, and the stretching protocol applied here did not mitigate the immobilization-induced muscle changes. Muscle disuse adversely affected several proteins involved in the transmission of forces between the intracellular and extracellular compartments. Thus, the 3-day rehabilitation period tested here did not provide sufficient time for the muscles to recover from the disuse maladaptations in animals undergoing postnatal development.

  6. 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

    An intramolecular electron-transfer process has previously been shown to take place between the Cys3--Cys26 radical-ion (RSSR-) produced pulse radiolytically and the Cu(II) ion in the blue single-copper protein, azurin [Farver, O. & Pecht, I. (1989) Proc. Natl Acad. Sci. USA 86, 6868-6972]. To fu...

  7. A combined kinetic push and thermodynamic pull as driving forces for outer membrane protein sorting and folding in bacteria.

    Science.gov (United States)

    Fleming, Karen G

    2015-10-05

    In vitro folding studies of outer membrane beta-barrels have been invaluable in revealing the lipid effects on folding rates and efficiencies as well as folding free energies. Here, the biophysical results are summarized, and these kinetic and thermodynamic findings are considered in terms of the requirements for folding in the context of the cellular environment. Because the periplasm lacks an external energy source the only driving forces for sorting and folding available within this compartment are binding or folding free energies and their associated rates. These values define functions for periplasmic chaperones and suggest a biophysical mechanism for the BAM complex. © 2015 The Author(s).

  8. Ab initio determination of polarizabilities and van der Waals coefficients of Li atoms using the relativistic coupled-cluster method

    NARCIS (Netherlands)

    Wansbeek, L. W.; Sahoo, B. K.; Timmermans, R. G. E.; Das, B. P.; Mukherjee, D.

    We report on a technique to determine the van der Waals coefficients of lithium (Li) atoms based on relativistic coupled-cluster theory. These quantities are determined using the imaginary parts of the scalar dipole and quadrupole polarizabilities, which are evaluated using an approach that we have

  9. 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.

  10. 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.

  11. 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)

  12. 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

  13. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

    Science.gov (United States)

    Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik

    2018-02-19

    Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.

  14. 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.

  15. The Second-Order Polarization Propagator Approximation (SOPPA) method coupled to the polarizable continuum model

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Solanko, Lukasz Michal; Nåbo, Lina J.

    2014-01-01

    We present an implementation of the Polarizable Continuum Model (PCM) in combination with the Second–Order Polarization Propagator Approximation (SOPPA) electronic structure method. In analogy with the most common way of designing ground state calculations based on a Second–Order Møller-Plesset (MP......2) wave function coupled to PCM, we introduce dynamical PCM solvent effects only in the Random Phase Approximation (RPA) part of the SOPPA response equations while the static solvent contribution is kept in both the RPA terms as well as in the higher order correlation matrix components of the SOPPA...... response equations. By dynamic terms, we refer to contributions that describe a change in environmental polarization which, in turn, reflects a change in the core molecular charge distribution upon an electronic excitation. This new combination of methods is termed PCM-SOPPA/RPA. We apply this newly...

  16. 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...

  17. Virtual Compton Scattering at MAMI and measurement of the proton generalized polarizabilities

    International Nuclear Information System (INIS)

    Roche, Julie

    1998-01-01

    We have measured the absolute unpolarized cross sections for photon electro-production of the proton with the Three-Spectrometer-Setup at MAMI at a momentum transfer q=600 MeV (or squared quadra-momentum of the virtual photon 0.33 GeV square) and a virtual photon polarization 0.62. The momentum for the outgoing real photon q' ranged from 33 to 111 MeV. We extracted two combinations of the generalized polarizabilities (GPs) of the proton. The reaction of interest is Virtual Compton Scattering off the proton. We can access to a measurement of the rigidity of the internal structure of the nucleon. Below pion production threshold but arbitrary squared quadra-momentum of the virtual photon, measured observables are the GPs. They generalize the concept of electric and magnetic polarizabilities already defined in Real Compton Scattering. Experimentally, the scattered electron was detected in coincidence with the recoiling proton in two high-resolution spectrometers. The photon emission process was selected by a cut on the missing mass squared distribution around zero. This PhD work describes the analysis work from raw data to absolute and precise cross sections (within a 3 pc statistical and 4 pc systematic accuracies). Our experiment at Mainz demonstrates that it is possible to measure two structure functions related to the GPs; extracted values are presented. These observables are compared with theoretical predictions and are very efficient to disentangle models of the non-perturbative structure of the nucleon. (author) [fr

  18. 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.

  19. 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

    Directory of Open Access Journals (Sweden)

    Elena Antonini

    2018-02-01

    Full Text Available 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.

  20. 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

  1. Polarizable charge equilibration model for predicting accurate electrostatic interactions in molecules and solids

    Science.gov (United States)

    Naserifar, Saber; Brooks, Daniel J.; Goddard, William A.; Cvicek, Vaclav

    2017-03-01

    Electrostatic interactions play a critical role in determining the properties, structures, and dynamics of chemical, biochemical, and material systems. These interactions are described well at the level of quantum mechanics (QM) but not so well for the various models used in force field simulations of these systems. We propose and validate a new general methodology, denoted PQEq, to predict rapidly and dynamically the atomic charges and polarization underlying the electrostatic interactions. Here the polarization is described using an atomic sized Gaussian shaped electron density that can polarize away from the core in response to internal and external electric fields, while at the same time adjusting the charge on each core (described as a Gaussian function) so as to achieve a constant chemical potential across all atoms of the system. The parameters for PQEq are derived from experimental atomic properties of all elements up to Nobelium (atomic no. = 102). We validate PQEq by comparing to QM interaction energy as probe dipoles are brought along various directions up to 30 molecules containing H, C, N, O, F, Si, P, S, and Cl atoms. We find that PQEq predicts interaction energies in excellent agreement with QM, much better than other common charge models such as obtained from QM using Mulliken or ESP charges and those from standard force fields (OPLS and AMBER). Since PQEq increases the accuracy of electrostatic interactions and the response to external electric fields, we expect that PQEq will be useful for a large range of applications including ligand docking to proteins, catalytic reactions, electrocatalysis, ferroelectrics, and growth of ceramics and films, where it could be incorporated into standard force fields as OPLS, AMBER, CHARMM, Dreiding, ReaxFF, and UFF.

  2. 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

    these substitutions are not in the microenvironment separating the electron donor and acceptor, they were expected to affect the LRET rate because of their effect on the redox potential of the copper site and thus on the driving force of the reaction, as well as on the reorganization energies of the copper site....... The rate of intramolecular electron transfer from RSSR- to Cu(II) in the wild-type P. aeruginosa azurin (delta G degrees = -68.9 kJ/mol) has previously been determined to be 44 +/- 7 s-1 at 298 K, pH 7.0. The [M44K]azurin mutant (delta G degrees = -75.3 kJ/mol) was now found to react considerably faster (k...... = 134 +/- 12 s-1 at 298 K, pH 7.0) while the [H35Q]azurin mutant (delta G degrees = -65.4 kJ/mol) exhibits, within experimental error, the same specific rate (k = 52 +/- 11 s-1, 298 K, pH 7.0) as that of the wild-type azurin. From the temperature dependence of these LRET rates the following activation...

  3. Hyperthermophile protein behavior: partially-structured conformations of Pyrococcus furiosus rubredoxin monomers generated through forced cold-denaturation and refolding.

    Directory of Open Access Journals (Sweden)

    Sanjeev Kumar Chandrayan

    Full Text Available Some years ago, we showed that thermo-chemically denatured, partially-unfolded forms of Pyrococcus furiosus triosephosphateisomerase (PfuTIM display cold-denaturation upon cooling, and heat-renaturation upon reheating, in proportion with the extent of initial partial unfolding achieved. This was the first time that cold-denaturation was demonstrated for a hyperthermophile protein, following unlocking of surface salt bridges. Here, we describe the behavior of another hyperthermophile protein, the small, monomeric, 53 residues-long rubredoxin from Pyrococcus furiosus (PfRd, which is one of the most thermostable proteins known to man. Like PfuTIM, PfRd too displays cold-denaturation after initial thermo-chemical perturbation, however, with two differences: (i PfRd requires considerably higher temperatures as well as higher concentrations of guanidium hydrochloride (Gdm.HCl than PfuTIM; (ii PfRd's cold-denaturation behavior during cooling after thermo-chemical perturbation is incompletely reversible, unlike PfuTIM's, which was clearly reversible (from each different conformation generated. Differential cold-denaturation treatments allow PfRd to access multiple partially-unfolded states, each of which is clearly highly kinetically-stable. We refer to these as 'Trishanku' unfolding intermediates (or TUIs. Fascinatingly, refolding of TUIs through removal of Gdm.HCl generates multiple partially-refolded, monomeric, kinetically-trapped, non-native 'Trishanku' refolding intermediates (or TRIs, which differ from each other and from native PfRd and TUIs, in structural content and susceptibility to proteolysis. We find that the occurrence of cold denaturation and observations of TUI and TRI states is contingent on the oxidation status of iron, with redox agents managing to modulate the molecule's behavior upon gaining access to PfRd's iron atom. Mass spectrometric examination provides no evidence of the formation of disulfide bonds, but other experiments

  4. Off-planar geometry and structural instability of EDO-TTF explained by using the extended debye polarizability model for bond angles.

    Science.gov (United States)

    Linker, Gerrit-Jan; van Duijnen, Piet Th; van Loosdrecht, Paul H M; Broer, Ria

    2012-07-05

    The geometry of ethylenedioxy-tetrathiafulvalene, EDO-TTF, plays an important role in the metal-insulator transition in the charge transfer salt (EDO-TTF)(2)PF(6). The planar and off-planar geometrical conformations of the EDO-TTF molecules are explained using an extended Debye polarizability model for the bond angle. The geometrical structure of EDO-TTF is dictated by its four sulfur bond angles and these are, in turn, determined by the polarizability of the sulfur atoms. With Hartree-Fock and second-order Møller-Plesset perturbation theory calculations on EDO-TTF, TTF, H(2)S, and their oxygen and selenium substituted counterparts we confirm this hypothesis. The Debye polarizability model for bond angles relates directly the optimum bond angle with the polarizability of the center atom. Considering the (EDO-TTF)(2)PF(6) material in this light proves to be very fruitful.

  5. Forces in yeast flocculation

    Science.gov (United States)

    El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Vincent, Stéphane P.; Abellán Flos, Marta; Hols, Pascal; Lipke, Peter N.; Dufrêne, Yves F.

    2015-01-01

    In the baker's yeast Saccharomyces cerevisiae, cell-cell adhesion (``flocculation'') is conferred by a family of lectin-like proteins known as the flocculin (Flo) proteins. Knowledge of the adhesive and mechanical properties of flocculins is important for understanding the mechanisms of yeast adhesion, and may help controlling yeast behaviour in biotechnology. We use single-molecule and single-cell atomic force microscopy (AFM) to explore the nanoscale forces engaged in yeast flocculation, focusing on the role of Flo1 as a prototype of flocculins. Using AFM tips labelled with mannose, we detect single flocculins on Flo1-expressing cells, showing they are widely exposed on the cell surface. When subjected to force, individual Flo1 proteins display two distinct force responses, i.e. weak lectin binding forces and strong unfolding forces reflecting the force-induced extension of hydrophobic tandem repeats. We demonstrate that cell-cell adhesion bonds also involve multiple weak lectin interactions together with strong unfolding forces, both associated with Flo1 molecules. Single-molecule and single-cell data correlate with microscale cell adhesion behaviour, suggesting strongly that Flo1 mechanics is critical for yeast flocculation. These results favour a model in which not only weak lectin-sugar interactions are involved in yeast flocculation but also strong hydrophobic interactions resulting from protein unfolding.

  6. Protein and lipid oxidative damage in streptozotocin-induced diabetic rats submitted to forced swimming test: the insulin and clonazepam effect.

    Science.gov (United States)

    Wayhs, Carlos Alberto Yasin; Manfredini, Vanusa; Sitta, Angela; Deon, Marion; Ribas, Graziela; Vanzin, Camila; Biancini, Giovana; Ferri, Marcelo; Nin, Maurício; Barros, Helena Maria Tannhauser; Vargas, Carmen Regla

    2010-09-01

    Diabetes may modify central nervous system functions and is associated with moderate cognitive deficits and changes in the brain, a condition that may be referred to as diabetic encephalopathy. The prevalence of depression in diabetic patients is higher than in the general population, and clonazepam is being used to treat this complication. Oxidative stress may play a role in the development of diabetes complications. We investigated oxidative stress parameters in streptozotocin-induced diabetic rats submitted to forced swimming test (STZ) and evaluated the effect of insulin (STZ-INS) and/or clonazepam (STZ-CNZ and STZ-INS-CNZ) acute treatment on these animal model. Oxidative damage to proteins measured as carbonyl content in plasma was significantly increased in STZ group compared to STZ treated groups. Malondialdehyde plasma levels were significantly reduced in STZ-INS and STZ-INS-CNZ groups when compared to STZ rats, being significantly reduced in STZ-INS-CNZ than STZ-INS rats. The activities of the antioxidant enzymes catalase, superoxide dismutase and glutathione peroxidase showed no significant differences among all groups of animals. These findings showed that protein and lipid damage occurs in this diabetes/depression animal model and that the associated treatment of insulin and clonazepam is capable to protect against oxidative damage in this experimental model.

  7. 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.

  8. Ab initio self-consistent calculations of the Compton profiles and polarizabilities of diamond and cubic boron nitride

    CERN Document Server

    Ayma, D; Lichanot, A

    1998-01-01

    Compton profiles, polarizabilities and related functions of diamond and cubic boron nitride have been investigated within the Hartree-Fock approximation and the density functional theory, calculated within the local density approximation and generalized gradient approximation, but without any explicit correlation correction for the Compton profiles. The correlation part already included in the standard uncorrected density functional theory is deduced from the comparison of the two types of calculation. The Compton profile and reciprocal-form-factor anisotropies, polarizability, dielectric constant and energy loss function of the two compounds are compared at the same level of accuracy. These properties are very close in spite of the rather different chemical bonds due to the charge transfer occurring in cubic boron nitride and gaps. (author)

  9. 4fn-15d centroid shift in lanthanides and relation with anion polarizability, covalency, and cation electronegativity

    International Nuclear Information System (INIS)

    Dorenbos, P.; Andriessen, J.; Eijk, C.W.E. van

    2003-01-01

    Data collected on the centroid shift of the 5d-configuration of Ce 3+ in oxide and fluoride compounds were recently analyzed with a model involving the correlated motion between 5d-electron and ligand electrons. The correlation effects are proportional to the polarizability of the anion ligands and it leads, like covalency, to lowering of the 5d-orbital energies. By means of ab initio Hartree-Fock-LCAO calculations including configuration interaction the contribution from covalency and correlated motion to the centroid shift are determined separately for Ce 3+ in various compounds. It will be shown that in fluoride compounds, covalency provides an insignificant contribution. In oxides, polarizability appears to be of comparable importance as covalency

  10. 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.

  11. Electric birefringence and streaming-electric birefringence of synthesized imogolite: the anisotropy of electric polarizability.

    Science.gov (United States)

    Matsumoto, Mitsuhiro; Koibuchi, Sae; Hayashi, Naoki

    2007-04-15

    Imogolite synthesized from sodium orthosilicate and aluminum trichloride was fractionated into four fractions by centrifuging at 12,000 x g (1h). The supernatant, which did not deposit by three times centrifugations, was used for all measurements. The signal of birefringence under a reversing electric pulse showed that the permanent dipole moment is negligibly small at low fields. The electric birefringence under a rectangular electric pulse is positive. The saturated value is proportional to the concentration of imogolite in the range of 0-0.1mg/ml and decreases rapidly with an increase of added salt concentration for NaCl and AgNO(3). It slightly depends on the pH of solution and is biggest in pure water. Then we have determined the anisotropy of electric polarizability (Deltaalpha) for imogolite in pure water at 0.05 mg/ml. Deltaalpha we obtained from the method decreases rapidly at low fields and slowly at high fields as shown in references [M. Matsumoto, Colloids Surf. A 148 (1999) 75, M. Matsumoto, Biophys. Chem. 58 (1996) 173]. It is approximately shown by the following expression, Deltaalpha=Deltaalpha(infinity)+(Deltaalpha(0)-Deltaalpha(infinity))/(1+KE), (Deltaalpha(0):Deltaalpha at E=0, Deltaalpha(infinity):Deltaalpha at E=infinity). Using this relation we can draw the curve of electric birefringence as a function of electric field and compare it with experimental values. The results, when Deltaalpha(0)=1.17x10(-28)Fm(2), Deltaalpha(infinity)=0.005x10(-28)Fm(2) and K=0.00031 m/V, are in good agreement with each other. In order to explain the reason why the anisotropy of electric polarizability rapidly decreases with an increase of electric field we propose that the difference of electrophoretic mobility between parts of colloidal particle causes the orientation of a rod like particle. The theoretical electric birefringence as a function of electric field we obtained is considerably in good agreement with the experimental values.

  12. Tunability of RF-Responses by Plasmonic Dielectric Amplification Using Branched e- -Polarizable C60-Adducts on Magnetic (Postprint)

    Science.gov (United States)

    2016-07-18

    energy can lead to the formation of polarizations at the surface region. Polarizability of this particular type of NPs, as a function of the size...Soumekh, M. Synthetic Aperture Radar Signal Processing with MATLAB Algorithms ; John Wiley & Sons: New York, 1999. (16) Kong, J. A. Electromagnetic Wave...FeOx NP core, was effectively released at the light-off stage to induce the intramolecular polarization of C60-DPAF adducts. Resulting charged

  13. 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)

  14. 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.

  15. Dipole polarizability of alkali-metal (Na, K, Rb)-alkaline-earth-metal (Ca, Sr) polar molecules: Prospects for alignment

    Science.gov (United States)

    Gopakumar, Geetha; Abe, Minori; Hada, Masahiko; Kajita, Masatoshi

    2014-06-01

    Electronic open-shell ground-state properties of selected alkali-metal-alkaline-earth-metal polar molecules are investigated. We determine potential energy curves of the 2Σ+ ground state at the coupled-cluster singles and doubles with partial triples (CCSD(T)) level of electron correlation. Calculated spectroscopic constants for the isotopes (23Na, 39K, 85Rb)-(40Ca, 88Sr) are compared with available theoretical and experimental results. The variation of the permanent dipole moment (PDM), average dipole polarizability, and polarizability anisotropy with internuclear distance is determined using finite-field perturbation theory at the CCSD(T) level. Owing to moderate PDM (KCa: 1.67 D, RbCa: 1.75 D, KSr: 1.27 D, RbSr: 1.41 D) and large polarizability anisotropy (KCa: 566 a.u., RbCa: 604 a.u., KSr: 574 a.u., RbSr: 615 a.u.), KCa, RbCa, KSr, and RbSr are potential candidates for alignment and orientation in combined intense laser and external static electric fields.

  16. 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.

  17. 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)

  18. Structural properties governing drug-plasma protein binding determined by high-performance liquid chromatography method.

    Science.gov (United States)

    Kamble, Sharad; Loadman, Paul; Abraham, Michael H; Liu, Xiangli

    2018-02-05

    The high-performance liquid chromatography (HPLC) method employing stationary phases immobilized with plasma proteins was used for this study to investigate the structural properties governing drug-plasma protein binding. A set of 65 compounds with a broad range of structural diversity (in terms of volume, hydrogen-bonding, polarity and electrostatic force) were selected for this purpose. The Abraham linear free energy relationship (LFER) analyses of the retention factors on the immobilized HSA (human serum albumin) and AGP (α 1 -acid glycoprotein) stationary phases showed that McGowan's characteristic molecular volume (V), dipolarity/polarizability (S) and hydrogen bond basicity (B) are the three significant molecular descriptors of solutes determining the interaction with immobilized plasma proteins, whereas excess molar refraction (E) is less important and hydrogen bond acidity (A) is not of statistical significance in both systems, for electrically neutral compounds. It was shown that ionised acids, as carboxylate anions, bind very strongly to the immobilized HSA stationary phase and that ionised bases, as cations bind strongly to the AGP stationary phase. This is the first time that the effect of ionised species on plasma protein binding has been determined quantitatively; the increased binding of acids to HSA is due almost entirely to acids in their ionised form. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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.

  20. 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.

  1. 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)

  2. 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.

  3. 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.

  4. Electrophoresis of a polarizable charged colloid with hydrophobic surface: A numerical study

    Science.gov (United States)

    Bhattacharyya, Somnath; Majee, Partha Sarathi

    2017-04-01

    We consider the electrophoresis of a charged colloid for a generalized situation in which the particle is considered to be polarizable and the surface exhibits hydrophobicity. The dielectric polarization of the particle creates a nonlinear dependence of the electrophoretic velocity on the applied electric field, and the core hydrophobicity amplifies the fluid convection in the Debye layer. Thus, a linear analysis is no longer applicable for this situation. The present analysis is based on the numerical solution of the nonlinear electrokinetic equations based on the Navier-Stokes-Nernst-Planck-Poisson equations coupled with the Laplace equation for the electric field within the dielectric particle. The hydrophobicity of the particle may influence its electric polarization by enhancing the convective transport of ions. The nonlinear effects, such as double-layer polarization and relaxation, are also influenced by the hydrophobicity of the particle surface. The present results compare well for a lower range of the applied electric field and surface charge density with the existing results for a perfectly dielectric particle with a hydrophobic surface based on the first-order perturbation analysis due to Khair and Squires [Phys. Fluids 21, 042001 (2009), 10.1063/1.3116664]. Dielectric polarization creates a reduction in particle electrophoretic velocity, and its impact is strong for a moderate range of Debye length. A quantitative measure of the nonlinear effects is demonstrated by comparing the electrophoretic velocity with an existing linear model.

  5. 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.

  6. 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

  7. Blackbody radiation shift, multipole polarizabilities, oscillator strengths, lifetimes, hyperfine constants, and excitation energies in Hg+

    International Nuclear Information System (INIS)

    Simmons, M.; Safronova, M. S.; Safronova, U. I.

    2011-01-01

    Excitation energies of the [Xe]4f 14 5d 10 ns, [Xe]4f 14 5d 10 np j , [Xe]4f 14 5d 10 nd j , [Xe]4f 14 5d 10 n ' f j , and [Xe]4f 14 5d 10 n ' g j states in Hg + are evaluated (n≤10, n ' ≤9, and [Xe]=1s 2 2s 2 2p 6 3s 2 3p 6 3d 10 4s 2 4p 6 4d 10 5s 2 5p 6 ). First-, second-, third-, and all-order Coulomb energies and first- and second-order Coulomb-Breit energies are calculated. Reduced matrix elements, oscillator strengths, and transition rates are determined for electric-dipole transitions, including the ns (n=6-11), np (n=6-10), nd (n=6-10), nf (n=5-9), and ng (n=5-9) states. Lifetime values are determined for all above-mentioned states. The ground state E1, E2, and E3 polarizabilities are evaluated. The hyperfine structure in 199 Hg + and 201 Hg + ions is investigated. The hyperfine A and B values are determined for the first low-lying levels up to n = 7. The quadratic Stark effect on hyperfine structure levels of 199 Hg + and 201 Hg + ground states is investigated. The calculated shift for the 199 Hg + (F = 1, M = 0) ↔ (F = 0, M = 0) transition is -0.0597(2) Hz/(kV/cm) 2 , in agreement with previous theoretical result -0.060(3) Hz/(kV/cm) 2 . These calculations provide a theoretical benchmark for comparison with experiment and theory and provide values of blackbody radiation shifts for microwave frequency standards with 199 Hg + and 201 Hg + ions.

  8. Electrochemical Solvent Reorganization Energies in the Framework of the Polarizable Continuum Model.

    Science.gov (United States)

    Ghosh, Soumya; Horvath, Samantha; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2014-05-13

    Electron transfer reactions at electrochemical interfaces play a critical role in a wide range of catalytic processes. A key parameter in the rate constant expressions for such processes is the reorganization energy, which reflects the energetic cost of the solute and solvent rearrangements upon electron transfer. In this paper, we present dielectric continuum methods for calculating the solvent reorganization energy for electrochemical processes. We develop a method for calculating the electrochemical solvent reorganization energies with molecular-shaped cavities within the framework of the polarizable continuum model (PCM). The electronic and inertial responses of the solvent are separated according to their respective time scales, and two limiting cases of the relation between the solute and solvent electrons are examined. The effects of the electrode are included with the integral equations formalism PCM (IEF-PCM), in which the molecule-solvent boundary is treated explicitly, but the effects of the electrode-solvent boundary are included through an external Green's function. This approach accounts for the effects of detailed molecular charge redistribution in a molecular-shaped cavity, as well as the electronic and inertial solvent responses and the effects of the electrode. The calculated total reorganization energies are in reasonable agreement with experimental measurements for a series of electrochemical systems. Inclusion of the effects of the electrode is found to be essential for obtaining even qualitatively accurate solvent reorganization energies. These approaches are applicable to a wide range of systems and can be extended to include other types of boundaries, such as a self-assembled monolayer or double layer separating the electrode and the molecule.

  9. Direct measurements of the frequency-dependent dielectrophoresis force.

    Science.gov (United States)

    Wei, Ming-Tzo; Junio, Joseph; Ou-Yang, H Daniel

    2009-01-02

    Dielectrophoresis (DEP), the phenomenon of directed motion of electrically polarizable particles in a nonuniform electric field, is promising for applications in biochemical separation and filtration. For colloidal particles in suspension, the relaxation of the ionic species in the shear layer gives rise to a frequency-dependent, bidirectional DEP force in the radio frequency range. However, quantification methods of the DEP force on individual particles with the pico-Newton resolution required for the development of theories and design of device applications are lacking. We report the use of optical tweezers as a force sensor and a lock-in phase-sensitive technique for analysis of the particle motion in an amplitude modulated DEP force. The coherent detection and sensing scheme yielded not only unprecedented sensitivity for DEP force measurements, but also provided a selectivity that clearly distinguishes the pure DEP force from all the other forces in the system, including electrophoresis, electro-osmosis, heat-induced convection, and Brownian forces, all of which can hamper accurate measurements through other existing methods. Using optical tweezers-based force transducers already developed in our laboratory, we have results that quantify the frequency-dependent DEP force and the crossover frequency of individual particles with this new experimental method.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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...

  17. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper

    2015-01-01

    of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation...

  18. Collision-induced Raman scattering by rare-gas atoms: The isotropic spectrum of Ne–Ne and its mean polarizability

    Energy Technology Data Exchange (ETDEWEB)

    Rachet, Florent; Chrysos, Michael, E-mail: michel.chrysos@univ-angers.fr [LUNAM Université, Université d’Angers, CNRS UMR 6200, Laboratoire MOLTECH-Anjou, 2 Bd Lavoisier, 49045 Angers (France); Dixneuf, Sophie [Forschungszentrum Jülich GmbH IEK-8, Troposphere, 52425 Jülich (Germany)

    2015-05-07

    We report the room-temperature isotropic collision-induced light scattering spectrum of Ne–Ne over a wide interval of Raman shifts, and we compare it with the only available experimental spectrum for that system as well as with spectra calculated quantum-mechanically with the employ of advanced ab initio-computed data for the incremental mean polarizability. The spectral range previously limited to 170 cm{sup −1} is now extended to 485 cm{sup −1} allowing us to successfully solve the inverse-scattering problem toward an analytic model for the mean polarizability that perfectly matches our measurements. We also report the depolarization ratio of the scattering process, lingering over the usefulness of this property for more stringent checks between the various polarizability models.

  19. Collision-induced Raman scattering by rare-gas atoms: The isotropic spectrum of Ne-Ne and its mean polarizability.

    Science.gov (United States)

    Rachet, Florent; Dixneuf, Sophie; Chrysos, Michael

    2015-05-07

    We report the room-temperature isotropic collision-induced light scattering spectrum of Ne-Ne over a wide interval of Raman shifts, and we compare it with the only available experimental spectrum for that system as well as with spectra calculated quantum-mechanically with the employ of advanced ab initio-computed data for the incremental mean polarizability. The spectral range previously limited to 170 cm(-1) is now extended to 485 cm(-1) allowing us to successfully solve the inverse-scattering problem toward an analytic model for the mean polarizability that perfectly matches our measurements. We also report the depolarization ratio of the scattering process, lingering over the usefulness of this property for more stringent checks between the various polarizability models.

  20. 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…

  1. Machine Learning Force Field Parameters from Ab Initio Data

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ying [Argonne; Li, Hui [Department; Pickard, Frank C. [Laboratory; Narayanan, Badri [Center; Sen, Fatih G. [Center; Chan, Maria K. Y. [Center; Computational; Sankaranarayanan, Subramanian K. R. S. [Center; Computational; Brooks, Bernard R. [Laboratory; Roux, Benoît [Department; Center; Computational

    2017-08-11

    Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.

  2. Force acting on an atom and a classical oscillator in an electromagnetic field

    International Nuclear Information System (INIS)

    Makarov, V. P.; Rukhadze, A. A.

    2010-01-01

    The expression for the force exerted by the field on an atom and averaged over the field period is derived in quantum-mechanical perturbation theory, in which a quasi-monochromatic electromagnetic field plays the role of a perturbation. An approximate solution is obtained to the classical (Newton) equation of motion in the same field for a harmonic isotropic oscillator. In both problems, the expressions for the force acting on a particle are completely identical if they are written in terms of the polarizability (of the atom and the oscillator). These results conform with the data obtained in macroscopic electrodynamics for rarefied media.

  3. 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...

  4. 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

  5. Analytical gradients for MP2, double hybrid functionals, and TD‐DFT with polarizable embedding described by fluctuating charges

    Science.gov (United States)

    Carnimeo, Ivan; Cappelli, Chiara

    2015-01-01

    A polarizable quantum mechanics (QM)/ molecular mechanics (MM) approach recently developed for Hartree–Fock (HF) and Kohn–Sham (KS) methods has been extended to energies and analytical gradients for MP2, double hybrid functionals, and TD‐DFT models, thus allowing the computation of equilibrium structures for excited electronic states together with more accurate results for ground electronic states. After a detailed presentation of the theoretical background and of some implementation details, a number of test cases are analyzed to show that the polarizable embedding model based on fluctuating charges (FQ) is remarkably more accurate than the corresponding electronic embedding based on a fixed charge (FX) description. In particular, a set of electronegativities and hardnesses has been optimized for interactions between QM and FQ regions together with new repulsion–dispersion parameters. After validation of both the numerical implementation and of the new parameters, absorption electronic spectra have been computed for representative model systems including vibronic effects. The results show remarkable agreement with full QM computations and significant improvement with respect to the corresponding FX results. The last part of the article provides some hints about computation of solvatochromic effects on absorption spectra in aqueous solution as a function of the number of FQ water molecules and on the use of FX external shells to improve the convergence of the results. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26399473

  6. HPr(His~P)-mediated Phosphorylation Differently Affects Counterflow and Proton Motive Force-driven Uptake via the Lactose Transport Protein of Streptococcus thermophilus

    NARCIS (Netherlands)

    Gunnewijk, M.G W; Poolman, B.

    2000-01-01

    The lactose transport protein (LacS) of Streptococcus thermophilus has a C-terminal hydrophilic domain that is homologous to IIA protein and protein domains of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). The IIA domain of LacS is phosphorylated on His-552 by the general

  7. Out-of-equilibrium relaxation of the thermal Casimir effect in a model polarizable material.

    Science.gov (United States)

    Dean, David S; Démery, Vincent; Parsegian, V Adrian; Podgornik, Rudolf

    2012-03-01

    Relaxation of the thermal Casimir or van der Waals force (the high temperature limit of the Casimir force) for a model dielectric medium is investigated. We start with a model of interacting polarization fields with a dynamics that leads to a frequency dependent dielectric constant of the Debye form. In the static limit, the usual zero frequency Matsubara mode component of the Casimir force is recovered. We then consider the out-of-equilibrium relaxation of the van der Waals force to its equilibrium value when two initially uncorrelated dielectric bodies are brought into sudden proximity. For the interaction between dielectric slabs, it is found that the spatial dependence of the out-of-equilibrium force is the same as the equilibrium one, but it has a time dependent amplitude, or Hamaker coefficient, which increases in time to its equilibrium value. The final relaxation of the force to its equilibrium value is exponential in systems with a single or finite number of polarization field relaxation times. However, in systems, such as those described by the Havriliak-Negami dielectric constant with a broad distribution of relaxation times, we observe a much slower power law decay to the equilibrium value.

  8. 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

  9. Forced marriage.

    Science.gov (United States)

    2007-06-01

    Guidelines to help A&E staff and other healthcare professionals who suspect cases of forced marriage were launched this month by the government. The guidelines provide practical advice on how to recognise the warning signs, and what to do if patients disclose that they have been, or are about to be, forced to marry. The guidelines, Dealing with Cases of Forced Marriage, are available at www.fco.gov.uk/forcedmarriage.

  10. Decreased specific force and power production of muscle fibers from myostatin-deficient mice are associated with a suppression of protein degradation

    OpenAIRE

    Mendias, Christopher L.; Kayupov, Erdan; Bradley, Joshua R.; Brooks, Susan V.; Claflin, Dennis R.

    2011-01-01

    Myostatin (MSTN) is a member of the transforming growth factor-β superfamily of cytokines and is a negative regulator of skeletal muscle mass. Compared with MSTN+/+ mice, the extensor digitorum longus muscles of MSTN−/− mice exhibit hypertrophy, hyperplasia, and greater maximum isometric force production (Fo), but decreased specific maximum isometric force (sFo; Fo normalized by muscle cross-sectional area). The reason for the reduction in sFo was not known. Studies in myotubes indicate that ...

  11. 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.

  12. Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein.

    Science.gov (United States)

    Tipmanee, Varomyalin; Oberhofer, Harald; Park, Mina; Kim, Kwang S; Blumberger, Jochen

    2010-12-01

    The acceleration of electron transfer (ET) rates in redox proteins relative to aqueous solutes can be attributed to the protein's ability to reduce the nuclear response or reorganization upon ET, while maintaining sufficiently high electronic coupling. Quantitative predictions of reorganization free energy remain a challenge, both experimentally and computationally. Using density functional calculations and molecular dynamics simulation with an electronically polarizable force field, we report reorganization free energies for intraprotein ET in four heme-containing ET proteins that differ in their protein fold, hydrophilicity, and solvent accessibility of the electron-accepting group. The reorganization free energies for ET from the heme cofactors of cytochrome c and b(5) to solvent exposed Ru-complexes docked to histidine residues at the surface of these proteins fall within a narrow range of 1.2-1.3 eV. Reorganization free energy is significantly lowered in a designed 4-helix bundle protein where both redox active cofactors are protected from the solvent. For all ET reactions investigated, the major components of reorganization are the solvent and the protein, with the solvent contributing close to or more than 50% of the total. In three out of four proteins, the protein reorganization free energy can be viewed as a collective effect including many residues, each of which contributing a small fraction. These results have important implications for the design of artificial electron transport proteins. They suggest that reorganization free energy may in general not be effectively controlled by single point mutations, but to a large extent by the degree of solvent exposure of the ionizable cofactors.

  13. Intermolecular polarizabilities in H{sub 2}-rare-gas mixtures (H{sub 2}–He, Ne, Ar, Kr, Xe): Insight from collisional isotropic spectral properties

    Energy Technology Data Exchange (ETDEWEB)

    Głaz, Waldemar, E-mail: glaz@kielich.amu.edu.pl; Bancewicz, Tadeusz [Nonlinear Optics Division, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland); Godet, Jean-Luc [Laboratoire de photonique d’Angers, Université d’Angers, 2 boulevard Lavoisier, 49045 Angers (France); Gustafsson, Magnus [Department of Chemistry and Molecular Biology, University of Gothenburg, SE 412 96 Gothenburg (Sweden); Maroulis, George; Haskopoulos, Anastasios [Department of Chemistry, University of Patras, GR-26500 Patras (Greece)

    2014-08-21

    The report presents results of theoretical and numerical analysis of the electrical properties related to the isotropic part of the polarizability induced by interactions within compounds built up of a hydrogen H{sub 2} molecule and a set of noble gas atoms, Rg, ranging from the least massive helium up to the heaviest xenon perturber. The Cartesian components of the collisional polarizabilities of the H{sub 2}–Rg systems are found by means of the quantum chemistry methods and their dependence on the intermolecular distance is determined. On the basis of these data, the spherical, symmetry adapted components of the trace polarizability are derived in order to provide data sets that are convenient for evaluating collisional spectral profiles of the isotropic polarized part of light scattered by the H{sub 2}–Rg mixtures. Three independent methods of numerical computing of the spectral intensities are applied at room temperature (295 K). The properties of the roto-translational profiles obtained are discussed in order to determine the role played by contributions corresponding to each of the symmetry adapted parts of the trace polarizability. By spreading the analysis over the collection of the H{sub 2}–Rg systems, evolution of the spectral properties with the growing masses of the supermolecular compounds can be observed.

  14. Off-Planar Geometry and Structural Instability of EDO-TTF Explained by Using the Extended Debye Polarizability Model for Bond Angles

    NARCIS (Netherlands)

    Linker, Gerrit-Jan; van Duijnen, Piet Th.; van Loosdrecht, Paul H. M.; Broer-Braam, Henderika

    2012-01-01

    The geometry of ethylenedioxy-tetrathiafulvalene, EDO-TTF, plays an important role in the metal-insulator transition in the charge transfer salt (EDO-TTF)(2)PF6. The planar and off-planar geometrical conformations of the EDO-TTF molecules are explained using an extended Debye polarizability model

  15. Intermolecular polarizabilities in H2-rare-gas mixtures (H2-He, Ne, Ar, Kr, Xe): insight from collisional isotropic spectral properties.

    Science.gov (United States)

    Głaz, Waldemar; Bancewicz, Tadeusz; Godet, Jean-Luc; Gustafsson, Magnus; Maroulis, George; Haskopoulos, Anastasios

    2014-08-21

    The report presents results of theoretical and numerical analysis of the electrical properties related to the isotropic part of the polarizability induced by interactions within compounds built up of a hydrogen H2 molecule and a set of noble gas atoms, Rg, ranging from the least massive helium up to the heaviest xenon perturber. The Cartesian components of the collisional polarizabilities of the H2-Rg systems are found by means of the quantum chemistry methods and their dependence on the intermolecular distance is determined. On the basis of these data, the spherical, symmetry adapted components of the trace polarizability are derived in order to provide data sets that are convenient for evaluating collisional spectral profiles of the isotropic polarized part of light scattered by the H2-Rg mixtures. Three independent methods of numerical computing of the spectral intensities are applied at room temperature (295 K). The properties of the roto-translational profiles obtained are discussed in order to determine the role played by contributions corresponding to each of the symmetry adapted parts of the trace polarizability. By spreading the analysis over the collection of the H2-Rg systems, evolution of the spectral properties with the growing masses of the supermolecular compounds can be observed.

  16. 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.

  17. Gelation of edible blue-green algae protein isolate (Spirulina platensis Strain Pacifica): thermal transitions, rheological properties, and molecular forces involved.

    Science.gov (United States)

    Chronakis, I S

    2001-02-01

    Proteins isolated from blue-green algae Spirulina platensis strain Pacifica were characterized by visible absorption, differential scanning calorimetry (DSC), viscometry, and dynamic oscillatory rheological measurements. Unique thermal unfolding, denaturation, aggregation, and gelation of the algal protein isolate are presented. DSC analysis showed that thermal transitions occur at about 67 and 109 degrees C at neutral pH. Calcium chloride stabilized the quaternary structure against denaturation and shifted the transitions at higher temperatures. Viscometric studies of Spirulina protein isolate as a function of temperature showed that the onset of the viscosity increase is closely related to the dissociation-denaturation process. Lower viscosities were observed for the protein solutions dissolved at pH 9 due to an increased protein solubility. Solutions of Spirulina protein isolate form elastic gels during heating to 90 degrees C. Subsequent cooling at ambient temperatures caused a further pronounced increase in the elastic moduli and network elasticity. Spirulina protein isolate has good gelling properties with fairly low minimum critical gelling concentrations of about 1.5 and 2.5 wt % in 0.1 M Tris buffer, pH 7, and with 0.02 M CaCl(2) in the same buffer, respectively. It is suggested that mainly the interactions of exposed hydrophobic regions generate the molecular association, initial aggregation, and gelation of the protein isolate during the thermal treatment. Hydrogen bonds reinforce the network rigidity of the protein on cooling and further stabilize the structure of Spirulina protein gels but alone are not sufficient to form a network structure. Intermolecular sulfhydryl and disulfide bonds were found to play a minor role for the network strength of Spirulina protein gels but affect the elasticity of the structures formed. Both time and temperature at isothermal heat-induced gelation within 40-80 degrees C affect substantially the network formation and

  18. 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.

  19. Aqueous solvation of As(OH)3: A Monte Carlo study with flexible polarizable classical interaction potentials

    Science.gov (United States)

    Hernández-Cobos, J.; Vargas, M. Cristina; Ramírez-Solís, A.; Ortega-Blake, I.

    2010-09-01

    A theoretical study of the hydration of arsenious acid is presented. This study included ab initio calculations and Monte Carlo simulations. The model potentials used for the simulations were ab initio derived and they include polarizability, nonadditivity, and molecular relaxation. It is shown that with these refined potentials it is possible to reproduce the available experimental evidence and therefore permit the study of clusters, as well as of the hydration process in solution. From the study of stepwise hydration and the Monte Carlo simulation of the condensed phase it is concluded that As(OH)3 presents a hydration scheme similar to an amphipathic molecule. This phenomenon is explained as due to the existence of both a positive electrostatic potential and a localized lone pair in the vicinity of As. These results are used to rationalize the known passage of As(OH)3 through aqua-glyceroporines.

  20. Water density and polarizability deduced from the refractive index determined by interferometric measurements up to 250 MPa.

    Science.gov (United States)

    Weiss, L; Tazibt, A; Tidu, A; Aillerie, M

    2012-03-28

    The refractive index of water is precisely determined in the visible light range as a function of the pressure until 250 MPa by means of a new measurement device that uses a special pipe tee included in an interferometer set. This technique allows revisiting the Bradley-Tait and Sellmeier equations to make them dependent on the wavelength and the pressure, respectively. The Bradley-Tait equation for the pressure dependence of the water refractive index is completed by a wavelength-dependent factor. Also, in the considered pressure and wavelength ranges, it is shown that the Sellmeier coefficients can be straightforwardly linked to the pressure, allowing the determination of the refractive index of water for either any wavelength or pressure. A new simple model allows the determination of the density of water as a function of the measured refractive index. Finally, the polarizability of water as function of pressure and wavelength is calculated by means of the Lorentz-Lorenz equation.

  1. Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Beerepoot, Maarten; 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...... 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...

  2. Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

    Science.gov (United States)

    Duchemin, Ivan; Jacquemin, Denis; Blase, Xavier

    2016-04-01

    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.

  3. 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.

  4. 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.

  5. Optical Forces at the Nanoscale: Size and Electrostatic Effects.

    Science.gov (United States)

    Rodríguez-Sevilla, Paloma; Prorok, Katarzyna; Bednarkiewicz, Artur; Marqués, Manuel I; García-Martín, Antonio; García Solé, José; Haro-González, Patricia; Jaque, Daniel

    2018-01-10

    The reduced magnitude of the optical trapping forces exerted over sub-200 nm dielectric nanoparticles complicates their optical manipulation, hindering the development of techniques and studies based on it. Improvement of trapping capabilities for such tiny objects requires a deep understanding of the mechanisms beneath them. Traditionally, the optical forces acting on dielectric nanoparticles have been only correlated with their volume, and the size has been traditionally identified as a key parameter. However, the most recently published research results have shown that the electrostatic characteristics of a sub-100 nm dielectric particle could also play a significant role. Indeed, at present it is not clear what optical forces depend. In this work, we designed a set of experiments in order to elucidate the different mechanism and properties (i.e., size and/or electrostatic properties) that governs the magnitude of optical forces. The comparison between experimental data and numerical simulations have shown that the double layer induced at nanoparticle's surface, not considered in the classical description of nanoparticle's polarizability, plays a relevant role determining the magnitude of the optical forces. Here, the presented results constitute the first step toward the development of the dielectric nanoparticle over which enhanced optical forces could be exerted, enabling their optical manipulation for multiples purposes ranging from fundamental to applied studies.

  6. 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

  7. Electrostatic Forces as Dominant Interactions Between Proteins and Polyanions: an ESI MS Study of Fibroblast Growth Factor Binding to Heparin Oligomers

    Science.gov (United States)

    Minsky, Burcu Baykal; Dubin, Paul L.; Kaltashov, Igor A.

    2017-04-01

    The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1). This growth factor forms 1:1, 2:1, and 3:1 protein/heparinoid complexes with both dp8 and dp10, and the fraction of bound protein is highly dependent on protein/heparinoid molar ratio. Multimeric complexes are preferentially formed on the highly sulfated Hp oligomers. Although a variety of oligomers appear to be binding-competent, there is a strong correlation between the affinity and the overall level of sulfation (the highest charge density polyanions binding FGF most strongly via multivalent interactions). These results show that the interactions between FGF-1 and Hp oligomers are primarily directed by electrostatics, and also demonstrate the power of ESI MS as a tool to study multiple binding equilibria between proteins and structurally heterogeneous polyanions.

  8. Time-Dependent Coupled Perturbed Hartree-Fock and Density-Functional-Theory Approach for Calculating Frequency-Dependent (Hyper)Polarizabilities with Nonorthogonal Localized Molecular Orbitals.

    Science.gov (United States)

    Peng, Daoling; Li, Shaopeng; Peng, Liang; Gu, Feng Long; Yang, Weitao

    2017-09-12

    The time-dependent coupled perturbed Hartree-Fock/density-functional-theory (TDHF/TDDFT) approach has been reformulated based on nonorthogonal localized molecular orbitals (NOLMOs). Based on the NOLMO Fock equation, we have derived the corresponding NOLMO-TDHF/TDDFT equations up to the third order, and the formula for the frequency-dependent (hyper)polarizabilities has been given. Our approach has been applied to calculate both static and dynamic (hyper)polarizabilities of molecules varying from small molecules to large molecules. The NOLMO-TDHF/TDDFT approach can reproduce the reference canonical molecular orbital (CMO) results for all of our testing calculations. With the help of ongoing development of optimized local virtual molecular orbitals, the NOLMO-TDHF/TDDFT approach would be a very efficient method for large system calculations and tp achieve linear scaling.

  9. 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.

  10. 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.

  11. Calculations of dipole and quadrupole polarizability radial functions for LiH and HF: A comparison of different linear response methods

    Czech Academy of Sciences Publication Activity Database

    Paidarová, Ivana; Sauer, S. P. A.

    2005-01-01

    Roč. 48, - (2005), s. 185-208 ISSN 0065-3276 R&D Projects: GA ČR GA203/04/2146; GA AV ČR 1ET400400410 Institutional research plan: CEZ:AV0Z40400503 Keywords : polarization propagator calculations * frequency-dependent polarizabilities * consistent-field calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.877, year: 2005

  12. Spin rotation and oscillations for high energy particles in a crystal and possibility to measure the quadrupole moments and tensor polarizabilities of elementary particles and nuclei

    OpenAIRE

    Baryshevsky, V. G.; Gurinovich, A. A.

    2005-01-01

    It is shown that particle motion in a bent (straight) crystal is accompanied by particle spin rotation and oscillations that allows to measure the tensor electric and magnetic polarizabilities of nuclei and elementary particles. It is shown that channelling of particles in either straight or bent crystal with the polarized nuclei could be used both to analyze polarization of high energy particles and polarize them.

  13. Computational insight into relations between electronic and vibrational polarizabilities within the two-state valence-bond charge-transfer model

    Czech Academy of Sciences Publication Activity Database

    Zalesny, R.; Bartkowiak, W.; Toman, Petr; Leszczynski, J.

    2007-01-01

    Roč. 337, 1-3 (2007), s. 77-80 ISSN 0301-0104 Grant - others:Polish Committee for Scientific Research and the Ministry of Education, Youth, and Sports of the Czech Republic(PL) CZ25 Institutional research plan: CEZ:AV0Z40500505 Keywords : polarizability * first hyperpolarizability * second hyperpolarizability * nonlinear optical properties Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.805, year: 2007

  14. Dipole polarizability of alkali-metal (Na, K, Rb)–alkaline-earth-metal (Ca, Sr) polar molecules: Prospects for alignment

    Energy Technology Data Exchange (ETDEWEB)

    Gopakumar, Geetha, E-mail: geetha@tmu.ac.jp; Abe, Minori; Hada, Masahiko [Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397 (Japan); JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); Kajita, Masatoshi [National Institute of Information and Communications Technology, Koganei, Tokyo 184-8795 (Japan)

    2014-06-14

    Electronic open-shell ground-state properties of selected alkali-metal–alkaline-earth-metal polar molecules are investigated. We determine potential energy curves of the {sup 2}Σ{sup +} ground state at the coupled-cluster singles and doubles with partial triples (CCSD(T)) level of electron correlation. Calculated spectroscopic constants for the isotopes ({sup 23}Na, {sup 39}K, {sup 85}Rb)–({sup 40}Ca, {sup 88}Sr) are compared with available theoretical and experimental results. The variation of the permanent dipole moment (PDM), average dipole polarizability, and polarizability anisotropy with internuclear distance is determined using finite-field perturbation theory at the CCSD(T) level. Owing to moderate PDM (KCa: 1.67 D, RbCa: 1.75 D, KSr: 1.27 D, RbSr: 1.41 D) and large polarizability anisotropy (KCa: 566 a.u., RbCa: 604 a.u., KSr: 574 a.u., RbSr: 615 a.u.), KCa, RbCa, KSr, and RbSr are potential candidates for alignment and orientation in combined intense laser and external static electric fields.

  15. Aquareovirus NS80 recruits viral proteins to its inclusions, and its C-terminal domain is the primary driving force for viral inclusion formation.

    Directory of Open Access Journals (Sweden)

    Ling Shao

    Full Text Available Cytoplasmic inclusion bodies formed in reovirus-infected cells are the sites of viral replication and assembly. Previous studies have suggested that the NS80 protein of aquareovirus may be involved in the formation of viral inclusion bodies. However, it remains unknown whether other viral proteins are involved in the process, and what regions of NS80 may act coordinately in mediating inclusion formation. Here, we observed that globular cytoplasmic inclusions were formed in virus-infected cells and viral proteins NS80 and NS38 colocalized in the inclusions. During transfection, singly expressed NS80 could form cytoplasmic inclusions and recruit NS38 and GFP-tagged VP4 to these structures. Further treatment of cells with nocodazole, a microtubule inhibitor, did not disrupt the inclusion, suggesting that inclusion formation does not rely on microtubule network. Besides, we identified that the region 530-742 of NS80 was likely the minimal region required for inclusion formation, and the C-tail, coiled-coil region as well as the conserved linker region were essential for inclusion phenotype. Moreover, with series deletions from the N-terminus, a stepwise conversion occurred from large condensed cytoplasmic to small nuclear inclusions, then to a diffused intracellular distribution. Notablely, we found that the nuclear inclusions, formed by NS80 truncations (471 to 513-742, colocalized with cellular protein β-catenin. These data indicated that NS80 could be a major mediator in recruiting NS38 and VP4 into inclusion structures, and the C-terminus of NS80 is responsible for inclusion formation.

  16. Cluster forcing

    DEFF Research Database (Denmark)

    Christensen, Thomas Budde

    , Portugal and New Zealand have adopted the concept. Public sector interventions that aim to support cluster development in industries most often focus upon economic policy goals such as enhanced employment and improved productivity, but rarely emphasise broader societal policy goals relating to e.......g. sustainability or quality of life. The purpose of this paper is to explore how and to what extent public sector interventions that aim at forcing cluster development in industries can support sustainable development as defined in the Brundtland tradition and more recently elaborated in such concepts as eco...... in 2000 by the Welsh Automotive Task Force under the Welsh Assembly Government. The Accelerate programme takes basically different two directions: The first one, which was the first to be launched, is concerned with the upgrading of existing supply chains in the automotive industry in Wales. The programme...

  17. 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...

  18. Dynamic polarizability of Rydberg atoms: Applicability of the near-free-electron approximation, gauge invariance, and the Dirac sea

    Science.gov (United States)

    Topcu, Turker; Derevianko, Andrei

    2013-10-01

    Ponderomotive energy shifts experienced by Rydberg atoms in optical fields are known to be well approximated by the classical quiver energy of a free electron. We examine such energy shifts quantum mechanically and elucidate how they relate to the ponderomotive shift of a free electron in off-resonant fields. We derive and evaluate corrections to the ponderomotive free-electron polarizability in the length and velocity (transverse or Coulomb) gauges, which agree exactly as mandated by the gauge invariance. We also show how the free electron value emerges from the Dirac equation through summation over the Dirac sea states. We find that the free-electron ac Stark shift comes as an expectation value of a term proportional to the square of the vector potential in the velocity gauge. On the other hand, the same dominant contribution can be obtained to first order via a series expansion of the exact energy shift from the second-order perturbation theory in the length gauge. Finally, we numerically examine the validity of the free-electron approximation. The correction to the free-electron value becomes smaller with increasing principal quantum number, and it is well below a percent for 60s states of Rb and Sr away from the resonances.

  19. Response calculations based on an independent particle system with the exact one-particle density matrix: polarizabilities.

    Science.gov (United States)

    Giesbertz, K J H; Gritsenko, O V; Baerends, E J

    2014-05-14

    Recently, we have demonstrated that the problems finding a suitable adiabatic approximation in time-dependent one-body reduced density matrix functional theory can be remedied by introducing an additional degree of freedom to describe the system: the phase of the natural orbitals [K. J. H. Giesbertz, O. V. Gritsenko, and E. J. Baerends, Phys. Rev. Lett. 105, 013002 (2010); K. J. H. Giesbertz, O. V. Gritsenko, and E. J. Baerends, J. Chem. Phys. 133, 174119 (2010)]. In this article we will show in detail how the frequency-dependent response equations give the proper static limit (ω → 0), including the perturbation in the chemical potential, which is required in static response theory to ensure the correct number of particles. Additionally we show results for the polarizability for H2 and compare the performance of two different two-electron functionals: the phase-including Löwdin-Shull functional and the density matrix form of the Löwdin-Shull functional.

  20. Unified many-body approach to van der Waals interactions based on semi-local polarizability functional

    Science.gov (United States)

    Hermann, Jan; Scheffler, Matthias; Tkatchenko, Alexandre

    Electromagnetic coupling of charge fluctuations leads to van der Waals (vdW) attraction in systems ranging from metal nanoparticles to dielectric materials. In this regard, broadly applicable and accurate description of vdW interactions in complex materials is an elusive and unsolved puzzle. Many promising approaches model various subsets of this general problem, but are limited in scope by the underlying parametrization (atomic models), in accuracy due to missing many-body interactions (nonlocal density functionals), or in efficiency by working with virtual orbital space (e.g., random-phase approximation). Here, we present a unifying method that combines key elements from different theories and accurately describes vdW interactions in covalent, ionic, and metallic systems. In particular, we employ a semi-local polarizability functional of the electron density and its gradient to parametrize material response and its coupling within the many-body dispersion framework, and demonstrate the generality of the method on binding in molecular dimers and crystals, carbon-based nanomaterials, oxides, and salts, as well as on adsorption of molecules on metal surfaces. Our approach allows consistent modelling of a wide spectrum of materials as well as hybrid materials with mixed bond types.

  1. 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.

  2. 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.

  3. 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.

  4. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

    Science.gov (United States)

    Liwo, Adam; Ołdziej, Stanisław; Czaplewski, Cezary; Kleinerman, Dana S; Blood, Philip; Scheraga, Harold A

    2010-03-09

    We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time.

  5. Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

    Science.gov (United States)

    Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

    2017-12-12

    London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the

  6. Resonance energy transfer and interface forces: quantum electrodynamical analysis

    Science.gov (United States)

    Bradshaw, David S.; Leeder, Jamie M.; Rodríguez, Justo; Andrews, David L.

    2007-01-01

    On the propagation of radiation with a suitably resonant optical frequency through a dense chromophoric system - a doped solid for example - photon capture is commonly followed by one or more near-field transfers of the resulting optical excitation, usually to closely neighboring chromophores. Since the process results in a change to the local electronic environment, it can be expected to also shift the electromagnetic interactions between the participant optical units, producing modified inter-particle forces. Significantly, it emerges that energy transfer, when it occurs between chromophores or particles with electronically dissimilar properties (such as differing polarizabilities), engenders hitherto unreported changes in the local potential energy landscape. This paper reports the results of quantum electrodynamical calculations which cast a new light on the physical link between these features. The theory also elucidates a significant relationship with Casimir-Polder forces; it transpires that there are clear and fundamental links between dispersion forces and resonance energy transfer. Based on the results, we highlight specific effects that can be anticipated when laser light propagates through an interface between two absorbing media. Both steady-state and pulsed excitation conditions are modeled and the consequences for interface forces are subjected to detailed analysis.

  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. Electrostatic force and torque description of generalized spheroidal particles in optical landscapes

    Science.gov (United States)

    Going, Ryan W.; Conover, Brandon L.; Escuti, Michael J.

    2008-08-01

    Optical trapping, mixing, and sorting of micro- and nano-scale particles of arbitrary shape (e.g., blood cells and nanorods) are but a few of the burgeoning applications of optical interference landscapes. Due to their non-invasive, non-contact manipulation potential, biologists and nanotechnologists alike are showing increased interest in this area and experimental results continue to be promising. A complete and reliable theoretical description of the particles' response within these fields will allow us to accurately predict their behavior and motion. We develop an electrostatic model of the optical force and torque on anisotropic particles in optical intensity gradients. The complete optical field is defined and a Maxwell stress tensor approach is taken to realize the force and torque induced by the electric field due to the polarizability of the particle. We utilize the properties of real dielectrics and steady state optical fields to extend this approach to the electrodynamic case inherent in optical trapping. We then compare our results against our recently reported form factor approach and use the differences to try to determine the importance of polarizability in optical trapping.

  9. Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models.

    Science.gov (United States)

    Liu, Fang; Luehr, Nathan; Kulik, Heather J; Martínez, Todd J

    2015-07-14

    The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10× faster than that with a conventional CPU-based implementation. Our improvements to the linear solver provide a further 3× acceleration. The overall calculations including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril.

  10. Open-ended formulation of self-consistent field response theory with the polarizable continuum model for solvation.

    Science.gov (United States)

    Di Remigio, Roberto; Beerepoot, Maarten T P; Cornaton, Yann; Ringholm, Magnus; Steindal, Arnfinn Hykkerud; Ruud, Kenneth; Frediani, Luca

    2016-12-21

    The study of high-order absorption properties of molecules is a field of growing importance. Quantum-chemical studies can help design chromophores with desirable characteristics. Given that most experiments are performed in solution, it is important to devise a cost-effective strategy to include solvation effects in quantum-chemical studies of these properties. We here present an open-ended formulation of self-consistent field (SCF) response theory for a molecular solute coupled to a polarizable continuum model (PCM) description of the solvent. Our formulation relies on the open-ended, density matrix-based quasienergy formulation of SCF response theory of Thorvaldsen, et al., [J. Chem. Phys., 2008, 129, 214108] and the variational formulation of the PCM, as presented by Lipparini et al., [J. Chem. Phys., 2010, 133, 014106]. Within the PCM approach to solvation, the mutual solute-solvent polarization is represented by means of an apparent surface charge (ASC) spread over the molecular cavity defining the solute-solvent boundary. In the variational formulation, the ASC is an independent, variational degree of freedom. This allows us to formulate response theory for molecular solutes in the fixed-cavity approximation up to arbitrary order and with arbitrary perturbation operators. For electric dipole perturbations, pole and residue analyses of the response functions naturally lead to the identification of excitation energies and transition moments. We document the implementation of this approach in the Dalton program package using a recently developed open-ended response code and the PCMSolver libraries and present results for one-, two-, three-, four- and five-photon absorption processes of three small molecules in solution.

  11. 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.

  12. 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

  13. Joining Forces

    DEFF Research Database (Denmark)

    Christiansen, Anne Mette

    2013-01-01

    The interest in Corporate Social Responsibility (CSR) has grown dramatically over the last three years in Greenland. A vast geographical area with a tiny population, Greenland has recently obtained self-government status and is going through a rapid development economically and socially...... as the country moves towards embracing extractive industries (oil, gas and mining) as a path to development. Both government, civil society and business are increasingly looking for new and innovative ways of joining forces across sectors to solve some of the country's many critical social issues. Greenlandic...... companies have over the last 23 years embraced the concept of strategic CSR and are increasingly engaging in cross-sector partnerships as part of their CSR strategy. The partnerships take different forms both in regards to number of partners, focus areas and level of strategic engagement. In the article...

  14. 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)

  15. 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](-).

  16. Theoretical study of binding of hydrated Zn(II) and Mg(II) cations to 5'-guanosine monophosphate. Toward polarizable molecular mechanics for DNA and RNA

    Czech Academy of Sciences Publication Activity Database

    Gresh, N.; Šponer, Judit E.; Špačková, Naďa; Leszczynski, J.; Šponer, Jiří

    2003-01-01

    Roč. 107, č. 33 (2003), s. 8669-8681 ISSN 1520-6106 R&D Projects: GA MŠk LN00A016 Grant - others:National Science Foundation(US) CREST 9805465; National Institutes of Health(US) RCMI G1 2RR13459-21; Wellcome Trust(GB) GR067507MF Institutional research plan: CEZ:AV0Z5004920 Keywords : polarizable molecular mechanics * quantum-chemical computations * hydrated cations Subject RIV: BO - Biophysics Impact factor: 3.679, year: 2003

  17. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: bimetallic binding site and structured waters.

    Science.gov (United States)

    Gresh, Nohad; El Hage, Krystel; Perahia, David; Piquemal, Jean-Philip; Berthomieu, Catherine; Berthomieu, Dorothée

    2014-11-05

    The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn-superoxide dismutase (SOD) has been inferred from high-resolution X-ray crystallography. Long-duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second-generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn-SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short-duration MD simulations of 296 waters solvating Cu/Zn-SOD. Six representative geometries are selected and energy-minimized. Single-point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest-energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments

  18. Comprehensive study of electronic polarizability and band gap of B2O3–Bi2O3–ZnO–SiO2 glass network

    Directory of Open Access Journals (Sweden)

    Iskandar Shahrim Mustafa

    2017-10-01

    Full Text Available Quaternary glasses were successfully fabricated using melt quenching technique based on the chemical compound composition (xBi2O3–(0.5−x ZnO–(0.2B2O3–(0.3SiO2, where (x=0.1, 0.2, 0.3, 0.4, 0.45 mole. The sources of SiO2 was produced from rice husk ash (RHA at 99.36% of SiO2. The Urbach energy was increased from 0.16eV to the 0.29eV as the mole of Bi2O3 increased in the glass structure. The indirect energy band gap is indicated in decrement pattern with 3.15eV towards 2.51eV. The results of Urbach energy and band gap energy that were obtained are due to the increment of Bi3+ ion in the glass network. The refractive indexes for the prepared glasses were evaluated at 2.36 to 2.54 based on the Lorentz–Lorentz formulation which correlated to the energy band gap. The calculated of molar polarizability, electronic polarizability and optical basicity exemplify fine complement to the Bi2O3 addition in the glass network. The glass sample was indicated in amorphous state.

  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. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    Science.gov (United States)

    Gould, Tim; Bučko, Tomáš

    2016-08-09

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (30% errors) in a small fraction of cases.

  1. Polarizable Density Embedding

    DEFF Research Database (Denmark)

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

    2017-01-01

    and diffuse basis sets that are otherwise questionable-due to electron spill-out effects-in standard embedding models. Based on our analysis, we find the PDE model to be robust and much more systematic than less sophisticated focused embedding models, and thus outline the PDE model as a very efficient...

  2. Spin polarizability of hyperons

    Indian Academy of Sciences (India)

    2014-11-04

    Nov 4, 2014 ... baryon system will have three terms of order p, the loop contribution of order p2, p3 and also counterterms of order p2 and p3. Hence, complete one-loop diagram to order O(p3) involves one insertion from L(1). φN and tree-level diagrams. In HBChPT, the amplitude for. Pramana – J. Phys., Vol. 83, No. 5 ...

  3. Periodic forces trigger a complex mechanical response in ubiquitin.

    Science.gov (United States)

    Szymczak, Piotr; Janovjak, Harald

    2009-07-17

    Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.

  4. 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

  5. Handbook of force transducers

    CERN Document Server

    Stefanescu, Dan Mihai

    2011-01-01

    Part I introduces the basic ""Principles and Methods of Force Measurement"" acording to a classification into a dozen of force transducers types: resistive, inductive, capacitive, piezoelectric, electromagnetic, electrodynamic, magnetoelastic, galvanomagnetic (Hall-effect), vibrating wires, (micro)resonators, acoustic and gyroscopic. Two special chapters refer to force balance techniques and to combined methods in force measurement. Part II discusses the ""(Strain Gauge) Force Transducers Components"", evolving from the classical force transducer to the digital / intelligent one, with the inco

  6. 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.

  7. Atomic Force Microscopy of Biochemically Tagged DNA

    Science.gov (United States)

    Murray, Matthew N.; Hansma, Helen G.; Bezanilla, Magdalena; Sano, Takeshi; Ogletree, D. Frank; Kolbe, William; Smith, Casandra L.; Cantor, Charles R.; Spengler, Sylvia; Hansma, Paul K.; Salmeron, Miquel

    1993-05-01

    Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphyloccocal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein.

  8. Ionization Energies, Electron Affinities, and Polarization Energies of Organic Molecular Crystals: Quantitative Estimations from a Polarizable Continuum Model (PCM)–Tuned Range-Separated Density Functional Approach

    KAUST Repository

    Sun, Haitao

    2016-05-16

    We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a non-empirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal-phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials.

  9. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    Science.gov (United States)

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.

  10. Investigation of the 4snf 1F3 Rydberg states of zinc and determination of the dipole polarizability of the Zn+ ion

    Science.gov (United States)

    Aisha, G.; Shah, M.; Shahzada, Shaista; Haq, S. U.; Shakeel, H.; Nadeem, Ali

    2018-04-01

    We report term energies and effective quantum numbers of the odd-parity 4snf 1F3 Rydberg series of zinc from 75,480 to 75,750 cm-1 energy range. The experiment was performed using three dye lasers simultaneously pumped by the second (532 nm) and third (355 nm) harmonics of a Q-switched Nd-YAG laser in conjunction with an atomic beam set-up. The new observation include the 4snf 1F3 (20 ≤ n ≤ 50) series excited from the 4s4d 1D2 intermediate level. In addition, the dipole polarizability of the zinc core is determined as αd = 18.33 ± 0.95 ao3 using the core polarization model, which is in consistence with the earlier reported experimental and theoretical results.

  11. StringForce

    DEFF Research Database (Denmark)

    Barendregt, Wolmet; Börjesson, Peter; Eriksson, Eva

    2017-01-01

    In this paper, we present the forced collaborative interaction game StringForce. StringForce is developed for a special education context to support training of collaboration skills, using readily available technologies and avoiding the creation of a "mobile bubble". In order to play StringForce ...

  12. Mechanical forces in skin disorders.

    Science.gov (United States)

    Hsu, Chao-Kai; Lin, Hsi-Hui; Harn, Hans I-Chen; Hughes, Michael W; Tang, Ming-Jer; Yang, Chao-Chun

    2018-03-08

    Mechanical forces are known to regulate homeostasis of the skin and play a role in the pathogenesis of skin diseases. The epidermis consists of keratinocytes that are tightly adhered to each other by cell junctions. Defects in keratins or desmosomal/hemidesmosomal proteins lead to the attenuation of mechanical strength and formation of intraepidermal blisters in the case of epidermolysis bullosa simplex. The dermis is rich in extracellular matrix, especially collagen, and provides the majority of tensile force in the skin. Keloid and hypertrophic scar, which is the result of over-production of collagen by fibroblasts during the wound healing, are associated with extrinsic tensile forces and changes of intrinsic mechanical properties of the cell. Increasing evidences shows that stiffness of the skin environment determines the regenerative ability during wound healing process. Mechanotransduction pathways are also involved in the morphogenesis and cyclic growth of hair follicles. The development of androgenetic alopecia is correlated to tensile forces generated by the fibrous tissue underlying the scalp. Acral melanoma predominantly occurs in the weight-bearing area of the foot suggesting the role of mechanical stress. Increased dermal stiffness from fibrosis might be the cause of recessive dystrophic epidermolysis bullosa associated squamous cell carcinoma. Strategies to change the mechanical forces or modify the mechanotransduction signals may lead to a new way to treat skin diseases and promote skin regeneration. Copyright © 2018 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  13. Quantum mechanical force field for water with explicit electronic polarization.

    Science.gov (United States)

    Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

    2013-08-07

    A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

  14. The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

    Science.gov (United States)

    Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

    2017-10-01

    In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

  15. Interfacial force measurements using atomic force microscopy

    NARCIS (Netherlands)

    Chu, L.

    2018-01-01

    Atomic Force Microscopy (AFM) can not only image the topography of surfaces at atomic resolution, but can also measure accurately the different interaction forces, like repulsive, adhesive and lateral existing between an AFM tip and the sample surface. Based on AFM, various extended techniques have

  16. Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations

    Science.gov (United States)

    Nemchinsky, V.; Khrabry, A.

    2018-02-01

    Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. It is shown that the flux density is not uniform along the surface. It is maximal at the nanoparticle tips.

  17. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions

    DEFF Research Database (Denmark)

    Steinmann, Casper; Bratholm, Lars Andersen; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we...

  18. Reactive Force Fields via Explicit Valency

    Science.gov (United States)

    Kale, Seyit

    Computational simulations are invaluable in elucidating the dynamics of biological macromolecules. Unfortunately, reactions present a fundamental challenge. Calculations based on quantum mechanics can predict bond formation and rupture; however they suffer from severe length- and time-limitations. At the other extreme, classical approaches provide orders of magnitude faster simulations; however they regard chemical bonds as immutable entities. A few exceptions exist, but these are not always trivial to adopt for routine use. We bridge this gap by providing a novel, pseudo-classical approach, based on explicit valency. We unpack molecules into valence electron pairs and atomic cores. Particles bear ionic charges and interact via pairwise-only potentials. The potentials are informed of quantum effects in the short-range and obey dissociation limits in the long-range. They are trained against a small set of isolated species, including geometries and thermodynamics of small hydrides and of dimers formed by them. The resulting force field captures the essentials of reactivity, polarizability and flexibility in a simple, seamless setting. We call this model LEWIS, after the chemical theory that inspired the use of valence pairs. Following the introduction in Chapter 1, we initially focus on the properties of water. Chapter 2 considers gas phase clusters. To transition to the liquid phase, Chapter 3 describes a novel pairwise long-range compensation that performs comparably to infinite lattice summations. The approach is suited to ionic solutions in general. In Chapters 4 and 5, LEWIS is shown to correctly predict the dipolar and quadrupolar response in bulk liquid, and can accommodate proton transfers in both acid and base. Efficiency permits the study of proton defects at dilutions not accessible to experiment or quantum mechanics. Chapter 6 discusses explicit valency approaches in other hydrides, forming the basis of a reactive organic force field. Examples of simple

  19. Labor Force Participation Rate

    Data.gov (United States)

    City and County of Durham, North Carolina — This thematic map presents the labor force participation rate of working-age people in the United States in 2010. The 2010 Labor Force Participation Rate shows the...

  20. Aerodynamic Lifting Force.

    Science.gov (United States)

    Weltner, Klaus

    1990-01-01

    Describes some experiments showing both qualitatively and quantitatively that aerodynamic lift is a reaction force. Demonstrates reaction forces caused by the acceleration of an airstream and the deflection of an airstream. Provides pictures of demonstration apparatus and mathematical expressions. (YP)

  1. Acoustic force spectroscopy

    NARCIS (Netherlands)

    Sitters, G.; Kamsma, D.; Thalhammer, G.; Ritsch-Marte, M.; Peterman, E.J.G.; Wuite, G.J.L.

    2015-01-01

    Force spectroscopy has become an indispensable tool to unravel the structural and mechanochemical properties of biomolecules. Here we extend the force spectroscopy toolbox with an acoustic manipulation device that can exert forces from subpiconewtons to hundreds of piconewtons on thousands of

  2. Forces in General Relativity

    Science.gov (United States)

    Ridgely, Charles T.

    2010-01-01

    Many textbooks dealing with general relativity do not demonstrate the derivation of forces in enough detail. The analyses presented herein demonstrate straightforward methods for computing forces by way of general relativity. Covariant divergence of the stress-energy-momentum tensor is used to derive a general expression of the force experienced…

  3. Cooperatively enhanced dipole forces from artificial atoms in trapped nanodiamonds

    Science.gov (United States)

    Juan, Mathieu L.; Bradac, Carlo; Besga, Benjamin; Johnsson, Mattias; Brennen, Gavin; Molina-Terriza, Gabriel; Volz, Thomas

    2017-03-01

    Optical trapping is a powerful tool to manipulate small particles, from micrometre-size beads in liquid environments to single atoms in vacuum. The trapping mechanism relies on the interaction between a dipole and the electric field of laser light. In atom trapping, the dominant contribution to the associated force typically comes from the allowed optical transition closest to the laser wavelength, whereas for mesoscopic particles it is given by the polarizability of the bulk material. Here, we show that for nanoscale diamond crystals containing a large number of artificial atoms, nitrogen-vacancy colour centres, the contributions from both the nanodiamond and the colour centres to the optical trapping strength can be simultaneously observed in a noisy liquid environment. For wavelengths around the zero-phonon line transition of the colour centres, we observe a 10% increase of overall trapping strength. The magnitude of this effect suggests that due to the large density of centres, cooperative effects between the artificial atoms contribute to the observed modification of the trapping strength. Our approach may enable the study of cooperativity in nanoscale solid-state systems and the use of atomic physics techniques in the field of nano-manipulation.

  4. Statistics of force networks

    Science.gov (United States)

    Tighe, Brian

    2009-03-01

    We study the statistics of contact forces in the force network ensemble, a minimal model of jammed granular media that emphasizes the role of vector force balance. We show that the force probability distribution can be calculated analytically by way of an analogy to equilibrium ensemble methods. In two dimensions the large force tail decays asymptotically as a Gaussian, distinct from earlier predictions, due to the existence of a conserved quantity related to the presence of local vector force balance. We confirm our predictions with highly accurate statistical sampling -- we sample the force distribution over more than 40 decades -- permitting unambiguous confrontation of theory with numerics. We show how the conserved quantity arises naturally within the context of any constant stress ensemble.

  5. Quantum fictitious forces

    DEFF Research Database (Denmark)

    Bialynicki-Birula, I; Cirone, M.A.; Dahl, Jens Peder

    2002-01-01

    We present Heisenberg's equation of motion for the radial variable of a free non-relativistic particle in D dimensions. The resulting radial force consists of three contributions: (i) the quantum fictitious force which is either attractive or repulsive depending on the number of dimensions, (ii......) a singular quantum force located at the origin, and (iii) the centrifugal force associated with non-vanishing angular momentum. Moreover, we use Heisenberg's uncertainty relation to introduce a lower bound for the kinetic energy of an ensemble of neutral particles. This bound is quadratic in the number...... of atoms and can be traced back to the repulsive quantum fictitious potential. All three forces arise for a free particle: "Force without force"....

  6. A synthetic peptide corresponding to the C-terminal 25 residues of phage MS2 coded lysis protein dissipates the protonmotive force in Escherichia coli membrane vesicles by generating hydrophilic pores

    NARCIS (Netherlands)

    Goessens, Wil H.F.; Driessen, Arnold J.M.; Wilschut, Jan; Duin, Jan van

    1988-01-01

    The RNA phage MS2 encodes a protein, 75 amino acids long, that is necessary and sufficient for lysis of the host cell. DNA deletion analysis has shown that the lytic activity is confined to the C-terminal half of the protein. We have examined the effects of a synthetic peptide, covering the

  7. Quantum master equation method based on the broken-symmetry time-dependent density functional theory: application to dynamic polarizability of open-shell molecular systems.

    Science.gov (United States)

    Kishi, Ryohei; Nakano, Masayoshi

    2011-04-21

    A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.

  8. Electronic polarizability, optical basicity and interaction parameter for Nd{sub 2}O{sub 3} doped lithium-zinc-phosphate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Algradee, M.A.; Sultan, M.; Samir, O.M.; Alwany, A.E.B. [Ibb University, Department of Physics, Faculty of Science, Ibb (Yemen)

    2017-08-15

    The Nd{sup 3+}-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 Nd{sub 2}O{sub 3} content were discussed in terms of different parameters such as non-bridging oxygen and different concentrations of Nd cation in glass system. (orig.)

  9. Description of the Charge Transfer States at the Pentacene/C60 Interface: Combining Range-Separated Hybrid Functionals with the Polarizable Continuum Model

    KAUST Repository

    Zheng, Zilong

    2016-06-24

    Density functional theory (DFT) approaches based on range-separated hybrid functionals are currently methods of choice for the description of the charge-transfer (CT) states in organic donor/acceptor solar cells. However, these calculations are usually performed on small-size donor/acceptor complexes and as result do not account for electronic polarization effects. Here, using a pentacene/C60 complex as a model system, we discuss the ability of long-range corrected (LCR) hybrid functionals in combination with the polarizable continuum model (PCM) to determine the impact of the solid-state environment on the CT states. The CT energies are found to be insensitive to the interactions with the dielectric medium when a conventional time-dependent DFT/PCM (TDDFT/PCM) approach is used. However, a decrease in the energy of the CT state in the framework of LRC functionals can be obtained by using a smaller range-separated parameter when going from an isolated donor/acceptor complex to the solid-state case.

  10. Accurate determination of the anisotropy factors and the phase differences of Raman polarizabilities in some uniaxial crystals: the case of lithium niobate.

    Science.gov (United States)

    Djiedeu, N; Mohamadou, B; Bourson, P; Aillerie, M

    2009-01-07

    The present study highlights self-consistently helpful improvements dedicated to overcoming the difficulty resulting from the fitting procedure of integrated Raman intensities recorded according to the rotation crystal method described earlier. To this end, the anisotropy factors of Raman polarizabilities and the corresponding relative phases are determined within the framework of the exact mathematical derivation of the phase factors. These are the relevant parameters of the Raman efficiency relations which are numerically difficult to obtain from the fitting of the integrated areas. The present theoretical approach is then applied to the modes of the A(1) and Ey symmetry species of the lithium niobate (LN) crystal point group. All the expressions of the Raman absolute intensities of the A(1) and Ey irreducible representations initially imply three parameters to be determined from the fitting computations. However, from the derived analytical expressions of the phase differences, the number of parameters involved in the fitting procedure is reduced from 3 to 2, thus improving the statistics of the numerical treatment.

  11. Nonlinear Optical Properties of XPh4 (X = B-, C, N+, P+): A New Class of Molecules with a Negative Third-Order Polarizability

    KAUST Repository

    Gieseking, Rebecca L.

    2015-06-22

    Organic π-conjugated materials have been widely used for a variety of nonlinear optical (NLO) applications. Molecules with negative real components Re(γ) of the third-order polarizability, which leads to nonlinear refraction in macroscopic systems, have important benefits for several NLO applications. However, few organic systems studied to date have negative Re(γ) in the long wavelength limit, and all inorganic materials show positive nonlinear refraction in this limit. Here, we introduce a new class of molecules of the form X(C6H5)4, where X = B-, C, N+, and P+, that have negative Re(γ). The molecular mechanism for the NLO properties in these systems is very different from those in typical linear conjugated systems: these systems have a band of excited states involving single-electron excitations within the π-system, several of which have significant coupling to the ground state. Thus, Re(γ) cannot be understood in terms of a simplified essential-state model and must be analyzed in the context of the full sum-over-states expression. Although Re(γ) is significantly smaller than that of other commonly-studied NLO chromophores, the introduction of a new molecular architecture offering the potential for a negative Re(γ) introduces new avenues of molecular design for NLO applications.

  12. Evaluation of the bond polarizabilities of zincblende-type semiconductors: Application to the Raman spectra of disordered GaSb/AlSb (001) superlattices

    Energy Technology Data Exchange (ETDEWEB)

    Berdekas, D. [Direction of High Schools Education of Larissa, Lykeio of Giannouli, Larissa (Greece); Ves, S. [School of Physics, Aristotle University of Thessaloniki (Greece)

    2012-08-15

    We derive expressions for the bond polarizability (BP) parameters involving only directly measurable quantities, such as dielectric and elasto-optic constants of the bulk crystal and apply them to zincblende-type crystals. The vibrational modes are calculated on the basis of an eleven (11) parameter rigid-ion model approximation (RIM). Having estimated the BP parameters for GaSb and AlSb bulk crystals, we calculate the Raman spectra away of resonance conditions for the vibrations of perfect and disordered (GaSb)1/(AlSb)1 (001) superlattices (SL). The disordered SL is approximated with primitive cells much larger than the primitive cell of the perfect 1 x 1 SL. Furthermore, we show that disorder modifies the Raman spectra of the perfect SL by introducing asymmetry as well as by the formation of additional peaks in both the acoustic and optical range of the Raman spectra. Puzzlingly, even a small degree of disorder, results in a blueshift of all modes frequencies, especially the strongest optical ones. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Relativistic Linear Restoring Force

    Science.gov (United States)

    Clark, D.; Franklin, J.; Mann, N.

    2012-01-01

    We consider two different forms for a relativistic version of a linear restoring force. The pair comes from taking Hooke's law to be the force appearing on the right-hand side of the relativistic expressions: d"p"/d"t" or d"p"/d["tau"]. Either formulation recovers Hooke's law in the non-relativistic limit. In addition to these two forces, we…

  14. RSOI: Force Deployment Bottleneck

    National Research Council Canada - National Science Library

    D'Amato, Mark

    1998-01-01

    This study uses The Theory Of Constraints (TOC) management methodology and recent military missions to show that RSOI operations are generally the limiting constraint to force deployment operations...

  15. Bi-Force

    DEFF Research Database (Denmark)

    Sun, Peng; Speicher, Nora K; Röttger, Richard

    2014-01-01

    outperformed existing tools with Bi-Force at least when following the evaluation protocols from Eren et al. Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. The software as well as all used datasets are publicly available at http://biclue.mpi-inf.mpg.de....... of pairwise similarities. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol in a recent review paper from Eren et al. (2013) (A...

  16. Intermolecular and surface forces

    CERN Document Server

    Israelachvili, Jacob N

    2011-01-01

    This reference describes the role of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids and solids, with a special focus on more complex colloidal, polymeric and biological systems. The book provides a thorough foundation in theories and concepts of intermolecular forces, allowing researchers and students to recognize which forces are important in any particular system, as well as how to control these forces. This third edition is expanded into three sections and contains five new chapters over the previous edition.· starts fr

  17. Macroscopic forces from supersymmetry

    CERN Document Server

    Dimopoulos, Savas K

    1996-01-01

    We argue that theories in which supersymmetry breaking originates at low energies often contain scalar particles that mediate coherent gravitational strength forces at distances less than a cm. We estimate the strength and range of these forces in several cases. Present limits on such forces are inadequate. However new techniques, such as those based on small cryogenic mechanical oscillators, may improve the present limits by ten orders of magnitude or discover new forces as weak as 1 \\% of gravity at distances down to 40 microns.

  18. Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Blædel, Kristoffer; Christensen, Anders S

    2013-01-01

    An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiq......An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules...... such as ubiquitin a reasonable speedup (up to a factor of six) is observed for up to 16 cores. The SCF convergence is greatly improved by PCM for proteins compared to the gas phase....

  19. Interactions between soy protein hydrolyzates and wheat proteins in noodle making dough.

    Science.gov (United States)

    Guo, Xingfeng; Sun, Xiaohong; Zhang, Yingying; Wang, Ruihong; Yan, Xin

    2018-04-15

    Soy protein hydrolyzate has been used as supplements in wheat flour to enhance the nutritional value of its products, but it may negatively affect the gluten properties simultaneously. In order to explore the mechanism of this effect, protein characteristics including disulfide bond, protein composition, intermolecular force of dough proteins, and atomic force microscope images of gluten were obtained. Results showed that disulfide bonds in dough increased when soy protein hydrolyzate was added, but glutenin macropolymer decreased. Atomic force microscope images showed that gluten were weakened by soy protein hydrolyzate. Based on these results, a model was developed to describe the interaction between soy protein hydrolyzates and wheat proteins: soy protein hydrolyzates linked with wheat proteins through disulfide bond, disrupted the glutenins polymerization, thus hindered gluten networks formation. The interaction between wheat proteins and soy protein hydrolyzates in noodle making dough could be described with this model reasonably. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Climate forcings and feedbacks

    Science.gov (United States)

    Hansen, James

    1993-01-01

    Global temperature has increased significantly during the past century. Understanding the causes of observed global temperature change is impossible in the absence of adequate monitoring of changes in global climate forcings and radiative feedbacks. Climate forcings are changes imposed on the planet's energy balance, such as change of incoming sunlight or a human-induced change of surface properties due to deforestation. Radiative feedbacks are radiative changes induced by climate change, such as alteration of cloud properties or the extent of sea ice. Monitoring of global climate forcings and feedbacks, if sufficiently precise and long-term, can provide a very strong constraint on interpretation of observed temperature change. Such monitoring is essential to eliminate uncertainties about the relative importance of various climate change mechanisms including tropospheric sulfate aerosols from burning of coal and oil smoke from slash and burn agriculture, changes of solar irradiance changes of several greenhouse gases, and many other mechanisms. The considerable variability of observed temperature, together with evidence that a substantial portion of this variability is unforced indicates that observations of climate forcings and feedbacks must be continued for decades. Since the climate system responds to the time integral of the forcing, a further requirement is that the observations be carried out continuously. However, precise observations of forcings and feedbacks will also be able to provide valuable conclusions on shorter time scales. For example, knowledge of the climate forcing by increasing CFC's relative to the forcing by changing ozone is important to policymakers, as is information on the forcing by CO2 relative to the forcing by sulfate aerosols. It will also be possible to obtain valuable tests of climate models on short time scales, if there is precise monitoring of all forcings and feedbacks during and after events such as a large volcanic eruption

  1. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  2. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  3. Elementary Particles and Forces.

    Science.gov (United States)

    Quigg, Chris

    1985-01-01

    Discusses subatomic particles (quarks, leptons, and others) revealed by higher accelerator energies. A connection between forces at this subatomic level has been established, and prospects are good for a description of forces that encompass binding atomic nuclei. Colors, fundamental interactions, screening, camouflage, electroweak symmetry, and…

  4. The forces in Nature

    CERN Multimedia

    CERN AC

    1998-01-01

    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 of phenomena in which they have a dominant role.

  5. Force generation within tissues during development

    Science.gov (United States)

    Kasza, Karen

    During embryonic development, multicellular tissues physically change shape, move, and grow. Changes in epithelial tissue organization are often accomplished by local movements of cells that are driven largely by forces generated by the motor protein myosin II. These forces are patterned to orient cell movements, resulting in changes in tissue shape and organization to build functional tissues and organs. To investigate the mechanisms of force generation in vivo, we use the fruit fly embryo as a model system. Spatial patterns of forces orient cell movements to drive rapid tissue elongation along the head-to-tail axis of the embryo. I will describe how studying embryos generated with engineered myosin variants provides insight into where, when, and how forces are generated to efficiently reorganize tissues. We found that a myosin variant that is locked-in to the active or ``on'' state accelerates cell movements, while two mutant myosin variants associated with human disease produce slowed cell movement. These myosin variants all disrupt tissue elongation, but live imaging and biophysical measurements reveal distinct effects on myosin organization and dynamics within cells and uncover mechanisms that control the spatial and temporal patterns of force generation. These studies shed light not only on how defects in force generation contribute to disease but also on physical principles at work in active, living materials.

  6. The Predictive Power of Electronic Polarizability for Tailoring the Refractivity of High Index Glasses Optical Basicity Versus the Single Oscillator Model

    Energy Technology Data Exchange (ETDEWEB)

    McCloy, John S.; Riley, Brian J.; Johnson, Bradley R.; Schweiger, Michael J.; Qiao, Hong (Amy); Carlie, Nathan

    2010-06-01

    Four compositions of high density (~8 g/cm3) heavy metal oxide glasses composed of PbO, Bi2O3, and Ga2O3 were produced and refractivity parameters (refractive index and density) were computed and measured. Optical basicity was computed using three different models – average electronegativity, ionic-covalent parameter, and energy gap – and the basicity results were used to compute oxygen polarizability and subsequently refractive index. Refractive indices were measured in the visible and infrared at 0.633 μm, 1.55 μm, 3.39 μm, 5.35 μm, 9.29 μm, and 10.59 μm using a unique prism coupler setup, and data were fitted to the Sellmeier expression to obtain an equation of the dispersion of refractive index with wavelength. Using this dispersion relation, single oscillator energy, dispersion energy, and lattice energy were determined. Oscillator parameters were also calculated for the various glasses from their oxide values as an additional means of predicting index. Calculated dispersion parameters from oxides underestimate the index by 3 to 4%. Predicted glass index from optical basicity, based on component oxide energy gaps, underpredicts the index at 0.633 μm by only 2%, while other basicity scales are less accurate. The predicted energy gap of the glasses based on this optical basicity overpredicts the Tauc optical gap as determined by transmission measurements by 6 to 10%. These results show that for this system, density, refractive index in the visible, and energy gap can be reasonably predicted using only composition, optical basicity values for the constituent oxides, and partial molar volume coefficients. Calculations such as these are useful for a priori prediction of optical properties of glasses.

  7. The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution.

    Science.gov (United States)

    Silva, Daniel L; Murugan, N Arul; Kongsted, Jacob; Rinkevicius, Zilvinas; Canuto, Sylvio; Ågren, Hans

    2012-07-19

    Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

  8. The Cytoskeleton and Force Response Mechanisms

    Science.gov (United States)

    Allen, Philip Goodwin

    2003-01-01

    The long term aim of this project was to define the mechanisms by which cells sense and respond to the physical forces experienced at 1g and missing in microgravity. Identification and characterization of the elements of the cells force response mechanism could provide pathways and molecules to serve as targets for pharmacological intervention to mitigate the pathologic effects of microgravity. Mechanical forces experienced by the organism can be transmitted to cells through molecules that allow cells to bind to the extracellular matrix and through other types of molecules which bind cells to each other. These molecules are coupled in large complexes of proteins to structural elements such as the actin cytoskeleton that give the cell the ability to sense, resist and respond to force. Application of small forces to tissue culture cells causes local elevation of intracellular calcium through stretch activated ion channels, increased tyrosine phosphorylation and a restructuring of the actin cytoskeleton. Using collagen coated iron oxide beads and strong magnets, we can apply different levels of force to cells in culture. We have found that force application causes the cells to polymerize actin at the site of mechanical deformation and unexpectedly, to depolymerize actin across the rest of the cell. Observations of GFP- actin expressing cells demonstrate that actin accumulates at the site of deformation within the first five minutes of force application and is maintained for many tens of minutes after force is removed. Consistent with the reinforcement of the cytoskeletal structures underlying the integrin-bead interaction, force also alters the motion of bound magnetic beads. This effect is seen following the removal of the magnetic field, and is only partially ablated by actin disruption with cytochalsin B. While actin is polymerizing locally at the site of force application, force also stimulates a global reduction in actin filament content within the cells. We have

  9. OOTW Force Design Tools

    Energy Technology Data Exchange (ETDEWEB)

    Bell, R.E.; Hartley, D.S.III; Packard, S.L.

    1999-05-01

    This report documents refined requirements for tools to aid the process of force design in Operations Other Than War (OOTWs). It recommends actions for the creation of one tool and work on other tools relating to mission planning. It also identifies the governmental agencies and commands with interests in each tool, from whom should come the user advisory groups overseeing the respective tool development activities. The understanding of OOTWs and their analytical support requirements has matured to the point where action can be taken in three areas: force design, collaborative analysis, and impact analysis. While the nature of the action and the length of time before complete results can be expected depends on the area, in each case the action should begin immediately. Force design for OOTWs is not a technically difficult process. Like force design for combat operations, it is a process of matching the capabilities of forces against the specified and implied tasks of the operation, considering the constraints of logistics, transport and force availabilities. However, there is a critical difference that restricts the usefulness of combat force design tools for OOTWs: the combat tools are built to infer non-combat capability requirements from combat capability requirements and cannot reverse the direction of the inference, as is required for OOTWs. Recently, OOTWs have played a larger role in force assessment, system effectiveness and tradeoff analysis, and concept and doctrine development and analysis. In the first Quadrennial Defense Review (QDR), each of the Services created its own OOTW force design tool. Unfortunately, the tools address different parts of the problem and do not coordinate the use of competing capabilities. These tools satisfied the immediate requirements of the QDR, but do not provide a long-term cost-effective solution.

  10. Forced magnetic reconnection

    Science.gov (United States)

    Vekstein, G.

    2017-10-01

    This is a tutorial-style selective review explaining basic concepts of forced magnetic reconnection. It is based on a celebrated model of forced reconnection suggested by J. B. Taylor. The standard magnetohydrodynamic (MHD) theory of this process has been pioneered by Hahm & Kulsrud (Phys. Fluids, vol. 28, 1985, p. 2412). Here we also discuss several more recent developments related to this problem. These include energetics of forced reconnection, its Hall-mediated regime, and nonlinear effects with the associated onset of the secondary tearing (plasmoid) instability.

  11. Rate of force development

    DEFF Research Database (Denmark)

    Maffiuletti, Nicola A; Aagaard, Per; Blazevich, Anthony J

    2016-01-01

    development and to discuss various methodological considerations inherent to its evaluation for research and clinical purposes. Rate of force development (1) seems to be mainly determined by the capacity to produce maximal voluntary activation in the early phase of an explosive contraction (first 50-75 ms......The evaluation of rate of force development during rapid contractions has recently become quite popular for characterising explosive strength of athletes, elderly individuals and patients. The main aims of this narrative review are to describe the neuromuscular determinants of rate of force...

  12. Traction force dynamics predict gap formation in activated endothelium

    International Nuclear Information System (INIS)

    Valent, Erik T.; Nieuw Amerongen, Geerten P. van; Hinsbergh, Victor W.M. van; Hordijk, Peter L.

    2016-01-01

    In many pathological conditions the endothelium becomes activated and dysfunctional, resulting in hyperpermeability and plasma leakage. No specific therapies are available yet to control endothelial barrier function, which is regulated by inter-endothelial junctions and the generation of acto-myosin-based contractile forces in the context of cell-cell and cell-matrix interactions. However, the spatiotemporal distribution and stimulus-induced reorganization of these integral forces remain largely unknown. Traction force microscopy of human endothelial monolayers was used to visualize contractile forces in resting cells and during thrombin-induced hyperpermeability. Simultaneously, information about endothelial monolayer integrity, adherens junctions and cytoskeletal proteins (F-actin) were captured. This revealed a heterogeneous distribution of traction forces, with nuclear areas showing lower and cell-cell junctions higher traction forces than the whole-monolayer average. Moreover, junctional forces were asymmetrically distributed among neighboring cells. Force vector orientation analysis showed a good correlation with the alignment of F-actin and revealed contractile forces in newly formed filopodia and lamellipodia-like protrusions within the monolayer. Finally, unstable areas, showing high force fluctuations within the monolayer were prone to form inter-endothelial gaps upon stimulation with thrombin. To conclude, contractile traction forces are heterogeneously distributed within endothelial monolayers and force instability, rather than force magnitude, predicts the stimulus-induced formation of intercellular gaps. - Highlights: • Endothelial monolayers exert dynamic- and heterogeneous traction forces. • High traction forces correlate with junctional areas and the F-actin cytoskeleton. • Newly formed inter-endothelial gaps are characterized by opposing traction forces. • Force stability is a key feature controlling endothelial permeability.

  13. Traction force dynamics predict gap formation in activated endothelium

    Energy Technology Data Exchange (ETDEWEB)

    Valent, Erik T.; Nieuw Amerongen, Geerten P. van; Hinsbergh, Victor W.M. van; Hordijk, Peter L., E-mail: p.hordijk@vumc.nl

    2016-09-10

    In many pathological conditions the endothelium becomes activated and dysfunctional, resulting in hyperpermeability and plasma leakage. No specific therapies are available yet to control endothelial barrier function, which is regulated by inter-endothelial junctions and the generation of acto-myosin-based contractile forces in the context of cell-cell and cell-matrix interactions. However, the spatiotemporal distribution and stimulus-induced reorganization of these integral forces remain largely unknown. Traction force microscopy of human endothelial monolayers was used to visualize contractile forces in resting cells and during thrombin-induced hyperpermeability. Simultaneously, information about endothelial monolayer integrity, adherens junctions and cytoskeletal proteins (F-actin) were captured. This revealed a heterogeneous distribution of traction forces, with nuclear areas showing lower and cell-cell junctions higher traction forces than the whole-monolayer average. Moreover, junctional forces were asymmetrically distributed among neighboring cells. Force vector orientation analysis showed a good correlation with the alignment of F-actin and revealed contractile forces in newly formed filopodia and lamellipodia-like protrusions within the monolayer. Finally, unstable areas, showing high force fluctuations within the monolayer were prone to form inter-endothelial gaps upon stimulation with thrombin. To conclude, contractile traction forces are heterogeneously distributed within endothelial monolayers and force instability, rather than force magnitude, predicts the stimulus-induced formation of intercellular gaps. - Highlights: • Endothelial monolayers exert dynamic- and heterogeneous traction forces. • High traction forces correlate with junctional areas and the F-actin cytoskeleton. • Newly formed inter-endothelial gaps are characterized by opposing traction forces. • Force stability is a key feature controlling endothelial permeability.

  14. Objective Force Warrior

    National Research Council Canada - National Science Library

    Shisler, Vernon

    2001-01-01

    This presentation concerns technology aimed at the dismounted soldier, Capstone demonstrations for FY06-07, fielding in the Objective Force time frame, strong interest in a lightweight weapon family...

  15. Packing force data correlations

    International Nuclear Information System (INIS)

    Heiman, S.M.

    1994-01-01

    One of the issues facing valve maintenance personnel today deals with an appropriate methodology for installing and setting valve packing that will minimize leak rates, yet ensure functionality of the the valve under all anticipated operating conditions. Several variables can affect a valve packing's ability to seal, such as packing bolt torque, stem finish, and lubrication. Stem frictional force can be an excellent overall indicator of some of the underlying conditions that affect the sealing characteristics of the packing and the best parameter to use when adjusting the packing. This paper addresses stem friction forces, analytically derives the equations related to these forces, presents a methodology for measuring these forces on valve stems, and attempts to correlate the data directly to the underlying variables

  16. Institutionalizing Security Force Assistance

    National Research Council Canada - National Science Library

    Binetti, Michael R

    2008-01-01

    .... It looks at the manner in which security assistance guidance is developed and executed. An examination of national level policy and the guidance from senior military and civilian leaders highlights the important role of Security Force Assistance...

  17. Hanscom Air Force Base

    Data.gov (United States)

    Federal Laboratory Consortium — MIT Lincoln Laboratory occupies 75 acres (20 acres of which are MIT property) on the eastern perimeter of Hanscom Air Force Base, which is at the nexus of Lexington,...

  18. On the fifth forces

    Science.gov (United States)

    Treder, Hans-Jürgen

    1991-03-01

    We discuss the possibility of “fifth forces” in relativistic gravitation theories of fourth order. The fifth force may be an analog to the “weak forces” in the theories of electroweak interactions.

  19. Bow Crushing Forces

    DEFF Research Database (Denmark)

    Pedersen, Preben Terndrup

    1996-01-01

    The purpose of these notes is to present a basis for the estimation of the internal collision forces between conventinal merchant vessels and large volume offshore structures in the form of gravity-supported offshore installations and bridges crossing international shipping routes.The main emphasis...... is on the presentation of impact loads on fixed offshore structures due to bow collisions. The crushing forces are determined as functions of vessels size, vessels speed, bow profile, collision angles and eccentric impacts....

  20. Security Force Assistance

    Science.gov (United States)

    2009-05-01

    Group 8-59. Cultures may be individualistic or collectivist in their orientation. An individualist culture is one in which the ties between...relatively little weight on offensive and defensive operations from a U.S. perspective . However, when U.S. forces accompany foreign security forces (FSF) in...precedence when conducting SFA. As a result, the brigade combat team (BCT) may be a supported command from a U.S. perspective as well as acting as

  1. Joint Force Fires Coordination: Towards a Joint Force Answer

    National Research Council Canada - National Science Library

    Fearn, William

    1997-01-01

    .... Components compete for decisive effect not only with each other but with the joint force. The contemporary joint force is confederated, the joint force headquarters a weak arbitration authority...

  2. Quantification of the electrostatic forces involved in the directed assembly of colloidal nanoparticles by AFM nanoxerography.

    Science.gov (United States)

    Palleau, E; Sangeetha, N M; Ressier, L

    2011-08-12

    Directed assembly of 10 nm dodecanethiol stabilized silver nanoparticles in hexane and 14 nm citrate stabilized gold nanoparticles in ethanol was performed by AFM nanoxerography onto charge patterns of both polarities written into poly(methylmethacrylate) thin films. The quasi-neutral silver nanoparticles were grafted on both positive and negative charge patterns while the negatively charged gold nanoparticles were selectively deposited on positive charge patterns only. Numerical simulations were conducted to quantify the magnitude, direction and spatial range of the electrophoretic and dielectrophoretic forces exerted by the charge patterns on these two types of nanoparticles in suspension taken as models. The simulations indicate that the directed assembly of silver nanoparticles on both charge patterns is due to the predominant dielectrophoretic forces, while the selective assembly of gold nanoparticles only on positive charge patterns is due to the predominant electrophoretic forces. The study also suggests that the minimum surface potential of charge patterns required for obtaining effective nanoparticle assembly depends strongly on the charge and polarizability of the nanoparticles and also on the nature of the dispersing solvent. Attractive electrostatic forces of about 2 × 10( - 2) pN in magnitude just above the charged surface appear to be sufficient to trap silver nanoparticles in hexane onto charge patterns and the value is about 2 pN for gold nanoparticles in ethanol, under the present experimental conditions. The numerical simulations used in this work to quantify the electrostatic forces operating in the directed assembly of nanoparticles from suspensions onto charge patterns can easily be extended to any kind of colloid and serve as an effective tool for a better comprehension and prediction of liquid-phase nanoxerography processes.

  3. Quantification of the electrostatic forces involved in the directed assembly of colloidal nanoparticles by AFM nanoxerography

    International Nuclear Information System (INIS)

    Palleau, E; Sangeetha, N M; Ressier, L

    2011-01-01

    Directed assembly of 10 nm dodecanethiol stabilized silver nanoparticles in hexane and 14 nm citrate stabilized gold nanoparticles in ethanol was performed by AFM nanoxerography onto charge patterns of both polarities written into poly(methylmethacrylate) thin films. The quasi-neutral silver nanoparticles were grafted on both positive and negative charge patterns while the negatively charged gold nanoparticles were selectively deposited on positive charge patterns only. Numerical simulations were conducted to quantify the magnitude, direction and spatial range of the electrophoretic and dielectrophoretic forces exerted by the charge patterns on these two types of nanoparticles in suspension taken as models. The simulations indicate that the directed assembly of silver nanoparticles on both charge patterns is due to the predominant dielectrophoretic forces, while the selective assembly of gold nanoparticles only on positive charge patterns is due to the predominant electrophoretic forces. The study also suggests that the minimum surface potential of charge patterns required for obtaining effective nanoparticle assembly depends strongly on the charge and polarizability of the nanoparticles and also on the nature of the dispersing solvent. Attractive electrostatic forces of about 2 x 10 -2 pN in magnitude just above the charged surface appear to be sufficient to trap silver nanoparticles in hexane onto charge patterns and the value is about 2 pN for gold nanoparticles in ethanol, under the present experimental conditions. The numerical simulations used in this work to quantify the electrostatic forces operating in the directed assembly of nanoparticles from suspensions onto charge patterns can easily be extended to any kind of colloid and serve as an effective tool for a better comprehension and prediction of liquid-phase nanoxerography processes.

  4. Course 2: Mechanics of Motor Proteins

    Science.gov (United States)

    Howard, J.

    1 Introduction 2 Cell motility and motor proteins 3 Motility assays 4 Single-molecules assays 5 Atomic structures 6 Proteins as machines 7 Chemical forces 8 Effect of force on chemical equilibria 9 Effect of force on the rates of chemical reactions 10 Absolute rate theories 11 Role of thermal fluctuations in motor reactions 12 A mechanochemical model for kinesin 13 Conclusions and outlook

  5. Website on Protein Interaction and Protein Structure Related Work

    Science.gov (United States)

    Samanta, Manoj; Liang, Shoudan; Biegel, Bryan (Technical Monitor)

    2003-01-01

    In today's world, three seemingly diverse fields - computer information technology, nanotechnology and biotechnology are joining forces to enlarge our scientific knowledge and solve complex technological problems. Our group is dedicated to conduct theoretical research exploring the challenges in this area. The major areas of research include: 1) Yeast Protein Interactions; 2) Protein Structures; and 3) Current Transport through Small Molecules.

  6. Sound of proteins

    DEFF Research Database (Denmark)

    2007-01-01

    In my group we work with Molecular Dynamics to model several different proteins and protein systems. We submit our modelled molecules to changes in temperature, changes in solvent composition and even external pulling forces. To analyze our simulation results we have so far used visual inspection...... and statistical analysis of the resulting molecular trajectories (as everybody else!). However, recently I started assigning a particular sound frequency to each amino acid in the protein, and by setting the amplitude of each frequency according to the movement amplitude we can "hear" whenever two aminoacids...

  7. Discrete persistent-chain model for protein binding on DNA.

    Science.gov (United States)

    Lam, Pui-Man; Zhen, Yi

    2011-04-01

    We describe and solve a discrete persistent-chain model of protein binding on DNA, involving an extra σ(i) at a site i of the DNA. This variable takes the value 1 or 0, depending on whether or not the site is occupied by a protein. In addition, if the site is occupied by a protein, there is an extra energy cost ɛ. For a small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA. For higher forces, the model can be solved numerically to obtain force-extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force-extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of nonspecific binding. ©2011 American Physical Society

  8. Complementarity of structure ensembles in protein-protein binding.

    Science.gov (United States)

    Grünberg, Raik; Leckner, Johan; Nilges, Michael

    2004-12-01

    Protein-protein association is often accompanied by changes in receptor and ligand structure. This interplay between protein flexibility and protein-protein recognition is currently the largest obstacle both to our understanding of and to the reliable prediction of protein complexes. We performed two sets of molecular dynamics simulations for the unbound receptor and ligand structures of 17 protein complexes and applied shape-driven rigid body docking to all combinations of representative snapshots. The crossdocking of structure ensembles increased the likelihood of finding near-native solutions. The free ensembles appeared to contain multiple complementary conformations. These were in general not related to the bound structure. We suggest that protein-protein binding follows a three-step mechanism of diffusion, free conformer selection, and refolding. This model combines previously conflicting ideas and is in better agreement with the current data on interaction forces, time scales, and kinetics.

  9. Tendon Force Transmission at the Nanoscale

    DEFF Research Database (Denmark)

    Svensson, René

    2013-01-01

    The subject of this study is connective tissues, in particular tendon. Connective tissues consist of an extracellular matrix made of the protein collagen, which is responsible for the mechanical integrity of the body. While connective tissues may appear simple, there are still many aspects...... of connective tissue function that are poorly understood. One such aspect is the microscopic mechanisms of force transmission through tendons over macroscopic distances. Force transmission is at the heart of tendon function, but the large range of scales in the hierarchical structure of tendons has made...... it difficult to tackle. The tendon hierarchy ranges from molecules (2 nm) over fibrils (200 nm), fibers (2 μm) and fascicles (200 μm) to tendons (10 mm), and to derive the mechanisms of force transmission it is necessary to know the mechanical behavior at each hierarchical level. The aim of the present work...

  10. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    Science.gov (United States)

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

  11. Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development.

    Science.gov (United States)

    Verstraelen, Toon; Vandenbrande, Steven; Heidar-Zadeh, Farnaz; Vanduyfhuys, Louis; Van Speybroeck, Veronique; Waroquier, Michel; Ayers, Paul W

    2016-08-09

    Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g., obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method, but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Scheffler scheme for dispersion interactions.

  12. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  13. Forces in strategy formation

    DEFF Research Database (Denmark)

    Steensen, Elmer Fly; Sanchez, Ron

    2008-01-01

    This chapter proposes that organizational strategy formation should be characterized theoretically as a process that is subject to several interacting forces, rather than represented by separate discrete decisionmodels or theoretic perspectives, as is commonly done in the strategic management...... literature. Based on an extensive review of relevant theory and empirical work in strategic decision-making, organizational change theory, cognitive and social psychology, and strategy processes, seven kinds of ''forces'' - rational, imposed, teleological, learning, political, heuristic, and social...... - are identified as interacting in and having significant influence on the strategy formation process. It is further argued that by applying a holistic ''forces-view'' of the significant and interacting influences on strategy formation, we can better understand the dynamics and challenges in managing the process...

  14. Quantum mode phonon forces between chainmolecules

    DEFF Research Database (Denmark)

    Bohr, Jakob

    2001-01-01

    A phenomenological description of the contributions of phonons to molecular force is developed. It uses an approximation to consider macromolecules as solid continua. The molecular modes of a molecule can then be characterized by a Debye-like description of the partition function. The resulting b....... For the later case, a significant change in zero-point energy is found. This may be the underlying cause for cold denaturation of proteins. (C) 2001 John Wiley & Sons, Inc....

  15. Monitoring developmental force distributions in reconstituted embryonic epithelia.

    Science.gov (United States)

    Przybyla, L; Lakins, J N; Sunyer, R; Trepat, X; Weaver, V M

    2016-02-01

    The way cells are organized within a tissue dictates how they sense and respond to extracellular signals, as cues are received and interpreted based on expression and organization of receptors, downstream signaling proteins, and transcription factors. Part of this microenvironmental context is the result of forces acting on the cell, including forces from other cells or from the cellular substrate or basement membrane. However, measuring forces exerted on and by cells is difficult, particularly in an in vivo context, and interpreting how forces affect downstream cellular processes poses an even greater challenge. Here, we present a simple method for monitoring and analyzing forces generated from cell collectives. We demonstrate the ability to generate traction force data from human embryonic stem cells grown in large organized epithelial sheets to determine the magnitude and organization of cell-ECM and cell-cell forces within a self-renewing colony. We show that this method can be used to measure forces in a dynamic hESC system and demonstrate the ability to map intracolony protein localization to force organization. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Modeling Molecular Systems at Extreme Pressure by an Extension of the Polarizable Continuum Model (PCM) Based on the Symmetry-Adapted Cluster-Configuration Interaction (SAC-CI) Method: Confined Electronic Excited States of Furan as a Test Case.

    Science.gov (United States)

    Fukuda, Ryoichi; Ehara, Masahiro; Cammi, Roberto

    2015-05-12

    Novel molecular photochemistry can be developed by combining high pressure and laser irradiation. For studying such high-pressure effects on the confined electronic ground and excited states, we extend the PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (SAC-configuration interaction) methods to the PCM-XP (extreme pressure) framework. By using the PCM-XP SAC/SAC-CI method, molecular systems in various electronic states can be confined by polarizable media in a smooth and flexible way. The PCM-XP SAC/SAC-CI method is applied to a furan (C4H4O) molecule in cyclohexane at high pressure (1-60 GPa). The relationship between the calculated free-energy and cavity volume can be approximately represented with the Murnaghan equation of state. The excitation energies of furan in cyclohexane show blueshifts with increasing pressure, and the extents of the blueshifts significantly depend on the character of the excitations. Particularly large confinement effects are found in the Rydberg states. The energy ordering of the lowest Rydberg and valence states alters under high-pressure. The pressure effects on the electronic structure may be classified into two contributions: a confinement of the molecular orbital and a suppression of the mixing between the valence and Rydberg configurations. The valence or Rydberg character in an excited state is, therefore, enhanced under high pressure.

  17. Electrochemical force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kalinin, Sergei V.; Jesse, Stephen; Collins, Liam F.; Rodriguez, Brian J.

    2017-01-10

    A system and method for electrochemical force microscopy are provided. The system and method are based on a multidimensional detection scheme that is sensitive to forces experienced by a biased electrode in a solution. The multidimensional approach allows separation of fast processes, such as double layer charging, and charge relaxation, and slow processes, such as diffusion and faradaic reactions, as well as capturing the bias dependence of the response. The time-resolved and bias measurements can also allow probing both linear (small bias range) and non-linear (large bias range) electrochemical regimes and potentially the de-convolution of charge dynamics and diffusion processes from steric effects and electrochemical reactivity.

  18. ForcePAD

    DEFF Research Database (Denmark)

    Lindemann, J.; Damkilde, Lars

    2009-01-01

    ForcePAD is a 2-dimensional finite element application that started as a concept application for finite element modeling. Over the course of 10 years the application has been evolved into an application that is used extensively in both an educational setting as well as a tool for design and engin......ForcePAD is a 2-dimensional finite element application that started as a concept application for finite element modeling. Over the course of 10 years the application has been evolved into an application that is used extensively in both an educational setting as well as a tool for design...

  19. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  20. Polarizability of a metallic surface

    International Nuclear Information System (INIS)

    Moraga, L.A.; Esparza, C.

    1981-01-01

    The surface dielectric operator for a semi-infinite 'Jellium' in the random phase approximation is calculated in a semi-analytical form, utilizing as zero-order approximation the Green's function for the finite height well potential. From this one, the interaction potential is calculated with different additional approximations. (L.C.) [pt

  1. Polarizational radiation or 'atomic' bremsstrahlung

    International Nuclear Information System (INIS)

    Ya Amusia, M.

    1992-01-01

    It is demonstrated that a new kind of continuum spectrum radiation exists, where the mechanism of formation is quite different from that of ordinary bremsstrahlung. The latter originates due to slowing down of the charged projectile in the target field, while the former, called polarization radiation or 'atomic' bremsstrahlung, is a result of radiation either of the target or the projectile particles dipolarly polarized during the collision process. Not only general formulae, but also results of concrete calculations are presented. These demonstrate, that for electron-atom collisions the atomic contribution to the total bremsstrahlung spectrum becomes dominant for photon energies near and above the atomic ionization potential. As to atom-atom or ion-atom collisions, the bremsstrahlung spectrum is completely determined by the atomic contribution. The specific features of the case when the incoming particles are relativistic are discussed at length. A number of examples of colliding pairs are considered, for which the atomic bremsstrahlung process is quite essential: A bare nucleus and an atom, pair of atoms, at least one of which is excited, electron, or atom interacting with a molecule. The same mechanism is essential also in formation of radiation in nuclear and elementary particle collisions. (orig.)

  2. Energy profile of nanobody–GFP complex under force

    International Nuclear Information System (INIS)

    Klamecka, Kamila; Severin, Philip M; Milles, Lukas F; Gaub, Hermann E; Leonhardt, Heinrich

    2015-01-01

    Nanobodies (Nbs)—the smallest known fully functional and naturally occuring antigen-binding fragments—have attracted a lot of attention throughout the last two decades. Exploring their potential beyond the current use requires more detailed characterization of their binding forces as those cannot be directly derived from the binding affinities. Here we used atomic force microscope to measure rupture force of the Nb–green fluorescent protein (GFP) complex in various pulling geometries and derived the energy profile characterizing the interaction along the direction of the pulling force. We found that—despite identical epitopes—the Nb binds stronger (41–56 pN) to enhanced GFP than to wild-type GFP (28–45 pN). Measured forces make the Nb–GFP pair a potent reference for investigating molecular forces in living systems both in and ex vivo. (paper)

  3. Energy profile of nanobody-GFP complex under force

    Science.gov (United States)

    Klamecka, Kamila; Severin, Philip M.; Milles, Lukas F.; Gaub, Hermann E.; Leonhardt, Heinrich

    2015-10-01

    Nanobodies (Nbs)—the smallest known fully functional and naturally occuring antigen-binding fragments—have attracted a lot of attention throughout the last two decades. Exploring their potential beyond the current use requires more detailed characterization of their binding forces as those cannot be directly derived from the binding affinities. Here we used atomic force microscope to measure rupture force of the Nb-green fluorescent protein (GFP) complex in various pulling geometries and derived the energy profile characterizing the interaction along the direction of the pulling force. We found that—despite identical epitopes—the Nb binds stronger (41-56 pN) to enhanced GFP than to wild-type GFP (28-45 pN). Measured forces make the Nb-GFP pair a potent reference for investigating molecular forces in living systems both in and ex vivo.

  4. due to Capillary Forces

    Directory of Open Access Journals (Sweden)

    Hassen M. Ouakad

    2009-01-01

    Full Text Available We present modeling and analysis for the static behavior and collapse instabilities of doubly-clamped and cantilever microbeams subjected to capillary forces. These forces can be as a result of a volume of liquid trapped underneath the microbeam during the rinsing and drying process in fabrication. The model considers the microbeam as a continuous medium, the capillary force as a nonlinear function of displacement, and accounts for the mid-plane stretching and geometric nonlinearities. The capillary force is assumed to be distributed over a specific length underneath the microbeam. The Galerkin procedure is used to derive a reduced-order model consisting of a set of nonlinear algebraic and differential equations that describe the microbeams static and dynamic behaviors. We study the collapse instability, which brings the microbeam from its unstuck configuration to touch the substrate and gets stuck in the so-called pinned configuration. We calculate the pull-in length that distinguishes the free from the pinned configurations as a function of the beam thickness and gap width for both microbeams. Comparisons are made with analytical results reported in the literature based on the Ritz method for linear and nonlinear beam models. The instability problem, which brings the microbeam from a pinned to adhered configuration is also investigated. For this case, we use a shooting technique to solve the boundary-value problem governing the deflection of the microbeams. The critical microbeam length for this second instability is also calculated.

  5. The fifth force

    International Nuclear Information System (INIS)

    Fischbach, E.; Sudarsky, D.; Szafer, A.; Talmadge, C.; Aronson, S.H.

    1986-01-01

    We present a phenomenological description of the ''fifth force'' which focuses on the implications of the existing data from satellite and geophysical measurements of gravity, the Eoetvoes experiment, decays into hyperphotons, and the energy-dependence of the K 0 - anti K 0 parameters

  6. Magnetic Force Microscopy

    NARCIS (Netherlands)

    Abelmann, Leon

    Principle of MFM In magnetic force microscopy (MFM), the magnetic stray field above a very flat specimen, or sample, is detected by placing a small magnetic element, the tip, mounted on a cantilever spring very close to the surface of the sample (Figure 1). Typical dimensions are a cantilever length

  7. Separation problems and forcing

    Czech Academy of Sciences Publication Activity Database

    Zapletal, Jindřich

    2013-01-01

    Roč. 13, č. 1 (2013), s. 1350002 ISSN 0219-0613 R&D Projects: GA AV ČR IAA100190902 Institutional research plan: CEZ:AV0Z10190503 Keywords : separation * set of uniqueness * forcing Subject RIV: BA - General Mathematics Impact factor: 0.364, year: 2012 http://www.worldscientific.com/doi/abs/10.1142/S0219061313500025

  8. Allegiance: Egypt Security Forces

    Science.gov (United States)

    2013-12-01

    expected after the uprising of 2011 never truly materialized; the Interior Ministry instituted various cosmetic changes, but its basic construct and...military forces located there. The masked men appeared to be shooting and the army responded, shooting back.284 Whatever the stories

  9. Activation force splines

    DEFF Research Database (Denmark)

    Engell-Nørregård, Morten Pol; Erleben, Kenny

    We present a method for simulating the active contraction of deformable models, usable for interactive animation of soft deformable objects. We present a novel physical principle as the governing equation for the coupling between the low dimensional 1D activation force model and the higher...

  10. Stretching to understand proteins - a survey of the protein data bank.

    Science.gov (United States)

    Sułkowska, Joanna I; Cieplak, Marek

    2008-01-01

    We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps.

  11. Fifth force, sixth force and all that

    International Nuclear Information System (INIS)

    Recami, E.; Tonin Zanchin, V.

    1988-01-01

    In the recent literature, a few claims appeared about possible deviations from the ordinary gravitational laws (both at the terrestrial and at the galactic level). The experimental evidence does not seem to be conclusive; nor its is clear if new forces are showing up, or if we have to accept actual deviations from Newton or Einstein gravitation (in the latter case, the validity of the very Equivalence Principle might be on the stage). In such a situation, the attempts by various authors at explaining the ''new effects'' just on the basis of the ordinary theory of General Relativity (for instance, in terms of quantum gravity) can be regarded as logically instance, in terms of quantum gravity) can be regarded as logically questionable. In this pedagogically oriented paper, the problem is approached within the classical realm, by exploring whether the possible new effects can be accounted for through minimal modifications of the standard formulatiaon of General Relativity: in particular, through exploitation and extension of the role of the cosmological constant

  12. Biodegradable Piezoelectric Force Sensor.

    Science.gov (United States)

    Curry, Eli J; Ke, Kai; Chorsi, Meysam T; Wrobel, Kinga S; Miller, Albert N; Patel, Avi; Kim, Insoo; Feng, Jianlin; Yue, Lixia; Wu, Qian; Kuo, Chia-Ling; Lo, Kevin W-H; Laurencin, Cato T; Ilies, Horea; Purohit, Prashant K; Nguyen, Thanh D

    2018-01-30

    Measuring vital physiological pressures is important for monitoring health status, preventing the buildup of dangerous internal forces in impaired organs, and enabling novel approaches of using mechanical stimulation for tissue regeneration. Pressure sensors are often required to be implanted and directly integrated with native soft biological systems. Therefore, the devices should be flexible and at the same time biodegradable to avoid invasive removal surgery that can damage directly interfaced tissues. Despite recent achievements in degradable electronic devices, there is still a tremendous need to develop a force sensor which only relies on safe medical materials and requires no complex fabrication process to provide accurate information on important biophysiological forces. Here, we present a strategy for material processing, electromechanical analysis, device fabrication, and assessment of a piezoelectric Poly-l-lactide (PLLA) polymer to create a biodegradable, biocompatible piezoelectric force sensor, which only employs medical materials used commonly in Food and Drug Administration-approved implants, for the monitoring of biological forces. We show the sensor can precisely measure pressures in a wide range of 0-18 kPa and sustain a reliable performance for a period of 4 d in an aqueous environment. We also demonstrate this PLLA piezoelectric sensor can be implanted inside the abdominal cavity of a mouse to monitor the pressure of diaphragmatic contraction. This piezoelectric sensor offers an appealing alternative to present biodegradable electronic devices for the monitoring of intraorgan pressures. The sensor can be integrated with tissues and organs, forming self-sensing bionic systems to enable many exciting applications in regenerative medicine, drug delivery, and medical devices.

  13. Force Exertion and Transmission in Cross-Linked Actin Networks

    Science.gov (United States)

    Stam, Samantha

    Cells are responsive to external cues in their environment telling them to proliferate or migrate within their surrounding tissue. Sensing of cues that are mechanical in nature, such stiffness of a tissue or forces transmitted from other cells, is believed to involve the cytoskeleton of a cell. The cytoskeleton is a complex network of proteins consisting of polymers that provide structural support, motor proteins that remodel these structures, and many others. We do not yet have a complete understanding of how cytoskeletal components respond to either internal or external mechanical force and stiffness. Such an understanding should involve mechanisms by which constituent molecules, such as motor proteins, are responsive to mechanics. Additionally, physical models of how forces are transmitted through biopolymer networks are necessary. My research has focused on networks formed by the cytoskeletal filament actin and the molecular motor protein myosin II. Actin filaments form networks and bundles that form a structural framework of the cell, and myosin II slides actin filaments. In this thesis, we show that stiffness of an elastic load that opposes myosin-generated actin sliding has a very sharp effect on the myosin force output in simulations. Secondly, we show that the stiffness and connectivity of cytoskeletal filaments regulates the contractility and anisotropy of network deformations that transmit force on material length scales. Together, these results have implications for predicting and interpreting the deformations and forces in biopolymeric active materials.

  14. Atomic Force Microscopy in Liquids

    Science.gov (United States)

    Weisenhorn, Albrecht Ludwig

    The atomic force microscope (AFM) was invented by Binnig, Quate, and Gerber in 1986 as an offspring of the very successful scanning tunneling microscope (STM), which Binnig and Rohrer invented in 1982 and for which they shared the Nobel prize. While the STM can only image conducting surfaces, the AFM has overcome this limitation. An AFM creates a three-dimensional image of the sample surface by raster scanning this surface under a sharp tip that is attached to a cantilever. The tip moves the cantilever up and down while going over "hills" and through "valleys" of the surface. The vertical motion of the cantilever deflects a laser beam that is reflected off the back of the cantilever toward a two-segment photodiode. The difference of the intensity of the two segments is used as the deflection signal. A feedback loop is used to keep the deflection signal constant by moving the sample surface up and down accordingly. This vertical motion gives a direct measurement of the surface height. The forces involved in the imaging process have been studied in air and water. Due to adsorbed layers on tip and sample surface when scanning in air (capillary condensation) the imaging forces are >10 ^{-7} N. If the tip and sample surface are immersed in water the forces can be reduced to {~}10^{ -9} N. An AFM with a large scanner can image up to tens of micrometers like an optical microscope. Zooming in allows one to get resolution of a few nanometers, which makes the AFM a natural continuation of the optical microscope towards higher magnification. Integrated circuit chips, photographic film, bacteria, red and white blood cells, purple membrane, polymerized Langmuir-Blodgett (LB) films, and stoma have been imaged at low and high magnification. The AFM has shown its power by imaging "hard" and "soft" surfaces with atomic and (sub)molecular resolution respectively. The "hard" crystalline surfaces of mica, graphite, RuCl_3, Ge(111), Bi(111), and zeolites (clinoptilolite (010

  15. Photothermal cantilever actuation for fast single-molecule force spectroscopy

    Science.gov (United States)

    Stahl, Stefan W.; Puchner, Elias M.; Gaub, Hermann E.

    2009-07-01

    Photothermal cantilever excitation provides a fast and easy to implement means to control the deflection of standard atomic force microscopy cantilevers. Minute heat pulses yield deflections on the order of several tens of nanometers or when the deflection is kept constant, forces of several hundreds of piconewton can be applied. In our case these pulses resulted in less than 1 K temperature changes at the sample position. Here we present and characterize the implementation of photothermal actuation for single-molecule force-spectroscopy experiments. When molecules are stretched under force-clamp conditions, fast control cycles that re-establish the pulling force after the rupture of molecular domains are essential for detecting the complete unfolding pattern with high precision. By combining the fast response of photothermal cantilever excitation with a conventional piezoactuator, a fast force-clamp with high accuracy and large working distances is reached. Simple feedback mechanisms and standard cantilever geometries lead to step response times of less than 90 μs, which is more than one order of magnitude faster than those of conventional force-clamp systems that are based only on piezo feedback. We demonstrate the fast and accurate performance of the setup by unfolding a protein construct consisting of one green fluorescent protein and eight surrounding immunoglobulin domains at constant force.

  16. Force Modulator System

    Energy Technology Data Exchange (ETDEWEB)

    Redmond Clark

    2009-04-30

    Many metal parts manufacturers use large metal presses to shape sheet metal into finished products like car body parts, jet wing and fuselage surfaces, etc. These metal presses take sheet metal and - with enormous force - reshape the metal into a fully formed part in a manner of seconds. Although highly efficient, the forces involved in forming metal parts also damage the press itself, limit the metals used in part production, slow press operations and, when not properly controlled, cause the manufacture of large volumes of defective metal parts. To date, the metal-forming industry has not been able to develop a metal-holding technology that allows full control of press forces during the part forming process. This is of particular importance in the automotive lightweighting efforts under way in the US automotive manufacturing marketplace. Metalforming Controls Technology Inc. (MC2) has developed a patented press control system called the Force Modulator that has the ability to control these press forces, allowing a breakthrough in stamping process control. The technology includes a series of hydraulic cylinders that provide controlled tonnage at all points in the forming process. At the same time, the unique cylinder design allows for the generation of very high levels of clamping forces (very high tonnages) in very small spaces; a requirement for forming medium and large panels out of HSS and AHSS. Successful production application of these systems testing at multiple stamping operations - including Ford and Chrysler - has validated the capabilities and economic benefits of the system. Although this technology has been adopted in a number of stamping operations, one of the primary barriers to faster adoption and application of this technology in HSS projects is system cost. The cost issue has surfaced because the systems currently in use are built for each individual die as a custom application, thus driving higher tooling costs. This project proposed to better

  17. Suicide and forced marriage.

    Science.gov (United States)

    Pridmore, Saxby; Walter, Garry

    2013-03-01

    The prevailing view that the vast majority of those who complete suicide have an underlying psychiatric disorder has been recently challenged by research on the contribution of "predicaments", in the absence of mental illness, to suicide. In this paper, we sought data to support the notion that forced marriage may lead to suicide without the presence of psychiatric disorder. Historical records, newspapers, and the electronic media were searched for examples. Two examples from ancient times and six from the last hundred years were located and described. These cases suggest that forced marriage may lead to suicide and complements earlier findings that loss of fortune, health, liberty, and reputation may lead to suicide in the absence of mental disorder.

  18. Quantum control of molecular vibrational and rotational excitations in a homonuclear diatomic molecule: A full three-dimensional treatment with polarization forces

    Science.gov (United States)

    Ren, Qinghua; Balint-Kurti, Gabriel G.; Manby, Frederick R.; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel

    2006-01-01

    The optimal control of the vibrational excitation of the hydrogen molecule [Balint-Kurti et al., J. Chem. Phys. 122, 084110 (2005)] utilizing polarization forces is extended to three dimensions. The polarizability of the molecule, to first and higher orders, is accounted for using explicit ab initio calculations of the molecular electronic energy in the presence of an electric field. Optimal control theory is then used to design infrared laser pulses that selectively excite the molecule to preselected vibrational-rotational states. The amplitude of the electric field of the optimized pulses is restricted so that there is no significant ionization during the process, and a new frequency sifting method is used to simplify the frequency spectrum of the pulse. The frequency spectra of the optimized laser pulses for processes involving rotational excitation are more complex than those relating to processes involving only vibrational excitation.

  19. Flora rapid reaction forces

    Directory of Open Access Journals (Sweden)

    Виктор Васильевич Туганаев

    2015-10-01

    Full Text Available Flora rapid reaction forces ­– there are explerents that have high productivity and weak competitiveness. Their innately functional allocation is to plant disturbed acres as soon as possible preventing by that biosphere homeostasis disturbance. Disturbed acres were used to take place in geological history. Nowadays they take especially big areas. Considering a historical line of Dactylis glomerata L. authors suggest to separate out an especial group of anthropochores which they call medieophytes

  20. Air Force Leadership Diversity

    Science.gov (United States)

    2017-04-06

    College, Air University, Maxwell AFB, AL. He grew up as part of an Air Force family, entered active duty in 1996, and is a career Aircraft Maintenance... artificially limit them to capping out at O-6 if we want to encourage diversity in our most senior leadership levels as we seek to create a stronger...but I am not sure it does. I find it interesting that as of 31 December 2016 the Deputy Chief of Staff for Intelligence , Surveillance and