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Sample records for molecules including nuclear

  1. High-order harmonic generation from polyatomic molecules including nuclear motion and a nuclear modes analysis

    SciTech Connect

    Madsen, C. B.; Abu-samha, M.; Madsen, L. B.

    2010-04-15

    We present a generic approach for treating the effect of nuclear motion in high-order harmonic generation from polyatomic molecules. Our procedure relies on a separation of nuclear and electron dynamics where we account for the electronic part using the Lewenstein model and nuclear motion enters as a nuclear correlation function. We express the nuclear correlation function in terms of Franck-Condon factors, which allows us to decompose nuclear motion into modes and identify the modes that are dominant in the high-order harmonic generation process. We show results for the isotopes CH{sub 4} and CD{sub 4} and thereby provide direct theoretical support for a recent experiment [S. Baker et al., Science 312, 424 (2006)] that uses high-order harmonic generation to probe the ultrafast structural nuclear rearrangement of ionized methane.

  2. High-order harmonic generation from polyatomic molecules including nuclear motion and a nuclear modes analysis

    NASA Astrophysics Data System (ADS)

    Madsen, C. B.; Abu-Samha, M.; Madsen, L. B.

    2010-04-01

    We present a generic approach for treating the effect of nuclear motion in high-order harmonic generation from polyatomic molecules. Our procedure relies on a separation of nuclear and electron dynamics where we account for the electronic part using the Lewenstein model and nuclear motion enters as a nuclear correlation function. We express the nuclear correlation function in terms of Franck-Condon factors, which allows us to decompose nuclear motion into modes and identify the modes that are dominant in the high-order harmonic generation process. We show results for the isotopes CH4 and CD4 and thereby provide direct theoretical support for a recent experiment [S. Baker , Science 312, 424 (2006)] that uses high-order harmonic generation to probe the ultrafast structural nuclear rearrangement of ionized methane.

  3. Nuclear Chemistry: Include It in Your Curriculum.

    ERIC Educational Resources Information Center

    Atwood, Charles H.; Sheline, R. K.

    1989-01-01

    Some of the topics that might be included in a nuclear chemistry section are explored. Offers radioactivity, closed shells in nuclei, energy of nuclear processes, nuclear reactions, and fission and fusion as topics of interest. Provided are ideas and examples for each. (MVL)

  4. Nuclear reactor shield including magnesium oxide

    DOEpatents

    Rouse, Carl A.; Simnad, Massoud T.

    1981-01-01

    An improvement in nuclear reactor shielding of a type used in reactor applications involving significant amounts of fast neutron flux, the reactor shielding including means providing structural support, neutron moderator material, neutron absorber material and other components as described below, wherein at least a portion of the neutron moderator material is magnesium in the form of magnesium oxide either alone or in combination with other moderator materials such as graphite and iron.

  5. Aerosol simulation including chemical and nuclear reactions

    SciTech Connect

    Marwil, E.S.; Lemmon, E.C.

    1985-01-01

    The numerical simulation of aerosol transport, including the effects of chemical and nuclear reactions presents a challenging dynamic accounting problem. Particles of different sizes agglomerate and settle out due to various mechanisms, such as diffusion, diffusiophoresis, thermophoresis, gravitational settling, turbulent acceleration, and centrifugal acceleration. Particles also change size, due to the condensation and evaporation of materials on the particle. Heterogeneous chemical reactions occur at the interface between a particle and the suspending medium, or a surface and the gas in the aerosol. Homogeneous chemical reactions occur within the aersol suspending medium, within a particle, and on a surface. These reactions may include a phase change. Nuclear reactions occur in all locations. These spontaneous transmutations from one element form to another occur at greatly varying rates and may result in phase or chemical changes which complicate the accounting process. This paper presents an approach for inclusion of these effects on the transport of aerosols. The accounting system is very complex and results in a large set of stiff ordinary differential equations (ODEs). The techniques for numerical solution of these ODEs require special attention to achieve their solution in an efficient and affordable manner. 4 refs.

  6. Theory of nuclear electric shielding in molecules

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Zanasi, R.

    1981-10-01

    In order to rationalize the effects of an external uniform electric field on a perturbed molecule, we introduce the concept of electric shielding as a tensor which determines the effective field at an arbitrary point in the molecular space. The fundamental properties of the nuclear shielding tensor are analyzed in the case of heteronuclear diatomics HF, HCl, and HBr. It is shown that this quantity is essential in accounting for the deformation of the molecular geometry induced by the external field. Uncoupled and coupled Hartree-Fock perturbation theory is applied in order to obtain quantitative estimates of the shieldings and their derivatives with respect to the interatomic distance in HF, HCl, HBr, H2O, NH3, and CH4 molecules. Accurate linear combination of atomic orbitals wave functions are prepared for the diatomics, and their quality is tested by evaluating a series of first- and second-order electric properties, giving fair agreement with corresponding experimental data. The reliability of the computed shielding is examined to obtain information on the vibrational contribution to the property and the role of the electronic correlation.

  7. Attosecond electronic and nuclear quantum photodynamics of the ozone molecule

    SciTech Connect

    Halász, G. J.; Perveaux, A.; Lasorne, B.; Gatti, F.; Robb, M. A.; Vibók, Á.

    2013-11-13

    Coupled electron-nuclear dynamics simulations are investigated for the ozone molecule on the attosecond time scale. The initial wavepacket is pumped as a coherent superposition of two or three electronic states.

  8. Energetics and Electronic Structures of C60 Included Within [n]Cyclacene Molecules

    NASA Astrophysics Data System (ADS)

    Kigure, Shota; Okada, Susumu

    2013-09-01

    We report the geometric and electronic structures of C60 included within cyclic hydrocarbon molecules, i.e., [n]cyclacene molecules. We found that the C60 included within the [n]cyclacene molecules ([n]cyclacene\\supsetC60) are energetically stable and that the inclusion reactions are exothermic for the [n]cyclacene molecules where n is larger than 16. Because of quantum confinement of the electronic states of the guest C60 molecule by the host [n]cyclacene, the electronic structure of [n]cyclacene\\supsetC60 is complex. The energy gap between the highest occupied states and the lowest unoccupied states is opened between the electronic states of the guest and host molecules.

  9. Calculations of nuclear electric shielding in molecules

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Zanasi, R.

    1980-05-01

    The electric shielding tensor at nuclei in the molecules H 2O, NH 3, CH 4 and CO has been evaluated via coupled Hartree-Fock perturbation theory. The average trace of the shielding tensor is linearly dependent on atomic electronegativities in the isoelectronic series H 2O, NH 3, CH 4.

  10. EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-09-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict (subcooled) liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  11. Covalent Binding on the Femtometer Scale: Nuclear Molecules

    NASA Astrophysics Data System (ADS)

    von Oertzen, Wolfram; Milin, Matko

    Nuclear molecules are objects having two or more individual clusters as centres with extra nucleons (usually neutrons) binding them. The clusters have to be strongly bound themselves, while they get bound into molecules due to the specific properties of the nucleus-nucleus potentials and exchange of nucleons. The molecular, quantum mechanical covalent binding effect via the exchange of neutrons is the dominant source of binding in many light nuclei, overcoming the Coulomb repulsion in such structures. This results in states having valence neutrons in the π and σ orbitals, known from molecules in atomic physics; in this paper we discuss the structural properties of such states in light nuclei. The interaction between clusters resulting in nuclear molecules should show a repulsive interaction at smaller distances. This is generally the case for strongly bound clusters, like α-particles (but also for the 12C and 16O nuclei)—due to the Pauli principle, nucleons penetrating the second cluster show then a strong repulsion effect. The particular properties of nuclear clusters needed for the formation of bound molecules is their intrinsic stiffness (a large gap to the first excited states), which inhibits their excitation and allows their survival in a two-centre configuration. A large number of strongly deformed nuclear states in light nuclei with neutron excess have been experimentally identified in the last decades, and some of them have been associated with covalent structures, mainly via their grouping into rotational bands. These results have been confirmed in many theoretical studies with nuclear cluster models, but also in model independent calculations, e.g. in the Antisymmetrized Molecular Dynamics approach, where no a priori cluster structure is assumed.

  12. Nanocoating of titanium implant surfaces with organic molecules. Polysaccharides including glycosaminoglycans.

    PubMed

    Gurzawska, Katarzyna; Svava, Rikke; Jørgensen, Niklas Rye; Gotfredsen, Klaus

    2012-12-01

    Long-term stability of titanium implants are dependent on a variety of factors. Nanocoating with organic molecules is one of the method used to improve osseointegration. Nanoscale modification of titanium implants affects surface properties, such as hydrophilicity, biochemical bonding capacity and roughness. This influences cell behaviour on the surface such as adhesion, proliferation and differentiation of cells as well as the mineralization of the extracellular matrix at the implant surfaces. The aim of the present systematic review was to describe organic molecules used for surface nanocoating with focus on polysaccharides including glycosaminoglycans, and how these molecules change surface properties, cell reactions and affect on osseointegartion. The included in vitro studies demonstrated increased cell adhesion, proliferation and mineralization of a number of the tested polysaccharide nanocoatings. The included in vivo studies, showed improvement of bone interface reactions measured as increased Bone-to-Implant Contact length and Bone Mineral Density adjacent to the polysaccharide coated surfaces. Based on existing literature, surface modification with polysaccharide and glycosaminoglycans appears to be an effective way to stimulate bone regeneration on bone-implant interface. PMID:23030010

  13. Novel nuclear magnetic resonance techniques for studying biological molecules

    SciTech Connect

    Laws, David D.

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone ({phi}/{psi}) dihedral angles by comparing experimentally determined {sup 13}C{sub a}, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of {alpha}-helical and {beta}-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly {beta}-sheet.

  14. Nuclear Spin Dependent Parity Violation in Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Altuntas, Emine; Cahn, Sidney; Demille, David; Kozlov, Mikhail

    2016-05-01

    Nuclear spin-dependent parity violation (NSD-PV) effects arise from exchange of the Z0 boson between electrons and the nucleus, and from interaction of electrons with the nuclear anapole moment, a parity-odd magnetic moment. The latter scales with nucleon number of the nucleus A as A 2 / 3 , whereas the Z0 coupling is independent of A. Thus the former is the dominant source of NSD-PV for nuclei with A >= 20. We study NSD-PV effects using diatomic molecules, where signals are dramatically amplified by bringing rotational levels of opposite parity close to degeneracy in a strong magnetic field. The NSD-PV interaction matrix element is measured using a Stark-interference technique. We present results that demonstrate statistical sensitivity to NSD-PV effects surpassing that of any previous atomic parity violation measurement, using the test system 138 Ba19 F. We report our progress on measuring and cancelling systematic effects due to combination of non-reversing stray E-fields, Enr with B-field inhomogeneities. Short-term prospects for measuring the nuclear anapole moment of 137 Ba19 F are discussed. In the long term, our technique is sufficiently general and sensitive to enable measurements across a broad range of nuclei.

  15. Nuclear Magnetic Resonance Coupling Constants and Electronic Structure in Molecules.

    ERIC Educational Resources Information Center

    Venanzi, Thomas J.

    1982-01-01

    Theory of nuclear magnetic resonance spin-spin coupling constants and nature of the three types of coupling mechanisms contributing to the overall spin-spin coupling constant are reviewed, including carbon-carbon coupling (neither containing a lone pair of electrons) and carbon-nitrogen coupling (one containing a lone pair of electrons).…

  16. Nuclear magnetic resonance of laser-polarized noble gases in molecules, materials and organisms

    SciTech Connect

    Goodson, Boyd M.

    1999-12-01

    Conventional nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are fundamentally challenged by the insensitivity that stems from the ordinarily low spin polarization achievable in even the strongest NMR magnets. However, by transferring angular momentum from laser light to electronic and nuclear spins, optical pumping methods can increase the nuclear spin polarization of noble gases by several orders of magnitude, thereby greatly enhancing their NMR sensitivity. This dissertation is primarily concerned with the principles and practice of optically pumped nuclear magnetic resonance (OPNMR). The enormous sensitivity enhancement afforded by optical pumping noble gases can be exploited to permit a variety of novel NMR experiments across many disciplines. Many such experiments are reviewed, including the void-space imaging of organisms and materials, NMR and MRI of living tissues, probing structure and dynamics of molecules in solution and on surfaces, and zero-field NMR and MRI.

  17. Nuclear Clusters and Covalent Molecules on the femto-scale

    SciTech Connect

    Oertzen, Wolfram von

    2010-04-30

    Nuclear clusters like alpha-particles light N = Z nuclei are the building blocks of nuclear molecules. With additional 'valence' neutrons, which find there place in quantum mechanical two-center orbits a variety of covalently bound states in nuclei have been established in the last decade: in isotopes of {sup 9-12}Be, {sup 13-14}C and {sup 21}Ne. More recently we have studied molecular states in {sup 18,19,20}O-isotopes using the ({sup 7}Li,p) reaction on {sup 12,13,14}C targets at E{sub lab}({sup 7}Li) = 44 MeV. The systematics of the energies and cross sections show rotational bands with high moments of inertia. These are characteristic of large deformations or molecular structures where the clusters are well separated. Generally the large scale shell model calculations are unable to reproduce these cluster bands. With two clusters of different size (e.g. ({sup 14}C x {sup 4}He), or ({sup 16}O x {sup 4}He)) intrinsically reflection asymmetric shapes arise. The molecular structures appear as rotational bands split into parity inversion doublets.

  18. An independent-atom-model description of ion-molecule collisions including geometric screening corrections

    NASA Astrophysics Data System (ADS)

    Lüdde, Hans Jürgen; Achenbach, Alexander; Kalkbrenner, Thilo; Jankowiak, Hans-Christian; Kirchner, Tom

    2016-04-01

    A new model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is introduced. The ion-molecule cross sections for net capture and net ionization are represented as weighted sums of atomic cross sections with weight factors that are determined from a geometric model of overlapping cross section areas. Results are presented for proton collisions with targets ranging from diatomic to complex polyatomic molecules. Significant improvement compared to simple additivity rule results and in general good agreement with experimental data are found. The flexibility of the approach opens up the possibility to study more detailed observables such as orientation-dependent and charge-state-correlated cross sections for a large class of complex targets ranging from biomolecules to atomic clusters.

  19. On the importance of nuclear quantum motions in near edge x-ray absorption fine structure (NEXAFS) spectroscopy of molecules

    SciTech Connect

    Schwartz, Craig P.; Uejio, Janel S.; Saykally, Richard J.; Prendergast, David

    2009-02-26

    We report the effects of sampling nuclear quantum motion with path integral molecular dynamics (PIMD) on calculations of the nitrogen K-edge spectra of two isolated organic molecules. S-triazine, a prototypical aromatic molecule occupying primarily its vibrational ground state at room temperature, exhibits substantially improved spectral agreement when nuclear quantum effects are included via PIMD, as compared to the spectra obtained from either a single fixed-nuclei based calculation or from a series of configurations extracted from a classical molecular dynamics trajectory. Nuclear quantum dynamics can accurately explain the intrinsic broadening of certain features. Glycine, the simplest amino acid, is problematic due to large spectral variations associated with multiple energetically accessible conformations at the experimental temperature. This work highlights the sensitivity of NEXAFS to quantum nuclear motions in molecules, and the necessity of accurately sampling such quantum motion when simulating their NEXAFS spectra.

  20. Generalization of atoms-in-molecules theory to include independent scaling of inner and outer shells

    NASA Astrophysics Data System (ADS)

    Ellison, Frank O.; Chen, Cheng

    1984-12-01

    Scaled atoms-in-molecules (SAIM) theory is required for obtaining diatomic fragment eigenvectors, and often useful for providing diatomic fragment potential energy curves, needed as input in the scaled diatomic-in-molecules (SDIM) method. Independent scaling of inner shells and valence shells is not admitted in the current formulation of SAIM. A new extension is developed here in which atomic eigenfunctions are partitioned into inner-shell and outer-shell components. These component functions are rigorously defined as solutions of two simultaneous eigenvalue equations; the Hamiltonians in these equations add to yield the original total atomic Hamiltonian. The component Hamiltonians so defined are shown to contain potential energy functions which are approximately homogeneous functions of degree minus one; hence, Coulomb-like. Thus, the inner-shell and outer-shell eigenfunctions may be scaled independently using methods generalized from standard scaled atoms-in-molecules (SAIM) theory. Preliminary applications to LiH, BeH, and Li2, and their positive ions, yield dissociation energies accurate to 7 kcal/mol or better.

  1. EVAPORATION: a new vapor pressure estimation method for organic molecules including non-additivity and intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-04-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict vapour pressure p0 of organic molecules needing only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: carbonyls, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  2. Some considerations of cold fusion including the calculation of fusion rates in molecules of hydrogen isotopes

    SciTech Connect

    Cowley, S.C.; Kulsrud, R.M.

    1989-11-01

    We calculate the fusion reaction rates in molecules of hydrogen isotopes. The rates are calculated analytically (for the first time) as an asymptotic expansion in the ratio of the electron mass to the reduced mass of the nucleii. The fusion rates of the P-D, D-D, and D-T reactions are given for a variable electron mass by a simple analytic formula. However, we do not know any mechanism by which a sufficiently localized electron in solid can have an effective mass' large enough to explain the result of Fleischman and Pons (FP). This calculation indicates that P-D rates should exceed D-D rates for D-D fusion rates less than approximately 10{sup {minus}23} per molecule per second. The D-D fusion rate is enhanced by a factor of 10{sup 5} at 10,000{degree}K if the excited vibrational states are populated with a Boltzmann distribution and the rotational excitations suppressed. The suggestion that experimental results could be explained by bombardment of cold deuterons by kilovolt deuterons is shown to be an unlikely from an energetic point of view. 12 refs., 3 figs., 1 tab.

  3. Monte Carlo calculations of diatomic molecule gas flows including rotational mode excitation

    NASA Technical Reports Server (NTRS)

    Yoshikawa, K. K.; Itikawa, Y.

    1976-01-01

    The direct simulation Monte Carlo method was used to solve the Boltzmann equation for flows of an internally excited nonequilibrium gas, namely, of rotationally excited homonuclear diatomic nitrogen. The semi-classical transition probability model of Itikawa was investigated for its ability to simulate flow fields far from equilibrium. The behavior of diatomic nitrogen was examined for several different nonequilibrium initial states that are subjected to uniform mean flow without boundary interactions. A sample of 1000 model molecules was observed as the gas relaxed to a steady state starting from three specified initial states. The initial states considered are: (1) complete equilibrium, (2) nonequilibrium, equipartition (all rotational energy states are assigned the mean energy level obtained at equilibrium with a Boltzmann distribution at the translational temperature), and (3) nonequipartition (the mean rotational energy is different from the equilibrium mean value with respect to the translational energy states). In all cases investigated the present model satisfactorily simulated the principal features of the relaxation effects in nonequilibrium flow of diatomic molecules.

  4. Zirconium-based alloys, nuclear fuel rods and nuclear reactors including such alloys, and related methods

    DOEpatents

    Mariani, Robert Dominick

    2014-09-09

    Zirconium-based metal alloy compositions comprise zirconium, a first additive in which the permeability of hydrogen decreases with increasing temperatures at least over a temperature range extending from 350.degree. C. to 750.degree. C., and a second additive having a solubility in zirconium over the temperature range extending from 350.degree. C. to 750.degree. C. At least one of a solubility of the first additive in the second additive over the temperature range extending from 350.degree. C. to 750.degree. C. and a solubility of the second additive in the first additive over the temperature range extending from 350.degree. C. to 750.degree. C. is higher than the solubility of the second additive in zirconium over the temperature range extending from 350.degree. C. to 750.degree. C. Nuclear fuel rods include a cladding material comprising such metal alloy compositions, and nuclear reactors include such fuel rods. Methods are used to fabricate such zirconium-based metal alloy compositions.

  5. Monitoring Nonadiabatic Electron-Nuclear Dynamics in Molecules by Attosecond Streaking of Photoelectrons.

    PubMed

    Kowalewski, Markus; Bennett, Kochise; Rouxel, Jérémy R; Mukamel, Shaul

    2016-07-22

    Streaking of photoelectrons has long been used for the temporal characterization of attosecond extreme ultraviolet pulses. When the time-resolved photoelectrons originate from a coherent superposition of electronic states, they carry additional phase information, which can be retrieved by the streaking technique. In this contribution we extend the streaking formalism to include coupled electron and nuclear dynamics in molecules as well as initial coherences. We demonstrate how streaked photoelectrons offer a novel tool for monitoring nonadiabatic dynamics as it occurs in the vicinity of conical intersections and avoided crossings. Streaking can provide high time resolution direct signatures of electronic coherences, which affect many primary photochemical and biological events. PMID:27494470

  6. Monitoring Nonadiabatic Electron-Nuclear Dynamics in Molecules by Attosecond Streaking of Photoelectrons

    NASA Astrophysics Data System (ADS)

    Kowalewski, Markus; Bennett, Kochise; Rouxel, Jérémy R.; Mukamel, Shaul

    2016-07-01

    Streaking of photoelectrons has long been used for the temporal characterization of attosecond extreme ultraviolet pulses. When the time-resolved photoelectrons originate from a coherent superposition of electronic states, they carry additional phase information, which can be retrieved by the streaking technique. In this contribution we extend the streaking formalism to include coupled electron and nuclear dynamics in molecules as well as initial coherences. We demonstrate how streaked photoelectrons offer a novel tool for monitoring nonadiabatic dynamics as it occurs in the vicinity of conical intersections and avoided crossings. Streaking can provide high time resolution direct signatures of electronic coherences, which affect many primary photochemical and biological events.

  7. Maria Goeppert Mayer: atoms, molecules and nuclear shells

    SciTech Connect

    Johnson, K.E.

    1986-09-01

    The mathematical physicist's early work in atomic and molecular physics, and her unfamiliarity with the ''fashions'' in nuclear physics, gave her the ideal preparation for solving the puzzle of the nuclear ''magic numbers.''

  8. Analytic dipole moment geometric derivatives from nuclear electric shielding in molecules. II. Application to two-heavy atom molecules

    NASA Astrophysics Data System (ADS)

    Zanasi, Riccardo; Lazzeretti, Paolo

    1986-11-01

    Calculations of dipole moment geometric derivatives for C2H4, C2H6, CH2O, CH3F, C2H2, HCN, and CH3OH molecules are presented. Satisfactory results are obtained by using a previously introduced analytical method, based on the evaluation of nuclear electric shieldings combined with the use of ``polarized'' basis sets. Computer efforts are maintained reasonably low.

  9. Searches for new interstellar molecules, including a tentative detection of aziridine and a possible detection of propenal

    NASA Technical Reports Server (NTRS)

    Dickens, J. E.; Irvine, W. M.; Nummelin, A.; Mollendal, H.; Saito, S.; Thorwirth, S.; Hjalmarson, A.; Ohishi, M.

    2001-01-01

    Rotational spectroscopy at millimeter wavelengths is a powerful means of investigating the chemistry of dense interstellar clouds. These regions can exhibit an interesting complement of gas phase molecules, including relatively complex organics. Here we report the tentative first astronomical detection of aziridine (ethylenimine), the possible detection of propenal (acrolein), and upper limits on the abundances of cyclopropenone, furan, hydroxyethanal (glycolaldehyde), thiohydroxylamine (NH2SH), and ethenol (vinyl alcohol) in various interstellar clouds.

  10. Theoretical predictions of the impact of nuclear dynamics and environment on core-level spectra of organic molecules

    NASA Astrophysics Data System (ADS)

    Prendergast, David; Schwartz, Craig; Uejio, Janel; Saykally, Richard

    2009-03-01

    Core-level spectroscopy provides an element-specific probe of local electronic structure and bonding, but linking details of atomic structure to measured spectra relies heavily on accurate theoretical interpretation. We present first principles simulations of the x-ray absorption of a range of organic molecules both in isolation and aqueous solvation, highlighting the spectral impact of internal nuclear motion as well as solvent interactions. Our approach uses density functional theory with explicit inclusion of the core-level excited state within a plane-wave supercell framework. Nuclear degrees of freedom are sampled using various molecular dynamics techniques. We indicate specific cases for molecules in their vibrational ground state at experimental conditions, where nuclear quantum effects must be included. Prepared by LBNL under Contract DE-AC02-05CH11231.

  11. Time-reversal symmetry violation in molecules induced by nuclear magnetic quadrupole moments.

    PubMed

    Flambaum, V V; DeMille, D; Kozlov, M G

    2014-09-01

    Recent measurements in paramagnetic molecules improved the limit on the electron electric dipole moment (EDM) by an order of magnitude. Time-reversal (T) and parity (P) symmetry violation in molecules may also come from their nuclei. We point out that nuclear T, P-odd effects are amplified in paramagnetic molecules containing deformed nuclei, where the primary effects arise from the T, P-odd nuclear magnetic quadrupole moment (MQM). We perform calculations of T, P-odd effects in the molecules TaN, ThO, ThF+, HfF+, YbF, HgF, and BaF induced by MQMs. We compare our results with those for the diamagnetic TlF molecule, where the T, P-odd effects are produced by the nuclear Schiff moment. We argue that measurements in molecules with MQMs may provide improved limits on the strength of T, P-odd nuclear forces, on the proton, neutron, and quark EDMs, on quark chromo-EDMs, and on the QCD θ term and CP-violating quark interactions. PMID:25238355

  12. Non-nuclear electron transport channels in hollow molecules

    NASA Astrophysics Data System (ADS)

    Zhao, Jin; Petek, Hrvoje

    2014-08-01

    Electron transport in inorganic semiconductors and metals occurs through delocalized bands formed by overlapping electron orbitals. Strong correlation of electronic wave functions with the ionic cores couples the electron and lattice motions, leading to efficient interaction and scattering that degrades coherent charge transport. By contrast, unoccupied electronic states at energies near the vacuum level with diffuse molecular orbitals may form nearly-free-electron bands with density maxima in non-nuclear interstitial voids, which are subject to weaker electron-phonon interaction. The position of such bands typically above the frontier orbitals, however, renders them unstable with respect to electronic interband relaxation and therefore unsuitable for charge transport. Through electronic-structure calculations, we engineer stable, non-nuclear, nearly-free-electron conduction channels in low-dimensional molecular materials by tailoring their electrostatic and polarization potentials. We propose quantum structures of graphane-derived Janus molecular sheets with spatially isolated conducting and insulating regions that potentially exhibit emergent electronic properties, as a paradigm for molecular-scale non-nuclear charge conductors; we also describe tuning of their electronic properties by application of external fields and calculate their electron-acoustic-phonon interaction.

  13. Non-nuclear Electron Transport Channels in Hollow Molecules

    SciTech Connect

    Zhao, Jin; Petek, Hrvoje

    2014-08-15

    Electron transport in inorganic semiconductors and metals occurs through delocalized bands formed by overlapping electron orbitals. Strong correlation of electronic wave functions with the ionic cores couples the electron and lattice motions, leading to efficient interaction and scattering that degrades coherent charge transport. By contrast, unoccupied electronic states at energies near the vacuum level with diffuse molecular orbitals may form nearly-free-electron bands with density maxima in non-nuclear interstitial voids, which are subject to weaker electron-phonon interaction. The position of such bands typically above the frontier orbitals, however, renders them unstable with respect to electronic interband relaxation and therefore unsuitable for charge transport. Through electronic-structure calculations, we engineer stable, non-nuclear, nearly-free-electron conduction channels in low-dimensional molecular materials by tailoring their electrostatic and polarization potentials. We propose quantum structures of graphane-derived Janus molecular sheets with spatially isolated conducting and insulating regions that potentially exhibit emergent electronic properties, as a paradigm for molecular-scale non-nuclear charge conductors; we also describe tuning of their electronic properties by application of external fields and calculate their electron–acoustic-phonon interaction.

  14. Measurement of the nuclear polarization of hydrogen and deuterium molecules using a Lamb-shift polarimeter

    SciTech Connect

    Engels, Ralf Gorski, Robert; Grigoryev, Kiril; Mikirtychyants, Maxim; Rathmann, Frank; Seyfarth, Hellmut; Ströher, Hans; Weiss, Philipp; Kochenda, Leonid; Kravtsov, Peter; Trofimov, Viktor; Tschernov, Nikolay; Vasilyev, Alexander; Vznuzdaev, Marat; Schieck, Hans Paetz gen.

    2014-10-15

    Lamb-shift polarimeters are used to measure the nuclear polarization of protons and deuterons at energies of a few keV. In combination with an ionizer, the polarization of hydrogen and deuterium atoms was determined after taking into account the loss of polarization during the ionization process. The present work shows that the nuclear polarization of hydrogen or deuterium molecules can be measured as well, by ionizing the molecules and injecting the H{sub 2}{sup +} (or D{sub 2}{sup +}) ions into the Lamb-shift polarimeter.

  15. Calculation of Ground State Rotational Populations for Kinetic Gas Homonuclear Diatomic Molecules including Electron-Impact Excitation and Wall Collisions

    SciTech Connect

    David R. Farley

    2010-08-19

    A model has been developed to calculate the ground-state rotational populations of homonuclear diatomic molecules in kinetic gases, including the effects of electron-impact excitation, wall collisions, and gas feed rate. The equations are exact within the accuracy of the cross sections used and of the assumed equilibrating effect of wall collisions. It is found that the inflow of feed gas and equilibrating wall collisions can significantly affect the rotational distribution in competition with non-equilibrating electron-impact effects. The resulting steady-state rotational distributions are generally Boltzmann for N≥3, with a rotational temperature between the wall and feed gas temperatures. The N=0,1,2 rotational level populations depend sensitively on the relative rates of electron-impact excitation versus wall collision and gas feed rates.

  16. Single-point single-molecule FRAP distinguishes inner and outer nuclear membrane protein distribution

    PubMed Central

    Mudumbi, Krishna C; Schirmer, Eric C; Yang, Weidong

    2016-01-01

    The normal distribution of nuclear envelope transmembrane proteins (NETs) is disrupted in several human diseases. NETs are synthesized on the endoplasmic reticulum and then transported from the outer nuclear membrane (ONM) to the inner nuclear membrane (INM). Quantitative determination of the distribution of NETs on the ONM and INM is limited in available approaches, which moreover provide no information about translocation rates in the two membranes. Here we demonstrate a single-point single-molecule FRAP microscopy technique that enables determination of distribution and translocation rates for NETs in vivo. PMID:27558844

  17. Single-point single-molecule FRAP distinguishes inner and outer nuclear membrane protein distribution.

    PubMed

    Mudumbi, Krishna C; Schirmer, Eric C; Yang, Weidong

    2016-01-01

    The normal distribution of nuclear envelope transmembrane proteins (NETs) is disrupted in several human diseases. NETs are synthesized on the endoplasmic reticulum and then transported from the outer nuclear membrane (ONM) to the inner nuclear membrane (INM). Quantitative determination of the distribution of NETs on the ONM and INM is limited in available approaches, which moreover provide no information about translocation rates in the two membranes. Here we demonstrate a single-point single-molecule FRAP microscopy technique that enables determination of distribution and translocation rates for NETs in vivo. PMID:27558844

  18. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches.

    PubMed

    Musser, Siegfried M; Grünwald, David

    2016-05-22

    Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells. PMID:26944195

  19. Energy-Level Related Nuclear-Spin Effects and Super-Hyperfine Spectral Patterns: how Molecules do Self-Nmr

    NASA Astrophysics Data System (ADS)

    Harter, William; Mitchell, Justin

    2009-06-01

    At several points in his defining works on molecular spectroscopy, Herzberg notes that ``because nuclear moments ldots are so very slight ldots transitions between species ldots are very strictly forbiddenldots '' Herzberg's most recent statement of such selection rules pertained to spherical top spin-species. It has since been shown that spherical top species (as well as those of lower symmetry molecules) converge exponentially with momentum quanta J and K to degenerate level clusters wherein even ``very slight'' nuclear fields and moments cause pervasive resonance and total spin species mixing. Ultra-high resolution spectra of Borde, et .al and Pfister et .al shows how SF_6 and SiF_4 Fluorine nuclear spin levels rearrange from total-spin multiplets to NMR-like patterns as their superfine structure converges. Similar super-hyperfine effects are anticipated for lower symmetry molecules exhibiting converging superfine level-clusters. Examples include PH_3 molecules and asymmetric tops. Following this we consider models that treat nuclear spins as coupled rotors undergoing generalized Hund-case transitions from spin-lab-momentum coupling to various spin-rotor correlations. G. A. Herzberg, Electronic Spectra of Polyatomic Molecules, (Von Norstrand Rheinhold 1966) p. 246. W G. Harter and C. W Patterson, Phys. Rev. A 19, 2277 (1979) W. G. Harter, Phys. Rev. A 24, 192 (1981). Ch. J. Borde, J. Borde, Ch. Breant, Ch. Chardonnet, A. Van Lerberghe, and Ch. Salomon, in Laser Spectroscopy VII, T. W Hensch and Y. R. Shen, eds. (Springer-Verlag, Berlin, 1985). O. Pfister, F. Guernet, G. Charton, Ch. Chardonnet, F. Herlemont, and J. Legrand, J. Opt. Soc. Am. B 10, 1521 (1993). O. Pfister, Ch. Chardonnet, and Ch. J. Bordè, Phys. Rev. Lett. 76, 4516 (1996) S. N. Yurchenko, W. Thiel, S. Patchkovskii, and P. Jensen, Phys. Chem. Chem. Phys.7, 573 (2005)

  20. MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

    NASA Astrophysics Data System (ADS)

    Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

    2012-08-01

    We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_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.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon

  1. Single-Molecule Imaging to Characterize the Transport Mechanism of the Nuclear Pore Complex.

    PubMed

    Jeremy, Grace; Stevens, James; Lowe, Alan R

    2016-01-01

    In the eukaryotic cell, a large macromolecular channel, known as the Nuclear Pore Complex (NPC), mediates all molecular transport between the nucleus and cytoplasm. In recent years, single-molecule fluorescence (SMF) imaging has emerged as a powerful tool to study the molecular mechanism of transport through the NPC. More recently, techniques such as single-molecule localization microscopy (SMLM) have enabled the spatial and temporal distribution of cargos, transport receptors and even structural components of the NPC to be determined with nanometre accuracy. In this protocol, we describe a method to study the position and/or motion of individual molecules transiting through the NPC with high spatial and temporal precision. PMID:27283299

  2. Polarization propagator approach to the dynamic nuclear electric shielding in LiH molecule

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Rossi, E.; Zanasi, R.

    1983-07-01

    The frequency dependence of the dipole electric polarizability and electric shielding tensors of hydrogen and lithium nuclei in the LiH molecule has been studied via some approximations to the polarization propagator method, i.e., STA, TDA, and RPA, allowing for dipole length, velocity, acceleration, and mixed formalisms. The RPA nuclear electric shieldings are in a fairly good agreement with the corresponding experimental data, a discrepancy being observed for the parallel component at the Li nucleus.

  3. Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging.

    PubMed

    Georgieva, Mariya; Cattoni, Diego I; Fiche, Jean-Bernard; Mutin, Thibaut; Chamousset, Delphine; Nollmann, Marcelo

    2016-08-01

    In order to study the detailed assembly and regulation mechanisms of complex structures and machineries in the cell, simultaneous in situ observation of all the individual interacting components should be achieved. Multi-color Single-Molecule Localization Microscopy (SMLM) is ideally suited for these quantifications. Here, we build on previous developments and thoroughly discuss a protocol for two-color SMLM combining PALM and STORM, including sample preparation details, image acquisition and data postprocessing analysis. We implement and evaluate a recently proposed colocalization analysis method (aCBC) that allows single-molecule colocalization quantification with the potential of revealing fine, nanometer-scaled, structural details of multicomponent complexes. Finally, using a doubly-labeled nuclear factor (Beaf-32) in Drosophila S2 cells we experimentally validate the colocalization quantification algorithm, highlight its advantages and discuss how using high molecular weight fluorescently labeled tags compromises colocalization precision in two-color SMLM experiments. PMID:27045944

  4. Relationship of sea level muon charge ratio to primary composition including nuclear target effects

    NASA Technical Reports Server (NTRS)

    Goned, A.; Shalaby, M.; Salem, A. M.; Roushdy, M.

    1985-01-01

    The discrepancy between the muon charge ratio observed at low energies and that calculated using pp data is removed by including nuclear target effects. Calculations at high energies show that the primary iron spectrum is expected to change slope from 2 to 2.2 to 2.4 to 2.5 for energies approx. 4 x 10 to the 3 GeV/nucleon if scaling features continue to the highest energies.

  5. Extensive spectroscopic calculations on 12 low-lying electronic states of AlN molecule including transition properties

    NASA Astrophysics Data System (ADS)

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2014-05-01

    Using the CASSCF method followed by the internally contracted MRCI approach in combination with the correlation-consistent basis sets, the potential energy curves (PECs) are calculated for the X3Π, A3Σ-, B3Σ+, C3Π, E3Δ, a1Σ+, b1Π, c1Δ, d1Σ+, e1Π, 23Σ- and 33Σ- electronic states of AlN molecule for internuclear separations from 0.1 to 1.0 nm. All the electronic states correlate to the three dissociation channels, Al(2Pu) + N(4Su), Al(2Pu) + N(2Du) and Al(2Pu) + N(2Pu). Of these 12 electronic states, only the 23Σ- possesses the double well. The PECs determined by the internally contracted MRCI approach are corrected for size-extensivity errors by means of the Davidson correction. The convergent behavior of present calculations is observed with respect to the basis set and level of theory. The effect of core-valence correlation and scalar relativistic corrections on the spectroscopic parameters is discussed. Scalar relativistic correction calculations are performed by the third-order Douglas-Kroll Hamiltonian approximation at the level of cc-pVTZ basis set. Core-valence correlation corrections are included with a cc-pCVTZ basis set. All the PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated by fitting the first ten vibrational levels when available, which are obtained by solving the ro-vibrational Schrödinger equation with the Numerov's method. The spectroscopic parameters are compared with those reported in the literature. Excellent agreement is found between the present results and the measurements. Analyses show that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. The Franck-Condon factors and radiative lifetimes of the transitions from the A3Σ-, B3Σ+, C3Π, a1Σ+ and b1Π electronic states to the ground state are calculated for several low vibrational levels, and some necessary discussion has been made.

  6. Extensive ab initio study of the electronic states of S2 molecule including spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Xing, Wei; Shi, Deheng; Sun, Jinfeng; Liu, Hui; Zhu, Zunlue

    2013-03-01

    The potential energy curves (PECs) of 15 Λ-S states and 24 Ω states generated from the 13 Λ-S bound states of the S2 molecule are investigated in detail using an ab initio quantum chemical method. The PECs are calculated for internuclear separations from 0.12 to 1.10 nm by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson modification (MRCI + Q). The spin-orbit (SO) coupling effect is accounted for by the Breit-Pauli Hamiltonian. To discuss the effect on the energy splitting by the core-electron correlations, the all-electron basis set, cc-pCVTZ with and without 2s2p correlations, is used for the SO coupling calculations of the A3 ? and B‧3Πg Λ-S states since their measurements can be found in the literature. By comparison, the cc-pCVTZ basis set with 2s2p correlations is chosen for the SO coupling calculations of 13 Λ-S bound states. To improve the quality of PECs, core-valence correlation and scalar relativistic corrections are included. Scalar relativistic correction calculations are made using the third-order Douglas-Kroll Hamiltonian (DKH3) approximation at the level of a cc-pV5Z basis set. Core-valence correlation corrections are taken into account with a cc-pCVTZ basis set. The spectroscopic parameters of 13 Λ-S bound states and 24 Ω states are calculated. With the PECs obtained by the MRCI + Q/aug-cc-pV6Z + CV + DK + SO calculations, the SO coupling splitting energies are 379.25 cm-1 between the A‧3 and A‧2 Ω state, 83.40 cm-1 between the A1 and A0- Ω state and 210.91 cm-1 between the B‧2 and B‧1 Ω state, which agree well with the corresponding measurements of 383, 77.51 and 209 cm-1, respectively. Moreover, other spectroscopic parameters are also in excellent agreement with the measurements. It demonstrates that the spectroscopic parameters of 24 Ω states reported here for the first time can be expected to be

  7. Pressuromodulation at the cell membrane as the basis for small molecule hormone and peptide regulation of cellular and nuclear function.

    PubMed

    Sarin, Hemant

    2015-01-01

    Building on recent knowledge that the specificity of the biological interactions of small molecule hydrophiles and lipophiles across microvascular and epithelial barriers, and with cells, can be predicted on the basis of their conserved biophysical properties, and the knowledge that biological peptides are cell membrane impermeant, it has been further discussed herein that cellular, and thus, nuclear function, are primarily regulated by small molecule hormone and peptide/factor interactions at the cell membrane (CM) receptors. The means of regulating cellular, and thus, nuclear function, are the various forms of CM Pressuromodulation that exist, which include Direct CM Receptor-Mediated Stabilizing Pressuromodulation, sub-classified as Direct CM Receptor-Mediated Stabilizing Shift Pressuromodulation (Single, Dual or Tri) or Direct CM Receptor-Mediated Stabilizing Shift Pressuromodulation (Single, Dual or Tri) cum External Cationomodulation (≥3+ → 1+); which are with respect to acute CM receptor-stabilizing effects of small biomolecule hormones, growth factors or cytokines, and also include Indirect CM- or CM Receptor-Mediated Pressuromodulation, sub-classified as Indirect 1ary CM-Mediated Shift Pressuromodulation (Perturbomodulation), Indirect 2ary CM Receptor-Mediated Shift Pressuromodulation (Tri or Quad Receptor Internal Pseudo-Cationomodulation: SS 1+), Indirect 3ary CM Receptor-Mediated Shift Pressuromodulation (Single or Dual Receptor Endocytic External Cationomodulation: 2+) or Indirect (Pseudo) 3ary CM Receptor-Mediated Shift Pressuromodulation (Receptor Endocytic Hydroxylocarbonyloetheroylomodulation: 0), which are with respect to sub-acute CM receptor-stabilizing effects of small biomolecules, growth factors or cytokines. As a generalization, all forms of CM pressuromodulation decrease CM and nuclear membrane (NM) compliance (whole cell compliance), due to pressuromodulation of the intracellular microtubule network and increases the exocytosis of pre

  8. Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping

    SciTech Connect

    Kruglyak, L.; Daly, M.J.; Lander, E.S. |

    1995-02-01

    Homozygosity mapping is a powerful strategy for mapping rare recessive traits in children of consanguineous marriages. Practical applications of this strategy are currently limited by the inability of conventional linkage analysis software to compute, in reasonable time, multipoint LOD scores for pedigrees with inbreeding loops. We have developed a new algorithm for rapid multipoint likelihood calculations in small pedigrees, including those with inbreeding loops. The running time of the algorithm grows, at most, linearly with the number of loci considered simultaneously. The running time is not sensitive to the presence of inbreeding loops, missing genotype information, and highly polymorphic loci. We have incorporated this algorithm into a software package, MAPMAKER/HOMOZ, that allows very rapid multipoint mapping of disease genes in nuclear families, including homozygosity mapping. Multipoint analysis with dozens of markers can be carried out in minutes on a personal workstation. 23 refs., 4 figs., 1 tab.

  9. Photo Library of the Nevada Site Office (Includes historical archive of nuclear testing images)

    DOE Data Explorer

    The Nevada Site Office makes available publicly released photos from their archive that includes photos from both current programs and historical activities. The historical collections include atmospheric and underground nuclear testing photos and photos of other events and people related to the Nevada Test Site. Current collections are focused on homeland security, stockpile stewardship, and environmental management and restoration. See also the Historical Film Library at http://www.nv.doe.gov/library/films/testfilms.aspx and the Current Film Library at http://www.nv.doe.gov/library/films/current.aspx. Current films can be viewed online, but only short clips of the historical films are viewable. They can be ordered via an online request form for a very small shipping and handling fee.

  10. Neutron monitoring systems including gamma thermometers and methods of calibrating nuclear instruments using gamma thermometers

    SciTech Connect

    Moen, Stephan Craig; Meyers, Craig Glenn; Petzen, John Alexander; Foard, Adam Muhling

    2012-08-07

    A method of calibrating a nuclear instrument using a gamma thermometer may include: measuring, in the instrument, local neutron flux; generating, from the instrument, a first signal proportional to the neutron flux; measuring, in the gamma thermometer, local gamma flux; generating, from the gamma thermometer, a second signal proportional to the gamma flux; compensating the second signal; and calibrating a gain of the instrument based on the compensated second signal. Compensating the second signal may include: calculating selected yield fractions for specific groups of delayed gamma sources; calculating time constants for the specific groups; calculating a third signal that corresponds to delayed local gamma flux based on the selected yield fractions and time constants; and calculating the compensated second signal by subtracting the third signal from the second signal. The specific groups may have decay time constants greater than 5.times.10.sup.-1 seconds and less than 5.times.10.sup.5 seconds.

  11. Molecular and structural characterization of dissolved organic matter from the deep ocean by FTICR-MS, including hydrophilic nitrogenous organic molecules

    USGS Publications Warehouse

    Reemtsma, T.; These, A.; Linscheid, M.; Leenheer, J.; Spitzy, A.

    2008-01-01

    Dissolved organic matter isolated from the deep Atlantic Ocean and fractionated into a so-called hydrophobic (HPO) fraction and a very hydrophilic (HPI) fraction was analyzed for the first time by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to resolve the molecular species, to determine their exact masses, and to calculate their molecular formulas. The elemental composition of about 300 molecules was identified. Those in the HPO fraction (14C age of 5100 year) are very similar to much younger freshwater fulvic acids, but less aromatic and more oxygenated molecules are more frequent. This trend continues toward the HPI fraction and may indicate biotic and abiotic aging processes that this material experienced since its primary production thousands of years ago. In the HPI fraction series of nitrogenous molecules containing one, two, or three nitrogens were identified by FTICR-MS. Product ion spectra of the nitrogenous molecules suggest that the nitrogen atoms in these molecules are included in the (alicyclic) backbone of these molecules, possibly in reduced form. These mass spectrometric data suggest that a large set of stable fulvic acids is ubiquitous in all aquatic compartments. Although sources may differ, their actual composition and structure appears to be quite similar and largely independent from their source, because they are the remainder of intensive oxidative degradation processes. ?? 2008 American Chemical Society.

  12. Theoretical methods for attosecond electron and nuclear dynamics: applications to the H2 molecule

    NASA Astrophysics Data System (ADS)

    Palacios, Alicia; Sanz-Vicario, José Luis; Martín, Fernando

    2015-12-01

    Attosecond science, born at the beginning of this century with the generation of the first bursts of light with durations shorter than a femtosecond, has opened the way to look at electron dynamics in atoms and molecules at its natural timescale. Thus controlling chemical reactions at the electronic level or obtaining time-resolved images of the electronic motion has become a goal for many physics and chemistry laboratories all over the world. The new experimental capabilities have spurred the development of sophisticated theoretical methods that can accurately predict phenomena occurring in the sub-fs timescale. This review provides an overview of the capabilities of existing theoretical tools to describe electron and nuclear dynamics resulting from the interaction of femto- and attosecond UV/XUV radiation with simple molecular targets. We describe one of these methods in more detail, the time-dependent Feshbach close-coupling (TDFCC) formalism, which has been used successfully over the years to investigate various attosecond phenomena in the hydrogen molecule and can easily be extended to other diatomics. In addition to describing the details of the method and discussing its advantages and limitations, we also provide examples of the new physics that one can learn by applying it to different problems: from the study of the autoionization decay that follows attosecond UV excitation to the imaging of the coupled electron and nuclear dynamics in H2 using different UV-pump/IR-probe and UV-pump/UV-probe schemes.

  13. Electric quadrupole polarizabilities of nuclear magnetic shielding in some small molecules.

    PubMed

    Ferraro, M B; Caputo, M C; Pagola, G I; Lazzeretti, P

    2008-01-28

    Computational procedures, based on (i) the Ramsey common origin approach and (ii) the continuous transformation of the origin of the quantum mechanical current density-diamagnetic zero (CTOCD-DZ), were applied at the Hartree-Fock level to determine electric quadrupole polarizabilities of nuclear magnetic shielding for molecules in the presence of a nonuniform electric field with a uniform gradient. The quadrupole polarizabilities depend on the origin of the coordinate system, but values of the magnetic field induced at a reference nucleus, determined via the CTOCD-DZ approach, are origin independent for any calculations relying on the algebraic approximation, irrespective of size and quality of the (gaugeless) basis set employed. On the other hand, theoretical estimates of the induced magnetic field obtained by single-origin methods are translationally invariant only in the limit of complete basis sets. Calculations of electric quadrupole polarizabilities of nuclear magnetic shielding are reported for H(2), HF, H(2)O, NH(3), and CH(4) molecules. PMID:18247940

  14. Electric quadrupole polarizabilities of nuclear magnetic shielding in some small molecules

    NASA Astrophysics Data System (ADS)

    Ferraro, M. B.; Caputo, M. C.; Pagola, G. I.; Lazzeretti, P.

    2008-01-01

    Computational procedures, based on (i) the Ramsey common origin approach and (ii) the continuous transformation of the origin of the quantum mechanical current density-diamagnetic zero (CTOCD-DZ), were applied at the Hartree-Fock level to determine electric quadrupole polarizabilities of nuclear magnetic shielding for molecules in the presence of a nonuniform electric field with a uniform gradient. The quadrupole polarizabilities depend on the origin of the coordinate system, but values of the magnetic field induced at a reference nucleus, determined via the CTOCD-DZ approach, are origin independent for any calculations relying on the algebraic approximation, irrespective of size and quality of the (gaugeless) basis set employed. On the other hand, theoretical estimates of the induced magnetic field obtained by single-origin methods are translationally invariant only in the limit of complete basis sets. Calculations of electric quadrupole polarizabilities of nuclear magnetic shielding are reported for H2, HF, H2O, NH3, and CH4 molecules.

  15. Body-fixed relativistic molecular Hamiltonian and its application to nuclear spin-rotation tensor: Linear molecules

    NASA Astrophysics Data System (ADS)

    Xiao, Yunlong; Liu, Wenjian

    2013-07-01

    The relativistic molecular Hamiltonian written in the body-fixed frame of reference is the basis for high-precision calculations of spectroscopic parameters involving nuclear vibrations and/or rotations. Such a Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is just developed for semi-rigid nonlinear molecules [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)], 10.1063/1.4797496. Yet, the formulation should somewhat be revised for linear molecules thanks to some unusual features arising from the redundancy of the rotation around the molecular axis. Nonetheless, the resulting isomorphic Hamiltonian is rather similar to that for nonlinear molecules. Consequently, the relativistic formulation of nuclear spin-rotation (NSR) tensor for linear molecules is very much the same as that for nonlinear molecules. So is the relativistic mapping between experimental NSR and NMR.

  16. Ionization potential of {sup 9}Be calculated including nuclear motion and relativistic corrections

    SciTech Connect

    Stanke, Monika; Kedziera, Dariusz; Bubin, Sergiy; Adamowicz, Ludwik

    2007-05-15

    Variational calculations employing explicitly correlated Gaussian functions have been performed for the ground states of {sup 9}Be and {sup 9}Be{sup +} including the nuclear motion [i.e., without assuming the Born-Oppenheimer (BO) approximation]. An approach based on the analytical energy gradient calculated with respect to the Gaussian exponential parameters was employed, leading to energies of the two systems noticeably improved over those found in the recent paper of Pachucki and Komasa [Phys. Rev. A 73, 052502 (2006)]. The non-BO wave functions were used to calculate the {alpha}{sup 2} relativistic corrections ({alpha}=e{sup 2}/({Dirac_h}/2{pi})c). With those corrections and the {alpha}{sup 3} and {alpha}{sup 4} corrections taken from Pachucki and Komasa, a new value of the ionization potential (IP) of {sup 9}Be was determined. It agrees very well with the most recent experimental IP.

  17. Squaring the cube: a family of octametallic lanthanide complexes including a Dy8 single-molecule magnet.

    PubMed

    Fang, Ming; Zhao, Hanhua; Prosvirin, Andrey V; Pinkowicz, Dawid; Zhao, Bin; Cheng, Peng; Wernsdorfer, Wolfgang; Brechin, Euan K; Dunbar, Kim R

    2013-10-01

    A series of isostructural octanuclear lanthanide complexes of general formula [Ln8(sao)4(μ3-OH)4(NO3)12(DMF)12] (Ln = Nd (), Sm (), Eu (), Gd (), Tb (), Dy (), Ho (), Er (); DMF = dimethylformamide) have been prepared via reactions of salicylaldoxime (saoH2), tetramethylammonium hydroxide (Me4NOH) with the appropriate lanthanide nitrate salt (Ln(NO3)3·6H2O). The metallic skeletons of the complexes describe [Ln4] tetrahedra encapsulated inside a [Ln4] square with the inner core stabilised through μ3-OH(-) ions and the periphery by μ4-sao(2-) ligands. The magnetic properties of compounds were investigated by dc and ac magnetometry. Temperature dependent ac magnetic susceptibility data reveal that the dysprosium analogue () displays an out-of-phase signal in the absence of an applied magnetic field indicative of slow relaxation of the magnetization typical of a Single-Molecule Magnet (SMM). Micro-SQUID measurements reveal temperature and sweep rate dependent hysteresis below 1.0 K. PMID:23943045

  18. Improved best estimate plus uncertainty methodology including advanced validation concepts to license evolving nuclear reactors

    SciTech Connect

    Unal, Cetin; Williams, Brian; Mc Clure, Patrick; Nelson, Ralph A

    2010-01-01

    Many evolving nuclear energy programs plan to use advanced predictive multi-scale multi-physics simulation and modeling capabilities to reduce cost and time from design through licensing. Historically, the role of experiments was primary tool for design and understanding of nuclear system behavior while modeling and simulation played the subordinate role of supporting experiments. In the new era of multi-scale multi-physics computational based technology development, the experiments will still be needed but they will be performed at different scales to calibrate and validate models leading predictive simulations. Cost saving goals of programs will require us to minimize the required number of validation experiments. Utilization of more multi-scale multi-physics models introduces complexities in the validation of predictive tools. Traditional methodologies will have to be modified to address these arising issues. This paper lays out the basic aspects of a methodology that can be potentially used to address these new challenges in design and licensing of evolving nuclear technology programs. The main components of the proposed methodology are verification, validation, calibration, and uncertainty quantification. An enhanced calibration concept is introduced and is accomplished through data assimilation. The goal is to enable best-estimate prediction of system behaviors in both normal and safety related environments. To achieve this goal requires the additional steps of estimating the domain of validation and quantification of uncertainties that allow for extension of results to areas of the validation domain that are not directly tested with experiments, which might include extension of the modeling and simulation (M&S) capabilities for application to full-scale systems. The new methodology suggests a formalism to quantify an adequate level of validation (predictive maturity) with respect to required selective data so that required testing can be minimized for cost

  19. Observing the attosecond dynamics of nuclear wavepackets in molecules by using high harmonic generation in mixed gases

    NASA Astrophysics Data System (ADS)

    Kanai, Tsuneto; Takahashi, Eiji J.; Nabekawa, Yasuo; Midorikawa, Katsumi

    2008-02-01

    We probe the attosecond dynamics of nuclear wavepackets in H2 and D2 molecules by measuring the relative phase of high harmonics generated in each molecule by using a novel method with a mixed gas of H2 and D2. We find that not only the single molecule responses but also the propagation effects of harmonics differ between the two isotopes and we conclude that in order to discuss the dynamics of molecules in the single molecule responses, the propagation effects need to be excluded from the raw harmonic signals. The measured relative phase as well as the intensity ratio are found to be monotonic functions of the harmonic order and are successfully reproduced by applying Feynman's path integral method fully to the dynamics of the nuclei and electrons in the molecules.

  20. Thermosetting polymer for dynamic nuclear polarization: Solidification of an epoxy resin mixture including TEMPO

    NASA Astrophysics Data System (ADS)

    Noda, Yohei; Kumada, Takayuki; Yamaguchi, Daisuke; Shamoto, Shin-ichi

    2015-03-01

    We investigated the dynamic nuclear polarization (DNP) of typical thermosetting polymers (two-component type epoxy resins; Araldite® Standard or Araldite® Rapid) doped with a (2,2,6,6-tetramethylpiperidine-1-yl)oxy (TEMPO) radical. The doping process was developed by carefully considering the decomposition of TEMPO during the solidification of the epoxy resin. The TEMPO electron spin in each two-component paste decayed slowly, which was favorable for our study. Furthermore, despite the dissolved TEMPO, the mixture of the two-component paste successfully solidified. With the resulting TEMPO-doped epoxy-resin samples, DNP experiments at 1.2 K and 3.35 T indicated a magnitude of a proton-spin polarization up to 39%. This polarization is similar to that (35%) obtained for TEMPO-doped polystyrene (PS), which is often used as a standard sample for DNP. To combine this solidification of TEMPO-including mixture with a resin-casting technique enables a creation of polymeric target materials with a precise and complex structure.

  1. Degradation of HaloTag-fused nuclear proteins using bestatin-HaloTag ligand hybrid molecules.

    PubMed

    Tomoshige, Shusuke; Naito, Mikihiko; Hashimoto, Yuichi; Ishikawa, Minoru

    2015-10-14

    We have developed a protein knockdown technology using hybrid small molecules designed as conjugates of a ligand for the target protein and a ligand for ubiquitin ligase cellular inhibitor of apoptosis protein 1 (cIAP1). However, this technology has several limitations. Here, we report the development of a novel protein knockdown system to address these limitations. In this system, target proteins are fused with HaloTag to provide a common binding site for a degradation inducer. We designed and synthesized small molecules consisting of alkyl chloride as the HaloTag-binding degradation inducer, which binds to HaloTag, linked to BE04 (2), which binds to cIAP1. Using this system, we successfully knocked down HaloTag-fused cAMP responsive element binding protein 1 (HaloTag-CREB1) and HaloTag-fused c-jun (HaloTag-c-jun), which are ligand-unknown nuclear proteins, in living cells. HaloTag-binding degradation inducers can be synthesized easily, and are expected to be useful as biological tools for pan-degradation of HaloTag-fused proteins. PMID:26338696

  2. Detection of molecules and cells using nuclear magnetic resonance with magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Rümenapp, Christine; Gleich, Bernhard; Mannherz, Hans Georg; Haase, Axel

    2015-04-01

    For the detection of small molecules, proteins or even cells in vitro, functionalised magnetic nanoparticles and nuclear magnetic resonance measurements can be applied. In this work, magnetic nanoparticles with the size of 5-7 nm were functionalised with antibodies to detect two model systems of different sizes, the protein avidin and Saccharomyces cerevisiae as the model organism. The synthesised magnetic nanoparticles showed a narrow size distribution, which was determined using transmission electron microscopy and dynamic light scattering. The magnetic nanoparticles were functionalised with the according antibodies via EDC/NHS chemistry. The binding of the antigen to magnetic nanoparticles was detected through the change in the NMR T2 relaxation time at 0.5 T (≈21.7 MHz). In case of a specific binding the particles cluster and the T2 relaxation time of the sample changes. The detection limit in buffer for FITC-avidin was determined to be 1.35 nM and 107 cells/ml for S. cerevisiae. For fluorescent microscopy the avidin molecules were labelled with FITC and for the detection of S. cerevisiae the magnetic nanoparticles were additionally functionalised with rhodamine. The binding of the particles to S. cerevisiae and the resulting clustering was also seen by transmission electron microscopy.

  3. Impact of nuclear lattice relaxation on the excitation energy transfer along a chain of π -conjugated molecules

    NASA Astrophysics Data System (ADS)

    Schmid, S. A.; Abbel, R.; Schenning, A. P. H. J.; Meijer, E. W.; Herz, L. M.

    2010-02-01

    We have investigated the extent to which delocalization of the ground-state and excited-state wave functions of a π -conjugated molecule affects the excitation energy transfer (EET) between such molecules. Using femtosecond photoluminescence spectroscopy, we experimentally monitored the EET along well-defined supramolecular chains of extended conjugated molecules. Comparison with Monte Carlo simulations reveals that only a model incorporating a localized emitter and delocalized absorber wave function accurately reproduces these data. Our findings demonstrate that self-localization of the initially excited state, following fast relaxation of the nuclear lattice, has a significant impact on the EET dynamics in molecular assemblies.

  4. Simplex and duplex polymerase chain reaction analysis of Herculex RW (59122) maize based on one reference molecule including separated fragments of 5' integration site and endogenous gene.

    PubMed

    Li, Xiang; Yang, Litao; Zhang, Jianzhong; Wang, Shu; Shen, Kailin; Pan, Liangwen; Zhang, Dabing

    2009-01-01

    Reference molecules, as positive controls and calibrators, have been recently developed in genetically modified organism analysis as a potential substitute for reference materials derived from plant raw materials. In this study, a novel reference molecule p59122, including the revealed 5' integration sequence of maize Herculex RW (59122), was constructed that was suitable for simplex and duplex event-specific qualitative and quantitative PCR detections. The LOD values were 10 copies both for simplex and duplex qualitative PCR when p59122 was used as the calibrator. These values were comparable to those of using genomic DNA samples with 0.01 and 0.05%, approximately 5 and 25 hyploid genomic DNA copies, respectively. The absolute LOD and LOQ values were confirmed to be as low as 10 and 25 copies of p59122 DNA both in simplex and duplex quantitative systems. Furthermore, ideal quantification data with low bias, SD and RSD values were obtained from the practical samples analyses in simplex and duplex real-time PCR systems using the reference molecule p59122 as a calibrator. All these results suggested that the developed reference molecule p59122 and the qualitative and quantitative PCR detection methods are suitable for identification and quantification of GM maize 59122 and its derived products. PMID:19916386

  5. Antitumor effect of dehydroxymethylepoxyquinomicin, a small molecule inhibitor of nuclear factor-κB, on glioblastoma

    PubMed Central

    Fukushima, Tsuyoshi; Kawaguchi, Makiko; Yorita, Kenji; Tanaka, Hiroyuki; Takeshima, Hideo; Umezawa, Kazuo; Kataoka, Hiroaki

    2012-01-01

    Glioblastoma is the most malignant type of brain tumor. Despite recent advances in therapeutic modalities, the prognosis of glioblastoma remains very poor. Recent studies have indicated that RelA/nuclear factor (NF)-κB is consistently activated in human glioblastoma. In this study, we searched for a new treatment modality for glioblastoma, by examining the effects of dehydroxymethylepoxyquinomicin (DHMEQ), a unique small molecule inhibitor of NF-κB. Addition of DHMEQ to cultured human glioblastoma cells inhibited the nuclear translocation of RelA. It also reduced the growth rate of human glioblastoma cells significantly in 6 cell lines and modestly in 3 among 10 cell lines examined. Then, we performed further analyses using 3 sensitive cell lines (U87, U251, and YKG-1). The growth retardation was accompanied by G2/M arrest in vitro. Increased apoptosis was observed in U87 and YKG-1, but not U251 cells after DHMEQ treatment. Then, we tested the efficacy of DHMEQ in chemoprevention through the use of a nude mouse model. Subcutaneous tumors formed by U87 or U251 cells were reduced by ∼40% in size by intraperitoneal administration of DHMEQ started immediately after implantation of the cells. DHMEQ treatment achieved statistically significant improvements in survival curves of mice intracranially implanted with U87 or U251 cells. Histological analysis revealed increased areas of necrosis, increased numbers of collapsed microvessels, decreased nuclear immunoreactivity of RelA, and decreased immunoreactivity of urokinase-type plasminogen activator in the DHMEQ-treated U87 tumor tissues. These results suggest that the targeting of NF-κB by DHMEQ may serve as a promising treatment modality in glioblastoma. PMID:21968049

  6. Characteristics of regional seismic waves from large explosive events including Korean nuclear explosions

    NASA Astrophysics Data System (ADS)

    Jo, Eunyoung; Lee, Ha-sung

    2015-04-01

    Three North Korean underground nuclear explosion (UNE) tests were conducted in 2006, 2009 and 2013. Discrimination of explosions from natural earthquakes is important in monitoring the seismic activity in the Korean Peninsula. The UNEs were well recorded by dense regional seismic networks in South Korea. The UNEs provide unique regional seismic waveforms with high signal-to-noise ratios. However, the continental crust in the Korean Peninsula changes abruptly into a transitional structure between continental and oceanic crusts across the eastern coast. The complex geological and tectonic structures around the Korean Peninsula cause significant variations in regional waveforms. Outstanding question is whether conventional discrimination techniques can be applicable for explosions including the North Korean UNEs. P/S amplitude ratios are widely used for seismic discrimination. To understand the regional shear-energy composition, we analyze the frequency contents of waveforms. The shear-energy contents for the UNEs are compared with those for natural earthquakes with comparable magnitudes. The result shows that the UNEs are successfully discriminated from earthquakes in the Korean Peninsula. We also analyze the explosive events from North Korean not UNEs to test the applicability of the discrimination technique. The result of high frequency Pn/Sn regional discrimination in the explosions show that as magnitude of event is smaller, available distance of discrimination is decreased particularly in high frequency range. The poor signal to noise ratio of Pn phase in the explosions, and inefficient propagation of Sn phase in the Western part of the peninsula frustrate Pn/Sn discriminant, while the UNEs show good performance using both discriminants because of propagation path effects in the eastern part of the peninsula.

  7. Analysis of advanced european nuclear fuel cycle scenarios including transmutation and economical estimates

    SciTech Connect

    Merino Rodriguez, I.; Alvarez-Velarde, F.; Martin-Fuertes, F.

    2013-07-01

    In this work the transition from the existing Light Water Reactors (LWR) to the advanced reactors is analyzed, including Generation III+ reactors in a European framework. Four European fuel cycle scenarios involving transmutation options have been addressed. The first scenario (i.e., reference) is the current fleet using LWR technology and open fuel cycle. The second scenario assumes a full replacement of the initial fleet with Fast Reactors (FR) burning U-Pu MOX fuel. The third scenario is a modification of the second one introducing Minor Actinide (MA) transmutation in a fraction of the FR fleet. Finally, in the fourth scenario, the LWR fleet is replaced using FR with MOX fuel as well as Accelerator Driven Systems (ADS) for MA transmutation. All scenarios consider an intermediate period of GEN-III+ LWR deployment and they extend for a period of 200 years looking for equilibrium mass flows. The simulations were made using the TR-EVOL code, a tool for fuel cycle studies developed by CIEMAT. The results reveal that all scenarios are feasible according to nuclear resources demand (U and Pu). Concerning to no transmutation cases, the second scenario reduces considerably the Pu inventory in repositories compared to the reference scenario, although the MA inventory increases. The transmutation scenarios show that elimination of the LWR MA legacy requires on one hand a maximum of 33% fraction (i.e., a peak value of 26 FR units) of the FR fleet dedicated to transmutation (MA in MOX fuel, homogeneous transmutation). On the other hand a maximum number of ADS plants accounting for 5% of electricity generation are predicted in the fourth scenario (i.e., 35 ADS units). Regarding the economic analysis, the estimations show an increase of LCOE (Levelized cost of electricity) - averaged over the whole period - with respect to the reference scenario of 21% and 29% for FR and FR with transmutation scenarios respectively, and 34% for the fourth scenario. (authors)

  8. Nuclear Reactor/Hydrogen Process Interface Including the HyPEP Model

    SciTech Connect

    Steven R. Sherman

    2007-05-01

    The Nuclear Reactor/Hydrogen Plant interface is the intermediate heat transport loop that will connect a very high temperature gas-cooled nuclear reactor (VHTR) to a thermochemical, high-temperature electrolysis, or hybrid hydrogen production plant. A prototype plant called the Next Generation Nuclear Plant (NGNP) is planned for construction and operation at the Idaho National Laboratory in the 2018-2021 timeframe, and will involve a VHTR, a high-temperature interface, and a hydrogen production plant. The interface is responsible for transporting high-temperature thermal energy from the nuclear reactor to the hydrogen production plant while protecting the nuclear plant from operational disturbances at the hydrogen plant. Development of the interface is occurring under the DOE Nuclear Hydrogen Initiative (NHI) and involves the study, design, and development of high-temperature heat exchangers, heat transport systems, materials, safety, and integrated system models. Research and development work on the system interface began in 2004 and is expected to continue at least until the start of construction of an engineering-scale demonstration plant.

  9. Nuclear matter equation of state including two-, three-, and four-nucleon correlations

    NASA Astrophysics Data System (ADS)

    Röpke, G.

    2015-11-01

    Light clusters (mass number A ≤4 ) in nuclear matter at subsaturation densities are described using a quantum statistical approach to calculate the quasiparticle properties and abundances of light elements. I review the formalism and approximations used and extend it with respect to the treatment of continuum correlations. Virial coefficients are derived from continuum contributions to the partial densities which depend on temperature, densities, and total momentum. The Pauli blocking is modified taking correlations in the medium into account. Both effects of continuum correlations lead to an enhancement of cluster abundances in nuclear matter at higher densities. Based on calculations for A =2 , estimates for the contributions with A =3 ,4 are given. The properties of light clusters and continuum correlations in dense matter are of interest for nuclear structure calculations, heavy-ion collisions, and astrophysical applications such as the formation of neutron stars in core-collapse supernovae.

  10. Nonlocal Nuclear Spin Quieting in Quantum Dot Molecules: Optically Induced Extended Two-Electron Spin Coherence Time

    NASA Astrophysics Data System (ADS)

    Chow, Colin M.; Ross, Aaron M.; Kim, Danny; Gammon, Daniel; Bracker, Allan S.; Sham, L. J.; Steel, Duncan G.

    2016-08-01

    We demonstrate the extension of coherence between all four two-electron spin ground states of an InAs quantum dot molecule (QDM) via nonlocal suppression of nuclear spin fluctuations in two vertically stacked quantum dots (QDs), while optically addressing only the top QD transitions. Long coherence times are revealed through dark-state spectroscopy as resulting from nuclear spin locking mediated by the exchange interaction between the QDs. Line shape analysis provides the first measurement of the quieting of the Overhauser field distribution correlating with reduced nuclear spin fluctuations.

  11. Nonlocal Nuclear Spin Quieting in Quantum Dot Molecules: Optically Induced Extended Two-Electron Spin Coherence Time.

    PubMed

    Chow, Colin M; Ross, Aaron M; Kim, Danny; Gammon, Daniel; Bracker, Allan S; Sham, L J; Steel, Duncan G

    2016-08-12

    We demonstrate the extension of coherence between all four two-electron spin ground states of an InAs quantum dot molecule (QDM) via nonlocal suppression of nuclear spin fluctuations in two vertically stacked quantum dots (QDs), while optically addressing only the top QD transitions. Long coherence times are revealed through dark-state spectroscopy as resulting from nuclear spin locking mediated by the exchange interaction between the QDs. Line shape analysis provides the first measurement of the quieting of the Overhauser field distribution correlating with reduced nuclear spin fluctuations. PMID:27563998

  12. Small molecule and peptide-mediated inhibition of Epstein-Barr virus nuclear antigen 1 dimerization

    SciTech Connect

    Kim, Sun Young; Song, Kyung-A; Kieff, Elliott; Kang, Myung-Soo

    2012-07-27

    Highlights: Black-Right-Pointing-Pointer Evidence that targeting EBNA1 dimer, an EBV onco-antigen, can be achievable. Black-Right-Pointing-Pointer A small molecule and a peptide as EBNA1 dimerization inhibitors identified. Black-Right-Pointing-Pointer Both inhibitors associated with EBNA1 and blocked EBNA1 DNA binding activity. Black-Right-Pointing-Pointer Also, prevented its dimerization, and repressed viral gene transcription. -- Abstract: Latent Epstein-Barr virus (EBV) infection is associated with human B cell lymphomas and certain carcinomas. EBV episome persistence, replication, and gene expression are dependent on EBV-encoded nuclear antigen 1 (EBNA1)'s DNA binding domain (DBD)/dimerization domain (DD)-mediated sequence-specific DNA binding activity. Homodimerization of EBNA1 is essential for EBNA1 DNA binding and transactivation. In this study, we characterized a novel small molecule EBNA1 inhibitor EiK1, screened from the previous high throughput screening (HTS). The EiK1 compound specifically inhibited the EBNA1-dependent, OriP-enhanced transcription, but not EBNA1-independent transcription. A Surface Plasmon Resonance Biacore assay revealed that EiK1 associates with EBNA1 amino acid 459-607 DBD/DD. Consistent with the SPR data, in vitro gel shift assays showed that EiK1 suppressed the activity of EBNA1 binding to the cognate familial repeats (FR) sequence, but not control RBP-J{kappa} binding to the J{kappa} site. Subsequently, a cross-linker-mediated in vitro multimerization assay and EBNA1 homodimerization-dependent yeast two-hybrid assay showed that EiK1 significantly inhibited EBNA1 dimerization. In an attempt to identify more highly specific peptide inhibitors, small peptides encompassing the EBNA1 DBD/DD were screened for inhibition of EBNA1 DBD-mediated DNA binding function. The small peptide P85, covering EBNA1 a.a. 560-574, significantly blocked EBNA1 DNA binding activity in vitro, prevented dimerization in vitro and in vivo, associated with

  13. Nuclear Rocket Test Facility Decommissioning Including Controlled Explosive Demolition of a Neutron-Activated Shield Wall

    SciTech Connect

    Michael Kruzic

    2007-09-01

    Located in Area 25 of the Nevada Test Site, the Test Cell A Facility was used in the 1960s for the testing of nuclear rocket engines, as part of the Nuclear Rocket Development Program. The facility was decontaminated and decommissioned (D&D) in 2005 using the Streamlined Approach For Environmental Restoration (SAFER) process, under the Federal Facilities Agreement and Consent Order (FFACO). Utilities and process piping were verified void of contents, hazardous materials were removed, concrete with removable contamination decontaminated, large sections mechanically demolished, and the remaining five-foot, five-inch thick radiologically-activated reinforced concrete shield wall demolished using open-air controlled explosive demolition (CED). CED of the shield wall was closely monitored and resulted in no radiological exposure or atmospheric release.

  14. Tabulated equation of state for supernova matter including full nuclear ensemble

    SciTech Connect

    Buyukcizmeci, N.; Botvina, A. S.; Mishustin, I. N.

    2014-07-01

    This is an introduction to the tabulated database of stellar matter properties calculated within the framework of the Statistical Model for Supernova Matter (SMSM). The tables present thermodynamical characteristics and nuclear abundances for 31 values of baryon density (10{sup –8} < ρ/ρ{sub 0} < 0.32, ρ{sub 0} = 0.15 fm{sup –3} is the normal nuclear matter density), 35 values of temperature (0.2 MeV < T < 25 MeV), and 28 values of electron-to-baryon ratio (0.02 < Y{sub e} < 0.56). The properties of stellar matter in β equilibrium are also considered. The main ingredients of the SMSM are briefly outlined, and the data structure and content of the tables are explained.

  15. Nuclear winter - Three-dimensional simulations including interactive transport, scavenging, and solar heating of smoke

    NASA Technical Reports Server (NTRS)

    Malone, R. C.; Auer, L. H.; Glatzmaier, G. A.; Wood, M. C.; Toon, O. B.

    1986-01-01

    A reexamination is conducted of the 'nuclear winter' hypothesis with a three-dimensional global model modified to allow for localized injection of smoke, its transport by the simulated winds, its absorption of sunlight, and its removal by model-simulated precipitation. Smoke injected into the troposphere is driven upward by solar heating. The tropopause, initially above the smoke, reforms below the heat smoke layer and separates it from precipitation below. Although much smoke is scavenged while the thermal structure is being altered, the residence time of the remaining smoke is greatly increased. Particularly for July conditions, a longer-lasting 'nuclear winter' effect is observed than was found in earlier modeling studies in which normal tropospheric residence times were assumed. In January the smaller solar flux in the northern hemisphere allows faster removal of smoke than in July. Significant cooling of the northern hemisphere continents is predicted; its dependence on season and injected smoke mass is described.

  16. Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution.

    PubMed

    Żurek-Biesiada, Dominika; Szczurek, Aleksander T; Prakash, Kirti; Mohana, Giriram K; Lee, Hyun-Keun; Roignant, Jean-Yves; Birk, Udo J; Dobrucki, Jurek W; Cremer, Christoph

    2016-05-01

    Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant(®) DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10(6) signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. PMID:26341267

  17. Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Meyer, Hans-Dieter

    2015-10-01

    Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

  18. Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

    SciTech Connect

    Meng, Qingyong; Meyer, Hans-Dieter

    2015-10-28

    Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

  19. Investigation of parameter-free model polarization potentials for electron-molecule scattering calculations including the nuclear motion

    SciTech Connect

    Morrison, M.A.; Saha, B.C.

    1986-10-01

    A correlation-polarization potential originally introduced by O'Connell and Lane (Phys. Rev. A 27, 1893 (1983)) is used in e-H/sub 2/ scattering calculations in which the vibrational motion of the target is taken into account. Eigenphase sums (as a function of internuclear separation) and cross sections for elastic scattering and for rovibrational excitations are compared to their counterparts calculated using the ab initio nonadiabatic model polarization potential of Gibson and Morrison (Phys. Rev. A 29, 2497 (1984)). At low energies, these scattering quantities are found to be quite sensitive to the treatment of polarization. To assess these model potentials, theoretical total, momentum transfer, and rotational- and vibrational-excitation cross sections are compared to experimental data.

  20. Differential two-body compound nuclear cross section, including the width-fluctuation corrections

    SciTech Connect

    Brown, D.; Herman, M.

    2014-09-02

    We figure out the compound angular differential cross sections, following mainly Fröbrich and Lipperheide, but with the angular momentum couplings that make sense for optical model work. We include the width-fluctuation correction along with calculations.

  1. Rotational partition functions for symmetric-top molecules

    NASA Astrophysics Data System (ADS)

    McDowell, Robin S.

    1990-08-01

    An improved expression is found for the rotational partition functions of symmetric-top molecules. The expression includes the effect of nuclear spin for molecules of C(3v) symmetry. The effect that centrifugal distortion of the rotating molecules has on these rigid-rotator formulations is considered. The nuclear-spin correction is generalized to symmetric-top molecules of other symmetries. The treatment is extended to nonplanar molecules that exhibit inversion doubling, with particular attention given to NH3.

  2. Magnetic-field-induced quadrupole coupling in the nuclear magnetic resonance of noble-gas atoms and molecules

    SciTech Connect

    Manninen, Pekka; Vaara, Juha; Pyykkoe, Pekka

    2004-10-01

    An analytic response theory formulation for the leading-order magnetic field-induced and field-dependent quadrupole splitting in nuclear magnetic resonance spectra is presented and demonstrated with first-principles calculations for {sup 21}Ne, {sup 36}Ar, and {sup 83}Kr in noble gas atoms. The case of molecules was studied for {sup 33}S in the sulphur hexafluoride molecule, as well as for {sup 47/49}Ti, {sup 91}Zr, and {sup 177,179}Hf in group(IV) tetrahalides. According to our calculations, the hitherto experimentally unknown field-induced quadrupole splitting in molecules rises to 10{sup 2} Hz for {sup 177,179}Hf nuclei in HfF{sub 4} and 10{sup 1} Hz for {sup 47/49}Ti in TiCl{sub 4}, and is hence of observable magnitude.

  3. An expanded Metrosideros (Myrtaceae) to include Carpolepis and Tepualia based on nuclear genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Metrosideros (Myrtaceae) comprises 50-60 species, found largely across the Pacific Islands. The relationships within this genus, including the circumscriptions of the subgenera Mearnsia and Metrosideros and their relationships with the other members of the tribe Metrosidereae, namely the N...

  4. Network of nuclear receptor ligands in multiple sclerosis: Common pathways and interactions of sex-steroids, corticosteroids and vitamin D3-derived molecules.

    PubMed

    Rolf, Linda; Damoiseaux, Jan; Hupperts, Raymond; Huitinga, Inge; Smolders, Joost

    2016-09-01

    Sex-steroids, corticosteroids and vitamin D3-derived molecules have all been subject to experimental studies and clinical trials in a plethora of autoimmune diseases. These molecules are all derived from cholesterol metabolites and are ligands for nuclear receptors. Ligation of these receptors results in direct regulation of multiple gene transcription involved in general homeostatic and adaptation networks, including the immune system. Indeed, the distinct ligands affect the function of both myeloid and lymphoid cells, eventually resulting in a less pro-inflammatory immune response which is considered beneficial in autoimmune diseases. Next to the immune system, also the central nervous system is prone to regulation by these nuclear receptor ligands. Understanding of the intricate interactions between sex-steroids, corticosteroids and vitamin D3 metabolites, on the one hand, and the immune and central nervous system, on the other hand, may reveal novel approaches to utilize these nuclear receptor ligands to full extent as putative treatments in multiple sclerosis, the prototypic immune-driven disease of the central nervous system. PMID:27395031

  5. Accurate spectroscopic calculations of the 17 Λ-S and 59 Ω states of the AsP molecule including the spin-orbit coupling effect

    NASA Astrophysics Data System (ADS)

    Shi, Deheng; Liu, Qionglan; Wang, Shuai; Sun, Jinfeng; Zhu, Zunlue

    2015-01-01

    The potential energy curves (PECs) of 59 Ω states generated from the 17 Λ-S states (X1Σ+, a3Σ+, 15Σ+, b3Δ, c3Π, 15Π, 25Σ+, 23Δ, 23Π, 33Σ+, A1Π, 23Σ+, 35Σ+, 17Σ+, 15Δ, 25Δ, and 25Π) of AsP molecule are studied for the first time for internuclear separations from about 0.10 to 1.10 nm. All the Λ-S states are contributed to the first three dissociation channels of AsP molecule except for the A1Π. The 23Σ+, 35Σ+, 17Σ+, 15Δ, 25Δ, and 25Π are found to be the repulsive states. The a3Σ+, 15Π, b3Δ, 17Σ+, 15Δ, 25Δ, and 25Π are found to be the inverted states. Each of the 33Σ+, c3Π, 23Π, 15Π, and 15Σ+ states has one potential barrier. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with Davidson correction. Core-valence correlation and scalar relativistic corrections are included. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling effect is accounted for. All these PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated for the bound states involved, and are compared with available measurements. Excellent agreement has been found between the present results and the measurements. It shows that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters is not obvious for all the Λ-S bound states except for few ones such as 15Σ+ and c3Π.

  6. Including screening in van der Waals corrected density functional theory calculations: The case of atoms and small molecules physisorbed on graphene

    SciTech Connect

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2014-03-28

    The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H{sub 2}, H{sub 2}O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.

  7. Including screening in van der Waals corrected density functional theory calculations: the case of atoms and small molecules physisorbed on graphene.

    PubMed

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2014-03-28

    The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H2, H2O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems. PMID:24697424

  8. Ultrafast x-ray-induced nuclear dynamics in diatomic molecules using femtosecond x-ray-pump-x-ray-probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Lehmann, C. S.; Picón, A.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Moonshiram, D.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-07-01

    The capability of generating two intense, femtosecond x-ray pulses with a controlled time delay opens the possibility of performing time-resolved experiments for x-ray-induced phenomena. We have applied this capability to study the photoinduced dynamics in diatomic molecules. In molecules composed of low-Z elements, K -shell ionization creates a core-hole state in which the main decay mode is an Auger process involving two electrons in the valence shell. After Auger decay, the nuclear wave packets of the transient two-valence-hole states continue evolving on the femtosecond time scale, leading either to separated atomic ions or long-lived quasibound states. By using an x-ray pump and an x-ray probe pulse tuned above the K -shell ionization threshold of the nitrogen molecule, we are able to observe ion dissociation in progress by measuring the time-dependent kinetic energy releases of different breakup channels. We simulated the measurements on N2 with a molecular dynamics model that accounts for K -shell ionization, Auger decay, and the time evolution of the nuclear wave packets. In addition to explaining the time-dependent feature in the measured kinetic energy release distributions from the dissociative states, the simulation also reveals the contributions of quasibound states.

  9. Accurate spectroscopic calculations of the 17 Λ-S and 59 Ω states of the AsP molecule including the spin-orbit coupling effect.

    PubMed

    Shi, Deheng; Liu, Qionglan; Wang, Shuai; Sun, Jinfeng; Zhu, Zunlue

    2015-01-25

    The potential energy curves (PECs) of 59 Ω states generated from the 17 Λ-S states (X(1)Σ(+), a(3)Σ(+), 1(5)Σ(+), b(3)Δ, c(3)Π, 1(5)Π, 2(5)Σ(+), 2(3)Δ, 2(3)Π, 3(3)Σ(+), A(1)Π, 2(3)Σ(+), 3(5)Σ(+), 1(7)Σ(+), 1(5)Δ, 2(5)Δ, and 2(5)Π) of AsP molecule are studied for the first time for internuclear separations from about 0.10 to 1.10nm. All the Λ-S states are contributed to the first three dissociation channels of AsP molecule except for the A(1)Π. The 2(3)Σ(+), 3(5)Σ(+), 1(7)Σ(+), 1(5)Δ, 2(5)Δ, and 2(5)Π are found to be the repulsive states. The a(3)Σ(+), 1(5)Π, b(3)Δ, 1(7)Σ(+), 1(5)Δ, 2(5)Δ, and 2(5)Π are found to be the inverted states. Each of the 3(3)Σ(+), c(3)Π, 2(3)Π, 1(5)Π, and 1(5)Σ(+) states has one potential barrier. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with Davidson correction. Core-valence correlation and scalar relativistic corrections are included. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling effect is accounted for. All these PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated for the bound states involved, and are compared with available measurements. Excellent agreement has been found between the present results and the measurements. It shows that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters is not obvious for all the Λ-S bound states except for few ones such as 1(5)Σ(+) and c(3)Π. PMID:25145917

  10. Spectroscopic and computational investigations on the origin of charge transfer between included neutral guest molecules and a functionalized anionic layered host.

    PubMed

    Dutta, Dipak; Tummanapelli, Anil Kumar

    2016-08-10

    Layered double hydroxides (LDHs) or anionic clays are an important class of ion-exchange materials, well known for drug and gene delivery and several other applications including catalysis, bioactive nanocomposite, electroactive and photoactive materials. Their structure is based on positively charged brucite-like inorganic sheets with the interlamellar space being occupied by charge-compensating exchangeable anions. In spite of having a vast scope many of the applications of LDHs are restricted as their host-guest chemistry is limited to ion-exchange reactions. Recently we have shown for the first time that charge-transfer interactions can be used as a driving force for the insertion of neutral guest molecules (ortho- and para-chloranil) within the galleries of an Mg-Al LDH by forming a charge-transfer complex with aniline pre-intercalated as p-aminobenzoate anion. Here, we have performed quantum chemical calculations in combination with molecular dynamics simulations to elucidate the nature of interactions, arrangement and the evaluation of electronic and Raman spectral signatures of the chloranil charge-transfer complex included within the galleries of the Mg-Al LDH. The natural bond orbital (NBO) analysis has been used to understand the nature and origin of the unidirectional charge-transfer that lead to the unusual insertion of chloranil in the galleries of the Mg-Al LDH. The NBO analysis reveals that a considerable amount of electronic charge redistribution occurs from the p-aminobenzoate to the chloranil during latter's insertion within the LDH galleries with a very negligible amount of back donation. This work is expected to pave the way for understanding the host-guest chemistry and targeted and controlled delivery of poorly soluble drugs. PMID:27461409

  11. Peptide binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes, and include HLA-B27-like alleles

    PubMed Central

    Mothé, Bianca R.; Southwood, Scott; Sidney, John; English, A. Michelle; Wriston, Amanda; Hoof, Ilka; Shabanowitz, Jeffrey; Hunt, Donald F.; Sette, Alessandro

    2013-01-01

    Chinese rhesus macaques are of particular interest in SIV/HIV research as these animals have prolonged kinetics of disease progression to AIDS, compared to their Indian counterparts, suggesting that they may be a better model for HIV. Nevertheless, the specific mechanism(s) accounting for these kinetics remains unclear. The study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide binding motifs, provides valuable information for measuring cellular immune responses and deciphering outcomes of infection and vaccine efficacy. In this study, we have provided detailed characterization of six prevalent Chinese rhesus macaque MHC class I alleles, yielding a combined phenotypic frequency of 29%. The peptide binding specificity of two of these alleles, Mamu-A2*01:02 and -B*010:01, as well as the previously characterized allele Mamu-B*003:01 (and Indian rhesus Mamu-B*003:01), was found to be analogous to that of alleles in the HLA-B27 supertype family. Specific alleles in the HLA-B27 supertype family, including HLA-B*27:05, have been associated with long-term non-progression to AIDS in humans. All six alleles characterized in the present study were found to have specificities analogous to HLA-supertype alleles. These data contribute to the concept that Chinese rhesus macaque MHC immunogenetics is more similar to HLA than their Indian rhesus macaque counterparts, and thereby warrant further studies to decipher the role of these alleles in the context of SIV infection. PMID:23417323

  12. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  13. Microhydration of caesium compounds: Cs, CsOH, CsI and Cs₂I₂ complexes with one to three H₂O molecules of nuclear safety interest.

    PubMed

    Sudolská, Mária; Cantrel, Laurent; Cernušák, Ivan

    2014-04-01

    Structure and thermodynamic properties (standard enthalpies of formation and Gibbs free energies) of hydrated caesium species of nuclear safety interest, Cs, CsOH, CsI and its dimer Cs₂I₂, with one up to three water molecules, are calculated to assess their possible existence in severe accident occurring to a pressurized water reactor. The calculations were performed using the coupled cluster theory including single, double and non-iterative triple substitutions (CCSD(T)) in conjunction with the basis sets (ANO-RCC) developed for scalar relativistic calculations. The second-order spin-free Douglas-Kroll-Hess Hamiltonian was used to account for the scalar relativistic effects. Thermodynamic properties obtained by these correlated ab initio calculations (entropies and thermal capacities at constant pressure as a function of temperature) are used in nuclear accident simulations using ASTEC/SOPHAEROS software. Interaction energies, standard enthalpies and Gibbs free energies of successive water molecules addition determine the ordering of the complexes. CsOH forms the most hydrated stable complexes followed by CsI, Cs₂I₂, and Cs. CsOH still exists in steam atmosphere even at quite high temperature, up to around 1100 K. PMID:24715048

  14. Calculation of the fourth-rank nuclear magnetic hypershielding of some small molecules

    NASA Astrophysics Data System (ADS)

    Pagola, G. I.; Caputo, M. C.; Ferraro, M. B.; Lazzeretti, P.

    2006-08-01

    A computational scheme has been implemented to evaluate magnetic hypershielding at the nuclei of a molecule in the presence of an external spatially uniform, time-independent magnetic field, accounting for cubic response contributions via Rayleigh-Schrödinger perturbation theory. Numerical estimates have been obtained for hydrogen and heavier atoms in H2 , HF, H2O , NH3 , and CH4 molecules at the coupled Hartree-Fock level of accuracy within the conventional common-origin approach. Gaugeless basis sets of increasing size and flexibility have been employed in a numerical test, to estimate the degree of convergence of theoretical tensor components. A further test for convergence has been carried out by evaluating properties for two different coordinate systems.

  15. NMR nuclear magnetic shielding anisotropy of linear molecules within the linear response within the elimination of the small component approach

    NASA Astrophysics Data System (ADS)

    Ruiz de Azúa, Martín C.; Giribet, Claudia G.; Melo, Juan I.

    2011-01-01

    The influence of the spin-Zeeman (SZ) operator in the evaluation of the spin-orbit effect on the nuclear magnetic shielding tensor in the context of the linear response within the elimination of the small component approach is critically discussed. It is shown that such term yields no contribution to the isotropic nuclear magnetic shielding constant, but it may be of great importance in the determination of individual tensor components, and particularly of the tensor anisotropy. In particular, an interesting relation between the SZ and orbital Zeeman contributions to the spin-orbit effect for the case of linear molecules is shown to hold. Numerical examples for the BrH, IH, and XeF2 molecules are presented which show that, provided the SZ term is taken into account, results of the individual shielding tensor components and the tensor anisotropy are in good agreement with those obtained by other theoretical methods, and particularly by the Dirac-Hartree-Fock approach.

  16. Gastric juice in congenital pernicious anemia contains no immunoreactive intrinsic factor molecule: study of three kindreds with variable ages at presentation, including a patient first diagnosed in adulthood.

    PubMed Central

    Carmel, R

    1983-01-01

    The mechanism responsible for the isolated intrinsic factor deficiency in congenital pernicious anemia is unknown. A new second-antibody radioimmunoassay capable of recognizing intrinsic factor independent of the molecule's ability to bind added cobalamin was used to study six patients from three kindreds with this disorder. One of the patients was first diagnosed at age 23 because of unusual circumstances in her case; yet the other patients also demonstrated great age variability at presentation of this presumably congenital disorder, even within the same kindred. The radioimmunoassay failed to detect immunoreactive intrinsic factor in any of the six patients, suggesting that elaboration of an abnormal molecule was not the pathogenetic mechanism. An unexpected incidental finding, contrasting with this observation in congenital pernicious anemia, was immunologic evidence that a previously described patient with familial R binder deficiency clearly elaborated an abnormal R binder molecule. PMID:6823973

  17. A cold, slow beam of TlF molecules for an improved probe for the nuclear Schiff moment

    NASA Astrophysics Data System (ADS)

    McCarron, Daniel; Edwards, Eustace; Steinecker, Matthew; Peck, Stephen; Hunter, Larry; Demille, David

    2016-05-01

    We present a new experimental effort to search for the nuclear Schiff moment (SM) using thallium fluoride (TlF) molecules. Our approach capitalizes on the strong internal electric field present in a polarized molecule to amplify the effect of the SM. We project a 25-fold improvement over the current state of the art sensitivity to certain underlying mechanisms such as the CP-violating QCD θ-parameter. Our recent measurements indicate that optical cycling is possible on the X1Σ+ -->B3Π1 electronic transition of TlF. Here a single laser will enable 100 photons to be scattered before an excited vibrational level is populated. This is sufficient for unit-efficiency fluorescence detection, rotational cooling, and state preparation. With a single repump laser, ~ 104 photons could be scattered, sufficient for transverse laser cooling that could substantially increase the brightness of the molecular beam. We report on the production of a cold and slow beam of TlF molecules from a cryogenic buffer gas beam source and present flux measurements for a range of TlF vaporization techniques. We also present our progress towards understanding the hyperfine structure in the B3Π1 state and its role in optical cycling.

  18. Nuclear Overhauser effect as a probe of molecular structure, dynamics and order of axially reorienting molecules in membranes.

    PubMed

    Davis, James H; Komljenović, Ivana

    2016-02-01

    The location, orientation, order and dynamics of cholesterol in model membranes have been well characterized, therefore cholesterol is an ideal molecule for developing new methods for studying structured molecules undergoing rapid axially symmetric reorientation. The use of (13)C filtering via short contact cross polarization transfer to (1)H allows the recovery of the weak cholesterol (1)H magic angle spinning NMR signals from beneath the strong phospholipid background in bicelles composed of chain perdeuterated dimyristoyl phosphatidylcholine/dicaproyl phosphatidylcholine/[3,4-(13)C]-cholesterol. Measurements of the nuclear Overhauser enhancement for (1)H nuclei located in the first ring of cholesterol are interpreted in terms of a simple two motion model consisting of axial reorientation, with a correlation time τ∥, and a slower reorientation of the diffusion axis relative to the bilayer normal, with correlation time τ⊥. This approach can be extended to other molecules which undergo rapid axial reorientation such as small membrane associated peptides. PMID:26607012

  19. Analytic dipole moment geometric derivatives from nuclear electric shielding in molecules

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Zanasi, R.

    1986-04-01

    We present ab initio calculations of dipole moment geometric derivatives for some first-row atom hydrides. Dipole moment derivatives, in terms of atomic polar tensors (APT), are equivalent to nuclear electric shieldings and were determined analytically, within the random phase approximation (RPA). Polarized basis sets were used, which give accurate results with small computer effort.

  20. Nuclear quadrupole moment-induced Cotton-Mouton effect in molecules

    SciTech Connect

    Fu, Li-juan E-mail: juha.vaara@iki.fi; Vaara, Juha E-mail: juha.vaara@iki.fi

    2014-01-14

    Nuclear magneto-optic effects could make important contributions to novel, high-sensitivity, and high-resolution spectroscopic and imaging methods that provide nuclear site-specific structural and dynamic information on molecular and materials systems. Here we present a first-principles electronic structure formulation of nuclear quadrupole moment-induced Cotton-Mouton effect in terms of response theory, as well as ab initio and density-functional theory calculations of this phenomenon for a series of molecular liquids: H{sub 2}O, CH{sub 3}NO{sub 2}, CH{sub 3}CH{sub 2}OH, C{sub 6}H{sub 6}, C{sub 6}H{sub 12} (cyclohexane), HI, XeF{sub 2}, WF{sub 5}Cl, and Pt(C{sub 2}dtp){sub 2}. The roles of basis-set convergence, electron correlation, and relativistic effects are discussed. The estimated order of magnitude of the overall ellipticities induced to linearly polarized light is 10{sup −3}–10{sup −7} rad/(M cm) for fully spin polarized nuclei. The cases with the largest presently obtained ellipticities should be detectable with modern instrumentation in the Voigt magneto-optic setup, particularly for the heavy nuclei.

  1. Two-dimensional nuclear magnetic resonance analysis of a labeled peptide bound to a class II major histocompatibility complex molecule.

    PubMed

    Driscoll, P C; Altman, J D; Boniface, J J; Sakaguchi, K; Reay, P A; Omichinski, J G; Appella, E; Davis, M M

    1993-07-20

    The formation of peptide/major histocompatibility complex (MHC) complexes and their subsequent recognition by T cells is a pivotal event in the initiation of an immune response. While X-ray crystal structures are now available for class I MHC/peptide complexes, little detailed structural information is known about the class II MHC equivalent, and there are no solution structure data for either. A 16 amino acid residue moth cytochrome c peptide (residues 88 to 103) was 13C-labeled for two-dimensional isotope-edited NMR analysis. The peptide was labeled either selectively in the methyl groups of alanine residues or uniformly at every carbon position, and bound to unlabeled soluble mouse I-Ek class II MHC molecules. Although alpha-helical in the native cytochrome c protein and with no uniform structure in solution, the peptide is bound to the I-Ek molecule with the alpha-carbon atoms of the 11 C-terminal residues held in the binding groove. This indicates that the class II MHC peptide binding site is somewhat larger than that of class I MHC molecules (> or = 11 amino acid residues versus 8 to 10 amino acid residues), consistent with recent data on eluted peptides. Despite the large size of the complex (approximately 70 kDa), nuclear Overhauser effects are clearly detectable between peptide side-chains and the MHC molecule. Indications of the buried or exposed nature of particular side-chains within the bound peptide are derived from the NMR data and these are used together with information from previous biological studies to propose a crude model of the interaction of the peptide with the groove of the MHC molecule. We find no evidence for a conformational change in the peptide/MHC complex in the spectra at pH 5.0 versus pH 7.0, despite a 40-fold faster on-rate for the peptide at the lower pH value. PMID:8393933

  2. Nuclear dynamics and spectator effects in resonant inelastic soft x-ray scattering of gas-phase water molecules

    SciTech Connect

    Weinhardt, Lothar; Benkert, Andreas; Meyer, Frank; Blum, Monika; Wilks, Regan G.; Yang, Wanli; Baer, Marcus; Reinert, Friedrich; and others

    2012-04-14

    The electronic structure of gas-phase H{sub 2}O and D{sub 2}O molecules has been investigated using resonant inelastic soft x-ray scattering (RIXS). We observe spectator shifts for all valence orbitals when exciting into the lowest three absorption resonances. Strong changes of the relative valence orbital emission intensities are found when exciting into the different absorption resonances, which can be related to the angular anisotropy of the RIXS process. Furthermore, excitation into the 4a{sub 1} resonance leads to nuclear dynamics on the time scale of the RIXS process; we find evidence for vibrational coupling and molecular dissociation in both, the spectator and the participant emission.

  3. Equation-of-motion approach to frequency-dependent nuclear electric shielding tensors in the HF molecule

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Rossi, E.; Zanasi, R.

    1983-03-01

    The frequency dependence of the dipole electric polarizability and electric shielding tensors of hydrogen and fluorine nuclei in the HF molecule has been investigated by means of the lower approximations to the equation-of-motion method-namely, the single-transition approximation (STA), the Tamm-Dancoff approximation (TDA), and the random-phase approximation (RPA)-within the framework of dipole length, velocity, acceleration, and mixed formalisms. Some relations are proved, concerning the relative magnitude of TDA and RPA polarizabilities and Thomas-Reich-Kuhn sum rules in the various formalisms. An interdependence between dynamic polarizabilities and nuclear shielding factors has been found. Good agreement with experimental static shielding factors has been obtained in the RPA calculation.

  4. Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement

    PubMed Central

    Martínez-Azorín, Mario; Crespo, Manuel B.; Juan, Ana; Fay, Michael F.

    2011-01-01

    Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and

  5. Pions are neither perturbative nor nonperturbative: Wilsonian renormalization-group analysis of nuclear effective field theory including pions

    SciTech Connect

    Harada, Koji; Kubo, Hirofumi; Yamamoto, Yuki

    2011-03-15

    Nuclear effective field theory (NEFT) including pions in the two-nucleon sector is examined from the Wilsonian renormalization group point of view. The pion exchange is cut off at the floating cutoff scale, {Lambda}, with the short-distance part being represented as contact interactions in accordance with the general principle of renormalization. We derive the nonperturbative renormalization group equations in the leading order of the nonrelativistic approximation in the operator space up to including O(p{sup 2}), and find the nontrivial fixed points in the {sup 1}S{sub 0} and {sup 3}S{sub 1}-{sup 3}D{sub 1} channels which are identified with those in the pionless NEFT. The scaling dimensions, which determine the power counting, of the contact interactions at the nontrivial fixed points are also identified with those in the pionless NEFT. We emphasize the importance of the separation of the pion exchange into the short-distance and the long-distance parts, since a part of the former is nonperturbative while the latter is perturbative.

  6. Identification of Novel Small Molecule Activators of Nuclear Factor-κB With Neuroprotective Action Via High-Throughput Screening

    PubMed Central

    Manuvakhova, Marina S.; Johnson, Guyla G.; White, Misti C.; Ananthan, Subramaniam; Sosa, Melinda; Maddox, Clinton; McKellip, Sara; Rasmussen, Lynn; Wennerberg, Krister; Hobrath, Judith V.; White, E. Lucile; Maddry, Joseph A.; Grimaldi, Maurizio

    2012-01-01

    Neuronal noncytokine-dependent p50/p65 nuclear factor-κB (the primary NF-κB complex in the brain) activation has been shown to exert neuroprotective actions. Thus neuronal activation of NF-κB could represent a viable neuroprotective target. We have developed a cell-based assay able to detect NF-κB expression enhancement, and through its use we have identified small molecules able to up-regulate NF-κB expression and hence trigger its activation in neurons. We have successfully screened approximately 300,000 compounds and identified 1,647 active compounds. Cluster analysis of the structures within the hit population yielded 14 enriched chemical scaffolds. One high-potency and chemically attractive representative of each of these 14 scaffolds and four singleton structures were selected for follow-up. The experiments described here highlighted that seven compounds caused noncanonical long-lasting NF-κB activation in primary astrocytes. Molecular NF-κB docking experiments indicate that compounds could be modulating NF-κB-induced NF-κB expression via enhancement of NF-κB binding to its own promoter. Prototype compounds increased p65 expression in neurons and caused its nuclear translocation without affecting the inhibitor of NF-κB (I-κB). One of the prototypical compounds caused a large reduction of glutamate-induced neuronal death. In conclusion, we have provided evidence that we can use small molecules to activate p65 NF-κB expression in neurons in a cytokine receptor-independent manner, which results in both long-lasting p65 NF-κB translocation/activation and decreased glutamate neurotoxicity. PMID:21046675

  7. Nuclear Fluxes in Diatomic Molecules Deduced from Pump-Probe Spectra with Spatiotemporal Resolutions down to 5 pm and 200 asec

    NASA Astrophysics Data System (ADS)

    Manz, Jörn; Pérez-Torres, Jhon Fredy; Yang, Yonggang

    2013-10-01

    When molecules move, their nuclei flow. The corresponding quantum observable, i.e., the nuclear flux density, was introduced by Schrödinger in 1926, but until now, it has not been measured. Here the first experimental results are deduced from high-resolution pump-probe measurements of the time-dependent nuclear densities in a vibrating diatomic molecule or molecular ion. The nuclear densities are converted to flux densities by means of the continuity equation. The flux densities are much more sensitive to time-dependent quantum effects than the densities. Applications to the sodium molecule and the deuterium molecular ion unravel four new effects; e.g., at the turns from bond stretch to compression, the flux of the nuclei exhibits multiple changes of directions, from small to large bond lengths, a phenomenon that we call the “quantum accordion.”

  8. Zearalenone Mycotoxin Affects Immune Mediators, MAPK Signalling Molecules, Nuclear Receptors and Genome-Wide Gene Expression in Pig Spleen

    PubMed Central

    Pistol, Gina Cecilia; Braicu, Cornelia; Motiu, Monica; Gras, Mihail Alexandru; Marin, Daniela Eliza; Stancu, Mariana; Calin, Loredana; Israel-Roming, Florentina; Berindan-Neagoe, Ioana; Taranu, Ionelia

    2015-01-01

    The toxicity of zearalenone (ZEA) was evaluated in swine spleen, a key organ for the innate and adaptative immune response. Weaned pigs were fed for 18 days with a control or a ZEA contaminated diet. The effect of ZEA was assessed on wide genome expression, pro- (TNF-α, IL-8, IL-6, IL-1β, IFN-γ) and anti-inflammatory (IL-10, IL-4) cytokines, other molecules involved in inflammatory processes (MMPs/TIMPs), as well as signaling molecules, (p38/JNK1/JNK2-MAPKs) and nuclear receptors (PPARγ/NFkB/AP-1/STAT3/c-JUN). Microarray analysis showed that 46% of total number of differentially expressed genes was involved in cellular signaling pathway, 13% in cytokine network and 10% in the inflammatory response. ZEA increased expression and synthesis of pro- inflammatory (TNF-α, IL-8, IL-6, IL-1β) and had no effect on IFN-γ, IL-4 and IL-10 cytokines in spleen. The inflammatory stimulation might be a consequence of JNK pathway activation rather than of p-38MAPK and NF-kB involvement whose gene and protein expression were suppressed by ZEA action. In summary, our findings indicated the role of ZEA as an immune disruptor at spleen level. PMID:26011631

  9. Zearalenone mycotoxin affects immune mediators, MAPK signalling molecules, nuclear receptors and genome-wide gene expression in pig spleen.

    PubMed

    Pistol, Gina Cecilia; Braicu, Cornelia; Motiu, Monica; Gras, Mihail Alexandru; Marin, Daniela Eliza; Stancu, Mariana; Calin, Loredana; Israel-Roming, Florentina; Berindan-Neagoe, Ioana; Taranu, Ionelia

    2015-01-01

    The toxicity of zearalenone (ZEA) was evaluated in swine spleen, a key organ for the innate and adaptative immune response. Weaned pigs were fed for 18 days with a control or a ZEA contaminated diet. The effect of ZEA was assessed on wide genome expression, pro- (TNF-α, IL-8, IL-6, IL-1β, IFN-γ) and anti-inflammatory (IL-10, IL-4) cytokines, other molecules involved in inflammatory processes (MMPs/TIMPs), as well as signaling molecules, (p38/JNK1/JNK2-MAPKs) and nuclear receptors (PPARγ/NFkB/AP-1/STAT3/c-JUN). Microarray analysis showed that 46% of total number of differentially expressed genes was involved in cellular signaling pathway, 13% in cytokine network and 10% in the inflammatory response. ZEA increased expression and synthesis of pro- inflammatory (TNF-α, IL-8, IL-6, IL-1β) and had no effect on IFN-γ, IL-4 and IL-10 cytokines in spleen. The inflammatory stimulation might be a consequence of JNK pathway activation rather than of p-38MAPK and NF-kB involvement whose gene and protein expression were suppressed by ZEA action. In summary, our findings indicated the role of ZEA as an immune disruptor at spleen level. PMID:26011631

  10. Adiabatic representation in the Coulomb three-body problem in the united-atom limit: Nuclear widths of the energy levels of the muonic molecule ttµ

    NASA Astrophysics Data System (ADS)

    Melezhik, V. S.

    2016-01-01

    We study the asymptotic behavior of the wave function of the system of three Coulomb particles in the united-atom limit in the adiabatic representation of the three-body problem. This result is used to calculate the nuclear widths of muonic-molecule energy levels. We discuss features of the approach with regard to excited states of the muonic molecule ttµ with a nonzero orbital angular momentum.

  11. Alternative approach to the standardization of NMR spectra. Direct measurement of nuclear magnetic shielding in molecules.

    PubMed

    Jackowski, Karol; Jaszuński, Michał; Wilczek, Marcin

    2010-02-25

    Exploring the relation between shielding constants, resonance frequencies and magnetic moments of the nuclei we demonstrate that nuclear magnetic shielding can be directly observed from NMR spectra. In this approach, the absolute shielding constants of all the nuclei can be related to a single reference scale, with atomic (3)He as the primary standard. The accuracy of the data obtained using our method is confirmed comparing the (1)H and (13)C shielding constants for a series of deuterated compounds with those determined analyzing the traditional chemical shifts. Since the use of helium-3 is not in general a practical alternative, we next transfer the reference standard to the (2)H signals of external lock solvents, in this way making the method easy and ready for application with most NMR spectrometers. Finally, we illustrate our new method with the measurements of the (2/1)H primary isotope effects in several liquid deuterated solvents. PMID:20112974

  12. Importin α: a key molecule in nuclear transport and non-transport functions.

    PubMed

    Miyamoto, Yoichi; Yamada, Kohji; Yoneda, Yoshihiro

    2016-08-01

    Importin α performs the indispensable role of ferrying proteins from the cytoplasm into the nucleus with a transport carrier, importin β1. Mammalian cells from mouse or human contain either six or seven importin α subtypes, respectively, each with a tightly regulated expression. Therefore, the combination of subtype expression in a cell defines distinct signaling pathways to achieve progressive changes in gene expression essential for cellular events, such as differentiation. Recent studies reveal that, in addition to nucleocytoplasmic transport, importin αs also serve non-transport functions. In this review, we first discuss the physiological significance of importin α as a nuclear transport regulator, and then focus on the functional diversities of importin αs based on their specific subcellular and cellular localizations, such as the nucleus and plasma membrane. These findings enrich our knowledge of how importin αs actively contribute to various cellular events. PMID:27289017

  13. Effect of nuclear mass on carrier-envelope-phase-controlled electron localization in dissociating molecules

    NASA Astrophysics Data System (ADS)

    Xu, Han; Xu, Tian-Yu; He, Feng; Kielpinski, D.; Sang, R. T.; Litvinyuk, I. V.

    2014-04-01

    We explore the effect of nuclear mass on the laser-driven electron localization process. We dissociate a mixed H2 and D2 target with intense, carrier-envelope-phase (CEP) stable 6 fs laser pulses and detect the products in a reaction microscope. We observe a very strong CEP-dependent asymmetry in proton and deuteron emission for low dissociation energy channels. This asymmetry is stronger for H2 than for D2. We also observe a large CEP offset between the asymmetry spectra for H2 and D2. Our theoretical simulations, based on a one-dimensional two-channel model, agree very well with the asymmetry spectra, but fail to account properly for the phase difference between the two isotopes.

  14. High-frequency, correlated nuclear and electron oscillations in molecules in intense laser fields

    NASA Astrophysics Data System (ADS)

    Bandrauk, André D.; Chelkowski, Szczepan; Lu, Huizhong

    2013-03-01

    We have solved numerically the time-dependent Schrödinger equation (TDSE) describing dissociative-ionization of a H2 (and of a D2) molecule exposed to intense short-pulse laser light in one dimension. From the time dependent wave function we calculated the total average acceleration of the two electrons and the relative proton acceleration and the average of internuclear distance. We find that the general shape of the power spectra of electron and proton motion is very similar except that for the electrons the peaks occur at odd harmonics whereas for protons the peaks occur at even harmonics. We relate this to the appearance of higher order polarizabilities. The wavelet time-frequency analysis shows that, surprisingly, time profiles of electron and proton accelerations are nearly identical for high order harmonics. The wavelet time profiles confirm predictions of the three-step quasi-classical model of harmonic generation by identifying several (up to three) electron return times with high precision.

  15. Biphenotypic sinonasal sarcoma: an expanded immunoprofile including consistent nuclear β-catenin positivity and absence of SOX10 expression.

    PubMed

    Rooper, Lisa M; Huang, Shih-Chiang; Antonescu, Cristina R; Westra, William H; Bishop, Justin A

    2016-09-01

    Biphenotypic sinonasal sarcoma (BSNS) is a recently recognized low-grade sarcoma that exhibits both neural and myogenic differentiation. This unique dual phenotype stems from recurrent rearrangements in PAX3, a transcription factor that promotes commitment along both lineages. While identification of PAX3 rearrangements by fluorescence in situ hybridization (FISH) can confirm a BSNS diagnosis, this assay is not widely available. This study evaluates whether an expanded immunohistochemical panel can facilitate recognition of BSNS without molecular analysis. Eleven cases of BSNS were identified from the surgical pathology archives of two academic medical centers. In 8 cases, the diagnosis was confirmed by FISH using custom probes for PAX3. In 3 cases, FISH failed but histologic and immunophenotypic findings were diagnostic for BSNS. All 11 BSNS (100%) were at least focally positive for S100 as well as calponin and/or smooth muscle actin. In addition, 10 (91%) of 11 expressed nuclear β-catenin, 8 (80%) of 10 expressed factor XIIIa, 4 (36%) of 11 expressed desmin, and 3 (30%) of 10 expressed myogenin. All 11 tumors were negative for SOX10. While no single marker resolves immunohistochemical overlap between BSNS and its histologic mimickers such as nerve sheath tumors, an extended immunohistochemical panel that includes β-catenin and SOX10 helps to support the diagnosis of BSNS without the need for gene rearrangement studies. PMID:27137987

  16. Simple expressions of the nuclear relaxation rate enhancement due to quadrupole nuclei in slowly tumbling molecules

    NASA Astrophysics Data System (ADS)

    Fries, Pascal H.; Belorizky, Elie

    2015-07-01

    For slowly tumbling entities or quasi-rigid lattices, we derive very simple analytical expressions of the quadrupole relaxation enhancement (QRE) of the longitudinal relaxation rate R1 of nuclear spins I due to their intramolecular magnetic dipolar coupling with quadrupole nuclei of arbitrary spins S ≥ 1. These expressions are obtained by using the adiabatic approximation for evaluating the time evolution operator of the quantum states of the quadrupole nuclei S. They are valid when the gyromagnetic ratio of the spin S is much smaller than that of the spin I. The theory predicts quadrupole resonant peaks in the dispersion curve of R1 vs magnetic field. The number, positions, relative intensities, Lorentzian shapes, and widths of these peaks are explained in terms of the following properties: the magnitude of the quadrupole Hamiltonian and the asymmetry parameter of the electric field gradient (EFG) acting on the spin S, the S-I inter-spin orientation with respect to the EFG principal axes, the rotational correlation time of the entity carrying the S-I pair, and/or the proper relaxation time of the spin S. The theory is first applied to protein amide protons undergoing dipolar coupling with fast-relaxing quadrupole 14N nuclei and mediating the QRE to the observed bulk water protons. The theoretical QRE agrees well with its experimental counterpart for various systems such as bovine pancreatic trypsin inhibitor and cartilages. The anomalous behaviour of the relaxation rate of protons in synthetic aluminium silicate imogolite nano-tubes due to the QRE of 27Al (S = 5/2) nuclei is also explained.

  17. Simple expressions of the nuclear relaxation rate enhancement due to quadrupole nuclei in slowly tumbling molecules

    SciTech Connect

    Fries, Pascal H.; Belorizky, Elie

    2015-07-28

    For slowly tumbling entities or quasi-rigid lattices, we derive very simple analytical expressions of the quadrupole relaxation enhancement (QRE) of the longitudinal relaxation rate R{sub 1} of nuclear spins I due to their intramolecular magnetic dipolar coupling with quadrupole nuclei of arbitrary spins S ≥ 1. These expressions are obtained by using the adiabatic approximation for evaluating the time evolution operator of the quantum states of the quadrupole nuclei S. They are valid when the gyromagnetic ratio of the spin S is much smaller than that of the spin I. The theory predicts quadrupole resonant peaks in the dispersion curve of R{sub 1} vs magnetic field. The number, positions, relative intensities, Lorentzian shapes, and widths of these peaks are explained in terms of the following properties: the magnitude of the quadrupole Hamiltonian and the asymmetry parameter of the electric field gradient (EFG) acting on the spin S, the S-I inter-spin orientation with respect to the EFG principal axes, the rotational correlation time of the entity carrying the S–I pair, and/or the proper relaxation time of the spin S. The theory is first applied to protein amide protons undergoing dipolar coupling with fast-relaxing quadrupole {sup 14}N nuclei and mediating the QRE to the observed bulk water protons. The theoretical QRE agrees well with its experimental counterpart for various systems such as bovine pancreatic trypsin inhibitor and cartilages. The anomalous behaviour of the relaxation rate of protons in synthetic aluminium silicate imogolite nano-tubes due to the QRE of {sup 27}Al (S = 5/2) nuclei is also explained.

  18. Complexation of the vulcanization accelerator tetramethylthiuram disulfide and related molecules with zinc compounds including zinc oxide clusters (Zn4O4).

    PubMed

    Steudel, Ralf; Steudel, Yana; Wong, Ming Wah

    2008-01-01

    Zinc chemicals are used as activators in the vulcanization of organic polymers with sulfur to produce elastic rubbers. In this work, the reactions of Zn(2+), ZnMe(2), Zn(OMe)(2), Zn(OOCMe)(2), and the heterocubane cluster Zn(4)O(4) with the vulcanization accelerator tetramethylthiuram disulfide (TMTD) and with the related radicals and anions Me(2)NCS(2)(*), Me(2)NCS(3)(*), Me(2)NCS(2)(-), and Me(2)NCS(3)(-) have been studied by quantum chemical methods at the MP2/6-31+G(2df,p)//B3LYP/6-31+G* level of theory. More than 35 zinc complexes have been structurally characterized and the energies of formation from their components calculated for the first time. The binding energy of TMTD as a bidendate ligand increases in the order ZnMe(2)molecule at the S-S bond on reaction with the Zn(4)O(4) cluster is predicted to be strongly exothermic, in sharp contrast to the endothermic S-S bond dissociation of the free molecule. The same holds for tetramethylthiuram trisulfide (TMTT). Surprisingly, the resulting complexes contain Zn-S as well as S-O bonds. The Zn(4)O(4) nanocluster serves here as a model for bulk zinc oxide used as an activator in rubber vulcanization by sulfur. The further uptake of sulfur atoms by the various complexes from S(8) or TMTD with formation of species derived from the radical Me(2)NCS(3)(*) or the trithiocarbamate anion Me(2)NCS(3)(-) is endothermic for mono- and dinuclear zinc dithiocarbamate (dtc) complexes such as [Zn(dtc)(2)] and [Zn(2)(dtc)(4)], but exothermic in the case of polynuclear zinc oxide species containing bridging ligands as in [Zn(4)O(4)(mu-S(2)CNMe(2))] and [Zn(4)O(4)(mu-dtc)]. Therefore, zinc oxide as a polynuclear species is predicted to promote the formation of trisulfido complexes, which are generally assumed to serve as catalysts for the transfer of

  19. Diversity of Dicotyledenous-Infecting Geminiviruses and Their Associated DNA Molecules in Southern Africa, Including the South-West Indian Ocean Islands

    PubMed Central

    Rey, Marie E. C.; Ndunguru, Joseph; Berrie, Leigh C.; Paximadis, Maria; Berry, Shaun; Cossa, Nurbibi; Nuaila, Valter N.; Mabasa, Ken G.; Abraham, Natasha; Rybicki, Edward P.; Martin, Darren; Pietersen, Gerhard; Esterhuizen, Lindy L.

    2012-01-01

    The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world. PMID:23170182

  20. Ab initio study of the positronation of the CaO and SrO molecules including calculation of annihilation rates.

    PubMed

    Buenker, Robert J; Liebermann, Heinz-Peter

    2012-07-15

    Ab initio multireference single- and double-excitation configuration interaction calculations have been performed to compute potential curves for ground and excited states of the CaO and SrO molecules and their positronic complexes, e(+)CaO, and e(+)SrO. The adiabatic dissociation limit for the (2)Σ(+) lowest states of the latter systems consists of the positive metal ion ground state (M(+)) and the OPs complex (e(+)O(-)), although the lowest energy limit is thought to be e(+)M + O. Good agreement is found between the calculated and experimental spectroscopic constants for the neutral diatomics wherever available. The positron affinity of the closed-shell X (1)Σ(+) ground states of both systems is found to lie in the 0.16-0.19 eV range, less than half the corresponding values for the lighter members of the alkaline earth monoxide series, BeO and MgO. Annihilation rates (ARs) have been calculated for all four positronated systems for the first time. The variation with bond distance is generally similar to what has been found earlier for the alkali monoxide series of positronic complexes, falling off gradually from the OPs AR value at their respective dissociation limits. The e(+)SrO system shows some exceptional behavior, however, with its AR value reaching a minimum at a relatively large bond distance and then rising to more than twice the OPs value close to its equilibrium distance. PMID:22522712

  1. Nuclear c-Abl-mediated tyrosine phosphorylation induces chromatin structural changes through histone modifications that include H4K16 hypoacetylation

    SciTech Connect

    Aoyama, Kazumasa; Fukumoto, Yasunori; Ishibashi, Kenichi; Kubota, Sho; Morinaga, Takao; Horiike, Yasuyoshi; Yuki, Ryuzaburo; Takahashi, Akinori; Nakayama, Yuji; Yamaguchi, Naoto

    2011-12-10

    c-Abl tyrosine kinase, which is ubiquitously expressed, has three nuclear localization signals and one nuclear export signal and can shuttle between the nucleus and the cytoplasm. c-Abl plays important roles in cell proliferation, adhesion, migration, and apoptosis. Recently, we developed a pixel imaging method for quantitating the level of chromatin structural changes and showed that nuclear Src-family tyrosine kinases are involved in chromatin structural changes upon growth factor stimulation. Using this method, we show here that nuclear c-Abl induces chromatin structural changes in a manner dependent on the tyrosine kinase activity. Expression of nuclear-targeted c-Abl drastically increases the levels of chromatin structural changes, compared with that of c-Abl. Intriguingly, nuclear-targeted c-Abl induces heterochromatic profiles of histone methylation and acetylation, including hypoacetylation of histone H4 acetylated on lysine 16 (H4K16Ac). The level of heterochromatic histone modifications correlates with that of chromatin structural changes. Adriamycin-induced DNA damage stimulates translocation of c-Abl into the nucleus and induces chromatin structural changes together with H4K16 hypoacetylation. Treatment with trichostatin A, a histone deacetylase inhibitor, blocks chromatin structural changes but not nuclear tyrosine phosphorylation by c-Abl. These results suggest that nuclear c-Abl plays an important role in chromatin dynamics through nuclear tyrosine phosphorylation-induced heterochromatic histone modifications.

  2. Enneanuclear [Ni6Ln3] Cages: [Ln(III)3] Triangles Capping [Ni(II)6] Trigonal Prisms Including a [Ni6Dy3] Single-Molecule Magnet.

    PubMed

    Canaj, Angelos B; Tzimopoulos, Demetrios I; Siczek, Milosz; Lis, Tadeusz; Inglis, Ross; Milios, Constantinos J

    2015-07-20

    The use of (2-(β-naphthalideneamino)-2-hydroxymethyl-1-propanol) ligand, H3L, in Ni/Ln chemistry has led to the isolation of three new isostructural [Ni(II)6Ln(III)3] metallic cages. More specifically, the reaction of Ni(ClO4)2·6H2O, the corresponding lanthanide nitrate salt, and H3L in MeCN, under solvothermal conditions in the presence of NEt3, led to the isolation of three complexes with the formulas [Ni6Gd3(OH)6(HL)6(NO3)3]·5.75MeCN·2Et2O·1.5H2O (1·5.75MeCN·2Et2O·1.5H2O), [Ni6Dy3(OH)6(HL)6(NO3)3]·2MeCN·2.7Et2O·2.4H2O (2·2MeCN·2.7Et2O·2.4H2O), and [Ni6Er3(OH)6(HL)6(NO3)3]·5.75MeCN·2Et2O·1.5H2O (3·5.75MeCN·2Et2O·1.5H2O). The structure of all three clusters describes a [Ln(III)3] triangle capping a [Ni(II)6] trigonal prism. Direct current magnetic susceptibility studies in the 5-300 K range for complexes 1-3 reveal the different nature of the magnetic interactions within the clusters: dominant antiferromagnetic exchange interactions for the Dy(III) and Er(III) analogues and dominant ferromagnetic interactions for the Gd(III) example. Alternating current magnetic susceptibility measurements under zero external dc field displayed fully formed temperature- and frequency-dependent out-of-phase peaks for the [Ni(II)6Dy(III)3] analogue, establishing its single molecule magnetism behavior with Ueff = 24 K. PMID:26135204

  3. Synthesis and Exploratory Catalysis of 3d Metals: Group-Transfer Reactions, and the Activation and Functionalization of Small Molecules Including Greenhouse Gases

    SciTech Connect

    Mindiola, Daniel J.

    2014-05-07

    Our work over the past three years has resulted in the development of electron rich and low-coordinate vanadium fragments, molecular nitrides of vanadium and parent imide systems of titanium, and the synthesis of phosphorus containing molecules of the 3d transition metal series. Likewise, with financial support from BES Division in DOE (DE-FG02-07ER15893), we now completed the full characterization of the first single molecular magnet (SMM) of Fe(III). We demonstrated that this monomeric form of Fe(III) has an unusual slow relaxation of the magnetization under zero applied field. To make matters more interesting, this system also undergoes a rare example of an intermediate to high-spin transition (an S = 3/2 to S = 5/2 transition). In 2010 we reported the synthesis of the first neutral and low-coordinate vanadium complexes having the terminal nitride functionality. We have now completed a full study to understand formation of the nitride ligand from the metastable azide precursor, and have also explored the reactivity of the nitride ligand in the context of incomplete and complete N-atom transfer. During the 2010-2013 period we also discovered a facile approach to assemble low-coordinate and low-valent vanadium(II) complexes and exploit their multielectron chemistry ranging from 1-3 electrons. Consequently, we can now access 3d ligand frameworks such as cyclo-P3 (and its corresponding radical anion), nitride radical anions and cations, low-coordinate vanadium oxo’s, and the first example of a vanadium thionitrosyl complex. A cis-divacant iron(IV) imido having some ligand centered radical has been also discovered, and we are in the process of elucidating its electronic structure (in particular the sign of zero field splitting and the origin of its magnitude), bonding and reactivity. We have also revisited some paramagnetic and classic metallocene compounds with S >1/2 ground states in order to understand their reactivity patterns and electronic structure. Lastly

  4. Comparative structure analyses of cystine knot-containing molecules with eight aminoacyl ring including glycoprotein hormones (GPH) alpha and beta subunits and GPH-related A2 (GPA2) and B5 (GPB5) molecules

    PubMed Central

    2009-01-01

    Background Cystine-knot (cys-knot) structure is found in a rather large number of secreted proteins and glycoproteins belonging to the TGFbeta and glycoprotein hormone (GPH) superfamilies, many of which are involved in endocrine control of reproduction. In these molecules, the cys-knot is formed by a disulfide (SS) bridge penetrating a ring formed by 8, 9 or 10 amino-acid residues among which four are cysteine residues forming two SS bridges. The glycoprotein hormones Follicle-Stimulating Hormone (FSH), Luteinizing Hormone (LH), Thyroid-Stimulating Hormone (TSH) and Chorionic Gonadotropin (CG) are heterodimers consisting of non-covalently associated alpha and beta subunits that possess cys-knots with 8-amino-acyl (8aa) rings. In order to get better insight in the structural evolution of glycoprotein hormones, we examined the number and organization of SS bridges in the sequences of human 8-aa-ring cys-knot proteins having 7 (gremlins), 9 (cerberus, DAN), 10 (GPA2, GPB5, GPHα) and 12 (GPHβ) cysteine residues in their sequence. Discussion The comparison indicated that the common GPH-alpha subunit exhibits a SS bridge organization ressembling that of DAN and GPA2 but possesses a unique bridge linking an additional cysteine inside the ring to the most N-terminal cysteine residue. The specific GPHbeta subunits also exhibit a SS bridge organization close to that of DAN but it has two additional C-terminal cysteine residues which are involved in the formation of the "seat belt" fastened by a SS "buckle" that ensures the stability of the heterodimeric structure of GPHs. GPA2 and GPB5 exhibit no cys residue potentially involved in interchain SS bridge and GPB5 does not possess a sequence homologous to that of the seatbelt in GPH β-subunits. GPA2 and GPB5 are thus not expected to form a stable heterodimer at low concentration in circulation. Summary The 8-aa cys-knot proteins GPA2 and GPB5 are expected to form a heterodimer only at concentrations above 0.1 microM: this

  5. Local vibrations in disordered solids studied via single-molecule spectroscopy: Comparison with neutron, nuclear, Raman scattering, and photon echo data

    NASA Astrophysics Data System (ADS)

    Vainer, Yu. G.; Naumov, A. V.; Kador, L.

    2008-06-01

    The energy spectrum of low-frequency vibrational modes (LFMs) in three disordered organic solids—amorphous polyisobutylene (PIB), toluene and deuterated toluene glasses, weakly doped with fluorescent chromophore molecules of tetra-tert-butylterrylene (TBT) has been measured via single-molecule (SM) spectroscopy. Analysis of the individual temperature dependences of linewidths of single TBT molecules allowed us to determine the values of the vibrational mode frequencies and the SM-LFM coupling constants for vibrations in the local environment of the molecules. The measured LFM spectra were compared with the “Boson peak” as measured in pure PIB by inelastic neutron scattering, in pure toluene glass by low-frequency Raman scattering, in doped toluene glass by nuclear inelastic scattering, and with photon echo data. The comparative analysis revealed close agreement between the spectra of the local vibrations as measured in the present study and the literature data of the Boson peak in PIB and toluene. The analysis has also the important result that weak doping of the disordered matrices with nonpolar probe molecules whose chemical composition is similar to that of the matrix molecules does not influence the observed vibrational dynamics markedly. The experimental data displaying temporal stability on the time scale of a few hours of vibrational excitation parameters in local surroundings was obtained for the first time both for polymer and molecular glass.

  6. 3D collapse of rotating stellar iron cores in general relativity including deleptonization and a nuclear equation of state.

    PubMed

    Ott, C D; Dimmelmeier, H; Marek, A; Janka, H-T; Hawke, I; Zink, B; Schnetter, E

    2007-06-29

    We present 2D and 3D simulations of the collapse of rotating stellar iron cores in general relativity employing a nuclear equation of state and an approximate treatment of deleptonization. We compare fully general relativistic and conformally flat evolutions and find that the latter treatment is sufficiently accurate for the core-collapse supernova problem. We focus on gravitational wave (GW) emission from rotating collapse, bounce, and early postbounce phases. Our results indicate that the GW signature of these phases is much more generic than previously estimated. We also track the growth of a nonaxisymmetric instability in one model, leading to strong narrow-band GW emission. PMID:17678077

  7. Nuclear factor kappaB dominant negative genetic constructs inhibit X-ray induction of cell adhesion molecules in the vascular endothelium.

    PubMed

    Hallahan, D E; Virudachalam, S; Kuchibhotla, J

    1998-12-01

    X-ray-induced expression of inflammatory mediators has been proposed to contribute to radiation injury in normal tissues. Radiation-inducible inflammatory mediators include the cell adhesion molecule (CAM) E-selectin and the intercellular adhesion molecule (ICAM)-1. Nuclear factor (NF)kappaB is activated by X-rays and may participate in the transcriptional regulation of each of these inflammatory mediators. To determine whether NFkappaB inhibition abrogates X-ray induction of inflammatory mediators, we used two experimental approaches including NFkappaB inhibitory drugs and a dominant negative genetic construct. Human umbilical vein endothelial cells (HUVEC) and human microvascular endothelial cells were treated with the NFkappaB inhibitors ALLN, PDTC, NAC, and MG132. After irradiation, E-selectin or ICAM-1 was measured by fluorescence-activated cell-sorting analysis. E-selectin and ICAM-1 expression was measured by use of immunofluorescence and fluorescence-activated cell-sorting analysis. E-selectin expression increased 7-fold, and ICAM-1 expression increased 4-fold after irradiation. All of the inhibitors attenuated E-selectin expression after irradiation. ALLN and MG132 attenuated radiation-induced ICAM expression. However, PDTC and NAC induced increased expression of ICAM-1 in HUVECs. Inhibition of X-ray induction of ICAM by these agents could not be demonstrated. In separate experiments, the NFkappaB dominant negative genetic construct was cotransfected with the promoter-reporter constructs by means of Lipofectin reagent. The ICAM promoter-reporter construct consists of the 1.2-kb segment of the human ICAM promoter upstream of the transcriptional start site linked to the luciferase reporter gene (pGL.FL-Luc). The E-selectin promoter-reporter construct consists of 525 bp upstream of the transcriptional start site of the human E-selectin promoter linked to the human growth hormone reporter gene (pE525-GH). Endothelial cells transfected with the ICAM-1 promoter

  8. The Evaluation of Lithium Hydride for Use in a Space Nuclear Reactor Shield, Including a Historical Perspective

    SciTech Connect

    D. Poeth

    2005-12-09

    LiH was one of the five primary shield materials the NRPCT intended to develop (along with beryllium, boron carbide, tungsten, and water) for potential Prometheus application. It was also anticipated that {sup 10}B metal would be investigated for feasibility at a low level of effort. LiH historically has been selected as a low mass, neutron absorption material for space shields (Systems for Nuclear Auxiliary Power (SNAP), Topaz, SP-100). Initial NRPCT investigations did not produce convincing evidence that LiH was desirable or feasible for a Prometheus mission due to material property issues (primarily swelling and hydrogen cover gas containment), and related thermal design complexity. Furthermore, if mass limits allowed, an option to avoid use of LiH was being contemplated to lower development costs and associated risks. However, LiH remains theoretically the most efficient neutron shield material per unit mass, and, with sufficient testing and development, could be an optimal material choice for future flights.

  9. Relativistic and electron-correlation effects on the nuclear magnetic resonance shieldings of molecules containing tin and lead atoms.

    PubMed

    Maldonado, Alejandro F; Aucar, Gustavo A

    2014-09-11

    The reference values for NMR magnetic shieldings, σ(ref), are of the highest importance when theoretical analysis of chemical shifts are envisaged. The fact that the nonrelativistically valid relationship among spin-rotation constants and magnetic shieldings is not any longer valid for heavy atoms requires that the search for σ(ref) for such atoms needs new strategies to follow. We present here results of σ(ref) that were obtained by applying our own simple procedure which mixes accurate experimental chemical shifts (δ) and theoretical magnetic shieldings (σ). We calculated σ(Sn) and σ(Pb) in a family of heavy-halogen-containing molecules. We found out that σ(ref)[Sn;Sn(CH3)4] in gas phase should be close to 3864.11 ± 20.05 ppm (0.5%). For Pb atom, σ(ref)[Pb;Pb(CH3)4] should be close to 14475.1 ± 500.7 ppm. Such theoretical values correspond to calculations with the relativistic polarization propagator method, RelPPA, at the RPA level of approach. They are closer to experimental values as compared to those obtained applying few different functionals such as PBE0, B3LYP, BLYP, BP86, KT2, and KT3 of the density functional theory, DFT. We studied tin and lead shieldings of the XY(4-n)Z(n) (X = Sn, Pb; Y, Z = H, F, Cl, Br, I) and PbH(4-n)I(n) (n = 0, 1, 2, 3, 4) family of compounds with four-component functionals as implemented in the DIRAC code. For these systems results of calculations with RelPPA-RPA are more reliable than DFT ones. We argue about why those DFT functionals must be modified in order to obtain more accurate results of NMR magnetic shieldings within the relativistic regime: first, there is a dependence among both electron-correlation and relativistic effects that should be introduced in some way in the functionals; and second, the DIRAC code uses standard nonrelativistic functionals and the functionals B3LYP and PBE0 were parametrized only with data taken from light elements. It can explain why they are not able to properly introduce

  10. A small molecule induces integrin β4 nuclear translocation and apoptosis selectively in cancer cells with high expression of integrin β4

    PubMed Central

    Liu, ShuYan; Ge, Di; Chen, LiNa; Zhao, Jing; Su, Le; Zhang, ShangLi; Miao, JunYing; Zhao, BaoXiang

    2016-01-01

    Increased integrin β4 (ITGB4) level is accompanied by malignant progression of multiple carcinomas. However, selective therapeutic strategies against cancer cells expressing a high level of ITGB4 have not been reported. Here, for the first time, we report that a chiral small molecule, SEC, selectively promotes apoptosis in cancer cells expressing a high level of ITGB4 by inducing ITGB4 nuclear translocation. Nuclear ITGB4 can bind to the ATF3 promoter region and activate the expression of ATF3, then upregulate the downstream pro-apoptosis genes. Furthermore, SEC promoted the binding of annexin A7 (ANXA7) to ITGB4 and increased ANXA7 GTPase activity. Activated ANXA7 promoted ITGB4 nuclear translocation by triggering ITGB4 phosphorylation at Y1494. SEC also inhibited the growth of xenograft tumors in the avian embryo model. We identified a small molecule, SEC, with selective pro-apoptosis effects on cancer cells with high expression of ITGB4, both in vitro and in vivo, by triggering the binding of ITGB4 and ANXA7, ITGB4 nuclear trafficking, and pro-apoptosis gene expression. PMID:26918348

  11. Coupled electron-nuclear dynamics in resonant 1 σ →2 π x-ray Raman scattering of CO molecules

    NASA Astrophysics Data System (ADS)

    Couto, Rafael C.; Guarise, Marco; Nicolaou, Alessandro; Jaouen, Nicolas; Chiuzbǎian, Gheorghe S.; Lüning, Jan; Ekholm, Victor; Rubensson, Jan-Erik; Sâthe, Conny; Hennies, Franz; Guimarães, Freddy F.; Ågren, Hans; Gel'mukhanov, Faris; Journel, Loïc; Simon, Marc; Kimberg, Victor

    2016-03-01

    We present a detailed experimental-theoretical analysis of O K -edge resonant 1 σ -2 π inelastic x-ray scattering (RIXS) from carbon monoxide with unprecedented energy resolution. We employ high-level ab initio calculations to compute the potential energy curves of the states involved in the RIXS process and simulate the measured RIXS spectra using the wave-packet-propagation formalism, including Coulomb coupling in the final-state manifold. The theoretical analysis allows us to explain all the key features of the experimental spectra, including some that were not seen before. First, we clearly show the interference effect between different RIXS channels corresponding to the transition via orthogonal Π1x and Π1y core-excited states of CO. Second, the RIXS region of 13 eV energy loss presents a triple structure, revealed only by the high-resolution measurement. In previous studies, this region was attributed solely to a valence state. Here we show a strong Coulomb mixing of the Rydberg and valence final states, which opens the forbidden RIXS channels to the "dark" final Rydberg states and drastically changes the RIXS profile. Third, using a combination of high-resolution experiment and high-level theory, we improve the |4 σ-12 π1> final-state potential-energy curve by fitting its bottom part with the experiment. Also, the coupling constants between Rydberg and valence states were refined via comparison with the experiment. Our results illustrate the large potential of the RIXS technique for advanced studies of highly excited states of neutral molecules.

  12. Charge and Nuclear Dynamics Induced by Deep Inner-Shell Multiphoton Ionization of CH3I Molecules by Intense X-ray Free-Electron Laser Pulses.

    PubMed

    Motomura, Koji; Kukk, Edwin; Fukuzawa, Hironobu; Wada, Shin-ichi; Nagaya, Kiyonobu; Ohmura, Satoshi; Mondal, Subhendu; Tachibana, Tetsuya; Ito, Yuta; Koga, Ryosuke; Sakai, Tsukasa; Matsunami, Kenji; Rudenko, Artem; Nicolas, Christophe; Liu, Xiao-Jing; Miron, Catalin; Zhang, Yizhu; Jiang, Yuhai; Chen, Jianhui; Anand, Mailam; Kim, Dong Eon; Tono, Kensuke; Yabashi, Makina; Yao, Makoto; Ueda, Kiyoshi

    2015-08-01

    In recent years, free-electron lasers operating in the true X-ray regime have opened up access to the femtosecond-scale dynamics induced by deep inner-shell ionization. We have investigated charge creation and transfer dynamics in the context of molecular Coulomb explosion of a single molecule, exposed to sequential deep inner-shell ionization within an ultrashort (10 fs) X-ray pulse. The target molecule was CH3I, methane sensitized to X-rays by halogenization with a heavy element, iodine. Time-of-flight ion spectroscopy and coincident ion analysis was employed to investigate, via the properties of the atomic fragments, single-molecule charge states of up to +22. Experimental findings have been compared with a parametric model of simultaneous Coulomb explosion and charge transfer in the molecule. The study demonstrates that including realistic charge dynamics is imperative when molecular Coulomb explosion experiments using short-pulse facilities are performed. PMID:26267186

  13. What Do Nuclear Spin Temperatures Tell Us About The Origin Of Comets? A Multi-molecule Study

    NASA Astrophysics Data System (ADS)

    Villanueva, Geronimo; Mumma, M. J.; Bonev, B. P.; DiSanti, M. A.; Magee-Sauer, K.; Gibb, E. L.; Paganini, L.; Radeva, Y. L.

    2012-10-01

    Comets are true remnants of our primordial Solar System, and provide unique clues to its formation and evolution, including the delivery of organics and water to our planet. A key indicator stored in the molecular structure of the nuclear ices is the spin temperature (Tspin), derived from spin-isomeric ratios (Rspin, e.g. ortho/para). At the time when cometary ices formed, the prevailing temperature defined the relative abundance of the different spin-isomeric species, and herewith Rspin and Tspin are normally treated as “remnant thermometers” probing the formation environments. Most of our knowledge of this indicator comes from measurements of ortho-para ratios in water and NH2, suggesting a common Tspin near 30K. This information is based on a restricted sample of comets, and the measurements are particularly sensitive to the molecular modeling technique and adopted spectral database. Here, we present new methodologies for extracting spin temperatures from ethane (C2H6), methane (CH4), and methanol (CH3OH), and describe advanced new models for ortho/para water (H2O) and ammonia (NH3). Our H2O analysis is based on the most complete fluorescence radiative transfer model to date, which incorporates 1,200 million transitions including those originating from high-energy levels that are activated in comets via non-resonance cascade. In a similar fashion, we developed non-resonance fluorescence models for NH3 and HCN, and quantum band models for the ν7 band of C2H6 and ν3 band of CH3OH. All models respect spin symmetry non-conversion radiative rules, and make use of a realistic Solar spectrum for the computation of fluorescence pumps. We applied these new methods to derive spin-isomeric ratios for H2O, CH4, C2H6, CH3OH and NH3 from three high-quality cometary datasets: 1) C/2007 W1 (Boattini), 2) C/2001 A2 (LINEAR), and 3) 8P/Tuttle. We compare our results with the measured organic compositions for these comets, and present possible formation and evolution

  14. Spin-labeled gel for the production of radical-free dynamic nuclear polarization enhanced molecules for NMR spectroscopy and imaging

    NASA Astrophysics Data System (ADS)

    McCarney, Evan R.; Han, Songi

    2008-02-01

    Dynamic nuclear polarization (DNP) has recently received much attention as a viable approach to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and the contrast of magnetic resonance imaging (MRI), where the significantly higher electron spin polarization of stable radicals is transferred to nuclear spins. In order to apply DNP-enhanced NMR and MRI signal to biological and in vivo systems, it is crucial to obtain highly polarized solution samples at ambient temperatures. As stable radicals are employed as the source for the DNP polarization transfer, it is also crucial that the highly polarized sample lacks residual radical concentration because the polarized molecules will be introduced to a biological system that will be sensitive to the presence of radicals. We developed an agarose-based porous media that is covalently spin-labeled with stable radicals. The loading of solvent accessible radical is sufficiently high and their mobility approximates that in solution, which ensures high efficiency for Overhauser mechanism induced DNP without physically releasing any measurable radical into the solution. Under ambient conditions at 0.35 T magnetic field, we measure the DNP enhancement efficiency of 1H signal of stagnant and continuously flowing water utilizing immobilized stable nitroxide radicals that contain two or three ESR hyperfine splitting lines and compare them to the performance of freely dissolved radicals.

  15. Tune-out wavelength around 413 nm for the helium 2 3S1 state including relativistic and finite-nuclear-mass corrections

    NASA Astrophysics Data System (ADS)

    Zhang, Yong-Hui; Tang, Li-Yan; Zhang, Xian-Zhou; Shi, Ting-Yun

    2016-05-01

    The tune-out wavelength at 413 nm for the 2 3S1 state of helium is expected to be sensitive to finite nuclear mass, relativistic, and quantum electrodynamic (QED) corrections, which provides a scheme for testing atomic structure theory [J. Mitroy and L.-Y. Tang, Phys. Rev. A 88, 052515 (2013), 10.1103/PhysRevA.88.052515]. In the present work, a large-scale full-configuration-interaction calculation based on both the Dirac-Coulomb-Breit Hamiltonian and the nonrelativistic Hamiltonian is performed for the dynamic dipole polarizabilities of helium in the 2 3S1 state. The tune-out wavelengths for the magnetic sublevels MJ=0 and MJ=±1 are determined to be 413.0801(4) nm and 413.0859(4) nm, respectively, at sub-ppm accuracy, including finite nuclear mass and relativistic corrections. Our value for the MJ=1 sublevel agrees with the measured value of 413.0938(20)(9) nm [B. M. Henson et al., Phys. Rev. Lett. 115, 043004 (2015), 10.1103/PhysRevLett.115.043004] at the level of 19 ppm. The discrepancy between these two values is mainly due to the uncalculated QED contribution. Our current value confirms quantitatively the prediction of Mitroy and Tang. Also, for the state of 2 3S1 we find that the corrections due to finite nuclear mass and relativistic effects to the static dipole polarizability of 315.7227(4)a03 are about 600 ppm and 310 ppm, respectively, which are about 1.4 and 5.4 times larger than those for the ground state. A measurement at the level of 10 ppm for the static dipole polarizability of helium in 2 3S1 can be used to determine the transition matrix element between 2 3S and 2 3P at the level of 10-5.

  16. A novel phylogeny of the Gelidiales (Rhodophyta) based on five genes including the nuclear CesA, with descriptions of Orthogonacladia gen. nov. and Orthogonacladiaceae fam. nov.

    PubMed

    Boo, Ga Hun; Le Gall, Line; Miller, Kathy Ann; Freshwater, D Wilson; Wernberg, Thomas; Terada, Ryuta; Yoon, Kyung Ju; Boo, Sung Min

    2016-08-01

    Although the Gelidiales are economically important marine red algae producing agar and agarose, the phylogeny of this order remains poorly resolved. The present study provides a molecular phylogeny based on a novel marker, nuclear-encoded CesA, plus plastid-encoded psaA, psbA, rbcL, and mitochondria-encoded cox1 from subsets of 107 species from all ten genera within the Gelidiales. Analyses of individual and combined datasets support the monophyly of three currently recognized families, and reveal a new clade. On the basis of these results, the new family Orthogonacladiaceae is described to accommodate Aphanta and a new genus Orthogonacladia that includes species previously classified as Gelidium madagascariense and Pterocladia rectangularis. Acanthopeltis is merged with Gelidium, which has nomenclatural priority. Nuclear-encoded CesA was found to be useful for improving the resolution of phylogenetic relationships within the Gelidiales and is likely to be valuable for the inference of phylogenetic relationship among other red algal taxa. PMID:27223999

  17. Attempts at Using Iamcalc to Analyze Low Frequency Rotational Spectra of Molecules with Internal Rotation and Nuclear Spins

    NASA Astrophysics Data System (ADS)

    Dewberry, Christopher T.; Cooke, Stephen A.

    2010-06-01

    Recent progress in the fitting and analyses of simple methyl rotors to simultaneously account for internal rotation and nuclear hyperfine terms will be presented. The analyses have been attempted using Herb Pickett's IAMCALC program which acts as a ``front end" for the powerful SPFIT/SPCAT software. Progress has been made by simply appending hyperfine parameters to an IAMCALC-prepared SPFIT input file. This work has been prompted by our recent high resolution spectral measurements in the 1 - 21 GHz region on species such as methanol and methyl nitrite. Data will be presented together with comments on the validity of the fitting approach.

  18. Cytoplasmic-nuclear trafficking of G1/S cell cycle molecules and adult human β-cell replication: a revised model of human β-cell G1/S control.

    PubMed

    Fiaschi-Taesch, Nathalie M; Kleinberger, Jeffrey W; Salim, Fatimah G; Troxell, Ronnie; Wills, Rachel; Tanwir, Mansoor; Casinelli, Gabriella; Cox, Amy E; Takane, Karen K; Srinivas, Harish; Scott, Donald K; Stewart, Andrew F

    2013-07-01

    Harnessing control of human β-cell proliferation has proven frustratingly difficult. Most G1/S control molecules, generally presumed to be nuclear proteins in the human β-cell, are in fact constrained to the cytoplasm. Here, we asked whether G1/S molecules might traffic into and out of the cytoplasmic compartment in association with activation of cell cycle progression. Cdk6 and cyclin D3 were used to drive human β-cell proliferation and promptly translocated into the nucleus in association with proliferation. In contrast, the cell cycle inhibitors p15, p18, and p19 did not alter their location, remaining cytoplasmic. Conversely, p16, p21, and p27 increased their nuclear frequency. In contrast once again, p57 decreased its nuclear frequency. Whereas proliferating β-cells contained nuclear cyclin D3 and cdk6, proliferation generally did not occur in β-cells that contained nuclear cell cycle inhibitors, except p21. Dynamic cytoplasmic-nuclear trafficking of cdk6 was confirmed using green fluorescent protein-tagged cdk6 and live cell imaging. Thus, we provide novel working models describing the control of cell cycle progression in the human β-cell. In addition to known obstacles to β-cell proliferation, cytoplasmic-to-nuclear trafficking of G1/S molecules may represent an obstacle as well as a therapeutic opportunity for human β-cell expansion. PMID:23493571

  19. Small Molecule Antagonists of the Nuclear Androgen Receptor for the Treatment of Castration-Resistant Prostate Cancer.

    PubMed

    Johnson, James K; Skoda, Erin M; Zhou, Jianhua; Parrinello, Erica; Wang, Dan; O'Malley, Katherine; Eyer, Benjamin R; Kazancioglu, Mustafa; Eisermann, Kurtis; Johnston, Paul A; Nelson, Joel B; Wang, Zhou; Wipf, Peter

    2016-08-11

    After a high-throughput screening campaign identified thioether 1 as an antagonist of the nuclear androgen receptor, a zone model was developed for structure-activity relationship (SAR) purposes and analogues were synthesized and evaluated in a cell-based luciferase assay. A novel thioether isostere, cyclopropane (1S,2R)-27, showed the desired increased potency and structural properties (stereospecific SAR response, absence of a readily oxidized sulfur atom, low molecular weight, reduced number of flexible bonds and polar surface area, and drug-likeness score) in the prostate-specific antigen luciferase assay in C4-2-PSA-rl cells to qualify as a new lead structure for prostate cancer drug development. PMID:27563404

  20. Benchmark calculations on the nuclear quadrupole-coupling parameters for open-shell molecules using non-relativistic and scalar-relativistic coupled-cluster methods

    SciTech Connect

    Cheng, Lan

    2015-08-14

    Quantum-chemical computations of nuclear quadrupole-coupling parameters for 24 open-shell states of small molecules based on non-relativistic and spin-free exact two-component (SFX2C) relativistic equation-of-motion coupled-cluster (EOM-CC) as well as spin-orbital-based restricted open-shell Hartree-Fock coupled-cluster (ROHF-CC) methods are reported. Relativistic effects, the performance of the EOM-CC and ROHF-CC methods for treating electron correlation, as well as basis-set convergence have been carefully analyzed. Consideration of relativistic effects is necessary for accurate calculations on systems containing third-row (K-Kr) and heavier elements, as expected, and the SFX2C approach is shown to be a useful cost-effective option here. Further, it is demonstrated that the EOM-CC methods constitute flexible and accurate alternatives to the ROHF-CC methods in the calculations of nuclear quadrupole-coupling parameters for open-shell states.

  1. Relativistic calculation of nuclear magnetic shielding tensor using the regular approximation to the normalized elimination of the small component. III. Introduction of gauge-including atomic orbitals and a finite-size nuclear model

    NASA Astrophysics Data System (ADS)

    Hamaya, S.; Maeda, H.; Funaki, M.; Fukui, H.

    2008-12-01

    The relativistic calculation of nuclear magnetic shielding tensors in hydrogen halides is performed using the second-order regular approximation to the normalized elimination of the small component (SORA-NESC) method with the inclusion of the perturbation terms from the metric operator. This computational scheme is denoted as SORA-Met. The SORA-Met calculation yields anisotropies, Δσ =σ∥-σ⊥, for the halogen nuclei in hydrogen halides that are too small. In the NESC theory, the small component of the spinor is combined to the large component via the operator σ⃗ṡπ⃗U/2c, in which π⃗=p⃗+A⃗, U is a nonunitary transformation operator, and c ≅137.036 a.u. is the velocity of light. The operator U depends on the vector potential A⃗ (i.e., the magnetic perturbations in the system) with the leading order c-2 and the magnetic perturbation terms of U contribute to the Hamiltonian and metric operators of the system in the leading order c-4. It is shown that the small Δσ for halogen nuclei found in our previous studies is related to the neglect of the U(0,1) perturbation operator of U, which is independent of the external magnetic field and of the first order with respect to the nuclear magnetic dipole moment. Introduction of gauge-including atomic orbitals and a finite-size nuclear model is also discussed.

  2. Nuclear factor-kappa B directs carcinoembryonic antigen-related cellular adhesion molecule 1 receptor expression in Neisseria gonorrhoeae-infected epithelial cells.

    PubMed

    Muenzner, Petra; Billker, Oliver; Meyer, Thomas F; Naumann, Michael

    2002-03-01

    The human-specific pathogen Neisseria gonorrhoeae expresses opacity-associated (Opa) protein adhesins that bind to various members of the carcinoembryonic antigen-related cellular adhesion molecule (CEACAM) family. In this study, we have analyzed the mechanism underlying N. gonorrhoeae-induced CEACAM up-regulation in epithelial cells. Epithelial cells represent the first barrier for the microbial pathogen. We therefore characterized CEACAM expression in primary human ovarian surface epithelial (HOSE) cells and found that CEACAM1-3 (L, S) and CEACAM1-4 (L, S) splice variants mediate an increased Opa(52)-dependent gonoccocal binding to HOSE cells. Up-regulation of these CEACAM molecules in HOSE cells is a direct process that takes place within 2 h postinfection and depends on close contact between microbial pathogen and HOSE cells. N. gonorrhoeae-triggered CEACAM1 up-regulation involves activation of the transcription factor nuclear factor kappaB (NF-kappaB), which translocates as a p50/p65 heterodimer into the nucleus, and an NF-kappaB-specific inhibitory peptide inhibited CEACAM1-receptor up-regulation in N. gonorrhoeae-infected HOSE cells. Bacterial lipopolysaccharides did not induce NF-kappaB and CEACAM up-regulation, which corresponds to our findings that HOSE cells do not express toll-like receptor 4. The ability of N. gonorrhoeae to up-regulate its epithelial receptor CEACAM1 through NF-kappaB suggests an important mechanism allowing efficient bacterial colonization during the initial infection process. PMID:11751883

  3. Stimulation of nuclear receptor REV-ERBs regulates tumor necrosis factor-induced expression of proinflammatory molecules in C6 astroglial cells.

    PubMed

    Morioka, Norimitsu; Tomori, Mizuki; Zhang, Fang Fang; Saeki, Munenori; Hisaoka-Nakashima, Kazue; Nakata, Yoshihiro

    2016-01-01

    Under physiological conditions, astrocytes maintain homeostasis in the CNS. Following inflammation and injury to the CNS, however, activated astrocytes produce neurotoxic molecules such as cytokines and chemokines, amplifying the initial molecular-cellular events evoked by inflammation and injury. Nuclear receptors REV-ERBα and REV-ERBβ (REV-ERBs) are crucial in the regulation of inflammation- and metabolism-related gene transcription. The current study sought to elucidate a role of REV-ERBs in rat C6 astroglial cells on the expression of inflammatory molecules following stimulation with the neuroinflammatory cytokine tumor necrosis factor (TNF). Stimulation of C6 cells with TNF (10 ng/ml) significantly increased the mRNA expression of CCL2, interleukin-6 (IL-6), inducible nitric oxide synthase (iNOS), and matrix metalloprotease (MMP)-9, but not fibroblast growth factor-2 (FGF-2), cyclooxygenase-2 (COX-2) and MMP-2. Treatment with either REV-ERB agonists GSK4112 or SR9009 significantly blocked TNF-induced upregulation of CCL2 mRNA and MMP-9 mRNA, but not IL-6 mRNA and iNOS mRNA expression. Furthermore, treatment with RGFP966, a selective histone deacetylase 3 (HDAC3) inhibitor, potently reversed the inhibitory effects of GSK4112 on TNF-induced expression of MMP-9 mRNA, but not CCL2 mRNA. Expression of Rev-erbs mRNA in C6 astroglial cells, primary cultured rat cortical and spinal astrocytes was confirmed by reverse transcription polymerase chain reaction. Together, the findings demonstrate an anti-inflammatory effect, downregulating of MMP-9 and CCL2 transcription, of astroglial REV-ERBs activation through HDAC3-dependent and HDAC3-independent mechanisms. PMID:26616049

  4. The effect of an iodine restricted including no sea foods diet, on technetium-99m thyroid scintigraphy: a neglected issue in nuclear medicine practice.

    PubMed

    Javadi, Hamid; Neshandarasli, Isa; Mogharrabi, Mehdi; Jalallat, Sara; Nabipour, Iraj; Assadi, Majid

    2012-01-01

    Although it is recommended to patients to avoid sea food and iodine-containing medications prior to iodine-131 (¹³¹I) scanning, the efficacy of this diet as for technetium-99m pertechnetate ((99m)Tc-P) thyroid scintigraphy is not well addressed in the literature. We evaluated a self-managed, outpatients, iodine restricted diet (IRD) designed to reduce total body iodine in preparation for such a scan. We have studied 39 patients who referred to our Department for multinodular goiter, 30 females and 9 males, aged:14-54 years and their (99m)Tc-P thyroid scintigraphy showed poor visualization of the thyroid gland. These patiens were living in regions with high consumption of sea foods went underwent a two-weeks iodine restriction including restriction of sea food diet for the reduction of iodine body content. These patients were called for a repeated scan after going on a IRD for at least two weeks. The two scans were compared visually, and by semiquantitative analysis. Semiquantitative analysis was applied in 8 regions of interest (ROI) by using Wilcoxon signed rank test. Thirty-six subjects had better quality scintigraphy images in the post IRD thyroid scan, as was visually assessed by two nuclear medicine physicians. Semiquantitatetively, there was a significant difference in the mean counts of ROI of the right and the left thyroid lobes in favor of the post IRD scans (P<0.05). In conclusion, this study suggests that in patients with multinodular goiter, living in regions with high consumption of sea foods a two-weeks diet for the reduction of iodine body content induces in most of the cases a slightly better diagnostic thyroid (99m)Tc-P scan. PMID:22413111

  5. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  6. Connection between energy relations of solids and molecules

    NASA Technical Reports Server (NTRS)

    Smith, John R.; Schlosser, Herbert; Leaf, William; Ferrante, John; Rose, James H.

    1989-01-01

    The universal energy relation, discovered for metallic and covalent solids as well as nuclear matter, is tested for diatomic molecules. It is found that it applies well to covalent diatomic bonds, but that ionic diatomic bonds are in a distinct class. A simple extension of the universal binding energy relation that includes the effects of ionicity ensues. It yields accurate prediction of spectroscopic data for both ionic and covalent bonds in 150 molecules. The form of the covalent part is given by the universal relation, suggesting an intimate relationship between the energetics of solids and diatomic molecules.

  7. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  8. Interstellar Molecules

    ERIC Educational Resources Information Center

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  9. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  10. Light, Including Ultraviolet

    PubMed Central

    Maverakis, Emanual; Miyamura, Yoshinori; Bowen, Michael P.; Correa, Genevieve; Ono, Yoko; Goodarzi, Heidi

    2009-01-01

    Ultraviolet (UV) light is intricately linked to the functional status of the cutaneous immune system. In susceptible individuals, UV radiation can ignite pathogenic inflammatory pathways leading to allergy or autoimmunity. In others, this same UV radiation can be used as a phototherapy to suppress pathogenic cutaneous immune responses. These vastly different properties are a direct result of UV light’s ability to ionize molecules in the skin and thereby chemically alter them. Sometimes these UV-induced chemical reactions are essential, the formation of pre-vitamin D3 from 7-dehydrocholesterol, for example. In other instances they can be potentially detrimental. UV radiation can ionize a cell’s DNA causing adjacent pyrimidine bases to chemically bond to each other. To prevent malignant transformation, a cell may respond to this UV-induced DNA damage by undergoing apoptosis. Although this pathway prevents skin cancer it also has the potential of inducing or exacerbating autoreactive immune responses by exposing the cell’s nuclear antigens. Ultaviolet-induced chemical reactions can activate the immune system by a variety of other mechanisms as well. In response to UV irradiation keratinocytes secrete cytokines and chemokines, which activate and recruit leukocytes to the skin. In some individuals UV-induced chemical reactions can synthesize novel antigens resulting in a photoallergy. Alternatively, photosensitizing molecules can damage cells by initiating sunburn-like phototoxic reactions. Herein we review all types of UV-induced skin reactions, especially those involving the immune system. PMID:20018479

  11. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  12. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  13. Configuration-interaction and Hylleraas configuration-interaction methods in valence-bond theory: Calculation of the nuclear shielding constant for the ground state of the hydrogen molecule

    SciTech Connect

    Komasa, J.; Cencek, W.; Rychlewski, J. )

    1992-09-01

    Values of the magnetic shielding constant in the ground state of the hydrogen molecule are calculated using explicitly correlated Gaussian functions. The total shielding at equilibrium amounts to 26.73 ppm.

  14. Correlation between Asian Dust and Specific Radioactivities of Fission Products Included in Airborne Samples in Tokushima, Shikoku Island, Japan, Due to the Fukushima Nuclear Accident

    NASA Astrophysics Data System (ADS)

    Sakama, M.; Nagano, Y.; Kitade, T.; Shikino, O.; Nakayama, S.

    2014-06-01

    Radioactive fission product 131I released from the Fukushima Daiichi Nuclear Power Plants (FD-NPP) was first detected on March 23, 2011 in an airborne aerosol sample collected at Tokushima, Shikoku Island, located in western Japan. Two other radioactive fission products, 134Cs and 137Cs were also observed in a sample collected from April 2 to 4, 2011. The maximum specific radioactivities observed in this work were about 2.5 to 3.5 mBq×m-3 in a airborne aerosol sample collected on April 6. During the course of the continuous monitoring, we also made our first observation of seasonal Asian Dust and those fission products associated with the FDNPP accident concurrently from May 2 to 5, 2011. We found that the specific radioactivities of 134Cs and 137Cs decreased drastically only during the period of Asian Dust. And also, it was found that this trend was very similar to the atmospheric elemental concentration (ng×m-3) variation of stable cesium (133Cs) quantified by elemental analyses using our developed ICP-DRC-MS instrument.

  15. Correlation between Asian Dust and Specific Radioactivities of Fission Products Included in Airborne Samples in Tokushima, Shikoku Island, Japan, Due to the Fukushima Nuclear Accident

    SciTech Connect

    Sakama, M.; Nagano, Y.; Kitade, T.; Shikino, O.; Nakayama, S.

    2014-06-15

    Radioactive fission product {sup 131}I released from the Fukushima Daiichi Nuclear Power Plants (FD-NPP) was first detected on March 23, 2011 in an airborne aerosol sample collected at Tokushima, Shikoku Island, located in western Japan. Two other radioactive fission products, {sup 134}Cs and {sup 137}Cs were also observed in a sample collected from April 2 to 4, 2011. The maximum specific radioactivities observed in this work were about 2.5 to 3.5 mBq×m{sup -3} in a airborne aerosol sample collected on April 6. During the course of the continuous monitoring, we also made our first observation of seasonal Asian Dust and those fission products associated with the FDNPP accident concurrently from May 2 to 5, 2011. We found that the specific radioactivities of {sup 134}Cs and {sup 137}Cs decreased drastically only during the period of Asian Dust. And also, it was found that this trend was very similar to the atmospheric elemental concentration (ng×m{sup -3}) variation of stable cesium ({sup 133}Cs) quantified by elemental analyses using our developed ICP-DRC-MS instrument.

  16. Polyatomic molecules under intense femtosecond laser irradiation.

    PubMed

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim V; Jackson, James E; Levine, Benjamin G; Dantus, Marcos

    2014-12-11

    Interaction of intense laser pulses with atoms and molecules is at the forefront of atomic, molecular, and optical physics. It is the gateway to powerful new tools that include above threshold ionization, high harmonic generation, electron diffraction, molecular tomography, and attosecond pulse generation. Intense laser pulses are ideal for probing and manipulating chemical bonding. Though the behavior of atoms in strong fields has been well studied, molecules under intense fields are not as well understood and current models have failed in certain important aspects. Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon excitation. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a "bag of atoms" during field induced ionization. In this article we present a set of experiments and theoretical calculations exploring the behavior of a large collection of aryl alkyl ketones when irradiated with intense femtosecond pulses. Specifically, we consider to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The set of molecules studied is further divided into smaller sets, sorted by type and position of functional groups. The pump-probe time-delay scans show that among positional isomers the variations in relative energies, which amount to only a few hundred millielectronvolts, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). High level ab initio quantum chemical calculations were performed to predict molecular dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose the

  17. Single-Molecule Tracking in Living Cells Using Single Quantum Dot Applications

    PubMed Central

    Baba, Koichi; Nishida, Kohji

    2012-01-01

    Revealing the behavior of single molecules in living cells is very useful for understanding cellular events. Quantum dot probes are particularly promising tools for revealing how biological events occur at the single molecule level both in vitro and in vivo. In this review, we will introduce how single quantum dot applications are used for single molecule tracking. We will discuss how single quantum dot tracking has been used in several examples of complex biological processes, including membrane dynamics, neuronal function, selective transport mechanisms of the nuclear pore complex, and in vivo real-time observation. We also briefly discuss the prospects for single molecule tracking using advanced probes. PMID:22896768

  18. Rotational partition functions for linear molecules

    NASA Astrophysics Data System (ADS)

    McDowell, Robin S.

    1988-01-01

    An accurate closed-form expression for the rotational partition function of linear polyatomic molecules in 1Sigma electronic states is derived, including the effect of nuclear spin (significant at very low temperatures) and of quartic and sextic centrifugal distortion terms (significant at moderate and high temperatures). The proper first-order quantum correction to the classical rigid-rotator partition function is shown to yield Qr = about 1/beta exp beta/3, where beta is defined as hcB / kT and B is the rotational constant in per cm; for beta of 0.2 or greater additional power-series terms in beta are necessary. Comparison between the results of this treatment and exact summations are made for HCN and C2H2 at temperatures from 2 to 5000 K, including separate evaluation of the conributions of nuclear spin and centrifugal distortion.

  19. Efficiency gains in tracer identification for nuclear imaging: can in vivo LC-MS/MS evaluation of small molecules screen for successful PET tracers?

    PubMed

    Joshi, Elizabeth M; Need, Anne; Schaus, John; Chen, Zhaogen; Benesh, Dana; Mitch, Charles; Morton, Stuart; Raub, Thomas J; Phebus, Lee; Barth, Vanessa

    2014-12-17

    Positron emission tomography (PET) imaging has become a useful noninvasive technique to explore molecular biology within living systems; however, the utility of this method is limited by the availability of suitable radiotracers to probe specific targets and disease biology. Methods to identify potential areas of improvement in the ability to predict small molecule performance as tracers prior to radiolabeling would speed the discovery of novel tracers. In this retrospective analysis, we characterized the brain penetration or peak SUV (standardized uptake value), binding potential (BP), and brain exposure kinetics across a series of known, nonradiolabeled PET ligands using in vivo LC-MS/MS (liquid chromatography coupled to mass spectrometry) and correlated these parameters with the reported PET ligand performance in nonhuman primates and humans available in the literature. The PET tracers studied included those reported to label G protein-coupled receptors (GPCRs), intracellular enzymes, and transporters. Additionally, data for each tracer was obtained from a mouse brain uptake assay (MBUA), previously published, where blood-brain barrier (BBB) penetration and clearance parameters were assessed and compared against similar data collected on a broad compound set of central nervous system (CNS) therapeutic compounds. The BP and SUV identified via nonradiolabeled LC-MS/MS, while different from the published values observed in the literature PET tracer data, allowed for an identification of initial criteria values we sought to facilitate increased potential for success from our early discovery screening paradigm. Our analysis showed that successful, as well as novel, clinical PET tracers exhibited BP of greater than 1.5 and peak SUVs greater than approximately 150% at 5 min post dose in rodents. The brain kinetics appeared similar between both techniques despite differences in tracer dose, suggesting linearity across these dose ranges. The assessment of tracers in a

  20. Overview of Non-nuclear Testing of the Safe, Affordable 30-kW Fission Engine, Including End-to-End Demonstrator Testing

    NASA Technical Reports Server (NTRS)

    VanDyke, M. K.; Martin, J. J.; Houts, M. G.

    2003-01-01

    Successful development of space fission systems will require an extensive program of affordable and realistic testing. In addition to tests related to design/development of the fission system, realistic testing of the actual flight unit must also be performed. At the power levels under consideration (3-300 kW electric power), almost all technical issues are thermal or stress related and will not be strongly affected by the radiation environment. These issues can be resolved more thoroughly, less expensively, and in a more timely fashing with nonnuclear testing, provided it is prototypic of the system in question. This approach was used for the safe, affordable fission engine test article development program and accomplished viz cooperative efforts with Department of Energy labs, industry, universiites, and other NASA centers. This Technical Memorandum covers the analysis, testing, and data reduction of a 30-kW simulated reactor as well as an end-to-end demonstrator, including a power conversion system and an electric propulsion engine, the first of its kind in the United States.

  1. Omega-3 fatty acid concentrate from Dunaliella salina possesses anti-inflammatory properties including blockade of NF-κB nuclear translocation.

    PubMed

    Chitranjali, T; Anoop Chandran, P; Muraleedhara Kurup, G

    2015-02-01

    The health benefits of omega-3 polyunsaturated fatty acids (ω-3 PUFA), mainly eicosapentaenoic acid (EPA 20:5) and docosahexaenoic acid (DHA, 22:6), have been long known. Although various studies have demonstrated the health benefits of ω-3 PUFA, the mechanisms of action of ω-3 PUFAs are still not completely understood. While the major commercial source is marine fish oil, in this study we suggest the marine micro algae, Dunaliella salina as an alternate source of omega-3 fatty acids. Treatment with this algal omega-3 fatty acid concentrate (Ds-ω-3 FA) resulted in significant down-regulation of LPS-induced production of TNF-α and IL-6 by peripheral blood mononuclear cells (PBMCs). The concentrate was also found to be a potent blocker of cyclooxygenase (COX-2) and matrix metalloproteinase (MMP-2 and MMP-9) expression. The present study reveals the anti-inflammatory properties of Ds-ω-3 FA concentrate including the inhibition of NF-κB translocation. PMID:25391558

  2. Positron binding to molecules

    NASA Astrophysics Data System (ADS)

    Danielson, J. R.

    2011-05-01

    While there is theoretical evidence that positrons can bind to atoms, calculations for molecules are much less precise. Unfortunately, there have been no measurements of positron-atom binding, due primarily to the difficulty in forming positron-atom bound states in two-body collisions. In contrast, positrons attach to molecules via Feshbach resonances (VFR) in which a vibrational mode absorbs the excess energy. Using a high-resolution positron beam, this VFR process has been studied to measure binding energies for more than 40 molecules. New measurements will be described in two areas: positron binding to relatively simple molecules, for which theoretical calculations appear to be possible; and positron binding to molecules with large permanent dipole moments, which can be compared to analogous, weakly bound electron-molecule (negative-ion) states. Binding energies range from 75 meV for CS2 (no dipole moment) to 180 meV for acetonitrile (CH3CN). Other species studied include aldehydes and ketones, which have permanent dipole moments in the range 2.5 - 3.0 debye. The measured binding energies are surprisingly large (by a factor of 10 to 100) compared to those for the analogous negative ions, and these differences will be discussed. New theoretical calculations for positron-molecule binding are in progress, and a recent result for acetonitrile will be discussed. This ability to compare theory and experiment represents a significant step in attempts to understand positron binding to matter. In collaboration with A. C. L. Jones, J. J. Gosselin, and C. M. Surko, and supported by NSF grant PHY 07-55809.

  3. Positronium ions and molecules

    NASA Technical Reports Server (NTRS)

    Ho, Y. K.

    1990-01-01

    Recent theoretical studies on positronium ions and molecules are discussed. A positronium ion is a three particle system consisting of two electrons in singlet spin state, and a positron. Recent studies include calculations of its binding energy, positron annihilation rate, and investigations of its doubly excited resonant states. A positronium molecule is a four body system consisting of two positrons and two electrons in an overall singlet spin state. The recent calculations of its binding energy against the dissociation into two positronium atoms, and studies of auto-detaching states in positronium molecules are discussed. These auto-dissociating states, which are believed to be part of the Rydberg series as a result of a positron attaching to a negatively charged positronium ion, Ps-, would appear as resonances in Ps-Ps scattering.

  4. Mind Molecules

    PubMed Central

    Snyder, Solomon H.

    2011-01-01

    Scientific styles vary tremendously. For me, research is largely about the unfettered pursuit of novel ideas and experiments that can test multiple ideas in a day, not a year, an approach that I learned from my mentor Julius “Julie” Axelrod. This focus on creative conceptualizations has been my métier since working in the summers during medical school at the National Institutes of Health, during my two years in the Axelrod laboratory, and throughout my forty-five years at Johns Hopkins University School of Medicine. Equally important has been the “high” that emerges from brainstorming with my students. Nothing can compare with the eureka moments when, together, we sense new insights and, better yet, when high-risk, high-payoff experiments succeed. Although I have studied many different questions over the years, a common theme emerges: simple biochemical approaches to understanding molecular messengers, usually small molecules. Equally important has been identifying, purifying, and cloning the messengers' relevant biosynthetic, degradative, or target proteins, at all times seeking potential therapeutic relevance in the form of drugs. In the interests of brevity, this Reflections article is highly selective, and, with a few exceptions, literature citations are only of findings of our laboratory that illustrate notable themes. PMID:21543333

  5. Conditions to obtain precise and true measurements of the intramolecular 13C distribution in organic molecules by isotopic 13C nuclear magnetic resonance spectrometry.

    PubMed

    Bayle, Kevin; Gilbert, Alexis; Julien, Maxime; Yamada, Keita; Silvestre, Virginie; Robins, Richard J; Akoka, Serge; Yoshida, Naohiro; Remaud, Gérald S

    2014-10-10

    Intramolecular (13)C composition gives access to new information on the (bio) synthetic history of a given molecule. Isotopic (13)C NMR spectrometry provides a general tool for measuring the position-specific (13)C content. As an emerging technique, some aspects of its performance are not yet fully delineated. This paper reports on (i) the conditions required to obtain satisfactory trueness and precision for the determination of the internal (13)C distribution, and (ii) an approach to determining the "absolute" position-specific (13)C content. In relation to (i), a precision of <1% can be obtained whatever the molecule on any spectrometer, once quantitative conditions are met, in particular appropriate proton decoupling efficiency. This performance is a prerequisite to the measurement of isotope fractionation either on the transformed or residual compound when a chemical reaction or process is being studied. The study of the trueness has revealed that the response of the spectrometer depends on the (13)C frequency range of the studied molecule, i.e. the chemical shift range. The "absolute value" and, therefore, the trueness of the (13)C NMR measurements has been assessed on acetic acid and by comparison to the results obtained on the fragments from COOH and CH3 by isotopic mass spectrometry coupled to a pyrolysis device (GC-Py-irm-MS), this technique being the reference method for acetic acid. Of the two NMR spectrometers used in this work, one gave values that corresponded to those obtained by GC-Py-irm-MS (thus, the "true" value) while the other showed a bias, which was dependent to the range covered by the resonance frequencies of the molecule. Therefore, the former can be used directly for studying isotope affiliations, while the latter can only be used directly for comparative data, for example in authenticity studies, but can also be used to obtain the true values by applying appropriate correction factors. The present study assesses several key protocol

  6. Irving Langmuir Prize in Chemical Physics Lecture: The Inner Machinery of Single Molecules: resolving the unresolved with the STM

    NASA Astrophysics Data System (ADS)

    Ho, Wilson

    2013-03-01

    The scanning tunneling microscope (STM) is a unique instrument that can probe and induce changes in a molecule with atomic scale resolution. Its operation is based on the current that flows between the tip and the substrate with the molecule sandwiched in between. Therefore, the STM can be used to understand the coupling of electrons to the different states and excitations in the molecule and to investigate the influence on them by its environment. From the spatial and energy dependences of the coupling to the charge, spin, and nuclear motions in the molecule, verification of and new insights into the quantum mechanical properties of molecules can be obtained, including the discovery of new conduction and energy transfer mechanisms. This understanding of electron-molecule interactions with the STM enables rational ways to control chemistry and the exploration of novel physical technologies based on molecules.

  7. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

    NASA Astrophysics Data System (ADS)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

  8. Nuclear weapons and nuclear war

    SciTech Connect

    Cassel, C.; McCally, M.; Abraham, H.

    1984-01-01

    This book examines the potential radiation hazards and environmental impacts of nuclear weapons. Topics considered include medical responsibility and thermonuclear war, the threat of nuclear war, nuclear weaponry, biological effects, radiation injury, decontamination, long-term effects, ecological effects, psychological aspects, the economic implications of nuclear weapons and war, ethics, civil defense, arms control, nuclear winter, and long-term biological consequences of nuclear war.

  9. 34 CFR 303.15 - Include; including.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Include; including. 303.15 Section 303.15 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION EARLY INTERVENTION PROGRAM FOR INFANTS AND TODDLERS...

  10. Analytic Empirical Potentials for BeH^+, BeD^+, and BeT^+ Including up to 4TH Order QED in the Long-Range and Predictions for the Halo Nucleonic Molecules 11BeH^+ and 14BeH^+.

    NASA Astrophysics Data System (ADS)

    Li Chun Fong, Lena C. M.; Lach, Grzegorz; Le Roy, Robert J.; Dattani, Nikesh S.

    2015-06-01

    The 13.81(8)s half-life of the halo nucleonic atom 11Be is orders of magnitude longer than those for any other halo nucleonic atom known, and makes Be-based diatomics the most promising candidates for the formation of the first halo nucleonic molecules. However, the 4e^- species LiH and BeH^+ are some of the first molecules for which the highest accuracy ab initio methods are not accessible, so empirical potential energy functions will be important for making predictions and for benchmarking how ab initio calculations break down at this transition from 3e^- to 4e^-. BeH^+ is also very light, and has one of the most extensive data sets involving a tritium isotopologue, making it a very useful benchmark for studying Born-Oppenheimer breakdown. We therefore seek to determine an empirical analytic potential energy function for BeH^+ that has as much precision as possible. To this end, all available spectroscopic data for all stable isotopologues of BeH^+ are analyzed in a standard direct-potential-fit procedure that uses least-squares fits to optimize the parameters defining an analytic potential. The ``Morse/Long-range'' (MLR) model used for the potential energy function incorporates the inverse-power long-range tail required by theory, and the calculation of the leading long-range coefficients C_4, C_6, C_7, and C_8 include non-adiabatic terms, and up to 4th order QED corrections. As a by-product, we have calculated some fundamental properties of 1e^- systems with unprecedented precision, such as the dipole, quadrupole, octupole, non-adiabatic, and mixed higher order polarizabilities of hydrogen, deuterium, and tritium. We provide good first estimates for the transition energies for the halo nucleonic species 11BeH^+ and 14BeH^+.

  11. Mechanical studies on single molecules: general considerations

    NASA Astrophysics Data System (ADS)

    Bensimon, David; Croquette, Vincent

    2015-10-01

    The following sections are included: * Elements of molecular biology * Advantages and drawbacks of single molecule studies * Order of magnitude of the relevant parameters at the single molecule level * Single molecule manipulation techniques * Comparison of the different techniques * DNA mechanical properties * Conclusion * Bibliography

  12. Quantum transport through aromatic molecules

    SciTech Connect

    Ojeda, J. H.; Rey-González, R. R.; Laroze, D.

    2013-12-07

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices.

  13. Molecules in interstellar clouds

    NASA Astrophysics Data System (ADS)

    Irvine, W. M.; Hjalmarson, A.; Rydbeck, O. E. H.

    The physical conditions and chemical compositions of the gas in interstellar clouds are reviewed in light of the importance of interstellar clouds for star formation and the origin of life. The Orion A region is discussed as an example of a giant molecular cloud where massive stars are being formed, and it is pointed out that conditions in the core of the cloud, with a kinetic temperature of about 75 K and a density of 100,000-1,000,000 molecules/cu cm, may support gas phase ion-molecule chemistry. The Taurus Molecular Clouds are then considered as examples of cold, dark, relatively dense interstellar clouds which may be the birthplaces of solar-type stars and which have been found to contain the heaviest interstellar molecules yet discovered. The molecular species identified in each of these regions are tabulated, including such building blocks of biological monomers as H2O, NH3, H2CO, CO, H2S, CH3CN and H2, and more complex species such as HCOOCH3 and CH3CH2CN.

  14. Epithelial Cell Adhesion Molecule

    PubMed Central

    Trzpis, Monika; McLaughlin, Pamela M.J.; de Leij, Lou M.F.H.; Harmsen, Martin C.

    2007-01-01

    The epithelial cell adhesion molecule (EpCAM, CD326) is a glycoprotein of ∼40 kd that was originally identified as a marker for carcinoma, attributable to its high expression on rapidly proliferating tumors of epithelial origin. Normal epithelia express EpCAM at a variable but generally lower level than carcinoma cells. In early studies, EpCAM was proposed to be a cell-cell adhesion molecule. However, recent insights revealed a more versatile role for EpCAM that is not limited only to cell adhesion but includes diverse processes such as signaling, cell migration, proliferation, and differentiation. Cell surface expression of EpCAM may actually prevent cell-cell adhesion. Here, we provide a comprehensive review of the current knowledge on EpCAM biology in relation to other cell adhesion molecules. We discuss the implications of the newly identified functions of EpCAM in view of its prognostic relevance in carcinoma, inflammatory pathophysiology, and tissue development and regeneration as well as its role in normal epithelial homeostasis. PMID:17600130

  15. Single Molecule Transcription Elongation

    PubMed Central

    Galburt, Eric A.; Grill, Stephan W.; Bustamante, Carlos

    2009-01-01

    Single molecule optical trapping assays have now been applied to a great number of macromolecular systems including DNA, RNA, cargo motors, restriction enzymes, DNA helicases, chromosome remodelers, DNA polymerases and both viral and bacterial RNA polymerases. The advantages of the technique are the ability to observe dynamic, unsynchronized molecular processes, to determine the distributions of experimental quantities and to apply force to the system while monitoring the response over time. Here, we describe the application of these powerful techniques to study the dynamics of transcription elongation by RNA polymerase II from Saccharomyces cerevisiae. PMID:19426807

  16. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  17. Intelligent distributed control for nuclear power plants. Final (third annual) technical progress report, September 1991--June 1993 (September 1989--June 1993): Includes no-cost extension period from September 1992--June 1993

    SciTech Connect

    Klevans, E.H.

    1993-12-31

    This project was initiated in September 1989 as a three year project to develop and demonstrate Intelligent Distributed Control (IDC) for Nuclear Power Plants. There were two primary goals of this research project. The first goal was to combine diagnostics and control to achieve a highly automated power plant as described by M.A. Schultz. The second goal was to apply this research to develop a prototype demonstration on an actual power plant system, the EBR-2 steam plant. Described in this Final (Third Annual) Technical Progress Report is the accomplishment of the project`s final milestone, an in-plant intelligent control experiment conducted on April 1, 1993. The development of the experiment included: simulation validation, experiment formulation and final programming, procedure development and approval, and experimental results. Other third year developments summarized in this report are: (1) a theoretical foundation for Reconfigurable Hybrid Supervisory Control, (2) a steam plant diagnostic system, (3) control console design tools and (4) other advanced and intelligent control.

  18. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  19. Small GTPase Rho signaling is involved in {beta}1 integrin-mediated up-regulation of intercellular adhesion molecule 1 and receptor activator of nuclear factor {kappa}B ligand on osteoblasts and osteoclast maturation

    SciTech Connect

    Hirai, Fumihiko; Nakayamada, Shingo; Okada, Yosuke; Saito, Kazuyoshi; Kurose, Hitoshi; Mogami, Akira; Tanaka, Yoshiya . E-mail: tanaka@med.uoeh-u.ac.jp

    2007-04-27

    We assessed the characteristics of human osteoblasts, focusing on small GTPase Rho signaling. {beta}1 Integrin were highly expressed on osteoblasts. Engagement of {beta}1 integrins by type I collagen augmented expression of intercellular adhesion molecule 1 (ICAM-1) and receptor activator of nuclear factor {kappa}B ligand (RANKL) on osteoblasts. Rho was activated by {beta}1 stimulation in osteoblasts. {beta}1 Integrin-induced up-regulation of ICAM-1 and RANKL was inhibited by transfection with adenoviruses encoding C3 transferase or pretreated with Y-27632, specific Rho and Rho-kinase inhibitors. Engagement of {beta}1 integrin on osteoblasts induced formation of tartrate-resistant acid phosphatase (TRAP)-positive multinuclear cells (MNC) in a coculture system of osteoblasts and peripheral monocytes, but this action was completely abrogated by transfection of C3 transferase. Our results indicate the direct involvement of Rho-mediated signaling in {beta}1 integrin-induced up-regulation of ICAM-1 and RANKL and RANKL-dependent osteoclast maturation. Thus, Rho-mediated signaling in osteoblasts seems to introduce major biases to bone resorption.

  20. Hexapole-Oriented Molecule Beams Scattered by Single Crystal Surfaces.

    NASA Astrophysics Data System (ADS)

    Curtiss, Thomas J.

    A newly constructed machine capable of producing beams of spatially oriented molecules is described in detail. Beam molecules are focused and state-selected by a 2.85 m electrostatic hexapole. The machine consists of seven differentially pumped chambers with an overall length from nozzle to final collimator in the surface scattering configuration of 3.78 m. For symmetric top molecules pure (>95%) {mid}JKM> rotational state selection has been achieved. The distribution of orientations among CH_3I beam molecules has been quantitatively measured using the photodissociation/multiphoton ionization time of flight technique. Results accord with simulated ion time of flight distributions using theoretical orientational probability distribution functions which include the nuclear hyperfine interaction. Oriented molecule beams of seven different molecules have been scattered by a graphite (0001) surface. The results show a large diversity in the sign and magnitude of the steric effects (i.e., "heads" vs. "tails"). The steric effects have been quantitatively measured, and have been analyzed in terms of a two component model: a trapping/desorption component and a direct scattering component. Analysis of the scattered angular distribution data yields estimates for the anisotropy of the trapping probability (e.g., for CHF_3 there is 25% higher trapping probability when the H "end" of the molecule is incident on the graphite surface than for the F_3 "end"). The magnitude of the steric effect is found to be a linear function of the degree of orientation of the beam molecules for all systems studied. Over the limited range of the present data, the steric effect increases with incident kinetic energy. A null steric effect result was observed for the scattering of oriented CH_3Cl by a W(110) surface. However, the initial sticking probability for randomly oriented CH_3Cl was measured to be unity. It is not surprising that there is no observable steric effect in the scattering of CH _3

  1. Nuclear Scans

    MedlinePlus

    Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...

  2. Spin tunneling in magnetic molecules

    NASA Astrophysics Data System (ADS)

    Kececioglu, Ersin

    In this thesis, we will focus on spin tunneling in a family of systems called magnetic molecules such as Fe8 and Mn12. This is comparatively new, in relation to other tunneling problems. Many issues are not completely solved and/or understood yet. The magnetic molecule Fe 8 has been observed to have a rich pattern of degeneracies in its magnetic spectrum. We focus on these degeneracies from several points of view. We start with the simplest anisotropy Hamiltonian to describe the Fe 8 molecule and extend our discussion to include higher order anisotropy terms. We give analytical expressions as much as we can, for the degeneracies in the semi-classical limit in both cases. We reintroduce jump instantons to the instanton formalism. Finally, we discuss the effect of the environment on the molecule. Our results, for all different models and techniques, agree well with both experimental and numerical results.

  3. Leucocyte cellular adhesion molecules.

    PubMed

    Yong, K; Khwaja, A

    1990-12-01

    Leucocytes express adhesion promoting receptors which mediate cell-cell and cell-matrix interactions. These adhesive interactions are crucial to the regulation of haemopoiesis and thymocyte maturation, the direction and control of leucocyte traffic and migration through tissues, and in the development of immune and non-immune inflammatory responses. Several families of adhesion receptors have been identified (Table). The leucocyte integrin family comprises 3 alpha beta heterodimeric membrane glycoproteins which share a common beta subunit, designated CD18. The alpha subunits of each of the 3 members, lymphocyte function associated antigen-1 (LFA-1), macrophage antigen-1 (Mac-1) and p150,95 are designated CD11a, b and c respectively. These adhesion molecules play a critical part in the immune and inflammatory responses of leucocytes. The leucocyte integrin family is, in turn, part of the integrin superfamily, members of which are evolutionally, structurally and functionally related. Another Integrin subfamily found on leucocytes is the VLA group, so-called because the 'very late activation antigens' VLA-1 and VLA-2 were originally found to appear late in T-cell activation. Members of this family function mainly as extracellular matrix adhesion receptors and are found both on haemopoietic and non-haemopoietic cells. They play a part in diverse cellular functions including tissue organisation, lymphocyte recirculation and T-cell immune responses. A third integrin subfamily, the cytoadhesins, are receptors on platelets and endothelial cells which bind extracellular matrix proteins. A second family of adhesion receptors is the immunoglobulin superfamily, members of which include CD2, LFA-3 and ICAM-1, which participate in T-cell adhesive interactions, and the antigen-specific receptors of T and B cells, CD4, CD8 and the MHC Class I and II molecules. A recently recognised family of adhesion receptors is the selectins, characterised by a common lectin domain. Leucocyte

  4. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  5. Mechanistic Control of Carcinoembryonic Antigen-related Cell Adhesion Molecule-1 (CEACAM1) Splice Isoforms by the Heterogeneous Nuclear Ribonuclear Proteins hnRNP L, hnRNP A1, and hnRNP M*

    PubMed Central

    Dery, Kenneth J.; Gaur, Shikha; Gencheva, Marieta; Yen, Yun; Shively, John E.; Gaur, Rajesh K.

    2011-01-01

    Carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) is expressed in a variety of cell types and is implicated in carcinogenesis. Alternative splicing of CEACAM1 pre-mRNA generates two cytoplasmic domain splice variants characterized by the inclusion (L-isoform) or exclusion (S-isoform) of exon 7. Here we show that the alternative splicing of CEACAM1 pre-mRNA is regulated by novel cis elements residing in exon 7. We report the presence of three exon regulatory elements that lead to the inclusion or exclusion of exon 7 CEACAM1 mRNA in ZR75 breast cancer cells. Heterologous splicing reporter assays demonstrated that the maintenance of authentic alternative splicing mechanisms were independent of the CEACAM1 intron sequence context. We show that forced expression of these exon regulatory elements could alter CEACAM1 splicing in HEK-293 cells. Using RNA affinity chromatography, three members of the heterogeneous nuclear ribonucleoprotein family (hnRNP L, hnRNP A1, and hnRNP M) were identified. RNA immunoprecipitation of hnRNP L and hnRNP A1 revealed a binding motif located central and 3′ to exon 7, respectively. Depletion of hnRNP A1 or L by RNAi in HEK-293 cells promoted exon 7 inclusion, whereas overexpression led to exclusion of the variable exon. By contrast, overexpression of hnRNP M showed exon 7 inclusion and production of CEACAM1-L mRNA. Finally, stress-induced cytoplasmic accumulation of hnRNP A1 in MDA-MB-468 cells dynamically alters the CEACAM1-S:CEACAM1:L ratio in favor of the l-isoform. Thus, we have elucidated the molecular factors that control the mechanism of splice-site recognition in the alternative splicing regulation of CEACAM1. PMID:21398516

  6. Nuclear Fuels.

    ERIC Educational Resources Information Center

    Nash, J. Thomas

    1983-01-01

    Trends in and factors related to the nuclear industry and nuclear fuel production are discussed. Topics addressed include nuclear reactors, survival of the U.S. uranium industry, production costs, budget cuts by the Department of Energy and U.S. Geological survey for resource studies, mining, and research/development activities. (JN)

  7. Molecules in the Spotlight

    SciTech Connect

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  8. Emerging small molecule drugs.

    PubMed

    Colin, Sophie; Chinetti-Gbaguidi, Giulia; Kuivenhoven, Jan A; Staels, Bart

    2015-01-01

    Dyslipidaemia is a major risk factor for cardiovascular diseases. Pharmacological lowering of LDL-C levels using statins reduces cardiovascular risk. However, a substantial residual risk persists especially in patients with type 2 diabetes mellitus. Because of the inverse association observed in epidemiological studies of HDL-C with the risk for cardiovascular diseases, novel therapeutic strategies to raise HDL-C levels or improve HDL functionality are developed as complementary therapy for cardiovascular diseases. However, until now most therapies targeting HDL-C levels failed in clinical trials because of side effects or absence of clinical benefits. This chapter will highlight the emerging small molecules currently developed and tested in clinical trials to pharmacologically modulate HDL-C and functionality including new CETP inhibitors (anacetrapib, evacetrapib), novel PPAR agonists (K-877, CER-002, DSP-8658, INT131 and GFT505), LXR agonists (ATI-111, LXR-623, XL-652) and RVX-208. PMID:25523004

  9. Monitoring Molecules: Insights and Progress

    PubMed Central

    2015-01-01

    In August, 2014, neuroscientists and physical scientists gathered together on the campus of the University of California, Los Angeles to discuss how to monitor molecules in neuroscience. This field has seen significant growth since its inception in the 1970s. Here, the advances in this field are documented, including its advance into understanding the actions that specific neurotransmitters mediate during behavior. PMID:25514501

  10. Introduction to nucleocytoplasmic transport: molecules and mechanisms.

    PubMed

    Peters, Reiner

    2006-01-01

    Nucleocytoplasmic transport, the exchange of matter between nucleus and cytoplasm, plays a fundamental role in human and other eukaryotic cells, affecting almost every aspect of health and disease. The only gate for the transport of small and large molecules as well as supramolecular complexes between nucleus and cytoplasm is the nuclear pore complex (NPC). The NPC is not a normal membrane transport protein (transporter). Composed of 500 to 1000 peptide chains, the NPC features a mysterious functional duality. For most molecules, it constitutes a molecular sieve with a blurred cutoff at approx 10 nm, but for molecules binding to phenylalanine-glycine (FG) motifs, the NPC appears to be a channel of approx 50 nm diameter, permitting bidirectional translocation at high speed. To achieve this, the NPC cooperates with soluble factors, the nuclear transport receptors, which shuttle between nuclear contents and cytoplasm. Here, we provide a short introduction to nucleocytoplasmic transport by describing first the structure and composition of the nuclear pore complex. Then, mechanisms of nucleocytoplasmic transport are discussed. Finally, the still essentially unresolved mechanisms by which nuclear transport receptors and transport complexes are translocated through the nuclear pore complex are considered, and a novel translocation model is suggested. PMID:16739728

  11. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

    NASA Astrophysics Data System (ADS)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

  12. Combining single-molecule manipulation and single-molecule detection.

    PubMed

    Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

    2014-10-01

    Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. PMID:25255052

  13. Nuclear power: Fourth edition

    SciTech Connect

    Deutsch, R.W.

    1986-01-01

    This book describes the basics of nuclear power generation, explaining both the benefits and the real and imagined risks of nuclear power. It includes a discussion of the Three Mile Island accident and its effects. Nuclear Power has been used in the public information programs of more than 100 utilities. The contents discussed are: Nuclear Power and People; Why Nuclear Power. Electricity produced by coal; Electricity produced by nuclear fuel; Nuclear plant sites in the United States; Short History of Commercial Nuclear Power; U.S. nuclear submarines, Regulation of Nuclear Power Plants; Licensing process, Nuclear Power Plant Operator Training; Nuclear power plant simulator, Are Nuclear Plants Safe.; Containment structure, Nuclear Power Plant Insurance; Is Radiation Dangerous.; Man-made radiation, What is Nuclear Fuel.; Fuel cycle for commercial nuclear power plants; Warm Water Discharge; Cooling tower; Protection of Radioactive Materials; Plutonium and Proliferation; Disposal of Radioactive Wastes; Are Alternate Energy Sources Available.; Nuclear Opposition; and Nuclear Power in the Future.

  14. Dipolar molecules in optical lattices.

    PubMed

    Sowiński, Tomasz; Dutta, Omjyoti; Hauke, Philipp; Tagliacozzo, Luca; Lewenstein, Maciej

    2012-03-16

    We study the extended Bose-Hubbard model describing an ultracold gas of dipolar molecules in an optical lattice, taking into account all on-site and nearest-neighbor interactions, including occupation-dependent tunneling and pair tunneling terms. Using exact diagonalization and the multiscale entanglement renormalization ansatz, we show that these terms can destroy insulating phases and lead to novel quantum phases. These considerable changes of the phase diagram have to be taken into account in upcoming experiments with dipolar molecules. PMID:22540482

  15. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  16. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  17. Pump apparatus including deconsolidator

    DOEpatents

    Sonwane, Chandrashekhar; Saunders, Timothy; Fitzsimmons, Mark Andrew

    2014-10-07

    A pump apparatus includes a particulate pump that defines a passage that extends from an inlet to an outlet. A duct is in flow communication with the outlet. The duct includes a deconsolidator configured to fragment particle agglomerates received from the passage.

  18. Development of novel small molecules for imaging and drug release

    NASA Astrophysics Data System (ADS)

    Cao, Yanting

    Small organic molecules, including small molecule based fluorescent probes, small molecule based drugs or prodrugs, and smart multifunctional fluorescent drug delivery systems play important roles in biological research, drug discovery, and clinical practices. Despite the significant progress made in these fields, the development of novel and diverse small molecules is needed to meet various demands for research and clinical applications. My Ph.D study focuses on the development of novel functional molecules for recognition, imaging and drug release. In the first part, a turn-on fluorescent probe is developed for the detection of intracellular adenosine-5'-triphosphate (ATP) levels based on multiplexing recognitions. Considering the unique and complicated structure of ATP molecules, a fluorescent probe has been implemented with improved sensitivity and selectivity due to two synergistic binding recognitions by incorporating of 2, 2'-dipicolylamine (Dpa)-Zn(II) for targeting of phospho anions and phenylboronic acid group for cis-diol moiety. The novel probe is able to detect intracellular ATP levels in SH-SY5Y cells. Meanwhile, the advantages of multiplexing recognition design concept have been demonstrated using two control molecules. In the second part, a prodrug system is developed to deliver multiple drugs within one small molecule entity. The prodrug is designed by using 1-(2-nitrophenyl)ethyl (NPE) as phototrigger, and biphenol biquaternary ammonium as the prodrug. With controlled photo activation, both DNA cross-linking agents mechlorethamine and o-quinone methide are delivered and released at the preferred site, leading to efficient DNA cross-links formation and cell death. The prodrug shows negligible cytotoxicity towards normal skin cells (Hekn cells) with and without UV activation, but displays potent activity towards cancer cells (HeLa cells) upon UV activation. The multiple drug release system may hold a great potential for practical application. In the

  19. Guidance molecules in lung cancer

    PubMed Central

    Nasarre, Patrick; Potiron, Vincent; Drabkin, Harry

    2010-01-01

    Guidance molecules were first described in the nervous system to control axon outgrowth direction. They are also widely expressed outside the nervous system where they control cell migration, tissue development and establishment of the vascular network. In addition, they are involved in cancer development, tumor angiogenesis and metastasis. This review is primarily focused on their functions in lung cancer and their involvement in lung development is also presented. Five guidance molecule families and their corresponding receptors are described, including the semaphorins/neuropilins/plexins, ephrins and Eph receptors, netrin/DCC/UNC5, Slit/Robo and Notch/Delta. In addition, the possibility to target these molecules as a therapeutic approach in cancer is discussed. PMID:20139699

  20. Uranium-mediated activation of small molecules.

    PubMed

    Arnold, Polly L

    2011-08-28

    Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power. PMID:21614341

  1. Electron Collisions with Large Molecules

    NASA Astrophysics Data System (ADS)

    McKoy, Vincent

    2006-10-01

    In recent years, interest in electron-molecule collisions has increasingly shifted to large molecules. Applications within the semiconductor industry, for example, require electron collision data for molecules such as perfluorocyclobutane, while almost all biological applications involve macromolecules such as DNA. A significant development in recent years has been the realization that slow electrons can directly damage DNA. This discovery has spurred studies of low-energy collisions with the constituents of DNA, including the bases, deoxyribose, the phosphate, and larger moieties assembled from them. In semiconductor applications, a key goal is development of electron cross section sets for plasma chemistry modeling, while biological studies are largely focused on understanding the role of localized resonances in inducing DNA strand breaks. Accurate calculations of low-energy electron collisions with polyatomic molecules are computationally demanding because of the low symmetry and inherent many-electron nature of the problem; moreover, the computational requirements scale rapidly with the size of the molecule. To pursue such studies, we have adapted our computational procedure, known as the Schwinger multichannel method, to run efficiently on highly parallel computers. In this talk, we will present some of our recent results for fluorocarbon etchants used in the semiconductor industry and for constituents of DNA and RNA. In collaboration with Carl Winstead, California Institute of Technology.

  2. Spectroscopic modeling of water molecule

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.

    2013-12-01

    This research is devoted to the vibrational spectroscopy inverse problem solution that gives a possibility to design a molecule and make conclusions about its geometry. The valence angle finding based on the usage of inverse spectral vibrational spectroscopy problem is a well-known task. 3N-matrix method was chosen to solve the proposed task. The usage of this method permits to make no assumptions about the molecule force field, besides it can be applied to molecules of matter in liquid state. Anharmonicity constants assessment is an important part of the valence angle finding. The reduction to zero vibrations is necessary because used matrix analytical expression were found in the harmonic approach. In order to find the single-valued inverse spectral problem of vibrational spectroscopy solution a shape parameter characterizing "mixing" of ω1 and ω2 vibrations forms must be found. The minimum of such a function Υ called a divergence parameter was found. This function characterizes method's accuracy. The valence angle assessment was reduced to the divergence parameter minimization. The β value concerning divergence parameter minimum was interpreted as the desired valence angle. The proposed method was applied for water molecule in liquid state: β = (88,8 ±1,7)° . The found angle fits the water molecule nearest surrounding tetrahedral model including hydrogen bond curvature in the first approximation.

  3. Optical modulator including grapene

    DOEpatents

    Liu, Ming; Yin, Xiaobo; Zhang, Xiang

    2016-06-07

    The present invention provides for a one or more layer graphene optical modulator. In a first exemplary embodiment the optical modulator includes an optical waveguide, a nanoscale oxide spacer adjacent to a working region of the waveguide, and a monolayer graphene sheet adjacent to the spacer. In a second exemplary embodiment, the optical modulator includes at least one pair of active media, where the pair includes an oxide spacer, a first monolayer graphene sheet adjacent to a first side of the spacer, and a second monolayer graphene sheet adjacent to a second side of the spacer, and at least one optical waveguide adjacent to the pair.

  4. Many-body physics of ultracold doublet sigma molecules in optical lattices

    NASA Astrophysics Data System (ADS)

    Shchedrin, Gavriil; Jaschke, Daniel; Han, Wei; Carr, Lincoln D.; Green, Dermot G.; Aldegunde, Jesus; Hutson, Jeremy M.

    2016-05-01

    The creation of ultracold polar molecules provides a unique opportunity to discover and explore new regimes in strongly interacting many-body quantum systems. Polar molecules have strong long-range dipole-dipole interactions that allow one to realize exotic phenomena such as topological phases and quantum magnetism. We explore quantum many-body systems formed by molecules in doublet sigma (2 Σ) states, with both electric dipole moments and electron spin S = 1 / 2 , but without electronic orbital momentum. The Hamiltonian for doublet sigma molecules includes molecular rotation terms, spin-rotation interaction, hyperfine terms including both spin-spin and nuclear electric quadrupole interactions, and molecular dipole-dipole interactions. The complete control of the molecular quantum states can be accomplished by applying electric and magnetic fields to molecules trapped in optical lattices. We provide the complete theoretical treatment for experimentally relevant doublet sigma molecules such as SrF and CaF and discuss the associated single-body and many-body physics. Funded by AFOSR and NSF.

  5. Small Molecule based Musculoskeletal Regenerative Engineering

    PubMed Central

    Lo, Kevin W.-H.; Jiang, Tao; Gagnon, Keith A.; Nelson, Clarke; Laurencin, Cato T.

    2014-01-01

    Clinicians and scientists working in the field of regenerative engineering are actively investigating a wide range of methods to promote musculoskeletal tissue regeneration. Small molecule-mediated tissue regeneration is emerging as a promising strategy for regenerating various musculoskeletal tissues and a large number of small molecule compounds have been recently discovered as potential bioactive molecules for musculoskeletal tissue repair and regeneration. In this review, we summarize the recent literature encompassing the past four years in the area of small bioactive molecule for promoting repair and regeneration of various musculoskeletal tissues including bone, muscle, cartilage, tendon, and nerve. PMID:24405851

  6. Giant molecules composed of polar molecules and atoms in mixed dimensions

    NASA Astrophysics Data System (ADS)

    Qi, Ran; Tan, Shina

    2014-05-01

    Two or three polar molecules, confined to one or two dimensions, can form stable bound states with a single atom living in three dimensions, if the molecule and the atom can interact resonantly such that their mixed dimensional scattering length is large. We call these bound states ``giant molecules'' since it's a molecule composed of smaller molecules and atoms. We study their properties using techniques including exact numerical solution, exact qunatum diffusion Monte Carlo (QMC), Born-Oppenheimer approximation (BOA), and semiclassical approximation. These bound states have a hierarchical structure reminiscent of the celestial systems.

  7. Adhesion molecules and receptors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adhesion molecules are necessary for leukocyte trafficking and differentiation. They serve to initiate cell-cell interactions under conditions of shear, and they sustain the cell-cell and cell-matrix interactions needed for cellular locomotion. They also can serve directly as signaling molecules act...

  8. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  9. Single-molecule junctions beyond electronic transport

    NASA Astrophysics Data System (ADS)

    Aradhya, Sriharsha V.; Venkataraman, Latha

    2013-06-01

    The idea of using individual molecules as active electronic components provided the impetus to develop a variety of experimental platforms to probe their electronic transport properties. Among these, single-molecule junctions in a metal-molecule-metal motif have contributed significantly to our fundamental understanding of the principles required to realize molecular-scale electronic components from resistive wires to reversible switches. The success of these techniques and the growing interest of other disciplines in single-molecule-level characterization are prompting new approaches to investigate metal-molecule-metal junctions with multiple probes. Going beyond electronic transport characterization, these new studies are highlighting both the fundamental and applied aspects of mechanical, optical and thermoelectric properties at the atomic and molecular scales. Furthermore, experimental demonstrations of quantum interference and manipulation of electronic and nuclear spins in single-molecule circuits are heralding new device concepts with no classical analogues. In this Review, we present the emerging methods being used to interrogate multiple properties in single molecule-based devices, detail how these measurements have advanced our understanding of the structure-function relationships in molecular junctions, and discuss the potential for future research and applications.

  10. Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions

    PubMed Central

    Bidlingmaier, Scott; Liu, Bin

    2016-01-01

    The identification of proteins that interact with small bioactive molecules is a critical but often difficult and time-consuming step in understanding cellular signaling pathways or molecular mechanisms of drug action. Numerous methods for identifying small molecule-interacting proteins have been developed and utilized, including affinity-based purification followed by mass spectrometry analysis, protein microarrays, phage display, and three-hybrid approaches. Although all these methods have been used successfully, there remains a need for additional techniques for analyzing small molecule-protein interactions. A promising method for identifying small molecule-protein interactions is affinity-based selection of yeast surface-displayed human proteome libraries. Large and diverse libraries displaying human protein fragments on the surface of yeast cells have been constructed and subjected to FACS-based enrichment followed by comprehensive exon microarray-based output analysis to identify protein fragments with affinity for small molecule ligands. In a recent example, a proteome-wide search has been successfully carried out to identify cellular proteins binding to the signaling lipids PtdIns(4,5)P2 and PtdIns(3,4,5)P3. Known phosphatidylinositide-binding proteins such as pleckstrin homology domains were identified, as well as many novel interactions. Intriguingly, many novel nuclear phosphatidylinositide-binding proteins were discovered. Although the existence of an independent pool of nuclear phosphatidylinositides has been known about for some time, their functions and mechanism of action remain obscure. Thus, the identification and subsequent study of nuclear phosphatidylinositide-binding proteins is expected to bring new insights to this important biological question. Based on the success with phosphatidylinositides, it is expected that the screening of yeast surface-displayed human proteome libraries will be of general use for the discovery of novel small

  11. Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions.

    PubMed

    Bidlingmaier, Scott; Liu, Bin

    2015-01-01

    The identification of proteins that interact with small bioactive molecules is a critical but often difficult and time-consuming step in understanding cellular signaling pathways or molecular mechanisms of drug action. Numerous methods for identifying small molecule-interacting proteins have been developed and utilized, including affinity-based purification followed by mass spectrometry analysis, protein microarrays, phage display, and three-hybrid approaches. Although all these methods have been used successfully, there remains a need for additional techniques for analyzing small molecule-protein interactions. A promising method for identifying small molecule-protein interactions is affinity-based selection of yeast surface-displayed human proteome libraries. Large and diverse libraries displaying human protein fragments on the surface of yeast cells have been constructed and subjected to FACS-based enrichment followed by comprehensive exon microarray-based output analysis to identify protein fragments with affinity for small molecule ligands. In a recent example, a proteome-wide search has been successfully carried out to identify cellular proteins binding to the signaling lipids PtdIns(4,5)P2 and PtdIns(3,4,5)P3. Known phosphatidylinositide-binding proteins such as pleckstrin homology domains were identified, as well as many novel interactions. Intriguingly, many novel nuclear phosphatidylinositide-binding proteins were discovered. Although the existence of an independent pool of nuclear phosphatidylinositides has been known about for some time, their functions and mechanism of action remain obscure. Thus, the identification and subsequent study of nuclear phosphatidylinositide-binding proteins is expected to bring new insights to this important biological question. Based on the success with phosphatidylinositides, it is expected that the screening of yeast surface-displayed human proteome libraries will be of general use for the discovery of novel small

  12. Electron attachment to the SF{sub 6} molecule

    SciTech Connect

    Smirnov, B. M. Kosarim, A. V.

    2015-09-15

    Various models for transition between electron and nuclear subsystems are compared in the case of electron attachment to the SF{sub 6} molecule. Experimental data, including the cross section of electron attachment to this molecule as a function of the electron energy and vibrational temperature, the rate constants of this process in swarm experiments, and the rates of the chemionization process involving Rydberg atoms and the SF{sub 6} molecule, are collected and treated. Based on the data and on the resonant character of electron capture into an autodetachment ion state in accordance with the Breit–Wigner formula, we find that intersection of the molecule and negative ion electron terms proceeds above the potential well bottom of the molecule with the barrier height 0.05–0.1 eV, and the transition between these electron terms has both the tunnel and abovebarrier character. The limit of small electron energies e for the electron attachment cross section at room vibrational temperature takes place at ε ≪ 2 meV, while in the range 2 meV ≪ ε ≪ 80 meV, the cross section is inversely proportional to ε. In considering the attachment process as a result of the interaction between the electron and vibrational degrees of freedom, we find the coupling factor f between them to be f = aT at low vibrational temperatures T with a ≈ 3 × 10{sup −4} K{sup −1}. The coupling factor is independent of the temperature at T > 400 K.

  13. Single molecule tracking

    DOEpatents

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  14. Single molecule tracking

    DOEpatents

    Shera, E.B.

    1987-10-07

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

  15. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  16. Kaposi's Sarcoma-Associated Herpesvirus Latency-Associated Nuclear Antigen and Angiogenin Interact with Common Host Proteins, Including Annexin A2, Which Is Essential for Survival of Latently Infected Cells

    PubMed Central

    Paudel, Nitika; Sadagopan, Sathish; Balasubramanian, Sandhya

    2012-01-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) infection and latency-associated nuclear antigen (LANA-1) upregulate the multifunctional protein angiogenin (ANG). Our studies demonstrate that silencing ANG or inhibiting its nuclear translocation downregulates KSHV LANA-1 expression and ANG is necessary for KSHV latency, anti-apoptosis and angiogenesis (Sadagopan et al., J. Virol. 83:3342–3364, 2009; Sadagopan et al., J Virol. 85:2666–2685, 2011). Here we show that LANA-1 interacts with ANG and colocalizes in latently infected endothelial telomerase-immortalized human umbilical vein endothelial (TIVE-LTC) cells. Mass spectrometric analyses of TIVE-LTC proteins immunoprecipitated by anti-LANA-1 and ANG antibodies identified 28 common cellular proteins such as ribosomal proteins, structural proteins, tRNA synthetases, metabolic pathway enzymes, chaperons, transcription factors, antioxidants, and ubiquitin proteosome proteins. LANA-1 and ANG interaction with one of the proteins, annexin A2, was validated. Annexin A2 has been shown to play roles in cell proliferation, apoptosis, plasmin generation, exocytosis, endocytosis, and cytoskeleton reorganization. It is also known to associate with glycolytic enzyme 3-phosphoglyceratekinase in the primer recognition protein (PRP) complex that interacts with DNA polymerase α in the lagging strand of DNA during replication. A higher level of annexin A2 is expressed in KSHV+ but not in Epstein-Barr virus (EBV)+ B-lymphoma cell lines. Annexin A2 colocalized with several LANA-1 punctate spots in KSHV+ body cavity B-cell lymphoma (BCBL-1) cells. In triple-staining analyses, we observed annexin A2-ANG-LANA-1, annexin A2-ANG, and ANG-LANA-1 colocalizations. Annexin A2 appeared as punctate nuclear dots in LANA-1-positive TIVE-LTC cells. In LANA-1-negative TIVE-LTC cells, annexin A2 was detected predominately in the cytoplasm, with some nuclear spots, and colocalization with ANG was observed mostly in the cytoplasm. Annexin A2

  17. Core-mass nonadiabatic corrections to molecules: H2, H2+, and isotopologues.

    PubMed

    Diniz, Leonardo G; Alijah, Alexander; Mohallem, José Rachid

    2012-10-28

    For high-precision calculations of rovibrational states of light molecules, it is essential to include non-adiabatic corrections. In the absence of crossings of potential energy surfaces, they can be incorporated in a single surface picture through coordinate-dependent vibrational and rotational reduced masses. We present a compact method for their evaluation and relate in particular the vibrational mass to a well defined nuclear core mass derived from a Mulliken analysis of the electronic density. For the rotational mass we propose a simple, but very effective parametrization. The use of these masses in the nuclear Schrödinger equation yields numerical data for the corrections of a much higher quality than can be obtained with optimized constant masses, typically better than 0.1 cm(-1). We demonstrate the method for H(2), H(2)(+), and singly deuterated isotopologues. Isotopic asymmetry does not present any particular difficulty. Generalization to polyatomic molecules is straightforward. PMID:23126719

  18. Engineering crystals of dendritic molecules.

    PubMed

    Lukin, Oleg; Schubert, Dirk; Müller, Claudia M; Schweizer, W Bernd; Gramlich, Volker; Schneider, Julian; Dolgonos, Grygoriy; Shivanyuk, Alexander

    2009-07-01

    A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. PMID:19549870

  19. Engineering crystals of dendritic molecules

    PubMed Central

    Lukin, Oleg; Schubert, Dirk; Müller, Claudia M.; Schweizer, W. Bernd; Gramlich, Volker; Schneider, Julian; Dolgonos, Grygoriy; Shivanyuk, Alexander

    2009-01-01

    A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. PMID:19549870

  20. Ultracold polar KRb molecules

    NASA Astrophysics Data System (ADS)

    Neyenhuis, Brian; Chotia, Amodsen; Moses, Steven; Ye, Jun; Jin, Deborah

    2011-05-01

    Ultracold polar molecules in the quantum degenerate regime open the possibility of realizing quantum gases with long-range, and spatially anisotropic, interparticle interactions. Currently, we can create a gas of ultracold fermionic ground-state KRb molecules in with a peak density of 1012 cm-3 and a temperature just 1.4 times the Fermi temperature. We will report on efforts to further cool this gas of molecules. One possibility is to evaporatively cool a spin-polarized molecular Fermi gas confined in quasi-2D, where we would rely on dipole-dipole interactions for rethermalization. We acknowledge funding from NIST, NSF, and AFOSR-MURI.

  1. Poisson's spot with molecules

    SciTech Connect

    Reisinger, Thomas; Holst, Bodil; Patel, Amil A.; Smith, Henry I.; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo

    2009-05-15

    In the Poisson-spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. In this paper we report the observation of Poisson's spot using a beam of neutral deuterium molecules. The wavelength independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson's spot a promising candidate for applications ranging from the study of large molecule diffraction to patterning with molecules.

  2. Poisson's spot with molecules

    NASA Astrophysics Data System (ADS)

    Reisinger, Thomas; Patel, Amil A.; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo; Smith, Henry I.; Holst, Bodil

    2009-05-01

    In the Poisson-spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. In this paper we report the observation of Poisson’s spot using a beam of neutral deuterium molecules. The wavelength independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson’s spot a promising candidate for applications ranging from the study of large molecule diffraction to patterning with molecules.

  3. Laser Spectroscopy of Atoms and Molecules.

    ERIC Educational Resources Information Center

    Schawlow, Arthur L.

    1978-01-01

    Surveys new laser techniques and a variety of spectroscopic experiments that can be used to detect, measure and study very small numbers of atoms on molecules. The range of applicability of these techniques is also included. (HM)

  4. Nuclear war: Opposing viewpoints

    SciTech Connect

    Szumski, B.

    1985-01-01

    This book presents opposing viewpoints on nuclear war. Topics discussed include: how nuclear would begin; would humanity survive; would civil defense work; will an arms agreement work; and can space weapons reduce the risk of nuclear war.

  5. A toy model for a diatomic molecule

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-08-01

    We introduce a toy model for a diatomic molecule which is based on coupling electronic and nuclear spins to a rigid rotor. Despite its simplicity, the model can be used scientifically to analyze and understand complex molecular hyperfine spectra. In addition, the model has educational value as a number of fundamental symmetries and conservation laws of the molecule can be studied. Because of its simple structure, the model can be readily implemented as a computer program with comparatively short computing times on the order of a few seconds.

  6. Nuclear astrophysics

    SciTech Connect

    Haxton, W.C.

    1992-12-31

    The problem of core-collapse supernovae is used to illustrate the many connections between nuclear astrophysics and the problems nuclear physicists study in terrestrial laboratories. Efforts to better understand the collapse and mantle ejection are also motivated by a variety of interdisciplinary issues in nuclear, particle, and astrophysics, including galactic chemical evolution, neutrino masses and mixing, and stellar cooling by the emission of new particles. The current status of theory and observations is summarized.

  7. Nuclear astrophysics

    SciTech Connect

    Haxton, W.C.

    1992-01-01

    The problem of core-collapse supernovae is used to illustrate the many connections between nuclear astrophysics and the problems nuclear physicists study in terrestrial laboratories. Efforts to better understand the collapse and mantle ejection are also motivated by a variety of interdisciplinary issues in nuclear, particle, and astrophysics, including galactic chemical evolution, neutrino masses and mixing, and stellar cooling by the emission of new particles. The current status of theory and observations is summarized.

  8. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  9. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  10. Polyatomic molecule vibrations

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Polyatomic molecule vibrations are analyzed as harmonic vibrations along normal coordinates. The energy eigenvalues are found for linear and nonlinear symmetric triatomic molecules for valence bond models of the potential function with arbitrary coupling coefficients; such models can usually be fitted to observed energy levels with reasonably good accuracy. Approximate normal coordinates for the H2O molecule are discussed. Degenerate vibrational modes such as occur in CO2 are analyzed and expressions for Fermi resonance between close-lying states of the same symmetry are developed. The bending modes of linear triatomic molecules are expressed in terms of Laguerre polynomials in cylindrical coordinates as well as in terms of Hermite polynomials in Cartesian coordinates. The effects of large-amplitude bending such as occur in the C3 molecule are analyzed, along with anharmonic effects, which split the usually degenerate bending mode energy levels. Finally, the vibrational frequencies, degeneracies, and symmetry properties of XY3, X2Y2, and XY4 type molecules are discussed.

  11. Objections to nuclear defence

    SciTech Connect

    Blake, N.; Pole, K.

    1984-01-01

    This book presents papers on nuclear deterrence. Topics considered include nuclear warfare, nuclear deterrence and the use of the just war doctrine, political aspects, human survival, moral aspects, the nuclear arms race, the ideology of nuclear deterrence, arms control, proliferation, and public opinion.

  12. Strategies on the nuclear-targeted delivery of genes

    PubMed Central

    Yao, Jing; Fan, Ying; Li, Yuanke; Huang, Leaf

    2016-01-01

    To improve the nuclear-targeted delivery of non-viral vectors, extensive effort has been carried out on the development of smart vectors which could overcome multiple barriers. The nuclear envelope presents a major barrier to transgene delivery. Viruses are capable of crossing the nuclear envelope to efficiently deliver their genome into the nucleus through the specialized protein components. However, non-viral vectors are preferred over viral ones because of the safety concerns associated with the latter. Non-viral delivery systems have been designed to include various types of components to enable nuclear translocation at the periphery of the nucleus. This review summarizes the progress of research regarding nuclear transport mechanisms. “Smart” non-viral vectors that have been modified by peptides and other small molecules are able to facilitate the nuclear translocation and enhance the efficacy of gene expression. The resulting technology may also enhance delivery of other macromolecules to the nucleus. PMID:23964565

  13. Nuclear safety

    NASA Technical Reports Server (NTRS)

    Buden, D.

    1991-01-01

    Topics dealing with nuclear safety are addressed which include the following: general safety requirements; safety design requirements; terrestrial safety; SP-100 Flight System key safety requirements; potential mission accidents and hazards; key safety features; ground operations; launch operations; flight operations; disposal; safety concerns; licensing; the nuclear engine for rocket vehicle application (NERVA) design philosophy; the NERVA flight safety program; and the NERVA safety plan.

  14. Understanding ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Julienne, Paul

    2009-05-01

    The successful production of a dense sample of ultracold ground state KRb polar molecules [1] opens the door to a new era of research with dipolar gases and lattices of such species. This feat was achieved by first associating a K and a Rb atom to make a weakly bound Feshbach molecule and then coherently transferring the population to the ground vibrational level of the molecule. This talk focuses on theoretical issues associated with making and using ultracold polar molecules, using KRb as an example [2]. Full understanding of this species and the processes by which it is made requires taking advantage of accurate molecular potentials [3], ab initio calculations [4], and the properties of the long-range potential. A highly accurate model is available for KRb for all bound states below the ground state separated atom limit and could be constructed for other species. The next step is to develop an understanding of the interactions between polar molecules, and their control in the ultracold domain. Understanding long-range interactions and threshold resonances will be crucial for future work. [1] K.-K. Ni, et al, Science 322, 231(2008). [2] P. S. Julienne, arXiv:0812:1233. [3] Pashov et al., Phys. Rev. A76, 022511 (2007). [4] S. Kotochigova, et al., arXiv:0901.1486.

  15. Molecules on ice

    SciTech Connect

    Clary, D.C.

    1996-03-15

    The ozone hole that forms in the spring months over the Antarctic is thought to be produced through a network of chemical reactions catalyzed by the surfaces of ice crystals in polar stratospheric clouds (PSCs). A reaction between chlorine reservoir molecules, such as HCl + ClONO{sub 2} > HNO{sub 3} + Cl{sub 2}, is kinetically forbidden in the gas phase but proceeds quickly on the surface of ice and produces Cl{sub 2} molecules that are photodissociated by sunlight to yield the Cl atoms that destroy ozone. This destructive chain of events begins when HCl molecules stick to the ice crystals, and the mechanism for this crucial sticking process has been the subject of much debate. Recent work describes a mechanism that explains how HCl sticks to ice. This article goes on to detail research focusing surface reactions in stratospheric chemistry. 9 refs., 1 fig.

  16. Atomic branching in molecules

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Rodríguez-Velázquez, Juan A.; Randić, Milan

    A graph theoretic measure of extended atomic branching is defined that accounts for the effects of all atoms in the molecule, giving higher weight to the nearest neighbors. It is based on the counting of all substructures in which an atom takes part in a molecule. We prove a theorem that permits the exact calculation of this measure based on the eigenvalues and eigenvectors of the adjacency matrix of the graph representing a molecule. The definition of this measure within the context of the Hückel molecular orbital (HMO) and its calculation for benzenoid hydrocarbons are also studied. We show that the extended atomic branching can be defined using any real symmetric matrix, as well as any Hermitian (self-adjoint) matrix, which permits its calculation in topological, geometrical, and quantum chemical contexts.

  17. Single-Molecule Bioelectronics

    PubMed Central

    Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

    2014-01-01

    Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  18. Single-molecule bioelectronics.

    PubMed

    Rosenstein, Jacob K; Lemay, Serge G; Shepard, Kenneth L

    2015-01-01

    Experimental techniques that interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. In this study, we review several technologies that can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  19. Photochemistry of interstellar molecules

    NASA Technical Reports Server (NTRS)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  20. Molecules in η Carinae

    NASA Astrophysics Data System (ADS)

    Loinard, Laurent; Menten, Karl M.; Güsten, Rolf; Zapata, Luis A.; Rodríguez, Luis F.

    2012-04-01

    We report the detection toward η Carinae of six new molecules, CO, CN, HCO+, HCN, HNC, and N2H+, and of two of their less abundant isotopic counterparts, 13CO and H13CN. The line profiles are moderately broad (~100 km s-1), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO+ do not appear to be underabundant in η Carinae. On the other hand, molecules containing nitrogen or the 13C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of η Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  1. Poisson's Spot with Molecules

    NASA Astrophysics Data System (ADS)

    Reisinger, Thomas; Patel, Amil; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo; Smith, Henry I.; Holst, Bodil

    2009-03-01

    In the Poisson-Spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. The Poisson spot is the last of the classical optics experiments to be realized with neutral matter waves. In this paper we report the observation of Poisson's Spot using a beam of neutral deuterium molecules. The wavelength-independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson's spot a promising candidate for applications ranging from the study of large-molecule diffraction and coherence in atom-lasers to patterning with large molecules.

  2. MOLECULES IN {eta} CARINAE

    SciTech Connect

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf; Zapata, Luis A.; Rodriguez, Luis F.

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  3. Nuclear APC.

    PubMed

    Neufeld, Kristi L

    2009-01-01

    Mutational inactivation of the tumor suppressor gene APC (Adenomatous polyposis coli) is thought to be an initiating step in the progression of the vast majority ofcolorectal cancers. Attempts to understand APC function have revealed more than a dozen binding partners as well as several subcellular localizations including at cell-cell junctions, associated with microtubules at the leading edge of migrating cells, at the apical membrane, in the cytoplasm and in the nucleus. The present chapter focuses on APC localization and functions in the nucleus. APC contains two classical nuclear localization signals, with a third domain that can enhance nuclear import. Along with two sets of nuclear export signals, the nuclear localization signals enable the large APC protein to shuttle between the nucleus and cytoplasm. Nuclear APC can oppose beta-catenin-mediated transcription. This down-regulation of nuclear beta-catenin activity by APC most likely involves nuclear sequestration of beta-catenin from the transcription complex as well as interaction of APC with transcription corepressor CtBP. Additional nuclear binding partners for APC include transcription factor activator protein AP-2alpha, nuclear export factor Crm1, protein tyrosine phosphatase PTP-BL and perhaps DNA itself. Interaction of APC with polymerase beta and PCNA, suggests a role for APC in DNA repair. The observation that increases in the cytoplasmic distribution of APC correlate with colon cancer progression suggests that disruption of these nuclear functions of APC plays an important role in cancer progression. APC prevalence in the cytoplasm of quiescent cells points to a potential function for nuclear APC in control of cell proliferation. Clear definition of APC's nuclear function(s) will expand the possibilities for early colorectal cancer diagnostics and therapeutics targeted to APC. PMID:19928349

  4. Towards single molecule switches.

    PubMed

    Zhang, Jia Lin; Zhong, Jian Qiang; Lin, Jia Dan; Hu, Wen Ping; Wu, Kai; Xu, Guo Qin; Wee, Andrew T S; Chen, Wei

    2015-05-21

    The concept of using single molecules as key building blocks for logic gates, diodes and transistors to perform basic functions of digital electronic devices at the molecular scale has been explored over the past decades. However, in addition to mimicking the basic functions of current silicon devices, molecules often possess unique properties that have no parallel in conventional materials and promise new hybrid devices with novel functions that cannot be achieved with equivalent solid-state devices. The most appealing example is the molecular switch. Over the past decade, molecular switches on surfaces have been intensely investigated. A variety of external stimuli such as light, electric field, temperature, tunneling electrons and even chemical stimulus have been used to activate these molecular switches between bistable or even multiple states by manipulating molecular conformations, dipole orientations, spin states, charge states and even chemical bond formation. The switching event can occur either on surfaces or in break junctions. The aim of this review is to highlight recent advances in molecular switches triggered by various external stimuli, as investigated by low-temperature scanning tunneling microscopy (LT-STM) and the break junction technique. We begin by presenting the molecular switches triggered by various external stimuli that do not provide single molecule selectivity, referred to as non-selective switching. Special focus is then given to selective single molecule switching realized using the LT-STM tip on surfaces. Single molecule switches operated by different mechanisms are reviewed and discussed. Finally, molecular switches embedded in self-assembled monolayers (SAMs) and single molecule junctions are addressed. PMID:25757483

  5. Plasmonic nanostructures: artificial molecules.

    PubMed

    Wang, Hui; Brandl, Daniel W; Nordlander, Peter; Halas, Naomi J

    2007-01-01

    This Account describes a new paradigm for the relationship between the geometry of metallic nanostructures and their optical properties. While the interaction of light with metallic nanoparticles is determined by their collective electronic or plasmon response, a compelling analogy exists between plasmon resonances of metallic nanoparticles and wave functions of simple atoms and molecules. Based on this insight, an entire family of plasmonic nanostructures, artificial molecules, has been developed whose optical properties can be understood within this picture: nanoparticles (nanoshells, nanoeggs, nanomatryushkas, nanorice), multi-nanoparticle assemblies (dimers, trimers, quadrumers), and a nanoparticle-over-metallic film, an electromagnetic analog of the spinless Anderson model. PMID:17226945

  6. How successful is nuclear targeting by nanocarriers?

    PubMed

    Tammam, Salma N; Azzazy, Hassan M E; Lamprecht, Alf

    2016-05-10

    The nucleus is ultimately the final target for many therapeutics treating various disorders including cancers, heart dysfunction and brain disorders. Owing to their specialized cell uptake and trafficking mechanisms, nanoparticles (NPs) allow drug targeting where degradation sensitive therapeutics could be delivered to their target tissues and cell in active form and sufficient concentration. However, it has recently become increasingly obvious that cytosolic internalization of a drug molecule does not entail its interaction with its subcellular target and hence careful nanoparticle design and optimization is required to enable nuclear targeting. This review, discusses the barriers to NP nuclear delivery; crossing the cell membrane, endo/lysosomal escape, cytoplasmic trafficking and finally nuclear entry focusing on how NP synthesis and modification could allow for bypassing each of the aforementioned barriers and successfully reaching the nucleus. Examples of nuclear targeted NPs are also discussed, stressing on the critical aspects of nuclear targeting and pointing out how the disease state might change the normal NP path and how such change could be exploited to increase efficiency of nuclear targeting. Finally, the criteria set for the evaluation of nanocarriers for nuclear delivery are discussed highlighting that quantitative rather than qualitative evaluation is required to evaluate how successful nanocarriers for nuclear delivery are, particularly with regards to the amount of drug delivered and released in the nucleus. PMID:26995759

  7. Engineering biological systems with synthetic RNA molecules

    PubMed Central

    Liang, Joe C.; Bloom, Ryan J.; Smolke, Christina D.

    2011-01-01

    RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors. PMID:21925380

  8. Bioactive molecules from sea hares.

    PubMed

    Kamiya, H; Sakai, R; Jimbo, M

    2006-01-01

    Sea hares, belonging to the order Opisthobranchia, subclass Gastropoda, are mollusks that have attracted many researchers who are interested in the chemical defense mechanisms of these soft and "shell-less" snails. Numbers of small molecules of dietary origin have been isolated from sea hares and some have ecologically relevant activities, such as fish deterrent activity or toxicity. Recently, however, greater attention has been paid to biomedically interesting sea hare isolates such as dolastatins, a series of antitumor peptide/macrolides isolated from Dolabella auricularia. Another series of bioactive peptide/macrolides, as represented by aplyronines, have been isolated from sea hares in Japanese waters. Although earlier studies indicated the potent antitumor activity of aplyronines, their clinical development has never been conducted because of the minute amount of compound available from the natural source. Recent synthetic studies, however, have made it possible to prepare these compounds and analogs for a structure-activity relationship study, and started to uncover their unique action mechanism towards their putative targets, microfilaments. Here, recent findings of small antitumor molecules isolated from Japanese sea hares are reviewed. Sea hares are also known to produce cytotoxic and antimicrobial proteins. In contrast to the small molecules of dietary origin, proteins are the genetic products of sea hares and they are likely to have some primary physiological functions in addition to ecological roles in the sea hare. Based on the biochemical properties and phylogenetic analysis of these proteins, we propose that they belong to one family of molecule, the "Aplysianin A family," although their molecular weights are apparently divided into two groups. Interestingly, the active principles in Aplysia species and Dolabella auricularia were shown to be L-amino acid oxidase (LAAO), a flavin enzyme that oxidizes an alpha-amino group of the substrate with

  9. Vibrational spectroscopy of polar molecules with superradiance

    NASA Astrophysics Data System (ADS)

    Lin, Guin-Dar; Yelin, Susanne F.

    2013-07-01

    We investigate cooperative phenomena and superradiance for vibrational transitions in polar molecule spectroscopy of high optical-depth samples. Such cooperativity comes from the build-up of inter-particle coherence through dipole-dipole interactions and leads to speed-up of decay processes. We compare our calculation to recent work and find very good agreement, suggesting that superradiant effects need to be taken into account in a wide variety of ultracold molecule experiments, including vibrational and rotational states.

  10. Prebiologically Important Interstellar Molecules

    NASA Astrophysics Data System (ADS)

    Kuan, Y.-J.; Huang, H.-C.; Charnley, S. B.; Tseng, W.-L.; Snyder, L. E.; Ehrenfreund, P.; Kisiel, Z.; Thorwirth, S.; Bohn, R. K.; Wilson, T. L.

    2004-06-01

    Understanding the organic chemistry of molecular clouds, particularly the formation of biologically important molecules, is fundamental to the study of the processes which lead to the origin, evolution and distribution of life in the Galaxy. Determining the level of molecular complexity attainable in the clouds, and the nature of the complex organic material available to protostellar disks and the planetary systems that form from them, requires an understanding of the possible chemical pathways and is therefore a central question in astrochemistry. We have thus searched for prebiologically important molecules in the hot molecular cloud cores: Sgr B2(N-LMH), W51 e1/e2 and Orion-KL. Among the molecules searched: Pyrimidine is the unsubstituted ring analogue for three of the DNA and RNA bases. 2H-Azirine and Aziridine are azaheterocyclic compounds. And Glycine is the simplest amino acid. Detections of these interstellar organic molecular species will thus have important implications for Astrobiology. Our preliminary results indicate a tentative detection of interstellar glycine. If confirmed, this will be the first detection of an amino acid in interstellar space and will greatly strengthen the thesis that interstellar organic molecules could have played a pivotal role in the prebiotic chemistry of the early Earth.

  11. Algebraic theory of molecules

    NASA Technical Reports Server (NTRS)

    Iachello, Franco

    1995-01-01

    An algebraic formulation of quantum mechanics is presented. In this formulation, operators of interest are expanded onto elements of an algebra, G. For bound state problems in nu dimensions the algebra G is taken to be U(nu + 1). Applications to the structure of molecules are presented.

  12. Mighty Molecule Models

    ERIC Educational Resources Information Center

    Brown, Tom; Rushton, Greg; Bencomo, Marie

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that…

  13. Diversity in Biological Molecules

    ERIC Educational Resources Information Center

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  14. The Science of Molecules

    ERIC Educational Resources Information Center

    Flory, Paul J.

    1974-01-01

    The author maintains that chemistry has a key role as the science of molecules and rejects the concept of chemistry as a branch of physics. The scope of chemistry, the philosophies underlying its practice, and the teaching of the subject also are discussed. (DT)

  15. DUO: Spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin–orbit, angular momenta, spin-rotational and spin–spin. Introducing the relevant couplings using so-called Born–Oppenheimer breakdown curves can correct non-adiabatic effects.

  16. Nanoelectronics of a DNA molecule

    NASA Astrophysics Data System (ADS)

    Albuquerque, E. L.; Fulco, U. L.; Caetano, E. W. S.; Freire, V. N.; Lyra, M. L.; Moura, F. A. B. F.

    2014-03-01

    We investigate the nanoelectronic properties of a double-strand quasiperiodic DNA molecule, modeled by a tight-binding effective Hamiltonian, which includes contributions from the nucleobasis system as well as the sugar-phosphate backbone. Our theoretical approach makes use of Dyson's equation together with a transfer-matrix treatment, to investigate the electronic density of states, the electronic transmissivity, and the current-voltage characteristic curves of sequences of a DNA finite segment.We compared the electronic transport found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22.

  17. OMG: Open Molecule Generator

    PubMed Central

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  18. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  19. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  20. Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials.

    PubMed

    Mayhall, Nicholas J; Raghavachari, Krishnan

    2011-05-10

    We present a new extrapolated fragment-based approach, termed molecules-in-molecules (MIM), for accurate energy calculations on large molecules. In this method, we use a multilevel partitioning approach coupled with electronic structure studies at multiple levels of theory to provide a hierarchical strategy for systematically improving the computed results. In particular, we use a generalized hybrid energy expression, similar in spirit to that in the popular ONIOM methodology, that can be combined easily with any fragmentation procedure. In the current work, we explore a MIM scheme which first partitions a molecule into nonoverlapping fragments and then recombines the interacting fragments to form overlapping subsystems. By including all interactions with a cheaper level of theory, the MIM approach is shown to significantly reduce the errors arising from a single level fragmentation procedure. We report the implementation of energies and gradients and the initial assessment of the MIM method using both biological and materials systems as test cases. PMID:26610128

  1. Trapping and manipulating single molecules of DNA

    NASA Astrophysics Data System (ADS)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  2. The reaction dynamics of alkali dimer molecules and electronically excited alkali atoms with simple molecules

    SciTech Connect

    Hou, H.

    1995-12-01

    This dissertation presents the results from the crossed molecular beam studies on the dynamics of bimolecular collisions in the gas phase. The primary subjects include the interactions of alkali dimer molecules with simple molecules, and the inelastic scattering of electronically excited alkali atoms with O2. The reaction of the sodium dimers with oxygen molecules is described in Chapter 2. Two reaction pathways were observed for this four-center molecule-molecule reaction, i.e. the formations of NaO2 + Na and NaO + NaO. NaO2 products exhibit a very anisotropic angular distribution, indicating a direct spectator stripping mechanism for this reaction channel. The NaO formation follows the bond breaking of O2, which is likely a result of a charge transfer from Na2 to the excited state orbital of O2-. The scattering of sodium dimers from ammonium and methanol produced novel molecules, NaNH3 and Na(CH3OH), respectively. These experimental observations, as well as the discussions on the reaction dynamics and the chemical bonding within these molecules, will be presented in Chapter 3. The lower limits for the bond dissociation energies of these molecules are also obtained. Finally, Chapter 4 describes the energy transfer between oxygen molecules and electronically excited sodium atoms.

  3. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  4. Strange skyrmion molecules

    NASA Astrophysics Data System (ADS)

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-01

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  5. Strange skyrmion molecules

    SciTech Connect

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-20

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  6. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  7. Model molecules mimicking asphaltenes.

    PubMed

    Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe

    2015-04-01

    Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed. PMID:25638443

  8. Photonic Molecule Lasers Revisited

    NASA Astrophysics Data System (ADS)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  9. Small Molecules from the Human Microbiota

    PubMed Central

    Donia, Mohamed S.; Fischbach, Michael A.

    2015-01-01

    Developments in the use of genomics to guide natural product discovery and a recent emphasis on understanding the molecular mechanisms of microbiota-host interactions have converged on the discovery of natural products from the human microbiome. Here, we review what is known about small molecules produced by the human microbiota. Numerous molecules representing each of the major metabolite classes have been found that have a variety of biological activities, including immune modulation and antibiosis. We discuss technologies that will affect how microbiota-derived molecules are discovered in the future, and consider the challenges inherent in finding specific molecules that are critical for driving microbe-host and microbe-microbe interactions and their biological relevance. PMID:26206939

  10. Understanding Polymer Properties through Imaging of Molecules.

    NASA Astrophysics Data System (ADS)

    Sheiko, Sergei

    2008-03-01

    The unique advantage of Scanning Probe Microscopy (SPM) is that it allows imaging of flexible polymer molecules, whose overall size and local curvature are below the optical resolution limit. The role of molecular visualization has grown to be especially profound with the synthesis of complex macromolecules whose structure is difficult to confirm using conventional techniques such as NMR and light scattering. This is especially true for molecules that are branched, heterogeneous, and polydisperse. Here, SPM images provide unambiguous proof of the molecular architecture along with accurate analysis of size, conformation, and ordering of molecules on surfaces. The unique advantage of SPM is that one obtains molecular dimensions in direct space. This offers more opportunities for statistical analysis including fractionation of molecules by size, branching topology, and chemical composition as well as sorting out the irrelevant species. Unlike molecular characterization of static molecules, it remains challenging to study molecules as they move and react on surfaces. We will discuss pioneering AFM studies of flowing monolayers one molecule at a time. Through use of AFM, the flow process was monitored over a broad range of length scales from the millimeter long precursor film all the way down to the movements of individual molecules within the film. Molecular imaging enabled independent measurements both the driving and frictional forces that control spreading rate. In these studies, one also discovered a new type of flow instability in polymer monolayers caused by flow-induced conformational transitions. Recently, molecular imaging has been successfully used to monitor adsorption-induced degradation of branched molecules. These experiments open an entirely new perspective in chemistry wherein the chemical bonds can be mechanically activated upon the physical contact of a macromolecule with a substrate. This research directly impacts coatings, lubrication, heterogeneous

  11. Protein folding at single-molecule resolution

    PubMed Central

    Ferreon, Allan Chris M.; Deniz, Ashok A.

    2011-01-01

    The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. PMID:21303706

  12. Nuclear analytical chemistry

    SciTech Connect

    Brune, D.; Forkman, B.; Persson, B.

    1984-01-01

    This book covers the general theories and techniques of nuclear chemical analysis, directed at applications in analytical chemistry, nuclear medicine, radiophysics, agriculture, environmental sciences, geological exploration, industrial process control, etc. The main principles of nuclear physics and nuclear detection on which the analysis is based are briefly outlined. An attempt is made to emphasise the fundamentals of activation analysis, detection and activation methods, as well as their applications. The book provides guidance in analytical chemistry, agriculture, environmental and biomedical sciences, etc. The contents include: the nuclear periodic system; nuclear decay; nuclear reactions; nuclear radiation sources; interaction of radiation with matter; principles of radiation detectors; nuclear electronics; statistical methods and spectral analysis; methods of radiation detection; neutron activation analysis; charged particle activation analysis; photon activation analysis; sample preparation and chemical separation; nuclear chemical analysis in biological and medical research; the use of nuclear chemical analysis in the field of criminology; nuclear chemical analysis in environmental sciences, geology and mineral exploration; and radiation protection.

  13. High-content screening identifies small molecules that remove nuclear foci, affect MBNL distribution and CELF1 protein levels via a PKC-independent pathway in myotonic dystrophy cell lines.

    PubMed

    Ketley, Ami; Chen, Catherine Z; Li, Xin; Arya, Sukrat; Robinson, Thelma E; Granados-Riveron, Javier; Udosen, Inyang; Morris, Glenn E; Holt, Ian; Furling, Denis; Chaouch, Soraya; Haworth, Ben; Southall, Noel; Shinn, Paul; Zheng, Wei; Austin, Christopher P; Hayes, Christopher J; Brook, J David

    2014-03-15

    Myotonic dystrophy (DM) is a multi-system neuromuscular disorder for which there is no treatment. We have developed a medium throughput phenotypic assay, based on the identification of nuclear foci in DM patient cell lines using in situ hybridization and high-content imaging to screen for potentially useful therapeutic compounds. A series of further assays based on molecular features of DM have also been employed. Two compounds that reduce and/or remove nuclear foci have been identified, Ro 31-8220 and chromomycin A3. Ro 31-8220 is a PKC inhibitor, previously shown to affect the hyperphosphorylation of CELF1 and ameliorate the cardiac phenotype in a DM1 mouse model. We show that the same compound eliminates nuclear foci, reduces MBNL1 protein in the nucleus, affects ATP2A1 alternative splicing and reduces steady-state levels of CELF1 protein. We demonstrate that this effect is independent of PKC activity and conclude that this compound may be acting on alternative kinase targets within DM pathophysiology. Understanding the activity profile for this compound is key for the development of targeted therapeutics in the treatment of DM. PMID:24179176

  14. The New Nuclear Nations.

    ERIC Educational Resources Information Center

    Spector, Leonard S.

    1990-01-01

    Explores the issue of nuclear proliferation, noting that the countries with nuclear capability now include Israel, South Africa, India, and Pakistan. Describes the role and problems of the United States in halting nuclearization. Supplies charts, maps, and information concerning the state of nuclear capability in each country. (NL)

  15. Atom-diatom scattering dynamics of spinning molecules

    SciTech Connect

    Eyles, C. J.; Floß, J.; Averbukh, I. Sh.; Leibscher, M.

    2015-01-14

    We present full quantum mechanical scattering calculations using spinning molecules as target states for nuclear spin selective atom-diatom scattering of reactive D+H{sub 2} and F+H{sub 2} collisions. Molecules can be forced to rotate uni-directionally by chiral trains of short, non-resonant laser pulses, with different nuclear spin isomers rotating in opposite directions. The calculations we present are based on rotational wavepackets that can be created in this manner. As our simulations show, target molecules with opposite sense of rotation are predominantly scattered in opposite directions, opening routes for spatially and quantum state selective scattering of close chemical species. Moreover, two-dimensional state resolved differential cross sections reveal detailed information about the scattering mechanisms, which can be explained to a large degree by a classical vector model for scattering with spinning molecules.

  16. Atom-diatom scattering dynamics of spinning molecules.

    PubMed

    Eyles, C J; Floss, J; Averbukh, I Sh; Leibscher, M

    2015-01-14

    We present full quantum mechanical scattering calculations using spinning molecules as target states for nuclear spin selective atom-diatom scattering of reactive D+H2 and F+H2 collisions. Molecules can be forced to rotate uni-directionally by chiral trains of short, non-resonant laser pulses, with different nuclear spin isomers rotating in opposite directions. The calculations we present are based on rotational wavepackets that can be created in this manner. As our simulations show, target molecules with opposite sense of rotation are predominantly scattered in opposite directions, opening routes for spatially and quantum state selective scattering of close chemical species. Moreover, two-dimensional state resolved differential cross sections reveal detailed information about the scattering mechanisms, which can be explained to a large degree by a classical vector model for scattering with spinning molecules. PMID:25591357

  17. New molecules for hippocampal development.

    PubMed

    Skutella, T; Nitsch, R

    2001-02-01

    Pathfinding by developing axons towards their proper targets is an essential step in establishing appropriate neuronal connections. Recent work involving cell culture assays and molecular biology strategies, including knockout animals, strongly indicates that a complex network of guidance signals regulates the formation of hippocampal connections during development. Outgrowing axons are routed towards the hippocampal formation by specific expression of long-range cues, which include secreted class 3 semaphorins, netrin 1 and Slit proteins. Local membrane- or substrate-anchored molecules, such as ligands of the ephrin A subclass, provide layer-specific positional information. Understanding the molecular mechanisms that underlie axonal guidance during hippocampal development might be of importance in making therapeutic use of sprouting fibers, which are produced following the loss of afferents in CNS lesion. PMID:11164941

  18. Thermodynamics of nuclear transport

    NASA Astrophysics Data System (ADS)

    Wang, Ching-Hao; Mehta, Pankaj; Elbaum, Michael

    Molecular transport across the nuclear envelope is important for eukaryotes for gene expression and signaling. Experimental studies have revealed that nuclear transport is inherently a nonequilibrium process and actively consumes energy. In this work we present a thermodynamics theory of nuclear transport for a major class of nuclear transporters that are mediated by the small GTPase Ran. We identify the molecular elements responsible for powering nuclear transport, which we term the ``Ran battery'' and find that the efficiency of transport, measured by the cargo nuclear localization ratio, is limited by competition between cargo molecules and RanGTP to bind transport receptors, as well as the amount of NTF2 (i.e. RanGDP carrier) available to circulate the energy flow. This picture complements our current understanding of nuclear transport by providing a comprehensive thermodynamics framework to decipher the underlying biochemical machinery. Pm and CHW were supported by a Simons Investigator in the Mathematical Modeling in Living Systems grant (to PM).

  19. Geometric phase and gauge connection in polyatomic molecules.

    PubMed

    Wittig, Curt

    2012-05-14

    Geometric phase is an interesting topic that is germane to numerous and varied research areas: molecules, optics, quantum computing, quantum Hall effect, graphene, and so on. It exists only when the system of interest interacts with something it perceives as exterior. An isolated system cannot display geometric phase. This article addresses geometric phase in polyatomic molecules from a gauge field theory perspective. Gauge field theory was introduced in electrodynamics by Fock and examined assiduously by Weyl. It yields the gauge field A(μ), particle-field couplings, and the Aharonov-Bohm phase, while Yang-Mills theory, the cornerstone of the standard model of physics, is a template for non-Abelian gauge symmetries. Electronic structure theory, including nonadiabaticity, is a non-Abelian gauge field theory with matrix-valued covariant derivative. Because the wave function of an isolated molecule must be single-valued, its global U(1) symmetry cannot be gauged, i.e., products of nuclear and electron functions such as χ(n)ψ(n) are forbidden from undergoing local phase transformation on R, where R denotes nuclear degrees of freedom. On the other hand, the synchronous transformations (first noted by Mead and Truhlar): ψ(n)→ψ(n)e(iζ) and simultaneously χ(n)→χ(n)e(-iζ), preserve single-valuedness and enable wave functions in each subspace to undergo phase transformation on R. Thus, each subspace is compatible with a U(1) gauge field theory. The central mathematical object is Berry's adiabatic connection i, which serves as a communication link between the two subsystems. It is shown that additions to the connection according to the gauge principle are, in fact, manifestations of the synchronous (e(iζ)/e(-iζ)) nature of the ψ(n) and χ(n) phase transformations. Two important U(1) connections are reviewed: qA(μ) from electrodynamics and Berry's connection. The gauging of SU(2) and SU(3) is reviewed and then used with molecules. The largest gauge

  20. Nuclear Speckles

    PubMed Central

    Spector, David L.; Lamond, Angus I.

    2011-01-01

    Nuclear speckles, also known as interchromatin granule clusters, are nuclear domains enriched in pre-mRNA splicing factors, located in the interchromatin regions of the nucleoplasm of mammalian cells. When observed by immunofluorescence microscopy, they usually appear as 20–50 irregularly shaped structures that vary in size. Speckles are dynamic structures, and their constituents can exchange continuously with the nucleoplasm and other nuclear locations, including active transcription sites. Studies on the composition, structure, and dynamics of speckles have provided an important paradigm for understanding the functional organization of the nucleus and the dynamics of the gene expression machinery. PMID:20926517

  1. Liquid-gas phase transition in nuclear matter including strangeness

    SciTech Connect

    Wang, P.; Leinweber, D.B.; Williams, A.G.; Thomas, A.W.

    2004-11-01

    We apply the chiral SU(3) quark mean field model to study the properties of strange hadronic matter at finite temperature. The liquid-gas phase transition is studied as a function of the strangeness fraction. The pressure of the system cannot remain constant during the phase transition, since there are two independent conserved charges (baryon and strangeness number). In a range of temperatures around 15 MeV (precise values depending on the model used) the equation of state exhibits multiple bifurcates. The difference in the strangeness fraction f{sub s} between the liquid and gas phases is small when they coexist. The critical temperature of strange matter turns out to be a nontrivial function of the strangeness fraction.

  2. Vibronic bands in the HOMO-LUMO excitation of linear polyyne molecules

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Tomonari; Wada, Yoriko; Iwahara, Naoya; Sato, Tohru

    2013-04-01

    Hydrogen-capped linear carbon chain molecules, namely polyynes H(C≡C)nH (n>=2), give rise to three excited states in the HOMO-LUMO excitation. Electric dipole transition from the ground state is fully allowed to one of the three excited states, while forbidden for the other two low-lying excited states. In addition to the strong absorption bands in the UV for the allowed transition, the molecules exhibit weak absorption and emission bands in the near UV and visible wavelength regions. The weak features are the vibronic bands in the forbidden transition. In this article, symmetry considerations are presented for the optical transitions in the centrosymmetric linear polyyne molecule. The argument includes Herzberg-Teller expansion for the state mixing induced by nuclear displacements along the normal coordinate of the molecule, intensity borrowing from fully allowed transitions, and inducing vibrational modes excited in the vibronic transition. The vibronic coupling considered here includes off-diagonal matrix elements for second derivatives along the normal coordinate. The vibronic selection rule for the forbidden transition is derived and associated with the transition moment with respect to the molecular axis. Experimental approaches are proposed for the assignment of the observed vibronic bands.

  3. Negative ions of polyatomic molecules.

    PubMed Central

    Christophorou, L G

    1980-01-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies. PMID:7428744

  4. Making More-Complex Molecules Using Superthermal Atom/Molecule Collisions

    NASA Technical Reports Server (NTRS)

    Shortt, Brian; Chutjian, Ara; Orient, Otto

    2008-01-01

    A method of making more-complex molecules from simpler ones has emerged as a by-product of an experimental study in outer-space atom/surface collision physics. The subject of the study was the formation of CO2 molecules as a result of impingement of O atoms at controlled kinetic energies upon cold surfaces onto which CO molecules had been adsorbed. In this study, the O/CO system served as a laboratory model, not only for the formation of CO2 but also for the formation of other compounds through impingement of rapidly moving atoms upon molecules adsorbed on such cold interstellar surfaces as those of dust grains or comets. By contributing to the formation of increasingly complex molecules, including organic ones, this study and related other studies may eventually contribute to understanding of the origins of life.

  5. COCIS: Markov processes in single molecule fluorescence

    PubMed Central

    Talaga, David S.

    2009-01-01

    This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the FPT distributions out of those states must be describable by a simple exponential law. The observation of non-exponential first-passage time distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system. PMID:19543444

  6. Newly detected molecules in dense interstellar clouds

    NASA Technical Reports Server (NTRS)

    Irvine, William M.; Ziurys, L. M.; Avery, L. W.; Matthews, H. E.; Friberg, P.

    1988-01-01

    The last year or so has seen the identification of several new interstellar molecules, including C2S, C3S, C5H, C6H, and (probably) HC2CHO in the cold, dark cloud TMC-1, and the discovery of the first interstellar phosphorus-containing molecule, PN, in the Orion 'plateau' source. Further interesting results include the observations of (C-13))3H2 and C3HD, and the first detection of HCOOH (formic acid) in a (C-13)3H2 cold cloud.

  7. Electric power monthly, September 1990. [Glossary included

    SciTech Connect

    Not Available

    1990-12-17

    The purpose of this report is to provide energy decision makers with accurate and timely information that may be used in forming various perspectives on electric issues. The power plants considered include coal, petroleum, natural gas, hydroelectric, and nuclear power plants. Data are presented for power generation, fuel consumption, fuel receipts and cost, sales of electricity, and unusual occurrences at power plants. Data are compared at the national, Census division, and state levels. 4 figs., 52 tabs. (CK)

  8. High-harmonic generation in aligned water molecules

    NASA Astrophysics Data System (ADS)

    Wang, Song; Devin, Julien; Hoffmann, Matthias; Cryan, James; Kaldun, Andreas; Bucksbaum, Philip

    2016-05-01

    In recent years, the use of high harmonic generation (HHG) in aligned molecular vapors has become a powerful tool to study ultrafast dynamics of electronic and nuclear wave packets. In our new experimental setup, we are able to orient H2 O and D2 O molecules using a single cycle terahertz (THz) pulse. Aligning water is especially interesting as the highest occupied molecular orbital (HOMO) of water contains a node in the xz plane of the molecular frame, allowing us to perform HHG from second highest occupied molecular orbital (HOMO-1) only, by setting the polarization of the fundamental laser along the z-axis of the aligned water molecules. We are particularly interested in the HOMO-1 state, as there is fast motion of the H-O-H angle leading to sub-wavelength dynamics. On this poster we present our all-optical alignment setup where HHG and single-cycle THz generation take place in high-vacuum, where measurements with arbitrary polarization angles between the two are possible. In addition, we discuss the effects of the molecular orientation on HHG, including symmetry breaking that could produce even harmonics and isotope effects between H2 O and D2 O due to different vibrational energies. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  9. Ultra-cold molecule production.

    SciTech Connect

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-12-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled.

  10. Spin squeezing a cold molecule

    NASA Astrophysics Data System (ADS)

    Bhattacharya, M.

    2015-12-01

    In this article we present a concrete proposal for spin squeezing the cold ground-state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. In contrast to existing work, we consider a single, noninteracting molecule with angular momentum greater than 1 /2 . Starting from an experimentally relevant effective Hamiltonian, we identify an adiabatic regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993), 10.1103/PhysRevA.47.5138], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T. Ng, and P. T. Leung, Phys. Rev. A 63, 055601 (2001), 10.1103/PhysRevA.63.055601], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989), 10.1103/PhysRevA.39.2969]. We then consider the situation in which nonadiabatic effects are quite large and show that the effective Hamiltonian supports spin squeezing even in this case. We provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounting for the effects of field misalignment. Our results have consequences for applications such as precision spectroscopy, techniques such as magnetometry, and stereochemical effects such as the orientation-to-alignment transition.

  11. Electronic spectroscopy of diatomic molecules

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.

    1994-01-01

    This article provides an overview of the principal computational approaches and their accuracy for the study of electronic spectroscopy of diatomic molecules. We include a number of examples from our work that illustrate the range of application. We show how full configuration interaction benchmark calculations were instrumental in improving the understanding of the computational requirements for obtaining accurate results for diatomic spectroscopy. With this understanding it is now possible to compute radiative lifetimes accurate to within 10% for systems involving first- and second-row atoms. We consider the determination of the infrared vibrational transition probabilities for the ground states of SiO and NO, based on a globally accurate dipole moment function. We show how we were able to assign the a(sup "5)II state of CO as the upper state in the recently observed emission bands of CO in an Ar matrix. We next discuss the assignment of the photoelectron detachment spectra of NO and the alkali oxide negative ions. We then present several examples illustrating the state-of-the-art in determining radiative lifetimes for valence-valence and valence-Rydberg transitions. We next compare the molecular spectroscopy of the valence isoelectronic B2, Al2, and AlB molecules. The final examples consider systems involving transition metal atoms, which illustrate the difficulty in describing states with different numbers of d electrons.

  12. Nonlinear Dynamics of Atom-Molecule Conversion

    NASA Astrophysics Data System (ADS)

    Fu, Li-Bin; Liu, Jie

    2014-03-01

    The creation of ultracold molecules has opened up new possibilities for studies on molecular matter waves, strongly interacting superfluids, high-precision molecular spectroscopy and coherent molecular optics. In an atomic Bose-Einstein condensate (BEC) and a degenerate Fermi-Fermi or Fermi-Bose mixture, magnetic Feshbach resonance or optical photoassociation (PA) technique has been used to create not only diatomic molecules but also more complex molecules. In this chapter, we focus on many issues of nonlinear dynamics of atom-molecule systems. In Sec. 1, on the basis of the two-channelmean-field approach, we study the manybody effects on the Landau-Zener(LZ) picture of two-body molecular production through dramatically distorting the energy levels near the Feshbach resonance. In Sec. 2, we investigate the Feshbach resonance with modulation of an oscillating magnetic field. In Sec. 3, we include the nonlinear interparticle collisions and focus on the linear instability induced by the collisions and the adiabatic fidelity of the atom-trimer dark state in a stimulated Raman adiabatic passage (STIRAP). In Sec. 4, we theoretically investigate conversion problem from atom to N-body polyatomic molecule in an ultracold bosonic system by implementing the generalized STIRAP. In the last section, we discuss role of two-body interactions in the Feshbach conversion of fermionic atoms to bosonic molecules.

  13. Self-Assemblies of novel molecules, VECAR

    NASA Astrophysics Data System (ADS)

    Shrestha, Bijay; Kim, Hye-Young; Lee, Soojin; Novak, Brian; Moldovan, Dorel

    2015-03-01

    VECAR is a newly synthesized molecule, which is an amphiphilic antioxidant molecule that consists of two molecular groups, vitamin-E and Carnosine, linked by a hydrocarbon chain. The hydrocarbon chain is hydrophobic and both vitamin-E and Carnosine ends are hydrophilic. In the synthesis process, the length of the hydrophobic chain of VECAR molecules can vary from the shortest (n =0) to the longest (n =18), where n indicates the number of carbon atoms in the chain. We conducted MD simulation studies of self-assembly of VECAR molecules in water using GROMACS on LONI HPC resources. Our study shows that there is a strong correlation between the shape and atomistic structure of the self-assembled nano-structures (SANs) and the chain-length (n) of VECAR molecules. We will report the results of data analyses including the atomistic structure of each SANs and the dynamic and energetic mechanisms of their formation as function of time. In summary, both VECAR molecules of chain-length n =18 and 9 form worm-like micelles, which may be used as a drug delivery system. This research is supported by the Louisiana Board of Regents-RCS Grant (LEQSF(2012-15)-RD-A-19).

  14. Soft Landing of Complex Molecules on Surfaces

    SciTech Connect

    Johnson, Grant E.; Hu, Qichi; Laskin, Julia

    2011-07-01

    Mass spectrometry is a versatile technique for identification and structural characterization of large molecules. The advent of soft ionization techniques such as electrospray (ESI) (1-2) has enabled ionization of a wide variety of complex molecules without significant \\fragmentation while non-thermal ion sources such as laser vaporization (3-4) and magnetron sputtering (5-6) have provided access to materials that cannot, currently, be produced through conventional techniques. Most mass spectrometry studies rely on ionization of a molecule of interest or a complex mixture followed by mass analysis. Alternatively, mass spectrometry may be used as a preparatory technique, in which mass-selected ions are deposited onto solid supports or into liquid materials (7-18). Preparatory mass spectrometry offers several unique advantages for deposition of complex molecules on substrates including the ability to generate high-purity uniform films (19-20), unprecedented selectivity and specificity of preparation of deposited species (11, 21-22), the ability to focus and pattern an ion beam (23-24), and flexibility in both ion formation (1, 3, 25-26) and mass selection (27-32) processes. This review will highlight applications of mass-selected deposition of complex molecules for selective immobilization of biological molecules and catalytically active complexes on substrates.

  15. Nuclear Sphingolipid Metabolism

    PubMed Central

    Lucki, Natasha C.; Sewer, Marion B.

    2014-01-01

    Nuclear lipid metabolism is implicated in various processes, including transcription, splicing, and DNA repair. Sphingolipids play roles in numerous cellular functions, and an emerging body of literature has identified roles for these lipid mediators in distinct nuclear processes. Different sphingolipid species are localized in various subnuclear domains, including chromatin, the nuclear matrix, and the nuclear envelope, where sphingolipids exert specific regulatory and structural functions. Sphingomyelin, the most abundant nuclear sphingolipid, plays both structural and regulatory roles in chromatin assembly and dynamics in addition to being an integral component of the nuclear matrix. Sphingosine-1-phosphate modulates histone acetylation, sphingosine is a ligand for steroidogenic factor 1, and nuclear accumulation of ceramide has been implicated in apoptosis. Finally, nuclear membrane–associated ganglioside GM1 plays a pivotal role in Ca2+ homeostasis. This review highlights research on the factors that control nuclear sphingolipid metabolism and summarizes the roles of these lipids in various nuclear processes. PMID:21888508

  16. The photodissociation and reaction dynamics of vibrationally excited molecules

    SciTech Connect

    Not Available

    1993-01-01

    We have used combined vibrational overtone excitation and laser induced fluorescence detection to study dissociation dynamics of hydroxylamine (NH[sub 2]OH), have performed our first laser induced grating experiments on water, and have begun assembling a new apparatus for preparing vibrationally excited molecules with simulated Raman excitation. We study role of vibrational excitation in photodissociation dynamics by using a vibrational state preparation technique, such as vibrational overtone excitation or stimulated Raman excitation, to create molecules with particular nuclear motions and then to excite that molecule to a dissociative electronic state.

  17. Covalent Chemistry beyond Molecules.

    PubMed

    Jiang, Juncong; Zhao, Yingbo; Yaghi, Omar M

    2016-03-16

    Linking molecular building units by covalent bonds to make crystalline extended structures has given rise to metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), thus bringing the precision and versatility of covalent chemistry beyond discrete molecules to extended structures. The key advance in this regard has been the development of strategies to overcome the "crystallization problem", which is usually encountered when attempting to link molecular building units into covalent solids. Currently, numerous MOFs and COFs are made as crystalline materials in which the large size of the constituent units provides for open frameworks. The molecular units thus reticulated become part of a new environment where they have (a) lower degrees of freedom because they are fixed into position within the framework; (b) well-defined spatial arrangements where their properties are influenced by the intricacies of the pores; and (c) ordered patterns onto which functional groups can be covalently attached to produce chemical complexity. The notion of covalent chemistry beyond molecules is further strengthened by the fact that covalent reactions can be carried out on such frameworks, with full retention of their crystallinity and porosity. MOFs are exemplars of how this chemistry has led to porosity with designed metrics and functionality, chemically-rich sequences of information within their frameworks, and well-defined mesoscopic constructs in which nanoMOFs enclose inorganic nanocrystals and give them new levels of spatial definition, stability, and functionality. PMID:26863450

  18. Small Molecules in the Treatment of Psoriasis.

    PubMed

    Torres, Tiago; Filipe, Paulo

    2015-08-01

    Preclinical Research Psoriasis is an inflammatory systemic skin disease that affects various parts of the body requiring long-term management due to its chronic nature. Available treatment options include topical, systemic or biological therapies, which have long-term limitations associated to toxicity, tolerability and risk for adverse effects requiring its intermittent use and close monitoring. Small molecules modulate proinflammatory cytokines, selectively inhibit signaling pathways and showing potential to treat inflammatory diseases in patients not responding to conventional treatments. Presently, small molecules available are phosphodiesterase 4 inhibitors or Janus kinase inhibitors. Other small molecules under development for psoriasis include fumaric acid esters, amygdalin analogs, protein kinase C inhibitors, mitogen-activated protein kinase inhibitors, spleen protein kinase inhibitors, other tyrosine kinase inhibitors, sphingosine 1-phosphate receptor agonists, and A3 adenosine receptor agonists. These new treatment options represent important advances in the development of specific drugs to respond to the goals of treatment and improve patient quality of life. PMID:26255795

  19. Electric Power Monthly, August 1990. [Glossary included

    SciTech Connect

    Not Available

    1990-11-29

    The Electric Power Monthly (EPM) presents monthly summaries of electric utility statistics at the national, Census division, and State level. The purpose of this publication is to provide energy decisionmakers with accurate and timely information that may be used in forming various perspectives on electric issues that lie ahead. Data includes generation by energy source (coal, oil, gas, hydroelectric, and nuclear); generation by region; consumption of fossil fuels for power generation; sales of electric power, cost data; and unusual occurrences. A glossary is included.

  20. Nuclear Power in China

    NASA Astrophysics Data System (ADS)

    Zhou, Yun

    2012-02-01

    In response to the Fukushima accident, China is strengthening its nuclear safety at reactors in operation, under construction and in preparation, including efforts to improve nuclear safety regulations and guidelines based on lessons learned from the accident. Although China is one of the major contributors in the global nuclear expansion, China's nuclear power industry is relatively young. Its nuclear safety regulators are less experienced compared to those in other major nuclear power countries. To realize China's resolute commitment to rapid growth of safe nuclear energy, detailed analyses of its nuclear safety regulatory system are required. This talk explains China's nuclear energy program and policy at first. It also explores China's governmental activities and future nuclear development after Fukushima accidents. At last, an overview of China's nuclear safety regulations and practices are provided. Issues and challenges are also identified for police makers, regulators, and industry professionals.

  1. Effects of Nuclear Weapons.

    ERIC Educational Resources Information Center

    Sartori, Leo

    1983-01-01

    Fundamental principles governing nuclear explosions and their effects are discussed, including three components of a nuclear explosion (thermal radiation, shock wave, nuclear radiation). Describes how effects of these components depend on the weapon's yield, its height of burst, and distance of detonation point. Includes effects of three…

  2. An easy approach for constructing vesicles by using aromatic molecules with β-cyclodextrin.

    PubMed

    Li, Shangyang; Zhang, Lin; Wang, Bo; Ma, Mingfang; Xing, Pengyao; Chu, Xiaoxiao; Zhang, Yimeng; Hao, Aiyou

    2015-03-01

    Vesicles were formed in aqueous solution using β-cyclodextrin (β-CD) complexes with a series of ultra-small aromatic molecules. The vesicles are easy to prepare without a complicated synthesis procedure and their structure was identified and characterized using various techniques, including transmission electron microscopy, atomic force microscopy and dynamic laser light scattering. Using the β-CD/l-phenylalanine system as a representative example, the structural factors that caused the self-assembly were revealed using proton nuclear magnetic resonance, Fourier transform infrared spectroscopy and X-ray diffraction. In addition, the vesicular architecture could be endowed with a diverse range of stimuli-responses, as a consequence of the selective addition of various guest molecules. It is anticipated that this novel assembly strategy could be further extended, and that it presents new opportunities for the development of nanocarriers and soft materials. PMID:25608115

  3. Molecular-beam spectroscopy of interhalogen molecules

    SciTech Connect

    Sherrow, S.A.

    1983-08-01

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.

  4. Electrokinetic concentration of charged molecules

    DOEpatents

    Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.; Garguilo, Michael G.

    2002-01-01

    A method for separating and concentrating charged species from uncharged or neutral species regardless of size differential. The method uses reversible electric field induced retention of charged species, that can include molecules and molecular aggregates such as dimers, polymers, multimers, colloids, micelles, and liposomes, in volumes and on surfaces of porous materials. The retained charged species are subsequently quantitatively removed from the porous material by a pressure driven flow that passes through the retention volume and is independent of direction thus, a multi-directional flow field is not required. Uncharged species pass through the system unimpeded thus effecting a complete separation of charged and uncharged species and making possible concentration factors greater than 1000-fold.

  5. Clinical nuclear medicine. [Handbook

    SciTech Connect

    Matin, P.

    1981-01-01

    ''Clinical Nuclear Medicine'' is an update to the author's ''Handbook of Clinical Nuclear Medicine.'' Sections on placental imaging, bone marrow imaging, biliary tract imaging and scintigraphy are included in the volume. (JMT)

  6. Biochips - Can molecules compute?

    NASA Astrophysics Data System (ADS)

    Tucker, J. B.

    1984-02-01

    In recent years the possibility has been considered to build 'biochip' computers, in which the silicon transistors of present machines would be replaced by large organic molecules or genetically engineered proteins. Two major advantages of such biochips over current devices would be related to vastly increased densities of computing elements, and entirely new styles of data processing, suited to such high-level tasks as pattern recognition and context-dependent analysis. The limitations of the semiconductor chip with respect to the density of elementary units due to size considerations and heat development could be overcome by making use of molecular switches. Attention is given to soliton switching, soliton logic, bulk molecular devices, analog biochips, 'intelligent' switches based on the employment of enzymes, robot vision, questions of biochip fabrication, protein engineering, and a strategy for the development of biochips.

  7. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another? PMID:17328425

  8. Ion-Molecule Chemistry in Titan's Ionosphere

    NASA Technical Reports Server (NTRS)

    Anicich, V. G.; McEwan, M. J.

    1996-01-01

    We present a summary of the information available from laboratory studies of ion-molecule reactions that is relevant to the chemistry occuring in Titan's ionopshere. Reaction information from the literature has been collated and we have measured many new reations, including some ion-atom reactions.

  9. Polarized nuclear target based on parahydrogen induced polarization

    SciTech Connect

    D. Budker, M.P. Ledbetter, S. Appelt, L.S. Bouchard, B. Wojtsekhowski

    2012-12-01

    We discuss a novel concept of a polarized nuclear target for accelerator fixed-target scattering experiments, which is based on parahydrogen induced polarization (PHIP). One may be able to reach a 33% free-proton polarization in the ethane molecule. The potential advantages of such a target include operation at zero magnetic field, fast ({approx}100 HZ) polarization oscillation (akin to polarization reversal), and operation with large intensity of an electron beam.

  10. Polarized nuclear target based on parahydrogen induced polarization

    NASA Astrophysics Data System (ADS)

    Budker, D.; Ledbetter, M. P.; Appelt, S.; Bouchard, L. S.; Wojtsekhowski, B.

    2012-12-01

    We discuss a novel concept of a polarized nuclear target for accelerator fixed-target scattering experiments, which is based on parahydrogen induced polarization (PHIP). One may be able to reach a 33% free-proton polarization in the ethane molecule. The potential advantages of such a target include operation at zero magnetic field, fast (˜100 Hz) polarization oscillation (akin to polarization reversal), and operation with large intensity of an electron beam.

  11. Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10.

    PubMed

    Yang, Wang-Yong; Gao, Rui; Southern, Mark; Sarkar, Partha S; Disney, Matthew D

    2016-01-01

    RNA is an important target for chemical probes of function and lead therapeutics; however, it is difficult to target with small molecules. One approach to tackle this problem is to identify compounds that target RNA structures and utilize them to multivalently target RNA. Here we show that small molecules can be identified to selectively bind RNA base pairs by probing a library of RNA-focused small molecules. A small molecule that selectively binds AU base pairs informed design of a dimeric compound (2AU-2) that targets the pathogenic RNA, expanded r(AUUCU) repeats, that causes spinocerebellar ataxia type 10 (SCA10) in patient-derived cells. Indeed, 2AU-2 (50 nM) ameliorates various aspects of SCA10 pathology including improvement of mitochondrial dysfunction, reduced activation of caspase 3, and reduction of nuclear foci. These studies provide a first-in-class chemical probe to study SCA10 RNA toxicity and potentially define broadly applicable compounds targeting RNA AU base pairs in cells. PMID:27248057

  12. Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10

    PubMed Central

    Yang, Wang-Yong; Gao, Rui; Southern, Mark; Sarkar, Partha S.; Disney, Matthew D.

    2016-01-01

    RNA is an important target for chemical probes of function and lead therapeutics; however, it is difficult to target with small molecules. One approach to tackle this problem is to identify compounds that target RNA structures and utilize them to multivalently target RNA. Here we show that small molecules can be identified to selectively bind RNA base pairs by probing a library of RNA-focused small molecules. A small molecule that selectively binds AU base pairs informed design of a dimeric compound (2AU-2) that targets the pathogenic RNA, expanded r(AUUCU) repeats, that causes spinocerebellar ataxia type 10 (SCA10) in patient-derived cells. Indeed, 2AU-2 (50 nM) ameliorates various aspects of SCA10 pathology including improvement of mitochondrial dysfunction, reduced activation of caspase 3, and reduction of nuclear foci. These studies provide a first-in-class chemical probe to study SCA10 RNA toxicity and potentially define broadly applicable compounds targeting RNA AU base pairs in cells. PMID:27248057

  13. VizieR Online Data Catalog: Partition functions for molecules and atoms (Barklem+, 2016)

    NASA Astrophysics Data System (ADS)

    Barklem, P. S.; Collet, R.

    2016-02-01

    The results and input data are presented in the following files. Table 1 contains dissociation energies from the literature, and final adopted values, for 291 molecules. The literature values are from the compilations of Huber & Herzberg (1979, Constants of Diatomic Molecules (Van Nostrand Reinhold), Luo (2007, Comprehensive Handbook of Chemical Bond Energies (CRC Press)) and G2 theory calculations of Curtiss et al. (1991, J. Chem. Phys., 94, 7221). Table 2 contains the input data for the molecular calculations including adopted dissociation energy, nuclear spins, molecular spectroscopic constants and their sources. There are 291 files, one for each molecule, labelled by the molecule name. The various molecular spectroscopic constants are as defined in the paper. Table 4 contains the first, second and third ionisation energies for all chemical elements from H to U. The data comes from the CRC Handbook of Chemistry and Physics (Haynes, W.M. 2010, CRC Handbook of Chemistry and Physics, 91st edn. (CRC Press, Taylor and Francis Group)). Table 5a contains a list of keys to bibliographic references for the atomic energy level data that was extracted from NIST Atomic Spectra Database and used in the present work to compute atomic partition functions. The citation keys are abbreviations of the full bibliographic references which are made available in Table 5b in BibTeX format. Table 5b contains the full bibliographic references for the atomic energy level data that was extracted from the NIST Atomic Spectra Database. Table 6 contains tabulated partition function data as a function of temperature for 291 molecules. Table 7 contains tabulated equilibrium constant data as a function of temperature for 291 molecules. Table 8 contains tabulated partition function data as a function of temperature for 284 atoms and ions. The paper should be consulted for further details. (10 data files).

  14. Modeling single-molecule detection statistics

    NASA Astrophysics Data System (ADS)

    Enderlein, Joerg; Robbins, David L.; Ambrose, W. P.; Goodwin, Peter M.; Keller, Richard A.

    1997-05-01

    We present experimental results of single B-phycoerythrin molecule detection in a fluid flow at different sample introduction rates. A new mathematical approach is used for calculating the resulting burst size distributions. The calculations are based upon a complete physical model including absorption, fluorescence and photobleaching characteristics of the fluorophore; its diffusion; the sample stream hydrodynamics; the spatially dependent optical detection efficiency; and the excitation laser beam characteristics. Special attention is paid to the phenomenon of `molecular noise'--fluctuations in the number of overlapping crossings of molecules through the detection volume. The importance of this study and its connections to experimental applications are discussed.

  15. Distal apolipoprotein C-III regulatory elements F to J act as a general modular enhancer for proximal promoters that contain hormone response elements. Synergism between hepatic nuclear factor-4 molecules bound to the proximal promoter and distal enhancer sites.

    PubMed

    Kardassis, D; Tzameli, I; Hadzopoulou-Cladaras, M; Talianidis, I; Zannis, V

    1997-01-01

    Transient transfection assays have shown that the distal apoC-III promoter segments that contain the regulatory elements F to J enhance the strength of the tandemly linked proximal apoA-I promoter 5- to 13-fold in hepatic (HepG2) cells. Activation in intestinal (CaCo-2) cells to levels comparable to those obtained in HepG2 cells requires a larger apoA-I promoter sequence that extends to nucleotide -1500 as well as the presence of hepatic nuclear factor-4 (HNF-4). The distal apoC-III regulatory elements can also enhance 4- to 8-fold the strength of the heterologous apoB promoter in HepG2 and CaCo-2 cells. Finally, these elements in the presence of HNF-4 enhance 14.5- to 18.5-fold the strength of the minimal adenovirus major late promoter linked to two copies of the hormone response element (HRE) AID of apoA-I in both HepG2 and CaCo-2 cells. In vitro mutagenesis of the promoter/enhancer cluster established that the enhancer activity is lost by a mutation in the HRE present in the 3' end of the regulatory element I (-736 to -714) and is reduced significantly by point mutations or deletions in one or more of the regulatory elements F to J of the apoC-III enhancer. The enhancer activity also requires the HREs of the proximal apoA-I promoter. The apoC-III enhancer can also restore the activity of the proximal apoA-I and apoB promoters that have been inactivated by mutations in CCAAT/enhancers binding protein binding sites, indicating that C/EBP may not participate in the synergistic activation of the promoter/enhancer cluster. The findings suggest that the regulatory elements F to J of the apoC-III promoter act as a general modular enhancer that can potentiate the strength of proximal promoters that contain HREs. Such potentiation in the HepG2 cells can be accounted for by synergistic interactions between HNF-4 or other nuclear hormone receptors bound to the proximal and distal HREs and SP1 or other factors bound to the apoC-III enhancer. Additional factors may be

  16. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    SciTech Connect

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  17. Microfluidic devices and methods including porous polymer monoliths

    DOEpatents

    Hatch, Anson V; Sommer, Gregory J; Singh, Anup K; Wang, Ying-Chih; Abhyankar, Vinay V

    2014-04-22

    Microfluidic devices and methods including porous polymer monoliths are described. Polymerization techniques may be used to generate porous polymer monoliths having pores defined by a liquid component of a fluid mixture. The fluid mixture may contain iniferters and the resulting porous polymer monolith may include surfaces terminated with iniferter species. Capture molecules may then be grafted to the monolith pores.

  18. Microfluidic devices and methods including porous polymer monoliths

    SciTech Connect

    Hatch, Anson V.; Sommer, Gregory j.; Singh, Anup K.; Wang, Ying-Chih; Abhyankar, Vinay

    2015-12-01

    Microfluidic devices and methods including porous polymer monoliths are described. Polymerization techniques may be used to generate porous polymer monoliths having pores defined by a liquid component of a fluid mixture. The fluid mixture may contain iniferters and the resulting porous polymer monolith may include surfaces terminated with iniferter species. Capture molecules may then be grafted to the monolith pores.

  19. Organ Preference of Cancer Metastasis and Metastasis-Related Cell Adhesion Molecules Including Carbohydrates.

    PubMed

    Kawaguchi, Takanori

    2016-01-01

    This review starts on one of our special interests, the organ preference of metastasis. We examined data on 1,117 autopsy cases and found that the organ distribution of metastasis of cancers of the lung, pancreas, stomach, colon, rectum, uterine cervix, liver, bile duct, and esophagus involved the lung, liver, adrenal gland, bone/bone marrow, lymph node, and pleura/peritoneum. Cancers of the kidney, thyroid, ovary, choriocarcinoma, and breast, however, manifested different metastatic patterns. The distribution of leukemia and lymphoma metastases was quite different from that of epithelial cancers. On the basis of experimental studies, we believe that the anatomical-mechanical hypothesis should be replaced by the microinjury hypothesis, which suggests that tissue microinjury induced by temporal tumor cell embolization is crucial for successful metastasis. This hypothesis may actually reflect the so-called inflammatory oncotaxis concept. To clarify the mechanisms underlying metastasis, we developed an experimental model system of a rat hepatoma AH7974 that embraced substrate adhesiveness. This model did not prove a relationship between substrate-adhesion potential and metastatic lung-colonizing potential of tumor cells, but metastatic potential was correlated with the expression of the laminin carbohydrate that was recognized by Griffonia (Bandeiraea) simplicifolia isolectin G4. Therefore, we investigated the relationship between carbohydrate expression profiles and metastasis and prognosis. We indeed found an intimate relationship between the carbohydrate expression of cancer cells and the progression of malignant tumors, organ preference of metastasis, metastatic potential of tumor cells, and prognosis of patients. PMID:26521885

  20. Beam dynamics in a storage ring for neutral (polar) molecules

    SciTech Connect

    Lambertson, Glen R.

    2003-05-01

    The force from a non-uniform electric field on the electric dipole moment of a molecule may be used to circulate and focus molecules in a storage ring. The nature of the forces from multipole electrodes for bending and focusing are described for strong-field-seeking and for weak-field-seeking molecules. Fringe-field forces are analyzed. Examples of storage ring designs are presented; these include long straight sections and provide bunching and acceleration.

  1. Sample preparation for single molecule localization microscopy.

    PubMed

    Allen, John R; Ross, Stephen T; Davidson, Michael W

    2013-11-21

    Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations. PMID:24084850

  2. Counterintuitive energy shifts in joint electron-nuclear-energy spectra of strong-field fragmentation of H2+

    NASA Astrophysics Data System (ADS)

    Wang, Zhuo; Li, Min; Zhou, Yueming; Li, Yang; Lan, Pengfei; Lu, Peixiang

    2016-01-01

    By numerically solving the time-dependent Schrödinger equation, we investigate electron-nuclear-energy sharing in strong-field fragmentation of the H2+ molecule. We find a counterintuitive energy shift in the joint electron-nuclear-energy spectrum. This energy shift becomes larger for lower nuclear energies. Through tracing the time evolution of the electron wave packet of bound states, we identify that the energy shift originates from the Stark effect due to the coupling of the ground state and the first exited state of the H2+ molecule in strong laser fields. We achieve a good agreement between the ab initio result and the analytic method that includes the Stark effect of molecules.

  3. Small Molecule Immunosensing Using Surface Plasmon Resonance

    PubMed Central

    Mitchell, John

    2010-01-01

    Surface plasmon resonance (SPR) biosensors utilize refractive index changes to sensitively detect mass changes at noble metal sensor surface interfaces. As such, they have been extensively applied to immunoassays of large molecules, where their high mass and use of sandwich immunoassay formats can result in excellent sensitivity. Small molecule immunosensing using SPR is more challenging. It requires antibodies or high-mass or noble metal labels to provide the required signal for ultrasensitive assays. Also, it can suffer from steric hindrance between the small antigen and large antibodies. However, new studies are increasingly meeting these and other challenges to offer highly sensitive small molecule immunosensor technologies through careful consideration of sensor interface design and signal enhancement. This review examines the application of SPR transduction technologies to small molecule immunoassays directed to different classes of small molecule antigens, including the steroid hormones, toxins, drugs and explosives residues. Also considered are the matrix effects resulting from measurement in chemically complex samples, the construction of stable sensor surfaces and the development of multiplexed assays capable of detecting several compounds at once. Assay design approaches are discussed and related to the sensitivities obtained. PMID:22163605

  4. Modelling the spectroscopic behaviour of hot molecules

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan

    2010-05-01

    At elevated temperatures the molecules absorb and emit light in a very complicated fashion which is hard to characterise on the basis of laboraroty measurement. Computed line lists of molecule transitions therefore provide a vital input for models of hot atmospheres. I will describe the calculation and use of such line lists including the BT2 water line list [1], which contains some 500 million distinct rotation-vibration transitions. This linelist proved crucial in the detection of water in extrasolar planet HD189733b and has been used extensively in atmospheric modelling. Illustrations will be given at the meeting. A new linelist for the ammonia molecule has just been completed [2] which shows that standard compilations for this molecule need to be improved. Progress on a more extensive linelist for hot ammonia and linelists for other molecules will be discussed at the meeting. [1] R.J. Barber, J. Tennyson, G.J. Harris and R.N. Tolchenov, Mon. Not. R. Astr. Soc., 368, 1087-1094 (2006) [2] S.N. Yurchenko, R.J. Barber, A. Yachmenev, W. Theil, P. Jensen and J. Tennyson, J. Phys. Chem. A, 113, 11845-11855 (2009).

  5. Electrochromic graphene molecules.

    PubMed

    Ji, Zhiqiang; Doorn, Stephen K; Sykora, Milan

    2015-04-28

    Polyclic aromatic hydrocarbons also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in situ on the surface of transparent nanocrystalline indium tin oxide (nc-ITO) electrodes and their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current, but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using a modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here, these were found to be E1,ox(0) = 0.77 ± 0.01 V and E2,ox(0) = 1.24 ± 0.02 V vs NHE for the first and second oxidation and E1,red(0) = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be nonideal. The nonideality factors associated with the oxidation and reduction processes are attributed to strong interactions between the GM redox centers. Under the conditions of potential cycling, GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component. PMID:25768313

  6. Electrochromic Graphene Molecules

    DOE PAGESBeta

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  7. Reactions of oriented molecules.

    PubMed

    Brooks, P R

    1976-07-01

    Beams of oriented molecules have been used to directly study geometrical requirements in chemical reactions. These studies have shown that reactivity is much greater in some orientations than others and demonstrated the existence of steric effects. For some reactions portions of the orientation results are in good accord with traditional views of steric hindrance, but for others it is clear that our chemical intuition needs recalibrating. Indeed, the information gained from simultaneously orienting the reactants and observing the scattering angle of the products may lead to new insights about the detailed mechanism of certain reactions. Further work must be done to extend the scope and detail of the studies described here. More detailed information is needed on the CH(3)I reaction and the CF(3)I reaction. The effects of alkyl groups of various sizes and alkali metals of various sizes are of interest. In addition, reactions where a long-lived complex is formed should be studied to see if orientation is important. Finally, it would be of interest to apply the technique to the sort of reactions that led to our interest in the first place: the S(N)2 displacements in alkyl halides where the fascinating Walden inversion occurs. PMID:17793988

  8. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole–dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  9. Adsorption kinetics of diatomic molecules.

    PubMed

    Burde, Jared T; Calbi, M Mercedes

    2014-05-01

    The adsorption dynamics of diatomic molecules on solid surfaces is examined by using a Kinetic Monte Carlo algorithm. Equilibration times at increasing loadings are obtained, and explained based on the elementary processes that lead to the formation of the adsorbed film. The ability of the molecules to change their orientation accelerates the overall uptake and leads to competitive kinetic behaviour between the different orientations. The dependence of the equilibration time on coverage follows the same decreasing trend obtained experimentally for ethane adsorption on closed-end carbon nanotube bundles. The exploration of molecule-molecule interaction effects on this trend provides relevant insights to understand the kinetic behaviour of other species, from simpler molecules to larger polyatomic molecules, adsorbing on surfaces with different binding strength. PMID:24654004

  10. Nuclear War and Science Teaching.

    ERIC Educational Resources Information Center

    Hobson, Art

    1983-01-01

    Suggests that science-related material on nuclear war be included in introductory courses. Lists nuclear war topics for physics, psychology, sociology, biology/ecology, chemistry, geography, geology/meteorology, mathematics, and medical science. Also lists 11 lectures on nuclear physics which include nuclear war topics. (JN)

  11. 8. VIEW OF RADIOGRAPHY EQUIPMENT, TEST METHODS INCLUDED RADIOGRAPHY AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. VIEW OF RADIOGRAPHY EQUIPMENT, TEST METHODS INCLUDED RADIOGRAPHY AND BETA BACKSCATTERING. (7/13/56) - Rocky Flats Plant, Non-Nuclear Production Facility, South of Cottonwood Avenue, west of Seventh Avenue & east of Building 460, Golden, Jefferson County, CO

  12. Trapping Single Molecules by Dielectrophoresis

    NASA Astrophysics Data System (ADS)

    Hölzel, Ralph; Calander, Nils; Chiragwandi, Zackary; Willander, Magnus; Bier, Frank F.

    2005-09-01

    We have trapped single protein molecules of R-phycoerythrin in an aqueous solution by an alternating electric field. A radio frequency voltage is applied to sharp nanoelectrodes and hence produces a strong electric field gradient. The resulting dielectrophoretic forces attract freely diffusing protein molecules. Trapping takes place at the electrode tips. Switching off the field immediately releases the molecules. The electric field distribution is computed, and from this the dielectrophoretic response of the molecules is calculated using a standard polarization model. The resulting forces are compared to the impact of Brownian motion. Finally, we discuss the experimental observations on the basis of the model calculations.

  13. Aromatic molecules as spintronic devices

    SciTech Connect

    Ojeda, J. H.; Orellana, P. A.; Laroze, D.

    2014-03-14

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

  14. Electrical Transport through Organic Molecules

    NASA Astrophysics Data System (ADS)

    Lau, C. N.; Chang, Shun-Chi; Williams, Stan

    2003-03-01

    We investigate electrical transport properties of single organic molecules using electromigration break junctions[1]. A self-assembled monolayer of various organic molecules such as 1,4-di(phenylethynyl-4'-methanethiol)benzene was grown on narrow metal wires, and single or a few molecules were incorporated into the junctions which were created by applying a large voltage and breaking the wires. The transport properties of these molecules were then measured at low temperatures. Latest experimental results will be discussed. [1] Park, J. et al, Nature, 417, 722 (2002); Liang W. et al, Nature, 417, 725 (2002).

  15. Nuclear Medicine

    MedlinePlus

    ... Parents/Teachers Resource Links for Students Glossary Nuclear Medicine What is nuclear medicine? What are radioactive tracers? ... funded researchers advancing nuclear medicine? What is nuclear medicine? Nuclear medicine is a medical specialty that uses ...

  16. Single-molecule spectroscopy and imaging over the decades.

    PubMed

    Moerner, W E; Shechtman, Yoav; Wang, Quan

    2015-01-01

    As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many

  17. Electrochromic Graphene Molecules

    SciTech Connect

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were found to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.

  18. CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule.

    PubMed

    Barletta, Paolo; Shirin, Sergei V; Zobov, Nikolai F; Polyansky, Oleg L; Tennyson, Jonathan; Valeev, Edward F; Császár, Attila G

    2006-11-28

    The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed. PMID:17144700

  19. Nuclear pursuits

    SciTech Connect

    Not Available

    1993-05-01

    This table lists quantities of warheads (in stockpile, peak number per year, total number built, number of known test explosions), weapon development milestones (developers of the atomic bomb and hydrogen bomb, date of first operational ICBM, first nuclear-powered naval SSN in service, first MIRVed missile deployed), and testing milestones (first fission test, type of boosted fission weapon, multistage thermonuclear test, number of months from fission bomb to multistage thermonuclear bomb, etc.), and nuclear infrastructure (assembly plants, plutonium production reactors, uranium enrichment plants, etc.). Countries included in the tally are the United States, Soviet Union, Britain, France, and China.

  20. Molecules into Cells: Specifying Spatial Architecture

    PubMed Central

    Harold, Franklin M.

    2005-01-01

    A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth. PMID:16339735

  1. Adhesion molecules in cutaneous inflammation.

    PubMed

    Barker, J N

    1995-01-01

    As in other organs, leukocyte adhesion molecules and their ligands play a major role in cutaneous inflammatory events both by directing leukocyte trafficking and by their effects on antigen presentation. Skin biopsies of inflamed skin from patients with diseases such as as psoriasis or atopic dermatitis reveal up-regulation of endothelial cell expression of P- and E-selectin, vascular cell adhesion molecule 1 and intercellular adhesion molecule 1. Studies of evolving lesions following UVB irradiation, Mantoux reaction or application of contact allergen, demonstrate that expression of these adhesion molecules parallels leukocyte infiltration into skin. When cutaneous inflammation is widespread (e.g. in erythroderma), soluble forms of these molecules are detectable in serum. In vitro studies predict that peptide mediators are important regulatory factors for endothelial adhesion molecules. Intradermal injection of the cytokines interleukin 1, tumour necrosis factor alpha and interferon gamma into normal human skin leads to induction of endothelial adhesion molecules with concomitant infiltration of leukocytes. In addition, neuropeptides rapidly induce P-selectin translocation to the cell membrane and expression of E-selectin. Adhesion molecules also play a crucial role as accessory molecules in the presentation of antigen to T lymphocytes by Langerhans' cells. Expression of selectin ligands by Langerhans' cells is up-regulated by various inflammatory stimuli, suggesting that adhesion molecules may be important in Langerhans' cell migration. The skin, because of its accessibility, is an ideal organ in which to study expression of adhesion molecules and their relationship to inflammatory events. Inflammatory skin diseases are common and inhibition of lymphocyte accumulation in skin is likely to prove of great therapeutic benefit. PMID:7587640

  2. Nitrogen molecule activation by excited states of copper

    SciTech Connect

    Sanchez-Zamora, M.; Novaro, O.; Ruiz, M.E. )

    1990-04-05

    Ab initio molecular orbital studies that include variational (with a multiconfiguration reference state of 200 states) and perturbational (including over 3 million configurations) configuration interaction calculations were addressed to the interaction of nitrogen molecules with copper. The Cu ground state {sup 2}S and first two excited states {sup 2}P and {sup 2}D were studied as they interact in different geometrical approaches (including side-on and end-on geometries) with ground-state N{sub 2} molecules.

  3. Performance of Bioactive Molecules on Cotton and Other Textiles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Four types of biologically active molecules were examined for their structure/activity relationships as applied to textile functionalization. Bio-molecules including enzymes, peptides, carbohydrates, and lipids have been found to retain their activity when linked to cotton fabrics. Wound dressing pr...

  4. X-ray characterization of solid small molecule organic materials

    SciTech Connect

    Billinge, Simon; Shankland, Kenneth; Shankland, Norman; Florence, Alastair

    2014-06-10

    The present invention provides, inter alia, methods of characterizing a small molecule organic material, e.g., a drug or a drug product. This method includes subjecting the solid small molecule organic material to x-ray total scattering analysis at a short wavelength, collecting data generated thereby, and mathematically transforming the data to provide a refined set of data.

  5. Molecules for Fluorescence Detection of Specific Chemicals

    NASA Technical Reports Server (NTRS)

    Fedor, Steve

    2008-01-01

    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  6. Disease allele-dependent small-molecule sensitivities in blood cells from monogenic diabetes

    PubMed Central

    Shaw, Stanley Y.; Blodgett, David M.; Ma, Maggie S.; Westly, Elizabeth C.; Clemons, Paul A.; Subramanian, Aravind; Schreiber, Stuart L.

    2011-01-01

    Even as genetic studies identify alleles that influence human disease susceptibility, it remains challenging to understand their functional significance and how they contribute to disease phenotypes. Here, we describe an approach to translate discoveries from human genetics into functional and therapeutic hypotheses by relating human genetic variation to small-molecule sensitivities. We use small-molecule probes modulating a breadth of targets and processes to reveal disease allele-dependent sensitivities, using cells from multiple individuals with an extreme form of diabetes (maturity onset diabetes of the young type 1, caused by mutation in the orphan nuclear receptor HNF4α). This approach enabled the discovery of small molecules that show mechanistically revealing and therapeutically relevant interactions with HNF4α in both lymphoblasts and pancreatic β-cells, including compounds that physically interact with HNF4α. Compounds including US Food and Drug Administration–approved drugs were identified that favorably modulate a critical disease phenotype, insulin secretion from β-cells. This method may suggest therapeutic hypotheses for other nonblood disorders. PMID:21183721

  7. NUCLEAR REACTOR CONTROL SYSTEM

    DOEpatents

    Epler, E.P.; Hanauer, S.H.; Oakes, L.C.

    1959-11-01

    A control system is described for a nuclear reactor using enriched uranium fuel of the type of the swimming pool and other heterogeneous nuclear reactors. Circuits are included for automatically removing and inserting the control rods during the course of normal operation. Appropriate safety circuits close down the nuclear reactor in the event of emergency.

  8. Revitalizing Nuclear Safety Research.

    ERIC Educational Resources Information Center

    National Academy of Sciences - National Research Council, Washington, DC.

    This report covers the general issues involved in nuclear safety research and points out the areas needing detailed consideration. Topics included are: (1) "Principles of Nuclear Safety Research" (examining who should fund, who should conduct, and who should set the agenda for nuclear safety research); (2) "Elements of a Future Agenda for Nuclear…

  9. Micro-Kelvin cold molecules.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-10-01

    We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.

  10. Featured Molecules: Sucrose and Vanillin

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-04-01

    The WebWare molecules of the month for April relate to the sense of taste. Apple Fool, the JCE Classroom Activity, mentions sucrose and vanillin and their use as flavorings. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  11. Proregenerative Properties of ECM Molecules

    PubMed Central

    Plantman, Stefan

    2013-01-01

    After traumatic injuries to the nervous system, regrowing axons encounter a complex microenvironment where mechanisms that promote regeneration compete with inhibitory processes. Sprouting and axonal regrowth are key components of functional recovery but are often counteracted by inhibitory molecules. This review covers extracellular matrix molecules that support neuron axonal outgrowth. PMID:24195084

  12. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  13. Enzyme molecules in solitary confinement.

    PubMed

    Liebherr, Raphaela B; Gorris, Hans H

    2014-01-01

    Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities. PMID:25221867

  14. Magnetoassociation of KRb Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

    2010-03-01

    I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231- 235.

  15. Magnetoassociation of KRb Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

    2010-03-01

    I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231-235.

  16. Molecule-hugging graphene nanopores.

    PubMed

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A; Branton, Daniel

    2013-07-23

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule's outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤ 0.6 nm along the length of the molecule. PMID:23836648

  17. Cold molecules, collisions and reactions

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-05-01

    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

  18. The influence of morphology on excitons in single conjugated molecules

    NASA Astrophysics Data System (ADS)

    Thiessen, Alexander

    The electronic properties of pi-conjugated molecules are strongly related to their molecular shape and morphology of assembly in three-dimensional space. Understanding the various structure-property relationships is relevant to the applications of these materials in optoelectronic devices such as organic light-emitting diodes, field effect transistors and photovoltaic cells. The fact that conjugated systems interact with visible light opens these materials to a plethora of noninvasive spectroscopic investigation techniques. In this work, electronic properties of different pi-conjugated systems are studied spectroscopically on the ensemble and the single molecule levels. Single molecule spectroscopy is advantageous in that it allows the investigation of the individual nuclear building blocks that contribute to the properties of the ensemble. Additionally, transient photoluminescence spectroscopy methods can provide useful insight into the temporal evolution of the emissive states. In combination with these methods, novel pi-conjugated model molecules are used to probe processes related to exciton dynamics. For the first time, the spatial localization of excited states is probed experimentally in a molecule with a circular chromophoric structure. In addition, a set of model molecules with different geometries is employed to study exciton relaxation in pi-conjugated systems. The molecular morphology is utilized to distinguish between processes such as nuclear reorganization and torsional relaxation. Furthermore, single molecule spectroscopy is used to study the electronic structure of individual polymer chains in the photovoltaic cell material poly-(3-hexylthiophene). Optical spectra of this polymer are known to change with the morphology of the bulk film. Single molecule studies reveal that individual polymer chains exhibit similar behavior and indicate that spectral diversity is an intrinsic property of single P3HT molecules. The main results of this work are the

  19. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  20. High performance photovoltaic applications using solution-processed small molecules.

    PubMed

    Chen, Yongsheng; Wan, Xiangjian; Long, Guankui

    2013-11-19

    Energy remains a critical issue for the survival and prosperity of humancivilization. Many experts believe that the eventual solution for sustainable energy is the use of direct solar energy as the main energy source. Among the options for renewable energy, photovoltaic technologies that harness solar energy offer a way to harness an unlimited resource and minimum environment impact in contrast with other alternatives such as water, nuclear, and wind energy. Currently, almost all commercial photovoltaic technologies use Si-based technology, which has a number of disadvantages including high cost, lack of flexibility, and the serious environmental impact of the Si industry. Other technologies, such as organic photovoltaic (OPV) cells, can overcome some of these issues. Today, polymer-based OPV (P-OPV) devices have achieved power conversion efficiencies (PCEs) that exceed 9%. Compared with P-OPV, small molecules based OPV (SM-OPV) offers further advantages, including a defined structure for more reproducible performance, higher mobility and open circuit voltage, and easier synthetic control that leads to more diversified structures. Therefore, while largely undeveloped, SM-OPV is an important emerging technology with performance comparable to P-OPV. In this Account, we summarize our recent results on solution-processed SM-OPV. We believe that solution processing is essential for taking full advantage of OPV technologies. Our work started with the synthesis of oligothiophene derivatives with an acceptor-donor-acceptor (A-D-A) structure. Both the backbone conjugation length and electron withdrawing terminal groups play an important role in the light absorption, energy levels and performance of the devices. Among those molecules, devices using a 7-thiophene-unit backbone and a 3-ethylrhodanine (RD) terminal unit produced a 6.1% PCE. With the optimized conjugation length and terminal unit, we borrowed from the results with P-OPV devices to optimize the backbone. Thus we

  1. Single-Molecule Electronics: Chemical and Analytical Perspectives.

    PubMed

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance. PMID:26048551

  2. Single-Molecule Electronics: Chemical and Analytical Perspectives

    NASA Astrophysics Data System (ADS)

    Nichols, Richard J.; Higgins, Simon J.

    2015-07-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  3. Energies, Polarizabilities, and Forces of Interacting Molecules at Long or Intermediate Range

    NASA Astrophysics Data System (ADS)

    Liang, Ying Q.

    Collision-induced molecular phenomena are widely researched subjects. In complement with other research, deriving new results to understand the nature and effects of the interaction between molecules at long or intermediate range is the main goal of this thesis. By applying Rayleigh-Schrodinger perturbation theory, we have obtained the molecular interaction energy to second order in terms of nonlocal polarizability densities. The derivation also includes the effects of an applied field. The nonlocal polarizability density alpha (r; r^', omega) plays a central role in this research. The polarizability density is a linear-response tensor that determines the electronic polarization induced at point r in a molecule, by an external electric field of frequency omega, acting at r^ '. When a nuclear position in the molecule shifts infinitesimally, we find that the change in alpha(r; r^', omega) is connected to the same hyperpolarizability beta_{alphabetagamma }(r; r^', omega, r^{' '}, 0) that describes the electronic charge distribution's response to external fields, i.e.: partialalpha_{ betagamma}(omega)/partial R ^{I}_alpha=int dr dr^' dr^ {''} beta _{betagammadelta}(r; r^', omega, r^{''}, 0) Z^{rm I} T_{deltaalpha}(r ^{''}, R^{rm I}). This is a generalization of the relationship between partialalpha_{beta gamma}(0)/partial R^{I} _alpha and beta_ {betagammadelta}(r; r^', r^ {''}).. Due to establishment of the relationships between partialalpha_{ betagamma}/partial R^{I }_alpha and beta _{betagammadelta}, we have obtained new analytical results for the forces acting on nuclei in a molecule. For the first time, we have proven the equivalence of forces from interaction energy calculations and those obtained via the Hellmann -Feynman theorem, order by order. We are also able to separate forces on nuclei in one of the interacting molecules (A) into those due to its "own" electrons vs. forces due to the charge distribution of the collision partner, B. By taking the long range

  4. Collision integrals for isotopic hydrogen molecules.

    NASA Technical Reports Server (NTRS)

    Brown, N. J.; Munn, R. J.

    1972-01-01

    The study was undertaken to determine the effects of reduced mass and differences in asymmetry on the collision integrals and thermal diffusion factors of isotopic hydrogen systems. Each system selected for study consisted of two diatoms, one in the j = 0 rotation state and the other in the j = 1 state. The molecules interacted with a Lennard-Jones type potential modified to include angular terms. A set of cross sections and collision integrals were obtained for each system.

  5. Excitation of muonic molecules ddμ and dtμ by super-intense attosecond soft X-ray laser pulses: Shaped post-laser-pulse muonic oscillations and enhancement of nuclear fusion

    NASA Astrophysics Data System (ADS)

    Bandrauk, André D.; Paramonov, Guennaddi K.

    2014-07-01

    The quantum dynamics of muonic molecular ions ddμ and dtμ excited by linearly polarized along the molecular (z)-axis super-intense laser pulses is studied beyond the Born-Oppenheimer approximation by the numerical solution of the time-dependent Schrödinger equation within a three-dimensional model, including the internuclear distance R and muon coordinates z and ρ. The peak-intensity of the super-intense laser pulses used in our simulations is I0 = 3.51 × 1022 W/cm2 and the wavelength is λl = 5 nm. In both ddμ and dtμ, expectation values and < ρ > of muon demonstrate "post-laser-pulse" oscillations after the ends of the laser pulses. In ddμ post-laser-pulse z-oscillations appear as shaped nonoverlapping "echo-pulses". In dtμ post-laser-pulse muonic z-oscillations appear as comparatively slow large-amplitude oscillations modulated with small-amplitude pulsations. The post-laser-pulse ρ-oscillations in both ddμ and dtμ appear, for the most part, as overlapping "echo-pulses". The post-laser-pulse oscillations do not occur if the Born-Oppenheimer approximation is employed. Power spectra generated due to muonic motion along both optically active z and optically passive ρ degrees of freedom are calculated. The fusion probability in dtμ can be increased by more than 11 times by making use of three sequential super-intense laser pulses. The energy released from the dt fusion in dtμ can by more than 20 GeV exceed the energy required to produce a usable muon and the energy of the laser pulses used to enhance the fusion. The possibility of power production from the laser-enhanced muon-catalyzed fusion is discussed.

  6. Small molecule control of bacterial biofilms

    PubMed Central

    Worthington, Roberta J.; Richards, Justin J.

    2012-01-01

    Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: 1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, 2) chemical library screening for compounds with anti-biofilm activity, and 3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity. PMID:22733439

  7. Molecules of significance in planetary aeronomy

    NASA Technical Reports Server (NTRS)

    Mohan, H.

    1979-01-01

    This monograph is basically devoted to spectroscopic information of the molecules of planetary interest. Only those molecules have been dealt with which have been confirmed spectroscopically to be present in the atmosphere of major planets of our solar system and play an important role in the aeronomy of the respective planets. An introduction giving the general conditions of planets and their atmospheres including the gaseous molecules is given. Some typical planetary spectra is presented and supported with a discussion on some basic concepts of optical absorption and molecular parameters that are important to the study of planetary atmospheres. Quantities like dipole moments, transition probabilities, Einstein coefficients and line strengths, radiative life times, absorption cross sections, oscillator strengths, line widths and profiles, equivalent widths, growth curves, bond strengths, electronic transition moments, Franck-Condon factors and r-centroids, etc., are discussed. Spectroscopic information and relevant data of 6 diatomic (HF, HCL, CO, H2, O2, N2) and 6 polyatomic (CO2, N2), O3, HeO, NH3, CH4) molecules are presented.

  8. SMPDB: The Small Molecule Pathway Database.

    PubMed

    Frolkis, Alex; Knox, Craig; Lim, Emilia; Jewison, Timothy; Law, Vivian; Hau, David D; Liu, Phillip; Gautam, Bijaya; Ly, Son; Guo, An Chi; Xia, Jianguo; Liang, Yongjie; Shrivastava, Savita; Wishart, David S

    2010-01-01

    The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in clinical metabolomics, transcriptomics, proteomics and systems biology. SMPDB provides exquisitely detailed, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the Human Metabolome Database (HMDB) or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable. SMPDB is available at: http://www.smpdb.ca. PMID:19948758

  9. Lesser-Known Molecules in Ovarian Carcinogenesis

    PubMed Central

    Lozneanu, Ludmila; Cojocaru, Elena; Giuşcă, Simona Eliza; Cărăuleanu, Alexandru; Căruntu, Irina-Draga

    2015-01-01

    Currently, the deciphering of the signaling pathways brings about new advances in the understanding of the pathogenic mechanism of ovarian carcinogenesis, which is based on the interaction of several molecules with different biochemical structure that, consequently, intervene in cell metabolism, through their role as regulators in proliferation, differentiation, and cell death. Given that the ensemble of biomarkers in OC includes more than 50 molecules the interest of the researchers focuses on the possible validation of each one's potential as prognosis markers and/or therapeutic targets. Within this framework, this review presents three protein molecules: ALCAM, c-FLIP, and caveolin, motivated by the perspectives provided through the current limited knowledge on their role in ovarian carcinogenesis and on their potential as prognosis factors. Their structural stability, once altered, triggers the initiation of the sequences characteristic for ovarian carcinogenesis, through their role as modulators for several signaling pathways, contributing to the disruption of cellular junctions, disturbance of pro-/antiapoptotic equilibrium, and alteration of transmission of the signals specific for the molecular pathways. For each molecule, the text is built as follows: (i) general remarks, (ii) structural details, and (iii) particularities in expression, from different tumors to landmarks in ovarian carcinoma. PMID:26339605

  10. Teaching Activities on Horizontal Nuclear Proliferation.

    ERIC Educational Resources Information Center

    Zola, John

    1990-01-01

    Provides learning activities concerning the horizontal proliferation of nuclear weapons. Includes step-by-step directions for four activities: (1) the life cycle of nuclear weapons; (2) nuclear nonproliferation: pros and cons; (3) the nuclear power/nuclear weapons connection; and (4) managing nuclear proliferation. (NL)

  11. Relative Sizes of Organic Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  12. Organic heterocyclic molecules become superalkalis.

    PubMed

    Reddy, G Naaresh; Giri, Santanab

    2016-09-21

    An organic molecule which behaves like a superalkali has been designed from an aromatic heterocyclic molecule, pyrrole. Using first-principles calculation and a systematic two-step approach, we can have superalkali molecules with a low ionization energy, even lower than that of Cs. Couple cluster (CCSD) calculation reveals that a new heterocycle, C3N2(CH3)5 derived from a well-known aromatic heterocycle, pyrrole (C4H5N) has an ionization energy close to 3.0 eV. A molecular dynamics calculation on C3N2(CH3)5 reveals that the structure is dynamically stable. PMID:27530344

  13. Nonsequential double ionization of molecules

    SciTech Connect

    Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Zakrzewski, Jakub; Eckhardt, Bruno

    2005-03-01

    Double ionization of diatomic molecules by short linearly polarized laser pulses is analyzed. We consider the final stage of the ionization process, that is the decay of a highly excited two electron molecule, which is formed after rescattering. The saddles of the effective adiabatic potential energy close to which simultaneous escape of electrons takes place are identified. Numerical simulations of the ionization of molecules show that the process can be dominated by either sequential or nonsequential events. In order to increase the ratio of nonsequential to sequential ionizations very short laser pulses should be applied.

  14. Resolving metal-molecule interfaces at single-molecule junctions

    PubMed Central

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-01-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT. PMID:27221947

  15. Resolving metal-molecule interfaces at single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-05-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT.

  16. Nuclear export of proteins and drug resistance in cancer

    PubMed Central

    Turner, Joel G.; Dawson, Jana; Sullivan, Daniel M.

    2015-01-01

    The intracellular location of a protein is crucial to its normal functioning in a cell. Cancer cells utilize the normal processes of nuclear-cytoplasmic transport through the nuclear pore complex of a cell to effectively evade anti-neoplastic mechanisms. CRM1-mediated export is increased in various cancers. Proteins that are exported in cancer include tumor-suppressive proteins such as retinoblastoma, APC, p53, BRAC1, FOXO proteins, INI1/hSNF5, galectin-3, Bok, nucleophosmin, RASSF2, Merlin, p21CIP, p27KIP1, N-WASP/FAK, estradiol receptor and Tob, drug targets topoisomerase I and IIα and BCR-ABL, and the molecular chaperone protein Hsp90. Here, we review in detail the current processes and known structures involved in the export of a protein through the nuclear pore complex. We also discuss the export receptor molecule CRM1 and its binding to the leucine-rich nuclear export signal of the cargo protein and the formation of a nuclear export trimer with RanGTP. The therapeutic potential of various CRM1 inhibitors will be addressed, including leptomycin B, ratjadone, KOS-2464, and specific small molecule inhibitors of CRM1, N-azolylacrylate analogs, FOXO export inhibitors, valtrate, acetoxychavicol acetate, CBS9106, and SINE inhibitors. We will also discuss examples of how drug resistance may be reversed by targeting the exported proteins topoisomerase IIα, BCR-ABL, and galectin-3. As effective and less toxic CRM1 export inhibitors become available, they may be used as both single agents and in combination with current chemotherapeutic drugs. We believe that the future development of low-toxicity, small-molecule CRM1 inhibitors may provide a new approach to treating cancer. PMID:22209898

  17. Unifying the rotational and permutation symmetry of nuclear spin states: Schur-Weyl duality in molecular physics.

    PubMed

    Schmiedt, Hanno; Jensen, Per; Schlemmer, Stephan

    2016-08-21

    In modern physics and chemistry concerned with many-body systems, one of the mainstays is identical-particle-permutation symmetry. In particular, both the intra-molecular dynamics of a single molecule and the inter-molecular dynamics associated, for example, with reactive molecular collisions are strongly affected by selection rules originating in nuclear-permutation symmetry operations being applied to the total internal wavefunctions, including nuclear spin, of the molecules involved. We propose here a general tool to determine coherently the permutation symmetry and the rotational symmetry (associated with the group of arbitrary rotations of the entire molecule in space) of molecular wavefunctions, in particular the nuclear-spin functions. Thus far, these two symmetries were believed to be mutually independent and it has even been argued that under certain circumstances, it is impossible to establish a one-to-one correspondence between them. However, using the Schur-Weyl duality theorem we show that the two types of symmetry are inherently coupled. In addition, we use the ingenious representation-theory technique of Young tableaus to represent the molecular nuclear-spin degrees of freedom in terms of well-defined mathematical objects. This simplifies the symmetry classification of the nuclear wavefunction even for large molecules. Also, the application to reactive collisions is very straightforward and provides a much simplified approach to obtaining selection rules. PMID:27544099

  18. Message in a molecule.

    PubMed

    Sarkar, Tanmay; Selvakumar, Karuthapandi; Motiei, Leila; Margulies, David

    2016-01-01

    Since ancient times, steganography, the art of concealing information, has largely relied on secret inks as a tool for hiding messages. However, as the methods for detecting these inks improved, the use of simple and accessible chemicals as a means to secure communication was practically abolished. Here, we describe a method that enables one to conceal multiple different messages within the emission spectra of a unimolecular fluorescent sensor. Similar to secret inks, this molecular-scale messaging sensor (m-SMS) can be hidden on regular paper and the messages can be encoded or decoded within seconds using common chemicals, including commercial ingredients that can be obtained in grocery stores or pharmacies. Unlike with invisible inks, however, uncovering these messages by an unauthorized user is almost impossible because they are protected by three different defence mechanisms: steganography, cryptography and by entering a password, which are used to hide, encrypt or prevent access to the information, respectively. PMID:27138465

  19. Message in a molecule

    PubMed Central

    Sarkar, Tanmay; Selvakumar, Karuthapandi; Motiei, Leila; Margulies, David

    2016-01-01

    Since ancient times, steganography, the art of concealing information, has largely relied on secret inks as a tool for hiding messages. However, as the methods for detecting these inks improved, the use of simple and accessible chemicals as a means to secure communication was practically abolished. Here, we describe a method that enables one to conceal multiple different messages within the emission spectra of a unimolecular fluorescent sensor. Similar to secret inks, this molecular-scale messaging sensor (m-SMS) can be hidden on regular paper and the messages can be encoded or decoded within seconds using common chemicals, including commercial ingredients that can be obtained in grocery stores or pharmacies. Unlike with invisible inks, however, uncovering these messages by an unauthorized user is almost impossible because they are protected by three different defence mechanisms: steganography, cryptography and by entering a password, which are used to hide, encrypt or prevent access to the information, respectively. PMID:27138465

  20. Moving Molecules and Mothball Madness.

    ERIC Educational Resources Information Center

    Strain, John

    1993-01-01

    Describes concrete demonstrations on the states of matter. In the first demonstration, students represent molecules; and, in the second demonstration, moth balls are heated to produce a change of state. (PR)

  1. Surface chemistry of deuterated molecules

    NASA Astrophysics Data System (ADS)

    Tielens, A. G. G. M.

    1983-03-01

    The chemical composition of grain mantles is calculated in order to determine the concentration of deuterated molecules relative to their hydrogenated counterparts in grain mantles. The computation takes into account reactions involving deuterium in the gas phase and on grain surfaces. The results show that the abundance of deuterium molecules in grain mantles is much higher than expected on the basis of the cosmic abundance ratio of D to H. HDCO has a relatively high abundance in grain mantles as compared to other deuterated molecules, due to the fact that H abstraction from HDCO has a lower activation barrier than D abstraction. The infrared characteristics of the calculated grain mantles are discussed and observational tests of the model calcultions are suggested. The contribution of grain surface chemistry to the concentration of molecules in the gas phase is briefly considered.

  2. Cobalt single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Yang, En-Che; Hendrickson, David N.; Wernsdorfer, Wolfgang; Nakano, Motohiro; Zakharov, Lev N.; Sommer, Roger D.; Rheingold, Arnold L.; Ledezma-Gairaud, Marisol; Christou, George

    2002-05-01

    A cobalt molecule that functions as a single-molecule magnet, [Co4(hmp)4(MeOH)4Cl4], where hmp- is the anion of hydroxymethylpyridine, is reported. The core of the molecule consists of four Co(II) cations and four hmp- oxygen atom ions at the corners of a cube. Variable-field and variable-temperature magnetization data have been analyzed to establish that the molecule has a S=6 ground state with considerable negative magnetoanisotropy. Single-ion zero-field interactions (DSz2) at each cobalt ion are the origin of the negative magnetoanisotropy. A single crystal of the compound was studied by means of a micro-superconducting quantum interference device magnetometer in the range of 0.040-1.0 K. Hysteresis was found in the magnetization versus magnetic field response of this single crystal.

  3. Molecule-hugging graphene nanopores

    PubMed Central

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel

    2013-01-01

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule. PMID:23836648

  4. Single-Molecule DNA Analysis

    NASA Astrophysics Data System (ADS)

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

    The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

  5. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  6. Nuclear power in space

    NASA Astrophysics Data System (ADS)

    Written and verbal testimony presented before the House Subcommittee on Energy Research and Development is documented. Current research efforts related to space nuclear power are discussed including the SP-100 Space Reactor Program, development of radioisotope thermoelectric generators, and the Advanced Nuclear Systems Program. Funding, research and test facilities, specific space mission requirements, and the comparison of solar and nuclear power systems are addressed. Witnesses included representatives from DOD, NASA, DOE, universities, and private industry.

  7. Collisional decoherence of polar molecules

    NASA Astrophysics Data System (ADS)

    Walter, Kai; Stickler, Benjamin A.; Hornberger, Klaus

    2016-06-01

    The quantum state of motion of a large and rotating polar molecule can lose coherence through the collisions with gas atoms. We show how the associated quantum master equation for the center of mass can be expressed in terms of the orientationally averaged differential and total scattering cross sections, for which we provide approximate analytic expressions. The master equation is then utilized to quantify collisional decoherence in a interference experiment with polar molecules.

  8. Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive.

    PubMed

    Childs-Disney, Jessica L; Hoskins, Jason; Rzuczek, Suzanne G; Thornton, Charles A; Disney, Matthew D

    2012-05-18

    RNA is an important drug target, but it is difficult to design or discover small molecules that modulate RNA function. In the present study, we report that rationally designed, modularly assembled small molecules that bind the RNA that causes myotonic dystrophy type 1 (DM1) are potently bioactive in cell culture models. DM1 is caused when an expansion of r(CUG) repeats, or r(CUG)(exp), is present in the 3' untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) mRNA. r(CUG)(exp) folds into a hairpin with regularly repeating 5'CUG/3'GUC motifs and sequesters muscleblind-like 1 protein (MBNL1). A variety of defects are associated with DM1, including (i) formation of nuclear foci, (ii) decreased translation of DMPK mRNA due to its nuclear retention, and (iii) pre-mRNA splicing defects due to inactivation of MBNL1, which controls the alternative splicing of various pre-mRNAs. Previously, modularly assembled ligands targeting r(CUG)(exp) were designed using information in an RNA motif-ligand database. These studies showed that a bis-benzimidazole (H) binds the 5'CUG/3'GUC motif in r(CUG)(exp.) Therefore, we designed multivalent ligands to bind simultaneously multiple copies of this motif in r(CUG)(exp). Herein, we report that the designed compounds improve DM1-associated defects including improvement of translational and pre-mRNA splicing defects and the disruption of nuclear foci. These studies may establish a foundation to exploit other RNA targets in genomic sequence. PMID:22332923

  9. Rationally Designed Small Molecules Targeting the RNA That Causes Myotonic Dystrophy Type 1 Are Potently Bioactive

    PubMed Central

    Childs-Disney, Jessica L.; Hoskins, Jason; Rzuczek, Suzanne G.; Thornton, Charles A.; Disney, Matthew D.

    2012-01-01

    RNA is an important drug target, but it is difficult to design or discover small molecules that modulate RNA function. In the present study, we report that rationally designed, modularly assembled small molecules that bind the RNA that causes myotonic dystrophy type 1 (DM1) are potently bioactive in cell culture models. DM1 is caused when an expansion of r(CUG) repeats, or r(CUG)exp, is present in the 3′ untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) mRNA. r(CUG)exp folds into a hairpin with regularly repeating 5′CUG/3′GUC motifs and sequester muscleblind-like 1 protein (MBNL1). A variety of defects are associated with DM1 including: (i) formation of nuclear foci, (ii) decreased translation of DMPK mRNA due to its nuclear retention, and (iii) pre-mRNA splicing defects due to inactivation of MBNL1, which controls the alternative splicing of various pre-mRNAs. Previously, modularly assembled ligands targeting r(CUG)exp were designed using information in an RNA motif-ligand database. These studies showed that a bis-benzimidazole (H) binds the 5′CUG/3′GUC motif in r(CUG)exp. Therefore, we designed multivalent ligands to bind multiple copies of this motif simultaneously in r(CUG)exp. Herein, we report that the designed compounds improve DM1-associated defects including improvement of translational and pre-mRNA splicing defects and the disruption of nuclear foci. These studies may establish a foundation to exploit other RNA targets in genomic sequence. PMID:22332923

  10. Nanochannel Based Single Molecule Recycling

    PubMed Central

    Lesoine, John F.; Venkataraman, Prahnesh A.; Maloney, Peter C.; Dumont, Mark

    2012-01-01

    We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering. PMID:22662745

  11. Computation of Free Molecular Flow in Nuclear Materials

    SciTech Connect

    Casella, Andrew M.; Loyalka, Sudarsham K.; Hanson, Brady D.

    2009-11-11

    Generally the transport of gases and vapors in nuclear materials is adequately described by the diffusion equation with an effective diffusion coefficient. There are instances however, such as transport through porous or cracked media (nuclear fuels, cladding and coating materials, fuel-cladding gap, graphite, rocks, soil) where the diffusion description has limitations. In general, molecular transport is governed by intermolecular forces and collisions (interactions between multiple gas/vapor molecules) and by molecule-surface interactions. However, if nano-scale pathways exist within these materials, as has been suggested, then molecular transport can be characterized as being in the free-molecular flow regime where intermolecular interactions can be ignored and flow is determined entirely by molecule-surface collisions. Our purpose in this investigation is to focus on free molecular transport in fine capillaries of a range of shapes and to explore the effect of geometry on this transport. We have employed Monte Carlo techniques in our calculations, and for simple geometries we have benchmarked our results against some analytical and previously available results. We have used Mathematica® which has exceptional built-in symbolic and graphical capabilities, permitting easy handling of the complicated geometries and good visualization of the results. Our computations provide insights into the role of geometry in molecular transport in nuclear materials with narrow pathways for flows, and also will be useful in guiding computations that include intermolecular collisions and more realistic gas-surface collision operators.

  12. Nuclear power and nuclear weapons

    SciTech Connect

    Vaughen, V.C.A.

    1983-01-01

    The proliferation of nuclear weapons and the expanded use of nuclear energy for the production of electricity and other peaceful uses are compared. The difference in technologies associated with nuclear weapons and nuclear power plants are described.

  13. Fluorescence Polarization Assays in Small Molecule Screening

    PubMed Central

    Lea, Wendy A.; Simeonov, Anton

    2011-01-01

    Importance of the field Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field has been symbolized by the facile adoption of FP in high-throughput screening (HTS) and small molecule drug discovery of an increasing range of target classes. Areas covered in this review The article provides a brief overview on the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including G-protein coupled receptors (GPCRs), enzymes and protein-protein interactions (PPIs). The strengths and weaknesses of this method, practical considerations in assay design, novel applications, and future directions are also discussed. What the reader will gain The reader will be informed of the most recent advancements and future directions of FP application to small molecule screening. Take home message In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor binding studies. PMID:22328899

  14. Symmetry Beyond Perturbation Theory: Floppy Molecules and Rotation-Vibration States

    NASA Astrophysics Data System (ADS)

    Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per

    2015-06-01

    In the customary approach to the theoretical description of the nuclear motion in molecules, the molecule is seen as a near-static structure rotating in space. Vibrational motion causing small structural deformations induces a perturbative treatment of the rotation-vibration interaction, which fails in fluxional molecules, where all vibrational motions are large compared to the linear extension of the molecule. An example is protonated methane (CH_5^+). For this molecule, customary theory fails to simulate reliably even the low-energy spectrum. Within the traditional view of rotation and vibration being near-separable, rotational and vibrational wavefunctions can be symmetry classified separately in the molecular symmetry (MS) group. In the present contribution we discuss a fundamental group theoretical approach to the problem of determining the symmetries of molecular rotation-vibration states. We will show that all MS groups discussed so far are subgroups of the special orthogonal group in three dimensions SO(3) This leads to a group theoretical foundation of the technique of equivalent rotations. The MS group of protonated methane (G240) represents, to the best of our knowledge, the first example of an MS group which is not a subgroup of SO(3) (nor of O(3) nor of SU(2)). Because of this, a separate symmetry classification of vibrational and rotational wavefunctions becomes impossible in this MS group, consistent with the fact that a decoupling of vibrational and rotational motion is impossible. We want to discuss the consequences of this. In conclusion, we show that the prototypical floppy molecule CH_5^+ represents a new class of molecules, where usual group theoretical methods for determining selection rules and spectral assignments fail so that new methods have to be developed. P. Kumar and D. Marx, Physical Chemistry Chemical Physics 8, 573 (2006) Z. Jin, B. J. Braams, and J. M. Bowman, The Journal of Physical Chemistry A 110, 1569 (2006) A. S. Petit, J. E

  15. Neoclassical Transport Including Collisional Nonlinearity

    SciTech Connect

    Candy, J.; Belli, E. A.

    2011-06-10

    In the standard {delta}f theory of neoclassical transport, the zeroth-order (Maxwellian) solution is obtained analytically via the solution of a nonlinear equation. The first-order correction {delta}f is subsequently computed as the solution of a linear, inhomogeneous equation that includes the linearized Fokker-Planck collision operator. This equation admits analytic solutions only in extreme asymptotic limits (banana, plateau, Pfirsch-Schlueter), and so must be solved numerically for realistic plasma parameters. Recently, numerical codes have appeared which attempt to compute the total distribution f more accurately than in the standard ordering by retaining some nonlinear terms related to finite-orbit width, while simultaneously reusing some form of the linearized collision operator. In this work we show that higher-order corrections to the distribution function may be unphysical if collisional nonlinearities are ignored.

  16. Families classification including multiopposition asteroids

    NASA Astrophysics Data System (ADS)

    Milani, Andrea; Spoto, Federica; Knežević, Zoran; Novaković, Bojan; Tsirvoulis, Georgios

    2016-01-01

    In this paper we present the results of our new classification of asteroid families, upgraded by using catalog with > 500,000 asteroids. We discuss the outcome of the most recent update of the family list and of their membership. We found enough evidence to perform 9 mergers of the previously independent families. By introducing an improved method of estimation of the expected family growth in the less populous regions (e.g. at high inclination) we were able to reliably decide on rejection of one tiny group as a probable statistical fluke. Thus we reduced our current list to 115 families. We also present newly determined ages for 6 families, including complex 135 and 221, improving also our understanding of the dynamical vs. collisional families relationship. We conclude with some recommendations for the future work and for the family name problem.

  17. TRAF molecules in cell signaling and in human diseases

    PubMed Central

    2013-01-01

    The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of intracellular proteins were originally identified as signaling adaptors that bind directly to the cytoplasmic regions of receptors of the TNF-R superfamily. The past decade has witnessed rapid expansion of receptor families identified to employ TRAFs for signaling. These include Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), T cell receptor, IL-1 receptor family, IL-17 receptors, IFN receptors and TGFβ receptors. In addition to their role as adaptor proteins, most TRAFs also act as E3 ubiquitin ligases to activate downstream signaling events. TRAF-dependent signaling pathways typically lead to the activation of nuclear factor-κBs (NF-κBs), mitogen-activated protein kinases (MAPKs), or interferon-regulatory factors (IRFs). Compelling evidence obtained from germ-line and cell-specific TRAF-deficient mice demonstrates that each TRAF plays indispensable and non-redundant physiological roles, regulating innate and adaptive immunity, embryonic development, tissue homeostasis, stress response, and bone metabolism. Notably, mounting evidence implicates TRAFs in the pathogenesis of human diseases such as cancers and autoimmune diseases, which has sparked new appreciation and interest in TRAF research. This review presents an overview of the current knowledge of TRAFs, with an emphasis on recent findings concerning TRAF molecules in signaling and in human diseases. PMID:23758787

  18. Transport of fullerene molecules along graphene nanoribbons

    PubMed Central

    Savin, Alexander V.; Kivshar, Yuri S.

    2012-01-01

    We study the motion of C60 fullerene molecules and short-length carbon nanotubes on graphene nanoribbons. We reveal that the character of the motion of C60 depends on temperature: for T < 150 K the main type of motion is sliding along the surface, but for higher temperatures the sliding is replaced by rocking and rolling. Modeling of the buckyball with an included metal ion demonstrates that this molecular complex undergoes a rolling motion along the nanoribbon with the constant velocity under the action of a constant electric field. The similar effect is observed in the presence of the heat gradient applied to the nanoribbon, but mobility of carbon structures in this case depends largely on their size and symmetry, such that larger and more asymmetric structures demonstrate much lower mobility. Our results suggest that both electorphoresis and thermophoresis can be employed to control the motion of carbon molecules and fullerenes. PMID:23259049

  19. Computer display and manipulation of biological molecules

    NASA Technical Reports Server (NTRS)

    Coeckelenbergh, Y.; Macelroy, R. D.; Hart, J.; Rein, R.

    1978-01-01

    This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

  20. Small molecule inhibition of RISC loading.

    PubMed

    Tan, Grace S; Chiu, Chun-Hao; Garchow, Barry G; Metzler, David; Diamond, Scott L; Kiriakidou, Marianthi

    2012-02-17

    Argonaute proteins are the core components of the microRNP/RISC. The biogenesis and function of microRNAs and endo- and exo- siRNAs are regulated by Ago2, an Argonaute protein with RNA binding and nuclease activities. Currently, there are no in vitro assays suitable for large-scale screening of microRNP/RISC loading modulators. We describe a novel in vitro assay that is based on fluorescence polarization of TAMRA-labeled RNAs loaded to human Ago2. Using this assay, we identified potent small-molecule inhibitors of RISC loading, including aurintricarboxylic acid (IC(50) = 0.47 μM), suramin (IC(50) = 0.69 μM), and oxidopamine HCL (IC(50) = 1.61 μM). Small molecules identified by this biochemical screening assay also inhibited siRNA loading to endogenous Ago2 in cultured cells. PMID:22026461

  1. Interstellar molecules - Formation in solar nebulae

    NASA Technical Reports Server (NTRS)

    Anders, E.

    1973-01-01

    Herbig's (1970) hypothesis that solar nebulae might be the principal source of interstellar grains and molecules is investigated. The investigation includes the determination of physical and chemical conditions in the early solar system. The production of organic compounds in the solar nebula is studied, and the compounds in meteorites are compared with those obtained in Miller-Urey and Fischer-Tropsch-type (FTT) reactions, taking into consideration aliphatic hydrocarbons, aromatic hydrocarbons, purines, pyrimidines, amino acids, porphyrins, and aspects of carbon-isotope fractionation. It is found that FTT reactions account reasonably well for all well-established features of organic matter in meteorites investigated. The distribution of compounds produced by FTT reactions is compared with the distribution of interstellar molecules. Biological implications of the results are considered.

  2. Nuclear Magnetic Conduits

    NASA Astrophysics Data System (ADS)

    Desantis, Rich

    2008-10-01

    Point charges are not conduits of magnetism. Vacuum gaps between charges prevent superconductivity. Magnetism occurs w/o charge velocity. A changing magnetic field can add magnetism, w/o magnetism's centripetal force adding speed. Voltage is not charge repulsion energy. Passing electrons through a stationary electron's field cannot reduce its field. Passing the external electrons through a charged capacitor's field discharges the capacitor. Chemical bonds extend between atoms. A superconductive magnet contains a superconductive molecule, the length of its wire. Superconductivity dictates that chemical bonding material is non-vacuum and non-point charge. Its unit is an electron/proton fusion called an ABION. Unpaired abions attract all other unpaired abions within or between atoms. Paired abions have reduced attraction for other abions. Helium is inert because its abions are paired. A lithium atom includes an unpaired abion. Superconductive abions are nuclear magnetic conduits. Equality of transference numbers in electrochemistry is evidence of conduits. In fuel cells and semiconductors, paired voltage-induced redox reactions convert lines of abions into conduits. This temporarily converts bulk insulators to conductors.

  3. Micro injector sample delivery system for charged molecules

    DOEpatents

    Davidson, James C.; Balch, Joseph W.

    1999-11-09

    A micro injector sample delivery system for charged molecules. The injector is used for collecting and delivering controlled amounts of charged molecule samples for subsequent analysis. The injector delivery system can be scaled to large numbers (>96) for sample delivery to massively parallel high throughput analysis systems. The essence of the injector system is an electric field controllable loading tip including a section of porous material. By applying the appropriate polarity bias potential to the injector tip, charged molecules will migrate into porous material, and by reversing the polarity bias potential the molecules are ejected or forced away from the tip. The invention has application for uptake of charged biological molecules (e.g. proteins, nucleic acids, polymers, etc.) for delivery to analytical systems, and can be used in automated sample delivery systems.

  4. Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

    PubMed Central

    Hines, Keegan E.; Bankston, John R.; Aldrich, Richard W.

    2015-01-01

    The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

  5. Computer systems for annotation of single molecule fragments

    DOEpatents

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  6. Electron-driven excitations and dissociation of molecules

    SciTech Connect

    Miller, Greg; Orel, Ann E.

    2015-02-13

    This program studied how energy is interchanged in electron and photon collisions with molecules leading to ex-citation and dissociation. Modern ab initio techniques, both for the photoionization and electron scattering, and the subsequent nuclear dynamics studies, are used to accurately treat these problems. This work addresses vibrational ex-citation and dissociative attachment following electron impact, and the dynamics following inner shell photoionzation. These problems are ones for which a full multi-dimensional treatment of the nuclear dynamics is essential and where non-adiabatic effects are expected to be important.

  7. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-01

    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules. PMID:26760444

  8. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  9. Dissociation dynamics of diatomic molecules in intense fields

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, Maia

    We study the dynamics of diatomic molecules (dimers) in intense IR and XUV laser fields theoretically and compare the results with measured data in collaboration with different experimental groups worldwide. The first three chapters of the thesis cover the introduction and the background on solving time-independent and time-dependent Schrodinger equation. The numerical results in this thesis are presented in four chapters, three of which are focused on diatomic molecules in IR fields. The last one concentrates on diatomic molecules in XUV pulses. The study of nuclear dynamics of H2 or D2 molecules in IR pulses is given in Chapter 4. First, we investigate the optimal laser parameters for observing field-induced bond softening and bond hardening in D2+. Next, the nuclear dynamics of H2 + molecular ions in intense laser fields are investigated by analyzing their fragment kinetic-energy release (KER) spectra as a function of the pump-probe delay τ Lastly, the electron localization is studied for long circularly polarized laser pulses. Chapter 5 covers the dissociation dynamics of O2+ in an IR laser field. The fragment KER spectra are analyzed as a function of the pump-probe delay τ Within the Born-Oppenheimer approximation, we calculate ab-initio adiabatic potential-energy curves and their electric dipole couplings, using the quantum chemistry code GAMESS. In Chapter 6, the dissociation dynamics of the noble gas dimer ions He 2+, Ne2+, Ar2 +, Kr2+, and Xe2 + is investigated in ultrashort pump and probe laser pulses of different wavelengths. We observe a striking "delay gap" in the pump-probe-delay-dependent KER spectrum only if the probe-pulse wavelength exceeds the pump-pulse wavelength. Comparing pump-probe-pulse-delay dependent KER spectra for different noble gas dimer cations, we quantitatively discuss quantum-mechanical versus classical aspects of the nuclear vibrational motion as a function of the nuclear mass. Chapter 7 focuses on diatomic molecules in XUV

  10. Nuclear rights - nuclear wrongs

    SciTech Connect

    Paul, E.F.; Miller, F.D.; Paul, J.; Ahrens, J.

    1986-01-01

    This book contains 11 selections. The titles are: Three Ways to Kill Innocent Bystanders: Some Conundrums Concerning the Morality of War; The International Defense of Liberty; Two Concepts of Deterrence; Nuclear Deterrence and Arms Control; Ethical Issues for the 1980s; The Moral Status of Nuclear Deterrent Threats; Optimal Deterrence; Morality and Paradoxical Deterrence; Immoral Risks: A Deontological Critique of Nuclear Deterrence; No War Without Dictatorship, No Peace Without Democracy: Foreign Policy as Domestic Politics; Marxism-Leninism and its Strategic Implications for the United States; Tocqueveille War.

  11. Small molecule annotation for the Protein Data Bank.

    PubMed

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. PMID:25425036

  12. Uniquely designed nuclear structures of lower eukaryotes.

    PubMed

    Iwamoto, Masaaki; Hiraoka, Yasushi; Haraguchi, Tokuko

    2016-06-01

    The nuclear structures of lower eukaryotes, specifically protists, often vary from those of yeasts and metazoans. Several studies have demonstrated the unique and fascinating features of these nuclear structures, such as a histone-independent condensed chromatin in dinoflagellates and two structurally distinct nuclear pore complexes in ciliates. Despite their unique molecular/structural features, functions required for formation of their cognate molecules/structures are highly conserved. This provides important information about the structure-function relationship of the nuclear structures. In this review, we highlight characteristic nuclear structures found in lower eukaryotes, and discuss their attractiveness as potential biological systems for studying nuclear structures. PMID:26963276

  13. Stochastic electrotransport selectively enhances the transport of highly electromobile molecules.

    PubMed

    Kim, Sung-Yon; Cho, Jae Hun; Murray, Evan; Bakh, Naveed; Choi, Heejin; Ohn, Kimberly; Ruelas, Luzdary; Hubbert, Austin; McCue, Meg; Vassallo, Sara L; Keller, Philipp J; Chung, Kwanghun

    2015-11-17

    Nondestructive chemical processing of porous samples such as fixed biological tissues typically relies on molecular diffusion. Diffusion into a porous structure is a slow process that significantly delays completion of chemical processing. Here, we present a novel electrokinetic method termed stochastic electrotransport for rapid nondestructive processing of porous samples. This method uses a rotational electric field to selectively disperse highly electromobile molecules throughout a porous sample without displacing the low-electromobility molecules that constitute the sample. Using computational models, we show that stochastic electrotransport can rapidly disperse electromobile molecules in a porous medium. We apply this method to completely clear mouse organs within 1-3 days and to stain them with nuclear dyes, proteins, and antibodies within 1 day. Our results demonstrate the potential of stochastic electrotransport to process large and dense tissue samples that were previously infeasible in time when relying on diffusion. PMID:26578787

  14. SPLINTS: small-molecule protein ligand interface stabilizers.

    PubMed

    Fischer, Eric S; Park, Eunyoung; Eck, Michael J; Thomä, Nicolas H

    2016-04-01

    Regulatory protein-protein interactions are ubiquitous in biology, and small molecule protein-protein interaction inhibitors are an important focus in drug discovery. Remarkably little attention has been given to the opposite strategy-stabilization of protein-protein interactions, despite the fact that several well-known therapeutics act through this mechanism. From a structural perspective, we consider representative examples of small molecules that induce or stabilize the association of protein domains to inhibit, or alter, signaling for nuclear hormone, GTPase, kinase, phosphatase, and ubiquitin ligase pathways. These SPLINTS (small-molecule protein ligand interface stabilizers) drive interactions that are in some cases physiologically relevant, and in others entirely adventitious. The diverse structural mechanisms employed suggest approaches for a broader and systematic search for such compounds in drug discovery. PMID:26829757

  15. Stochastic electrotransport selectively enhances the transport of highly electromobile molecules

    PubMed Central

    Kim, Sung-Yon; Cho, Jae Hun; Murray, Evan; Bakh, Naveed; Choi, Heejin; Ohn, Kimberly; Ruelas, Luzdary; Hubbert, Austin; McCue, Meg; Vassallo, Sara L.; Keller, Philipp J.; Chung, Kwanghun

    2015-01-01

    Nondestructive chemical processing of porous samples such as fixed biological tissues typically relies on molecular diffusion. Diffusion into a porous structure is a slow process that significantly delays completion of chemical processing. Here, we present a novel electrokinetic method termed stochastic electrotransport for rapid nondestructive processing of porous samples. This method uses a rotational electric field to selectively disperse highly electromobile molecules throughout a porous sample without displacing the low-electromobility molecules that constitute the sample. Using computational models, we show that stochastic electrotransport can rapidly disperse electromobile molecules in a porous medium. We apply this method to completely clear mouse organs within 1–3 days and to stain them with nuclear dyes, proteins, and antibodies within 1 day. Our results demonstrate the potential of stochastic electrotransport to process large and dense tissue samples that were previously infeasible in time when relying on diffusion. PMID:26578787

  16. Application of Recognition Tunneling in Single Molecule Identification

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan

    Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.

  17. Investigating single molecule adhesion by atomic force spectroscopy.

    PubMed

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-01-01

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment. PMID:25867282

  18. Laser Methods in the Study of Nuclei, Atoms and Molecules

    NASA Astrophysics Data System (ADS)

    Inamura, Takashi T.

    2005-01-01

    The VIth International Workshop on Application of Lasers in Atomic Nuclei Research was held at Adam Mickiewicz University, Poznan in Poland from May 24 to 27, 2004. Its title this year was "Laser methods in the study of nuclei, atoms and molecules". Some topics are reviewed from a viewpoint of the atomic physics contribution to nuclear physics and its applications. It is suggested how this meeting should be organized in the future by taking the new geopolitics into account.

  19. Polarizabilities of Adsorbed and Assembled Molecules: Measuring the Conductance through Buried Contacts

    PubMed Central

    2010-01-01

    We have measured the polarizabilities of four families of molecules adsorbed to Au{111} surfaces, with structures ranging from fully saturated to fully conjugated, including single-molecule switches. Measured polarizabilities increase with increasing length and conjugation in the adsorbed molecules and are consistent with theoretical calculations. For single-molecule switches, the polarizability reflects the difference in substrate−molecule electronic coupling in the ON and OFF conductance states. Calculations suggest that the switch between the two conductance states is correlated with an oxidation state change in a nitro functional group in the switch molecules. PMID:21077677

  20. Room temperature single molecule microscopes

    SciTech Connect

    Ambrose, W.P.; Goodwin, P.M.; Enderlein, G.; Semin, D.J.; Keller, R.A.

    1997-12-31

    We have developed three capabilities to image the locations of and interrogate immobilized single fluorescent molecules: near-field scanning optical, confocal scanning optical, and wide-field epi-fluorescence microscopy. Each microscopy has its own advantages. Near-field illumination can beat the diffraction limit. Confocal microscopy has high brightness and temporal resolution. Wide-field has the quickest (parallel) imaging capability. With confocal microscopy, we have verified that single fluorescent spots in our images are due to single molecules by observing photon antibunching. Using all three microscopies, we have observed that xanthene molecules dispersed on dry silica curiously exhibit intensity fluctuations on millisecond to minute time scales. We are exploring the connection between the intensity fluctuations and fluctuations in individual photophysical parameters. The fluorescence lifetimes of Rhodamine 6G on silica fluctuate. The complex nature of the intensity and lifetime fluctuations is consistent with a mechanism that perturbs more than one photophysical parameter.

  1. Report Card on Nuclear Power

    ERIC Educational Resources Information Center

    Novick, Sheldon

    1974-01-01

    Problems facing the nuclear power industry include skyrocketing construction costs, technical failures, fuel scarcity, power plant safety, and the disposal of nuclear wastes. Possible solutions include: reductions in nuclear power plant construction, a complete moratorium on new plant construction, the construction of fast breeder reactors and the…

  2. Small-Molecule Hormones: Molecular Mechanisms of Action

    PubMed Central

    Budzińska, Monika

    2013-01-01

    Small-molecule hormones play crucial roles in the development and in the maintenance of an adult mammalian organism. On the molecular level, they regulate a plethora of biological pathways. Part of their actions depends on their transcription-regulating properties, exerted by highly specific nuclear receptors which are hormone-dependent transcription factors. Nuclear hormone receptors interact with coactivators, corepressors, basal transcription factors, and other transcription factors in order to modulate the activity of target genes in a manner that is dependent on tissue, age and developmental and pathophysiological states. The biological effect of this mechanism becomes apparent not earlier than 30–60 minutes after hormonal stimulus. In addition, small-molecule hormones modify the function of the cell by a number of nongenomic mechanisms, involving interaction with proteins localized in the plasma membrane, in the cytoplasm, as well as with proteins localized in other cellular membranes and in nonnuclear cellular compartments. The identity of such proteins is still under investigation; however, it seems that extranuclear fractions of nuclear hormone receptors commonly serve this function. A direct interaction of small-molecule hormones with membrane phospholipids and with mRNA is also postulated. In these mechanisms, the reaction to hormonal stimulus appears within seconds or minutes. PMID:23533406

  3. Phase structure of soliton molecules

    SciTech Connect

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Boehm, M.; Mitschke, F.

    2007-06-15

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E-fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  4. Phase structure of soliton molecules

    NASA Astrophysics Data System (ADS)

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Böhm, M.; Mitschke, F.

    2007-06-01

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E -fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  5. Orbital molecules in electronic materials

    SciTech Connect

    Attfield, J. Paul

    2015-04-01

    Orbital molecules are made up of coupled orbital states on several metal ions within an orbitally ordered (and sometimes also charge-ordered) solid such as a transition metal oxide. Spin-singlet dimers are known in many materials, but recent discoveries of more exotic species such as 18-electron heptamers in AlV{sub 2}O{sub 4} and magnetic 3-atom trimerons in magnetite (Fe{sub 3}O{sub 4}) have shown that orbital molecules constitute a general new class of quantum electronic states in solids.

  6. Nonadiabatic reaction of energetic molecules.

    PubMed

    Bhattacharya, Atanu; Guo, Yuanqing; Bernstein, Elliot R

    2010-12-21

    Energetic materials store a large amount of chemical energy that can be readily converted into mechanical energy via decomposition. A number of different ignition processes such as sparks, shocks, heat, or arcs can initiate the excited electronic state decomposition of energetic materials. Experiments have demonstrated the essential role of excited electronic state decomposition in the energy conversion process. A full understanding of the mechanisms for the decomposition of energetic materials from excited electronic states will require the investigation and analysis of the specific topography of the excited electronic potential energy surfaces (PESs) of these molecules. The crossing of multidimensional electronic PESs creates a funnel-like topography, known as conical intersections (CIs). CIs are well established as a controlling factor in the excited electronic state decomposition of polyatomic molecules. This Account summarizes our current understanding of the nonadiabatic unimolecular chemistry of energetic materials through CIs and presents the essential role of CIs in the determination of decomposition pathways of these energetic systems. Because of the involvement of more than one PES, a decomposition process involving CIs is an electronically nonadiabatic mechanism. Based on our experimental observations and theoretical calculations, we find that a nonadiabatic reaction through CIs dominates the initial decomposition process of energetic materials from excited electronic states. Although the nonadiabatic behavior of some polyatomic molecules has been well studied, the role of nonadiabatic reactions in the excited electronic state decomposition of energetic molecules has not been well investigated. We use both nanosecond energy-resolved and femtosecond time-resolved spectroscopic techniques to determine the decomposition mechanism and dynamics of energetic species experimentally. Subsequently, we employ multiconfigurational methodologies (such as, CASSCF

  7. Piezoresistivity in single DNA molecules

    PubMed Central

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π–π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  8. Piezoresistivity in single DNA molecules

    NASA Astrophysics Data System (ADS)

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-09-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes.

  9. Piezoresistivity in single DNA molecules.

    PubMed

    Bruot, Christopher; Palma, Julio L; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  10. Selection and Biosensor Application of Aptamers for Small Molecules

    PubMed Central

    Pfeiffer, Franziska; Mayer, Günter

    2016-01-01

    Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging. PMID:27379229

  11. Laser cooling of internal degrees of freedom of molecules

    NASA Astrophysics Data System (ADS)

    Horchani, R.

    2016-08-01

    Optical pumping techniques using laser fields combined with photo-association of ultracold atoms leads to control of the vibrational and/or rotational population of molecules. In this study, we review the basic concepts and main steps that should be followed, including the excitation schemes and detection techniques used to achieve ro-vibrational cooling of Cs2 molecules. We also discuss the extension of this technique to other molecules. In addition, we present a theoretical model used to support the experiment. These simulations can be widely used for the preparation of various experiments because they allow the optimization of several important experimental parameters.

  12. Toward Triplet Ground State LiNa Molecules

    NASA Astrophysics Data System (ADS)

    Jamison, Alan; Rvachov, Timur; Jing, Li; Jiang, Yijun; Zwierlein, Martin; Ketterle, Wolfgang

    2015-05-01

    We present progress toward creation of ultracold ground-state triplet LiNa molecules. This molecule is expected to have a long lifetime in the triplet ground state due to its fermionic nature, large rotational constant, and weak spin-orbit coupling. The triplet state has both electric and magnetic dipole moments, affording unique opportunities in quantum simulation and ultracold chemistry. Our progress includes the first observation of triplet excited states in this molecule, achieved through photoassociation of ultracold mixtures of 6-Li and Na. We compare experimental results to a variety of near-dissociation expansions as well as ab initio potentials.

  13. Selection and Biosensor Application of Aptamers for Small Molecules.

    PubMed

    Pfeiffer, Franziska; Mayer, Günter

    2016-01-01

    Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging. PMID:27379229

  14. Biomedical applications of single molecule detection

    NASA Astrophysics Data System (ADS)

    Kelso, D. M.

    1997-05-01

    The search for increased sensitivity of bio-analytical techniques has recently shifted from signal generation to detection. While enzyme amplifiers and chemiluminescent reporters developed by chemists over the last two decades gradually moved detection limits to the attomol level, it has taken engineers only a few years to reach single- molecule sensitivity with the development of new instrumentation. A number of different approaches have successfully achieved single-molecule fluorescence detection including confocal and near-field scanning optical microscopy, photon-counting cameras, fluorescence- correlation and time-gated spectroscopy. They detect labels immobilized on substrates, diffusing in solution and flowing in electro-osmotic and hydrodynamically focused streams. Biotechnology has created numerous application s for single- molecule detection. In research labs, it can dramatically increase the rate of DNA sequencing, screen libraries for products of directed evolution, and characterize compounds in drug discovery programs. In medical diagnostics, ultra- sensitive detection technologies can be used for genetic screening, detection of infectious diseases, or multi- analyte profiles. It can be applied to immunoassays as well as DNA or RNA hybridization assays.

  15. Crystal structure prediction of rigid molecules.

    PubMed

    Elking, Dennis M; Fusti-Molnar, Laszlo; Nichols, Anthony

    2016-08-01

    A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r(6) dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups. PMID:27484371

  16. Single Molecule Dynamics of Branched DNA Polymers

    NASA Astrophysics Data System (ADS)

    Mai, Danielle; Sing, Charles; Schroeder, Charles

    This work focuses on extending the field of single polymer dynamics to topologically complex polymers. Here, we report the direct observation of DNA-based branched polymers. Recently, we recently demonstrated a two-step synthesis method to generate star, H-shaped, and comb polymers for single molecule visualization. Following synthesis, we use single-color or dual-color single molecule fluorescence microscopy to directly visualize branched polymer dynamics in flow, in particular tracking side branches and backbones independently. In this way, our imaging method allows for characterization of molecular properties, including quantification of polymer contour length and branch distributions. Moving beyond characterization, we use molecular rheology and single molecule techniques to study the dynamics of single branched polymers in flow. Here, we utilize precision microfluidics to directly observe branched DNA polymer conformations during transient stretching, steady-state extension, and relaxation from high stretch. We specifically measure backbone end-to-end distance as a function of time. Experiments and Brownian dynamics simulations show that branched polymer relaxation is a strong function of the number of branches and position of branch points along the main chain backbone.

  17. Extracellular Matrix Molecules: Potential Targets in Pharmacotherapy

    PubMed Central

    Järveläinen, Hannu; Sainio, Annele; Koulu, Markku; Wight, Thomas N.; Penttinen, Risto

    2009-01-01

    The extracellular matrix (ECM) consists of numerous macromolecules classified traditionally into collagens, elastin, and microfibrillar proteins, proteoglycans including hyaluronan, and noncollagenous glycoproteins. In addition to being necessary structural components, ECM molecules exhibit important functional roles in the control of key cellular events such as adhesion, migration, proliferation, differentiation, and survival. Any structural inherited or acquired defect and/or metabolic disturbance in the ECM may cause cellular and tissue alterations that can lead to the development or progression of disease. Consequently, ECM molecules are important targets for pharmacotherapy. Specific agents that prevent theexcess accumulation of ECM molecules in the vascular system, liver, kidney, skin, and lung; alternatively, agents that inhibit the degradation of the ECM in degenerative diseases such as osteoarthritis would be clinically beneficial. Unfortunately, until recently, the ECM in drug discovery has been largely ignored. However, several of today's drugs that act on various primary targets affect the ECM as a byproduct of the drugs' actions, and this activity may in part be beneficial to the drugs' disease-modifying properties. In the future, agents and compounds targeting directly the ECM will significantly advance the treatment of various human diseases, even those for which efficient therapies are not yet available. PMID:19549927

  18. Classification models for safe drug molecules.

    PubMed

    Madan, A K; Bajaj, Sanjay; Dureja, Harish

    2013-01-01

    Frequent failure of drug candidates during development stages remains the major deterrent for an early introduction of new drug molecules. The drug toxicity is the major cause of expensive late-stage development failures. An early identification/optimization of the most favorable molecule will naturally save considerable cost, time, human efforts and minimize animal sacrifice. (Quantitative) Structure Activity Relationships [(Q)SARs] represent statistically derived predictive models correlating biological activity (including desirable therapeutic effect and undesirable side effects) of chemicals (drugs/toxicants/environmental pollutants) with molecular descriptors and/or properties. (Q)SAR models which categorize the available data into two or more groups/classes are known as classification models. Numerous techniques of diverse nature are being presently employed for development of classification models. Though there is an increasing use of classification models for prediction of either biological activity or toxicity, the future trend will naturally be towards the development of classification models capable of simultaneous prediction of biological activity, toxicity, and pharmacokinetic parameters so as to accelerate development of bioavailable safe drug molecules. PMID:23086839

  19. Signaling Molecules: Hydrogen Sulfide and Polysulfide

    PubMed Central

    2015-01-01

    Abstract Significance: Hydrogen sulfide (H2S) has been recognized as a signaling molecule as well as a cytoprotectant. It modulates neurotransmission, regulates vascular tone, and protects various tissues and organs, including neurons, the heart, and kidneys, from oxidative stress and ischemia-reperfusion injury. H2S is produced from l-cysteine by cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and 3-mercaptopyruvate sulfurtransferase (3MST) along with cysteine aminotransferase. Recent Advances: In addition to these enzymes, we recently identified a novel pathway to produce H2S from d-cysteine, which involves d-amino acid oxidase (DAO) along with 3MST. These enzymes are localized in the cytoplasm, mitochondria, and peroxisomes. However, some enzymes translocate to organelles under specific conditions. Moreover, H2S-derived potential signaling molecules such as polysulfides and HSNO have been identified. Critical Issues: The physiological stimulations, which trigger the production of H2S and its derivatives and maintain their local levels, remain unclear. Future Directions: Understanding the regulation of the H2S production and H2S-derived signaling molecules and the specific stimuli that induce their release will provide new insights into the biology of H2S and therapeutic development in diseases involving these substances. Antioxid. Redox Signal. 22, 362–376. PMID:24800864

  20. (Aerodynamic focusing of particles and heavy molecules)

    SciTech Connect

    de la Mora, J.F.

    1990-01-08

    By accelerating a gas containing suspended particles or large molecules through a converging nozzle, the suspended species may be focused and therefore used to write fine lines on a surface. Our objective was to study the limits on how narrow this focal region could be as a function of particle size. We find that, for monodisperse particles with masses m{sub p} some 3.6 {times} 10{sup 5} times larger than the molecular mass m of the carrier gas (diameters above some 100{angstrom}), there is no fundamental obstacle to directly write submicron features. However, this conclusion has been verified experimentally only with particles larger than 0.1 {mu}m. Experimental, theoretical and numerical studies on the defocusing role of Brownian motion for very small particles or heavy molecules have shown that high resolution (purely aerodynamic) focusing is impossible with volatile molecules whose masses are typically smaller than 1000 Dalton. For these, the minimal focal diameter after optimization appears to be 5{radical}(m/m{sub p}) times the nozzle diameter d{sub n}. But combinations of focused lasers and aerodynamic focusing appear as promising for direct writing with molecular precursors. Theoretical and numerical schemes capable of predicting the evolution of the focusing beam, including Brownian motion effects, have been developed, although further numerical work would be desirable. 11 refs.

  1. Expression of adhesion molecules in leprosy lesions.

    PubMed Central

    Sullivan, L; Sano, S; Pirmez, C; Salgame, P; Mueller, C; Hofman, F; Uyemura, K; Rea, T H; Bloom, B R; Modlin, R L

    1991-01-01

    Leprosy presents as a clinical spectrum that is precisely paralleled by a spectrum of immunological reactivity. The disease provides a useful and accessible model, in this case in the skin, in which to study the dynamics of cellular immune responses to an infectious pathogen, including the role of adhesion molecules in those responses. In lesions characterized by strong delayed-type hypersensitivity against Mycobacterium leprae (tuberculoid, reversal reaction, and Mitsuda reaction), the overlying epidermis exhibited pronounced keratinocyte intracellular adhesion molecule 1 (ICAM-1) expression and contained lymphocytes expressing the ICAM-1 ligand, LFA-1. Conversely, in lesions in which delayed-type hypersensitivity was lacking (lepromatous), keratinocyte ICAM-1 expression was low and LFA-1+ lymphocytes were rare. Expression of these adhesion molecules on the cells within the dermal granulomas was equivalent throughout the spectrum of leprosy. The percentage of lymphocytes in these granulomas containing mRNA coding for gamma interferon and tumor necrosis factor alpha, synergistic regulators of ICAM-1 expression, paralleled epidermal ICAM-1 expression. In lesions of erythema nodosum leprosum, a reactional state of lepromatous leprosy thought to be due to immune complex deposition, keratinocyte ICAM-1 expression and gamma interferon mRNA+ cells were both prominent. Antibodies to LFA-1 and ICAM-1 blocked the response of both alpha beta and gamma delta T-cell clones in vitro to mycobacteria. Overall, the expression of adhesion molecules by immunocompetent epidermal cells, as well as the cytokines which regulate such expression, correlates with the outcome of the host response to infection. Images PMID:1718871

  2. Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding.

    PubMed

    Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka

    2015-07-31

    Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS(SV40)) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS(SV40) in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS(SV40) formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS(SV40) likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS(SV40) can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. PMID:26032495

  3. Spectroscopy and reactions of molecules important in chemical evolution

    NASA Technical Reports Server (NTRS)

    Becker, R. S.

    1974-01-01

    The research includes: (1) hot hydrogen atom reactions in terms of the nature of products produced, mechanism of the reactions and the implication and application of such reactions for molecules existing in interstellar clouds, in planetary atmospheres, and in chemical evolution; (2) photochemical reactions that can lead to molecules important in chemical evolution, interstellar clouds and as constituents in planetary atmospheres; and (3) spectroscopic and theoretical properties of biomolecules and their precursors and where possible, use these to understand their photochemical behavior.

  4. Interstellar molecules. [detection from Copernicus satellite UV absorption data

    NASA Technical Reports Server (NTRS)

    Drake, J. F.

    1974-01-01

    The Princeton equipment on the Copernicus satellite provides the means to study interstellar molecules between the satellite and stars from 20 to 1000 pc distant. The study is limited to stars relatively unobscured by dust which strongly attenuates the ultraviolet continuum flux used as a source to probe the interstellar medium. Of the 14 molecules searched for only three have been detected including molecular hydrogen, molecular HD, and carbon monoxide.

  5. Nucleic Acids as Information Molecules.

    ERIC Educational Resources Information Center

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  6. Nanodevices for Single Molecule Studies

    NASA Astrophysics Data System (ADS)

    Craighead, H. G.; Stavis, S. M.; Samiee, K. T.

    During the last two decades, biotechnology research has resulted in progress in fields as diverse as the life sciences, agriculture and healthcare. While existing technology enables the analysis of a variety of biological systems, new tools are needed for increasing the efficiency of current methods, and for developing new ones altogether. Interest has grown in single molecule analysis for these reasons.

  7. Dialkylresorcinols as bacterial signaling molecules

    PubMed Central

    Brameyer, Sophie; Kresovic, Darko; Bode, Helge B.; Heermann, Ralf

    2015-01-01

    It is well recognized that bacteria communicate via small diffusible molecules, a process termed quorum sensing. The best understood quorum sensing systems are those that use acylated homoserine lactones (AHLs) for communication. The prototype of those systems consists of a LuxI-like AHL synthase and a cognate LuxR receptor that detects the signal. However, many proteobacteria possess LuxR receptors, yet lack any LuxI-type synthase, and thus these receptors are referred to as LuxR orphans or solos. In addition to the well-known AHLs, little is known about the signaling molecules that are sensed by LuxR solos. Here, we describe a novel cell–cell communication system in the insect and human pathogen Photorhabdus asymbiotica. We identified the LuxR homolog PauR to sense dialkylresorcinols (DARs) and cyclohexanediones (CHDs) instead of AHLs as signals. The DarABC synthesis pathway produces the molecules, and the entire system emerged as important for virulence. Moreover, we have analyzed more than 90 different Photorhabdus strains by HPLC/MS and showed that these DARs and CHDs are specific to the human pathogen P. asymbiotica. On the basis of genomic evidence, 116 other bacterial species are putative DAR producers, among them many human pathogens. Therefore, we discuss the possibility of DARs as novel and widespread bacterial signaling molecules and show that bacterial cell–cell communication goes far beyond AHL signaling in nature. PMID:25550519

  8. Nuclear imaging in pediatrics

    SciTech Connect

    Siddiqui, A.R.

    1985-01-01

    The author's intent is to familiarize practicing radiologists with the technical aspects and interpretation of nuclear medicine procedures in children and to illustrate the indications for nuclear medicine procedures in pediatric problems. Pediatric doses, dosimetry, sedation, and injection techniques, organ systems, oncology and infection, testicular scanning and nuclear crystography, pediatric endocrine and skeletal systems, ventilation and perfusion imaging of both congenital and acquired pediatric disorders, cardiovascular problems, gastrointestinal, hepatobiliary, reticuloendothelial studies, and central nervous system are all topics which are included and discussed.

  9. Assessing the nuclear age

    SciTech Connect

    Ackland, L.; McGuire, S.

    1986-01-01

    This book presents papers on nuclear weapons and arms control. Topics considered include historical aspects, the arms race, nuclear power, flaws in the non-proliferation treaty, North-South issues, East-West confrontation, Soviet decision making with regard to national defense, US and Soviet perspectives on national security, ballistic missile defense (''Star Wars''), political aspects, nuclear winter, stockpiles, US foreign policy, and military strategy.

  10. Method of monitoring photoactive organic molecules in-situ during gas-phase deposition of the photoactive organic molecules

    SciTech Connect

    Forrest, Stephen R.; Vartanian, Garen; Rolin, Cedric

    2015-06-23

    A method for in-situ monitoring of gas-phase photoactive organic molecules in real time while depositing a film of the photoactive organic molecules on a substrate in a processing chamber for depositing the film includes irradiating the gas-phase photoactive organic molecules in the processing chamber with a radiation from a radiation source in-situ while depositing the film of the one or more organic materials and measuring the intensity of the resulting photoluminescence emission from the organic material. One or more processing parameters associated with the deposition process can be determined from the photoluminescence intensity data in real time providing useful feedback on the deposition process.

  11. Finding small molecules for the 'next Ebola'.

    PubMed

    Ekins, Sean; Southan, Christopher; Coffee, Megan

    2015-01-01

    The current Ebola virus epidemic may provide some suggestions of how we can better prepare for the next pathogen outbreak. We propose several cost effective steps that could be taken that would impact the discovery and use of small molecule therapeutics including: 1. text mine the literature, 2. patent assignees and/or inventors should openly declare their relevant filings, 3. reagents and assays could be commoditized, 4. using manual curation to enhance database links, 5. engage database and curation teams, 6. consider open science approaches, 7. adapt the "box" model for shareable reference compounds, and 8. involve the physician's perspective. PMID:25949804

  12. Ultrafast X-ray Scattering from Molecules.

    PubMed

    Kirrander, Adam; Saita, Kenichiro; Shalashilin, Dmitrii V

    2016-03-01

    We present a theoretical framework for the analysis of ultrafast X-ray scattering experiments using nonadiabatic quantum molecular dynamics simulations of photochemical dynamics. A detailed simulation of a pump-probe experiment in ethylene is used to examine the sensitivity of the scattering signal to simulation parameters. The results are robust with respect to the number of wavepackets included in the total expansion of the molecular wave function. Overall, the calculated scattering signals correlate closely with the dynamics of the molecule. PMID:26717255

  13. Long-range interactions between chiral molecules

    SciTech Connect

    Salam, A.

    2015-01-22

    Results of molecular quantum electrodynamics calculations of discriminatory interactions between two chiral molecules undergoing resonance energy transfer, van der Waals dispersion, and optical binding are presented. A characteristic feature of the theory is that the radiation field is quantized with signals consequently propagating between centres at the speed of light. In order to correctly describe optically active chromophores, it is necessary to include magnetic as well as electric dipole coupling terms in the time-dependent perturbation theory computations. Recent work investigating the effect of an absorptive and dispersive chiral medium on the rate of migration of energy will also be discussed.

  14. Nuclear Medicine.

    ERIC Educational Resources Information Center

    Badawi, Ramsey D.

    2001-01-01

    Describes the use of nuclear medicine techniques in diagnosis and therapy. Describes instrumentation in diagnostic nuclear medicine and predicts future trends in nuclear medicine imaging technology. (Author/MM)

  15. Anti-Stokes-enhanced tunneling ionization of molecules

    NASA Astrophysics Data System (ADS)

    Kornev, Aleksei S.; Zon, Boris A.

    2012-10-01

    We consider the influence of vibrational motion of nuclei on the tunneling ionization of a molecule in a strong light field. Unlike the molecular Ammosov-Delone-Krainov (MO-ADK) model [X. M. Tong , Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.66.033402 66, 033402 (2002)], the Franck-Condon factors that take into consideration the quantization of nuclear vibrations are introduced in the theory. Modification of the vibrational motion of nuclei by the external field leads to the time-dependent constant in the asymptotic form of the electronic wave function. This in turn leads to a more significant modification of the Keldysh theory for the tunnel effect in molecules as compared to the MO-ADK model. We take into account the possibility of vibrational quantum numbers changing in a neutral molecule and in a molecular ion in the process of the tunneling ionization, which in principle enables one to get molecular ions of a certain isotopic composition if the vibrational states of the neutral molecules with this isotopic composition are pumped before ionization. We present numerical results illustrating this possibility for the isotopes of a hydrogen molecule.

  16. Towards understanding the hydrogen molecule in ZnO

    NASA Astrophysics Data System (ADS)

    Koch, S. G.; Lavrov, E. V.; Weber, J.

    2014-11-01

    The hydrogen molecule H2 (or "hidden" hydrogen) in ZnO is studied by Raman scattering spectroscopy. It is shown that H2 is practically a free rotator stable up to 700 ∘C , which is formed by two mobile interstitial hydrogen atoms. The concentration profile of the hydrogen molecule anticorrelates with hydrogen substituting for oxygen (HO) created at the sample surface during the high temperature hydrogenation. The H2 dissociation at elevated temperatures in the bulk regenerates interstitial (HBC) hydrogen, whereas the formation of HO and hydrogen out-diffusion are dominant decay channels of the molecule near the surface. The latter mechanisms are responsible for the lower stability of H2 in the subsurface region. An ortho-para conversion between the nuclear spin states 1 and 0 of the molecule at 79 K was found to occur within 7.5 h, whereas the back conversion at room temperature occurs faster than 0.5 h. A shift in frequency of the H2 local vibrational mode with annealing time and temperature is associated with the thermal anneal of lattice imperfections. The coupling of transitions between rotational states of the molecule and lattice phonons influences the ro-vibrational properties. Interstitial lattice sites and/or larger vacancy clusters are preferred trapping centers for H2 in ZnO.

  17. Coherent Dynamics Following Strong Field Ionization of Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim; Jackson, James; Levine, Benjamin; Dantus, Marcos

    2015-03-01

    Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon strong field ionization. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a ``bag of atoms'' during field induced ionization. We consider here to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The delay scans show that among positional isomers the variations in relative energies, amounting to only a few hundred meVs, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). Ab initio calculations were performed to predict dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose that single electron ionization occurs within an optical cycle with the electron carrying away essentially all of the energy, leaving behind little internal energy in the cation. Evidence for this observation comes from coherent vibrational motion governed by the potential energy surface of the ground state of the cation. Subsequent fragmentation of the cation takes place as a result of further photon absorption modulated by one- and two-photon resonances, which provide sufficient energy to overcome the dissociation energy.

  18. Cell Adhesion Molecules in Chemically-Induced Renal Injury

    PubMed Central

    Prozialeck, Walter C.; Edwards, Joshua R.

    2007-01-01

    Cell adhesion molecules are integral cell-membrane proteins that maintain cell-cell and cell-substrate adhesion, and in some cases, act as regulators of intracellular signaling cascades. In the kidney, cell adhesion molecules such as the cadherins, the catenins, ZO-1, occludin and the claudins are essential for maintaining the epithelial polarity and barrier integrity that are necessary for the normal absorption/excretion of fluid and solutes. A growing volume of evidence indicates that these cell adhesion molecules are important early targets for a variety of nephrotoxic substances including metals, drugs, and venom components. In addition, it is now widely appreciated that molecules such as ICAM-1, the integrins and selectins play important roles in the recruitment of leukocytes and inflammatory responses that are associated with nephrotoxic injury. This review summarizes the results of recent in vitro and in vivo studies indicating that these cell adhesion molecules may be primary molecular targets in many types of chemically-induced renal injury. Some of the specific agents that are discussed include Cd, Hg, Bi, cisplatin, aminoglycoside antibiotics, S-(1,2-dichlorovinyl-L-cysteine) (DCVC) and various venom toxins. This review also includes a discussion of the various mechanisms by which these substances can affect cell adhesion molecules in the kidney. PMID:17316817

  19. Nuclear data for nuclear transmutation

    SciTech Connect

    Harada, Hideo

    2009-05-04

    Current status on nuclear data for the study of nuclear transmutation of radioactive wastes is reviewed, mainly focusing on neutron capture reactions. It is stressed that the highest-precision frontier research in nuclear data measurements should be a key to satisfy the target accuracies on the nuclear data requested for realizing the nuclear transmutation.

  20. History of Nuclear India

    NASA Astrophysics Data System (ADS)

    Chaturvedi, Ram

    2000-04-01

    India emerged as a free and democratic country in 1947, and entered into the nuclear age in 1948 by establishing the Atomic Energy Commission (AEC), with Homi Bhabha as the chairman. Later on the Department of Atomic Energy (DAE) was created under the Office of the Prime Minister Jawahar Lal Nehru. Initially the AEC and DAE received international cooperation, and by 1963 India had two research reactors and four nuclear power reactors. In spite of the humiliating defeat in the border war by China in 1962 and China's nuclear testing in 1964, India continued to adhere to the peaceful uses of nuclear energy. On May 18, 1974 India performed a 15 kt Peaceful Nuclear Explosion (PNE). The western powers considered it nuclear weapons proliferation and cut off all financial and technical help, even for the production of nuclear power. However, India used existing infrastructure to build nuclear power reactors and exploded both fission and fusion devices on May 11 and 13, 1998. The international community viewed the later activity as a serious road block for the Non-Proliferation Treaty and the Comprehensive Test Ban Treaty; both deemed essential to stop the spread of nuclear weapons. India considers these treaties favoring nuclear states and is prepared to sign if genuine nuclear disarmament is included as an integral part of these treaties.

  1. New antimicrobial molecules and new antibiotic strategies.

    PubMed

    Rodríguez de Castro, Felipe; Naranjo, Olga Rajas; Marco, Javier Aspa; Violán, Jordi Solé

    2009-04-01

    Drug options for treatment of infections are increasingly limited. The pharmaceutical industry has found it difficult to discover new antimicrobial agents, and only two novel classes of antibiotics, the oxazolidinones and the cyclic lipopeptides, have entered the market since the late 1960s. Few new agents have reached the market in the last decade with potential interest for community-acquired pneumonia (CAP) treatment, including linezolid (the first oxazolidinone in clinical use), new fluoroquinolones, cefditoren, ertapenem, and telithromycin. Agents currently in clinical development include other novel quinolones and ketolides, broad-spectrum cephalosporin derivatives, faropenem, several glycopeptides, and iclaprim. Other molecules are considered to be promising candidates for the future. In addition to the foregoing agents, alternative treatment approaches have also been introduced into clinical practice, which include the administration of the appropriate antimicrobials in a timely manner and the consideration of the pharmacokinetic-pharmacodynamic properties of the agent(s). PMID:19296416

  2. Nuclear Security for Floating Nuclear Power Plants

    SciTech Connect

    Skiba, James M.; Scherer, Carolynn P.

    2015-10-13

    Recently there has been a lot of interest in small modular reactors. A specific type of these small modular reactors (SMR,) are marine based power plants called floating nuclear power plants (FNPP). These FNPPs are typically built by countries with extensive knowledge of nuclear energy, such as Russia, France, China and the US. These FNPPs are built in one country and then sent to countries in need of power and/or seawater desalination. Fifteen countries have expressed interest in acquiring such power stations. Some designs for such power stations are briefly summarized. Several different avenues for cooperation in FNPP technology are proposed, including IAEA nuclear security (i.e. safeguards), multilateral or bilateral agreements, and working with Russian design that incorporates nuclear safeguards for IAEA inspections in non-nuclear weapons states

  3. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale

    PubMed Central

    Szczurek, Aleksander; Xing, Jun; Birk, Udo J.; Cremer, Christoph

    2016-01-01

    Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50–100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field. PMID:27446198

  4. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale.

    PubMed

    Szczurek, Aleksander; Xing, Jun; Birk, Udo J; Cremer, Christoph

    2016-01-01

    Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50-100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field. PMID:27446198

  5. Cold collisions between boson or fermion molecules

    SciTech Connect

    Kajita, Masatoshi

    2004-01-01

    We theoretically investigate collisions between electrostatically trapped cold polar molecules and compare boson and fermion isotopes. Evaporative cooling seems possible for fermion molecules as the ratio of the collision loss cross section to the elastic collision cross section (R) gets smaller as the molecular temperature T lowers. With boson molecules, R gets larger as T lowers, which makes evaporative cooling difficult. The elastic collision cross section between fermion molecules can be larger than that for boson molecules with certain conditions.

  6. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  7. Circulating adhesion molecules in obstructive sleep apnea and cardiovascular disease

    PubMed Central

    Pak, Victoria M.; Grandner, Michael A.; Pack, Allan I.

    2013-01-01

    SUMMARY Over 20 years of evidence indicates a strong association between obstructive sleep apnea (OSA) and cardiovascular disease. Although inflammatory processes have been heavily implicated as an important link between the two, the mechanism for this has not been conclusively established. Atherosclerosis may be one of the mechanisms linking OSA to cardiovascular morbidity. This review addresses the role of circulating adhesion molecules in patients with OSA, and how these may be part of the link between cardiovascular disease and OSA. There is evidence for the role of adhesion molecules in cardiovascular disease risk. Some studies, albeit with small sample sizes, also show higher levels of adhesion molecules in patients with OSA compared to controls. There are also studies that show that levels of adhesion molecules diminish with continuous positive airway pressure therapy. Limitations of these studies include small sample sizes, cross-sectional sampling, and inconsistent control for confounding variables known to influence adhesion molecule levels. There are potential novel therapies to reduce circulating adhesion molecules in patients with OSA to diminish cardiovascular disease. Understanding the role of cell adhesion molecules generated in OSA will help elucidate one mechanistic link to cardiovascular disease in patients with OSA. PMID:23618532

  8. Clinical Nuclear Pharmacy Clerkship

    ERIC Educational Resources Information Center

    Dunson, George L.; Christopherson, William J., Jr.

    1977-01-01

    The School of Pharmacy, University of the Pacific, and the Pharmacy Service, Letterman Army Medical Center, initiated a 15-week clinical nuclear pharmacy clerkship in 1975. It includes basic nuclear medical science, technical competency, professional competency, and special interest emphasis. (LBH)

  9. TRAINING NUCLEAR TECHNICIANS.

    ERIC Educational Resources Information Center

    KOVNER, EDGAR A.

    PROBLEMS CONFRONTED BY PLANNERS OF NUCLEAR PROGRAMS AT THE TECHNICIAN LEVEL INCLUDE (1) LACK OF PRECEDENT IN CURRICULUM, COURSE OUTLINES, AND GRADUATE PLACEMENT, (2) DIFFICULTY IN DETERMINING COSTS OF LABORATORY CONSTRUCTION, EQUIPMENT, AND OPERATION, AND (3) REQUIREMENT OF ATOMIC ENERGY COMMISSION LICENSES IN NUCLEAR OCCUPATIONS. A 92-SEMESTER…

  10. Coupled Hartree-Fock calculations of atomic polar tensors and the dipole polarisability of the benzene molecule

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Malagoli, M.; Zanasi, R.

    1990-03-01

    Coupled Hartree-Fock perturbation theory has been applied within the framework of high-quality basis sets to estimate the Hartree-Fock limit for the nuclear electric shielding tensors and the electric polarisability of the benzene molecule.

  11. Answers to Questions: Nuclear Energy.

    ERIC Educational Resources Information Center

    Department of Energy, Washington, DC. Nuclear Energy Office.

    Electricity is an increasingly important part of our everyday lives. Its versatility allows one to heat, cool, and light homes; cook meals; watch television; listen to music; power computers; make medical diagnosis and treatment; explore the vastness of space; and study the tiniest molecules. Nuclear energy, second to coal, surpasses natural gas,…

  12. Dissociative Ionization of Aromatic and Heterocyclic Molecules

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    2003-01-01

    Space radiation poses a major health hazard to humans in space flight. The high-energy charged particles in space radiation ranging from protons to high atomic number, high-energy (HZE) particles, and the secondary species they produce, attack DNA, cells, and tissues. Of the potential hazards, long-term health effects such as carcinogenesis are likely linked to the DNA lesions caused by secondary electrons in the 1 - 30 eV range. Dissociative ionization (DI) is one of the electron collision processes that can damage the DNA, either directly by causing a DNA lesion, or indirectly by producing radicals and cations that attack the DNA. To understand this process, we have developed a theoretical model for DI. Our model makes use of the fact that electron motion is much faster than nuclear motion and assumes DI proceeds through a two-step process. The first step is electron-impact ionization resulting in a particular state of the molecular ion in the geometry of the neutral molecule. In the second step the ion undergoes unimolecular dissociation. Thus the DI cross section sigma(sup DI)(sub a) for channel a is given by sigma(sup DI)(sub a) = sigma(sup I)(sub a) P(sub D) with sigma(sup I)(sub a) the ionization cross section of channel a and P(sub D) the dissociation probability. This model has been applied to study the DI of H2O, NH3, and CH4, with results in good agreement with experiment. The ionization cross section sigma(sup I)(sub a) was calculated using the improved binary encounter-dipole model and the unimolecular dissociation probability P(sub D) obtained by following the minimum energy path determined by the gradients and Hessians of the electronic energy with respect to the nuclear coordinates of the ion. This model is used to study the DI from the low-lying channels of benzene and pyridine to understand the different product formation in aromatic and heterocyclic molecules. DI study of the DNA base thymine is underway. Solvent effects will also be discussed.

  13. X(3872): charmonium or molecule?

    SciTech Connect

    Nefediev, A. V.

    2011-05-23

    A theoretical analysis of the recent experimental data from the Belle and BABAR Collaborations on the charmonium state X(3872) is performed. The analysis takes into account the proximity of an S-wave mesonic threshold and a possible presence of molecule component in the resonance wave function, finite width of the molecule constituents, and a possible interference in the final state. In particular, a model-independent approach is formulated, based on the Flatte parametrisation of near-threshold observables as well as on the Weinberg analysis of the nature of weakly bound systems generalised to the case of unstable constituents. Conclusion is made that the X(3872) is generated dynamically by a strong coupling of the bare {chi}{sub c1} charmonium to the DD-bar* hadronic channel, with a large admixture of the DD-bar* molecular component.

  14. Electrochemical detection of single molecules.

    PubMed

    Fan, F R; Bard, A J

    1995-02-10

    The electrochemical behavior of a single molecule can be observed by trapping a small volume of a dilute solution of the electroactive species between an ultramicroelectrode tip with a diameter of approximately 15 nanometers and a conductive substrate. A scanning electrochemical microscope was used to adjust the tip-substrate distance ( approximately 10 nanometers), and the oxidation of [(trimethylammonio)methyl] ferrocene (Cp(2)FeTMA(+)) to Cp(2)FeTMA(2+) was carried out. The response was stochastic, and anodic current peaks were observed as the molecule moved into and out of the electrode-substrate gap. Similar experiments were performed with a solution containing two redox species, ferrocene carboxylate (Cp(2)FeCOO(-)) and Os(bpy)(3)(2+) (bpy is 2,2'-bipyridyl). PMID:17813918

  15. Comprehensive Nuclear Materials

    SciTech Connect

    Konings, Dr. Rudy J. M.; Allen, Todd R.; Stoller, Roger E; Yamanaka, Prof. Shinsuke

    2012-01-01

    This book encompasses a rich seam of current information on the vast and multidisciplinary field of nuclear materials employed in fission and prototype fusion systems. Discussion includes both historical and contemporary international research in nuclear materials, from Actinides to Zirconium alloys, from the worlds leading scientists and engineers. Synthesizes pertinent current science to support the selection, assessment, validation and engineering of materials in extreme nuclear environments. The work discusses the major classes of materials suitable for usage in nuclear fission, fusion reactors and high power accelerators, and for diverse functions in fuels, cladding, moderator and control materials, structural, functional, and waste materials.

  16. Discovering new bioactive molecules from microbial sources

    PubMed Central

    Monciardini, Paolo; Iorio, Marianna; Maffioli, Sonia; Sosio, Margherita; Donadio, Stefano

    2014-01-01

    There is an increased need for new drug leads to treat diseases in humans, animals and plants. A dramatic example is represented by the need for novel and more effective antibiotics to combat multidrug-resistant microbial pathogens. Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity, despite a decreased interest by large pharmaceutical companies. Novel approaches must be implemented to decrease the chances of rediscovering the tens of thousands of known natural products. In this review, we present an overview of natural product screening, focusing particularly on microbial products. Different approaches can be implemented to increase the probability of finding new bioactive molecules. We thus present the rationale and selected examples of the use of hypersensitive assays; of accessing unexplored microorganisms, including the metagenome; and of genome mining. We then focus our attention on the technology platform that we are currently using, consisting of approximately 70 000 microbial strains, mostly actinomycetes and filamentous fungi, and discuss about high-quality screening in the search for bioactive molecules. Finally, two case studies are discussed, including the spark that arose interest in the compound: in the case of orthoformimycin, the novel mechanism of action predicted a novel structural class; in the case of NAI-112, structural similarity pointed out to a possible in vivo activity. Both predictions were then experimentally confirmed. PMID:24661414

  17. Simple molecules as complex systems.

    PubMed

    Furtenbacher, Tibor; Arendás, Péter; Mellau, Georg; Császár, Attila G

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H2(16)O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an "ultra-small-world" property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  18. Molecules in the early universe

    SciTech Connect

    Lepp, S.; Shull, J.M.

    1984-05-15

    We present calculations of the formation of astrophysically interesting molecules (H/sub 2/, HD, LiH, and HeH/sup +/) by gas-phase reactions during the postrecombination epoch (redshifts z = 300-30). In standard Friedmann cosmological models, H/sub 2//Hroughly-equal10/sup -6/, HD/H/sub 2/roughly-equal10/sup -4.5/, and LiH/H/sub 2/roughly-equal10/sup -6.5/. These molecules may dominate the cooling and trigger the collapse of primordial gas clouds. The dipole rotational transitions of HD and LiH are particularly important at high density and low temperature. Additional molecules form during spherical collapse of these clouds, their rotational cooling keeps the gas temperature between 400 and 1500 K over 12 decades of density increase until the H/sub 2/ lines become optically thick. The existence of molecular coolants at high redshift has significant implications for the first generation of stars and for thermal instabilities in intergalactic matter.

  19. Simple molecules as complex systems

    PubMed Central

    Furtenbacher, Tibor; Árendás, Péter; Mellau, Georg; Császár, Attila G.

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H216O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an “ultra-small-world” property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  20. A single-molecule diode

    PubMed Central

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-01-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

  1. Functional molecules in electronic circuits.

    PubMed

    Weibel, Nicolas; Grunder, Sergio; Mayor, Marcel

    2007-08-01

    Molecular electronics is a fascinating field of research contributing to both fundamental science and future technological achievements. A promising starting point for molecular devices is to mimic existing electronic functions to investigate the potential of molecules to enrich and complement existing electronic strategies. Molecules designed and synthesized to be integrated into electronic circuits and to perform an electronic function are presented in this article. The focus is set in particular on rectification and switching based on molecular devices, since the control over these two parameters enables the assembly of memory units, likely the most interesting and economic application of molecular based electronics. Both historical and contemporary solutions to molecular rectification are discussed, although not exhaustively. Several examples of integrated molecular switches that respond to light are presented. Molecular switches responding to an electrochemical signal are also discussed. Finally, supramolecular and molecular systems with intuitive application potential as memory units due to their hysteretic switching are highlighted. Although a particularly attractive feature of molecular electronics is its close cooperation with neighbouring disciplines, this article is written from the point of view of a chemist. Although the focus here is largely on molecular considerations, innovative contributions from physics, electro engineering, nanotechnology and other scientific disciplines are equally important. However, the ability of the chemist to correlate function with structure, to design and to provide tailor-made functional molecules is central to molecular electronics. PMID:17637951

  2. Methods And Devices For Characterizing Duplex Nucleic Acid Molecules

    DOEpatents

    Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen

    2005-08-30

    Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

  3. The Dipole Polarizability of a Water Molecule in Liquid Water

    NASA Astrophysics Data System (ADS)

    Distasio, Robert; Maitra, Rahul

    The dipole polarizability, α, provides a measure of the tendency of a molecule or material to deform (or polarize) in the presence of an electric field. Within the framework of density functional theory (DFT), we present a hierarchy of first principles based approaches for computing α of a molecule located in the condensed phase. This hierarchy includes a successive treatment of both short-range (hybridization, Pauli exchange-repulsion, etc.) and long-range (Coulomb) electrodynamical response screening in the computation of α, while simultaneously accounting for the surrounding condensed-phase environment. Utilizing highly accurate liquid water configurations generated from van der Waals inclusive hybrid DFT based ab initio molecular dynamics, we computed α for a given water molecule in liquid water as a first application of this approach. Our findings will be compared and contrasted with α computed for an isolated gas-phase water molecule.

  4. Carbon Monoxide as a Signaling Molecule in Plants.

    PubMed

    Wang, Meng; Liao, Weibiao

    2016-01-01

    Carbon monoxide (CO), a gaseous molecule, has emerged as a signaling molecule in plants, due to its ability to trigger a series of physiological reactions. This article provides a brief update on the synthesis of CO, its physiological functions in plant growth and development, as well as its roles in abiotic stress tolerance such as drought, salt, ultraviolet radiation, and heavy metal stress. CO has positive effects on seed germination, root development, and stomatal closure. Also, CO can enhance plant abiotic stress resistance commonly through the enhancement of antioxidant defense system. Moreover, CO shows cross talk with other signaling molecules including NO, phytohormones (IAA, ABA, and GA) and other gas signaling molecules (H2S, H2, CH4). PMID:27200045

  5. Reactive oxygen species, essential molecules, during plant-pathogen interactions.

    PubMed

    Camejo, Daymi; Guzmán-Cedeño, Ángel; Moreno, Alexander

    2016-06-01

    Reactive oxygen species (ROS) are continually generated as a consequence of the normal metabolism in aerobic organisms. Accumulation and release of ROS into cell take place in response to a wide variety of adverse environmental conditions including salt, temperature, cold stresses and pathogen attack, among others. In plants, peroxidases class III, NADPH oxidase (NOX) locates in cell wall and plasma membrane, respectively, may be mainly enzymatic systems involving ROS generation. It is well documented that ROS play a dual role into cells, acting as important signal transduction molecules and as toxic molecules with strong oxidant power, however some aspects related to its function during plant-pathogen interactions remain unclear. This review focuses on the principal enzymatic systems involving ROS generation addressing the role of ROS as signal molecules during plant-pathogen interactions. We described how the chloroplasts, mitochondria and peroxisomes perceive the external stimuli as pathogen invasion, and trigger resistance response using ROS as signal molecule. PMID:26950921

  6. Cell Adhesion Molecules and Ubiquitination—Functions and Significance

    PubMed Central

    Homrich, Mirka; Gotthard, Ingo; Wobst, Hilke; Diestel, Simone

    2015-01-01

    Cell adhesion molecules of the immunoglobulin (Ig) superfamily represent the biggest group of cell adhesion molecules. They have been analyzed since approximately 40 years ago and most of them have been shown to play a role in tumor progression and in the nervous system. All members of the Ig superfamily are intensively posttranslationally modified. However, many aspects of their cellular functions are not yet known. Since a few years ago it is known that some of the Ig superfamily members are modified by ubiquitin. Ubiquitination has classically been described as a proteasomal degradation signal but during the last years it became obvious that it can regulate many other processes including internalization of cell surface molecules and lysosomal sorting. The purpose of this review is to summarize the current knowledge about the ubiquitination of cell adhesion molecules of the Ig superfamily and to discuss its potential physiological roles in tumorigenesis and in the nervous system. PMID:26703751

  7. Molecules and Methods for Super-Resolution Imaging

    PubMed Central

    Thompson, Michael A.; Biteen, Julie S.; Lord, Samuel J.; Conley, Nicholas R.; Moerner, W. E.

    2011-01-01

    By looking at a fluorescently labeled structure one molecule at a time, it is possible to side-step the optical diffraction limit and obtain “super-resolution” images of small nanostructures. In the Moerner Lab, we seek to develop both molecules and methods to extend super-resolution fluorescence imaging. Methodologies and protocols for designing and characterizing fluorophores with switchable fluorescence required for super-resolution imaging are reported. These fluorophores include azido-DCDHF molecules, covalently linked Cy3–Cy5 dimers, and also the first example of a photoswitchable fluorescent protein, enhanced yellow fluorescent protein (EYFP). The imaging of protein superstructures in living Caulobacter crescentus bacteria is used as an example of the power of super-resolution imaging by single-molecule photoswitching to extract information beyond the diffraction limit. Finally, a new method is described for obtaining three-dimensional super-resolution information using a double-helix point-spread function. PMID:20627152

  8. Carbon Monoxide as a Signaling Molecule in Plants

    PubMed Central

    Wang, Meng; Liao, Weibiao

    2016-01-01

    Carbon monoxide (CO), a gaseous molecule, has emerged as a signaling molecule in plants, due to its ability to trigger a series of physiological reactions. This article provides a brief update on the synthesis of CO, its physiological functions in plant growth and development, as well as its roles in abiotic stress tolerance such as drought, salt, ultraviolet radiation, and heavy metal stress. CO has positive effects on seed germination, root development, and stomatal closure. Also, CO can enhance plant abiotic stress resistance commonly through the enhancement of antioxidant defense system. Moreover, CO shows cross talk with other signaling molecules including NO, phytohormones (IAA, ABA, and GA) and other gas signaling molecules (H2S, H2, CH4). PMID:27200045

  9. Interactions Between Ground-State Nitrogen Atoms and Molecules

    NASA Technical Reports Server (NTRS)

    Vanderslice, Joseph T.; Mason, Edward A.; Lippincott, Ellis R.

    1959-01-01

    Potential-energy curves for nitrogen atom (N-N) interactions corresponding to the X (1)Sigma(sup +, sub g), A (3)Sigma(sup +, sub u), (5)Sigma(sup +, sub g), (7)Sigma(sup +, sub u), B (3) Pi(sub g), C (3)(Pi(su u)and a (1)Pi(sub g) states of the nitrogen molecule N2 as well as curves for the atom-molecules (N-N2) and molecule-molecule (N2-N2) interactions have been calculated. All calculations have been based as nearly as possible on experimental data, including spectroscopically determined vibrational energy levels, scattering cross sections of atomic beams in gases, and measured vibrational relaxation times. In cases where experimental data were not available, approximate quantum-mechanical calculations have been made. Results obtained by these various methods are remarkably consistent with one another and are believed to have good accuracy.

  10. [Recent progress in nuclear magnetic resonance spectrum for drug research and development].

    PubMed

    Zhong, Jun; Jiang, Xue-mei

    2015-01-01

    In the process of modern drug research, the new methods and technologies which can detect drug molecules' chemical composition, structure and interaction with biomolecules are always the key scientific problems people care about. Spectra (including IR, UV and NMR) are the most common analytical methods, of which NMR can obtain detailed parameter about the nucleus of organic molecules through researching the laws of nuclear transition in the impact of surrounding chemical environment. The parameter contains rich information about the chemical composition, structure and interaction with other molecules of organic molecules. In many complex environments, such as liquid, solid or gas state, even biological in situ environment, NMR can provide molecules' chemical composition, atomic-resolution three-dimensional structure, information of interaction with each other and dynamic process, especially the information about drug interacting with biomacromolecules. In recent years, the applications of nuclear magnetic resonance spectrum in drug research and development are more and more widespread. This paper reviewed its recent progress in structure and dynamic of targeted biological macromolecules, drug design and screening and drug metabolism in drug research and development. In the first part, we gave a brief introduction of nuclear magnetic resonance technology and its applications in drug research. In the second part, we explained the basic principles briefly and summarized progress in methods and techniques for drug research. In the third part, we discussed applications of nuclear magnetic resonance ir structure and dynamic of targeted biological macromolecules, drug design and screening and drug metabolism in detail. The conclusions were stated in the last part. PMID:25993865

  11. NUCLEAR DATA RESOURCES FOR ADVANCED ANALYSIS AND SIMULATION.

    SciTech Connect

    PRITYCHENKO, B.

    2006-06-05

    The mission of the National Nuclear Data Center (NNDC) includes collection, evaluation, and dissemination of nuclear physics data for basic nuclear research and applied nuclear technologies. In 2004, to answer the needs of nuclear data users, NNDC completed a project to modernize storage and management of its databases and began offering new nuclear data Web services. Examples of nuclear reaction, nuclear structure and decay database applications along with a number of nuclear science codes are also presented.

  12. MHCcluster, a method for functional clustering of MHC molecules.

    PubMed

    Thomsen, Martin; Lundegaard, Claus; Buus, Søren; Lund, Ole; Nielsen, Morten

    2013-09-01

    The identification of peptides binding to major histocompatibility complexes (MHC) is a critical step in the understanding of T cell immune responses. The human MHC genomic region (HLA) is extremely polymorphic comprising several thousand alleles, many encoding a distinct molecule. The potentially unique specificities remain experimentally uncharacterized for the vast majority of HLA molecules. Likewise, for nonhuman species, only a minor fraction of the known MHC molecules have been characterized. Here, we describe a tool, MHCcluster, to functionally cluster MHC molecules based on their predicted binding specificity. The method has a flexible web interface that allows the user to include any MHC of interest in the analysis. The output consists of a static heat map and graphical tree-based visualizations of the functional relationship between MHC variants and a dynamic TreeViewer interface where both the functional relationship and the individual binding specificities of MHC molecules are visualized. We demonstrate that conventional sequence-based clustering will fail to identify the functional relationship between molecules, when applied to MHC system, and only through the use of the predicted binding specificity can a correct clustering be found. Clustering of prevalent HLA-A and HLA-B alleles using MHCcluster confirms the presence of 12 major specificity groups (supertypes) some however with highly divergent specificities. Importantly, some HLA molecules are shown not to fit any supertype classification. Also, we use MHCcluster to show that chimpanzee MHC class I molecules have a reduced functional diversity compared to that of HLA class I molecules. MHCcluster is available at www.cbs.dtu.dk/services/MHCcluster-2.0. PMID:23775223

  13. Nuclear Science References Database

    SciTech Connect

    Pritychenko, B.; Běták, E.; Singh, B.; Totans, J.

    2014-06-15

    The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energy Agency (http://www-nds.iaea.org/nsr)

  14. Safe use of atomic (Nuclear) power (Nuclear Safety)

    NASA Astrophysics Data System (ADS)

    Sidorenko, V. A.

    2013-12-01

    The established concept of ensuring safety for nuclear power sources is presented; the influence of severe accidents on nuclear power development is considered, including the accident at a Japan NPP in 2011, as well as the role of state regulation of nuclear safety.

  15. Dynamics of hadronic molecule in one-boson exchange approach and possible heavy flavor molecules

    SciTech Connect

    Ding Guijun; Liu Jiafeng; Yan Mulin

    2009-03-01

    We extend the one pion exchange model at quark level to include the short distance contributions coming from {eta}, {sigma}, {rho} and {omega} exchange. This formalism is applied to discuss the possible molecular states of DD*/DD*, BB*/BB*, DD*, BB*, the pseudoscalar-vector systems with C=B=1 and C=-B=1 respectively. The ''{delta} function'' term contribution and the S-D mixing effects have been taken into account. We find the conclusions reached after including the heavier mesons exchange are qualitatively the same as those in the one pion exchange model. The previous suggestion that 1{sup ++} BB*/BB* molecule should exist, is confirmed in the one-boson exchange model, whereas DD* bound state should not exist. The DD*/DD* system can accommodate a 1{sup ++} molecule close to the threshold, the mixing between the molecule and the conventional charmonium has to be considered to identify this state with X(3872). For the BB* system, the pseudoscalar-vector systems with C=B=1 and C=-B=1, near threshold molecular states may exist. These bound states should be rather narrow, isospin is violated and the I=0 component is dominant. Experimental search channels for these states are suggested.

  16. Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Guehr, Markus; Vecchione, Theodore; Robinson, Matthew S.; Li, Renkai; Hartmann, Nick; Shen, Xiaozhe; Coffee, Ryan; Corbett, Jeff; Fry, Alan; Gaffney, Kelly; Gorkhover, Tais; Hast, Carsten; Jobe, Keith; Makasyuk, Igor; Reid, Alexander; Robinson, Joseph; Vetter, Sharon; Wang, Fenglin; Weathersby, Stephen; Yoneda, Charles; Centurion, Martin; Wang, Xijie

    2016-04-01

    Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angström spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 Å) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule. In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.

  17. Atlas of nuclear medicine

    SciTech Connect

    Van Nostrand, D. ); Baum, S. )

    1988-01-01

    This book contains the proceeding on the atlas of nuclear medicine. Topics covered include: Radionuclide esophageal transit studies, Iodine-131 neck and chest scintigraphy, Indium-111 white blood cell imaging, and Pediatric radionuclide lymphography.

  18. Water molecules orientation in surface layer

    NASA Astrophysics Data System (ADS)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  19. Drosophila Cajal bodies: accessories not included

    PubMed Central

    Matera, A. Gregory

    2006-01-01

    Cajal bodies are nuclear sites of small ribonucleoprotein (RNP) remodeling and maturation. A recent study describes the discovery of the Drosophila Cajal body, revealing some interesting insights into the subnuclear organization of RNA processing machineries among different species. PMID:16533940

  20. Gating Immunity and Death at the Nuclear Pore Complex.

    PubMed

    Dasso, Mary; Fontoura, Beatriz M A

    2016-09-01

    The nuclear pore complex is the primary conduit for nuclear import and export of molecules. In this issue, Gu et al. uncover a novel mechanism in which immune signaling and programmed cell death require nuclear pore rearrangement and release of sequestered cyclin-dependent kinase inhibitors to elicit immunity and death. PMID:27610561