WorldWideScience

Sample records for atomic conformational transition

  1. Transition probabilities for atoms

    International Nuclear Information System (INIS)

    Kim, Y.K.

    1980-01-01

    Current status of advanced theoretical methods for transition probabilities for atoms and ions is discussed. An experiment on the f values of the resonance transitions of the Kr and Xe isoelectronic sequences is suggested as a test for the theoretical methods

  2. Atomic cranks and levers control sugar ring conformations

    International Nuclear Information System (INIS)

    Zhang Qingmin; Lee, Gwangrog; Marszalek, Piotr E

    2005-01-01

    In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of β-1→4-linked D-glucose, and amylose, composed of α-1→4-linked D-glucose. In contrast to β-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, α-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1→6-linked polysaccharides: pustulan, a β-1→6-linked glucan, and dextran, a α-1→6-linked glucan. Forced rotations about the C 5 -C 6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C 5 -C 6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance

  3. Electromagnetic transitions in the atom

    International Nuclear Information System (INIS)

    Ulehla, I.; Suk, M.; Trka, Z.

    1990-01-01

    Methods to achieve excitation of atoms are outlined and conditions necessary for the occurrence of electromagnetic transitions in the atomic shell are given. Radiative transitions between the energy states of the atom include stimulated absorption, spontaneous emission, and stimulated emission. Selection rules applying to the majority of observed transitions are given. The parity concept is explained. It is shown how the electromagnetic field and its interaction with the magnetic moment of the atom lead to a disturbance of the energy states of the atom and the occurrence of various electro-optical and magneto-optical phenomena. The Stark effect and electron spin resonance are described. X-rays and X-ray spectra, the Auger effect and the internal photoeffect are also dealt with. The principle of the laser is explained. (M.D.). 22 figs., 1 tab

  4. Frustration-guided motion planning reveals conformational transitions in proteins.

    Science.gov (United States)

    Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; van den Bedem, Henry

    2017-10-01

    Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25 Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/. © 2017 Wiley Periodicals, Inc.

  5. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan

    2014-10-07

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  6. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan; Uyaver, Sahin; Sun, Shuyu

    2014-01-01

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  7. Parity nonconservation in Zeeman atomic transitions

    International Nuclear Information System (INIS)

    Kraftmakher, A.Ya.

    1990-01-01

    The abilities to observe the parity violation at the radiofrequency transitions between the hyperfine and Zeeman terms of the atomic levels are considered. The E-1 amplitudes fo the Zeeman transitions of heavy atoms in weak magnetic fields are larger, than for the light atoms hyperfine transitions at the same wavelength. 9 refs

  8. Prediction of conformationally dependent atomic multipole moments in carbohydrates.

    Science.gov (United States)

    Cardamone, Salvatore; Popelier, Paul L A

    2015-12-15

    The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings. © 2015 Wiley Periodicals, Inc.

  9. Vibration atomic layer deposition for conformal nanoparticle coating

    Energy Technology Data Exchange (ETDEWEB)

    Park, Suk Won; Woo Kim, Jun; Jong Choi, Hyung; Hyung Shim, Joon, E-mail: shimm@korea.ac.kr [School of Mechanical Engineering, Korea University, Seoul 136-701 (Korea, Republic of)

    2014-01-15

    A vibration atomic layer deposition reactor was developed for fabricating a conformal thin-film coating on nanosize particles. In this study, atomic layer deposition of 10–15-nm-thick Al{sub 2}O{sub 3} films was conducted on a high-surface-area acetylene black powder with particle diameters of 200–250 nm. Intense vibration during the deposition resulted in the effective separation of particles, overcoming the interparticle agglomeration force and enabling effective diffusion of the precursor into the powder chunk; this phenomenon led to the formation of a conformal film coating on the nanopowder particles. It was also confirmed that the atomic layer deposition Al{sub 2}O{sub 3} films initially grew on the high-surface-area acetylene black powder particles as discrete islands, presumably because chemisorption of the precursor and water occurred only on a few sites on the high-surface-area acetylene black powder surface. Relatively sluggish growth of the films during the initial atomic layer deposition cycles was identified from composition analysis.

  10. Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

    Science.gov (United States)

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2014-03-01

    A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

  11. Transition from LEDCOP to ATOMIC

    International Nuclear Information System (INIS)

    Magee, N.H.; Abdallah, J.; Colgan, J.; Hakel, P.; Kilcrease, D.P.; Mazevet, S.; Sherrill, M.E.; Fontes, C.J.; Zhang, H.

    2004-01-01

    This paper discusses the development of the ATOMIC code, a new low to mid Z opacity code, which will replace the current Los Alamos low Z opacity code LEDCOP. The ATOMIC code is based on the FINE code, long used by the Los Alamos group for spectral comparisons in local thermodynamic equilibrium (LTE) and for non-LTE calculations, both utilizing the extensive databases from the atomic physics suite of codes based on the work of R.D. Cowan. Many of the plasma physics packages in LEDCOP, such as line broadening and free-free absorption, are being transferred to the new ATOMIC code. A new equation of state (EOS) model is being developed to allow higher density calculations than were possible with either the FINE or LEDCOP codes. Extensive modernization for both ATOMIC and the atomic physics code suites, including conversion to Fortran 90 and parallelization, are underway to speed up the calculations and to allow the use of expanded databases for both the LTE opacity tables and the non-LTE calculations. Future plans for the code will be outlined, including considerations for new generation opacity tables.

  12. The E1 transitions in kaonic atoms

    International Nuclear Information System (INIS)

    Qureshi, I.E.

    1984-01-01

    The electric dipole transition rates in kanonic atoms are calculated by using distorted relativistic wave functions. The kaon-nucleus strong interaction which is responsible for the distortion of atomic states is considered to be proportional to the nuclear density and the effective isospin-averaged kaon-nucleon scattering length. Six atoms have been studied for which the last observed X-rays correspond to 3d-2p, 4f-3d, 5g-4f, 6h-5g, 7i-6h and 8j-7i transitions. It is found that the electric dipole transition rate is enhanced by an amount (0.3-7.6)x10 13 s -1 . (orig.)

  13. Resonant quantum transitions in trapped antihydrogen atoms.

    Science.gov (United States)

    Amole, C; Ashkezari, M D; Baquero-Ruiz, M; Bertsche, W; Bowe, P D; Butler, E; Capra, A; Cesar, C L; Charlton, M; Deller, A; Donnan, P H; Eriksson, S; Fajans, J; Friesen, T; Fujiwara, M C; Gill, D R; Gutierrez, A; Hangst, J S; Hardy, W N; Hayden, M E; Humphries, A J; Isaac, C A; Jonsell, S; Kurchaninov, L; Little, A; Madsen, N; McKenna, J T K; Menary, S; Napoli, S C; Nolan, P; Olchanski, K; Olin, A; Pusa, P; Rasmussen, C Ø; Robicheaux, F; Sarid, E; Shields, C R; Silveira, D M; Stracka, S; So, C; Thompson, R I; van der Werf, D P; Wurtele, J S

    2012-03-07

    The hydrogen atom is one of the most important and influential model systems in modern physics. Attempts to understand its spectrum are inextricably linked to the early history and development of quantum mechanics. The hydrogen atom's stature lies in its simplicity and in the accuracy with which its spectrum can be measured and compared to theory. Today its spectrum remains a valuable tool for determining the values of fundamental constants and for challenging the limits of modern physics, including the validity of quantum electrodynamics and--by comparison with measurements on its antimatter counterpart, antihydrogen--the validity of CPT (charge conjugation, parity and time reversal) symmetry. Here we report spectroscopy of a pure antimatter atom, demonstrating resonant quantum transitions in antihydrogen. We have manipulated the internal spin state of antihydrogen atoms so as to induce magnetic resonance transitions between hyperfine levels of the positronic ground state. We used resonant microwave radiation to flip the spin of the positron in antihydrogen atoms that were magnetically trapped in the ALPHA apparatus. The spin flip causes trapped anti-atoms to be ejected from the trap. We look for evidence of resonant interaction by comparing the survival rate of trapped atoms irradiated with microwaves on-resonance to that of atoms subjected to microwaves that are off-resonance. In one variant of the experiment, we detect 23 atoms that survive in 110 trapping attempts with microwaves off-resonance (0.21 per attempt), and only two atoms that survive in 103 attempts with microwaves on-resonance (0.02 per attempt). We also describe the direct detection of the annihilation of antihydrogen atoms ejected by the microwaves.

  14. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Barry J Grant

    2009-03-01

    Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

  15. Quantum phase transitions in atomic nuclei

    International Nuclear Information System (INIS)

    Zamfir, N.V.

    2005-01-01

    Studies of quantum phase transitions in mesoscopic systems and applications to atomic nuclei are presented. Analysis in terms of the Interacting Boson Model shows that the main features persist even for moderate number of particles. Experimental evidence in rare-earth nuclei is discussed. New order and control parameters for systems with the same number of particles are proposed. (author)

  16. Resonant quantum transitions in trapped antihydrogen atoms

    CERN Document Server

    Amole, C; Baquero-Ruiz, M; Bertsche, W; Bowe, P D; Butler, E; Capra, A; Cesar, C L; Charlton, M; Deller, A; Donnan, P H; Eriksson, S; Fajans, J; Friesen, T; Fujiwara, M C; Gill, D R; Gutierrez, A; Hangst, J S; Hardy, W N; Hayden, M E; Humphries, A J; Isaac, C A; Jonsell, S; Kurchaninov, L; Little, A; Madsen, N; McKenna, J T K; Menary, S; Napoli, S C; Nolan, P; Olchanski, K; Olin, A; Pusa, P; Rasmussen, C Ø; Robicheaux, F; Sarid, E; Shields, C R; Silveira, D M; Stracka, S; So, C; Thompson, R I; van der Werf, D P; Wurtele, J S

    2012-01-01

    The hydrogen atom is one of the most important and influential model systems in modern physics. Attempts to understand its spectrum are inextricably linked to the early history and development of quantum mechanics. The hydrogen atom’s stature lies in its simplicity and in the accuracy with which its spectrum can be measured1 and compared to theory. Today its spectrum remains a valuable tool for determining the values of fundamental constants and for challenging the limits of modern physics, including the validity of quantum electrodynamics and—by comparison with measurements on its antimatter counterpart, antihydrogen—the validity of CPT (charge conjugation, parity and time reversal) symmetry. Here we report spectroscopy of a pure antimatter atom, demonstrating resonant quantum transitions in antihydrogen. We have manipulated the internal spin state2, 3 of antihydrogen atoms so as to induce magnetic resonance transitions between hyperfine levels of the positronic ground state. We used resonant microwave...

  17. Stimulated transitions in resonant atom Majorana mixing

    Science.gov (United States)

    Bernabéu, José; Segarra, Alejandro

    2018-02-01

    Massive neutrinos demand to ask whether they are Dirac or Majorana particles. Majorana neutrinos are an irrefutable proof of physics beyond the Standard Model. Neutrinoless double electron capture is not a process but a virtual Δ L = 2 mixing between a parent A Z atom and a daughter A ( Z - 2) excited atom with two electron holes. As a mixing between two neutral atoms and the observable signal in terms of emitted two-hole X-rays, the strategy, experimental signature and background are different from neutrinoless double beta decay. The mixing is resonantly enhanced for almost degeneracy and, under these conditions, there is no irreducible background from the standard two-neutrino channel. We reconstruct the natural time history of a nominally stable parent atom since its production either by nature or in the laboratory. After the time periods of atom oscillations and the decay of the short-lived daughter atom, at observable times the relevant "stationary" states are the mixed metastable long-lived state and the non-orthogonal short-lived excited state, as well as the ground state of the daughter atom. We find that they have a natural population inversion which is most appropriate for exploiting the bosonic nature of the observed atomic transitions radiation. Among different observables of the atom Majorana mixing, we include the enhanced rate of stimulated X-ray emission from the long-lived metastable state by a high-intensity X-ray beam: a gain factor of 100 can be envisaged at current XFEL facilities. On the other hand, the historical population of the daughter atom ground state can be probed by exciting it with a current pulsed optical laser, showing the characteristic absorption lines: the whole population can be excited in a shorter time than typical pulse duration.

  18. Laser induced popcornlike conformational transition of nanodiamond as a nanoknife

    International Nuclear Information System (INIS)

    Chang, C.-C.; Chen, P.-H.; Chu, H.-L.; Lee, T.-C.; Chou, C.-C.; Chao, J.-I; Su, C.-Y.; Chen, J.S.; Tsai, J.-S.; Tsai, C.-M.; Ho, Y.-P.; Sun, K.W.; Cheng, C.-L.; Chen, F.-R.

    2008-01-01

    Nanodiamond (ND) is surrounded by layers of graphite on its surface. This unique structure feature creates unusual fluorescence spectra, which can be used as an indicator to monitor its surface modification. Meanwhile, the impurity, nitroso (C-N=O) inside the ND can be photolyzed by two-photon absorption, releasing NO to facilitate the formation of a sp 3 diamond structure in the core of ND and transforming it into a sp 2 graphite structure. Such a conformational transition enlarges the size of ND from 8 to 90 nm, resulting in a popcornlike structure. This transition reaction may be useful as nanoknives in biomedical application

  19. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  20. The atomic structure of transition metal clusters

    International Nuclear Information System (INIS)

    Riley, S.J.

    1995-01-01

    Chemical reactions are used to probe the atomic (geometrical) structure of isolated clusters of transition metal atoms. The number of adsorbate molecules that saturate a cluster, and/or the binding energy of molecules to cluster surfaces, are determined as a function of cluster size. Systematics in these properties often make it possible to propose geometrical structures consistent with the experimental observations. We will describe how studies of the reactions of cobalt and nickel clusters with ammonia, water, and nitrogen provide important and otherwise unavailable structural information. Specifically, small (less than 20 atoms) clusters of cobalt and nickel atoms adopt entirely different structures, the former having packing characteristic of the bulk and the latter having pentagonal symmetry. These observations provide important input for model potentials that attempt to describe the local properties of transition metals. In particular, they point out the importance of a proper treatment of d-orbital binding in these systems, since cobalt and nickel differ so little in their d-orbital occupancy

  1. Atomic Transition Probabilities Scandium through Manganese

    International Nuclear Information System (INIS)

    Martin, G.A.; Fuhr, J.R.; Wiese, W.L.

    1988-01-01

    Atomic transition probabilities for about 8,800 spectral lines of five iron-group elements, Sc(Z = 21) to Mn(Z = 25), are critically compiled, based on all available literature sources. The data are presented in separate tables for each element and stage of ionization and are further subdivided into allowed (i.e., electric dipole-E1) and forbidden (magnetic dipole-M1, electric quadrupole-E2, and magnetic quadrupole-M2) transitions. Within each data table the spectral lines are grouped into multiplets, which are in turn arranged according to parent configurations, transition arrays, and ascending quantum numbers. For each line the transition probability for spontaneous emission and the line strength are given, along with the spectroscopic designation, the wavelength, the statistical weights, and the energy levels of the upper and lower states. For allowed lines the absorption oscillator strength is listed, while for forbidden transitions the type of transition is identified (M1, E2, etc.). In addition, the estimated accuracy and the source are indicated. In short introductions, which precede the tables for each ion, the main justifications for the choice of the adopted data and for the accuracy rating are discussed. A general introduction contains a discussion of our method of evaluation and the principal criteria for our judgements

  2. Relativistic effects in atomic inner-shell transitions

    International Nuclear Information System (INIS)

    Chen, M.H.

    1982-01-01

    Theoretical calculations of atomic inner-shell transition rates based on independent-particle models are reviewed. Factors affecting inner-shell transition rates are examined, particularly the effects of relativity. 48 references, 5 figures

  3. First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction

    International Nuclear Information System (INIS)

    Zhao Xiu-Qin; Liu Ni; Liang Jiu-Qing

    2017-01-01

    In this article, we use the spin coherent state transformation and the ground state variational method to theoretically calculate the ground function. In order to consider the influence of the atom-atom interaction on the extended Dicke model’s ground state properties, the mean photon number, the scaled atomic population and the average ground energy are displayed. Using the self-consistent field theory to solve the atom-atom interaction, we discover the system undergoes a first-order quantum phase transition from the normal phase to the superradiant phase, but a famous Dicke-type second-order quantum phase transition without the atom-atom interaction. Meanwhile, the atom-atom interaction makes the phase transition point shift to the lower atom-photon collective coupling strength. (paper)

  4. The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

    Science.gov (United States)

    Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.

    2012-01-01

    To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the Cα atoms of G60 at switch 2 and G10 at the P-loop and the N-Cα-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition. PMID:22359497

  5. Interplay of Nitrogen-Atom Inversion and Conformational Inversion in Enantiomerization of 1H-1-Benzazepines.

    Science.gov (United States)

    Ramig, Keith; Subramaniam, Gopal; Karimi, Sasan; Szalda, David J; Ko, Allen; Lam, Aaron; Li, Jeffrey; Coaderaj, Ani; Cavdar, Leyla; Bogdan, Lukasz; Kwon, Kitae; Greer, Edyta M

    2016-04-15

    A series of 2,4-disubstituted 1H-1-benzazepines, 2a-d, 4, and 6, were studied, varying both the substituents at C2 and C4 and at the nitrogen atom. The conformational inversion (ring-flip) and nitrogen-atom inversion (N-inversion) energetics were studied by variable-temperature NMR spectroscopy and computations. The steric bulk of the nitrogen-atom substituent was found to affect both the conformation of the azepine ring and the geometry around the nitrogen atom. Also affected were the Gibbs free energy barriers for the ring-flip and the N-inversion. When the nitrogen-atom substituent was alkyl, as in 2a-c, the geometry of the nitrogen atom was nearly planar and the azepine ring was highly puckered; the result was a relatively high-energy barrier to ring-flip and a low barrier to N-inversion. Conversely, when the nitrogen-atom substituent was a hydrogen atom, as in 2d, 4, and 6, the nitrogen atom was significantly pyramidalized and the azepine ring was less puckered; the result here was a relatively high energy barrier to N-inversion and a low barrier to ring-flip. In these N-unsubstituted compounds, it was found computationally that the lowest-energy stereodynamic process was ring-flip coupled with N-inversion, as N-inversion alone had a much higher energy barrier.

  6. Auger transitions in singly and multiply ionized atoms

    International Nuclear Information System (INIS)

    Mehlhorn, W.

    1978-01-01

    Some recent progress in Auger and autoionizing electron spectrometry of free metal atoms and of multiply ionized atoms is reviewed. The differences which arise between the spectra of atoms in the gaseous and the solid state are due to solid state effects. This will be shown for Cd as an example. The super Coster-Kronig transitions 3p-3d 2 (hole notation) and Coster-Kronig transitions 3p-3d 4s have been measured and compared with free-atom calculations for free Zn atoms. The experimental width GAMMA(3p)=(2.1+-0.2)eV found for the free atom agrees with the value obtained for solid Zn but is considerably smaller than the theoretical value for the free atom. Autoionizing spectra of Na following an L-shell excitation or ionization by different particles are compared and discussed. The nonisotropic angular distribution of electrons from the transition 2p 5 3s 2 2 Psub(3/2)→2p 6 +e - is compared with theoretical calculations. Two examples for Auger spectrometry of multiply ionized atoms are given: (1) excitation of neon target atoms by light and heavy ions, and (2) excitation of projectile ions Be + and B + in single gas collisions with CH 4 . A strong alignment of the excited atoms has also been found here

  7. Conformal invariance at a deconfinement phase transition in (2+1) dimensions

    International Nuclear Information System (INIS)

    Christensen, J.; Damgaard, P.H.

    1990-08-01

    The conformal dimension of the Polyakov line at the deconfinement phase transition of (2+1)-dimensional SU(2) lattice gauge theory is determined numerically using two-dimensional finite size conformal field theory. Excellent agreement with two-dimensional Ising model values is found for both the renormalized coupling on a spatially toroidal geometry and the conformal dimensions on a finite-width strip geometry. (orig.)

  8. First Order Electroweak Phase Transition from (Non)Conformal Extensions of the Standard Model

    DEFF Research Database (Denmark)

    Sannino, Francesco; Virkajärvi, Jussi

    2015-01-01

    We analyse and compare the finite-temperature electroweak phase transition properties of classically (non)conformal extensions of the Standard Model. In the classically conformal scenarios the breaking of the electroweak symmetry is generated radiatively. The models feature new scalars coupled co...... the associated models are testable at the upcoming Large Hadron Collider run two experiments....

  9. Identification of key residues for protein conformational transition using elastic network model.

    Science.gov (United States)

    Su, Ji Guo; Xu, Xian Jin; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin

    2011-11-07

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

  10. Model for pairing phase transition in atomic nuclei

    International Nuclear Information System (INIS)

    Schiller, A.; Guttormsen, M.; Hjorth-Jensen, M.; Rekstad, J.; Siem, S.

    2002-01-01

    A model is developed which allows the investigation and classification of the pairing phase transition in atomic nuclei. The regions of the parameter space are discussed for which a pairing phase transition can be observed. The model parameters include number of particles, attenuation of pairing correlations with increasing seniority, single-particle level spacing, and pairing gap parameter

  11. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.

    Science.gov (United States)

    Zhitnikova, M Y; Shestopalova, A V

    2017-11-01

    The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.

  12. Model analysis of molecular conformations in terms of weak interactions between non bonded atoms

    International Nuclear Information System (INIS)

    Lombardi, E.

    1988-01-01

    The aim of the present paper is to establish a reliable basis for the evaluation of stable conformations and rotational barriers for molecules, with possible applications to systems of biological interest. It is proceeded in two steps: first, the effect of chemical environment on orbitals of a given atom is studied for diatomic units, adopting a valence-bond approach and considering, as prototypes, the two simplest series of diatomic molecules with one valence electron each, i.e. the alkali diatomics and the alkali hydrides. In the model, the orbital of the hydrogen atom by a simple (''1S'') gaussian function, the valence orbital of an alkali atom by a function (r 2 -a 2 ) times a simple gaussian (''2S'' gaussian). Dissociation energies D e and equilibrium distances R e are calculated using a scanning procedure. Agreement with experiment is quantitative for the alkali diatomics. For alkali hydrides, good agreement is obtained only if validity of a rule β e R e =constant, for the two atoms separately, is postulated; β e is the characteristic parameter of a ''1S'' gaussian (hydrogen) or a ''2S'' gaussian (alkali atom) function. In a second step, the authors assume validity of the same rule in conformational analysis for any single bonded A-B molecule with A=C, O, N, P, Si, Ge and B=H, or a halogen atom. Gauge β e values for H, F and C are obtained by fitting experimental rotational barriers in C 2 H 6 , C 2 F 6 and C 3 H 8 . Stable conformation of, and barriers to rotation in, ethane-like rotors are determined, applying first-order exchange perturbation theory, in terms of two- and many-center exchange interactions in cluster of non-bonded atoms. Some 60 molecules are analyzed. Agreement with experiments is strikngly good except for a few systematic deviation. Reasons for such discrepancies are discussed

  13. Nuclear transitions induced by atomic excitations

    International Nuclear Information System (INIS)

    Dyer, P.; Bounds, J.A.; Haight, R.C.; Luk, T.S.

    1988-01-01

    In the two-step pumping scheme for a gamma-ray laser, an essential step is that of exciting the nucleus from a long-lived storage isomer to a nearby short- lived state that then decays to the upper lasing level. An experiment is in progress to induce this transfer by first exciting the atomic electrons with UV photons. The incident photons couple well to the electrons, which then couple via a virtual photon to the nucleus. As a test case, excitation of the 235 U nucleus is being sought, using a high- brightness UV laser. The excited nuclear state, having a 26- minute half-life, decays by internal conversion, resulting in emission of an atomic electron. A pulsed infrared laser produces an atomic beam of 235 U which is then bombarded by the UV laser beam. Ions are collected, and conversion electrons are detected by a channel electron multiplier. In preliminary experiments, an upper limit of 7 x 10 -5 has been obtained for the probability of exciting a 235 U atom in the UV beam for one picosecond at an intensity of about 10 15 W/cm 2 . Experiments with higher sensitivities and at higher UV beam intensities are underway

  14. QED theory of multiphoton transitions in atoms and ions

    Science.gov (United States)

    Zalialiutdinov, Timur A.; Solovyev, Dmitry A.; Labzowsky, Leonti N.; Plunien, Günter

    2018-03-01

    This review surveys the quantum theory of electromagnetic radiation for atomic systems. In particular, a review of current theoretical studies of multiphoton processes in one and two-electron atoms and highly charged ions is provided. Grounded on the quantum electrodynamics description the multiphoton transitions in presence of cascades, spin-statistic behaviour of equivalent photons and influence of external electric fields on multiphoton in atoms and anti-atoms are discussed. Finally, the nonresonant corrections which define the validity of the concept of the excited state energy levels are introduced.

  15. NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

    Science.gov (United States)

    Sekhar, Ashok; Kay, Lewis E

    2013-08-06

    The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

  16. Phase Transitions, Geometrothermodynamics, and Critical Exponents of Black Holes with Conformal Anomaly

    Directory of Open Access Journals (Sweden)

    Jie-Xiong Mo

    2014-01-01

    Full Text Available We investigate the phase transitions of black holes with conformal anomaly in canonical ensemble. Some interesting and novel phase transition phenomena have been discovered. It is shown that there are striking differences in both Hawking temperature and phase structure between black holes with conformal anomaly and those without it. Moreover, we probe in detail the dependence of phase transitions on the choice of parameters. The results show that black holes with conformal anomaly have much richer phase structure than those without it. There would be two, only one, or no phase transition points depending on the parameters. The corresponding parameter regions are derived both numerically and graphically. Geometrothermodynamics are built up to examine the phase structure we have discovered. It is shown that Legendre invariant thermodynamic scalar curvature diverges exactly where the specific heat diverges. Furthermore, critical behaviors are investigated by calculating the relevant critical exponents. And we prove that these critical exponents satisfy the thermodynamic scaling laws.

  17. Measurements of atomic transition probabilities in highly ionized atoms by fast ion beams

    International Nuclear Information System (INIS)

    Martinson, I.; Curtis, L.J.; Lindgaerd, A.

    1977-01-01

    A summary is given of the beam-foil method by which level lifetimes and transition probabilities can be determined in atoms and ions. Results are presented for systems of particular interest for fusion research, such as the Li, Be, Na, Mg, Cu and Zn isoelectronic sequences. The available experimental material is compared to theoretical transition probabilities. (author)

  18. Relativistic Transitions in the Hydrogenic Atoms

    CERN Document Server

    Boudet, R

    2009-01-01

    When one approaches the study of the quantal relativistic theory of the electron, one may be surprised by the gap which lies between the frame of the experiments, i.e. the real geometry of the space and time, and the abstraction of the complex matrices and spinors formalism employed in the presentation of the theory. This book uses a theory of the electron, introduced by David Hestenes, in which the mathematical language is the same as the one of the geometry of the space and time. Such a language not only allows one to find again the well known results concerning the one-electron atoms theory but furthermore leads easily to the resolution of problems considered for a long time without solution.

  19. Atomic final-state effects in nuclear transitions

    International Nuclear Information System (INIS)

    Griffiths, A.; Vogel, P.

    1991-01-01

    The interaction of a nuclear gamma radiation with the atomic electron cloud gives rise to a phase shift in the nuclear electromagnetic transition amplitude. The resulting interference parameters ξ(πL) are of significance to the analysis of time-reversal experiments. We calculate these parameters for E1, E2, E3, M1, and M2 gamma transitions in a number of nuclei. We also discuss the implication of these results for simultaneous parity- and time-reversal-violating experiments

  20. Experimental First Order Pairing Phase Transition in Atomic Nuclei

    International Nuclear Information System (INIS)

    Moretto, L G; Larsen, A C; Giacoppo, F; Guttormsen, M; Siem, S

    2015-01-01

    The natural log of experimental nuclear level densities at low energy is linear with energy. This can be interpreted in terms of a nearly 1st order phase transition from a superfluid to an ideal gas of quasi particles. The transition temperature coincides with the BCS critical temperature and yields gap parameters in good agreement with the values extracted from even- odd mass differences from rotational states. This converging evidence supports the relevance of the BCS theory to atomic nuclei

  1. Phase transition and gravitational wave phenomenology of scalar conformal extensions of the Standard Model

    Energy Technology Data Exchange (ETDEWEB)

    Marzola, Luca; Racioppi, Antonio; Vaskonen, Ville [National Institute of Chemical Physics and Biophysics, Tallinn (Estonia)

    2017-07-15

    Thermal corrections in classically conformal models typically induce a strong first-order electroweak phase transition, thereby resulting in a stochastic gravitational background that could be detectable at gravitational wave observatories. After reviewing the basics of classically conformal scenarios, in this paper we investigate the phase transition dynamics in a thermal environment and the related gravitational wave phenomenology within the framework of scalar conformal extensions of the Standard Model. We find that minimal extensions involving only one additional scalar field struggle to reproduce the correct phase transition dynamics once thermal corrections are accounted for. Next-to-minimal models, instead, yield the desired electroweak symmetry breaking and typically result in a very strong gravitational wave signal. (orig.)

  2. Self-limiting atomic layer deposition of conformal nanostructured silver films

    International Nuclear Information System (INIS)

    Golrokhi, Zahra; Chalker, Sophia; Sutcliffe, Christopher J.; Potter, Richard J.

    2016-01-01

    Graphical abstract: - Highlights: • We grow metallic silver by direct liquid injection thermal atomic layer deposition. • Highly conformal silver nanoparticle coatings on high aspect ratio surfaces. • An ALD temperature growth window between 123 and 128 °C is established. • ALD cycles provides sub nanometre control of silver growth. • Catalytic dehydrogenation ALD mechanism has been elucidated by in-situ QCM. - Abstract: The controlled deposition of ultra-thin conformal silver nanoparticle films is of interest for applications including anti-microbial surfaces, plasmonics, catalysts and sensors. While numerous techniques can produce silver nanoparticles, few are able to produce highly conformal coatings on high aspect ratio surfaces, together with sub-nanometre control and scalability. Here we develop a self-limiting atomic layer deposition (ALD) process for the deposition of conformal metallic silver nanoparticle films. The films have been deposited using direct liquid injection ALD with ((hexafluoroacetylacetonato)silver(I)(1,5-cyclooctadiene)) and propan-1-ol. An ALD temperature window between 123 and 128 °C is identified and within this range self-limiting growth is confirmed with a mass deposition rate of ∼17.5 ng/cm"2/cycle. The effects of temperature, precursor dose, co-reactant dose and cycle number on the deposition rate and on the properties of the films have been systematically investigated. Under self-limiting conditions, films are metallic silver with a nano-textured surface topography and nanoparticle size is dependent on the number of ALD cycles. The ALD reaction mechanisms have been elucidated using in-situ quartz crystal microbalance (QCM) measurements, showing chemisorption of the silver precursor, followed by heterogeneous catalytic dehydrogenation of the alcohol to form metallic silver and an aldehyde.

  3. Shake-off processes at the electron transitions in atoms

    International Nuclear Information System (INIS)

    Matveev, V.I.; Parilis, Eh.S.

    1982-01-01

    Elementary processes in multielectron atoms - radiative and Auger transitions, photoionization and ionization by an electron impact etc. are usually followed by the relaxation of electron shells. The conditions under which such multielectron problem could be solved in the shake-off approximation are considered. The shake-off processes occurring. as a result of the electron transitions are described from the general point of view. The common characteristics and peculiar features of this type of excitation in comparison with the electron shake-off under nuclear transformations are pointed out. Several electron shake-off processes are considered, namely: radiative Auger effect, the transition ''two electrons-one photon'', dipole ionization, spectral line broadening, post collision interaction, Auger decay stimulated by collision with fast electrons, three-electron Auger transitions: double and half Auger effect. Their classification is given according to the type of the electron transition causing the shake-off process. The experimental data are presented and the methods of theoretical description are reviewed. Other similar effects, which could follow the transitions in electron shells are pointed out. The deduction of shake-off approximation is presented, and it is pointed out that this approach is analogous to the distorted waves approximation in the theory of scattering. It was shown that in atoms the shake-off approximation is a very effective method, which allows to obtain the probability of different electronic effects

  4. Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

    Science.gov (United States)

    Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

    2017-11-01

    Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

  5. Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

    Science.gov (United States)

    Lee, Eunsang; Paul, Wolfgang

    2018-02-01

    A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

  6. Atomic structure of non-stoichiometric transition metal carbides

    International Nuclear Information System (INIS)

    Moisy-Maurice, Virginie.

    1981-10-01

    Different kinds of experimental studies of the atomic arrangement in non-stoichiometric transition metal carbides are proposed: the ordering of carbon vacancies and the atomic static displacements are the main subjects studied. Powder neutron diffraction on TiCsub(1-x) allowed us to determine the order-disorder transition critical temperature -Tsub(c) approximately 770 0 C- in the TiCsub(0.52-0.67) range, and to analyze at 300 K the crystal structure of long-range ordered samples. A neutron diffuse scattering quantitative study at 300 K of short-range order in TiCsub(0.76), TiCsub(0.79) and NbCsub(0.73) single crystals is presented: as in Ti 2 Csub(1+x) and Nb 6 C 5 superstructures, vacancies avoid to be on each side of a metal atom. Besides, the mean-square carbon atom displacements from their sites are small, whereas metal atoms move radially about 0.03 A away from vacancies. These results are in qualitative agreement with EXAFS measurements at titanium-K edge of TiCsub(1-x). An interpretation of ordering in term of short-range interaction pair potentials between vacancies is proposed [fr

  7. H/L transition time estimation in JET using conformal predictors

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, S., E-mail: sergio.gonzalez@ciemat.es [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Vega, J. [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Murari, A. [Consorzio RFX, Associazione EURATOM/ENEA per la Fusione, Padova 4-25127 (Italy); Pereira, A. [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Dormido-Canto, S.; Ramirez, J.M. [Departamento de Informatica y Automatica, UNED, Madrid 28040 (Spain)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer H/L transitions have been predicted using H/L and L/H models. Black-Right-Pointing-Pointer Models have been built using conformal predictors to hedge the prediction with confidence and credibility measures. Black-Right-Pointing-Pointer Models have been trained using linear and radial basis function kernels. Black-Right-Pointing-Pointer Conformal measures have proven their usefulness to validate data-driven models. - Abstract: Recent advances in data mining allow the automatic recognition of physical phenomena in the databases of fusion devices without human intervention. This is important to create large databases of physical events (thereby increasing the statistical relevance) in an unattended manner. Important examples are the L/H and H/L transitions. In this contribution, a novel technique is introduced to automatically locate H/L transitions in JET by using conformal predictors. The focus is on H/L transitions because typically there is not a clear signature in the time series of the most widely available signals to recognize the change of confinement. Conformal predictors hedge their prediction by means of two parameters: confidence and credibility. The technique has been based on binary supervised classifiers to separate the samples of the respective confinement modes. Results with several underlying classifiers are presented.

  8. pH-Driven Ordering Transitions in Liquid Crystal Induced by Conformational Changes of Cardiolipin.

    Science.gov (United States)

    Sidiq, Sumyra; Verma, Indu; Pal, Santanu Kumar

    2015-04-28

    We report an investigation of interfacial phenomena occurring at aqueous-liquid crystal (LC) interfaces that triggers an orientational ordering transition of the LC in the presence of cardiolipin (CL) by varying pH, salt concentration and valence. In particular, the effects of three different conformational isomeric forms of the CL are observed to cause the response of the LC ordering to vary significantly from one to another at those interfaces. An ordering transition of the LC was observed when the CL is mostly in undissociated (at pH 2) and/or in bicyclic (at pH 4) conformation in which LC shows changes in the optical appearance from bright to dark. By contrast, no change in the optical appearance of the LC was observed when the pH of the system increases to 8 or higher in which the CL mostly exists in the open conformation. Fluorescence microscopy measurements further suggest that pH-dependent conformational forms of the CL have different ability to self-assemble (thus different packing efficiency) at aqueous-LC interfaces leading to dissimilar orientational behavior of the LC. Specifically, we found that change in headgroup-headgroup repulsion of the central phosphatidyl groups of the CL plays a key role in tuning the lipid packing efficiency and thus responses to interfacial phenomena. Orientational ordering transition of the LC was also observed as a function of increasing the ionic strength (buffer capacity) and strongly influenced in the presence of mono and divalent cations. Langmuir-Blodgett (LB) and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements provide further insight in modulation of the lipid packing efficiency and alkyl chain conformation of the CL at different pH and ionic conditions. Overall, the results presented in this paper establish that LCs offer a promising approach to differentiate different conformations (label free detection) of the CL through ordering transition of the LC at aqueous

  9. Conformity and structure of titanium oxide films grown by atomic layer deposition on silicon substrates

    Energy Technology Data Exchange (ETDEWEB)

    Jogi, Indrek [University of Tartu, Institute of Experimental Physics and Technology, Taehe 4, 51010, Tartu (Estonia)], E-mail: indrek.jogi@ut.ee; Paers, Martti; Aarik, Jaan; Aidla, Aleks [University of Tartu, Institute of Physics, Riia 142, 51014, Tartu (Estonia); Laan, Matti [University of Tartu, Institute of Experimental Physics and Technology, Taehe 4, 51010, Tartu (Estonia); Sundqvist, Jonas; Oberbeck, Lars; Heitmann, Johannes [Qimonda Dresden GmbH and Co. OHG, Koenigsbruecker Strasse 180, 01099, Dresden (Germany); Kukli, Kaupo [University of Tartu, Institute of Experimental Physics and Technology, Taehe 4, 51010, Tartu (Estonia)

    2008-06-02

    Conformity and phase structure of atomic layer deposited TiO{sub 2} thin films grown on silicon substrates were studied. The films were grown using TiCl{sub 4} and Ti(OC{sub 2}H{sub 5}){sub 4} as titanium precursors in the temperature range from 125 to 500 {sup o}C. In all cases perfect conformal growth was achieved on patterned substrates with elliptical holes of 7.5 {mu}m depth and aspect ratio of about 1:40. Conformal growth was achieved with process parameters similar to those optimized for the growth on planar wafers. The dominant crystalline phase in the as-grown films was anatase, with some contribution from rutile at relatively higher temperatures. Annealing in the oxygen ambient resulted in (re)crystallization whereas the effect of annealing depended markedly on the precursors used in the deposition process. Compared to films grown from TiCl{sub 4}, the films grown from Ti(OC{sub 2}H{sub 5}){sub 4} were transformed into rutile in somewhat greater extent, whereas in terms of step coverage the films grown from Ti(OC{sub 2}H{sub 5}){sub 4} remained somewhat inferior compared to the films grown from TiCl{sub 4}.

  10. Conformal atomic layer deposition of alumina on millimeter tall, vertically-aligned carbon nanotube arrays.

    Science.gov (United States)

    Stano, Kelly L; Carroll, Murphy; Padbury, Richard; McCord, Marian; Jur, Jesse S; Bradford, Philip D

    2014-11-12

    Atomic layer deposition (ALD) can be used to coat high aspect ratio and high surface area substrates with conformal and precisely controlled thin films. Vertically aligned arrays of multiwalled carbon nanotubes (MWCNTs) with lengths up to 1.5 mm were conformally coated with alumina from base to tip. The nucleation and growth behaviors of Al2O3 ALD precursors on the MWCNTs were studied as a function of CNT surface chemistry. CNT surfaces were modified through a series of post-treatments including pyrolytic carbon deposition, high temperature thermal annealing, and oxygen plasma functionalization. Conformal coatings were achieved where post-treatments resulted in increased defect density as well as the extent of functionalization, as characterized by X-ray photoelectron spectroscopy and Raman spectroscopy. Using thermogravimetric analysis, it was determined that MWCNTs treated with pyrolytic carbon and plasma functionalization prior to ALD coating were more stable to thermal oxidation than pristine ALD coated samples. Functionalized and ALD coated arrays had a compressive modulus more than two times higher than a pristine array coated for the same number of cycles. Cross-sectional energy dispersive X-ray spectroscopy confirmed that Al2O3 could be uniformly deposited through the entire thickness of the vertically aligned MWCNT array by manipulating sample orientation and mounting techniques. Following the ALD coating, the MWCNT arrays demonstrated hydrophilic wetting behavior and also exhibited foam-like recovery following compressive strain.

  11. Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB

    Directory of Open Access Journals (Sweden)

    Beibei eWang

    2015-04-01

    Full Text Available The tripartite efflux pump assembly AcrAB-TolC is the major multidrug resistance transporter in E. coli. The inner membrane transporter AcrB is a homotrimer, energized by the proton movement down the transmembrane electrochemical gradient. The asymmetric crystal structures of AcrB with three monomers in distinct conformational states (access (A, binding (B and extrusion (E support a functional rotating mechanism, in which each monomer of AcrB cycles among the three states in a concerted way. However, the relationship between the conformational changes during functional rotation and drug translocation has not been totally understood. Here, we explored the conformational changes of the AcrB homotrimer during the ABE→BEA transition in different substrate-binding states using targeted MD simulations. It was found that the dissociation of substrate from the distal binding pocket of B monomer is closely related to the concerted conformational changes in the translocation pathway, especially the side chain reorientation of Phe628 and Tyr327. A second substrate binding at the proximal binding pocket of A monomer evidently accelerates the conformational transitions as well as substrate dissociation in B monomer. The acceleration effect of the multi-substrate binding mode provides a molecular explanation for the positive cooperativity observed in the kinetic studies of substrate efflux and deepens our understanding of the functional rotating mechanism of AcrB.

  12. Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases.

    Science.gov (United States)

    Wong, Chung F

    2016-01-01

    This short article examines the usefulness of fast simulations of conformational transition paths in elucidating enzymatic mechanisms and guiding drug discovery for protein kinases. It applies the transition path method in the MOIL software package to simulate the paths of conformational transitions between six pairs of structures from the Protein Data Bank. The structures along the transition paths were found to resemble experimental structures that mimic transient structures believed to form during enzymatic catalysis or conformational transitions, or structures that have drug candidates bound. These findings suggest that such simulations could provide quick initial insights into the enzymatic mechanisms or pathways of conformational transitions of proteins kinases, or could provide structures useful for aiding structure-based drug design. © 2015 The Protein Society.

  13. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

    Directory of Open Access Journals (Sweden)

    Joseph L Baker

    2013-04-01

    Full Text Available Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon

  14. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

    Science.gov (United States)

    Baker, Joseph L; Biais, Nicolas; Tama, Florence

    2013-04-01

    Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD) simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon stretching.

  15. 4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

    Science.gov (United States)

    2011-01-01

    Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible. PMID:21733172

  16. Non vertical vibronic transitions in atom molecule collisions

    International Nuclear Information System (INIS)

    Klomp, U.C.

    1982-01-01

    This thesis is mainly devoted to an experimental and theoretical study on vibronic transitions which occur in collisions between an alkali atom and several diatomic molecules. An experimental study on electron and ion production in repulsive Cs-CO and Cs-N 2 collisions, and in Cs-NO and Cs-O 2 non-repulsive collisions is presented. The experimental data are discussed in terms of some existing models. It is clear that a new consistent theory on vibronic transitions is needed to explain the experimental data. Such a theory is presented, and it is shown that some existing models are limiting cases of this theory. An experimental study on the relative probabilities for ion and electron production in collisions between a Na, K or Cs atom and an O 2 or NO molecule is also described. These experiments suggest that the incident velocity of the alkali atoms has a predominant influence on the relative probabilities for ion and electron production in these collisions. (Auth.)

  17. A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

    International Nuclear Information System (INIS)

    Tronrud, Dale E.; Karplus, P. Andrew

    2011-01-01

    A script was created to allow SHELXL to use the new CDL v.1.2 stereochemical library which defines the target values for main-chain bond lengths and angles as a function of the residue’s ϕ/ψ angles. Test refinements using this script show that the refinement behavior of structures at resolutions even better than 1 Å is substantially enhanced by the use of the new conformation-dependent ideal geometry paradigm. To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, a script was written that creates a restraint file for the SHELXL refinement program. It was found that the use of this library allows models to be created that have a substantially better fit to main-chain bond angles and lengths without degrading their fit to the X-ray data even at resolutions near 1 Å. For models at much higher resolution (∼0.7 Å), the refined model for parts adopting single well occupied positions is largely independent of the restraints used, but these structures still showed much smaller r.m.s.d. residuals when assessed with the CDL. Examination of the refinement tests across a wide resolution range from 2.4 to 0.65 Å revealed consistent behavior supporting the use of the CDL as a next-generation restraint library to improve refinement. CDL restraints can be generated using the service at http://pgd.science.oregonstate.edu/cdl_shelxl/

  18. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    Science.gov (United States)

    Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

    2013-12-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  19. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    International Nuclear Information System (INIS)

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine

    2013-01-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties

  20. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    Energy Technology Data Exchange (ETDEWEB)

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)

    2013-12-21

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  1. Solid-to-hybrid transitioning armature railgun with non-conforming-to-prejudice bore profile

    Science.gov (United States)

    Solberg, Jerome Michael

    2012-12-04

    An improved railgun, railgun barrel, railgun projectile, and railgun system for accelerating a solid-to-hybrid transitioning armature projectile using a barrel having a bore that does not conform to a cross-sectional profile of the projectile, to contact and guide the projectile only by the rails in a low pressure bore volume so as to minimize damage, failure, and/or underperformance caused by plasma armatures, insulator ablation, and/or restrikes.

  2. An intracellular interaction network regulates conformational transitions in the dopamine transporter

    DEFF Research Database (Denmark)

    Kniazeff, Julie; Shi, Lei; Løland, Claus Juul

    2008-01-01

    Neurotransmitter:sodium symporters (NSS)(1) mediate sodium-dependent reuptake of neurotransmitters from the synaptic cleft and are targets for many psychoactive drugs. The crystal structure of the prokaryotic NSS protein, LeuT, was recently solved at high resolution; however, the mechanistic...... and the intracellular milieu. The mechanism that emerges from these findings may be unique to the NSS family, where the local disruption of ionic interactions modulates the transition of the transporter between the outward- and inward-facing conformations....

  3. Laser Assisted Free-Free Transition in Electron - Atom Collision

    Science.gov (United States)

    Sinha, C.; Bhatia, A. K.

    2011-01-01

    Free-free transition is studied for electron-Hydrogen atom system in ground state at very low incident energies in presence of an external homogeneous, monochromatic and linearly polarized laser field. The incident electron is considered to be dressed by the laser in a non perturbative manner by choosing the Volkov solutions in both the channels. The space part of the scattering wave function for the electron is solved numerically by taking into account the effect of electron exchange, short range as well as of the long range interactions. Laser assisted differential as well as elastic total cross sections are calculated for single photon absorption/emission in the soft photon limit, the laser intensity being much less than the atomic field intensity. A strong suppression is noted in the laser assisted cross sections as compared to the field free situations. Significant difference is noted in the singlet and the triplet cross sections.

  4. Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

    Science.gov (United States)

    Bian, Liujiao; Ji, Xu

    2014-01-01

    Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

  5. Ru nanostructure fabrication using an anodic aluminum oxide nanotemplate and highly conformal Ru atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Woo-Hee; Park, Sang-Joon; Son, Jong-Yeog; Kim, Hyungjun [Department of Material Science and Engineering, POSTECH Pohang University of Science and Technology, San 31, Hyoja-Dong, Nam-Gu, Pohang 790-784 (Korea, Republic of)

    2008-01-30

    We fabricated metallic nanostructures directly on Si substrates through a hybrid nanoprocess combining atomic layer deposition (ALD) and a self-assembled anodic aluminum oxide (AAO) nanotemplate. ALD Ru films with Ru(DMPD)(EtCp) as a precursor and O{sub 2} as a reactant exhibited high purity and low resistivity with negligible nucleation delay and low roughness. These good growth characteristics resulted in the excellent conformality for nanometer-scale vias and trenches. Additionally, AAO nanotemplates were fabricated directly on Si and Ti/Si substrates through a multiple anodization process. AAO nanotemplates with various hole sizes (30-100 nm) and aspect ratios (2:1-20:1) were fabricated by controlling the anodizing process parameters. The barrier layers between AAO nanotemplates and Si substrates were completely removed by reactive ion etching (RIE) using BCl{sub 3} plasma. By combining the ALD Ru and the AAO nanotemplate, Ru nanostructures with controllable sizes and shapes were prepared on Si and Ti/Si substrates. The Ru nanowire array devices as a platform for sensor devices exhibited befitting properties of good ohmic contact and high surface/volume ratio.

  6. Colloquium: Excitons in atomically thin transition metal dichalcogenides

    Science.gov (United States)

    Wang, Gang; Chernikov, Alexey; Glazov, Mikhail M.; Heinz, Tony F.; Marie, Xavier; Amand, Thierry; Urbaszek, Bernhard

    2018-04-01

    Atomically thin materials such as graphene and monolayer transition metal dichalcogenides (TMDs) exhibit remarkable physical properties resulting from their reduced dimensionality and crystal symmetry. The family of semiconducting transition metal dichalcogenides is an especially promising platform for fundamental studies of two-dimensional (2D) systems, with potential applications in optoelectronics and valleytronics due to their direct band gap in the monolayer limit and highly efficient light-matter coupling. A crystal lattice with broken inversion symmetry combined with strong spin-orbit interactions leads to a unique combination of the spin and valley degrees of freedom. In addition, the 2D character of the monolayers and weak dielectric screening from the environment yield a significant enhancement of the Coulomb interaction. The resulting formation of bound electron-hole pairs, or excitons, dominates the optical and spin properties of the material. Here recent progress in understanding of the excitonic properties in monolayer TMDs is reviewed and future challenges are laid out. Discussed are the consequences of the strong direct and exchange Coulomb interaction, exciton light-matter coupling, and influence of finite carrier and electron-hole pair densities on the exciton properties in TMDs. Finally, the impact on valley polarization is described and the tuning of the energies and polarization observed in applied electric and magnetic fields is summarized.

  7. Potential of Transition Metal Atoms Embedded in Buckled Monolayer g-C3N4 as Single-Atom Catalysts

    KAUST Repository

    Li, Shu-Long

    2017-10-27

    We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C3N4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C3N4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C3N4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C3N4 gives rise to promising single-atom catalysts at low temperature.

  8. Potential of Transition Metal Atoms Embedded in Buckled Monolayer g-C3N4 as Single-Atom Catalysts

    KAUST Repository

    Li, Shu-Long; Kan, Xiang; Yin, Hui; Gan, Li-Yong; Schwingenschlö gl, Udo; Zhao, Yong

    2017-01-01

    We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C3N4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C3N4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C3N4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C3N4 gives rise to promising single-atom catalysts at low temperature.

  9. M1 and E2 transitions in the ground-state configuration of atomic ...

    Indian Academy of Sciences (India)

    have calculated the forbidden transition (M1 and E2) parameters such as transition energies, log- arithmic weighted ... Keywords. Forbidden transitions; transition energies; logarithmic weighted oscillator strengths; .... optimizing the energy function based on the non-relativistic Hamiltonian of an atom,. HNR = N. ∑ j=1. (12∇ ...

  10. Origin of the transition voltage in gold–vacuum–gold atomic junctions

    KAUST Repository

    Wu, Kunlin

    2012-12-13

    The origin and the distance dependence of the transition voltage of gold-vacuum-gold junctions are investigated by employing first-principles quantum transport simulations. Our calculations show that atomic protrusions always exist on the electrode surface of gold-vacuum-gold junctions fabricated using the mechanically controllable break junction (MCBJ) method. The transition voltage of these gold-vacuum-gold junctions with atomically sharp electrodes is determined by the local density of states (LDOS) of the apex gold atom on the electrode surface rather than by the vacuum barrier shape. More specifically, the absolute value of the transition voltage roughly equals the rising edge of the LDOS peak contributed by the 6p atomic orbitals of the gold atoms protruding from the electrode surface, whose local Fermi level is shifted downwards when a bias voltage is applied. Since the LDOS of the apex gold atom depends strongly on the exact shape of the electrode, the transition voltage is sensitive to the variation of the atomic configuration of the junction. For asymmetric junctions, the transition voltage may also change significantly depending on the bias polarity. Considering that the occurrence of the transition voltage requires the electrode distance to be larger than a critical value, the interaction between the two electrodes is actually rather weak. Consequently, the LDOS of the apex gold atom is mainly determined by its local atomic configuration and the transition voltage only depends weakly on the electrode distance as observed in the MCBJ experiments. © 2013 IOP Publishing Ltd.

  11. Origin of the transition voltage in gold–vacuum–gold atomic junctions

    International Nuclear Information System (INIS)

    Wu Kunlin; Bai Meilin; Hou Shimin; Sanvito, Stefano

    2013-01-01

    The origin and the distance dependence of the transition voltage of gold–vacuum–gold junctions are investigated by employing first-principles quantum transport simulations. Our calculations show that atomic protrusions always exist on the electrode surface of gold–vacuum–gold junctions fabricated using the mechanically controllable break junction (MCBJ) method. The transition voltage of these gold–vacuum–gold junctions with atomically sharp electrodes is determined by the local density of states (LDOS) of the apex gold atom on the electrode surface rather than by the vacuum barrier shape. More specifically, the absolute value of the transition voltage roughly equals the rising edge of the LDOS peak contributed by the 6p atomic orbitals of the gold atoms protruding from the electrode surface, whose local Fermi level is shifted downwards when a bias voltage is applied. Since the LDOS of the apex gold atom depends strongly on the exact shape of the electrode, the transition voltage is sensitive to the variation of the atomic configuration of the junction. For asymmetric junctions, the transition voltage may also change significantly depending on the bias polarity. Considering that the occurrence of the transition voltage requires the electrode distance to be larger than a critical value, the interaction between the two electrodes is actually rather weak. Consequently, the LDOS of the apex gold atom is mainly determined by its local atomic configuration and the transition voltage only depends weakly on the electrode distance as observed in the MCBJ experiments. (paper)

  12. Theory of collisional excitation transition between Rydberg states of atoms. Non-inertial mechanism

    International Nuclear Information System (INIS)

    Kaulakys, B.P.

    1982-01-01

    The transitions between highly states of an atom due to the collision of its core with another atom are considered. The cross sections of the change of highly excited electron angular momentum, in the case of the transitions when the main quantum number is constant, are expressed in terms of transport cross sections of the perturbing atom scattering on the ion of Rydberg atom. It is shown that the cross sections of the momentum mixing at thermal rapidities are lower than the cross sections of the atom-ion elastic scattering

  13. Inelastic transitions of atoms and molecules induced by van der Waals interaction with a surface

    International Nuclear Information System (INIS)

    Baudon, J.; Hamamda, M.; Boustimi, M.; Bocvarski, V.; Taillandier-Loize, T.; Dutier, G.; Perales, F.; Ducloy, M.

    2012-01-01

    Inelastic processes occuring in thermal-velocity metastable atoms and molecules passing at a mean distance (1–100 nm) are investigated. These processes are caused by the quadrupolar part of the van der Waals interaction: fine-structure transitions in atoms (Ar ∗ , Kr ∗ ), rovibrational transitions in N 2 ∗ ( 3 Σ u + ), transitions among magnetic sub-levels in the presence of a magnetic field.

  14. Transition from 2-D radiotherapy to 3-D conformal and intensity modulated radiotherapy

    International Nuclear Information System (INIS)

    2008-05-01

    Cancer is one of the leading causes of death globally and radiotherapy is currently an essential component in the management of cancer patients, either alone or in combination with surgery or chemotherapy, both for cure or palliation. It is now recognized that safe and effective radiotherapy service needs not only substantial capital investment in radiotherapy equipment and specially designed facilities but also continuous investment in maintenance and upgrading of the equipment to comply with the technical progress, but also in training the staff. The recent IAEA-TECDOC publication 'Setting up a Radiotherapy Programme: Clinical, Medical Physics, Radiation Protection and Safety Aspects' provides general guidelines for designing and implementing radiotherapy services in Member States. Advances in computer technology have enabled the possibility of transitioning from basic 2- dimensional treatment planning and delivery (2-D radiotherapy) to a more sophisticated approach with 3-dimensional conformal radiotherapy (3-D CRT). Whereas 2-D radiotherapy can be applied with simple equipment, infrastructure and training, transfer to 3-D conformal treatments requires more resources in technology, equipment, staff and training. A novel radiation treatment approach using Intensity Modulated Radiation Therapy (IMRT) that optimizes the delivery of radiation to irregularly shaped tumour volumes demands even more sophisticated equipment and seamless teamwork, and consequentially more resources, advanced training and more time for treatment planning and verification of dose delivery than 3-D CRT. Whereas 3-D CRT can be considered as a standard, IMRT is still evolving. Due to the increased interest of Member States to the modern application of radiotherapy the IAEA has received a number of requests for guidance coming from radiotherapy departments that wish to upgrade their facilities to 3-D CRT and IMRT through Technical Cooperation programme. These requests are expected to increase

  15. X-ray transition yields of low-Z kaonic atoms produced in Kapton

    Energy Technology Data Exchange (ETDEWEB)

    Bazzi, M. [INFN, Laboratori Nazionali di Frascati, C.P. 13, Via E. Fermi 40, I-00044 Frascati (Roma) (Italy); Beer, G. [Department of Physics and Astronomy, University of Victoria, P.O. Box 1700 STN CNC, Victoria, BC V8W 2Y2 (Canada); Berucci, C. [INFN, Laboratori Nazionali di Frascati, C.P. 13, Via E. Fermi 40, I-00044 Frascati (Roma) (Italy); Stefan-Meyer-Institut für subatomare Physik, Boltzmanngasse 3, 1090 Wien (Austria); Bombelli, L. [Politecnico di Milano, Dipartimento di Elettronica e Informazione, Piazza L. da Vinci 32, I-20133 Milano (Italy); Bragadireanu, A.M. [INFN, Laboratori Nazionali di Frascati, C.P. 13, Via E. Fermi 40, I-00044 Frascati (Roma) (Italy); IFIN-HH, Institutul National pentru Fizica si Inginerie Nucleara Horia Hulubei, Reactorului 30, Magurele (Romania); Cargnelli, M. [Stefan-Meyer-Institut für subatomare Physik, Boltzmanngasse 3, 1090 Wien (Austria); Curceanu, C.; D' Uffizi, A. [INFN, Laboratori Nazionali di Frascati, C.P. 13, Via E. Fermi 40, I-00044 Frascati (Roma) (Italy); Fiorini, C. [Politecnico di Milano, Dipartimento di Elettronica e Informazione, Piazza L. da Vinci 32, I-20133 Milano (Italy); Ghio, F. [INFN Sezione di Roma I and Instituto Superiore di Sanita, I-00161 Roma (Italy); Guaraldo, C. [INFN, Laboratori Nazionali di Frascati, C.P. 13, Via E. Fermi 40, I-00044 Frascati (Roma) (Italy); Hayano, R.S. [University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo (Japan); Iliescu, M. [INFN, Laboratori Nazionali di Frascati, C.P. 13, Via E. Fermi 40, I-00044 Frascati (Roma) (Italy); Ishiwatari, T., E-mail: tomoichi.ishiwatari@assoc.oeaw.ac.at [Stefan-Meyer-Institut für subatomare Physik, Boltzmanngasse 3, 1090 Wien (Austria); Iwasaki, M. [RIKEN, Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); and others

    2013-10-23

    The X-ray transition yields of kaonic atoms produced in Kapton polyimide (C{sub 22}H{sub 10}N{sub 2}O{sub 5}) were measured for the first time in the SIDDHARTA experiment. X-ray yields of the kaonic atoms with low atomic numbers (Z=6,7, and 8) and transitions with high principal quantum numbers (n=5–8) were determined. The relative yields of the successive transitions in the same atoms and the yield ratios of carbon-to-nitrogen (C:N) and carbon-to-oxygen (C:O) for the same transitions were also determined. These X-ray yields provide important information for understanding the capture ratios and cascade mechanisms of kaonic atoms produced in a compound material, such as Kapton.

  16. Optimization of the performance of rf transitions for the TUNL atomic beam polarized ion source

    International Nuclear Information System (INIS)

    Crosson, E.R.; Clegg, T.B.; Karwowski, H.J.; Lemieux, S.K.

    1991-01-01

    We have utilized the spin-dependence of the cross section for electron impact ionization of H 0 and D 0 atoms in the ionizer of our atomic beam polarized ion source to study the performance of the rf transitions which provide the nuclear polarization of the atomic beam. Switching the rf transitions on and off modulates the output polarized current. This modulation is observed using a lock-in amplifier and provides a fast and reliable method for optimization of transition unit parameters. (orig.)

  17. The effect of conformational transition of gelatin-polysaccharide polyelectrolyte complex on its functional properties

    Directory of Open Access Journals (Sweden)

    Tomáš Valenta

    2017-01-01

    Full Text Available The blends of gelatin and shear-thinning hydrocolloids (guar gum, kappa-carrageenan and xanthan gum were examined to determine the effect of the conformational change on the functional properties of the solutions. The polyelectrolyte complexes of 0.5% gelatin/0.5% polysaccharide in 70 mM KCl or 70 mM NaCl were investigated by the laboratory rheometer and conductivity meter in the temperature range 25 - 45 °C. The rheological data were fitted by the power-law and Herschel-Bulkley model to obtain the flow parameters. The functional properties of the samples were substantially affected by the conformational change of the polysaccharide, as well as by the type of the hydrocolloid and salt solution. There was an evident change of viscosity and conductivity of the solutions upon heating, corresponding to the helix-coil transition of the polysaccharide at temperature about 35 °C. The type of the salt solvent had an effect on the gelation properties of the samples. Gelatin/kappa-carrageenan blend in NaCl provided a gel of high consistency at ambient temperature (20 - 25 °C, whereas the blend in KCl did not gel in the studied temperature range. The potential stability of the blends was determined by zeta-potential analysis. The low values of ζ-potential indicate that the gelatin/polysaccharide blends are electrically unstable systems which tend to coagulate. The mixtures of gelatin/polysaccharide electrostatic complexes may have a great potential in many food applications.

  18. Behaviour of tunnelling transition rate of argon atom exposed to ...

    Indian Academy of Sciences (India)

    in the strong laser field ionization of atoms and molecules. ... state in the discrete spectrum and the final state in the continuum of a quantum system in ... In this paper we used the ADK model to describe the tunnel ionization of atoms and.

  19. Origin of the transition voltage in gold–vacuum–gold atomic junctions

    KAUST Repository

    Wu, Kunlin; Bai, Meilin; Sanvito, Stefano; Hou, Shimin

    2012-01-01

    The origin and the distance dependence of the transition voltage of gold-vacuum-gold junctions are investigated by employing first-principles quantum transport simulations. Our calculations show that atomic protrusions always exist on the electrode

  20. Forbidden atomic transitions driven by an intensity-modulated laser trap.

    Science.gov (United States)

    Moore, Kaitlin R; Anderson, Sarah E; Raithel, Georg

    2015-01-20

    Spectroscopy is an essential tool in understanding and manipulating quantum systems, such as atoms and molecules. The model describing spectroscopy includes the multipole-field interaction, which leads to established spectroscopic selection rules, and an interaction that is quadratic in the field, which is not often employed. However, spectroscopy using the quadratic (ponderomotive) interaction promises two significant advantages over spectroscopy using the multipole-field interaction: flexible transition rules and vastly improved spatial addressability of the quantum system. Here we demonstrate ponderomotive spectroscopy by using optical-lattice-trapped Rydberg atoms, pulsating the lattice light and driving a microwave atomic transition that would otherwise be forbidden by established spectroscopic selection rules. This ability to measure frequencies of previously inaccessible transitions makes possible improved determinations of atomic characteristics and constants underlying physics. The spatial resolution of ponderomotive spectroscopy is orders of magnitude better than the transition frequency would suggest, promising single-site addressability in dense particle arrays for quantum computing applications.

  1. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Science.gov (United States)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-04-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  2. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    International Nuclear Information System (INIS)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-01-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  3. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Energy Technology Data Exchange (ETDEWEB)

    Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao [Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); The HKUST Shenzhen Research Institute, Shenzhen (China)

    2016-04-21

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  4. Metal-Insulator Transition Revisited for Cold Atoms in Non-Abelian Gauge Potentials

    International Nuclear Information System (INIS)

    Satija, Indubala I.; Dakin, Daniel C.; Clark, Charles W.

    2006-01-01

    We discuss the possibility of realizing metal-insulator transitions with ultracold atoms in two-dimensional optical lattices in the presence of artificial gauge potentials. For Abelian gauges, such transitions occur when the magnetic flux penetrating the lattice plaquette is an irrational multiple of the magnetic flux quantum. Here we present the first study of these transitions for non-Abelian U(2) gauge fields. In contrast to the Abelian case, the spectrum and localization transition in the non-Abelian case is strongly influenced by atomic momenta. In addition to determining the localization boundary, the momentum fragments the spectrum. Other key characteristics of the non-Abelian case include the absence of localization for certain states and satellite fringes around the Bragg peaks in the momentum distribution and an interesting possibility that the transition can be tuned by the atomic momenta

  5. Los Alamos Opacities: Transition from LEDCOP to ATOMIC

    International Nuclear Information System (INIS)

    Magee, N.H.; Abdallah, J.; Colgan, J.; Hakel, P.; Kilcrease, D.P.; Mazevet, S.; Sherrill, M.; Fontes, C.J.; Zhang, H.L.

    2004-01-01

    This paper discusses the development of the ATOMIC code, a new low to mid Z opacity code, which will replace the current Los Alamos low Z opacity code LEDCOP. The ATOMIC code is based on the FINE code, long used by the Los Alamos group for spectral comparisons in local thermodynamic equilibrium (LTE) and for non-LTE calculations, utilizing the extensive databases from the atomic physics suite of codes based on the work of R. D. Cowan. Many of the plasma physics packages in LEDCOP, such as line broadening and free-free absorption, are being transferred to the new ATOMIC code. A new equation of state (EOS) model is being developed to allow higher density calculations than were possible with either the FINE or LEDCOP codes. Extensive modernization for both ATOMIC and the atomic physics code suites, including conversion to Fortran 90 and parallelization, are under way to speed up the calculations and to allow the use of expanded databases for both the LTE opacity tables and the non-LTE calculations. Future plans will be outlined, including considerations for new generation opacity tables

  6. Conformational transitions and interactions underlying the function of membrane embedded receptor protein kinases.

    Science.gov (United States)

    Bocharov, Eduard V; Sharonov, Georgy V; Bocharova, Olga V; Pavlov, Konstantin V

    2017-09-01

    Among membrane receptors, the single-span receptor protein kinases occupy a broad but specific functional niche determined by distinctive features of the underlying transmembrane signaling mechanisms that are briefly overviewed on the basis of some of the most representative examples, followed by a more detailed discussion of several hierarchical levels of organization and interactions involved. All these levels, including single-molecule interactions (e.g., dimerization, liganding, chemical modifications), local processes (e.g. lipid membrane perturbations, cytoskeletal interactions), and larger scale phenomena (e.g., effects of membrane surface shape or electrochemical potential gradients) appear to be closely integrated to achieve the observed diversity of the receptor functioning. Different species of receptor protein kinases meet their specific functional demands through different structural features defining their responses to stimulation, but certain common patterns exist. Signaling by receptor protein kinases is typically associated with the receptor dimerization and clustering, ligand-induced rearrangements of receptor domains through allosteric conformational transitions with involvement of lipids, release of the sequestered lipids, restriction of receptor diffusion, cytoskeleton and membrane shape remodeling. Understanding of complexity and continuity of the signaling processes can help identifying currently neglected opportunities for influencing the receptor signaling with potential therapeutic implications. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Symmetry-forbidden intervalley scattering by atomic defects in monolayer transition-metal dichalcogenides

    DEFF Research Database (Denmark)

    Kaasbjerg, Kristen; Martiny, Johannes H. J.; Low, Tony

    2017-01-01

    protectionmechanism against intervalley scattering in monolayer TMDs. The predicteddefectdependent selection rules for intervalley scattering can be verified viaFourier transform scanning tunneling spectroscopy (FT-STS), and provide aunique identification of, e.g., atomic vacancy defects (M vs X). Our findingsare......Intervalley scattering by atomic defects in monolayer transition metaldichalcogenides (TDMs; MX2) presents a serious obstacle for applicationsexploiting their unique valley-contrasting properties. Here, we show that thesymmetry of the atomic defects can give rise to an unconventional...

  8. Analysis of an ATP-induced conformational transition of ABC transporter MsbA using a coarse-grained model.

    Science.gov (United States)

    Arai, Naoki; Furuta, Tadaomi; Sakurai, Minoru

    2017-01-01

    Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.

  9. Reversible conformational transition gives rise to 'zig-zag' temperature dependence of the rate constant of irreversible thermoinactivation of enzymes.

    Science.gov (United States)

    Levitsky VYu; Melik-Nubarov, N S; Siksnis, V A; Grinberg VYa; Burova, T V; Levashov, A V; Mozhaev, V V

    1994-01-15

    We have obtained unusual 'zig-zag' temperature dependencies of the rate constant of irreversible thermoinactivation (k(in)) of enzymes (alpha-chymotrypsin, covalently modified alpha-chymotrypsin, and ribonuclease) in a plot of log k(in) versus reciprocal temperature (Arrhenius plot). These dependencies are characterized by the presence of both ascending and descending linear portions which have positive and negative values of the effective activation energy (Ea), respectively. A kinetic scheme has been suggested that fits best for a description of these zig-zag dependencies. A key element of this scheme is the temperature-dependent reversible conformational transition of enzyme from the 'low-temperature' native state to a 'high-temperature' denatured form; the latter form is significantly more stable against irreversible thermoinactivation than the native enzyme. A possible explanation for a difference in thermal stabilities is that low-temperature and high-temperature forms are inactivated according to different mechanisms. Existence of the suggested conformational transition was proved by the methods of fluorescence spectroscopy and differential scanning calorimetry. The values of delta H and delta S for this transition, determined from calorimetric experiments, are highly positive; this fact underlies a conclusion that this heat-induced transition is caused by an unfolding of the protein molecule. Surprisingly, in the unfolded high-temperature conformation, alpha-chymotrypsin has a pronounced proteolytic activity, although this activity is much smaller than that of the native enzyme.

  10. Observation of electric quadrupole transitions to Rydberg nd states of ultracold rubidium atoms

    NARCIS (Netherlands)

    Tong, D.; Farooqi, S.M.; Kempen, van E.G.M.; Pavlovic, Z.; Stanojevic, J.; Coté, R.; Eyler, E.E.; Gould, P.L.

    2009-01-01

    We report the observation of dipole-forbidden, but quadrupole-allowed, one-photon transitions to high-Rydberg states in Rb. Using pulsed uv excitation of ultracold atoms in a magneto-optical trap, we excite 5s¿nd transitions over a range of principal quantum numbers n=27–59. Compared to

  11. Atomic Layer Deposition Alumina-Passivated Silicon Nanowires: Probing the Transition from Electrochemical Double-Layer Capacitor to Electrolytic Capacitor.

    Science.gov (United States)

    Gaboriau, Dorian; Boniface, Maxime; Valero, Anthony; Aldakov, Dmitry; Brousse, Thierry; Gentile, Pascal; Sadki, Said

    2017-04-19

    Silicon nanowires were coated by a 1-5 nm thin alumina layer by atomic layer deposition (ALD) in order to replace poorly reproducible and unstable native silicon oxide by a highly conformal passivating alumina layer. The surface coating enabled probing the behavior of symmetric devices using such electrodes in the EMI-TFSI electrolyte, allowing us to attain a large cell voltage up to 6 V in ionic liquid, together with very high cyclability with less than 4% capacitance fade after 10 6 charge/discharge cycles. These results yielded fruitful insights into the transition between an electrochemical double-layer capacitor behavior and an electrolytic capacitor behavior. Ultimately, thin ALD dielectric coatings can be used to obtain hybrid devices exhibiting large cell voltage and excellent cycle life of dielectric capacitors, while retaining energy and power densities close to the ones displayed by supercapacitors.

  12. Off-resonant transitions in the collective dynamics of multi-level atomic ensembles

    DEFF Research Database (Denmark)

    Miroshnychenko, Yevhen; Mølmer, Klaus

    2013-01-01

    We study the contributions of off-resonant transitions to the dynamics of a system of N multi-level atoms sharing one excitation and interacting with the quantized vector electromagnetic field. The rotating wave approximation significantly simplifies the derivation of the equations of motion...... describing the collective atomic dynamics, but it leads to an incorrect expression for the dispersive part of the atom–atom interaction terms. For the case of two-level atoms and a scalar electromagnetic field, it turns out that the atom–atom interaction can be recovered correctly if integrals over...... the photon mode frequencies are extended to incorporate negative values. We explicitly derive the atom–atom interaction for multi-level atoms, coupled to the full vector electromagnetic field, and we recover also in this general case the validity of the results obtained by the extension to negative...

  13. Formation and structural phase transition in Co atomic chains on a Cu(775) surface

    International Nuclear Information System (INIS)

    Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.; Klavsyuk, A. L.

    2017-01-01

    The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomic spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.

  14. Formation and structural phase transition in Co atomic chains on a Cu(775) surface

    Energy Technology Data Exchange (ETDEWEB)

    Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.; Klavsyuk, A. L., E-mail: klavsyuk@physics.msu.ru [Moscow State University (Russian Federation)

    2017-01-15

    The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomic spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.

  15. Nonlinear narrow Doppler-free resonances for optical transitions and annihilation radiation of a positronium atom

    International Nuclear Information System (INIS)

    Letokhov, V.S.; Minogin, V.G.

    1976-01-01

    The possibilities of obtaining narrow resonances without the Doppler broadening for transition between the fine structure levels of the ground and first excited states of a positronium atom are considered. An analysis is carried out of the conditions required for observation of the narrow resonances of saturation of single quantum absorption in the 1S-2P transitions and observation of narrow two-photon absorption resonances in the 1S-2S transitions. It is shown that narrow 2γ annihilation radiation lines of a positronium atom may be obtained with a width much smaller than the Doppler one

  16. Lineshape-asymmetry elimination in weak atomic transitions driven by an intense standing wave field

    Science.gov (United States)

    Antypas, Dionysios; Fabricant, Anne; Budker, Dmitry

    2018-05-01

    Owing to the ac-Stark effect, the lineshape of a weak optical transition in an atomic beam can become significantly distorted, when driven by an intense standing wave field. We use an Yb atomic beam to study the lineshape of the 6s2 1S0 -> 5d6s 3D1 transition, which is excited with light circulating in a Fabry-Perot resonator. We demonstrate two methods to avoid the distortion of the transition profile. Of these, one relies on the operation of the resonator in multiple longitudinal modes, and the other in multiple transverse modes.

  17. A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

    Science.gov (United States)

    Xu, Guoyan G; Zhang, Yan; Mercedes-Camacho, Ana Y; Etzkorn, Felicia A

    2011-11-08

    The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.

  18. Reduced-Amide Inhibitor of Pin1 Binds in a Conformation Resembling a Twisted-Amide Transition State†

    Science.gov (United States)

    Xu, Guoyan G.; Zhang, Yan; Mercedes-Camacho, Ana Y.; Etzkorn, Felicia A.

    2011-01-01

    The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R–pSer–Ψ[CH2N]–Pro–2-(indol-3-yl)-ethylamine, 1 (R = fluorenylmethoxycarbonyl, Fmoc), and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC50 value of 6.3 μM, which is 4.5-fold better inhibition for Pin1 than our comparable ground state analogue, a cis-amide alkene isostere containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination, and resulted in an IC50 value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser, and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1. PMID:21980916

  19. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn; Zhu, Weiliang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Shi, Jiye, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [UCB Pharma, 216 Bath Road, Slough SL1 4EN (United Kingdom)

    2015-03-28

    The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.

  20. Extremely short pulses via stark modulation of the atomic transition frequencies.

    Science.gov (United States)

    Radeonychev, Y V; Polovinkin, V A; Kocharovskaya, Olga

    2010-10-29

    We propose a universal method to produce extremely short pulses of electromagnetic radiation in various spectral ranges. The essence of the method is a resonant interaction of radiation with atoms under the conditions of adiabatic periodic modulation of atomic transition frequencies by a far-off-resonant control laser field via dynamic Stark shift of the atomic levels and proper adjustment of the control field intensity and frequency, as well as the optical depth of the medium. The potential of the method is illustrated by an example in a hydrogenlike atomic system.

  1. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

    Directory of Open Access Journals (Sweden)

    Qing Wang

    2016-05-01

    Full Text Available Free energy calculations of the potential of mean force (PMF based on the combination of targeted molecular dynamics (TMD simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35. The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.

  2. Nonequilibrium Quantum Phase Transition in a Hybrid Atom-Optomechanical System

    Science.gov (United States)

    Mann, Niklas; Bakhtiari, M. Reza; Pelster, Axel; Thorwart, Michael

    2018-02-01

    We consider a hybrid quantum many-body system formed by a vibrational mode of a nanomembrane, which interacts optomechanically with light in a cavity, and an ultracold atom gas in the optical lattice of the out-coupled light. The adiabatic elimination of the light field yields an effective Hamiltonian which reveals a competition between the force localizing the atoms and the membrane displacement. At a critical atom-membrane interaction, we find a nonequilibrium quantum phase transition from a localized symmetric state of the atom cloud to a shifted symmetry-broken state, the energy of the lowest collective excitation vanishes, and a strong atom-membrane entanglement arises. The effect occurs when the atoms and the membrane are nonresonantly coupled.

  3. Transfer matrix treatment of atomic chemisorption on transition metal surface

    International Nuclear Information System (INIS)

    Mariz, A.M.; Koiller, B.

    1980-05-01

    The atomic adsorption of hydrogen on paramagnetic nickel 100 surface is studied, using the Green's function formalism and the transfer matrix technique, which allows the treatment of the geometry of the system in a simple manner. Electronic correlation at the adatom orbital in a self consistent Hartree-Fock approach is incorporated. The adsorption energy, local density of states and charge transfer between the solid and the adatom are calculated for different crystal structures (sc and fcc) and adatom positions at the surface. The results are discussed in comparison with other theories and with available experimental data, with satisfactory agreement. (Author) [pt

  4. The importance of atomic and molecular correlation on the bonding in transition metal compounds

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Walch, Stephen P.

    1986-01-01

    The determination of accurate spectroscopic parameters for molecular systems containing transition metal atoms is shown to require extensive data sets and a high level correlation treatment, and techniques and their limitations are considered. Extensive results reported on the transition metal atoms, hydrides, oxides, and dimers makes possible the design of a calculation to correctly describe the mixing of different atomic asymptotes, and to give a correct balance between molecular bonding and exchange interactions. Examples considered include the dipole moment of the 2Delta state of NiH, which can help determine the mixture of 3d(8)4s(2) and 3d(9)4s(1) in the NiH wavefunction, and the bonding in CrO, where an equivalent description of the relative energies associated with the Cr 3d-3d atomic exchange and the Cr-O bond is important.

  5. Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase

    International Nuclear Information System (INIS)

    Okai, Masahiko; Yamamura, Akihiro; Hayakawa, Kou; Tsutsui, Shiho; Miyazono, Ken-ichi; Lee, Woo-Cheol; Nagata, Koji; Inoue, Yumiko; Tanokura, Masaru

    2017-01-01

    Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75–80 °C and in the pH range of 6.8–7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 °C. We also determined the crystal structure of TthCP at 2.6 Å resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a C α RMSD value of 2.2 Å; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with C α RMSD values of 0.84 and 0.53 Å, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction. - Highlights: • The enzyme activity of TthCP was inhibited moderately by Tris molecule. • We solved the crystal structure of TthCP at 2.6 Å resolution. • The crystal structure of TthCP revealed both the open and closed conformations.

  6. Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM).

    Science.gov (United States)

    Wu, Heng-Liang; Tong, Yujin; Peng, Qiling; Li, Na; Ye, Shen

    2016-01-21

    The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.

  7. Calculating Relativistic Transition Matrix Elements for Hydrogenic Atoms Using Monte Carlo Methods

    Science.gov (United States)

    Alexander, Steven; Coldwell, R. L.

    2015-03-01

    The nonrelativistic transition matrix elements for hydrogen atoms can be computed exactly and these expressions are given in a number of classic textbooks. The relativistic counterparts of these equations can also be computed exactly but these expressions have been described in only a few places in the literature. In part, this is because the relativistic equations lack the elegant simplicity of the nonrelativistic equations. In this poster I will describe how variational Monte Carlo methods can be used to calculate the energy and properties of relativistic hydrogen atoms and how the wavefunctions for these systems can be used to calculate transition matrix elements.

  8. Experimental study of linear magnetic dichroism in photoionization satellite transitions of atomic rubidium

    International Nuclear Information System (INIS)

    Jaenkaelae, K.; Alagia, M.; Feyer, V.; Richter, R.; Prince, K. C.

    2011-01-01

    Laser orientation in the initial state has been used to study the properties of satellite transitions in inner-shell photoionization of rubidium atoms. The linear magnetic dichroism in the angular distribution (LMDAD) has been utilized to probe the continuum waves of orbital angular momentum conserving monopole, and angular momentum changing conjugate satellites, accompanying the 4p ionization of atomic Rb. We show experimentally that LMDAD of both types of satellite transitions is nonzero and that LMDAD of monopole satellites, measured as a function of photon energy, mimics the LMDAD of direct photoionization, whereas the LMDAD of conjugate transitions deviates drastically from that trend. The results indicate that conjugate transitions cannot be described theoretically without explicit inclusion of electron-electron interaction. The present data can thus be used as a very precise test of current models for photoionization.

  9. Matrix elements and transition probabilities of interaction of electromagnetic field with a hydrogen-like atom

    International Nuclear Information System (INIS)

    Rajput, B.S.

    1977-01-01

    Using the reduced expansions of second quantized electromagnetic vector potential operator in terms of irreducible representations of Pioncare group in the interaction Hamiltonian, the exact matrix elements of interaction of electromagnetic field with a hydrogenic atom have been derived and the contributions of transitions for different combinations of angular momentum quantum numbers to the transition probabilities of various lines in Lyman-, Balmer-, and Paschen-series have been computed. (author)

  10. Recent progress in the studies of atomic spectra and transition probabilities by beam-foil spectroscopy

    International Nuclear Information System (INIS)

    Martinson, I.

    1982-01-01

    A review is given of recent studies of atomic structure (in particular atomic spectra, energy levels and transition probabilities) using fast beams from ion accelerators. Thanks to improved spectral resolution detailed and quite accurate studies of energy levels are now possible, a number of such results will be discussed. The non-autoionizing, multiply excited levels in atoms and ions (including negative ions) are being vigorously investigated at present, some new results will be reported. The accuracy in lifetime determinations continues to improve, and several new ways for reduction of cascading effects have been developed. Some selected examples of recent progress in lifetime measurements are also included. (orig.)

  11. Emission and electron transitions in an atom interacting with an ultrashort electromagnetic pulse

    International Nuclear Information System (INIS)

    Matveev, V.I.

    2003-01-01

    Electron transitions and emission of an atom interacting with a spatially inhomogeneous ultrashort electromagnetic pulse are considered. The excitation and ionization probabilities are obtained as well as the spectra and cross sections of the reemission of such a pulse by atoms. By way of an example, one- and two-electron inelastic processes accompanying the interaction of ultrashort pulses with hydrogen- and helium-like atoms are considered. The developed technique makes it possible to take into account exactly the spatial nonuniformity of the ultrashort pulse field and photon momenta in the course of reemission

  12. NiCo_2O_4@TiN Core-shell Electrodes through Conformal Atomic Layer Deposition for All-solid-state Supercapacitors

    International Nuclear Information System (INIS)

    Wang, Ruiqi; Xia, Chuan; Wei, Nini; Alshareef, Husam N.

    2016-01-01

    Highlights: • NiCo_2O_4 nanostructures are prepared via a simple hydrothermal method. • Outer shell of TiN is then grown through conformal atomic layer deposition. • Electrodes exhibit significantly enhanced rate capability with TiN coating. • Solid-state polymer electrolyte is employed to improve cycling stability. • Full devices show a stack power density of 58.205 mW cm"−"3 at 0.061 mWh cm"−"3. - Abstract: Ternary transition metal oxides such as NiCo_2O_4 show great potential as supercapacitor electrode materials. However, the unsatisfactory rate performance of NiCo_2O_4 may prove to be a major hurdle to its commercial usage. Herein, we report the development of NiCo_2O_4@TiN core–shell nanostructures for all-solid-state supercapacitors with significantly enhanced rate capability. We demonstrate that a thin layer of TiN conformally grown by atomic layer deposition (ALD) on NiCo_2O_4 nanofiber arrays plays a key role in improving their electrical conductivity, mechanical stability, and rate performance. Fabricated using the hybrid NiCo_2O_4@TiN electrodes, the symmetric all-solid-state supercapacitor exhibited an impressive stack power density of 58.205 mW cm"−"3 at a stack energy density of 0.061 mWh cm"−"3. To the best of our knowledge, these values are the highest of any NiCo_2O_4-based all-solid-state supercapacitor reported. Additionally, the resulting NiCo_2O_4@TiN all-solid-state device displayed outstanding cycling stability by retaining 70% of its original capacitance after 20,000 cycles at a high current density of 10 mA cm"−"2. These results illustrate the promise of ALD-assisted hybrid NiCo_2O_4@TiN electrodes within sustainable and integrated energy storage applications.

  13. Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.

    Science.gov (United States)

    Li, Qufei; Wanderling, Sherry; Sompornpisut, Pornthep; Perozo, Eduardo

    2014-02-01

    Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting ('down') and activated ('up') conformations of the KvAP VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states, using site-directed spin-labeling and EPR spectroscopic methods. Solvent accessibility and interhelical distance determinations suggest that KvAP gates through S4 movements involving an ∼3-Å upward tilt and simultaneous ∼2-Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a new model of gating that combines structural rearrangements and electric-field remodeling.

  14. Ab initio theory of noble gas atoms in bcc transition metals.

    Science.gov (United States)

    Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; Gan, Jian

    2018-06-18

    Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe). Our charge density analysis indicates that the strong polarization of nearest-neighbor metal atoms by noble gas interstitials is the electronic origin of their high formation energies. Such polarization becomes more significant with an increasing gas atom size and interstitial charge density in the host bcc metal, which explains the similar trend followed by the unrelaxed formation energies of noble gas interstitials. Upon allowing for local relaxation, nearby metal atoms move farther away from gas interstitials in order to decrease polarization, albeit at the expense of increasing the elastic strain energy. Such atomic relaxation is found to play an important role in governing both the energetics and site preference of noble gas atoms in bcc metals. Our most notable finding is that the fully relaxed formation energies of noble gas interstitials are strongly correlated with the elastic shear modulus of the bcc metal, and the physical origin of this unexpected correlation has been elucidated by our theoretical analysis based on the effective-medium theory. The kinetic behavior of noble gas atoms and their interaction with pre-existing vacancies in bcc transition metals have also been discussed in this work.

  15. First-principles studies on 3d transition metal atom adsorbed twin graphene

    Science.gov (United States)

    Li, Lele; Zhang, Hong; Cheng, Xinlu; Miyamoto, Yoshiyuki

    2018-05-01

    Twin graphene is a new two-dimensional semiconducting carbon allotrope which is proposed recently. The structural, magnetic and electronic properties are investigated for 3d transition metal (TM) atom adsorbed twin graphene by means of GGA+U calculations. The results show most of single 3d transition metal atom except Zn can make twin graphene magnetization. The adsorption of single TM atom can also make the twin graphene systems turn to half metal (V adsorption), half-semiconductor (Fe adsorption) or metal (Sc, Cr, Mn, Co and Cu adsorption). The semiconducting nature still exists for Ti, Ni and Zn adsorption. All the 3d TM adatoms belong to n-type doping for transferring charge to the neighboring C atoms and have strong covalent bond with these C atoms. The influence of Hubbard U value on half-metallic V adsorbed system is also considered. As the U increases, the system can gradually transform from metal to half metal and metal. The effect of the coverage is investigated for two TM atoms (Sc-Fe) adsorption, too. We can know TM atoms adsorbed twin graphene have potentials to be spintronic device and nanomagnets from the results.

  16. Reversible switching of fluorophore property based on intrinsic conformational transition of adenylate kinase during its catalytic cycle.

    Science.gov (United States)

    Fujii, Akira; Hirota, Shun; Matsuo, Takashi

    2013-07-17

    Adenylate kinase shows a conformational transition (OPEN and CLOSED forms) during substrate binding and product release to mediate the phosphoryl transfer between ADP and ATP/AMP. The protein motional characteristics will be useful to construct switching systems of fluorophore properties caused by the catalytic cycle of the enzyme. This paper demonstrates in situ reversible switching of a fluorophore property driven by the conformational transition of the enzyme. The pyrene-conjugated mutant adenylate kinase is able to switch the monomer/excimer emission property of pyrene on addition of ADP or P(1)P(5)-di(adenosine-5')pentaphosphate (Ap5A, a transition state analog). The observation under the dilute condition (~0.1 μM) indicates that the emission spectral change was caused by the motion of a protein molecule and not led by protein-protein interactions through π-π stacking of pyrene rings. The switching can be reversibly conducted by using hexokinase-coupling reaction. The fashion of the changes in emission intensities at various ligand concentrations is different between ADP, Mg(2+)-bound ADP, and Mg(2+)-bound Ap5A. The emission property switching is repeatable by a sequential addition of a substrate in a one-pot process. It is proposed that the property of a synthetic molecule on the enzyme surface is switchable in response to the catalytic cycle of adenylate kinase.

  17. Circular dichroism of magnetically induced transitions for D2 lines of alkali atoms

    Science.gov (United States)

    Tonoyan, A.; Sargsyan, A.; Klinger, E.; Hakhumyan, G.; Leroy, C.; Auzinsh, M.; Papoyan, A.; Sarkisyan, D.

    2018-03-01

    In this letter we study magnetic circular dichroism in alkali atoms exhibiting asymmetric behaviour of magnetically induced transitions. The magnetic field \\textbf{B}\\parallel\\textbf{k} induces transitions between Δ F = +/-2 hyperfine levels of alkali atoms and in the range of ∼0.1{\\text{--}}3 \\text{kG} magnetic field, the intensities of these transitions experience significant enhancement. We have inferred a general rule applicable for the D 2 lines of all alkali atoms, that is the transition intensity enhancement is around four times larger for the case of σ+ than for σ- excitation for Δ F = +2 , whereas it is several hundreds of thousand times larger in the case of σ- than that for σ+ polarization for Δ F = -2 . This asymmetric behaviour results in circular dichroism. For experimental verification we employed half-wavelength-thick atomic vapor nanocells using a derivative of the selective reflection technique, which provides a sub-Doppler spectroscopic linewidth (∼50 \\text{MHz} ). The presented theoretical curves well describe the experimental results. This effect can find applications particularly in parity violation experiments.

  18. Glauber amplitudes for transitions from low lying states in hydrogen atom by charged particle impact

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, S; Srivastava, M K [Roorkee Univ. (India). Dept. of Physics

    1977-07-01

    The Glauber amplitudes for the general transition nlm ..-->.. n'1'm' in charged particle - hydrogen atom collisions have been obtained in the form of a one-dimensional integral. The final expression involves only a few hypergeometric functions if n is not too large and is particularly suited to study excitation to highly excited states from a low lying state.

  19. Dark states and interferences in cascade transitions of ultracold atoms in a cavity

    International Nuclear Information System (INIS)

    Arun, R.; Agarwal, G.S.

    2002-01-01

    We examine the competition among one- and two-photon processes in an ultracold, three-level atom undergoing cascade transitions as a result of its interaction with a bimodal cavity. We show parameter domains where two-photon transitions are dominant, and we also study the effect of two-photon emission on the mazer action in the cavity. The two-photon emission leads to the loss of detailed balance and therefore we obtain the photon statistics of the cavity field by the numerical integration of the master equation. The photon distribution in each cavity mode exhibits sub- and super-Poissonian behaviors depending on the strength of atom-field coupling. The photon distribution becomes identical to a Poisson distribution when the atom-field coupling strengths of the modes are equal

  20. Two-dimensional transition metal dichalcogenides as atomically thin semiconductors: opportunities and challenges.

    Science.gov (United States)

    Duan, Xidong; Wang, Chen; Pan, Anlian; Yu, Ruqin; Duan, Xiangfeng

    2015-12-21

    The discovery of graphene has ignited intensive interest in two-dimensional layered materials (2DLMs). These 2DLMs represent a new class of nearly ideal 2D material systems for exploring fundamental chemistry and physics at the limit of single-atom thickness, and have the potential to open up totally new technological opportunities beyond the reach of existing materials. In general, there are a wide range of 2DLMs in which the atomic layers are weakly bonded together by van der Waals interactions and can be isolated into single or few-layer nanosheets. The van der Waals interactions between neighboring atomic layers could allow much more flexible integration of distinct materials to nearly arbitrarily combine and control different properties at the atomic scale. The transition metal dichalcogenides (TMDs) (e.g., MoS2, WSe2) represent a large family of layered materials, many of which exhibit tunable band gaps that can undergo a transition from an indirect band gap in bulk crystals to a direct band gap in monolayer nanosheets. These 2D-TMDs have thus emerged as an exciting class of atomically thin semiconductors for a new generation of electronic and optoelectronic devices. Recent studies have shown exciting potential of these atomically thin semiconductors, including the demonstration of atomically thin transistors, a new design of vertical transistors, as well as new types of optoelectronic devices such as tunable photovoltaic devices and light emitting devices. In parallel, there have also been considerable efforts in developing diverse synthetic approaches for the rational growth of various forms of 2D materials with precisely controlled chemical composition, physical dimension, and heterostructure interface. Here we review the recent efforts, progress, opportunities and challenges in exploring the layered TMDs as a new class of atomically thin semiconductors.

  1. Electron-nuclear. gamma. transition spectrum of a nucleus in a multicharged atomic ion

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, L N; Letokhov, V S

    1987-08-01

    The nuclear emission of absorption spectrum of an atom possesses a set of electron satelites which are due to an alternation of the state of the electron shell. It is shown that the mechanism of formation of the satellites might be different for neutral atoms and high-charge ions. In the first case (loose electron shell) a ''shaking'' of the shell resulting from the interaction between the nucleus and ..gamma.. quantum is predominant. In the second case (rigid electron shell) the mechanism involves a direct interaction between the ..gamma.. quantum and electrons. The second mechanism is important in the case of dipole nuclear transitions and dominates at ..gamma.. quantum energies transition multiplicity do not pertain to the second mechanism. Consequently, the satellite spectrum is much enriched and transitions between the fine and hyperfine structure components, transitions and transitions which do not involve a change in the electron configuration can be considered. The relative intensities of the satellites are determined by the smallest parameter ..mu../sub p//sup 2lambda/ (lambda is the nuclear transition multipole order, ..mu../sub p/ approx. 12 ..pi.. is the relative proton mass and z the core mass). In the spectrum of the plasma source the electron satellites corresponding to the ..gamma.. quantum emission and absorption lines are not overlapped by the Doppler contour of the ..gamma.. line.

  2. Closing of Coster-Kronig transitions in multiply ionised gold atoms

    International Nuclear Information System (INIS)

    Banas, D.; Braziewicz, J.; Czarnota, M.; Fijal, I.; Jaskola, M.; Korman, A.; Kretschmer, W.; Pajek, M.; Semaniak, J.

    2003-01-01

    The paper discusses the effect of closing of L- and M-shell Coster-Kronig (CK) transitions in multiply ionised Au atoms, for which the selected CK transitions become energetically forbidden. This effect plays an important role when the Coster-Kronig energy for single-hole configuration is relatively low, being comparable with a change of the electronic binding energies in multiply ionised atom. We show, by using a simplified model, that for gold the effect of closing of CK transitions occurs for strong L 1 -L 3 M 4,5 transition for the L 1 -subshell as well as the M 3 -M 5 N 6,7 and M 4 -M 5 O 3,4 CK transitions for the M 3 - and M 4 -subshell, respectively. We demonstrate that the discussed effect of closing CK transitions substantially changes the X-ray fluorescence and Coster-Kronig yields and thus has to be considered in interpretation of X-rays excited by heavy ion impact

  3. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

    Directory of Open Access Journals (Sweden)

    Massimo Lai

    2015-01-01

    Full Text Available Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be

  4. Optically trapped atom interferometry using the clock transition of large 87Rb Bose-Einstein condensates

    International Nuclear Information System (INIS)

    Altin, P A; McDonald, G; Doering, D; Debs, J E; Barter, T H; Close, J D; Robins, N P; Haine, S A; Hanna, T M; Anderson, R P

    2011-01-01

    We present a Ramsey-type atom interferometer operating with an optically trapped sample of 10 6 Bose-condensed 87 Rb atoms. We investigate this interferometer experimentally and theoretically with an eye to the construction of future high precision atomic sensors. Our results indicate that, with further experimental refinements, it will be possible to produce and measure the output of a sub-shot-noise-limited, large atom number BEC-based interferometer. The optical trap allows us to couple the |F=1, m F =0)→|F=2, m F =0) clock states using a single photon 6.8 GHz microwave transition, while state selective readout is achieved with absorption imaging. We analyse the process of absorption imaging and show that it is possible to observe atom number variance directly, with a signal-to-noise ratio ten times better than the atomic projection noise limit on 10 6 condensate atoms. We discuss the technical and fundamental noise sources that limit our current system, and present theoretical and experimental results on interferometer contrast, de-phasing and miscibility.

  5. Competition between font face="Symbol">Lfont>- and V-type transitions in interference stabilization of Rydberg atoms.

    Science.gov (United States)

    Fedorov, M; Poluektov, N

    1998-01-19

    The problem of Interference Stabilization of Rydberg atoms is considered. Two kinds of Raman-type transitions can be responsible for the effect: L-type transitions via the continuum and V-type transitions via lower resonant atomic levels. The main distinctions between L- and V- stabilization are described. The conditions under which each of these two effects can exist are found and discussed.

  6. Two-photon transitions in hydrogen atoms embedded in weakly coupled plasmas

    International Nuclear Information System (INIS)

    Paul, S.; Ho, Y. K.

    2008-01-01

    The pseudostate method has been applied to calculate energy eigenvalues and corresponding eigenfunctions of the hydrogen atom in Debye plasma environments. Resonant two-photon transition rates from the ground state of atomic hydrogen to 2s and 3s excited states have been computed as a function of photon frequency in the length and velocity gauges for different Debye lengths. A two-photon transparency is found in correspondence to each resonance for 1s-3s. The transparency frequency and resonance enhancement frequency vary significantly with the Debye length.

  7. Photoemission from solids: the transition from solid-state to atomic physics

    International Nuclear Information System (INIS)

    Shirley, D.A.

    1980-08-01

    As the photon energy is increased, photoemission from solids undergoes a slow transition from solid-state to atomic behavior. However, throughout the energy range hν = 10 to 1000 eV or higher both types of phenomena are present. Thus angle-resolved photoemission can only be understood quantitatively if each experimenter recognizes the presence of band-structure, photoelectron diffraction, and photoelectron asymmetry effects. The quest for this understanding will build some interesting bridges between solid-state and atomic physics and should also yield important new insights about the phenomena associated with photoemission

  8. NiCo2O4@TiN Core-shell Electrodes through Conformal Atomic Layer Deposition for All-solid-state Supercapacitors

    KAUST Repository

    Wang, Renqi

    2016-03-04

    Ternary transition metal oxides such as NiCo2O4 show great promise as supercapacitor electrode materials. However, the unsatisfactory rate performance of NiCo2O4 may prove to be a major hurdle to its commercial usage. Herein, we report the development of NiCo2O4@TiN core–shell nanostructures for all-solid-state supercapacitors with significantly enhanced rate capability. We demonstrate that a thin layer of TiN conformally grown by atomic layer deposition (ALD) on NiCo2O4 nanofiber arrays plays a key role in improving their electrical conductivity, mechanical stability, and rate performance. Fabricated using the hybrid NiCo2O4@TiN electrodes, the symmetric all-solid-state supercapacitor exhibited an impressive stack power density of 58.205 mW cm−3 at a stack energy density of 0.061 mWh cm−3. To the best of our knowledge, these values are the highest of any NiCo2O4-based all-solid-state supercapacitor reported. Additionally, the resulting NiCo2O4@TiN all-solid-state device displayed outstanding cycling stability by retaining 70% of its original capacitance after 20,000 cycles at a high current density of 10 mA cm−2. These results illustrate the promise of ALD-assisted hybrid NiCo2O4@TiN electrodes for sustainable and integrated energy storage applications.

  9. NiCo2O4@TiN Core-shell Electrodes through Conformal Atomic Layer Deposition for All-solid-state Supercapacitors

    KAUST Repository

    Wang, Renqi; Xia, Chuan; Wei, Nini; Alshareef, Husam N.

    2016-01-01

    Ternary transition metal oxides such as NiCo2O4 show great promise as supercapacitor electrode materials. However, the unsatisfactory rate performance of NiCo2O4 may prove to be a major hurdle to its commercial usage. Herein, we report the development of NiCo2O4@TiN core–shell nanostructures for all-solid-state supercapacitors with significantly enhanced rate capability. We demonstrate that a thin layer of TiN conformally grown by atomic layer deposition (ALD) on NiCo2O4 nanofiber arrays plays a key role in improving their electrical conductivity, mechanical stability, and rate performance. Fabricated using the hybrid NiCo2O4@TiN electrodes, the symmetric all-solid-state supercapacitor exhibited an impressive stack power density of 58.205 mW cm−3 at a stack energy density of 0.061 mWh cm−3. To the best of our knowledge, these values are the highest of any NiCo2O4-based all-solid-state supercapacitor reported. Additionally, the resulting NiCo2O4@TiN all-solid-state device displayed outstanding cycling stability by retaining 70% of its original capacitance after 20,000 cycles at a high current density of 10 mA cm−2. These results illustrate the promise of ALD-assisted hybrid NiCo2O4@TiN electrodes for sustainable and integrated energy storage applications.

  10. Theoretical Study of Energy Levels and Transition Probabilities of Boron Atom

    Science.gov (United States)

    Tian Yi, Zhang; Neng Wu, Zheng

    2009-08-01

    Full Text PDF Though the electrons configuration for boron atom is simple and boron atom has long been of interest for many researchers, the theoretical studies for properties of BI are not systematic, there are only few results reported on energy levels of high excited states of boron, and transition measurements are generally restricted to transitions involving ground states and low excited states without considering fine structure effects, provided only multiplet results, values for transitions between high excited states are seldom performed. In this article, by using the scheme of the weakest bound electron potential model theory calculations for energy levels of five series are performed and with the same method we give the transition probabilities between excited states with considering fine structure effects. The comprehensive set of calculations attempted in this paper could be of some value to workers in the field because of the lack of published calculations for the BI systems. The perturbations coming from foreign perturbers are taken into account in studying the energy levels. Good agreement between our results and the accepted values taken from NIST has been obtained. We also reported some values of energy levels and transition probabilities not existing on the NIST data bases.

  11. Optical nonlinearities of excitonic states in atomically thin 2D transition metal dichalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Soh, Daniel Beom Soo [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Proliferation Signatures Discovery and Exploitation Department

    2017-08-01

    We calculated the optical nonlinearities of the atomically thin monolayer transition metal dichalcogenide material (particularly MoS2), particularly for those linear and nonlinear transition processes that utilize the bound exciton states. We adopted the bound and the unbound exciton states as the basis for the Hilbert space, and derived all the dynamical density matrices that provides the induced current density, from which the nonlinear susceptibilities can be drawn order-by-order via perturbative calculations. We provide the nonlinear susceptibilities for the linear, the second-harmonic, the third-harmonic, and the kerr-type two-photon processes.

  12. Relativistic many-body theory of atomic transitions: the relativistic equation-of-motion approach

    International Nuclear Information System (INIS)

    Huang, K.N.

    1981-01-01

    An equation-of-motion approach is used to develop the relativistic many-body theory of atomic transitions. The relativistic equations of motion for transition matrices are formulated using techniques of quantum field theory. To reduce the equation of motion to a tractable form which is appropriate for numerical calculations, a graphical method is employed to resolve the complication arising from the antisymmetrization and angular momentum coupling. The relativistic equation-of-motion method allows an ab initio treatment of correlation and relativistic effects in both closed- and open-shell many-body systems. A special case of the present formulation reduces to the relativistic random-phase approximation

  13. Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

    Science.gov (United States)

    Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

    2016-01-01

    Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties. PMID:27870845

  14. Quantum Phase Transition in a Cold Atomic Spin-Boson Mixture

    Science.gov (United States)

    Orth, Peter P.; Stanic, Ivan; Le Hur, Karyn

    2008-03-01

    We theoretically implement a spin array in a tunable bosonic environment using cold bosonic atoms with two (hyperfine) ground states, trapped by different potentials [1]. The first specie lies in a deep optical lattice with tightly confining wells and forms a spin array; spin-up/down corresponds to occupation by one/no atom at each site. The second specie forms a superfluid reservoir. Different species are coupled coherently via laser transitions and collisions. Whereas the laser coupling mimics a transverse field for the spins, the coupling to the reservoir phonons (sound modes) induces a ferromagnetic (Ising) coupling as well as dissipation. This results in a peculiar ferro-paramagnetic quantum phase transition where the effect of dissipation can be studied in a controllable manner. [1] Peter P. Orth, Ivan Stanic, and Karyn Le Hur, arXiv:0711.2309 [cond-mat.other].

  15. Higher order Stark effect and transition probabilities on hyperfine structure components of hydrogen like atoms

    Energy Technology Data Exchange (ETDEWEB)

    Pal' chikov, V.G. [National Research Institute for Physical-Technical and Radiotechnical Measurements - VNIIFTRI (Russian Federation)], E-mail: vitpal@mail.ru

    2000-08-15

    A quantum-electrodynamical (QED) perturbation theory is developed for hydrogen and hydrogen-like atomic systems with interaction between bound electrons and radiative field being treated as the perturbation. The dependence of the perturbed energy of levels on hyperfine structure (hfs) effects and on the higher-order Stark effect is investigated. Numerical results have been obtained for the transition probability between the hfs components of hydrogen-like bismuth.

  16. Thermodynamic Analysis of the Conformational Transition in Aqueous Solutions of Isotactic and Atactic Poly(Methacrylic Acid and the Hydrophobic Effect

    Directory of Open Access Journals (Sweden)

    Ksenija Kogej

    2016-04-01

    Full Text Available The affinity of amphiphilic compounds for water is important in various processes, e.g., in conformational transitions of biopolymers, protein folding/unfolding, partitioning of drugs in the living systems, and many others. Herein, we study the conformational transition of two isomer forms of poly(methacrylic acid (PMA, isotactic (iPMA and atactic (aPMA, in water. These isomers are chemically equivalent and differ only in the arrangement of functional groups along the chain. A complete thermodynamic analysis of the transition of the PMA chains from the compact to the extended form (comprising the conformational transition in water in the presence of three alkali chlorides is conducted by determining the free energy, enthalpy, and entropy changes of the process as a function of temperature, and therefrom also the heat capacity change. The heat capacity change of the transition is positive (+20 J/K mol for aPMA and negative (−50 J/K mol for iPMA. This result suggests a different affinity of PMA isomers for water. The conformational transition of iPMA is parallel to the transfer of polar solutes into water, whereas that of aPMA agrees with the transfer of nonpolar solutes into water.

  17. First observation of the strongly forbidden transition 1S0 - 3P0 in Strontium, for an atomic clock with trapped atoms

    International Nuclear Information System (INIS)

    Courtillot, I.

    2003-11-01

    This thesis reports the first results towards the realization of an optical clock using trapped strontium atoms. This set up would combine advantages of the different approaches commonly used to develop an atomic frequency standard. The first part describes the cold atoms source which is implemented. A magneto-optical trap operating on the 1 S 0 - 1 P 1 transition at 461 nm is loaded from an atomic beam decelerated by a Zeeman slower. The 461 nm laser is obtained by sum-frequency mixing in a potassium titanyl phosphate (KTP) crystal. The second part is devoted to the different stages developed to achieve the direct excitation of the 1 S 0 - 3 P 0 clock transition in 87 Sr. This line has a theoretical natural width of 10 -3 Hz. Before this detection, we obtained an estimate of the resonance frequency by measuring absolute frequencies of several allowed optical transitions. (author)

  18. First row transition metal atoms embedded in multivacancies in a rippled graphene system

    Science.gov (United States)

    Mombrú, Dominique; Faccio, Ricardo; Mombrú, Alvaro W.

    2018-03-01

    Ab-initio calculations based on density functional theory (DFT) have been performed to study systems where a first row transition metal atom is embedded in a rippled graphene due to the existence of an 8-order multivacancy. In addition to these cases, also the inclusion of a zinc atom, with a 3d10 electron configuration, was also studied. Structural distortions and magnetic response for each system were studied. A correlation was found for the magnitude of the rippling and the distortion in the vacancy. Variation in the trends was found for Cu and Zn cases, which were explained on the basis of the filling of the 3dx2-y2 orbital. All the systems exhibit lower magnetic moment in comparison to the metal-less system. The quenching of the magnetic moment due to the carbon atoms in the vacancy is observed for Sc and Cu.

  19. The general expression for the transition amplitude of two-photon ionization of atomic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Karule, E [Institute of Atomic Physics and Spectroscopy, University of Latvia, Raina Boulevard 19, Riga, LV-1586 (Latvia); Moine, B [Universite Paris Sud, 91405 Orsay Cedex (France)

    2003-05-28

    Two-photon ionization of atomic hydrogen with an excess photon is revisited. The non-relativistic dipole approximation and Coulomb Green function (CGF) formalism are applied. Using the CGF Sturmian expansion straightforwardly, one gets the radial transition amplitude in the form of an infinite sum over Gauss hypergeometric functions which are polynomials. It is convergent if all intermediate states are in the discrete spectrum. In the case of two-photon ionization with an excess photon, when photoionization is also possible, intermediate states are in the continuum. We performed the explicit summation over intermediate states and got a simple general expression for the radial transition amplitude in the form of a finite sum over Appell hypergeometric functions, which are not polynomials. An Appell function may be expressed as an infinite sum over Gauss functions. In the case of ionization by an excess photon, Gauss functions are transformed to give a convergent radial transition amplitude for the whole region. The generalized cross sections for two-photon above-threshold ionization of atomic hydrogen in the ground state and excited states calculated by us agree very well with results of previous calculations. Generalized cross sections for two-photon ionization of positronium in the ground state are obtained by scaling those for atomic hydrogen.

  20. Precision spectroscopy of the 2S-4P transition in atomic hydrogen

    Science.gov (United States)

    Maisenbacher, Lothar; Beyer, Axel; Matveev, Arthur; Grinin, Alexey; Pohl, Randolf; Khabarova, Ksenia; Kolachevsky, Nikolai; Hänsch, Theodor W.; Udem, Thomas

    2017-04-01

    Precision measurements of atomic hydrogen have long been successfully used to extract fundamental constants and to test bound-state QED. However, both these applications are limited by measurements of hydrogen lines other than the very precisely known 1S-2S transition. Moreover, the proton r.m.s.charge radius rp extracted from electronic hydrogen measurements currently disagrees by 4 σ with the much more precise value extracted from muonic hydrogen spectroscopy. We have measured the 2S-4P transition in atomic hydrogen using a cryogenic beam of hydrogen atoms optically excited to the initial 2S state. The first order Doppler shift of the one-photon 2S-4P transition is suppressed by actively stabilized counter-propagating laser beams and time-of-flight resolved detection. Quantum interference between excitation paths can lead to significant line distortions in our system. We use an experimentally verified, simple line shape model to take these distortions into account. With this, we can extract a new value for rp and the Rydberg constant R∞ with comparable accuracy as the combined previous H world data.

  1. Neutral currents and parity breakdown in atomic transitions: three proposed experiments

    International Nuclear Information System (INIS)

    Bloom, S.D.

    1976-01-01

    This paper describes three proposed experiments for observing the breakdown of parity in atomic transitions due to the exchange of neutral, parity-violating currents arising from some of the new gauge models (e.g., the Weinberg model) for the weak interaction. The experiments are based on exploiting a suggestion, by Bouchiat and Bouchiat, that modern laser technology be utilized to produce intense, monochromatic, and polarized photon beams with which to excite forbidden atomic transitions of the basic form parallel ns 1 / 2 broken bracket → parallel n's 1 / 2 broken bracket. The asymmetries (of the order of 10 -4 ) in the de-exitation processes then signal the presence of the parity-violating components due to the neutral currents. In all three experiments suggested here, the use of multiple (uncollimated)atomic beams as targets forms a basic part, and their advantages over a temperature-equilibrium vapor are described. The first experiment uses 55 Cs atomic beams as a target; the second uses 37 Rb in conjunction with a superstrong magnetic field (approximately 80 kG); the third uses 81 Tl and requires frequency doubling of the exciting laser beam. All three experiments appear to be quite feasible, and, given the requisite equipment (much of which is or soon will be commercially available), they could yield definitive results in a period of a few months

  2. Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

    International Nuclear Information System (INIS)

    Oka, Yurie; Yanao, Tomohiro; Koon, Wang Sang

    2015-01-01

    This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions

  3. Conformation transitions of blood proteins under influence of physical factors on microwave dielectric method

    International Nuclear Information System (INIS)

    Gorobchenko, O.A.; Nikolov, O.T.; Gatash, S.V.

    2006-01-01

    In this article, the influence of γ-irradiation and temperature on albumin and fibrinogen conformation and dielectric properties of protein solutions have been studied by the microwave dielectric method. Both the values of the real part ε' (dielectric permittivity) and the imaginary part ε'' (dielectric losses) of the complex dielectric permittivity of the aqueous solution of bovine serum albumin and human fibrinogen as functions of temperature and γ-irradiation dose have been obtained. The time of dielectric relaxation of water molecules in the protein solutions was calculated. The hydration of the albumin and fibrinogen molecules was determined. The temperature dependencies of hydration are non-monotonous and have a number of characteristic features at the temperatures 30-34 and 44-47 deg. C for serum albumin, and 24 and 32 deg. C for fibrinogen

  4. Reversible and irreversible conformational transitions in myoglobin: role of hydrated amino acid ionic liquid.

    Science.gov (United States)

    Sankaranarayanan, Kamatchi; Sathyaraj, Gopal; Nair, B U; Dhathathreyan, A

    2012-04-12

    Hydrated phenylalanine ionic liquid (Phe-IL) has been used to solubilize myoglobin (Mb). Structural stability of Mb in Phe-IL analyzed using fluorescence and circular dichroism spectroscopy shows that for low levels of hydration of Phe-IL there is a large red shift in the fluorescence emission wavelength and the protein transforms to complete β sheet from its native helical conformation. Rehydration or dilution reverses the β sheet to an α helix which on aging organizes to micrometer-sized fibrils. At concentrations higher than 200 μM, the protein changes from β to a more random coiled structure. Organization of the protein in Phe-IL in a Langmuir film at the air/water interface has been investigated using the surface pressure-molecular area isotherm and shows nearly the same surface tension for both pure Mb and Mb in Phe-IL. Scanning electron microscopy of the films of Mb in Phe-IL transferred using the Langmuir-Blodgett film technique show layered morphology. This study shows that the conformation of Mb is completely reversible going from β → helix → β sheet up to 200 μM of Phe-IL. Similar surface tension values for Mb in water and in Phe-IL suggests that direct ion binding interactions with the protein coupled with the change in local viscosity from the IL seems to not only alter the secondary structure of individual proteins but also drives the self-assembly of the protein molecules leading finally to fibril formation.

  5. Effects of finite temperature on two-photon transitions in a Rydberg atom in a high-Q cavity

    International Nuclear Information System (INIS)

    Puri, R.R.; Joshi, A.

    1989-01-01

    The effects of cavity temperature on an effective two-level atom undergoing two-photon transitions in a high-Q cavity are investigated. The quantum statistical properties of the field and the dynamical properties of the atom in this case are studied and compared with those for an atom making one-photon transitions between the two levels. The analysis is based on the solution of the equation for the density matrix in the secular approximation which is known to be a valid approximation in the case of a Rydberg atom in a high-Q cavity. (orig.)

  6. Selection rule engineering of forbidden transitions of a hydrogen atom near a nanogap

    Science.gov (United States)

    Kim, Hyunyoung Y.; Kim, Daisik S.

    2018-01-01

    We perform an analytical study on the allowance of forbidden transitions for a hydrogen atom placed near line dipole sources, mimicking light emanating from a one-dimensional metallic nanogap. It is shown that the rapid variation of the electric field vector, inevitable in the near zone, completely breaks the selection rule of Δl=±1. While the forbidden transitions between spherically symmetric S states, such as 2S to 1S or 3S to 1S (Δl=0), are rather robust against selection rule breakage, Δl=±2 transitions such as between 3D and 1S or 3D and 2S states are very vulnerable to the spatial variation of the perturbing electric field. Transitions between 2S and 3D states are enhanced by many orders of magnitude, aided by the quadratic nature of both the perturbing Hamiltonian and D wavefunctions. The forbidden dipole moment, which approaches one Bohr radius times the electric charge in the vicinity of the gap, can be written in a simple closed form owing to the one-dimensional nature of our gap. With large enough effective volume together with the symmetric nature of the excited state wavefunctions, our work paves way towards atomic physics application of infinitely long nanogaps.

  7. Theoretical expression of the internal conversion coefficient of a M1 transition between two atomic states

    International Nuclear Information System (INIS)

    Attallah, F.; Chemin, J.F.; Scheurer, J.N.; Karpeshin, F.; Harston, M.

    1997-01-01

    We have established a general relation for the expression of the internal conversion of an M 1 transition a 1s electronic state to an empty ns electronic bound state. Under the hypothesis that the density of the electron level ρ n satisfies the condition ρ n Γ >> 1 (where Γ is the total width of the excited atomic state) a calculation in the first order gives a relation for the internal conversion coefficient.This relation shows that the internal conversion coefficient takes a resonant character when the nuclear energy transition is smaller than the binding energy of the 1s electron. An application of this relation to an M 1 transition in the case of the ion 125 T e with a charge state Q = 45 and an 1s electron binding energy E B 45 = 35.581 KeV gives the value for the internal conversion coefficient R = 5.7

  8. Electronic structure and magnetic properties of substitutional transition-metal atoms in GaN nanotubes

    International Nuclear Information System (INIS)

    Zhang Min; Shi Jun-Jie

    2014-01-01

    The electronic structure and magnetic properties of the transition-metal (TM) atoms (Sc—Zn, Pt and Au) doped zigzag GaN single-walled nanotubes (NTs) are investigated using first-principles spin-polarized density functional calculations. Our results show that the bindings of all TM atoms are stable with the binding energy in the range of 6–16 eV. The Sc- and V-doped GaN NTs exhibit a nonmagnetic behavior. The GaN NTs doped with Ti, Mn, Ni, Cu and Pt are antiferromagnetic. On the contrary, the Cr-, Fe-, Co-, Zn- and Au-doped GaN NTs show the ferromagnetic characteristics. The Mn- and Co-doped GaN NTs induce the largest local moment of 4μ B among these TM atoms. The local magnetic moment is dominated by the contribution from the substitutional TM atom and the N atoms bonded with it. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  9. Atomic Origins of Monoclinic-Tetragonal (Rutile) Phase Transition in Doped VO 2 Nanowires

    KAUST Repository

    Asayesh-Ardakani, Hasti

    2015-10-12

    There has been long-standing interest in tuning the metal-insulator phase transition in vanadium dioxide (VO) via the addition of chemical dopants. However, the underlying mechanisms by which doping elements regulate the phase transition in VO are poorly understood. Taking advantage of aberration-corrected scanning transmission electron microscopy, we reveal the atomistic origins by which tungsten (W) dopants influence the phase transition in single crystalline WVO nanowires. Our atomically resolved strain maps clearly show the localized strain normal to the (122¯) lattice planes of the low W-doped monoclinic structure (insulator). These strain maps demonstrate how anisotropic localized stress created by dopants in the monoclinic structure accelerates the phase transition and lead to relaxation of structure in tetragonal form. In contrast, the strain distribution in the high W-doped VO structure is relatively uniform as a result of transition to tetragonal (metallic) phase. The directional strain gradients are furthermore corroborated by density functional theory calculations that show the energetic consequences of distortions to the local structure. These findings pave the roadmap for lattice-stress engineering of the MIT behavior in strongly correlated materials for specific applications such as ultrafast electronic switches and electro-optical sensors.

  10. Atomic Origins of Monoclinic-Tetragonal (Rutile) Phase Transition in Doped VO2 Nanowires.

    Science.gov (United States)

    Asayesh-Ardakani, Hasti; Nie, Anmin; Marley, Peter M; Zhu, Yihan; Phillips, Patrick J; Singh, Sujay; Mashayek, Farzad; Sambandamurthy, Ganapathy; Low, Ke-Bin; Klie, Robert F; Banerjee, Sarbajit; Odegard, Gregory M; Shahbazian-Yassar, Reza

    2015-11-11

    There has been long-standing interest in tuning the metal-insulator phase transition in vanadium dioxide (VO2) via the addition of chemical dopants. However, the underlying mechanisms by which doping elements regulate the phase transition in VO2 are poorly understood. Taking advantage of aberration-corrected scanning transmission electron microscopy, we reveal the atomistic origins by which tungsten (W) dopants influence the phase transition in single crystalline WxV1-xO2 nanowires. Our atomically resolved strain maps clearly show the localized strain normal to the (122̅) lattice planes of the low W-doped monoclinic structure (insulator). These strain maps demonstrate how anisotropic localized stress created by dopants in the monoclinic structure accelerates the phase transition and lead to relaxation of structure in tetragonal form. In contrast, the strain distribution in the high W-doped VO2 structure is relatively uniform as a result of transition to tetragonal (metallic) phase. The directional strain gradients are furthermore corroborated by density functional theory calculations that show the energetic consequences of distortions to the local structure. These findings pave the roadmap for lattice-stress engineering of the MIT behavior in strongly correlated materials for specific applications such as ultrafast electronic switches and electro-optical sensors.

  11. Atomic Origins of Monoclinic-Tetragonal (Rutile) Phase Transition in Doped VO 2 Nanowires

    KAUST Repository

    Asayesh-Ardakani, Hasti; Nie, Anmin; Marley, Peter M.; Zhu, Yihan; Phillips, Patrick J.; Singh, Sujay; Mashayek, Farzad; Sambandamurthy, Ganapathy; Low, Ke Bin; Klie, Robert F.; Banerjee, Sarbajit; Odegard, Gregory M.; Shahbazian-Yassar, Reza

    2015-01-01

    There has been long-standing interest in tuning the metal-insulator phase transition in vanadium dioxide (VO) via the addition of chemical dopants. However, the underlying mechanisms by which doping elements regulate the phase transition in VO are poorly understood. Taking advantage of aberration-corrected scanning transmission electron microscopy, we reveal the atomistic origins by which tungsten (W) dopants influence the phase transition in single crystalline WVO nanowires. Our atomically resolved strain maps clearly show the localized strain normal to the (122¯) lattice planes of the low W-doped monoclinic structure (insulator). These strain maps demonstrate how anisotropic localized stress created by dopants in the monoclinic structure accelerates the phase transition and lead to relaxation of structure in tetragonal form. In contrast, the strain distribution in the high W-doped VO structure is relatively uniform as a result of transition to tetragonal (metallic) phase. The directional strain gradients are furthermore corroborated by density functional theory calculations that show the energetic consequences of distortions to the local structure. These findings pave the roadmap for lattice-stress engineering of the MIT behavior in strongly correlated materials for specific applications such as ultrafast electronic switches and electro-optical sensors.

  12. Atoms

    International Nuclear Information System (INIS)

    Fuchs, Alain; Villani, Cedric; Guthleben, Denis; Leduc, Michele; Brenner, Anastasios; Pouthas, Joel; Perrin, Jean

    2014-01-01

    Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)

  13. Atomic Data Revisions for Transitions Relevant to Observations of Interstellar, Circumgalactic, and Intergalactic Matter

    Energy Technology Data Exchange (ETDEWEB)

    Cashman, Frances H.; Kulkarni, Varsha P. [Department of Physics and Astronomy, University of South Carolina, Columbia, SC 29208 (United States); Kisielius, Romas; Bogdanovich, Pavel [Institute of Theoretical Physics and Astronomy, Vilnius University, Saulėtekio al. 3, LT-10222 Vilnius (Lithuania); Ferland, Gary J. [Department of Physics and Astronomy, University of Kentucky, Lexington, KY 40506 (United States)

    2017-05-01

    Measurements of element abundances in galaxies from astrophysical spectroscopy depend sensitively on the atomic data used. With the goal of making the latest atomic data accessible to the community, we present a compilation of selected atomic data for resonant absorption lines at wavelengths longward of 911.753 Å (the H i Lyman limit), for key heavy elements (heavier than atomic number 5) of astrophysical interest. In particular, we focus on the transitions of those ions that have been observed in the Milky Way interstellar medium (ISM), the circumgalactic medium (CGM) of the Milky Way and/or other galaxies, and the intergalactic medium (IGM). We provide wavelengths, oscillator strengths, associated accuracy grades, and references to the oscillator strength determinations. We also attempt to compare and assess the recent oscillator strength determinations. For about 22% of the lines that have updated oscillator strength values, the differences between the former values and the updated ones are ≳0.1 dex. Our compilation will be a useful resource for absorption line studies of the ISM, as well as studies of the CGM and IGM traced by sight lines to quasars and gamma-ray bursts. Studies (including those enabled by future generations of extremely large telescopes) of absorption by galaxies against the light of background galaxies will also benefit from our compilation.

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

    International Nuclear Information System (INIS)

    Kharchenko, V.F.

    2015-01-01

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

  15. Spin-dependent electronic transport properties of transition metal atoms doped α-armchair graphyne nanoribbons

    Science.gov (United States)

    Fotoohi, Somayeh; Haji-Nasiri, Saeed

    2018-04-01

    Spin-dependent electronic transport properties of single 3d transition metal (TM) atoms doped α-armchair graphyne nanoribbons (α-AGyNR) are investigated by non-equilibrium Green's function (NEGF) method combined with density functional theory (DFT). It is found that all of the impurity atoms considered in this study (Fe, Co, Ni) prefer to occupy the sp-hybridized C atom site in α-AGyNR, and the obtained structures remain planar. The results show that highly localized impurity states are appeared around the Fermi level which correspond to the 3d orbitals of TM atoms, as can be derived from the projected density of states (PDOS). Moreover, Fe, Co, and Ni doped α-AGyNRs exhibit magnetic properties due to the strong spin splitting property of the energy levels. Also for each case, the calculated current-voltage characteristic per super-cell shows that the spin degeneracy in the system is obviously broken and the current becomes strongly spin dependent. Furthermore, a high spin-filtering effect around 90% is found under the certain bias voltages in Ni doped α-AGyNR. Additionally, the structure with Ni impurity reveals transfer characteristic that is suitable for designing a spin current switch. Our findings provide a high possibility to design the next generation spin nanodevices with novel functionalities.

  16. Monte Carlo simulations of phase transitions and lattice dynamics in an atom-phonon model for spin transition compounds

    International Nuclear Information System (INIS)

    Apetrei, Alin Marian; Enachescu, Cristian; Tanasa, Radu; Stoleriu, Laurentiu; Stancu, Alexandru

    2010-01-01

    We apply here the Monte Carlo Metropolis method to a known atom-phonon coupling model for 1D spin transition compounds (STC). These inorganic molecular systems can switch under thermal or optical excitation, between two states in thermodynamical competition, i.e. high spin (HS) and low spin (LS). In the model, the ST units (molecules) are linked by springs, whose elastic constants depend on the spin states of the neighboring atoms, and can only have three possible values. Several previous analytical papers considered a unique average value for the elastic constants (mean-field approximation) and obtained phase diagrams and thermal hysteresis loops. Recently, Monte Carlo simulation papers, taking into account all three values of the elastic constants, obtained thermal hysteresis loops, but no phase diagrams. Employing Monte Carlo simulation, in this work we obtain the phase diagram at T=0 K, which is fully consistent with earlier analytical work; however it is more complex. The main difference is the existence of two supplementary critical curves that mark a hysteresis zone in the phase diagram. This explains the pressure hysteresis curves at low temperature observed experimentally and predicts a 'chemical' hysteresis in STC at very low temperatures. The formation and the dynamics of the domains are also discussed.

  17. Compact Optical Atomic Clock Based on a Two-Photon Transition in Rubidium

    Science.gov (United States)

    Martin, Kyle W.; Phelps, Gretchen; Lemke, Nathan D.; Bigelow, Matthew S.; Stuhl, Benjamin; Wojcik, Michael; Holt, Michael; Coddington, Ian; Bishop, Michael W.; Burke, John H.

    2018-01-01

    Extralaboratory atomic clocks are necessary for a wide array of applications (e.g., satellite-based navigation and communication). Building upon existing vapor-cell and laser technologies, we describe an optical atomic clock, designed around a simple and manufacturable architecture, that utilizes the 778-nm two-photon transition in rubidium and yields fractional-frequency instabilities of 4 ×10-13/√{τ (s ) } for τ from 1 to 10 000 s. We present a complete stability budget for this system and explore the required conditions under which a fractional-frequency instability of 1 ×10-15 can be maintained on long time scales. We provide a precise characterization of the leading sensitivities to external processes, including magnetic fields and fluctuations of the vapor-cell temperature and 778-nm laser power. The system is constructed primarily from commercially available components, an attractive feature from the standpoint of the commercialization and deployment of optical frequency standards.

  18. Coherent, atomically thin transition-metal dichalcogenide superlattices with engineered strain

    Science.gov (United States)

    Xie, Saien; Tu, Lijie; Han, Yimo; Huang, Lujie; Kang, Kibum; Lao, Ka Un; Poddar, Preeti; Park, Chibeom; Muller, David A.; DiStasio, Robert A.; Park, Jiwoong

    2018-03-01

    Epitaxy forms the basis of modern electronics and optoelectronics. We report coherent atomically thin superlattices in which different transition metal dichalcogenide monolayers—despite large lattice mismatches—are repeated and laterally integrated without dislocations within the monolayer plane. Grown by an omnidirectional epitaxy, these superlattices display fully matched lattice constants across heterointerfaces while maintaining an isotropic lattice structure and triangular symmetry. This strong epitaxial strain is precisely engineered via the nanoscale supercell dimensions, thereby enabling broad tuning of the optical properties and producing photoluminescence peak shifts as large as 250 millielectron volts. We present theoretical models to explain this coherent growth and the energetic interplay governing the ripple formation in these strained monolayers. Such coherent superlattices provide building blocks with targeted functionalities at the atomically thin limit.

  19. n l -> n' l' transition rates in electron and proton - Rydberg atom collision

    Science.gov (United States)

    Vrinceanu, Daniel

    2017-04-01

    Electrons and protons drive the recombination dynamics of highly excited Rydberg atoms in cold rarefied plasmas found in astrophysical conditions such as primordial recombination or star formation in H-II clouds. It has been recognized that collisions induce both energy and angular momentum transitions in Rydberg atoms, although in different proportions, depending on the initial state, temperature and the given species considered in the collision (electron or proton). Most studies focused on one collision type at a time, under the assumption that collision types are independent or their effects are not competing. The classical Monte-Carlo trajectory simulations presented in this work calculate the rates for both energy and angular momentum transfers and show their interdependence. For example, energy transfer with small angular momentum change are more efficient for target states with initial large angular momentum. The author acknowledges support received from the National Science Foundation through a Grant for the Center for Research on Complex Networks (HRD-1137732).

  20. Low-lying nuclear levels and radiative transitions in hadronic atoms

    International Nuclear Information System (INIS)

    Popov, V.S.; Kudryavtsev, A.E.; Lisin, V.I.; Mur, V.D.

    1985-01-01

    The analytic theory of nuclear level shifts permit the position of the nuclear level perturbing the Coulomb spectrum to be calculated on the basis of the magnitude of the level shift of a hadron atom. As an example the K -4 He atom is discussed. The experimental data on the 2p-level shift indicate that a weakly bound p-state with a binding energy and width epsilon approximately γ approximately 0.5 MeV may exist in the system. The probabilities for radiative transitions to this level and the cross section for its creation in a nuclear reaction with 6 Li are calculated. The possible existence of weakly coupled K - and anti p states for other light nuclei is discussed. An exact solution of the model Coulomb problem with short range interaction is obtained and this permits the limits of validity of the initial approximations to be determined

  1. Phase transitions and pairing signature in strongly attractive Fermi atomic gases

    International Nuclear Information System (INIS)

    Guan, X. W.; Bortz, M.; Batchelor, M. T.; Lee, C.

    2007-01-01

    We investigate pairing and quantum phase transitions in the one-dimensional two-component Fermi atomic gas in an external field. The phase diagram, critical fields, magnetization, and local pairing correlation are obtained analytically via the exact thermodynamic Bethe ansatz solution. At zero temperature, bound pairs of fermions with opposite spin states form a singlet ground state when the external field H c1 . A completely ferromagnetic phase without pairing occurs when the external field H>H c2 . In the region H c1 c2 , we observe a mixed phase of matter in which paired and unpaired atoms coexist. The phase diagram is reminiscent of that of type II superconductors. For temperatures below the degenerate temperature and in the absence of an external field, the bound pairs of fermions form hard-core bosons obeying generalized exclusion statistics

  2. Mott Transition of Fermionic Atoms in a Three-Dimensional Optical Trap

    International Nuclear Information System (INIS)

    Helmes, R. W.; Rosch, A.; Costi, T. A.

    2008-01-01

    We study theoretically the Mott metal-insulator transition for a system of fermionic atoms confined in a three-dimensional optical lattice and a harmonic trap. We describe an inhomogeneous system of several thousand sites using an adaptation of dynamical mean-field theory solved efficiently with the numerical renormalization group method. Above a critical value of the on-site interaction, a Mott-insulating phase appears in the system. We investigate signatures of the Mott phase in the density profile and in time-of-flight experiments

  3. Activation barriers for series of exothermic homologous reactions. VI. Reactions of lanthanide and transition metal atoms.

    Science.gov (United States)

    Blue, Alan S.; Fontijn, Arthur

    2001-09-01

    Semiempirical configuration interaction (SECI) theory to predict activation barriers, E, as given by k(T)=ATn exp(-E(RT), has been applied to homologous series of lanthanide (LN) and transition metal (TM) atom oxidation reactions. This was achieved by considering as homologous series reactions of elements differing only by the number of electrons in one subshell. Comparison between SECI and experimental results leads to an average deviation for the LN+N2O reactions of 0.66 kJ mol-1, and up to 5.5 kJ mol-1 for other series. Thirty-one activation barriers are reported.

  4. Relativistic many-body theory of atomic transitions. The relativistic equation-of-motion approach

    International Nuclear Information System (INIS)

    Huang, K.

    1982-01-01

    An equation-of-motion approach is used to develop the relativistic many-body theory of atomic transitions. The relativistic equations of motion for transition matrices are formulated with the use of techniques of quantum-field theory. To reduce the equations of motion to a tractable form which is appropriate for numerical calculations, a graphical method to resolve the complication arising from the antisymmetrization and angular-momentum coupling is employed. The relativistic equation-of-motion method allows an ab initio treatment of correlation and relativistic effects in both closed- and open-shell many-body systems. A special case of the present formulation reduces to the relativistic random-phase approximation

  5. Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

    Science.gov (United States)

    Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

    2017-06-14

    Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

  6. Protein conformational transitions at the liquid-gas interface as studied by dilational surface rheology.

    Science.gov (United States)

    Noskov, Boris A

    2014-04-01

    Experimental results on the dynamic dilational surface elasticity of protein solutions are analyzed and compared. Short reviews of the protein behavior at the liquid-gas interface and the dilational surface rheology precede the main sections of this work. The kinetic dependencies of the surface elasticity differ strongly for the solutions of globular and non-globular proteins. In the latter case these dependencies are similar to those for solutions of non-ionic amphiphilic polymers and have local maxima corresponding to the formation of the distal region of the surface layer (type I). In the former case the dynamic surface elasticity is much higher (>60 mN/m) and the kinetic dependencies are monotonical and similar to the data for aqueous dispersions of solid nanoparticles (type II). The addition of strong denaturants to solutions of bovine serum albumin and β-lactoglobulin results in an abrupt transition from the type II to type I dependencies if the denaturant concentration exceeds a certain critical value. These results give a strong argument in favor of the preservation of the protein globular structure in the course of adsorption without any denaturants. The addition of cationic surfactants also can lead to the non-monotonical kinetic dependencies of the dynamic surface elasticity indicating destruction of the protein tertiary and secondary structures. The addition of anionic surfactants gives similar results only for the protein solutions of high ionic strength. The influence of cationic surfactants on the local maxima of the kinetic dependencies of the dynamic surface elasticity for solutions of a non-globular protein (β-casein) differs from the influence of anionic surfactants due to the heterogeneity of the charge distribution along the protein chain. In this case one can use small admixtures of ionic surfactants as probes of the adsorption mechanism. The effect of polyelectrolytes on the kinetic dependencies of the dynamic surface elasticity of protein

  7. Atomic Structure of a Spinel-like Transition Al2O3 (100) Surface

    DEFF Research Database (Denmark)

    Jensen, Thomas Nørregaard; Meinander, Kristoffer; Helveg, Stig

    2014-01-01

    We study a crystalline epitaxial alumina thin film with the characteristics of a spinel-type transition Al2O3(100) surface by using atom-resolved noncontact atomic force microscopy and density functional theory. It is shown that the films are terminated by an Al-O layer rich in Al vacancies......, exhibiting a strong preference for surface hydroxyl group formation in two configurations. The transition alumina films are crystalline and perfectly stable in ambient atmospheres, a quality which is expected to open the door to new fundamental studies of the surfaces of transition aluminas....

  8. Atomic scale 0-π transition and pairing symmetry in a Josephson junction with a ferromagnetic insulator

    International Nuclear Information System (INIS)

    Kawabata, S.; Kashiwaya, S.; Tanaka, Y.; Golubov, A. A.; Asano, Y.

    2011-01-01

    Full text: A superconducting ring with a π-junction made from superconductor (S) / ferromagnetic- metal (FM) / superconductor (S) exhibits a spontaneous current without an external magnetic field and the corresponding magnetic flux is half a flux quantum in the ground state. Such a π-ring provides so-called 'quiet qubit' that can be efficiently decoupled from the fluctuation of the external field. However, the usage of FM gives rise to strong Ohmic dissipation. Therefore, the realization of π-junctions without FM is highly desired for qubit applications. We theoretically consider the possibility of the π-junction formation in the mesoscopic Josephson junctions with ferromagnetic insulators (FI) by taking into account the band structure of such materials explicitly. In the case of the fully polarized FIs, e.g., La 2 BaCuO 5 (LBCO) and K 2 CuF 4 , we found the formation of a π-junction and a novel atomic-scale 0-π transition induced by increasing the FI thickness LF. In this talk, I will discuss a thermal stability and material-parameter dependences of the atomic-scale 0-π transition as well as possibility of the odd-frequency pairing in such systems. (author)

  9. Electron-nuclear γ transition spectrum of a nucleus in a multicharged atomic ion

    International Nuclear Information System (INIS)

    Ivanov, L.N.; Letokhov, V.S.

    1987-01-01

    The nuclear emission of absorption spectrum of an atom possesses a set of electron satelites which are due to an alternation of the state of the electron shell. It is shown that the mechanism of formation of the satellites might be different for neutral atoms and high-charge ions. In the first case (loose electron shell) a ''shaking'' of the shell resulting from the interaction between the nucleus and γ quantum is predominant. In the second case (rigid electron shell) the mechanism involves a direct interaction between the γ quantum and electrons. The second mechanism is important in the case of dipole nuclear transitions and dominates at γ quantum energies p 2λ (λ is the nuclear transition multipole order, μ p ∼ 1/2 π is the relative proton mass and z the core mass). In the spectrum of the plasma source the electron satellites corresponding to the γ quantum emission and absorption lines are not overlapped by the Doppler contour of the γ line

  10. An interface between the nuclear physics and the atomic physics; how to measure nuclear times observing atomic transitions

    International Nuclear Information System (INIS)

    Pinho, A.G. de

    1985-01-01

    Recent observations are related in which processes resulting from the ionization in ion-atom collisions are observed in coincidence with nuclear processes (where the incidence ion nucleus hits the target atom nucleus). The delay introduced by the nuclear reaction contaminates the results of the atomic collision and manifest itself either in the X rays (positrons) emitted in the joined atom system or in the X rays (Auger electrons) emitted by separeted atoms, after the collision. Both effects serve to obtain information on the reaction times (in general much less then 10 -16 sec). Following this line, other experimental possibilities are discussed. (L.C.) [pt

  11. Few electron transitions in atomic collisions. Final report, September 1, 1992--December 31, 1995

    Energy Technology Data Exchange (ETDEWEB)

    McGuire, J.

    1997-04-01

    During the past three years we have evaluated probabilities and cross sections for few and multiple electron transitions in atomic collisions. Our studies included interactions of atoms and molecules with incident protons, bare ions, electrons, positrons, anti-protons, ions carrying electrons and photons. We also: studied the inter-relation between collisions with charged particles and collisions involving various processes with photons. This work has complemented various studies of collisions of atoms with charged particles and with photons as well as more general efforts to understand the nature of multi-electron systems. Our aim has been to begin with relatively simple two electron systems and to focus on fast processes in which there is too little time for complicated processes to occur. We have used a variety of computational techniques, but we emphasize those appropriate for fast collisions in which we hope to obtain insight into the physical nature of the process itself. We generally considered systems in which experimental data was available.

  12. Conformational studies of self-organized regioregular poly(3-dodecylthiophene)s using non-contact atomic force microscopy in ultra high vacuum condition

    International Nuclear Information System (INIS)

    Tanaka, Shukichi; Grevin, Benjamin; Rannou, Patrice; Suzuki, Hitoshi; Mashiko, Shinro

    2006-01-01

    Conformations of one of the variations of π-conjugated poly-alkylthiophene, poly(3-dodecylthiophene)s (P3DDT)s on the surface in ultra high vacuum (UHV) were investigated by non-contact atomic force microscopy (NC-AFM) operated by frequency-modulation mode (FM-mode). From individual molecules to several multi-layered ones, polymer chains on the surface were clearly resolved on conducting highly oriented pyrolytic graphite (HOPG) substrates and insulating mica ones, respectively. Solvent evaporation was found to have two stages, which influenced the diffusion, ordering, and adhesion processes of polymer chains on the substrate. To keep the ordered conformations of deposited polymer chains when they are transferred from ambient condition to UHV, these evaporation processes should be carefully considered. The initial conformation of polymers on the substrate was found to depend strongly on the lattice matching conditions and interactions between polymers and substrates. Formations of stripe-like structures of P3DDT polymers were found on the mica substrates, which is promising for device application

  13. Phase transitions in an Ising model for monolayers of coadsorbed atoms

    International Nuclear Information System (INIS)

    Lee, H.H.; Landau, D.P.

    1979-01-01

    A Monte Carlo method is used to study a simple S=1 Ising (lattice-gas) model appropriate for monolayers composed of two kinds of atoms on cubic metal substrates H = K/sub nn/ Σ/sub nn/ S 2 /sub i/zS 2 /sub j/z + J/sub nnn/ Σ/sub nnn/ S/sub i/zS/sub j/z + Δ Σ/sub i/ S 2 /sub i/z (where nn denotes nearest-neighbor and nnn next-nearest-neighbor pairs). The phase diagram is determined over a wide range of Δ and T for K/sub nn//J/sub nnn/=1/4. For small (or negative) Δ we find an antiferromagnetic 2 x 1 ordered phase separated from the disordered state by a line of second-order phase transitions. The 2 x 1 phase is separated by a line of first-order transitions from a c (2 x 2) phase which appears for larger Δ. The 2 x 1 and c (2 x 2) phases become simultaneously critical at a bicritical point and the phase boundary of the c (2 x 2) → disordered transition shows a tricritical point

  14. Accurate Cross Sections for Excitation of Resonance Transitions in Atomic Oxygen

    Science.gov (United States)

    Tayal, S. S.

    2004-01-01

    Electron collision excitation cross sections for the resonance 2p(sup)4 (sup 3)P-2p(sup 3)3s (sup 3)S(sup 0), 2p(sup 4) (sup 3)P-2p(sup 3)3d (sup 3)D(sup 0), 2p4 (sup 3)P-2p(sup 3)3s (sup 3)D(sup 0), 2p(sup 4) (sup 3)P-2p(sup 3)3s (sup 3)P(sup 0) and 2p(sup 4) (sup 3)P-2s2p(sup 5) (sup 3)P(sup 0) transitions have been calculated by using the R matrix with a pseudostates approach for incident electron energies from near threshold to 100 eV. The excitation of these transition sgives rise to strong atomic oxygen emission features at 1304, 1027, 989, 878, and 792 Angstrom in the spectra of several planetary atmospheres. We included 22 spectroscopic bound and autoionizing states and 30 pseudostates in the close-coupling expansion. The target wave functions are chosen to properly account for the important correlation and relaxation effects. The effect of coupling to the continuum is included through the use of pseudostates. The contribution of the ionization continuum is significant for resonance transitions. Measured absolute direct excitation cross sections of 0 I are reported by experimental groups from the Jet Propulsion Laboratory and Johns Hopkins University. Good agreement is noted for the 2p(sup)4 (sup 3)P-2p(sup 3)3s (sup 3)S(sup 0) transition (lambda 1304 Ang) with measured cross sections from both groups that agree well with each other. There is disagreement between experiments for other transitions. Our results support the measured cross sections from the Johns Hopkins University for the 2p(sup 4) (sup 3)P-2p(sup 3)3d (sup 3)D(sup 0) and 2p4 (sup 3)P-2p(sup 3)3s (sup 3)D(sup 0) transitions, while for the 2p4 (sup 3)P-2p(sup 3)3s (sup 3)D(sup 0) transition the agreement is switched to the measured cross sections from the Jet Propulsion Laboratory.

  15. Measurement of the population densities in Gd atomic vapor using diode laser absorption spectroscopy in UV transitions

    International Nuclear Information System (INIS)

    Kwon, Duck Hee; Jung, E. C.; Ko, Kwang Hoon; Kim, Tack Soo

    2003-01-01

    We report on the ultraviolet laser absorption spectroscopy of atomic Gd at 394-554 nm where two transition lines are place very closely by using a frequency-doubled beam of external-cavity diode laser (ECDL). One is from 999.121 to 26337.071 cm -1 and the other from 0 to 25337.755 cm -1 . If two transition lines are placed closely within a continuous fine tuning range, the real-time measurement of the atomic excitation temperature is possible without any significant time consumption because at least two transition lines originating from different low-lying energy levels need to be investigated for the Boltzmann-plot. Since the spectral difference between the two transitions is only about 0.195 cm -1 (5.85 GHz), it is possible to record both the absorption spectra simultaneously as shown in Fig. 1. But the transition probabilities (or oscillator strengths) of these lines have not been measured accurately yet to the best of our knowledge. We report on the newly measured transition probabilities by analyzing their absorption spectra at known vapor density conditions. The simultaneous measurement of the atomic excitation temperature and the vapor density demonstrated. In addition we present another ultraviolet laser absorption spectroscopy of atomic Gd at 403.540 nm by means of a commercial blue diode laser and investigate the characteristics of the blue diode laser as well.

  16. Oligomeric rare-earth metal cluster complexes with endohedral transition metal atoms

    Energy Technology Data Exchange (ETDEWEB)

    Steinberg, Simon; Zimmermann, Sina; Brühmann, Matthias; Meyer, Eva; Rustige, Christian; Wolberg, Marike; Daub, Kathrin; Bell, Thomas; Meyer, Gerd, E-mail: gerd.meyer@uni-koeln.de

    2014-11-15

    Comproportionation reactions of rare-earth metal trihalides (RX{sub 3}) with the respective rare-earth metals (R) and transition metals (T) led to the formation of 22 oligomeric R cluster halides encapsulating T, in 19 cases for the first time. The structures of these compounds were determined by single-crystal X-ray diffraction and are composed of trimers ((T{sub 3}R{sub 11})X{sub 15}-type, P6{sub 3}/m), tetramers ((T{sub 4}R{sub 16})X{sub 28}(R{sub 4}) (P-43m), (T{sub 4}R{sub 16})X{sub 20} (P4{sub 2}/nnm), (T{sub 4}R{sub 16})X{sub 24}(RX{sub 3}){sub 4} (I4{sub 1}/a) and (T{sub 4}R{sub 16})X{sub 23} (C2/m) types of structure) and pentamers ((Ru{sub 5}La{sub 14}){sub 2}Br{sub 39}, Cc) of (TR{sub r}){sub n} (n=2–5) clusters. These oligomers are further enveloped by inner (X{sup i}) as well as outer (X{sup a}) halido ligands, which possess diverse functionalities and interconnect like oligomers through i–i, i–a and/or a–i bridges. The general features of the crystal structures for these new compounds are discussed and compared to literature entries as well as different structure types with oligomeric T centered R clusters. Dimers and tetramers originating from the aggregation of (TR{sub 6}) octahedra via common edges are more frequent than trimers and pentamers, in which the (TR{sub r}) clusters share common faces. - Graphical abstract: Rare earth-metal cluster complexes with endohedral transition metal atoms (TR{sub 6}) may connect via common edges or faces to form dimers, trimers, tetramers and pentamers of which the tetramers are the most prolific. Packing effects and electron counts play an important role. - Highlights: • Rare-earth metal cluster complexes encapsulate transition metal atoms. • Oligomers are built via connection of octahedral clusters via common edges or faces. • Dimers through pentamers with closed structures are known. • Tetramers including a tetrahedron of endohedral atoms are the most prolific.

  17. Atom

    International Nuclear Information System (INIS)

    Auffray, J.P.

    1997-01-01

    The atom through centuries, has been imagined, described, explored, then accelerated, combined...But what happens truly inside the atom? And what are mechanisms who allow its stability? Physicist and historian of sciences, Jean-Paul Auffray explains that these questions are to the heart of the modern physics and it brings them a new lighting. (N.C.)

  18. Conformality lost

    International Nuclear Information System (INIS)

    Kaplan, David B.; Lee, Jong-Wan; Son, Dam T.; Stephanov, Mikhail A.

    2009-01-01

    We consider zero-temperature transitions from conformal to nonconformal phases in quantum theories. We argue that there are three generic mechanisms for the loss of conformality in any number of dimensions: (i) fixed point goes to zero coupling, (ii) fixed point runs off to infinite coupling, or (iii) an IR fixed point annihilates with a UV fixed point and they both disappear into the complex plane. We give both relativistic and nonrelativistic examples of the last case in various dimensions and show that the critical behavior of the mass gap behaves similarly to the correlation length in the finite temperature Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions, ξ∼exp(c/|T-T c | 1/2 ). We speculate that the chiral phase transition in QCD at large number of fermion flavors belongs to this universality class, and attempt to identify the UV fixed point that annihilates with the Banks-Zaks fixed point at the lower end of the conformal window.

  19. Long Spin-Relaxation Times in a Transition-Metal Atom in Direct Contact to a Metal Substrate.

    Science.gov (United States)

    Hermenau, Jan; Ternes, Markus; Steinbrecher, Manuel; Wiesendanger, Roland; Wiebe, Jens

    2018-03-14

    Long spin-relaxation times are a prerequisite for the use of spins in data storage or nanospintronics technologies. An atomic-scale solid-state realization of such a system is the spin of a transition-metal atom adsorbed on a suitable substrate. For the case of a metallic substrate, which enables the direct addressing of the spin by conduction electrons, the experimentally measured lifetimes reported to date are on the order of only hundreds of femtoseconds. Here, we show that the spin states of iron atoms adsorbed directly on a conductive platinum substrate have a surprisingly long spin-relaxation time in the nanosecond regime, which is comparable to that of a transition metal atom decoupled from the substrate electrons by a thin decoupling layer. The combination of long spin-relaxation times and strong coupling to conduction electrons implies the possibility to use flexible coupling schemes to process the spin information.

  20. Computerization of atomic level and transition data for the first and second ionization states of the elements hydrogen through phosphorous

    International Nuclear Information System (INIS)

    Henry, E.A.

    1976-01-01

    A computerized data base of atomic energy levels and atomic transition data has been developed from data published by the National Bureau of Standards. These data are of potential use for laser application. The MASTER CONTROL data-base management system is used. These computerized data can be requested from the ERDA Computer Program Exchange and Information Center of the Argonne National Laboratory or from the National Technical Information Service of the U.S. Department of Commerce

  1. Atomic transition energies and the variation of the fine-structure constant α

    International Nuclear Information System (INIS)

    Borschevsky, Anastasia; Eliav, Ephraim; Ishikawa, Yasuyuki; Kaldor, Uzi

    2006-01-01

    Relativistic energy shifts of atomic excitation energies, showing the dependence of these energies on the value of the fine-structure constant α, are needed to extract past changes in α from spectra of distant quasars. These shifts are calculated by the Fock-space coupled cluster method and its extrapolated intermediate Hamiltonian extension, which allow high-accuracy treatment of electron correlation. The accuracy of the method is tested by comparing 33 transition energies in heavy atoms (obtained with the laboratory α) with experiment; the average error is 258 cm -1 , and the largest error is 711 cm -1 . This may be compared with an average error of 432 cm -1 and a maximum error of 2150 cm -1 in the work of Dzuba et al., who reported most of the available energy shift calculations. The enhanced accuracy is due to more extensive inclusion of electron correlation. To obtain the energy shifts, we repeated the calculations with different values of α (within 0.1% of the current value). Our shifts differ by up to 30% from the values given by Dzuba et al., with an average difference of 9%. Based on the better quality of the present-day excitation energies, we believe the energy shifts reported here are more accurate than earlier work

  2. Elastic fields, dipole tensors, and interaction between self-interstitial atom defects in bcc transition metals

    Science.gov (United States)

    Dudarev, S. L.; Ma, Pui-Wai

    2018-03-01

    Density functional theory (DFT) calculations show that self-interstitial atom (SIA) defects in nonmagnetic body-centered-cubic (bcc) metals adopt strongly anisotropic configurations, elongated in the direction [S. Han et al., Phys. Rev. B 66, 220101 (2002), 10.1103/PhysRevB.66.220101; D. Nguyen-Manh et al., Phys. Rev. B 73, 020101 (2006), 10.1103/PhysRevB.73.020101; P. M. Derlet et al., Phys. Rev. B 76, 054107 (2007), 10.1103/PhysRevB.76.054107; S. L. Dudarev, Annu. Rev. Mater. Res. 43, 35 (2013), 10.1146/annurev-matsci-071312-121626]. Elastic distortions, associated with such anisotropic atomic structures, appear similar to distortions around small prismatic dislocation loops, although the extent of this similarity has never been quantified. We derive analytical formulas for the dipole tensors of SIA defects, which show that, in addition to the prismatic dislocation looplike character, the elastic field of a SIA defect also has a significant isotropic dilatation component. Using empirical potentials and DFT calculations, we parametrize dipole tensors of defects for all the nonmagnetic bcc transition metals. This enables a quantitative evaluation of the energy of elastic interaction between the defects, which also shows that in a periodic three-dimensional simple cubic arrangement of crowdions, long-range elastic interactions between a defect and all its images favor a orientation of the defect.

  3. Theoretical studies of atomic transitions: Progress report, March 15, 1985-March 14, 1988

    International Nuclear Information System (INIS)

    Froese Fischer, C.

    1987-09-01

    Allowed and forbidden transitions have been studied for a number of atomic systems of interest in astrophysics, laser physics, or fusion research. All calculations have been based on the multiconfiguration Hartree-Fock (MCHF) method extended to include relativistic corrections in the Breit-Pauli approximation. The computer codes for this atomic structure software package were transferred to the CRAY supercomputer and modified for more convenient computation. Techniques were developed to enhance the range of problems considered, by either increasing the accuracy of prediction or increasing the complexity of problems considered. An example is the prediction of a bound state for Ca - for which experimental evidence was inconclusive. Several different types of problems have been considered. A study of energy levels and lifetimes of a Rydberg series can given insight into electronic structure and explain deviations from regular behavior, and a number of such studies were performed. With the MCHF + Breit-Pauli approach it has been possible to determine a large portion of a spectrum. In core excited quartets of Na, autoionization along spin-orbit mixing and term dependence were all important in predicting lifetimes in excellent agreement with the most recent experiments. Some photoionization studies were performed which, like autoionization require the calculation of continuum functions. Finally, an attempt was made to combine the MCHF method with many-body perturbation theory so as to build on the strengths of both. 13 refs., 2 figs., 3 tabs

  4. Electron impact excitation of the n = 2 to n = 3 transition in atomic hydrogen near threshold

    Science.gov (United States)

    Hata, J.; Morgan, L. A.; McDowell, M. R. C.

    1980-06-01

    Close-coupling calculations of electron impact excitation of the n = 2 to n = 3 transition of atomic hydrogen at energies below the n = 4 threshold are presented. The algebraic variational close-coupling code of Morgan (1980) with an eighteen-state basis was used to obtain cross sections at eight impact energies from 2.04 to 2.45 eV, and calculations in a six-state close-coupling model were compared with the six-state calculations of Burke et al. (1967). The six-state values are found to be in satisfactory agreement with the exception of the singlet contribution to the 2s-3s transition. Near the n = 3 threshold the cross section obtained in the full calculation is found to be almost a factor of 2 lower than that predicted by Johnson (1972), thus explaining in part the discrepancy between Johnson's results and experiments on hydrogen plasmas. Estimates of rate coefficients based on the cross sections and assuming a Maxwellian velocity distribution, however, are shown to remain in disagreement with experiment.

  5. Transitions from order to disorder in multiple dark and multiple dark-bright soliton atomic clouds

    International Nuclear Information System (INIS)

    Wang, Wenlong; Kevrekidis, P. G.

    2015-01-01

    We have performed a systematic study quantifying the variation of solitary wave behavior from that of an ordered cloud resembling a 'crystalline' configuration to that of a disordered state that can be characterized as a soliton 'gas'. As our illustrative examples, we use both one-component, as well as two-component, one-dimensional atomic gases very close to zero temperature, where in the presence of repulsive interatomic interactions and of a parabolic trap, a cloud of dark (dark-bright) solitons can form in the one- (two-) component system. We corroborate our findings through three distinct types of approaches, namely a Gross-Pitaevskii type of partial differential equation, particle-based ordinary differential equations describing the soliton dynamical system, and Monte Carlo simulations for the particle system. In addition, we define an 'empirical' order parameter to characterize the order of the soliton lattices and study how this changes as a function of the strength of the 'thermally' (i.e., kinetically) induced perturbations. As may be anticipated by the one-dimensional nature of our system, the transition from order to disorder is gradual without, apparently, a genuine phase transition ensuing in the intermediate regime

  6. Chemically assisted release of transition metals in graphite vaporizers for atomic spectrometry

    International Nuclear Information System (INIS)

    Katskov, Dmitri; Darangwa, Nicholas; Grotti, Marco

    2006-01-01

    The processes associated with the vaporization of microgram samples and modifiers in a graphite tube ET AAS were investigated by the example of transition metals. The vapor absorption spectra and vaporization behavior of μg-amounts Cd, Zn, Cu, Ag, Au, Ni, Co, Fe, Mn and Cr were studied using the UV spectrometer with CCD detector, coupled with a continuum radiation source. The pyrocoated, Ta or W lined tubes, with Ar or He as internal gases, and filter furnace were employed in the comparative experiments. It was found that the kinetics of atomic vapor release changed depending on the specific metal-substrate-gas combination; fast vaporization at the beginning was followed by slower 'tailing.' The absorption continuum, overlapped by black body radiation at longer wavelengths, accompanied the fast vaporization mode for all metals, except Cd and Zn. The highest intensity of the continuum was observed in the pyrocoated tube with Ar. For Cu and Ag the molecular bands overlapped the absorption continuum; the continuum and bands were suppressed in the filter furnace. It is concluded that the exothermal interaction of sample vapor with the material of the tube causes the energy evolution in the gas phase. The emitted heat is dispersed near the tube wall in the protective gas and partially transferred back to the surface of the sample, thus facilitating the vaporization. The increased vapor flow causes over-saturation and gas-phase condensation in the absorption volume at some distance from the wall, where the gas temperature is not affected by the reaction. The condensation is accompanied by the release of phase transition energy via black body radiation and atomic emission. The particles of condensate and molecular clusters cause the scattering of light and molecular absorption; slow decomposition of the products of the sample vapor-substrate reaction produces the 'tailing' of atomic absorption signal. The interaction of graphite with metal vapor or oxygen, formed in the

  7. Anderson Transition of Cold Atoms with Synthetic Spin-Orbit Coupling in Two-Dimensional Speckle Potentials

    Science.gov (United States)

    Orso, Giuliano

    2017-03-01

    We investigate the metal-insulator transition occurring in two-dimensional (2D) systems of noninteracting atoms in the presence of artificial spin-orbit interactions and a spatially correlated disorder generated by laser speckles. Based on a high order discretization scheme, we calculate the precise position of the mobility edge and verify that the transition belongs to the symplectic universality class. We show that the mobility edge depends strongly on the mixing angle between Rashba and Dresselhaus spin-orbit couplings. For equal couplings a non-power-law divergence is found, signaling the crossing to the orthogonal class, where such a 2D transition is forbidden.

  8. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg

    International Nuclear Information System (INIS)

    Hay, P.J.; Wadt, W.R.

    1985-01-01

    Ab initio effective core potentials (ECP's) have been generated to replace the Coulomb, exchange, and core-orthogonality effects of the chemically inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series relative ECP's have been generated which also incorporate the mass--velocity and Darwin relativistic effects into the potential. The ab initio ECP's should facilitate valence electron calculations on molecules containing transition-metal atoms with accuracies approaching all-electron calculations at a fraction of the computational cost. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3d,4s,4p), (4d,5s,5p), and (5d,6s,6p) orbitals of the first, second, and third transition series atoms, respectively. All-electron and valence-electron atomic excitation energies are also compared for the low-lying states of Sc--Hg, and the valence-electron calculations are found to reproduce the all-electron excitation energies (typically within a few tenths of an eV)

  9. Influence of a transition metal atom on the geometry and electronic structure of Mg and Mg-H clusters

    International Nuclear Information System (INIS)

    Siretskiy, M.Yu.; Shelyapina, M.G.; Fruchart, D.; Miraglia, S.; Skryabina, N.E.

    2009-01-01

    We report on the study of (MgH 2 ) n + M complexes (M = Ti or Ni) carried out within the framework of the cluster density functional theory (DFT) method. The influence of such transition metal atoms on the cluster geometry and electronic structure is discussed considering the stability of MgH 2 hydride.

  10. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

    Directory of Open Access Journals (Sweden)

    MacKerell Alexander D

    2007-03-01

    Full Text Available Abstract Background The N-terminal SH2 domain (N-SH2 of the non-receptor tyrosine phosphatase SHP-2 is involved both in localization of SHP-2 by recognition of phosphotyrosine (pY peptides and self-inhibition of SHP-2 phosphatase activity through the formation of a protein – protein interface with the phosphatase domain. Mutations that disrupt this interface break the coupling between pY-peptide binding cleft conformation and self-inhibition, thereby increasing both SHP-2 phosphatase activity and pY-peptide binding affinity, and are associated with the congenital condition Noonan syndrome and various pediatric leukemias. To better characterize the molecular process involved in N-SH2 pY-dependent binding, we have applied explicit-solvent molecular dynamics simulations to study the closed-to-open transition of the N-SH2 pY-peptide binding cleft. Results The existence of stable conformations in the left-handed helical and the extended regions of Tyr66 φ/ψ space prevent rapid interconversion of the backbone and create a conformational switch such that Tyr66 in a left-handed helical backbone conformation results in an open cleft and in an extended backbone conformation results in a closed cleft. The stable conformations arise from deep, well-localized free-energy minima in the left-handed helical and extended regions of the Tyr66 φ/ψ map. Changing the Tyr66 backbone conformation from extended to left-handed helical induces a closed-to-open transition in the cleft, and the reverse change in backbone conformation induces the reverse, open-to-closed transition. In the open-cleft state, weak solvent-exposed interactions involving the sidechains of Tyr66, Asp40, Lys55, and Gln57 serve to anchor the Tyr66 sidechain to the surface of the protein and away from the binding cleft entrance, thereby facilitating pY-peptide access to the binding cleft. Conclusion The simulations point to a regulatory role for Tyr66 and surrounding residues in SHP-2 function

  11. Ultrabright multikilovolt x-ray source: saturated amplification on noble gas transition arrays from hollow atom states

    Science.gov (United States)

    Rhodes, Charles K.; Boyer, Keith

    2004-02-17

    An apparatus and method for the generation of ultrabright multikilovolt x-rays from saturated amplification on noble gas transition arrays from hollow atom states is described. Conditions for x-ray amplification in this spectral region combine the production of cold, high-Z matter, with the direct, selective multiphoton excitation of hollow atoms from clusters using ultraviolet radiation and a nonlinear mode of confined, self-channeled propagation in plasmas. Data obtained is consistent with the presence of saturated amplification on several transition arrays of the hollow atom Xe(L) spectrum (.lambda..about.2.9 .ANG.). An estimate of the peak brightness achieved is .about.10.sup.29 .gamma..multidot.s.sup.-1.multidot.mm.sup.-2.multidot.mr.sup.-2 (0.1% Bandwidth).sup.-1, that is .about.10.sup.5 -fold higher than presently available synchotron technology.

  12. Multiplicity dependence of matrix-induced frequency shifts for atomic transitions of the group 12 metals in rare gas solids

    International Nuclear Information System (INIS)

    Laursen, S.L.; Cartland, H.E.

    1991-01-01

    Atomic resonances of the group 12 metal atoms, Hg, Cd, and Zn, undergo frequency shifts from the gas phase atomic line when trapped in rare gas matrices of Ar, Kr, and Xe at 12 K. As expected, the shifts are approximately linear in polarizability of the rare gas, but the slope of this line depends on whether the transition in question is 1 P 1 left-arrow 1 S 0 or 3 P 1 left-arrow 1 S 0 . Thus the matrix-induced frequency shift is dependent on the singlet or triplet nature of the excited state as well as on the matrix material. This dependence on multiplicity is discussed in terms of interactions between the excited-state atomic orbitals and the matrix. The results are compared to matrix studies of other metals and to related gas-phase work on diatomic van der Waals complexes of group 12 metals with rare gases

  13. Investigating the particle to fibre transition threshold during electrohydrodynamic atomization of a polymer solution

    Energy Technology Data Exchange (ETDEWEB)

    Husain, O.; Lau, W.; Edirisinghe, M.; Parhizkar, M., E-mail: maryam.parhizkar.09@ucl.ac.uk

    2016-08-01

    Electrohydrodynamic atomization (EHDA) is a key research area for producing micro and nano-sized structures. This process can be categorized into two main operating regimes: electrospraying for particle generation and electrospinning for fibre production. Producing particles/fibres of the desired size or morphology depends on two main factors; properties of the polymeric solution used and the processing conditions including flow rate, applied voltage and collection distance. In this work the particle-fibre transition region was analyzed by changing the polymer concentration of PLGA poly (lactic-co-glycolic acid) in acetone between 2 and 25 wt%. Subsequently the processing conditions were adjusted to study the optimum transition parameters. Additionally the EHDA configuration was also modified by adding a metallic plate to observe the deposition area. The diameter and the distance of the plate from the capillary tip were adjusted to investigate variations in particle and fibre morphologies as well. It was found that complete transition from particles to fibres occurs at 20 wt% indicating concentration to be the dominant criterion. Low flow rates yielded fibres without beads. However the applied voltage and distance between the tip of the nozzle jetting the polymer solution and collector (working distance) did not yield definitive results. Reducing the collector distance and increasing applied voltages produces smooth as well as beaded fibres. Addition of a metal plate reduces particle size by ~ 1 μm; the fibre size increases especially with increasing plate diameter while bead density and size reduces when the disc is fixed closer to the capillary tip. Additionally, the deposition area is reduced by 70% and 57% with the addition of metal plates of 30 mm and 60 mm, respectively. The results indicate that a metal plate can be utilized further to tune the particle/fibre size and morphology and this also significantly increases the yield of EHDA process which is

  14. Measurement of dipole-moment in atomic transitions under strong external magnetic field

    International Nuclear Information System (INIS)

    Nittoh, Koichi; Kuwako, Akira; Ikehara, Tadashi; Yoshida, Tadashi; Watanabe, Takasi; Yoguchi, Itaru; Suzuki, Kazuhiro.

    1996-01-01

    Obtaining an accurate value of the electric dipole moment μ is essential in the fields of laser application technologies. A direct way of measuring the electric dipole moment μ is to observe the Rabi-oscillation which manifests itself in the coherent photo-excitation behavior of atoms. In the case of the elements which have large angular momenta, identifying the Rabi-oscillation in their excitation behavior becomes rather difficult. We proposed an accurate and straightforward method of determining the electric-dipole moment μ between multi-fold degenerate levels. The point is to remove the degeneracy by applying an external magnetic field with the aid of the Zeeman effect and, then, to realize a degeneration free coherent excitation. As a result, we can observe the Rabi-oscillations explicitly in the excitation υs. laser-fluence curves. The present method provides a reliable basis of experimental determination of μ. As an example, we applied the present method to a transition to 0-17,362 cm -1 level in uranium and obtained the value μ=0.86±0.06 (Debye). (author)

  15. MODELING THE ATOMIC-TO-MOLECULAR TRANSITION AND CHEMICAL DISTRIBUTIONS OF TURBULENT STAR-FORMING CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)

    2013-06-10

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.

  16. Precision spectroscopy of the 2S-4P{sub 1/2} transition in atomic hydrogen on a cold thermal beam of optically excited 2S atoms

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Axel; Kolachevsky, Nikolai; Alnis, Janis; Yost, Dylan C.; Matveev, Arthur; Parthey, Christian G.; Pohl, Randolf; Udem, Thomas [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Khabarova, Ksenia [FSUE ' VNIIFTRI' , 141570 Moscow (Russian Federation); Haensch, Theodor W. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet, 80799 Muenchen (Germany)

    2013-07-01

    The 'proton size puzzle', i.e. the discrepancy between the values for the proton r.m.s. charge radius deduced from precision spectroscopy of atomic hydrogen and electron-proton-scattering on one side and the value deduced from muonic hydrogen spectroscopy on the other side, has been persisting for more than two years now. Although huge efforts have been put into trying to resolve this discrepancy from experimental and theoretical side, no convincing argument could be found so far. In this talk, we report on a unique precision spectroscopy experiment on atomic hydrogen, which is aiming to bring some light to the hydrogen part of the puzzle: In contrast to any previous high resolution experiment probing a transition frequency between the meta-stable 2S state and a higher lying nL state (n=3,4,6,8,12, L=S,P,D), our measurement of the 2S-4P{sub 1/2} transition frequency is the first experiment being performed on a cold thermal beam of hydrogen atoms optically excited to the 2S state. We will discuss how this helps to efficiently suppresses leading systematic effects of previous measurements and present the preliminary results we obtained so far.

  17. Optically trapped atom interferometry using the clock transition of large {sup 87}Rb Bose-Einstein condensates

    Energy Technology Data Exchange (ETDEWEB)

    Altin, P A; McDonald, G; Doering, D; Debs, J E; Barter, T H; Close, J D; Robins, N P [Department of Quantum Science, ARC Centre of Excellence for Quantum Atom Optics, the Australian National University, ACT 0200 (Australia); Haine, S A [School of Mathematics and Physics, ARC Centre of Excellence for Quantum-Atom Optics, The University of Queensland, Queensland 4072 (Australia); Hanna, T M [Joint Quantum Institute, National Institute of Standards and Technology and University of Maryland, 100 Bureau Drive, Stop 8423, Gaithersburg, MD 20899-8423 (United States); Anderson, R P, E-mail: paul.altin@anu.edu.au [School of Physics, Monash University, VIC 3800 (Australia)

    2011-06-15

    We present a Ramsey-type atom interferometer operating with an optically trapped sample of 10{sup 6} Bose-condensed {sup 87}Rb atoms. We investigate this interferometer experimentally and theoretically with an eye to the construction of future high precision atomic sensors. Our results indicate that, with further experimental refinements, it will be possible to produce and measure the output of a sub-shot-noise-limited, large atom number BEC-based interferometer. The optical trap allows us to couple the |F=1, m{sub F}=0){yields}|F=2, m{sub F}=0) clock states using a single photon 6.8 GHz microwave transition, while state selective readout is achieved with absorption imaging. We analyse the process of absorption imaging and show that it is possible to observe atom number variance directly, with a signal-to-noise ratio ten times better than the atomic projection noise limit on 10{sup 6} condensate atoms. We discuss the technical and fundamental noise sources that limit our current system, and present theoretical and experimental results on interferometer contrast, de-phasing and miscibility.

  18. Electronic Transitions in Conformationally Controlled Tetrasilanes with a Wide Range of SiSiSiSi Dihedral Angles

    Czech Academy of Sciences Publication Activity Database

    Tsuji, H.; Fogarty, H. A.; Ehara, M.; Fukuda, R.; Casher, D. L.; Tamao, K.; Nakatsuji, H.; Michl, Josef

    2014-01-01

    Roč. 20, č. 30 (2014), s. 9431-9441 ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : conformational effects * electronic spectra * SAC-CI calculations * silicon * UV/Vis spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 5.731, year: 2014

  19. Theoretical studies of atomic transitions. Progress report, March 15, 1985-March 14, 1986

    International Nuclear Information System (INIS)

    Fischer, C.F.

    1986-01-01

    A brief description of the research program for atomic studies is given. The program includes an effort to combine the Multi-Configuration Hartree-Fock (MCHF) method with Many-Body Perturbation Theory and the development of a database system for atomic data generated by the atomic structure package. 6 refs

  20. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Bhardwaj, Anshul [Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107 (United States); Casjens, Sherwood R. [University of Utah School of Medicine, Salt Lake City, UT 84112 (United States); Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu [Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107 (United States)

    2014-02-01

    This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

  1. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

    International Nuclear Information System (INIS)

    Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino

    2014-01-01

    This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility

  2. Diode laser operating on an atomic transition limited by an isotope ⁸⁷Rb Faraday filter at 780 nm.

    Science.gov (United States)

    Tao, Zhiming; Hong, Yelong; Luo, Bin; Chen, Jingbiao; Guo, Hong

    2015-09-15

    We demonstrate an extended cavity Faraday laser system using an antireflection-coated laser diode as the gain medium and the isotope (87)Rb Faraday anomalous dispersion optical filter (FADOF) as the frequency selective device. Using this method, the laser wavelength works stably at the highest transmission peak of the isotope (87)Rb FADOF over the laser diode current from 55 to 140 mA and the temperature from 15°C to 35°C. Neither the current nor the temperature of the laser diode has significant influence on the output frequency. Compared with previous extended cavity laser systems operating at frequencies irrelevant to spectacular atomic transition lines, the laser system realized here provides a stable laser source with the frequency operating on atomic transitions for many practical applications.

  3. Roughness of the SiC/SiO{sub 2} vicinal interface and atomic structure of the transition layers

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Peizhi; Li, Guoliang; Duscher, Gerd, E-mail: gduscher@utk.edu [Department of Materials Science and Engineering, The University of Tennessee, Knoxville, Tennessee 37996 (United States); Sharma, Yogesh K.; Ahyi, Ayayi C.; Isaacs-Smith, Tamara; Williams, John R.; Dhar, Sarit [Department of Physics, Auburn University, Auburn, Alabama 36849 (United States)

    2014-11-01

    The SiC/SiO{sub 2} interface is generally considered to be the cause for the reduced electron mobility of SiC power devices. Previous studies have shown a correlation between the mobility and the transition layer width at the SiC/SiO{sub 2} interface. The authors investigated this interface with atomic resolution Z-contrast imaging and electron energy-loss spectroscopy, and discovered that this transition region was due to the roughness of the vicinal interface. The roughness of a vicinal interface consisted of atomic steps and facets deviating from the ideal off-axis cut plane. The authors conclude that this roughness is limiting the mobility in the channels of SiC MOSFETs.

  4. Transition metal atoms absorbed on MoS2/h-BN heterostructure: stable geometries, band structures and magnetic properties.

    Science.gov (United States)

    Wu, Yanbing; Huang, Zongyu; Liu, Huating; He, Chaoyu; Xue, Lin; Qi, Xiang; Zhong, Jianxin

    2018-06-15

    We have studied the stable geometries, band structures and magnetic properties of transition-metal (V, Cr, Mn, Fe, Co and Ni) atoms absorbed on MoS2/h-BN heterostructure systems by first-principles calculations. By comparing the adsorption energies, we find that the adsorbed transition metal (TM) atoms prefer to stay on the top of Mo atoms. The results of the band structure without spin-orbit coupling (SOC) interaction indicate that the Cr-absorbed systems behave in a similar manner to metals, and the Co-absorbed system exhibits a half-metallic state. We also deduce that the V-, Mn-, Fe-absorbed systems are semiconductors with 100% spin polarization at the HOMO level. The Ni-absorbed system is a nonmagnetic semiconductor. In contrast, the Co-absorbed system exhibits metallic state, and the bandgap of V-absorbed system decreases slightly according to the SOC calculations. In addition, the magnetic moments of all the six TM atoms absorbed on the MoS2/h-BN heterostructure systems decrease when compared with those of their free-standing states.

  5. Outer-shell transitions in collisions between multiply charged ions and atoms

    International Nuclear Information System (INIS)

    Bloemen, E.W.P.

    1980-01-01

    The study of collisions between multiply charged ions and atoms (molecules) is of importance in different areas of research. Usually, the most important process is capture of an electron from the target atom into the projectile ion. In most cases the electron goes to an excited state of the projectile ion. These electron capture processes are studied. The author also studied direct excitation of the target atom and of the projectile ion. (Auth.)

  6. Holographic research on phase transitions for a five dimensional AdS black hole with conformally coupled scalar hair

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hui-Ling, E-mail: LHL51759@126.com [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu, 610054 (China); College of Physics Science and Technology, Shenyang Normal University, Shenyang 110034 (China); Yang, Shu-Zheng, E-mail: szyangcwnu@126.com [Institute of Theoretical Physics, China West Normal University, Nanchong 637002 (China); Zu, Xiao-Tao, E-mail: xtzu@uestc.edu.cn [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu, 610054 (China)

    2017-01-10

    In the framework of holography, we survey the phase structure for a higher dimensional hairy black hole including the effects of the scalar field hair. It is worth emphasizing that, not only black hole entropy, but also entanglement entropy and two point correlation function exhibit the Van der Waals-like phase transition in a fixed scalar charge ensemble. Furthermore, by making use of numerical computation, we show that the Maxwell's equal area law is valid for the first order phase transition. In addition, we also discuss how the hair parameter affects the black hole's phase transition.

  7. Light-pulse atom interferometric device

    Science.gov (United States)

    Biedermann, Grant; McGuinness, Hayden James Evans; Rakholia, Akash; Jau, Yuan-Yu; Schwindt, Peter; Wheeler, David R.

    2016-03-22

    An atomic interferometric device useful, e.g., for measuring acceleration or rotation is provided. The device comprises at least one vapor cell containing a Raman-active chemical species, an optical system, and at least one detector. The optical system is conformed to implement a Raman pulse interferometer in which Raman transitions are stimulated in a warm vapor of the Raman-active chemical species. The detector is conformed to detect changes in the populations of different internal states of atoms that have been irradiated by the optical system.

  8. Magnetic properties of Mg12O12 nanocage doped with transition metal atoms (Mn, Fe, Co and Ni): DFT study

    Science.gov (United States)

    Javan, Masoud Bezi

    2015-07-01

    Binding energy of the Mg12O12 nanocage doped with transition metals (TM=Mn, Fe, Co and Ni) in endohedrally, exohedrally and substitutionally forms were studied using density functional theory with the generalized gradient approximation exchange-correlation functional along 6 different paths inside and outside of the Mg12O12 nanocage. The most stable structures were determined with full geometry optimization near the minimum of the binding energy curves of all the examined paths inside and outside of the Mg12O12 nanocage. The results reveal that for all stable structures, the Ni atom has a larger binding energy than the other TM atoms. It is also found that for all complexes additional peaks contributed by TM-3d, 4s and 4p states appear in the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) gap of the host MgO cluster. The mid-gap states are mainly due to the hybridization between TM-3d, 4s and 4p orbitals and the cage π orbitals. The magnetic moment of the endohedrally doped TM atoms in the Mg12O12 are preserved to some extent due to the interaction between the TM and Mg12O12 nanocage, in contrast to the completely quenched magnetic moment of the Fe and Ni atoms in the Mg11(TM)O12 complexes. Furthermore, charge population analysis shows that charge transfer occurs from TM atom to the cage for endohedrally and substitutionally doping.

  9. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

  10. Electronic and magnetic properties of 1T-HfS{sub 2} by doping transition-metal atoms

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xu, E-mail: zhaoxu@htu.cn [College of Physics and Electronic Engineering, Henan Normal University, Xinxiang, Henan 453007 (China); Wang, Tianxing; Wang, Guangtao [College of Physics and Electronic Engineering, Henan Normal University, Xinxiang, Henan 453007 (China); Dai, Xianqi [College of Physics and Electronic Engineering, Henan Normal University, Xinxiang, Henan 453007 (China); Department of Physics, Zhengzhou Normal University, Zhengzhou, Henan 450044 (China); Xia, Congxin [College of Physics and Electronic Engineering, Henan Normal University, Xinxiang, Henan 453007 (China); Yang, Lin [School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007 (China)

    2016-10-15

    Highlights: • Pristine 1T-HfS{sub 2} is a semiconductor with indirect gaps of 1.250 eV • Magnetism can be observed for V, Cr, Mn, Fe, Co, and Cu doping. • Strong p–d hybridization was found between TM 3d orbitals and S 3p orbitals. • V-doped 1T-HfS{sub 2} is ideal for spin injection. - Abstract: We explored the electronic and magnetic properties of 1T-HfS{sub 2} doped by transition metal (TM) atom using the first-principles calculation. We doped the transition metal atoms from the IIIB to VIB groups in nonmagnetic 1T-HfS{sub 2}. Numerical results show that the pristine 1T-HfS{sub 2} is a semiconductor with indirect gaps of 1.250 eV. Magnetism can be observed for V, Cr, Mn, Fe, Co, and Cu doping. The polarized charges mainly arise from the localized 3d electrons of the TM atom. The strong p–d hybridization was found between the 3d orbitals of TM and 3p orbitals of S. The substituted 1T-HfS{sub 2} can be a metal, semiconductor or half-metal. Analysis of the band structure and magnetic properties indicates that TM-doped HfS{sub 2} (TM = V, Fe, Cu) are promising systems to explore two-dimensional diluted magnetic semiconductors. The formation energy calculations also indicate that it is energetically favorable and relatively easier to incorporate transition metal atom into the HfS{sub 2} under S-rich experimental conditions. In contrast, V-doped HfS{sub 2} has relatively wide half-metallic gap and low formation energy. So V-doped 1T-HfS{sub 2} is ideal for spin injection, which is important for application in semiconductor spintronics.

  11. TRANSITION METAL CATALYSIS IN CONTROLLED RADICAL POLYMERIZATION: ATOM TRANSFER RADICAL POLYMERIZATION. (R826735)

    Science.gov (United States)

    Novel and diversified macromolecular structures, which include polymers with designed topologies (top), compostions (middle), and functionalities (bottom), can be prepared by atom transfer radical polymerization processes. These polymers can be synthesized from a large variety of...

  12. Towards Precision Measurement of the 21S0-31D2 Two-Photon Transition in Atomic Helium

    Science.gov (United States)

    Huang, Yi-Jan; Guan, Yu-Chan; Suen, Te-Hwei; Wang, Li-Bang; Shy, Jow-Tsong

    2017-04-01

    We intend to accurately measure the frequency for 2S-3D two-photon transition and to deduce the 2S ionization energy to an accuracy below 100 kHz from the theoretical calculation of the 3D state. In this talk, we present a precision measurement of the 21S0 -31D2 two-photon transition in atomic helium at 1009 nm. A master oscillator power amplifier (MOPA) is seeded by an external cavity diode laser (ECDL) is constructed to generate more than 700 mW laser power with TEM00 beam profile at 1009 nm. To observe the two-photon transition, a helium cell is placed inside a power enhancement optical cavity and the helium atoms at 21S metastable level are prepared by a pulsed RF discharge and monitor the 668 nm 31D2 to 21P1 fluorescence after RF discharge is turned off . The absolute frequency metrology of the ECDL is carried out by an Er-fiber optical frequency comb (OFC). The two-photon spectrum is obtained by tuning the repetition frequency of the OFC. The 21S0-31D2 frequency is determined to be 594414291.967 (80) MHz in He-4. More results will be presented at the annual meeting.

  13. Calculation of probabilities of rotational transitions of two-atom molecules in the collision with heavy particles

    International Nuclear Information System (INIS)

    Vargin, A.N.; Ganina, N.A.; Konyukhov, V.K.; Selyakov, V.I.

    1975-01-01

    The problem of calculation of collisional probabilities of rotational transitions (CPRT) in molecule-molecule and molecule-atom interactions in a three-dimensional space has been solved in this paper. A quasiclassical approach was used. The calculation of collisional probabilities of rotational transitions trajectory was carried out in the following way. The particle motion trajectory was calculated by a classical method and the time dependence of the perturbation operator was obtained, its averaging over wave functions of initial and finite states produced CPRT. The classical calculation of the molecule motion trajectory was justified by triviality of the de Broglie wavelength, compared with characteristic atomic distances, and by triviality of a transfered rotational quantum compared with the energy of translational motion of particles. The results of calculation depend on the chosen interaction potential of collisional particles. It follows from the Messy criterion that the region of nonadiabaticity of interaction may be compared with internuclear distances of a molecule. Therefore, for the description of the interaction a short-range potential is required. Analytical expressions were obtained appropriate for practical calculations for one- and two-quantum rotational transitions of diatomic molecules. The CPRT was averaged over the Maxwell distribution over velocities and analytical dependences on a gas temperature were obtained. The results of the numerical calculation of probabilities for the HCl-HCl, HCl-He, CO-CO interactions are presented to illustrate the method

  14. Ab initio study of neutral (TiO2)n clusters and their interactions with water and transition metal atoms

    International Nuclear Information System (INIS)

    Çakır, D; Gülseren, O

    2012-01-01

    We have systematically investigated the growth behavior and stability of small stoichiometric (TiO 2 ) n (n = 1-10) clusters as well as their structural, electronic and magnetic properties by using the first-principles plane wave pseudopotential method within density functional theory. In order to find out the ground state geometries, a large number of initial cluster structures for each n has been searched via total energy calculations. Generally, the ground state structures for the case of n = 1-9 clusters have at least one monovalent O atom, which only binds to a single Ti atom. However, the most stable structure of the n = 10 cluster does not have any monovalent O atom. On the other hand, Ti atoms are at least fourfold coordinated for the ground state structures for n ≥ 4 clusters. Our calculations have revealed that clusters prefer to form three-dimensional structures. Furthermore, all these stoichiometric clusters have nonmagnetic ground state. The formation energy and the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap for the most stable structure of (TiO 2 ) n clusters for each n have also been calculated. The formation energy and hence the stability increases as the cluster size grows. In addition, the interactions between the ground state structure of the (TiO 2 ) n cluster and a single water molecule have been studied. The binding energy (E b ) of the H 2 O molecule exhibits an oscillatory behavior with the size of the clusters. A single water molecule preferably binds to the cluster Ti atom through its oxygen atom, resulting an average binding energy of 1.1 eV. We have also reported the interaction of the selected clusters (n = 3, 4, 10) with multiple water molecules. We have found that additional water molecules lead to a decrease in the binding energy of these molecules to the (TiO 2 ) n clusters. Finally, the adsorption of transition metal (TM) atoms (V, Co and Pt) on the n = 10 cluster has been

  15. Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Haruki Nakamura

    2012-02-01

    Full Text Available The phosphorylated kinase-inducible activation domain (pKID adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.

  16. Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption

    Directory of Open Access Journals (Sweden)

    Arundhati Banerjee

    2016-01-01

    Full Text Available Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

  17. Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption.

    Science.gov (United States)

    Banerjee, Arundhati; Ray, Sujay

    2016-01-01

    Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

  18. Steered molecular dynamics simulations of a bacterial type IV pilus reveal characteristics of an experimentally-observed, force-induced conformational transition

    Science.gov (United States)

    Baker, Joseph; Biais, Nicolas; Tama, Florence

    2011-10-01

    Type IV pili (T4P) are long, filamentous structures that emanate from the cellular surface of many infectious bacteria. They are built from a 158 amino acid long subunit called pilin. T4P can grow to many micrometers in length, and can withstand large tension forces. During the infection process, pili attach themselves to host cells, and therefore naturally find themselves under tension. We investigated the response of a T4 pilus to a pulling force using the method of steered molecular dynamics (SMD) simulation. Our simulations expose to the external environment an amino acid sequence initially hidden in the native filament, in agreement with experimental data. Therefore, our simulations might be probing the initial stage of the transition to a force-induced conformation of the T4 pilus. Additional exposed amino acid sequences that might be useful targets for drugs designed to mitigate bacterial infection were also predicted.

  19. CO2 electroreduction performance of a single transition metal atom supported on porphyrin-like graphene: a computational study.

    Science.gov (United States)

    Wang, Zhongxu; Zhao, Jingxiang; Cai, Qinghai

    2017-08-30

    Searching for low-cost, efficient, and stable electrocatalysts for CO 2 electroreduction (CO 2 ER) reactions is highly desirable for the reduction of CO 2 emission and its conversion into useful products, but remains a great challenge. In this work, single transition metal atoms supported on porphyrin-like graphene catalysts, i.e., TMN 4 /graphene, acting as electrocatalysts for CO 2 reduction were explored by means of comprehensive density functional theory (DFT) computations. Our results revealed that these anchored TM atoms possess high stability due to their strong hybridization with the unsaturated N atoms of the substrate and function as the active sites. On the basis of the calculated adsorption strength of CO 2 ER intermediates, we have identified that single Co, Rh, and Ir atoms exhibit superior catalytic activity towards CO 2 reduction. In particular, CH 3 OH is the preferred product of CO 2 ER on the CoN 4 /graphene catalyst with an overpotential of 0.59 V, while the RhN 4 /graphene and IrN 4 /graphene catalysts prefer to reduce CO 2 to CH 2 O with an overpotential of 0.35 and 0.29 V, respectively. Our work may open a new avenue for the development of catalytic materials with high efficiency for CO 2 electroreduction.

  20. Sub-doppler spectroscopy based on the transit relaxation of atomic particles in a thin gas cell

    International Nuclear Information System (INIS)

    Azad, Izmailov

    2011-01-01

    This paper is the review of methods, achievements, and possibilities of the recently elaborated high-resolution laser spectroscopy based on sub-doppler absorption, fluorescence and polarization resonances (on centers of quantum transitions), which arise because of the specific optical selection of comparatively slow-speed atoms or molecules in a thin cell with a rarefied gas. It is considered two following mechanisms of such velocity selection of atomic particles connected with their flight durations between walls of the thin cell : 1) optical pumping of sublevels of the ground atomic term and 2) optical excitation of long-lived metastable quantum levels. Theoretical bases of elaborated spectroscopy methods are presented. In case of the optical pumping mechanism, experimental technique and results on the record of sub-doppler spectral structure of Cs and Rb atoms and on the frequency stabilization of diode lasers by given methods are described. Perspectives of further development and applications of this new direction of the high-resolution spectroscopy are discussed

  1. An investigation of one- versus two-dimensional semiclassical transition state theory for H atom abstraction and exchange reactions.

    Science.gov (United States)

    Greene, Samuel M; Shan, Xiao; Clary, David C

    2016-02-28

    We investigate which terms in Reduced-Dimensionality Semiclassical Transition State Theory (RD SCTST) contribute most significantly in rate constant calculations of hydrogen extraction and exchange reactions of hydrocarbons. We also investigate the importance of deep tunneling corrections to the theory. In addition, we introduce a novel formulation of the theory in Jacobi coordinates. For the reactions of H atoms with methane, ethane, and cyclopropane, we find that a one-dimensional (1-D) version of the theory without deep tunneling corrections compares well with 2-D SCTST results and accurate quantum scattering results. For the "heavy-light-heavy" H atom exchange reaction between CH3 and CH4, deep tunneling corrections are needed to yield 1-D results that compare well with 2-D results. The finding that accurate rate constants can be obtained from derivatives of the potential along only one dimension further validates RD SCTST as a computationally efficient yet accurate rate constant theory.

  2. Conformal Nets II: Conformal Blocks

    Science.gov (United States)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-08-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  3. Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems

    OpenAIRE

    Setiawan, F.; Sengupta, K.; Spielman, I. B.; Sau, Jay D.

    2015-01-01

    We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signat...

  4. Multiconfiguration Hartree--Fock method for atomic energy levels and transition probabilities

    International Nuclear Information System (INIS)

    Fischer, C.F.

    1978-01-01

    The effect of correlation in the motion of electrons in a many-electron system is considered in the theoretical determination of atomic properties. The correlation effects are computed using the configuration interaction. Restriction is made to the discussion of outer processes of neutral atoms or ions of low degree of ionization in which the relativistic effects are small. The first-order theory, the 3p,3d state of Al II, correlation in the 3d/sup n/ shell, and f-values in the presence of cross-overs are discussed. 29 references

  5. Fast, clash-free RNA conformational morphing using molecular junctions.

    Science.gov (United States)

    Héliou, Amélie; Budday, Dominik; Fonseca, Rasmus; van den Bedem, Henry

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  6. Interfacing transitions of different alkali atoms and telecom bands using one narrowband photon pair source

    DEFF Research Database (Denmark)

    Schunk, Gerhard; Vogl, Ulrich; Strekalov, Dmitry V.

    2015-01-01

    Quantum information technology strongly relies on the coupling of optical photons with narrowband quantum systems, such as quantum dots, color centers, and atomic systems. This coupling requires matching the optical wavelength and bandwidth to the desired system, which presents a considerable pro...

  7. Estimation of Enthalpy of Formation of Liquid Transition Metal Alloys: A Modified Prescription Based on Macroscopic Atom Model of Cohesion

    Science.gov (United States)

    Raju, Subramanian; Saibaba, Saroja

    2016-09-01

    The enthalpy of formation Δo H f is an important thermodynamic quantity, which sheds significant light on fundamental cohesive and structural characteristics of an alloy. However, being a difficult one to determine accurately through experiments, simple estimation procedures are often desirable. In the present study, a modified prescription for estimating Δo H f L of liquid transition metal alloys is outlined, based on the Macroscopic Atom Model of cohesion. This prescription relies on self-consistent estimation of liquid-specific model parameters, namely electronegativity ( ϕ L) and bonding electron density ( n b L ). Such unique identification is made through the use of well-established relationships connecting surface tension, compressibility, and molar volume of a metallic liquid with bonding charge density. The electronegativity is obtained through a consistent linear scaling procedure. The preliminary set of values for ϕ L and n b L , together with other auxiliary model parameters, is subsequently optimized to obtain a good numerical agreement between calculated and experimental values of Δo H f L for sixty liquid transition metal alloys. It is found that, with few exceptions, the use of liquid-specific model parameters in Macroscopic Atom Model yields a physically consistent methodology for reliable estimation of mixing enthalpies of liquid alloys.

  8. Density Functional Theory of Open-Shell Systems. The 3d-Series Transition-Metal Atoms and Their Cations.

    Science.gov (United States)

    Luo, Sijie; Averkiev, Boris; Yang, Ke R; Xu, Xuefei; Truhlar, Donald G

    2014-01-14

    The 3d-series transition metals (also called the fourth-period transition metals), Sc to Zn, are very important in industry and biology, but they provide unique challenges to computing the electronic structure of their compounds. In order to successfully describe the compounds by theory, one must be able to describe their components, in particular the constituent atoms and cations. In order to understand the ingredients required for successful computations with density functional theory, it is useful to examine the performance of various exchange-correlation functionals; we do this here for 4s(N)3d(N') transition-metal atoms and their cations. We analyze the results using three ways to compute the energy of the open-shell states: the direct variational method, the weighted-averaged broken symmetry (WABS) method, and a new broken-symmetry method called the reinterpreted broken symmetry (RBS) method. We find the RBS method to be comparable in accuracy with the WABS method. By examining the overall accuracy in treating 18 multiplicity-changing excitations and 10 ionization potentials with the RBS method, 10 functionals are found to have a mean-unsigned error of systems, the M06-L functional is the most accurate. And by combining the results with our previous studies of p-block and 4d-series elements as well as databases for alkyl bond dissociation, main-group atomization energies, and π-π noncovalent interactions, we find five functionals, namely, PW6B95, MPW1B95, M08-SO, SOGGA11-X, and MPWB1K, to be highly recommended. We also studied the performance of PW86 and C09 exchange functionals, which have drawn wide interest in recent studies due to their claimed ability to reproduce Hartree-Fock exchange at long distance. By combining them with four correlation functionals, we find the performance of the resulting functionals disappointing both for 3d transition-metal chemistry and in broader tests, and thus we do not recommend PW86 and C09 as components of generalized

  9. Adsorption of 3d transition metal atoms on graphene-like gallium nitride monolayer: A first-principles study

    Science.gov (United States)

    Chen, Guo-Xiang; Li, Han-Fei; Yang, Xu; Wen, Jun-Qing; Pang, Qing; Zhang, Jian-Min

    2018-03-01

    We study the structural, electronic and magnetic properties of 3d transition metal (TM) atoms (Cr, Mn, Fe, Co, Ni and Cu) adsorbed GaN monolayer (GaN-ML) using first-principles calculations. The results show that, for 6 different TM adatoms, the most stable adsorption sites are the same. The adsorption of TM atoms results in significant lattice distortions. A covalent chemical bonding character between TM adatom and GaN-ML is found in TM adsorbed systems. Except for Ni adsorbed system, all TM adsorbed systems show spin polarization implying that the adsorption of TM induces magnetization. The magnetic moments of the adsorbed systems are concentrated on the TM adatoms and the nearest-neighbor N atoms of the adsorption site contributed slightly. Our analysis shows that the GaN-ML properties can be effectively modulated by TM adsorption, and exhibit various electronic and magnetic properties, such as magnetic metals (Fe adsorption), half-metal (Co adsorption), and spin gapless semiconductor (Cu adsorption). These present properties of TM adsorbed GaN-ML may be of value in electronics and spintronics applications.

  10. Ion-channeling study of anomalous atomic displacements at the superconducting transition in high-Tc materials

    International Nuclear Information System (INIS)

    Rehn, L.E.; Sharma, R.P.; Baldo, P.M.

    1991-01-01

    Ion channeling along the [001] direction in high-quality single crystals of (Y/Er)Ba 2 Cu 3 O 7-x revealed an abrupt change in displace-ments in the a-b plane of the Cu and O atoms at the superconducting transition, T c ; normal 'Debye-like' vibrations were found for the Y/Er and Ba atoms. The anomalous change in Cu-O displacements was found to shift directly with stoichiometry-induced changes in T c , implying a direct link between the observed phonon anomaly and the superconducting transition. Recent measurements of ion-channeling along the [001] axis in (Bi 1.7 Pb 0.3 )Sr 2 Ca 1 Cu 2 O x single-crystals revealed a similar change at T c , suggesting that this phonon anomaly is a general feature of high-T c superconductivity. In order to identify more specifically the crystallographic directions and displacement amplitudes associated with the anomalous phonon behavior, axial channeling scans using RBS, as well as characteristic x-ray production, were taken at several temperatures between 30 and 300K along the [301] and [331] directions of YBa 2 Cu 3 O 7-x single crystals. Twins present in the specimens, and the existing static atomic displacements present along these directions, caused the channeling to be poorer along these axes compared to the (001) direction. Also, a much stronger dependence of the minimum yield on depth was observed. However, since only one twin variant generally dominated over sufficiently wide areas of the specimens, reasonably good (approx 10 percent) minimum yields could be obtained along the appropriate [331] axis, and detwinned crystals produced good results along [301]. (author). 27 refs.; 5 figs

  11. Conformal house

    DEFF Research Database (Denmark)

    Ryttov, Thomas Aaby; Sannino, Francesco

    2010-01-01

    fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions...... at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms...

  12. The role of electron localization in the atomic structure of transition-metal 13-atom clusters: the example of Co13, Rh13, and Hf13.

    Science.gov (United States)

    Piotrowski, Maurício J; Piquini, Paulo; Cândido, Ladir; Da Silva, Juarez L F

    2011-10-14

    The crystalline structure of transition-metals (TM) has been widely known for several decades, however, our knowledge on the atomic structure of TM clusters is still far from satisfactory, which compromises an atomistic understanding of the reactivity of TM clusters. For example, almost all density functional theory (DFT) calculations for TM clusters have been based on local (local density approximation--LDA) and semilocal (generalized gradient approximation--GGA) exchange-correlation functionals, however, it is well known that plain DFT fails to correct the self-interaction error, which affects the properties of several systems. To improve our basic understanding of the atomic and electronic properties of TM clusters, we report a DFT study within two nonlocal functionals, namely, the hybrid HSE (Heyd, Scuseria, and Ernzerhof) and GGA+U functionals, of the structural and electronic properties of the Co(13), Rh(13), and Hf(13) clusters. For Co(13) and Rh(13), we found that improved exchange-correlation functionals decrease the stability of open structures such as the hexagonal bilayer (HBL) and double simple-cubic (DSC) compared with the compact icosahedron (ICO) structure, however, DFT-GGA, DFT-GGA+U, and DFT-HSE yield very similar results for Hf(13). Thus, our results suggest that the DSC structure obtained by several plain DFT calculations for Rh(13) can be improved by the use of improved functionals. Using the sd hybridization analysis, we found that a strong hybridization favors compact structures, and hence, a correct description of the sd hybridization is crucial for the relative energy stability. For example, the sd hybridization decreases for HBL and DSC and increases for ICO in the case of Co(13) and Rh(13), while for Hf(13), the sd hybridization decreases for all configurations, and hence, it does not affect the relative stability among open and compact configurations.

  13. Inelastic Transitions in Slow Collisions of Anti-Hydrogen with Hydrogen Atoms

    Science.gov (United States)

    Harrison, Robert; Krstic, Predrag

    2007-06-01

    We calculate excited adiabatic states and nonadiabatic coupling matrix elements of a quasimolecular system containing hydrogen and anti-hydrogen atoms, for a range of internuclear distances from 0.2 to 20 Bohrs. High accuracy is achieved by exact diagonalization of the molecular Hamiltionian in a large Gaussian basis. Nonadiabatic dynamics was calculated by solving MOCC equations. Positronium states are included in the consideration.

  14. Successive phase transitions in perovskites. II. Cell distortion and atomic displacements

    Energy Technology Data Exchange (ETDEWEB)

    Aleksandrov, K S; Pozdnyakova, L A; Orlova, T A [AN SSSR, Novosibirsk. Inst. Fiziki; Krasnoyarskij Gosudarstvennyj Univ. (USSR))

    1977-01-01

    A method is suggested for evaluating the structural and thermodynamic parameters from cell distortions at phase transformation. The method was applied for investigation of successive phase transformations in CsPbCl/sub 3/ and CsSrCl/sub 3/ crystals. By studying the temperature dependencies of the lattice parameters, the phase stereo groups for these crystals were established; the respective rotation angles and atom displacements were also evaluated.

  15. Collective vector method for calculation of E1 moments in atomic transition arrays

    International Nuclear Information System (INIS)

    Bloom, S.D.; Goldberg, A.

    1985-10-01

    The CV (collective vector) method for calculating E1 moments for a transition array is described and applied in two cases, herein denoted Z26A and Z26B, pertaining to two different configurations of iron VI. The basic idea of the method is to create a CV from each of the parent (''initial state'') state-vectors of the transition array by application of the E1 operator. The moments of each of these CV's, referred to the parent energy, are then the rigorous moments for that parent, requiring no state decomposition of the manifold of daughter state-vectors. Since, in cases of practical interest, the daughter manifold can be orders of magnitude larger in size than the parent manifold, this makes possible the calculation of many moments higher than the second in situations hitherto unattainable via standard methods. The combination of the moments of all the parents, with proper statistical weighting, then yields the transition array moments from which the transition strength distribution can be derived by various procedures. We describe two of these procedures: (1) The well-known GC (Gram-Charlier) expansion in terms of Hermite polynomials, (2) The Lanczos algorithm or Stieltjes imaging method, also called herein the delta expansion. Application is made in the cases of Z26A (50 lines) and Z26B (5523 lines) and the relative merits and shortcomings of the two procedures are discussed. 10 refs., 15 figs., 2 tabs

  16. Studying the Adhesion Force and Glass Transition of Thin Polystyrene Films by Atomic Force Microscopy

    DEFF Research Database (Denmark)

    Kang, Hua; Qian, Xiaoqin; Guan, Li

    2018-01-01

    microscopy (AFM)-based forcedistance curve to study the relaxation dynamics and the film thickness dependence of glass transition temperature (T-g) for normal thin polystyrene (PS) films supported on silicon substrate. The adhesion force (F-ad) between AFM tip and normal thin PS film surfaces...

  17. Evidence for a new class of many-electron Auger transitions in atoms

    International Nuclear Information System (INIS)

    Lee, I.; Wehlitz, R.; Becker, U.; Amusia, M.Ya.; Academy of Sciences, Saint Petersburg

    1993-01-01

    The possibility of the joint decay of two holes and one excited electron is discussed as one way many-electron Auger transitions can take place. It is shown that existing experimental decay spectra of resonantly excited states in krypton and xenon exhibit weak lines which may be associated with this new type of Auger process. (Author)

  18. Prediction of the transition energies of atomic No and Lr by the intermediate Hamiltonian coupled cluster method

    International Nuclear Information System (INIS)

    Borschevsky, A.; Eliav, E.; Kaldor, U.; Vilkas, M.J.; Ishikawa, Y.

    2007-01-01

    Complete text of publication follows: Measurements of the spectroscopic properties of the superheavy elements present a serious challenge to the experimentalist. Their short lifetimes and the low quantities of their production necessitate reliable prediction of transition energies to avoid the need for broad wavelength scans and to assist in identifying the lines. Thus, reliable high-accuracy calculations are necessary prior and parallel to experimental research. Nobelium and Lawrencium are at present the two most likely candidates for spectroscopic measurements, with the first experiments planned at GSI, Darmstadt. The intermediate Hamiltonian (IH) coupled cluster method is applied to the ionization potentials, electron affinities, and excitation energies of atomic nobelium and lawrencium. Large basis sets are used (37s31p26d21f16g11h6i). All levels of a particular atom are obtained simultaneously by diagonalizing the IH matrix. The matrix elements correspond to all excitations from correlated occupied orbitals to virtual orbitals in a large P space, and are 'dressed' by folding in excitations to higher virtual orbitals (Q space) at the coupled cluster singles-and-doubles level. Lamb-shift corrections are included. The same approach was applied to the lighter homologues of Lr and No, lutetium and ytterbium, for which many transition energies are experimentally known, in order to assess the accuracy of the calculation. The average absolute error of 20 excitation energies of Lu is 423 cm -1 , and the error limits for Lr are therefore put at 700 cm -1 . Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20,000-30,000 cm -1 , are 7p → 8s at 20,100 cm -1 and 7p →p 7d at 28,100 cm -1 . In case of Yb, the calculated ionization potential was within 20 cm -1 of the experiment, and the average error of the 20 lowest calculated excitations was about 300 cm -1 . Hence, the error limits of nobelium are set to 800 cm -1

  19. Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

    Science.gov (United States)

    Sullivan, David C; Lim, Carmay

    2006-08-24

    Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

  20. Controlling magnetism of MoS2 sheets by embedding transition-metal atoms and applying strain.

    Science.gov (United States)

    Zhou, Yungang; Su, Qiulei; Wang, Zhiguo; Deng, Huiqiu; Zu, Xiaotao

    2013-11-14

    Prompted by recent experimental achievement of transition metal (TM) atoms substituted in MoS2 nanostructures during growth or saturating existing vacancies (Sun et al., ACS Nano, 2013, 7, 3506; Deepak et al., J. Am. Chem. Soc., 2007, 129, 12549), we explored, via density functional theory, the magnetic properties of a series of 3d TM atoms substituted in a MoS2 sheet, and found that Mn, Fe, Co, Ni, Cu and Zn substitutions can induce magnetism in the MoS2 sheet. The localizing unpaired 3d electrons of TM atoms respond to the introduction of a magnetic moment. Depending on the species of TM atoms, the substituted MoS2 sheet can be a metal, semiconductor or half-metal. Remarkably, the applied elastic strain can be used to control the strength of the spin-splitting of TM-3d orbitals, leading to an effective manipulation of the magnetism of the TM-substituted MoS2 sheet. We found that the magnetic moment of the Mn- and Fe-substituted MoS2 sheets can monotonously increase with the increase of tensile strain, while the magnetic moment of Co-, Ni-, Cu- and Zn-substituted MoS2 sheets initially increases and then decreases with the increase of tensile strain. An instructive mechanism was proposed to qualitatively explain the variation of magnetism with elastic strain. The finding of the magnetoelastic effect here is technologically important for the fabrication of strain-driven spin devices on MoS2 nanostructures, which allows us to go beyond the current scope limited to the spin devices within graphene and BN-based nanostructures.

  1. Transition from the constant ion mobility regime to the ion-atom charge-exchange regime for bounded collisional plasmas

    International Nuclear Information System (INIS)

    Poggie, Jonathan; Sternberg, Natalia

    2005-01-01

    A numerical and analytical study of a planar, collisional, direct-current, plasma-wall problem is presented. The fluid model for the problem is first validated by comparing numerical solutions with experimental data for low-pressure (∼0.1 Pa) electrode sheaths with wall potentials on the order of -100 V. For electric potential, ion number density, and ion velocity, good agreement was found between theory and experiment from within the sheath out to the bulk plasma. The frictional drag resulting from ion-neutral collisions is described by a model incorporating both linear and quadratic velocity terms. In order to study the transition from the constant ion mobility regime (linear friction) to the ion-atom charge-exchange collision regime (quadratic friction), the theoretical model was examined numerically for a range of ion temperatures and ion-neutral collision rates. It was found that the solution profiles in the quasineutral plasma depend on the ion temperature. For low ion temperatures they are governed mainly by the ion-atom charge-exchange regime, whereas for high temperatures they are governed by the constant ion mobility regime. Quasineutral plasma models corresponding to these two limiting cases were solved analytically. In particular, an analytical plasma solution is given for the ion-atom charge exchange regime that includes the effects of ion inertia. In contrast to the quasineutral plasma, the sheath is always governed for low to moderate collision rates by the ion-atom charge-exchange regime, independent of the ion temperature. Varying the collision rate, it was shown that when the wall potential is sufficiently high, the sheath cannot be considered collisionless, even if the collision rate is quite small

  2. Search for Pauli exclusion principle violating atomic transitions and electron decay with a p-type point contact germanium detector

    Energy Technology Data Exchange (ETDEWEB)

    Abgrall, N.; Bradley, A.W.; Chan, Y.D.; Mertens, S.; Poon, A.W.P. [Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA (United States); Arnquist, I.J.; Hoppe, E.W.; Kouzes, R.T.; LaFerriere, B.D.; Orrell, J.L. [Pacific Northwest National Laboratory, Richland, WA (United States); Avignone, F.T. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); University of South Carolina, Department of Physics and Astronomy, Columbia, SC (United States); Barabash, A.S.; Konovalov, S.I.; Yumatov, V. [National Research Center ' ' Kurchatov Institute' ' Institute for Theoretical and Experimental Physics, Moscow (Russian Federation); Bertrand, F.E.; Galindo-Uribarri, A.; Radford, D.C.; Varner, R.L.; White, B.R.; Yu, C.H. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); Brudanin, V.; Shirchenko, M.; Vasilyev, S.; Yakushev, E.; Zhitnikov, I. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Busch, M. [Duke University, Department of Physics, Durham, NC (United States); Triangle Universities Nuclear Laboratory, Durham, NC (United States); Buuck, M.; Cuesta, C.; Detwiler, J.A.; Gruszko, J.; Guinn, I.S.; Leon, J.; Robertson, R.G.H. [University of Washington, Department of Physics, Center for Experimental Nuclear Physics and Astrophysics, Seattle, WA (United States); Caldwell, A.S.; Christofferson, C.D.; Dunagan, C.; Howard, S.; Suriano, A.M. [South Dakota School of Mines and Technology, Rapid City, SD (United States); Chu, P.H.; Elliott, S.R.; Goett, J.; Massarczyk, R.; Rielage, K. [Los Alamos National Laboratory, Los Alamos, NM (United States); Efremenko, Yu. [University of Tennessee, Department of Physics and Astronomy, Knoxville, TN (United States); Ejiri, H. [Osaka University, Research Center for Nuclear Physics, Ibaraki, Osaka (Japan); Finnerty, P.S.; Gilliss, T.; Giovanetti, G.K.; Henning, R.; Howe, M.A.; MacMullin, J.; Meijer, S.J.; O' Shaughnessy, C.; Rager, J.; Shanks, B.; Trimble, J.E.; Vorren, K.; Xu, W. [Triangle Universities Nuclear Laboratory, Durham, NC (United States); University of North Carolina, Department of Physics and Astronomy, Chapel Hill, NC (United States); Green, M.P. [North Carolina State University, Department of Physics, Raleigh, NC (United States); Oak Ridge National Laboratory, Oak Ridge, TN (United States); Triangle Universities Nuclear Laboratory, Durham, NC (United States); Guiseppe, V.E.; Tedeschi, D.; Wiseman, C. [University of South Carolina, Department of Physics and Astronomy, Columbia, SC (United States); Jasinski, B.R. [University of South Dakota, Department of Physics, Vermillion, SD (United States); Keeter, K.J. [Black Hills State University, Department of Physics, Spearfish, SD (United States); Kidd, M.F. [Tennessee Tech University, Cookeville, TN (United States); Martin, R.D. [Queen' s University, Department of Physics, Engineering Physics and Astronomy, Kingston, ON (Canada); Romero-Romero, E. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); University of Tennessee, Department of Physics and Astronomy, Knoxville, TN (United States); Vetter, K. [Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA (United States); University of California, Department of Nuclear Engineering, Berkeley, CA (United States); Wilkerson, J.F. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); Triangle Universities Nuclear Laboratory, Durham, NC (United States); University of North Carolina, Department of Physics and Astronomy, Chapel Hill, NC (United States)

    2016-11-15

    A search for Pauli-exclusion-principle-violating K{sub α} electron transitions was performed using 89.5 kg-d of data collected with a p-type point contact high-purity germanium detector operated at the Kimballton Underground Research Facility. A lower limit on the transition lifetime of 5.8 x 10{sup 30} s at 90% C.L. was set by looking for a peak at 10.6 keV resulting from the X-ray and Auger electrons present following the transition. A similar analysis was done to look for the decay of atomic K-shell electrons into neutrinos, resulting in a lower limit of 6.8 x 10{sup 30} s at 90% C.L. It is estimated that the Majorana Demonstrator, a 44 kg array of p-type point contact detectors that will search for the neutrinoless double-beta decay of {sup 76}Ge, could improve upon these exclusion limits by an order of magnitude after three years of operation. (orig.)

  3. Transition probabilities for lines of Cr II, Na II and Sb I by laser produced plasma atomic emission spectroscopy

    International Nuclear Information System (INIS)

    Gonzalez, A. M.; Ortiz, M.; Campos, J.

    1995-01-01

    Absolute transition probabilities for lines of CR II, Na II and Sb I were determined by emission spectroscopy of laser induced plasmas. the plasma was produced focusing the emission of a pulsed Nd-Yag laser on solid samples containing the atom in study. the light arising from the plasma region was collected by and spectrometer. the detector used was a time-resolved optical multichannel analyzer (OMA III EG and G). The wavelengths of the measured transitions range from 2000 sto 4100 A. The spectral resolution of the system was 0. 2 A. The method can be used in insulators materials as Cl Na crystals and in metallic samples as Al-Cr and Sn-Sn alloys. to avoid self-absorption effects the alloys were made with low Sb or Cr content. Relative transition probabilities have been determined from measurements of emission-line intensities and were placed on an absolute scale by using, where possible, accurate experimental lifetime values form the literature or theoretical data. From these measurements, values for plasma temperature (8000-24000 K), electron densities (∼∼ 10''16 cm ''-3) and self-absorption coefficients have been obtained. (Author) 56 refs

  4. Transition probabilities for lines of Cr II, Na II and Sb I by laser produced plasma atomic emission spectroscopy

    International Nuclear Information System (INIS)

    Gonzalez, A.M.; Ortiz, M.; Campos, J.

    1995-09-01

    Absolute transition probabilities for lines of Cr II, Na II and Sb I were determined by emission spectroscopy of laser induced plasmas. The plasma was produced focusing the emission of a pulsed Nd-Yag laser on solid samples containing the atom in study. The light arising from the plasma region was collected by and spectrometer. the detector used was a time-resolved optical multichannel analyzer (OMA III EG and G). The wavelengths of the measured transitions range from 2000 to 4100 A. The spectral resolution of the system was 0.2 A. The method can be used in insulators materials as Cl Na crystals and in metallic samples as Al-Cr and Sn-Sb alloys. To avoid self-absorption effects the alloys were made with low Sb or Cr content. Relative transition probabilities have been determined from measurements of emission-line intensities and were placed on an absolute scale by using, where possible, accurate experimental lifetime values form the literature or theoretical data. From these measurements, values for plasma temperature (8000-24000K), electron densities (approx 10 ''16 cm''-3) and self-absorption coefficients have been obtained

  5. Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems

    Science.gov (United States)

    Setiawan, F.; Sengupta, K.; Spielman, I. B.; Sau, Jay D.

    2015-11-01

    We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signatures of the TPT. We apply this strategy to study the TPT into a Majorana-carrying topological phase predicted in one-dimensional spin-orbit-coupled Fermi gases with attractive interactions. The resulting spin-resolved momentum distribution, computed by self-consistently solving the time-dependent Bogoliubov-de Gennes equations, exhibits Kibble-Zurek scaling and Stückelberg oscillations characteristic of the TPT. We discuss parameter regimes where the TPT is experimentally accessible.

  6. Visualization of the evolution of charged droplet formation and jet transition in electrostatic atomization

    Energy Technology Data Exchange (ETDEWEB)

    Huo, Yuanping, E-mail: huoyuanping@gmail.com; Wang, Junfeng, E-mail: wangjunfeng@ujs.edu.cn; Zuo, Ziwen; Fan, Yajun [School of Energy and Power Engineering, Jiangsu University, 212013 Zhenjiang (China)

    2015-11-15

    A detailed experimental study on the evolution of charged droplet formation and jet transition from a capillary is reported. By means of high-speed microscopy, special attention has been paid to the dynamics of the liquid thread and satellite droplets in the dripping mode, and a method for calculating the surface charge on the satellite droplet is proposed. Jet transition behavior based on the electric Bond number has been visualized, droplet sizes and velocities are measured to obtain the ejection characteristic of the spray plume, and the charge and hydrodynamic relaxation are linked to give explanations for ejection dynamics with different properties. The results show that the relative length is very sensitive to the hydrodynamic relaxation time. The magnitude of the electric field strength dominates the behavior of coalescence and noncoalescence, with the charge relationship between the satellite droplet and the main droplet being clear for every noncoalescence movement. Ejection mode transitions mainly depend on the magnitude of the electric Bond number, and the meniscus dynamics is determined by the ratio of the charge relaxation time to the hydrodynamic relaxation time.

  7. Radiative transitions from Rydberg states of lithium atoms in a blackbody radiation environment

    Science.gov (United States)

    Glukhov, I. L.; Ovsiannikov, V. D.

    2012-05-01

    The radiative widths induced by blackbody radiation (BBR) were investigated for Rydberg states with principal quantum number up to n = 1000 in S-, P- and D-series of the neutral lithium atom at temperatures T = 100-3000 K. The rates of BBR-induced decays and excitations were compared with the rates of spontaneous decays. Simple analytical approximations are proposed for accurate estimations of the ratio of thermally induced decay (excitation) rates to spontaneous decay rates in wide ranges of states and temperatures.

  8. Spintronic and transport properties of linear atomic strings of transition metals (Fe, Co, Ni)

    Energy Technology Data Exchange (ETDEWEB)

    Tyagi, Neha, E-mail: nehatyagi.phy@gmail.com [Department of Applied Physics, Delhi Technological University, New Delhi (India); Jaiswal, Neeraj K. [Discipline of Physics, PDPM-Indian Institute of Information Technology, Design & Manufacturing, Jabalpur (India); Srivastava, Pankaj [Nanomaterials Research Group, ABV-Indian Institute of Information Technology & Management, Gwalior (India)

    2016-05-06

    In the present work, first-principles investigations have been performed to study the spintronic and transport properties of linear atomic strings of Fe, Co and Ni. The structural stabilities of the considered strings were compared on the basis of binding energies which revealed that all the strings are energetically feasible to be achieved. Further, all the considered strings are found to be ferromagnetic and the observed magnetic moment ranges from 1.38 to 1.71 μ{sub B}. The observed transport properties and high spin polarization points towards their potential for nano interconnects and spintronic applications.

  9. Superconducting transition temperature and the formation of closed electron shells in the atoms of superconducting compounds

    International Nuclear Information System (INIS)

    Chapnik, I.M.

    1985-01-01

    The relationship between the regularities in the tansition temperature (T/sub c/) values in analogous compounds (having the same structure and stoichiometry) and the formation of the closed electron shells outside inert gas shells in the atoms of the variable component of the 158 intermetallic superconducting compounds has been discussed. The T/sub c/ data for compounds of the elements from the first long period of the Periodic Table (K to Se) are compared with the T/sub c/ data for the analogous compounds of the elements from the second long period (Rb to Te)

  10. Atomic structures and covalent-to-metallic transition of lead clusters Pbn (n=2-22)

    International Nuclear Information System (INIS)

    Wang Baolin; Zhao Jijun; Chen Xiaoshuang; Shi Daning; Wang Guanghou

    2005-01-01

    The lowest-energy structures and electronic properties of the lead clusters are studied by density-functional-theory calculations with Becke-Lee-Yang-Parr gradient correction. The lowest-energy structures of Pb n (n=2-22) clusters are determined from a number of structural isomers, which are generated from empirical genetic algorithm simulations. The competition between atom-centered compact structures and layered stacking structures leads to the alternative appearance of the two types of structures as global minimum. The size evolution of geometric and electronic properties from covalent bonding towards bulk metallic behavior in Pb clusters is discussed

  11. First observation of the strongly forbidden transition {sup 1}S{sub 0} - {sup 3}P{sub 0} in Strontium, for an atomic clock with trapped atoms; Premiere observation de la transition fortement interdite {sup 1}S{sub 0} - {sup 3}P{sub 0} du strontium, pour une horloge optique a atomes pieges

    Energy Technology Data Exchange (ETDEWEB)

    Courtillot, I

    2003-11-01

    This thesis reports the first results towards the realization of an optical clock using trapped strontium atoms. This set up would combine advantages of the different approaches commonly used to develop an atomic frequency standard. The first part describes the cold atoms source which is implemented. A magneto-optical trap operating on the {sup 1}S{sub 0}-{sup 1}P{sub 1} transition at 461 nm is loaded from an atomic beam decelerated by a Zeeman slower. The 461 nm laser is obtained by sum-frequency mixing in a potassium titanyl phosphate (KTP) crystal. The second part is devoted to the different stages developed to achieve the direct excitation of the {sup 1}S{sub 0}-{sup 3}P{sub 0} clock transition in {sup 87}Sr. This line has a theoretical natural width of 10{sup -3} Hz. Before this detection, we obtained an estimate of the resonance frequency by measuring absolute frequencies of several allowed optical transitions. (author)

  12. Electron impact excitation of complex atoms and ions. Pt. 2: forbidden transitions in Ni+

    International Nuclear Information System (INIS)

    Watts, M.S.T.; Berrington, K.A.; Burke, P.G.

    1996-01-01

    This letter reports the first application of the new R-matrix program package RMATRX II to electron impact excitation of a near neutral open d-shell ion. In this calculation for Ni + , all states corresponding to the configuration 3d 9 , 3d 8 4s and 3d 8 4p have been included in the expansion of the total wavefunction. Thermally averaged collision strengths for forbidden transitions involving the even parity states are presented in tabular form for temperatures between 5000 K and 20 000 K. The importance of including accurate C1 expansions for both the target and the (N + 1)-electron terms is demonstrated. (Author)

  13. Relativistic calculations of one-photon bound-free transition amplitudes in hydrogenic atoms

    International Nuclear Information System (INIS)

    Simo, E.; Kwato Njock, M.G.

    2005-04-01

    Photoionization transition matrix of hydrogenic systems are investigated theoretically within the framework of the tensorial formalism with relativistic arguments. Calculations are carried out exactly, without approximation. We derive continuum second-order Dirac-Coulomb Sturmian functions. The numerical simulation of our results is performed in the dipole approximation. We test our theory on selected nucleus from the Periodic Table. The results of the fully relativistic calculations are compared with those of the quasi-relativistic calculations. A conclusion is drawn about the level of reliability of the quite simplified quasi-relativistic approach. (author)

  14. Laser spectroscopy of the 4s4p(3) P-2-4s3d(1) D-2 transition on magnetically trapped calcium atoms

    NARCIS (Netherlands)

    Dammalapati, U.; Norris, I.; Burrows, C.; Riis, E.

    2011-01-01

    Laser excitation of the 4s4p(3) P-2-4s3d(1) D-2 transition in atomic calcium has been observed and the wavelength determined to 1530.5298(6) nm. The metastable 4s4p(3) P-2 atoms were magnetically trapped in the quadrupole magnetic field of a magneto-optical trap. This state represents the only

  15. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    Energy Technology Data Exchange (ETDEWEB)

    López-Moreno, S., E-mail: sinlopez@uacam.mx [Centro de Investigación en Corrosión, Universidad Autónoma de Campeche, Av. Héroe de Nacozari 480, Campeche, Campeche 24029 (Mexico); Romero, A. H. [Physics Department, West Virginia University, Morgantown, West Virginia 26506-6315 (United States)

    2015-04-21

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O{sub 2} molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

  16. Engineering giant magnetic anisotropy in single-molecule magnets by dimerizing heavy transition-metal atoms

    Science.gov (United States)

    Qu, Jiaxing; Hu, Jun

    2018-05-01

    The search for single-molecule magnets with large magnetic anisotropy energy (MAE) is essential for the development of molecular spintronics devices for use at room temperature. Through systematic first-principles calculations, we found that an Os–Os or Ir–Ir dimer embedded in the (5,5‧-Br2-salophen) molecule gives rise to a large MAE of 41.6 or 51.4 meV, respectively, which is large enough to hold the spin orientation at room temperature. Analysis of the electronic structures reveals that the top Os and Ir atoms play the most important part in the total spin moments and large MAEs of the molecules.

  17. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    Science.gov (United States)

    López-Moreno, S.; Romero, A. H.

    2015-04-01

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

  18. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    International Nuclear Information System (INIS)

    López-Moreno, S.; Romero, A. H.

    2015-01-01

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O 2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered

  19. Direct observation of phase transition of GeSbTe thin films by Atomic Force Microscope

    Energy Technology Data Exchange (ETDEWEB)

    Yang Fei [National Laboratory of Solid State Microstructures and Jiangsu Provincial Key Laboratory of Photonic and Electronic Materials Sciences and Technology, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Xu Ling, E-mail: xuling@nju.edu.cn [National Laboratory of Solid State Microstructures and Jiangsu Provincial Key Laboratory of Photonic and Electronic Materials Sciences and Technology, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Zhang Rui; Geng Lei; Tong Liang; Xu Jun [National Laboratory of Solid State Microstructures and Jiangsu Provincial Key Laboratory of Photonic and Electronic Materials Sciences and Technology, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Su Weining; Yu Yao [National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093 (China); Ma Zhongyuan; Chen Kunji [National Laboratory of Solid State Microstructures and Jiangsu Provincial Key Laboratory of Photonic and Electronic Materials Sciences and Technology, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China)

    2012-10-01

    Graphical abstract: Nano-sized marks on GST thin film were fabricated using Conductive-AFM (Atomic Force Microscope). The AFM morphology images show that the marks are ablated at the center and a raised ring surrounding it. Highlights: Black-Right-Pointing-Pointer Microstructure of GeSbTe thin films was characterized by XRD and AFM. Black-Right-Pointing-Pointer Annealing and applying electrical field can induce crystallization on thin film. Black-Right-Pointing-Pointer Conductive-AFM was used to modify the surface of GeSbTe thin film. - Abstract: GeSbTe (GST) thin films were deposited on quartz substrates using electron beam evaporation system and then annealed in nitrogen atmosphere at different temperatures, ranging from 20 Degree-Sign C to 300 Degree-Sign C. X-ray diffraction (XRD) and Atomic Force microscope (AFM) measurements were used to characterize the as-deposited and post-annealed thin films. Annealing treatment was found to induce changes on microstructure, surface roughness and grain size, indicating that with the increase of annealing temperature, the amorphous GST films first changed to face-centered-cubic (fcc) phase and then the stable hexagonal (hex) phase. Meanwhile, conductive-AFM (C-AFM) was used to produce crystallized GST dots on thin films. I-V spectroscopy results show that GST films can switch from amorphous state to crystalline state at threshold voltage. After switching, I-V curve exhibits ohmic characteristic, which is usually observed in crystallized GST films. By applying repeated I-V spectroscopies on the thin films, crystallized nuclei were observed. As the times of I-V spectroscopies increases, the area of written dots increases, and the center of the mark begin to ablate. The AFM images show that the shape of marks is an ablated center with a raised ring surrounding it.

  20. Optical and Excitonic Properties of Atomically Thin Transition-Metal Dichalcogenides

    Science.gov (United States)

    Berkelbach, Timothy C.; Reichman, David R.

    2018-03-01

    Starting with the isolation of a single sheet of graphene, the study of layered materials has been one of the most active areas of condensed matter physics, chemistry, and materials science. Single-layer transition-metal dichalcogenides are direct-gap semiconducting analogs of graphene that exhibit novel electronic and optical properties. These features provide exciting opportunities for the discovery of both new fundamental physical phenomena as well as innovative device platforms. Here, we review the progress associated with the creation and use of a simple microscopic framework for describing the optical and excitonic behavior of few-layer transition-metal dichalcogenides, which is based on symmetry, band structure, and the effective interactions between charge carriers in these materials. This approach provides an often quantitative account of experiments that probe the physics associated with strong electron–hole interactions in these quasi two-dimensional systems and has been successfully employed by many groups to both describe and predict emergent excitonic behavior in these layered semiconducting systems.

  1. Transportation Conformity

    Science.gov (United States)

    This section provides information on: current laws, regulations and guidance, policy and technical guidance, project-level conformity, general information, contacts and training, adequacy review of SIP submissions

  2. Transitions between the fine structure components of C+ in collision with atomic hydrogen

    International Nuclear Information System (INIS)

    Bazet, J.F.; Harel, C.; McCarroll, R.; Riera, A.

    1975-01-01

    The cross section for excitation of the 2 Psub(1/2)- 2 Psub(3/2) transition in thermal C + ( 2 P)-H( 2 S) collisions is calculated in the framework of the semiclassical approximation using the potential energy curves of the 1 Σ, 1 π, 3 π, 3 Σ states of CH + , determined by an exchange perturbation method. Full account is taken of the exchange interaction and of the trajectory effects induced by the long range polarization potential. For low energies E, such that E/k 350 K, sigma depends on the exchange interaction. The cross section, which presents a maximum of 130a 2 0 for E/k approximately equal to 180 K, is lower by about 50% than that calculated by Weisheit and Lane. The cooling function due to C + -H collisions in the interstellar clouds is computed as a function of the kinetic temperature of the medium. (orig.) [de

  3. Workers’ Conformism

    Directory of Open Access Journals (Sweden)

    Nikolay Ivantchev

    2013-10-01

    Full Text Available Conformism was studied among 46 workers with different kinds of occupations by means of two modified scales measuring conformity by Santor, Messervey, and Kusumakar (2000 – scale for perceived peer pressure and scale for conformism in antisocial situations. The hypothesis of the study that workers’ conformism is expressed in a medium degree was confirmed partly. More than a half of the workers conform in a medium degree for taking risk, and for the use of alcohol and drugs, and for sexual relationships. More than a half of the respondents conform in a small degree for anti-social activities (like a theft. The workers were more inclined to conform for risk taking (10.9%, then – for the use of alcohol, drugs and for sexual relationships (8.7%, and in the lowest degree – for anti-social activities (6.5%. The workers who were inclined for the use of alcohol and drugs tended also to conform for anti-social activities.

  4. Metal–semiconductor transition in atomically thin Bi2Sr2Co2O8 nanosheets

    Directory of Open Access Journals (Sweden)

    Yang Wang

    2014-09-01

    Full Text Available Two-dimensional layered materials have attracted considerable attention since the discovery of graphene. Here we demonstrate that the layered Bi2Sr2Co2O8 (BSCO can be mechanically exfoliated into single- or few-layer nanosheets. The BSCO nanosheets with four or more layers display bulk metallic characteristics, while the nanosheets with three or fewer layers have a layer-number-dependent semiconducting characteristics. Charge transport in bilayer or trilayer BSCO nanosheets exhibits Mott 2D variable-range-hopping (VRH conduction throughout 2 K–300 K, while the charge transport in monolayers follows the Mott-VRH law above a crossover temperature of 75 K, and is governed by Efros and Shklovskii-VRH laws below 75 K. Disorder potentials and Coulomb charging both contribute to the transport gap of these nanodevices. Our study reveals a distinct layer number-dependent metal-to-semiconductor transition in a new class of 2D materials, and is of great significance for both fundamental investigations and practical devices.

  5. Observation of double resonant laser induced transitions in the $v = n - l - 1 = 2$ metastable cascade of antiprotonic helium-4 atoms

    CERN Document Server

    Hayano, R S; Tamura, H; Torii, H A; Hori, Masaki; Maas, F E; Morita, N; Kumakura, M; Sugai, I; Hartmann, F J; Daniel, H; Von Egidy, T; Ketzer, B; Pohl, R; Horváth, D; Eades, John; Widmann, E; Yamazaki, T

    1997-01-01

    A new laser-induced resonant transition in the $v=n-l-1=2$ metastable cascade of antiprotonic $^4$He atoms has been found by using a double resonance technique. This was done by setting the first laser to the already known 470.724 nm resonance ($(n,l)=(37,34)\\rightarrow (36,33)$), while the $(38,35)\\rightarrow (37,34)$ transition was searched for with the second laser. The resonant transition was found at wavelength of 529.622$\\pm$0.003 nm, showing excellent agreement with a recent prediction of Korobov.

  6. Quantum incommensurate skyrmion crystals and commensurate to in-commensurate transitions in cold atoms and materials with spin-orbit couplings in a Zeeman field

    Science.gov (United States)

    Sun, Fadi; Ye, Jinwu; Liu, Wu-Ming

    2017-08-01

    In this work, we study strongly interacting spinor atoms in a lattice subject to a two dimensional (2d) anisotropic Rashba type of spin orbital coupling (SOC) and an Zeeman field. We find the interplay between the Zeeman field and the SOC provides a new platform to host rich and novel classes of quantum commensurate and in-commensurate phases, excitations and phase transitions. These commensurate phases include two collinear states at low and high Zeeman field, two co-planar canted states at mirror reflected SOC parameters respectively. Most importantly, there are non-coplanar incommensurate Skyrmion (IC-SkX) crystal phases surrounded by the four commensurate phases. New excitation spectra above all the five phases, especially on the IC-SKX phase are computed. Three different classes of quantum commensurate to in-commensurate transitions from the IC-SKX to its four neighboring commensurate phases are identified. Finite temperature behaviors and transitions are discussed. The critical temperatures of all the phases can be raised above that reachable by current cold atom cooling techniques simply by tuning the number of atoms N per site. In view of recent impressive experimental advances in generating 2d SOC for cold atoms in optical lattices, these new many-body phenomena can be explored in the current and near future cold atom experiments. Applications to various materials such as MnSi, {Fe}}0.5 {Co}}0.5Si, especially the complex incommensurate magnetic ordering in Li2IrO3 are given.

  7. Optical to ultraviolet spectra of sandwiches of benzene and transition metal atoms: Time dependent density functional theory and many-body calculations

    DEFF Research Database (Denmark)

    Martinez, Jose Ignacio; García Lastra, Juan Maria; Lopez, M. J.

    2010-01-01

    The optical spectra of sandwich clusters formed by transition metal atoms (titanium, vanadium, and chromium) intercalated between parallel benzene molecules have been studied by time-dependent density functional theory (TDDFT) and many-body perturbation theory. Sandwiches with different number...

  8. Application of an excited state LDA exchange energy functional for the calculation of transition energy of atoms within time-independent density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Shamim, Md; Harbola, Manoj K, E-mail: sami@iitk.ac.i, E-mail: mkh@iitk.ac.i [Department of Physics, Indian Institute of Technology, Kanpur 208 016 (India)

    2010-11-14

    Transition energies of a new class of excited states (two-gap systems) of various atoms are calculated in time-independent density functional formalism by using a recently proposed local density approximation exchange energy functional for excited states. It is shown that the excitation energies calculated with this functional compare well with those calculated with exact exchange theories.

  9. Application of an excited state LDA exchange energy functional for the calculation of transition energy of atoms within time-independent density functional theory

    International Nuclear Information System (INIS)

    Shamim, Md; Harbola, Manoj K

    2010-01-01

    Transition energies of a new class of excited states (two-gap systems) of various atoms are calculated in time-independent density functional formalism by using a recently proposed local density approximation exchange energy functional for excited states. It is shown that the excitation energies calculated with this functional compare well with those calculated with exact exchange theories.

  10. Conformal Infinity

    Directory of Open Access Journals (Sweden)

    Frauendiener Jörg

    2000-08-01

    Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, ``conformal infinity'' is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  11. Conformal Infinity.

    Science.gov (United States)

    Frauendiener, Jörg

    2004-01-01

    The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  12. Conformal Infinity

    Directory of Open Access Journals (Sweden)

    Frauendiener Jörg

    2004-01-01

    Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  13. General Conformity

    Science.gov (United States)

    The General Conformity requirements ensure that the actions taken by federal agencies in nonattainment and maintenance areas do not interfere with a state’s plans to meet national standards for air quality.

  14. Conformal Infinity

    OpenAIRE

    Frauendiener, J?rg

    2000-01-01

    The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory...

  15. Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons.

    Science.gov (United States)

    Greene, Samuel M; Shan, Xiao; Clary, David C

    2015-12-17

    Quantum mechanical methods for calculating rate constants are often intractable for reactions involving many atoms. Semiclassical transition state theory (SCTST) offers computational advantages over these methods but nonetheless scales exponentially with the number of degrees of freedom (DOFs) of the system. Here we present a method with more favorable scaling, reduced-dimensionality SCTST (RD SCTST), that treats only a subset of DOFs of the system explicitly. We apply it to three H abstraction and exchange reactions for which two-dimensional potential energy surfaces (PESs) have previously been constructed and evaluated using RD quantum scattering calculations. We differentiated these PESs to calculate harmonic frequencies and anharmonic constants, which were then used to calculate cumulative reaction probabilities and rate constants by RD SCTST. This method yielded rate constants in good agreement with quantum scattering results. Notably, it performed well for a heavy-light-heavy reaction, even though it does not explicitly account for corner-cutting effects. Recent extensions to SCTST that improve its treatment of deep tunneling were also evaluated within the reduced-dimensionality framework. The success of RD SCTST in this study suggests its potential applicability to larger systems.

  16. Modulating the electronic and magnetic properties of bilayer borophene via transition metal atoms intercalation: from metal to half metal and semiconductor.

    Science.gov (United States)

    Zhang, Xiuyun; Sun, Yi; Ma, Liang; Zhao, Xinli; Yao, Xiaojing

    2018-07-27

    Borophene, a two-dimensional monolayer made of boron atoms, has attracted wide attention due to its appealing properties. Great efforts have been devoted to fine tuning its electronic and magnetic properties for desired applications. Herein, we theoretically investigate the versatile electronic and magnetic properties of bilayer borophene (BLB) intercalated by 3d transition metal (TM) atoms, TM@BLBs (TM = Ti-Fe), using ab initio calculations. Four allotropes of AA-stacking (α 1 -, β-, β 12 - and χ 3 -) BLBs with different intercalation concentrations of TM atoms are considered. Our results show that the TM atoms are strongly bonded to the borophene layers with fairly large binding energies, around 6.31 ∼ 15.44 eV per TM atom. The BLBs with Cr and Mn intercalation have robust ferromagnetism, while for the systems decorated with Fe atoms, fruitful magnetic properties, such as nonmagnetic, ferromagnetic or antiferromagnetic, are identified. In particular, the α 1 - and β-BLBs intercalated by Mn or Fe atom can be transformed into a semiconductor, half metal or graphene-like semimetal. Moreover, some heavily doped TM@BLBs expose high Curie temperatures above room temperature. The attractive properties of TM@BLBs entail an efficient way to modulate the electronic and magnetic properties of borophene sheets for advanced applications.

  17. Unique Reactivity of Transition Metal Atoms Embedded in Graphene to CO, NO, O₂ and O Adsorption: A First-Principles Investigation.

    Science.gov (United States)

    Chu, Minmin; Liu, Xin; Sui, Yanhui; Luo, Jie; Meng, Changgong

    2015-10-27

    Taking the adsorption of CO, NO, O₂ and O as probes, we investigated the electronic structure of transition metal atoms (TM, TM = Fe, Co, Ni, Cu and Zn) embedded in graphene by first-principles-based calculations. We showed that these TM atoms can be effectively stabilized on monovacancy defects on graphene by forming plausible interactions with the C atoms associated with dangling bonds. These interactions not only give rise to high energy barriers for the diffusion and aggregation of the embedded TM atoms to withstand the interference of reaction environments, but also shift the energy levels of TM-d states and regulate the reactivity of the embedded TM atoms. The adsorption of CO, NO, O₂ and O correlates well with the weight averaged energy level of TM-d states, showing the crucial role of interfacial TM-C interactions on manipulating the reactivity of embedded TM atoms. These findings pave the way for the developments of effective monodispersed atomic TM composites with high stability and desired performance for gas sensing and catalytic applications.

  18. Conformation radiotherapy and conformal radiotherapy

    International Nuclear Information System (INIS)

    Morita, Kozo

    1999-01-01

    In order to coincide the high dose region to the target volume, the 'Conformation Radiotherapy Technique' using the multileaf collimator and the device for 'hollow-out technique' was developed by Prof. S. Takahashi in 1960. This technique can be classified a type of 2D-dynamic conformal RT techniques. By the clinical application of this technique, the late complications of the lens, the intestine and the urinary bladder after radiotherapy for the maxillary cancer and the cervical cancer decreased. Since 1980's the exact position and shape of the tumor and the surrounding normal tissues can be easily obtained by the tremendous development of the CT/MRI imaging technique. As a result, various kinds of new conformal techniques such as the 3D-CRT, the dose intensity modulation, the tomotherapy have been developed since the beginning of 1990'. Several 'dose escalation study with 2D-/3D conformal RT' is now under way to improve the treatment results. (author)

  19. TRANSIT

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. TRANSIT. SYSTEM: DETERMINE 2D-POSITION GLOBALLY BUT INTERMITTENT (POST-FACTO). IMPROVED ACCURACY. PRINCIPLE: POLAR SATELLITES WITH INNOVATIONS OF: GRAVITY-GRADIENT ATTITUDE CONTROL; DRAG COMPENSATION. WORKS ...

  20. Molecular insight into conformational transmission of human P-glycoprotein

    International Nuclear Information System (INIS)

    Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

    2013-01-01

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp

  1. The excitation functions of 4s-4p and 3d-4p transitions in Ni atoms sputtered from metallic targets by Ar+ ions

    International Nuclear Information System (INIS)

    Dabrowski, P.; Gabla, L.; Pedrys, R.

    1981-01-01

    The intensities of spectral lines corresponding to 4s-4p and 3d-4p transitions in Ni atoms sputtered from metallic targets by Ar + ions were measured. The energy of primary ions was varied from 4 keV to 10 keV. Both single crystal and polycrystalline targets were used at various temperatures including ferromagnetic and paramagnetic phases. The excitation functions calculated from experimental data can be explained only by the assumption that the promotion of the electrons occurs during energetic binary collisions of atomic particles in the solid. (orig.)

  2. Impact of buffer gas quenching on the 1S0 → 1P1 ground-state atomic transition in nobelium

    International Nuclear Information System (INIS)

    Chhetri, P.; Lautenschlaeger, F.; Ackermann, D.; Backe, H.; Lauth, W.; Block, M.; Duellmann, C.E.; Goetz, S.; Cheal, B.; Wraith, C.; Even, J.; Ferrer, R.; Giacoppo, F.; Hessberger, F.P.; Khuyagbaatar, J.; Kishor Mistry, A.; Raeder, S.; Yakushev, A.; Kaleja, O.; Kunz, P.; Laatiaoui, M.; Minaya Ramirez, E.; Walther, T.

    2017-01-01

    Using the sensitive Radiation Detected Resonance Ionization Spectroscopy (RADRIS) technique an optical transition in neutral nobelium (No, Z = 102) was identified. A remnant signal when delaying the ionizing laser indicated the influence of a strong buffer gas induced de-excitation of the optically populated level. A subsequent investigation of the chemical homologue, ytterbium (Yb, Z = 70), enabled a detailed study of the atomic levels involved in this process, leading to the development of a rate equation model. This paves the way for characterizing resonance ionization spectroscopy (RIS) schemes used in the study of nobelium and beyond, where atomic properties are currently unknown. (authors)

  3. Conformal Gravity

    International Nuclear Information System (INIS)

    Hooft, G.

    2012-01-01

    The dynamical degree of freedom for the gravitational force is the metric tensor, having 10 locally independent degrees of freedom (of which 4 can be used to fix the coordinate choice). In conformal gravity, we split this field into an overall scalar factor and a nine-component remainder. All unrenormalizable infinities are in this remainder, while the scalar component can be handled like any other scalar field such as the Higgs field. In this formalism, conformal symmetry is spontaneously broken. An imperative demand on any healthy quantum gravity theory is that black holes should be described as quantum systems with micro-states as dictated by the Hawking-Bekenstein theory. This requires conformal symmetry that may be broken spontaneously but not explicitly, and this means that all conformal anomalies must cancel out. Cancellation of conformal anomalies yields constraints on the matter sector as described by some universal field theory. Thus black hole physics may eventually be of help in the construction of unified field theories. (author)

  4. Conformational changes in glycine tri- and hexapeptide

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2006-01-01

    conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods...... also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids....

  5. Stability and properties of quasi-stable conformational states in the LH2 light-harvesting complex of Rbl. acidophilus bacteria formed by hexacoordination of bacteriochlorophyll a magnesium atom

    Science.gov (United States)

    Belov, Aleksandr S.; Khokhlov, Daniil V.; Glebov, Ilya O.; Poddubnyy, Vladimir V.; Eremin, Vadim V.

    2017-06-01

    Single-molecule spectroscopic experiments on several light-harvesting complexes revealed the existence of a set of metastable conformational states with different spectroscopic properties and lifetimes spanning from milliseconds to tens of seconds. In the absence of explicit structural data, a number of probable structural changes underlying the observed spectroscopic shifts were proposed. We examine the donor-acceptor interaction between the magnesium atom and the acetyl group of the adjacent bacteriochlorophylls a as a possible origin of metastable conformational states in the LH2 light-harvesting complex of Rbl. acidophilus bacteria. The results of QM/MM and molecular dynamics simulations show that such ligation can occur at room temperature and leads to one metastable coordination bond per pair of bacteriochlorophylls in the B850 ring. According to the results of Poisson-TrESP modeling, such coordination lowers the energies of the excited states of the complex by up to 163 cm-1 which causes red spectral shift of the B850 band.

  6. Adsorption of alkali, alkaline-earth, simple and 3d transition metal, and nonmetal atoms on monolayer MoS2

    Directory of Open Access Journals (Sweden)

    X. D. Li

    2015-05-01

    Full Text Available Single adsorption of different atoms on pristine two-dimensional monolayer MoS2 have been systematically investigated by using density functional calculations with van der Waals correction. The adatoms cover alkali metals, alkaline earth metals, main group metal, 3d-transition metals, coinage metal and nonmetal atoms. Depending on the adatom type, metallic, semimetallic or semiconducting behavior can be found in direct bandgap monolayer MoS2. Additionally, local or long-range magnetic moments of two-dimensional MoS2 sheet can also attained through the adsorption. The detailed atomic-scale knowledge of single adsorption on MoS2 monolayer is important not only for the sake of a theoretical understanding, but also device level deposition technological application.

  7. Adsorption of alkali, alkaline-earth, simple and 3d transition metal, and nonmetal atoms on monolayer MoS{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Li, X. D.; Fang, Y. M.; Wu, S. Q., E-mail: zzhu@xmu.edu.cn, E-mail: wsq@xmu.edu.cn [Department of Physics and Institute of Theoretical Physics and Astrophysics, Xiamen University, Xiamen 361005 (China); Zhu, Z. Z., E-mail: zzhu@xmu.edu.cn, E-mail: wsq@xmu.edu.cn [Department of Physics and Institute of Theoretical Physics and Astrophysics, Xiamen University, Xiamen 361005 (China); Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005 (China)

    2015-05-15

    Single adsorption of different atoms on pristine two-dimensional monolayer MoS{sub 2} have been systematically investigated by using density functional calculations with van der Waals correction. The adatoms cover alkali metals, alkaline earth metals, main group metal, 3d-transition metals, coinage metal and nonmetal atoms. Depending on the adatom type, metallic, semimetallic or semiconducting behavior can be found in direct bandgap monolayer MoS{sub 2}. Additionally, local or long-range magnetic moments of two-dimensional MoS{sub 2} sheet can also attained through the adsorption. The detailed atomic-scale knowledge of single adsorption on MoS{sub 2} monolayer is important not only for the sake of a theoretical understanding, but also device level deposition technological application.

  8. Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

    DEFF Research Database (Denmark)

    Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

    2017-01-01

    activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

  9. Intra- and inter-atomic optical transitions of Fe, Co, and Ni ferrocyanides studied using first-principles many-electron calculations

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Shinta, E-mail: s-watanabe@nucl.nagoya-u.ac.jp, E-mail: j-onoe@nucl.nagoya-u.ac.jp; Sawada, Yuki; Nakaya, Masato; Yoshino, Masahito; Nagasaki, Takanori; Onoe, Jun, E-mail: s-watanabe@nucl.nagoya-u.ac.jp, E-mail: j-onoe@nucl.nagoya-u.ac.jp [Department of Materials, Physics and Energy Engineering, Graduated School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Kameyama, Tatsuya; Torimoto, Tsukasa [Department of Crystalline Materials Science, Graduated School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Inaba, Yusuke; Takahashi, Hideharu; Takeshita, Kenji [Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, 2-12-1-N1-16 O-okayama, Meguro-ku, Tokyo 152-8550 (Japan)

    2016-06-21

    We have investigated the electronic structures and optical properties of Fe, Co, and Ni ferrocyanide nanoparticles using first-principles relativistic many-electron calculations. The overall features of the theoretical absorption spectra for Fe, Ni, and Co ferrocyanides calculated using a first-principles many-electron method well reproduced the experimental one. The origins of the experimental absorption spectra were clarified by performing a configuration analysis based on the many-electron wave functions. For Fe ferrocyanide, the experimental absorption peaks originated from not only the charge-transfer transitions from Fe{sup 2+} to Fe{sup 3+} but also the 3d-3d intra-transitions of Fe{sup 3+} ions. In addition, the spin crossover transition of Fe{sup 3+} predicted by the many-electron calculations was about 0.24 eV. For Co ferrocyanide, the experimental absorption peaks were mainly attributed to the 3d-3d intra-transitions of Fe{sup 2+} ions. In contrast to the Fe and Co ferrocyanides, Ni ferrocyanide showed that the absorption peaks originated from the 3d-3d intra-transitions of Ni{sup 3+} ions in a low-energy region, while from both the 3d-3d intra-transitions of Fe{sup 2+} ions and the charge-transfer transitions from Fe{sup 2+} to Ni{sup 3+} in a high-energy region. These results were quite different from those of density-functional theory (DFT) calculations. The discrepancy between the results of DFT calculations and those of many-electron calculations suggested that the intra- and inter-atomic transitions of transition metal ions are significantly affected by the many-body effects of strongly correlated 3d electrons.

  10. Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (phi-psi) space

    NARCIS (Netherlands)

    Liu, Z.; Ensing, B.; Moore, P.B.

    2011-01-01

    The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (phi-psi) conformational space. The FES is obtained from metadynamics simulations with five commonly used

  11. Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.

    Science.gov (United States)

    Silvaroli, Josie A; Arne, Jason M; Chelstowska, Sylwia; Kiser, Philip D; Banerjee, Surajit; Golczak, Marcin

    2016-04-15

    Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Measuring the mechanical properties of molecular conformers

    Science.gov (United States)

    Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

    2015-09-01

    Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

  13. Magnetic properties of Mg{sub 12}O{sub 12} nanocage doped with transition metal atoms (Mn, Fe, Co and Ni): DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Javan, Masoud Bezi, E-mail: javan.masood@gmail.com

    2015-07-01

    Binding energy of the Mg{sub 12}O{sub 12} nanocage doped with transition metals (TM=Mn, Fe, Co and Ni) in endohedrally, exohedrally and substitutionally forms were studied using density functional theory with the generalized gradient approximation exchange-correlation functional along 6 different paths inside and outside of the Mg{sub 12}O{sub 12} nanocage. The most stable structures were determined with full geometry optimization near the minimum of the binding energy curves of all the examined paths inside and outside of the Mg{sub 12}O{sub 12} nanocage. The results reveal that for all stable structures, the Ni atom has a larger binding energy than the other TM atoms. It is also found that for all complexes additional peaks contributed by TM-3d, 4s and 4p states appear in the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) gap of the host MgO cluster. The mid-gap states are mainly due to the hybridization between TM-3d, 4s and 4p orbitals and the cage π orbitals. The magnetic moment of the endohedrally doped TM atoms in the Mg{sub 12}O{sub 12} are preserved to some extent due to the interaction between the TM and Mg{sub 12}O{sub 12} nanocage, in contrast to the completely quenched magnetic moment of the Fe and Ni atoms in the Mg{sub 11}(TM)O{sub 12} complexes. Furthermore, charge population analysis shows that charge transfer occurs from TM atom to the cage for endohedrally and substitutionally doping. - Highlights: • Binding energy of the Mg{sub 12}O{sub 12} nanocage doped with transition metals was studied. • The most stable structures were determined near the minimum of the binding energy. • The encapsulated Ni atom has a larger binding energy than the other TM atoms. • Magnetic moment of the endohedrally doped TM atoms in the Mg{sub 12}O{sub 12} are preserved.

  14. Technical Note: Effect of explicit M and N-shell atomic transitions on a low-energy x-ray source

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Peter G. F., E-mail: peter.watson@mail.mcgill.ca; Seuntjens, Jan [Medical Physics Unit, McGill University, Montreal, Quebec H4A 3J1 (Canada)

    2016-04-15

    Purpose: In EGSnrc, atomic transitions to and from the M and N-shells are treated in an average way by default. This approach is justified in which the energy difference between explicit and average M and N-shell binding energies is less than 1 keV, and for most applications can be considered negligible. However, for simulations of low energy x-ray sources on thin, high-Z targets, characteristic x-rays can make up a significant portion of the source spectra. As of release V4-2.4.0, EGSnrc has included an option to enable a more complete algorithm of all atomic transitions available in the EADL compilation. In this paper, the effect of M and N-shell averaging on the calculation of half-value layer (HVL) and relative depth dose (RDD) curve of a 50 kVp intraoperative x-ray tube with a thin gold target was investigated. Methods: A 50 kVp miniature x-ray source with a gold target (The INTRABEAM System, Carl Zeiss, Germany) was modeled with the EGSnrc user code cavity, both with and without M and N-shell averaging. From photon fluence spectra simulations, the source HVLs were determined analytically. The same source model was then used with egs-chamber to calculate RDD curves in water. Results: A 4% increase of HVL was reported when accounting for explicit M and N-shell transitions, and up to a 9% decrease in local relative dose for normalization at 3 mm depth in water. Conclusions: The EGSnrc default of using averaged M and N-shell binding energies has an observable effect on the HVL and RDD of a low energy x-ray source with high-Z target. For accurate modeling of this class of devices, explicit atomic transitions should be included.

  15. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

    Science.gov (United States)

    Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

    2014-02-01

    Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

  16. Atomic frequency reference at 1033 nm for ytterbium (Yb)-doped fiber lasers and applications exploiting a rubidium (Rb) 5S_1/2 to 4D_5/2 one-colour two-photon transition

    Science.gov (United States)

    Roy, Ritayan; Condylis, Paul C.; Johnathan, Yik Jinen; Hessmo, Björn

    2017-04-01

    We demonstrate a two-photon transition of rubidium (Rb) atoms from the ground state (5$S_{1/2}$) to the excited state (4$D_{5/2}$), using a home-built ytterbium (Yb)-doped fiber amplifier at 1033 nm. This is the first demonstration of an atomic frequency reference at 1033 nm as well as of a one-colour two-photon transition for the above energy levels. A simple optical setup is presented for the two-photon transition fluorescence spectroscopy, which is useful for frequency stabilization for a broad class of lasers. This spectroscopy has potential applications in the fiber laser industry as a frequency reference, particularly for the Yb-doped fiber lasers. This two-photon transition also has applications in atomic physics as a background- free high- resolution atom detection and for quantum communication, which is outlined in this article.

  17. Confocal absorption spectral imaging of MoS2: optical transitions depending on the atomic thickness of intrinsic and chemically doped MoS2.

    Science.gov (United States)

    Dhakal, Krishna P; Duong, Dinh Loc; Lee, Jubok; Nam, Honggi; Kim, Minsu; Kan, Min; Lee, Young Hee; Kim, Jeongyong

    2014-11-07

    We performed a nanoscale confocal absorption spectral imaging to obtain the full absorption spectra (over the range 1.5-3.2 eV) within regions having different numbers of layers and studied the variation of optical transition depending on the atomic thickness of the MoS2 film. Three distinct absorption bands corresponding to A and B excitons and a high-energy background (BG) peak at 2.84 eV displayed a gradual redshift as the MoS2 film thickness increased from the monolayer, to the bilayer, to the bulk MoS2 and this shift was attributed to the reduction of the gap energy in the Brillouin zone at the K-point as the atomic thickness increased. We also performed n-type chemical doping of MoS2 films using reduced benzyl viologen (BV) and the confocal absorption spectra modified by the doping showed a strong dependence on the atomic thickness: A and B exciton peaks were greatly quenched in the monolayer MoS2 while much less effect was shown in larger thickness and the BG peak either showed very small quenching for 1 L MoS2 or remained constant for larger thicknesses. Our results indicate that confocal absorption spectral imaging can provide comprehensive information on optical transitions of microscopic size intrinsic and doped two-dimensional layered materials.

  18. Atomic-Resolution Visualization of Distinctive Chemical Mixing Behavior of Ni, Co and Mn with Li in Layered Lithium Transition-Metal Oxide Cathode Materials

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Pengfei; Zheng, Jianming; Lv, Dongping; Wei, Yi; Zheng, Jiaxin; Wang, Zhiguo; Kuppan, Saravanan; Yu, Jianguo; Luo, Langli; Edwards, Danny J.; Olszta, Matthew J.; Amine, Khalil; Liu, Jun; Xiao, Jie; Pan, Feng; Chen, Guoying; Zhang, Jiguang; Wang, Chong M.

    2015-07-06

    Capacity and voltage fading of layer structured cathode based on lithium transition metal oxide is closely related to the lattice position and migration behavior of the transition metal ions. However, it is scarcely clear about the behavior of each of these transition metal ions. We report direct atomic resolution visualization of interatomic layer mixing of transition metal (Ni, Co, Mn) and lithium ions in layer structured oxide cathodes for lithium ion batteries. Using chemical imaging with aberration corrected scanning transmission electron microscope (STEM) and DFT calculations, we discovered that in the layered cathodes, Mn and Co tend to reside almost exclusively at the lattice site of transition metal (TM) layer in the structure or little interlayer mixing with Li. In contrast, Ni shows high degree of interlayer mixing with Li. The fraction of Ni ions reside in the Li layer followed a near linear dependence on total Ni concentration before reaching saturation. The observed distinctively different behavior of Ni with respect to Co and Mn provides new insights on both capacity and voltage fade in this class of cathode materials based on lithium and TM oxides, therefore providing scientific basis for selective tailoring of oxide cathode materials for enhanced performance.

  19. Sub-doppler spectroscopy based on the transit relaxation of atomic particles in a thin gas cell

    International Nuclear Information System (INIS)

    Izmailov, Azad

    2010-01-01

    This paper is the review of methods, achievements and possibilities of the recently elaborated high-resolution laser spectroscopy based on sub-doppler absorption, fluorescence and polarization resonances, which arise because of the specific optical selection of comparatively slow-speed atoms in a thin cell with rarefied gas. It was considered two following mechanisms of such a velocity selection of atomic particles connected with their flight durations between walls of the thin cell : 1) optical pumping of sublevels of the ground atomic term and 2) optical excitation of long-lived quantum levels. Theoretical bases of elaborated spectroscopy methods are presented. In case of the optical pumping mechanism, experimental technique and results on the record of sub-doppler spectral structure of Cs and Rb atoms and on the frequency stabilization of diode lasers by given methods are described. Perspectives of further development and applications of this new direction of the high-resolution spectroscopy are discussed

  20. One step beyond the electric dipole approximation: An experiment to observe the 5p → 6p forbidden transition in atomic rubidium

    Science.gov (United States)

    Ponciano-Ojeda, F.; Hernández-Gómez, S.; Mojica-Casique, C.; Ruiz-Martínez, E.; López-Hernández, O.; Colín-Rodríguez, R.; Ramírez-Martínez, F.; Flores-Mijangos, J.; Sahagún, D.; Jáuregui, R.; Jiménez-Mier, J.

    2018-01-01

    An advanced undergraduate experiment to study the 5 P 3 / 2 → 6 P 3 / 2 electric quadrupole transition in rubidium atoms is presented. The experiment uses two external cavity diode lasers, one operating at the D2 rubidium resonance line and the other built with commercial parts to emit at 911 nm. The lasers produce the 5 s → 5 p → 6 p excitation sequence in which the second step is the forbidden transition. Production of atoms in the 6 P 3 / 2 state is observed by detection of the 420 nm fluorescence that results from electric dipole decay into the ground state. Lines whose widths are significantly narrower than the Doppler width are used to study the hyperfine structure of the 6 P 3 / 2 state in rubidium. The spectra illustrate characteristics unique to electric dipole forbidden transitions, like the electric quadrupole selection rules; they are also used to show general aspects of two-color laser spectroscopy such as velocity selection and hyperfine pumping.

  1. Studies of highly ionized atoms using internal conversion: 197Au, 57Fe; electric monopole transitions in 40Ca, 42Ca, and 44Ca

    International Nuclear Information System (INIS)

    Ulrickson, M.A.

    1975-01-01

    By using heavy-ion reactions, highly ionized electronic states of atoms may be produced. The interaction between excited nuclear levels and the surrounding atomic electrons via internal conversion allows the nucleus to be used as a probe of the electronic structure of the highly ionized atoms. Studies of such atoms were undertaken for strongly internally converted nuclear levels in 197 Au and 57 Fe. The nuclear levels were Coulomb excited by using 16 O and 32 S beams. Simultaneous measurement of the lifetime of the 77-keV state of 197 Au in both neutral gold atoms and gold atoms with mean charge +10 resulted in a measured change in the internal conversion coefficient of Δalpha/alpha equals - 1.7 +- 3.0)10 -3 . This result is consistent with calculations using a Hartree-Fock--Slater program. Measurements of the electric monopole strengths for 0 + → 0 + transitions were undertaken to determine the amount of core-deformation in calcium nuclei. The E0 strengths for the decays of the 0 + states at 5.21 MeV in 40 C, 1.84 MeV in 42 Ca, and 1.88 MeV in 44 Ca were observed. The branching ratios for the subsequent E0 pair decays were measured by observing the coincident annihilation radiation from the e + member of the pair in coincidence with protons feeding the state in the cases of 42 Ca and 44 Ca, and by observing the actual coincident e + --e - pair together with protons feeding the state in the case of 40 Ca. The resulting E0 strengths (rho less than or equal to 0.06, rho = 0.34 +- 0.03, rho = 0.30 +- 0.10 for 40 Ca, 42 Ca, and 44 Ca respectively) agree with theoretical descriptions

  2. The polarization-angular structure and elliptical dichroism of the cross sections for three-photon bound-bound transitions in atoms

    International Nuclear Information System (INIS)

    Manakov, N.L.; Merem'yanin, A.V.

    1997-01-01

    Using the electric dipole approximation, we present, in invariant form, the cross section of an arbitrary three-photon transition between the discrete states of an atom with total angular momenta J i and J f . The cross section contains scalar and mixed products of the photon polarization vectors, and invariant atomic parameters dependent only on the photon frequencies. We determine the number of independent atomic parameters at fixed values of J i and J f and obtain their explicit expressions in terms of the reduced composite dipole matrix elements. The polarization dependence of the cross sections is expressed in terms of the degrees l and ξ of linear and circular photon polarizations. We analyze the phenomenon of dissipation-induced circular dichroism in three-photon processes, i.e., the difference Δ of the cross sections for opposite signs of the degree of circular polarization of all the photons. We study in detail the case of two identical photons and the phenomenon of elliptical dichroism, when Δ∼lξ holds and dichroism occurs only when the photons are elliptically polarized, with 0< vertical bar ξ vertical bar <1. Finally, we discuss the dissipation-induced effects of atom polarization in three-photon processes involving linearly polarized or unpolarized photons

  3. Correlation between catalytic activity and bonding and coordination number of atoms and molecules on transition metal surfaces: theory and experimental evidence

    International Nuclear Information System (INIS)

    Falicov, L.M.; Somorjai, G.A.

    1985-01-01

    Correlation between catalytic activity and low-energy local electronic fluctuation in transition metals is proposed. A theory and calculations are presented which indicate that maximum electronic fluctuants take place at high-coordination metal sites. Either (i) atomically rough surfaces that expose to the reactant molecules atoms with large numbers of nonmagnetic or weakly magnetic neighbors in the first or second layer at the surface or (ii) stepped and kinked surfaces are the most active in carrying out structure-sensitive catalytic reactions. The synthesis of ammonia from N 2 and H 2 over iron and rhenium surfaces, 1 H 2 / 2 H 2 exchange over stepped platinum crystal surfaces at low pressures, and the hydrogenolysis (C - C bond breaking) of isobutane at kinked platinum crystal surfaces are presented as experimental evidence in support of the theory

  4. Spatio-temporal coherent control of atomic systems: weak to strong field transition and breaking of symmetry in 2D maps

    Energy Technology Data Exchange (ETDEWEB)

    Suchowski, H; Natan, A; Bruner, B D; Silberberg, Y [Physics of Complex Systems, Weizmann Institute of Science, Rehovot (Israel)], E-mail: haim.suchowski@weizmann.ac.il

    2008-04-14

    Coherent control of resonant and non-resonant two-photon absorption processes was examined using a spatio-temporal pulse-shaping technique. By utilizing a combination of temporal focusing and femtosecond pulse-shaping techniques, we spatially control multiphoton absorption processes in a completely deterministic manner. Distinctive symmetry properties emerge through two-dimensional mapping of spatio-temporal data. These symmetries break down in the transition to strong fields, revealing details of strong-field effects such as power broadenings and dynamic Stark shifts. We also present demonstrations of chirp-dependent population transfer in atomic rubidium, as well as the spatial separation of resonant and non-resonant excitation pathways in atomic caesium.

  5. Spatio-temporal coherent control of atomic systems: weak to strong field transition and breaking of symmetry in 2D maps

    International Nuclear Information System (INIS)

    Suchowski, H; Natan, A; Bruner, B D; Silberberg, Y

    2008-01-01

    Coherent control of resonant and non-resonant two-photon absorption processes was examined using a spatio-temporal pulse-shaping technique. By utilizing a combination of temporal focusing and femtosecond pulse-shaping techniques, we spatially control multiphoton absorption processes in a completely deterministic manner. Distinctive symmetry properties emerge through two-dimensional mapping of spatio-temporal data. These symmetries break down in the transition to strong fields, revealing details of strong-field effects such as power broadenings and dynamic Stark shifts. We also present demonstrations of chirp-dependent population transfer in atomic rubidium, as well as the spatial separation of resonant and non-resonant excitation pathways in atomic caesium

  6. Computationally efficient analytic representations of relativistic bound-bound, bound-unbound and unbound-unbound transition matrix elements of hydrogenic atoms

    International Nuclear Information System (INIS)

    Soldatov, A.; Seke, J.; Adam, G.; Polak, M.

    2008-01-01

    Full text: A closed analytic form for relativistic transition matrix elements between bound-bound, bound-unbound and unbound-unbound relativistic eigenstates of hydrogenic atoms by using the plane-wave expansion for the electromagnetic-field vector potential was derived in a form convenient for large-scale numerical calculations in QED. By applying the obtained formulae, these transition matrix elements can be evaluated analytically and numerically. These exact matrix elements, which to our knowledge have not been calculated as yet, are of great importance in the analysis of various atom-field interaction processes where retardation effects cannot be ignored. The ultimate goal of the ongoing research is to develop a general universal calculation technique for Seke's approximation and renormalization method in QED, for which the usage of the plane vector expansion for the vector potential is a preferable choice. However, our primary interest lies in the Lamb-shift calculation. Our nearest objective is to carry out the plain-style relativistic calculations of the Lamb shift of the energy levels of hydrogen-like atoms and ions from first principles in the second and higher perturbative orders, using the corresponding convenient as well as novel expressions for the magnitude in question as they stand, i.e. without any additional approximations. Due to that there is no way to achieve all the above-declared goals without recourse to large-scale laborious and time-consuming high-precision numerical calculations, having the transition matrix elements of all possible types in an analytic, convenient for their efficient numerical evaluation form, would be highly advantageous and even unavoidable, especially for calculations of various QED effects in higher perturbative orders be it, equally, in traditional or novel approach. (author)

  7. Electron-impact excitation of atomic-argon 3p54s-3p55p spectral transitions

    International Nuclear Information System (INIS)

    Bogdanova, I.P.; Yurgenson, S.V.

    1990-01-01

    Cross sections of excitation of some spectral lines of argon corresponding to transitions from 3p 5 5p-levels are measured using a pulsed electron beam. Cross sections of level excitation are estimated. It is shown that in transition from 3p 5 4p-levels to 3p 5 5p-levels, the cross section of levels by means of the electron impact decreases 20 times

  8. Quadrupole and monopole generalized oscillator strength for 2p-3p, 2p-4p transition of neon atomic in the velocity formulation

    International Nuclear Information System (INIS)

    Gomis, L; Diedhiou, I; Tall, M S; Diallo, S; Diatta, C S; Niassy, B

    2007-01-01

    The quadrupole and monopole generalized oscillator strengths (GOS) as a function of momentum transfer are calculated for the 2p-3p and 2p-4p transitions of the neon atom using the analytical Hartree-Fock (HF) wavefunctions for the ground-state and the wavefunctions for the excited states which are obtained numerically from the modified HF Slater equation. Calculations are carried out by using the HF method and random phase approximation with exchange in the velocity formulation. The positions and the number of the extrema in the GOS have received particular attention in the evaluation. Our calculated monopole GOS of 2p-3p transition in velocity form reveals one maximum located between the experimental and theoretical results of other authors. The disagreement between our first maximum of the quadrupole GOS 2p-3p transition with the experimental and other theoretical ones is unimportant. The extrema of the monopole and quadrupole GOS of 2p-4p transition are given in this paper. The results of velocity form study also show that the electron correlation effects are important around the maxima and are found to influence the positions of the extrema insignificantly

  9. Conformal invariance and two-dimensional physics

    International Nuclear Information System (INIS)

    Zuber, J.B.

    1993-01-01

    Actually, physicists and mathematicians are very interested in conformal invariance: geometric transformations which keep angles. This symmetry is very important for two-dimensional systems as phase transitions, string theory or node mathematics. In this article, the author presents the conformal invariance and explains its usefulness

  10. General Information for Transportation and Conformity

    Science.gov (United States)

    Transportation conformity is required by the Clean Air Act section 176(c) (42 U.S.C. 7506(c)) to ensure that federal funding and approval are given to highway and transit projects that are consistent with SIP.

  11. Reactivity of transition metal atoms supported or not on TiO2(110) toward CO and H adsorption

    KAUST Repository

    Helali, Zeineb; Jedidi, Abdesslem; Markovits, Alexis; Minot, Christian; Abderrabba, Manef Ben

    2015-01-01

    Following our strategy to analyze the metal–support interaction, we present periodic DFT calculations for adsorption of metal atoms on a perfect rutile TiO2(110) surface (at low coverage, θ = 1/3) to investigate the interaction of an individual

  12. An atomic force microscopy study on the transition from mushrooms to octopus surface ''micelles'' by changing the solvent quality

    NARCIS (Netherlands)

    Stamouli, A.; Pelletier, E.; Koutsos, V; van der Vegte, E.W.; Hadziioannou, G

    1996-01-01

    Atomic force microscopy (AFM) is used to study the behavior of a diblock copolymer onto a solid surface while the solvent quality is changed. In a first step, the copolymer poly(2-vinylpyridine)/polystyrene (P2VP/PS) is adsorbed onto mica from a selective solvent (the PS block is well solvated and

  13. Observation of the Forbidden Magnetic Dipole Transition 6{sup 2}P{sub ½} --> 7{sup 2}P{sub ½} in Atomic Thallium

    Science.gov (United States)

    Chu, S.

    1976-10-01

    A measurement of the 6{sup 2}P{sub ½} --> 7{sup 2}P{sub ½} forbidden magnetic dipole matrix element in atomic thallium is described. A pulsed, linearly polarized dye laser tuned to the transition frequency is used to excite the thallium vapor from the 6{sup 2}P{sub ½} ground state to the 7{sup 2}P{sub ½} excited state. Interference between the magnetic dipole M1 amplitude and a static electric field induced E1 amplitude results in an atomic polarization of the 7{sup 2}P{sub ½} state, and the subsequent circular polarization of 535 nm fluorescence. The circular polarization is seen to be proportional to / as expected, and measured for several transitions between hyperfine levels of the 6{sup 2}P{sub ½} and 7{sup 2}P{sub ½} states. The result is = -(2.11 +- 0.30) x 10{sup -5} parallel bar e parallel bar dirac constant/2mc, in agreement with theory.

  14. Remote sensing of atomic oxygen: Some observational difficulties in the use of the forbidden O I λ 1173-angstrom and O I λ 1641-angstrom transitions

    International Nuclear Information System (INIS)

    Erdman, P.W.; Zipf, E.C.

    1987-01-01

    Recent sounding rocket and satellite studies suggest that simultaneous measurements of the O I λ989-angstrom and λ1,304-angstrom resonance lines and of the forbidden λ1,172.6-angstrom and λ1641.3-angstrom transitions which also originate from the 3s'3D degree and 3s 3S degree states would form the basis of a useful remote sensing technique for measuring the O I density and optical of a planetary or stellar atmosphere. Because the λ1,172.6-angstrom and λ1641.3-angstrom emissions are weak lines and are emitted in a wavelength region rich in spectral features, it is important to determine whether typical flight instruments can make measurements with sufficient spectral purity so that the remote sensing observations will yield accurate results. We have made a detailed, high-resolution study of the far ultraviolet emission features in the regions surrounding the atomic oxygen transitions at λ1,172.6-angstrom and λ1,641.3-angstrom. These spectra, which were excited by electron impact on O 2 and N 2 , are presented in an attempt to display some potential sources of interference in aeronomical measurements of these O I lines. Both atomic and molecular emissions are found, and the spectral resolution necessary to make unambiguous measurements is discussed

  15. Infrared diode-laser measurements of some atomic helium (4He I 1s nl) fine-structure transitions: comment

    International Nuclear Information System (INIS)

    Kono, A.

    1987-01-01

    Five recently measured 4 He I transitions involving nS, nP, and nD levels (n = 3--8, Δn = 0,2) are compared with theoretical energy levels having estimated uncertainties that are comparable with those of the experimental results (--10 -3 cm -1 ) [T.J. Sears S. C. Foster, and A. R. W. McKellar, J. Opt. Soc. Am. B3, 1037 (1986)]. The agreement between theory and experiment is generally good, but considerable discrepancy exists for one transition

  16. Conformal Tachyons

    CERN Document Server

    Tomaschitz, R

    2000-01-01

    We study tachyons conformally coupled to the background geometry of a Milne universe. The causality of superluminal signal transfer is scrutinized in this context. The cosmic time of the comoving frame determines a distinguished time order for events connected by superluminal signals. An observer can relate his rest frame to the galaxy frame, and compare so the time order of events in his proper time to the cosmic time order. All observers can in this way arrive at identical conclusions on the causality of events connected by superluminal signals. An unambiguous energy concept for tachyonic rays is defined by means of the cosmic time of the comoving reference frame, without resorting to an antiparticle interpretation. On that basis we give an explicit proof that no signals can be sent into the past of observers. Causality violating signals are energetically forbidden, as they would have negative energy in the rest frame of the emitting observer. If an observer emits a superluminal signal, the tachyonic respon...

  17. Nonlinear magneto-optical rotation produced by atoms near a J=1→J=0 transition

    International Nuclear Information System (INIS)

    Roscinski, Vitalij; Czub, Janusz; Miklaszewski, Wieslaw

    2004-01-01

    The nonlinear magneto-optical rotation in a medium consisting of J=1→J=0 atoms placed in a static magnetic field is studied. The density matrix approach and irreducible atomic basis are used to describe the state of the atomic system. The stationary propagation equations for two collinear laser beams with perpendicular circular polarizations are derived and analyzed in the case of the magnetic field perpendicular to the light propagation direction. The effect of the linear polarization rotation toward the direction parallel or perpendicular to the magnetic field vector and lossless propagation of the resulting light are predicted. The conversion of the circularly polarized beam into linearly polarized one is shown. The propagation of the leading edges of switched on cw-laser beams and their stationary propagation are analyzed numerically. The dependence of the considered effects on the light detuning and on the additional magnetic field component parallel to the light propagation direction is discussed. The destructive role of the collisional relaxation is demonstrated

  18. Ultracold lithium-6 atoms in the BEC-BCS crossover: experiments and the construction of a new apparatus; Atomes de lithium-6 ultra froids dans la transition BEC-BCS: experiences et construction d'un montage experimental

    Energy Technology Data Exchange (ETDEWEB)

    Teichmann, M

    2007-09-15

    We use a fermionic gas of Lithium-6 as a model system to study superfluidity. The limiting cases of superfluidity are Bose-Einstein condensation (BEC) and superconductivity, described by the theory by Bardeen, Cooper and Schrieffer (BCS). In Lithium-6 gases, we can explore the whole range between the two cases, known as the BEC-BCS crossover, using a Feshbach resonance. We study the change of the momentum distribution of the gas in this cross-over and compare to theoretical models. We also investigate the hydrodynamic expansion, characteristic for a superfluid gas. We observe a sudden change of the ellipticity of the gas close to the transition to the superfluid phase. Moreover, we localized heteronuclear Feshbach resonances between {sup 6}Li and {sup 7}Li. We are currently constructing a second generation of the experimental setup. An new laser system, based on high power laser diodes, was developed. Changes in the vacuum chamber, including a complete reconstruction of the Zeeman slower, have increased the atomic flux, allowing us to increase the repetition rate of our experiment. Modifications of the geometry of the magnetic traps lead to a higher number of trapped atoms. (author)

  19. Ultracold lithium-6 atoms in the BEC-BCS crossover: experiments and the construction of a new apparatus; Atomes de lithium-6 ultra froids dans la transition BEC-BCS: experiences et construction d'un montage experimental

    Energy Technology Data Exchange (ETDEWEB)

    Teichmann, M

    2007-09-15

    We use a fermionic gas of Lithium-6 as a model system to study superfluidity. The limiting cases of superfluidity are Bose-Einstein condensation (BEC) and superconductivity, described by the theory by Bardeen, Cooper and Schrieffer (BCS). In Lithium-6 gases, we can explore the whole range between the two cases, known as the BEC-BCS crossover, using a Feshbach resonance. We study the change of the momentum distribution of the gas in this cross-over and compare to theoretical models. We also investigate the hydrodynamic expansion, characteristic for a superfluid gas. We observe a sudden change of the ellipticity of the gas close to the transition to the superfluid phase. Moreover, we localized heteronuclear Feshbach resonances between {sup 6}Li and {sup 7}Li. We are currently constructing a second generation of the experimental setup. An new laser system, based on high power laser diodes, was developed. Changes in the vacuum chamber, including a complete reconstruction of the Zeeman slower, have increased the atomic flux, allowing us to increase the repetition rate of our experiment. Modifications of the geometry of the magnetic traps lead to a higher number of trapped atoms. (author)

  20. Conformal field theory in conformal space

    International Nuclear Information System (INIS)

    Preitschopf, C.R.; Vasiliev, M.A.

    1999-01-01

    We present a new framework for a Lagrangian description of conformal field theories in various dimensions based on a local version of d + 2-dimensional conformal space. The results include a true gauge theory of conformal gravity in d = (1, 3) and any standard matter coupled to it. An important feature is the automatic derivation of the conformal gravity constraints, which are necessary for the analysis of the matter systems

  1. Relativistic calculation of Kβ hypersatellite energies and transition probabilities for selected atoms with 13 ≤ Z ≤ 80

    International Nuclear Information System (INIS)

    Costa, A M; Martins, M C; Santos, J P; Indelicato, P; Parente, F

    2006-01-01

    Energies and transition probabilities of Kβ hypersatellite lines are computed using the Dirac-Fock model for several values of Z throughout the periodic table. The influence of the Breit interaction on the energy shifts from the corresponding diagram lines and on the Kβ h 1 /Kβ h 3 intensity ratio is evaluated. The widths of the double-K hole levels are calculated for Al and Sc. The results are compared to experiment and to other theoretical calculations

  2. Theoretical spectroscopic studies of the atomic transitions and lifetimes of low-lying states in Ti IV

    International Nuclear Information System (INIS)

    Mandal, Subhasish; Dixit, Gopal; Majumder, Sonjoy; Sahoo, B K; Chaudhuri, R K

    2008-01-01

    The astrophysically important electric quadrupole (E2) and magnetic dipole (M1) transitions for the low-lying states of triply ionized titanium (Ti IV) are calculated very accurately using a state-of-the-art all-order many-body theory called coupled cluster (CC) method in the relativistic framework. Different many-body correlations of the CC theory has been estimated by studying the core and valence electron excitations to the unoccupied states. The calculated excitation energies of different states are in excellent agreement with the measurements. Also, we compare our calculated electric dipole (E1) amplitudes of few transitions with recent many-body calculations by others. The lifetimes of the low-lying states of Ti IV have been estimated and long lifetime is found for the first excited 3d 2 D 5/2 state, which suggested that Ti IV may be one of the useful candidates for many fundamental studies of physics. Most of the forbidden transition results reported here are not available in the literature, to the best of our knowledge

  3. Optical spectroscopy of an atomic nucleus: Progress toward direct observation of the {sup 229}Th isomer transition

    Energy Technology Data Exchange (ETDEWEB)

    Hehlen, Markus P., E-mail: hehlen@lanl.gov [Los Alamos National Laboratory, Mailstop E549, Los Alamos, NM 87545 (United States); Greco, Richard R. [Los Alamos National Laboratory, Mailstop E549, Los Alamos, NM 87545 (United States); Rellergert, Wade G.; Sullivan, Scott T. [Department of Physics and Astronomy, University of California, Los Angeles, CA 90095 (United States); DeMille, David [Department of Physics, Yale University, New Haven, CT 06511 (United States); Jackson, Robert A. [School of Physical and Geographical Sciences, Keele University, Keele, Staffordshire ST5 5BG (United Kingdom); Hudson, Eric R. [Department of Physics and Astronomy, University of California, Los Angeles, CA 90095 (United States); Torgerson, Justin R. [Los Alamos National Laboratory, Mailstop E549, Los Alamos, NM 87545 (United States)

    2013-01-15

    The nucleus of the thorium-229 isotope possesses a first excited nuclear state ({sup 229m}Th) at an exceptionally low energy of 7.8{+-}0.5 eV above the nuclear ground state ({sup 229g}Th), as determined by earlier indirect measurements. This is the only nuclear excited state known that is within the range of optical spectroscopy. This paper reports progress toward detecting the {sup 229m}Th state directly by luminescence spectroscopy in the vacuum ultraviolet spectral region. The estimated natural linewidth of the {sup 229g}Th{r_reversible}{sup 229m}Th isomer transition of 2{pi} Multiplication-Sign 0.1 to 2{pi} Multiplication-Sign 10 mHz is expected to broaden to {approx}10 kHz for {sup 229}Th{sup 4+} doped into a suitable crystal. The factors governing the choice of crystal system and the substantial challenges in acquiring a sufficiently large quantity of {sup 229}Th are discussed. We show that the {sup 229g}Th{r_reversible}{sup 229m}Th transition energy can be identified to within 0.1 nm by luminescence excitation and luminescence spectroscopy using the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory. This would open the door for subsequent laser-based measurements of the isomer transition and future applications of {sup 229}Th in nuclear clocks. We also show that {sup 233}U-doped materials should produce an intrinsic, continuous, and sufficiently high rate of {sup 229m}Th{yields}{sup 229g}Th luminescence and could be a useful aid in the initial direct search of the isomer transition. - Highlights: Black-Right-Pointing-Pointer Thorium-229 has a long-lived nuclear excited state. Black-Right-Pointing-Pointer It is the only known nuclear isomer within the reach of optical spectroscopy. Black-Right-Pointing-Pointer Thorium-229 doped fluoride crystals may offer sufficiently high luminescence rates. Black-Right-Pointing-Pointer Luminescence excitation spectroscopy in the vacuum ultraviolet spectral region may enable the first direct observation of

  4. Code ATOM for calculation of atomic characteristics

    International Nuclear Information System (INIS)

    Vainshtein, L.A.

    1990-01-01

    In applying atomic physics to problems of plasma diagnostics, it is necessary to determine some atomic characteristics, including energies and transition probabilities, for very many atoms and ions. Development of general codes for calculation of many types of atomic characteristics has been based on general but comparatively simple approximate methods. The program ATOM represents an attempt at effective use of such a general code. This report gives a brief description of the methods used, and the possibilities of and limitations to the code are discussed. Characteristics of the following processes can be calculated by ATOM: radiative transitions between discrete levels, radiative ionization and recombination, collisional excitation and ionization by electron impact, collisional excitation and ionization by point heavy particle (Born approximation only), dielectronic recombination, and autoionization. ATOM explores Born (for z=1) or Coulomb-Born (for z>1) approximations. In both cases exchange and normalization can be included. (N.K.)

  5. Reexamination of M2,3 atomic level widths and L1M2,3 transition energies of elements 69≤Z≤95

    Science.gov (United States)

    Fennane, K.; Berset, M.; Dousse, J.-Cl.; Hoszowska, J.; Raboud, P.-A.; Campbell, J. L.

    2013-11-01

    We report on high-resolution measurements of the photoinduced L1M2 and L1M3 x-ray emission lines of 69Tm, 70Yb, 71Lu, 73Ta, 74W, 75Re, 77Ir, 81Tl, 83Bi, and 95Am. From the linewidths of the measured transitions an accurate set of M2 and M3 level widths is determined assuming for the L1 level widths the values reported by Raboud [P.-A. Raboud et al., Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.65.022512 65, 022512 (2002)]. Furthermore, the present experimental M2,3 data set is extended to 80Hg, 90Th, and 92U, using former L1M2,3 high-resolution x-ray emission spectroscopy measurements performed by our group. A detailed comparison of the M2 and M3 level widths determined in the present work with those recommended by Campbell and Papp [J. L. Campbell and T. Papp, At. Data Nucl. Data TablesADNDAT0092-640X10.1006/adnd.2000.0848 77, 1 (2001)] and other available experimental data as well as theoretical predictions is done. The observed abrupt changes of the M2,3 level widths versus atomic number Z can be explained satisfactorily by the cutoffs and onsets of the M2M4N1, respectively M3M4N3,4,5 and M3M5N2,3 Coster-Kronig transitions deduced from the semiempirical (Z+1) approximation. As a spin-off result of this study, precise L1M2 and L1M3 transition energies are obtained for the investigated elements. A very good agreement with transition energies calculated within the many-body perturbation theory is found.

  6. Transition-state analysis of a Vmax mutant of AMP nucleosidase by the application of heavy-atom kinetic isotope effects

    International Nuclear Information System (INIS)

    Parkin, D.W.; Mentch, F.; Banks, G.A.; Horenstein, B.A.; Schramm, V.L.

    1991-01-01

    The transition state of the V max mutant of AMP nucleosidase from Azotobacter vinelandii has been characterized by heavy-atom kinetic isotope effects in the presence and absence of MgATP, the allosteric activator. The enzyme catalyzes hydrolysis of the N-glycosidic bond of AMP at approximately 2% of the rate of the normal enzyme with only minor changes in the K m for substrate, the activation constant for MgATP, and the K i for formycin 5'-phosphate, a tight-binding competitive inhibitor. Isotope effects were measured as a function of the allosteric activator concentration that increases the turnover number of the enzyme from 0.006 s -1 . The kinetic isotope effects were measured with the substrates [1'- 3 H]AMP, [2'- 2 H]AMP, [9- 15 N]AMP, and [1',9- 14 C, 15 N]AMP. All substrates gave significant kinetic isotope effects in a pattern that establishes that the reaction expresses intrinsic kinetic isotope effects in the presence or absence of MgATP. Transition-state analysis using bond-energy and bond-order vibrational analysis indicated that the transition state for the mutant enzyme has a similar position in the reaction coordinate compared to that for the normal enzyme. The mutant enzyme is less effective in stabilizing the carbocation-like intermediate and in the ability to protonate N7 of adenine to create a better leaving group. This altered transition-state structure was confirmed by an altered substrate specificity for the mutant protein

  7. Reactivity of transition metal atoms supported or not on TiO2(110) toward CO and H adsorption

    KAUST Repository

    Helali, Zeineb

    2015-04-01

    Following our strategy to analyze the metal–support interaction, we present periodic DFT calculations for adsorption of metal atoms on a perfect rutile TiO2(110) surface (at low coverage, θ = 1/3) to investigate the interaction of an individual metal atom, M, with TiO2 and its consequence on the coadsorption of H and CO over M/TiO2. M under investigation varies in a systematic way from K to Zn. It is found that the presence of the support decreases or increases the strength of M–H or M–CO interaction according to the nature of M. The site of the adsorption for H and the formation of HCO/M also depend on M. From the left- to the right-hand side of the period, C and O both interact while O progressively detaches from M. On the contrary, for M = Fe–Cu, CO dissociation is more likely to happen. For CO and H coadsorption, two extreme cases emerge: For Ni, the hydrogen adsorbed should easily move on the support and CO dissociation is more likely. For Ti or Sc, H is easily coadsorbed with CO on the metal and CO hydrogenation could be the initial step. © 2015, Springer-Verlag Berlin Heidelberg.

  8. An MD simulation of interactions between self-interstitial atoms and edge dislocation in bcc transition metals

    Energy Technology Data Exchange (ETDEWEB)

    Kamiyama, H. (Aomori Public College, 153-4 Yamazaki, Goushi-zawa, Aomori 030-01 (Japan)); Rafii-Tabar, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Kawazoe, Y. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Matsui, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan))

    1994-09-01

    According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))

  9. An MD simulation of interactions between self-interstitial atoms and edge dislocation in bcc transition metals

    International Nuclear Information System (INIS)

    Kamiyama, H.; Rafii-Tabar, H.; Kawazoe, Y.; Matsui, H.

    1994-01-01

    According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers ''below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))

  10. Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

    Science.gov (United States)

    Chakraborty, Debayan; Wales, David J

    2018-01-04

    The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.

  11. Detection of nanocrystallinity by X-ray absorption spectroscopy in thin film transition metal/rare-earth atom, elemental and complex oxides

    International Nuclear Information System (INIS)

    Edge, L.F.; Schlom, D.G.; Stemmer, S.; Lucovsky, G.; Luning, J.

    2006-01-01

    Nanocrystallinity has been detected in the X-ray absorption spectra of transition metal and rare-earth oxides by (i) removal of d-state degeneracies in the (a) Ti and Sc L 3 spectra of TiO 2 and LaScO 3 , respectively, and (b) O K 1 spectra of Zr(Hf)O 2 , Y 2 O 3 , LaScO 3 and LaAlO 3 , and by the (ii) detection of the O-atom vacancy in the O K 1 edge ZrO 2 -Y 2 O 3 alloys. Spectroscopic detection is more sensitive than X-ray diffraction with a limit of ∼2 nm as compared to >5 mm. Other example includes detection of ZrO 2 nanocrystallinity in phase-separated Zr(Hf) silicate alloys

  12. First-Principles Calculations for Chemical Reaction between Sodium Diethyldithiocarbamate and Transition-Metal (Cr) atom to Produce Cr(DDC)3 and Cr(DDC)2ODDC

    Science.gov (United States)

    Setiyanto, Henry; Muhida, Rifki; Kishi, Tomoya; Rempillo, Ofelia; Rahman, Mahmudur; Dipojono, Hermawan Kresno; Di\\ {n}o, Wilson Agerico; Matsumoto, Shigeno; Kasai, Hideaki

    2006-10-01

    We investigate the chemical reaction between a Cr transition-metal atom and sodium diethyldithiocarbamate (NaDDC), a complexing agent used to detect and extract Cr in human blood samples. Using density-functional-theory-based calculations, we determine their stable structures of Cr(DDC)2ODDC and Cr(DDC)3 complexes and obtain their dissociation energies. We found dissociation energies of -10.66 and -3.24 eV for Cr(DDC)2ODDC and Cr(DDC)3 complexes, respectively. Hence, on the basis of dissociation energies, we have verified that the reaction of NaDDC with Cr produces Cr(DDC)2ODDC as a major product.

  13. Atomic Spectra Database (ASD)

    Science.gov (United States)

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  14. Investigation of light-induced conformation changes in spiropyran-modified succinylated poly(L-lysine).

    Science.gov (United States)

    Cooper, T M; Stone, M O; Natarajan, L V; Crane, R L

    1995-08-01

    To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(L-lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide alpha-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- vs dark-adapted solutions (6.38 +/- 0.03 M-1 vs 6.56 +/- 0.03 M-1), but not for the nucleation parameter sigma (1.2 +/- 0.4 10(-3) vs 1.3 +/- 0.3 x 10(-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Louisiana SIP: LAC 33:III Ch. 14 Subchap B, 1431 to 1434--Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded, or Approved Under Title 23 U.S.C. or the Federal Transit Laws

    Science.gov (United States)

    Louisiana SIP: LAC 33:III Ch. 14 Subchap B, 1431 to 1434--Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded, or Approved Under Title 23 U.S.C. or the Federal Transit Laws

  16. Magnetic engineering in InSe/black-phosphorus heterostructure by transition-metal-atom Sc-Zn doping in the van der Waals gap

    Science.gov (United States)

    Ding, Yi-min; Shi, Jun-jie; Zhang, Min; Zhu, Yao-hui; Wu, Meng; Wang, Hui; Cen, Yu-lang; Guo, Wen-hui; Pan, Shu-hang

    2018-07-01

    Within the framework of the spin-polarized density-functional theory, we have studied the electronic and magnetic properties of InSe/black-phosphorus (BP) heterostructure doped with 3d transition-metal (TM) atoms from Sc to Zn. The calculated binding energies show that TM-atom doping in the van der Waals (vdW) gap of InSe/BP heterostructure is energetically favorable. Our results indicate that magnetic moments are induced in the Sc-, Ti-, V-, Cr-, Mn- and Co-doped InSe/BP heterostructures due to the existence of non-bonding 3d electrons. The Ni-, Cu- and Zn-doped InSe/BP heterostructures still show nonmagnetic semiconductor characteristics. Furthermore, in the Fe-doped InSe/BP heterostructure, the half-metal property is found and a high spin polarization of 100% at the Fermi level is achieved. The Cr-doped InSe/BP has the largest magnetic moment of 4.9 μB. The Sc-, Ti-, V-, Cr- and Mn-doped InSe/BP heterostructures exhibit antiferromagnetic ground state. Moreover, the Fe- and Co-doped systems display a weak ferromagnetic and paramagnetic coupling, respectively. Our studies demonstrate that the TM doping in the vdW gap of InSe/BP heterostructure is an effective way to modify its electronic and magnetic properties.

  17. Laser spectroscopy of the 5P3/2 → 6Pj (j = 1/2 and 3/2) electric dipole forbidden transitions in atomic rubidium

    Science.gov (United States)

    Ponciano-Ojeda, F.; Hernández-Gómez, S.; Mojica-Casique, C.; Hoyos, L. M.; Flores-Mijangos, J.; Ramírez-Martínez, F.; Sahagún, D.; Jáuregui, R.; Jiménez-Mier, J.

    2018-04-01

    Doppler-free optical double-resonance spectroscopy is used to study the 5S1/2 → 5P3/2 → 6Pj (j = 3/2,1/2) excitation sequence in room-temperature rubidium atoms. This involves a 5S1/2 → 5P3/2 electric dipole preparation step followed by the 5P3/2 → 6Pj electric quadrupole excitation. The electric dipole forbidden transitions occur at 911.0 nm (j = 3/2) and 917.5 nm (j = 1/2). Production of atoms in the 6Pj states is detected by observing their direct decay to the ground state through emission of blue photons (λ ≈ 420 nm). A detailed experimental and theoretical study of the dependence on the relative linear polarizations of excitation beams is made. It is shown that specific electric quadrupole selection rules over magnetic quantum numbers are directly related to the relative orientation of the linear polarization of the excitation beams.

  18. Conformational dependence of a protein kinase phosphate transfer reaction

    Science.gov (United States)

    Labute, Montiago; Henkelman, Graeme; Tung, Chang-Shung; Fenimore, Paul; McMahon, Ben

    2007-03-01

    Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005).

  19. Complementary Strategies for Directed C(sp3 )-H Functionalization: A Comparison of Transition-Metal-Catalyzed Activation, Hydrogen Atom Transfer, and Carbene/Nitrene Transfer.

    Science.gov (United States)

    Chu, John C K; Rovis, Tomislav

    2018-01-02

    The functionalization of C(sp 3 )-H bonds streamlines chemical synthesis by allowing the use of simple molecules and providing novel synthetic disconnections. Intensive recent efforts in the development of new reactions based on C-H functionalization have led to its wider adoption across a range of research areas. This Review discusses the strengths and weaknesses of three main approaches: transition-metal-catalyzed C-H activation, 1,n-hydrogen atom transfer, and transition-metal-catalyzed carbene/nitrene transfer, for the directed functionalization of unactivated C(sp 3 )-H bonds. For each strategy, the scope, the reactivity of different C-H bonds, the position of the reacting C-H bonds relative to the directing group, and stereochemical outcomes are illustrated with examples in the literature. The aim of this Review is to provide guidance for the use of C-H functionalization reactions and inspire future research in this area. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Disordering of two-dimensional oxyxgen lattices on Mo(011) initiated by electron transitions in oxygen and molybdenum atoms

    International Nuclear Information System (INIS)

    Zasimovich, I.N.; Klimenko, E.V.; Naumovets, A.G.

    1988-01-01

    The first observation of electron-induced disordering (EID) of the submonolayer film of heavier adsorbate-oxygen is reported. The investigation of energy dependence of the effective cross section of this process, which points to the fact that EID can be initiated by the electron transitions not only in adatoms, but in the substrate, is also presented. When irradiating by electrons, the sample surface cooled up to 77 K, intensity of diffraction reflects of the (2x2) and (6x2) structures decreases rather quickly, but the reflects of more dense (6x1) lattice do not practically attenuate. The conclusions are made that the knowledge of physical factors, determining the probability of radiation defect formation in an adfilm, gives the possibility either to avoid disordering, if it is undesirable, or to use it to control the surface properties

  1. First-Principles Study on the Adsorption Properties of Transition-Metal Atoms on CaO(001) Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Byung Deok [University of Seoul, Seoul (Korea, Republic of); Jang, Young-Rok [Incheon National University, Incheon (Korea, Republic of)

    2017-03-15

    By using first-principles electronic-structure calculations based on the density functional theory, we systematically investigated the adsorption properties of transition-metal (TM) adatoms on CaO(001) surfaces. Optimized adsorption structures and energetics of TM adatoms on CaO(001) are reported for various adsorption structures. The results are different from those of TM adatoms on MgO(001). Concomitantly, this suggests different dynamical properties of TM adatoms on CaO(001) surfaces as compared with TM adatoms on MgO(001) surfaces. Also performed was an analysis of the electronic structures of the TM adatoms on CaO(001) by using the energy positions of the adsorbate states with respect to the valence band maximum of CaO. The results are discussed in connection with the charge states of the TM adatoms on doped CaO(001).

  2. GOT C+ Survey of [CII] 158 μm Emission: Atomic to Molecular Cloud Transitions in the Inner Galaxy

    Science.gov (United States)

    Velusamy, T.; Langer, W. D.; Willacy, K.; Pineda, J. L.; Goldsmith, P. F.

    2013-03-01

    We present the results of the distribution of CO-dark H2 gas in a sample of 2223 interstellar clouds in the inner Galaxy (l=-90° to +57°) detected in the velocity resolved [CII] spectra observed in the GOT C+ survey using the Herschel HIFI. We analyze the [CII] intensities along with the ancillary HI, 12CO and 13CO data for each cloud to determine their evolutionary state and to derive the H2 column densities in the C+ and C+/CO transition layers in the cloud. We discuss the overall Galactic distribution of the [CII] clouds and their properties as a function Galactic radius. GOT C+ results on the global distribution of [CII] clouds and CO-dark H2 gas traces the FUV intensity and star formation rate in the Galactic disk.

  3. Holographic multiverse and conformal invariance

    Energy Technology Data Exchange (ETDEWEB)

    Garriga, Jaume [Departament de Física Fonamental i Institut de Ciències del Cosmos, Universitat de Barcelona, Martí i Franquès 1, 08193 Barcelona (Spain); Vilenkin, Alexander, E-mail: jaume.garriga@ub.edu, E-mail: vilenkin@cosmos.phy.tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, 212 College Ave., Medford, MA 02155 (United States)

    2009-11-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

  4. Holographic multiverse and conformal invariance

    International Nuclear Information System (INIS)

    Garriga, Jaume; Vilenkin, Alexander

    2009-01-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV

  5. An autopsy study of histopathological changes in the urinary bladder transitional epithelium of atomic bomb survivors, 1960 - 1983

    International Nuclear Information System (INIS)

    Eto, Ryozo; Ishimaru, Toranosuke; Tokunaga, Masayoshi

    1988-01-01

    From the ABCC-RERF Life Span Study extended sample, there were 4,499 cases in the Pathology Study sample of atomic bomb survivors who had come to autopsy in the period 1960 - 83. Among 370 subjects who were heavily exposed with an estimated dose (T65D) of 100 rad or more, 72 (about 20 %) of them, whose urinary bladder epithelia had been preserved satisfactorily to suit the purpose of this study, were sampled as the index group. An equal number of control subjects were selected from the unexposed group individually, matched with the index cases by city, sex, age at death, and year of death. However, cases with marked epithelial autolysis and those pathologically diagnosed as urinary bladder cancer were previously excluded from both the index group and control subjects. These 72 pairs of autopsy cases were pathologically studied for the presence or absence of epithelial lesions of the urinary bladder, namely, hyperplasia, dysplasia and carcinoma-in-situ, and the frequencies of appearance of these lesions were compared statistically by χ 2 test based on a case-control study design. Carcinoma-in-situ and severe dysplasia were detected in neither the index cases nor the control cases. The risk was relatively higher in the index group than in the control subjects for both hyperplasia and dysplasia (mild and moderate), in particular the relative risk of papillary hyperplasia being about 4.0, but as the total number of cases were small, this was not statistically significant. (author)

  6. Hybrid compounds of Keggin polyoxotungstate with transition metal ion as the central atom. Synthesis, structure and properties

    Science.gov (United States)

    Li, Xiao-Min; Chen, Ya-Guang; Shi, Tian

    2016-02-01

    The compounds (Hbipy)2[Co(bipy)2(H2O)4]2(CoW12O40)·2bipy·7H2O (1) and [Ni2(Hbipy)2(bipy)(H2O)4(H2W12O40)]·5H2O (2) (bipy = 4,4-bipyridine) were synthesized hydrothermally and characterized by elemental analysis, IR spectroscopy, TG analyses, solid ultraviolet diffuse spectroscopy and single crystal X-ray diffraction method. In 1 the complex ions, [Co(bipy)2(H2O)4]2+, construct a supramolecular layer through π-π stacking interaction. The heteropolyanions with central Co atom and supramolecular layers are linked by hydrogen bonds. In 2 a 2D structure is formed from metatungstate anions and binuclear Ni-bipy complexes through the coordination of metatungstate anions and bipy to Ni ions. Between the layers and bipyridine molecules are the hydrogen bond interactions. The formation of 1 and 2 shows that the solution acidity and metal ions influence greatly the structure of the compounds. Solid ultraviolet diffusion results indicate that the compounds 1 and 2 are potential semiconductor materials. In 1 and 2 there exists a weak antiferromagnetic interaction.

  7. Quasi-atoms

    International Nuclear Information System (INIS)

    Armbruster, P.

    1976-01-01

    The concept of a quasi-atom is discussed, and several experiments are described in which molecular or quasi-atomic transitions have been observed. X-ray spectra are shown for these experiments in which heavy ion projectiles were incident on various targets and the resultant combined system behaved as a quasi-atom. This rapidly developing field has already given new insight into atomic collision phenomena. (P.J.S.)

  8. Theoretical Investigation on Single-Wall Carbon Nanotubes Doped with Nitrogen, Pyridine-Like Nitrogen Defects, and Transition Metal Atoms

    Directory of Open Access Journals (Sweden)

    Michael Mananghaya

    2012-01-01

    Full Text Available This study addresses the inherent difficulty in synthesizing single-walled carbon nanotubes (SWCNTs with uniform chirality and well-defined electronic properties through the introduction of dopants, topological defects, and intercalation of metals. Depending on the desired application, one can modify the electronic and magnetic properties of SWCNTs through an appropriate introduction of imperfections. This scheme broadens the application areas of SWCNTs. Under this motivation, we present our ongoing investigations of the following models: (i (10, 0 and (5, 5 SWCNT doped with nitrogen (CNxNT, (ii (10, 0 and (5, 5 SWCNT with pyridine-like defects (3NV-CNxNT, (iii (10, 0 SWCNT with porphyrine-like defects (4ND-CNxNT. Models (ii and (iii were chemically functionalized with 14 transition metals (TMs: Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Pt and Au. Using the spin-unrestricted density functional theory (DFT, stable configurations, deformations, formation and binding energies, the effects of the doping concentration of nitrogen, pyridine-like and porphyrine-like defects on the electronic properties were all examined. Results reveal that the electronic properties of SWCNTs show strong dependence on the concentration and configuration of nitrogen impurities, its defects, and the TMs adsorbed.

  9. Atomic-scale study of the amorphous-to-crystalline phase transition mechanism in GeTe thin films

    CERN Document Server

    Mantovan, R.; Mokhles Gerami, A.; Mølholt, T. E.; Wiemer, C.; Longo, M.; Gunnlaugsson, H. P.; Johnston, K.; Masenda, H.; Naidoo, D.; Ncube, M.; Bharuth-Ram, K.; Fanciulli, M.; Gislason, H. P.; Langouche, G.; Ólafsson, S.; Weyer, G.

    The underlying mechanism driving the structural amorphous-to-crystalline transition in Group VI chalcogenides is still a matter of debate even in the simplest GeTe system. We exploit the extreme sensitivity of 57Fe emission Mössbauer spectroscopy, following dilute implantation of 57Mn (T½ = 1.5 min) at ISOLDE/CERN, to study the electronic charge distribution in the immediate vicinity  of the 57Fe probe substituting Ge (FeGe), and to interrogate the local environment of FeGe over the amorphous-crystalline phase transition in GeTe thin films. Our results show that the local structure  of as-sputtered amorphous GeTe is a combination of tetrahedral and defect-octahedral sites. The main effect of the crystallization is the conversion from tetrahedral to defect-free octahedral sites.  We discover that only the tetrahedral fraction in amorphous GeTe participates to the change of the FeGe-Te chemical bond...

  10. Atomic-fluorescence spectrophotometry

    International Nuclear Information System (INIS)

    Bakhturova, N.F.; Yudelevich, I.G.

    1975-01-01

    Atomic-fluorescence spectrophotometry, a comparatively new method for the analysis of trace quantities, has developed rapidly in the past ten years. Theoretical and experimental studies by many workers have shown that atomic-fluorescence spectrophotometry (AFS) is capable of achieving a better limit than atomic absorption for a large number of elements. The present review examines briefly the principles of atomic-fluorescence spectrophotometry and the types of fluorescent transition. The excitation sources, flame and nonflame atomizers, used in AFS are described. The limits of detection achieved up to the present, using flame and nonflame methods of atomization are given

  11. Principles of Atomic Structure and the Valence Electron Configurations of the Transition Elements%原子构造原理与过渡元素原子的价电子组态

    Institute of Scientific and Technical Information of China (English)

    刘承东

    2001-01-01

    According to the Aufbau build-up principle and the order of filling atomic orbits, the valence electron configuration of ground state atoms of the d-block transition elements seems only to be (n-1) dx-2ns2(x here denotes the number of the electron in (n-1) d and ns orbits). But the result of the spectra test shows that the atomic electron structure of the d-block transition elements also has the configurations (n-1) dx-1 ns1 and (n-1) dx nso. These two types of electron configurations are usually considered as "out of the ordinary". In addition, the another important phenomenon is that the electronic structure of the atoms for all of the elements can not attain the configuration (n-1)d6 ns1. The reasons why these exceptional electron configurations can be formed and why the configuration (n-1) d 6 ns1 can not exist are not properly understood and at present no theory of the many-electron atom structure is entirely satisfactory[1-7]. For this, it seems that the theoretical difficulty lies in accounting for the diversification of electron configurations and for the non-existence of configuration (n-1) d6 ns1 as we did not pay more attention to the control effect of symmetry principle in atom structure. We know that the stability of a mass system depends on the mechanics conservation law in the system and each conservation law is always relative to the invariance of the certain symmetry. In atom structure, the main interaction is the electromagnetic interaction. So the stability of atom structure system must be bounded up with the symmetry of the electromagnetic interaction in the atom system. The direct expression of this interconnection is that,when the electrons are allotted to the orbits with energy equivalent or close to one another in many-electron atoms, they would always distribute themselves in such a way that there is a relative highest symmetry configuration. That is to say, the way of the distribution of electrons(include electron spin states) in orbits is

  12. Polarization dependence of double-resonance optical pumping and electromagnetically induced transparency in the 5S1/2-5P3/2-5D5/2 transition of 87Rb atoms

    International Nuclear Information System (INIS)

    Moon, Han Seb; Noh, Heung-Ryoul

    2011-01-01

    The polarization dependence of double-resonance optical pumping (DROP) in the ladder-type electromagnetically induced transparency (EIT) of the 5S 1/2 -5P 3/2 -5D 5/2 transition of 87 Rb atoms is studied. The transmittance spectra in the 5S 1/2 (F=2)-5P 3/2 (F'=3)-5D 5/2 (F''=2,3,4) transition were observed as caused by EIT, DROP, and saturation effects in the various polarization combinations between the probe and coupling lasers. The features of the double-structure transmittance spectra in the 5S 1/2 (F=2)-5P 3/2 (F'=3)-5D 5/2 (F''=4) cycling transition were attributed to the difference in saturation effect according to the transition routes between the Zeeman sublevels and the EIT according to the two-photon transition probability.

  13. Application of Internal Standard Method for Several 3d-Transition Metallic Elements in Flame Atomic Absorption Spectrometry Using a Multi-wavelength High-resolution Spectrometer.

    Science.gov (United States)

    Toya, Yusuke; Itagaki, Toshiko; Wagatsuma, Kazuaki

    2017-01-01

    We investigated a simultaneous internal standard method in flame atomic absorption spectrometry (FAAS), in order to better the analytical precision of 3d-transition metals contained in steel materials. For this purpose, a new spectrometer system for FAAS, comprising a bright xenon lamp as the primary radiation source and a high-resolution Echelle monochromator, was employed to measure several absorption lines at a wavelength width of ca. 0.3 nm at the same time, which enables the absorbances of an analytical line and also an internal standard line to be estimated. In considering several criteria for selecting an internal standard element and the absorption line, it could be suggested that platinum-group elements: ruthenium, rhodium, or palladium, were suitable for an internal standard element to determine the 3d-transition metal elements, such as titanium, iron, and nickel, by measuring an appropriate pair of these absorption lines simultaneously. Several variances of the absorption signal, such as a variation in aspirated amounts of sample solution and a short-period drift of the primary light source, would be corrected and thus reduced, when the absorbance ratio of the analytical line to the internal standard line was measured. In Ti-Pd, Ni-Rh, and Fe-Ru systems chosen as typical test samples, the repeatability of the signal respnses was investigated with/without the internal standard method, resulting in better precision when the internal standard method was applied in the FAAS with a nitrous oxide-acetylene flame rather than an air-acetylene flame.

  14. A conformational study of protonated noradrenaline by UV-UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method.

    Science.gov (United States)

    Wako, Hiromichi; Ishiuchi, Shun-Ichi; Kato, Daichi; Féraud, Géraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe; Fujii, Masaaki

    2017-05-03

    The conformer-selected ultraviolet (UV) and infrared (IR) spectra of protonated noradrenaline were measured using an electrospray/cryogenic ion trap technique combined with photo-dissociation spectroscopy. By comparing the UV photo dissociation (UVPD) spectra with the UV-UV hole burning (HB) spectra, it was found that five conformers coexist under ultra-cold conditions. Based on the spectral features of the IR dip spectra of each conformer, two different conformations on the amine side chain were identified. Three conformers (group I) were assigned to folded and others (group II) to extended structures by comparing the observed IR spectra with the calculated ones. Observation of the significantly less-stable extended conformers strongly suggests that the extended structures are dominant in solution and are detected in the gas phase by kinetic trapping. The conformers in each group are assignable to rotamers of OH orientations in the catechol ring. By comparing the UV-UV HB spectra and the calculated Franck-Condon spectra obtained by harmonic vibrational analysis of the S 1 state, with the aid of relative stabilization energies of each conformer in the S 0 state, the absolute orientations of catechol OHs of the observed five conformers were successfully determined. It was found that the 0-0 transition of one folded conformer is red-shifted by about 1000 cm -1 from the others. The significant red-shift was explained by a large contribution of the πσ* state to S 1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.

  15. Conformational kinetics of aliphatic tails

    Science.gov (United States)

    Ferrarini, Alberta; Moro, Giorgio; Nordio, Pier Luigi

    The master equation describing the random walk between sites identified with the stable conformers of a chain molecule, represents the extension to the time domain of the Rotational Isomeric State model. The asymptotic analysis of the multidimensional diffusion equation in the continuous torsional variables subjected to the configurational potential, provides a rigorous justification for the discrete models, and it supplies, without resorting to phenomenological parameters, molecular definitions of the kinetic rates for the conformational transitions occurring at each segment of the chain. The coupling between the torsional variables is fully taken into account, giving rise to cooperative effects. A complete calculation of the specific correlation functions which describe the time evolution of the angular functions probed by N.M.R. and dielectric relaxation measurements, has been performed for alkyl chains attached to a massive core. The resulting behaviour has been compared with the decay of trans and gauche populations of specific bonds, expressed in terms of suitable correlation functions whose time integrals lead quite naturally to the definition of effective kinetic constants for the conformational transitions.

  16. Viscous conformal gauge theories

    DEFF Research Database (Denmark)

    Toniato, Arianna; Sannino, Francesco; Rischke, Dirk H.

    2017-01-01

    We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories.......We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories....

  17. Conformal Einstein spaces

    International Nuclear Information System (INIS)

    Kozameh, C.N.; Newman, E.T.; Tod, K.P.

    1985-01-01

    Conformal transformations in four-dimensional. In particular, a new set of two necessary and sufficient conditions for a space to be conformal to an Einstein space is presented. The first condition defines the class of spaces conformal to C spaces, whereas the last one (the vanishing of the Bach tensor) gives the particular subclass of C spaces which are conformally related to Einstein spaces. (author)

  18. Modification of Ni-Rich FCG NMC and NCA Cathodes by Atomic Layer Deposition: Preventing Surface Phase Transitions for High-Voltage Lithium-Ion Batteries

    Science.gov (United States)

    Mohanty, Debasish; Dahlberg, Kevin; King, David M.; David, Lamuel A.; Sefat, Athena S.; Wood, David L.; Daniel, Claus; Dhar, Subhash; Mahajan, Vishal; Lee, Myongjai; Albano, Fabio

    2016-05-01

    The energy density of current lithium-ion batteries (LIBs) based on layered LiMO2 cathodes (M = Ni, Mn, Co: NMC; M = Ni, Co, Al: NCA) needs to be improved significantly in order to compete with internal combustion engines and allow for widespread implementation of electric vehicles (EVs). In this report, we show that atomic layer deposition (ALD) of titania (TiO2) and alumina (Al2O3) on Ni-rich FCG NMC and NCA active material particles could substantially improve LIB performance and allow for increased upper cutoff voltage (UCV) during charging, which delivers significantly increased specific energy utilization. Our results show that Al2O3 coating improved the NMC cycling performance by 40% and the NCA cycling performance by 34% at 1 C/-1 C with respectively 4.35 V and 4.4 V UCV in 2 Ah pouch cells. High resolution TEM/SAED structural characterization revealed that Al2O3 coatings prevented surface-initiated layered-to-spinel phase transitions in coated materials which were prevalent in uncoated materials. EIS confirmed that Al2O3-coated materials had significantly lower increase in the charge transfer component of impedance during cycling. The ability to mitigate degradation mechanisms for Ni-rich NMC and NCA illustrated in this report provides insight into a method to enable the performance of high-voltage LIBs.

  19. Superspace conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Quella, Thomas [Koeln Univ. (Germany). Inst. fuer Theoretische Physik; Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2013-07-15

    Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

  20. Superspace conformal field theory

    International Nuclear Information System (INIS)

    Quella, Thomas

    2013-07-01

    Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

  1. Conformation and hydrogen bonding in 4-Aminobutanol

    Science.gov (United States)

    Khalil, Andrew S.; Duguay, Taylor M.; Lavrich, Richard J.

    2017-06-01

    Rotational spectra of the most abundant and four 13C isotopomers of 4-aminobutanol have been recorded in natural abundance using a Fourier-transform microwave spectrometer. For the most abundant isotopomer, 56 hyperfine components from the fifteen a- and b-type transitions measured were fit to the quadupole coupling constants, χaa = -3.843(3) MHz, χbb = 1.971(3) MHz. Rotational and centrifugal distortion constants determined from fits of the resulting unsplit line centers to the Watson A-reduction Hamiltonian are A = 4484.893(3) MHz, B = 2830.721(1) MHz, C = 1942.9710(3) MHz, ΔJ = 0.98(3) kHz, ΔJK = 1.4(1) kHz, ΔK = - 2.6(5) kHz, δJ = 0.27(1) kHz, and δK = 1.7(1) kHz. Between nine and eleven rotational transitions were measured for the 13C isotopes and rotational constants were determined by fixing the distortion constants to the values found for the normal isotope. The five sets of moments of inertia were used to determine the 4-aminobutanol substitution structure as well to perform a least-squares fit of the lowest energy ab initio structure. The heavy atom coordinates determined from these two methods are in excellent agreement. The conformation of 4-aminobutanol is stabilized by an intramolecular hydrogen bond from the alcohol proton to amino nitrogen with a resulting hydrogen bond distance of 1.891 Å. The experimental structure is consistent with the lowest energy ab initio [MP2/6-311++G(d,p)] structure.

  2. Atomic-level characterization of the activation mechanism of SERCA by calcium.

    Directory of Open Access Journals (Sweden)

    L Michel Espinoza-Fonseca

    Full Text Available We have performed molecular dynamics (MD simulations to elucidate, in atomic detail, the mechanism by which the sarcoplasmic reticulum Ca(2+-ATPase (SERCA is activated by Ca(2+. Crystal structures suggest that activation of SERCA occurs when the cytoplasmic head-piece, in an open (E1 conformation stabilized by Ca(2+, undergoes a large-scale open-to-closed (E1 to E2 transition that is induced by ATP binding. However, spectroscopic measurements in solution suggest that these structural states (E1 and E2 are not tightly coupled to biochemical states (defined by bound ligands; the closed E2 state predominates even in the absence of ATP, in both the presence and absence of Ca(2+. How is this loose coupling consistent with the high efficiency of energy transduction in the Ca(2+-ATPase? To provide insight into this question, we performed long (500 ns all-atom MD simulations starting from the open crystal structure, including a lipid bilayer and water. In both the presence and absence of Ca(2+, we observed a large-scale open-to-closed conformational transition within 400 ns, supporting the weak coupling between structural and biochemical states. However, upon closer inspection, it is clear that Ca(2+ is necessary and sufficient for SERCA to reach the precise geometrical arrangement necessary for activation of ATP hydrolysis. Contrary to suggestions from crystal structures, but in agreement with solution spectroscopy, the presence of ATP is not required for this activating transition. Principal component analysis showed that Ca(2+ reshapes the free energy landscape of SERCA to create a path between the open conformation and the activated closed conformation. Thus the malleability of the free energy landscape is essential for SERCA efficiency, ensuring that ATP hydrolysis is tightly coupled to Ca(2+ transport. These results demonstrate the importance of real-time dynamics in the formation of catalytically competent conformations of SERCA, with broad

  3. Electron scattering studies of selected electric and magnetic dipole and quadrupole transitions in light and heavy nuclei, the new multipole giant resonances and atomic transitions - recent results from the DALINAC

    International Nuclear Information System (INIS)

    Richter, A.

    1977-01-01

    Recent experimental work from the Darmstadt electron linear accelerator (DALINAC) is briefly summarized. Particular emphasis is given to the following topics: high resolution inelastic electron scattering (ΔE approximately 30 keV FWHM) has been used to study the radiative width and magnetization density of the 2 + , T = 1 state at 16.11 MeV in 12 C, E2 strength distribution in 28 Si below an excitation energy of 13 MeV and the isospin forbidden E1 electroexcitation of the 1 - , T = 0 state at 6.95 MeV in 40 Ca. High resolution inelastic electron scattering was also employed to determine certain M1 transitions in 14 N, 28 Si, 39 K, 58 Ni, 90 Zr and 208 Pb and the M2 strength distribution in the two heaviest nuclei. At medium energy resolution (ΔE approximately 200 keV FWHM) spectra at various angles and bombarding energies have been measured from (4-31) MeV for 208 Pb. They are being analyzed in order to determine E0, E1, E2, E3 and M1 giant resonance strength in the continuum. The Z and E dependence and the scaling behaviour of the atomic inner shell ionization cross section at relativistic electron impact is studied on gaseous and solid targets. (orig./BJ) [de

  4. Solid state protein monolayers: Morphological, conformational, and functional properties

    Science.gov (United States)

    Pompa, P. P.; Biasco, A.; Frascerra, V.; Calabi, F.; Cingolani, R.; Rinaldi, R.; Verbeet, M. Ph.; de Waal, E.; Canters, G. W.

    2004-12-01

    We have studied the morphological, conformational, and electron-transfer (ET) function of the metalloprotein azurin in the solid state, by a combination of physical investigation methods, namely atomic force microscopy, intrinsic fluorescence spectroscopy, and scanning tunneling microscopy. We demonstrate that a "solid state protein film" maintains its nativelike conformation and ET function, even after removal of the aqueous solvent.

  5. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

    and the Commission regarding a directive’s outcome, play a much more strategic role than has to date acknowledged in the transposition literature. Whereas disagreement of a member state delays conformable transposition, it speeds up non-conformable transposition. Disagreement of the Commission only prolongs...... the transposition process. We therefore conclude that a stronger focus on an effective sanctioning mechanism is warranted for safeguarding compliance with directives....

  6. Electronic Transitions in Conformationally Controlled Peralkylated Hexasilanes

    Czech Academy of Sciences Publication Activity Database

    Kanazawa, Y.; Tsuji, H.; Ehara, M.; Fukuda, R.; Casher, D. L.; Tamao, K.; Nakatsuji, H.; Michl, Josef

    2016-01-01

    Roč. 17, č. 19 (2016), s. 3010-3022 ISSN 1439-4235 Institutional support: RVO:61388963 Keywords : configuration interaction * density functional calculations * magnetic circular dichroism * oligosilanes * UV/Vis spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.075, year: 2016

  7. Frequency chain to measure the 2S-8S/8D transitions in atomic hydrogen: measurement of the Rydberg constant in frequency unit; Chaine de frequence optique pour mesurer les transitions 2S-8S/8D dans l'atome d'hydrogene: mesure de la constante de Rydberg en unite de frequence

    Energy Technology Data Exchange (ETDEWEB)

    Nez, F

    1993-10-15

    The aim of this thesis is to make a pure measurement of the frequency of the 2S-8S/8D two-photon transition in atomic hydrogen. In that purpose we have built a frequency chain in which hydrogen frequencies are compared with the difference of two optical standards, the methane stabilized He-Ne laser (3.39 {mu}m) and the iodine stabilized He-Ne laser (633 nm). The radiation from a home made Ti-sapphire laser (TS2) at 778 nm is mixed, in a LiIO{sub 3} crystal, with the one of a auxiliary He-Ne laser at 3.39 {mu}m to produce a synthesized radiation at 633 nm. The frequency of the Ti-sapphire (TS1) laser used for the two photon excitation is 89 GHz away from the one of TS2. To compare these two lasers, we have used a Schottky diode. The two lasers and a microwave radiation at 89 GHz, produced by a Gunn diode, are focused on the Schottky diode. The Gunn diode is phase locked on an ultra-stable quartz oscillator. In this way, we have linked an optical frequency of atomic hydrogen to the cesium clock without interferometry. From our measurements, we have deduced a new value of the Rydberg constant: R{sub {infinity}} equals 109737.3156834 (24) cm{sup -1} with an uncertainty of 2.2 10{sup -11}. Our uncertainty is near the one of the Q.E.D calculations giving the theoretical values of the energy levels. This value, which is currently the most precise available, is in good agreement with the recent result obtained from the 1S-2S and 2S-4D transitions. (author)

  8. Conformal solids and holography

    Science.gov (United States)

    Esposito, A.; Garcia-Saenz, S.; Nicolis, A.; Penco, R.

    2017-12-01

    We argue that a SO( d) magnetic monopole in an asymptotically AdS space-time is dual to a d-dimensional strongly coupled system in a solid state. In light of this, it would be remiss of us not to dub such a field configuration solidon. In the presence of mixed boundary conditions, a solidon spontaneously breaks translations (among many other symmetries) and gives rise to Goldstone excitations on the boundary — the phonons of the solid. We derive the quadratic action for the boundary phonons in the probe limit and show that, when the mixed boundary conditions preserve conformal symmetry, the longitudinal and transverse sound speeds are related to each other as expected from effective field theory arguments. We then include backreaction and calculate the free energy of the solidon for a particular choice of mixed boundary conditions, corresponding to a relevant multi-trace deformation of the boundary theory. We find such free energy to be lower than that of thermal AdS. This suggests that our solidon undergoes a solid-to-liquid first order phase transition by melting into a Schwarzschild-AdS black hole as the temperature is raised.

  9. UV light induced insulator-metal transition in ultra-thin ZnO/TiO{sub x} stacked layer grown by atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Saha, D., E-mail: sahaphys@gmail.com, E-mail: pmisra@rrcat.gov.in; Misra, P., E-mail: sahaphys@gmail.com, E-mail: pmisra@rrcat.gov.in; Joshi, M. P.; Kukreja, L. M. [Laser Materials Processing Division, Raja Ramanna Centre for Advanced Technology, Indore 452 013 (India)

    2016-08-28

    In the present study, atomic layer deposition has been used to grow a series of Ti incorporated ZnO thin films by vertically stacking different numbers (n = 1–7) of ZnO/TiO{sub x} layers on (0001) sapphire substrates. The effects of defect states mediated chemisorption of O{sub 2} and/OH groups on the electrical properties of these films have been investigated by illuminating the samples under UV light inside a high vacuum optical cryostat. The ultra-thin film having one stacked layer (n = 1) did not show any change in its electrical resistance upon UV light exposure. On the contrary, marginal drop in the electrical resistivity was measured for the samples with n ≥ 3. Most surprisingly, the sample with n = 2 (thickness ∼ 12 nm) showed an insulator to metal transition upon UV light exposure. The temperature dependent electrical resistivity measurement on the as grown film (n = 2) showed insulating behaviour, i.e., diverging resistivity on extrapolation to T→ 0 K. However, upon UV light exposure, it transformed to a metallic state, i.e., finite resistivity at T → 0 K. Such an insulator-metal transition plausibly arises due to the de-trapping of conduction electrons from the surface defect sites which resulted in an upward shift of the Fermi level above the mobility edge. The low-temperature electron transport properties on the insulating film (n = 2) were investigated by a combined study of zero field electrical resistivity ρ(T) and magnetoresistance (MR) measurements. The observed negative MR was found to be in good agreement with the magnetic field induced suppression of quantum interference between forward-going paths of tunnelling electrons. Both ρ(T) and MR measurements provided strong evidence for the Efros-Shklovskii type variable range hopping conduction in the low-temperature (≤40 K) regime. Such studies on electron transport in ultra-thin n-type doped ZnO films are crucial to achieve optimum functionality

  10. Bill authorizing the ratification of the protocol amending the Protocol on transitional provisions annexed to the Treaty on European Union, to the Treaty on the Functioning of the European Union and to the Treaty establishing the European Atomic Energy Community

    International Nuclear Information System (INIS)

    2010-01-01

    After an indication of the European Parliament composition, this text describes the transitional provisions adopted as the Lisbon Treaty did not come into effect before the European elections held in June 2009. The document also provides the protocol text signed by the Members States and which amended the protocol on transitional provisions annexed to the Treaty on the European Union, to the Treaty on the Functioning of the European Union and to the Treaty establishing the European Atomic Energy Community. The last part of the document discusses the administrative and legal consequences of this protocol. It also recalls the history of the negotiations and indicates the present status of signatures and ratifications

  11. Toward TeV Conformality

    International Nuclear Information System (INIS)

    Appelquist, T.; Fleming, G. T.; Neil, E. T.; Avakian, A.; Babich, R.; Brower, R. C.; Cohen, S. D.; Rebbi, C.; Schaich, D.; Cheng, M.; Vranas, P.; Clark, M. A.; Kiskis, J.; Osborn, J. C.

    2010-01-01

    We study the chiral properties of an SU(3) gauge theory with N f massless Dirac fermions in the fundamental representation when N f is increased from 2 to 6. For N f =2, our lattice simulations lead to a value of /F 3 , where F is the Nambu-Goldstone-boson decay constant and is the chiral condensate, which agrees with the measured QCD value. For N f =6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N f increases further, toward the critical value for transition from confinement to infrared conformality.

  12. The 2P1/2 → 2P3/2 laser transition in atomic iodine and the problem of search for signals from extraterrestrial intelligence

    International Nuclear Information System (INIS)

    Kutaev, Yu F; Mankevich, S K; Nosach, O Yu; Orlov, E P

    2007-01-01

    It is proposed to search for signals from extraterrestrial intelligence (ETI) at a wavelength of 1.315 μm of the laser 2 P 1/2 → 2 P 3/2 transition in the atomic iodine, which can be used for this purpose as the natural frequency reference. The search at this wavelength is promising because active quantum filters (AQFs) with the quantum sensitivity limit have been developed for this wavelength, which are capable of receiving laser signals, consisting of only a few photons, against the background of emission from a star under study. In addition, high-power iodine lasers emitting diffraction-limited radiation at 1.315 μm have been created, which highly developed ETI also can have. If a ETI sends in our direction a diffraction-limited 10-ns, 1-kJ laser pulse with the beam diameter of 10 m, a receiver with an AQF mounted on a ten-meter extra-atmospheric optical telescope can detect this signal at a distance of up to 300 light years, irrespective of the ETI position on the celestial sphere. The realisation of the projects for manufacturing optical telescopes of diameter 30 m will increase the research range up to 2700 light years. A weak absorption of the 1.315-μm radiation in the Earth atmosphere (the signal is attenuated by less than 20%) allows the search for ETI signals by using ground telescopes equipped with adaptive optical systems. (laser applications and other topics in quantum electronics)

  13. Generative Models of Conformational Dynamics

    Science.gov (United States)

    Langmead, Christopher James

    2014-01-01

    Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GrAphical Models of Energy LANdscapes), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc) from long timescale simulation data. PMID:24446358

  14. Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

    Energy Technology Data Exchange (ETDEWEB)

    Asadinezhad, Ahmad, E-mail: asadinezhad@cc.iut.ac.ir; Kelich, Payam

    2017-01-15

    Highlights: • Poly (trimethylene terephthalate) (PTT) conformation adopts a folded shape near nanofiller surface. • Graphene and carbon nanotube with different size and chemistry were simulated. • Graphene functionalization induces stronger confinement on PTT chain conformation. • PTT chain motion alters in dynamics mode as it becomes adsorbed onto nanofillers. • PTT reveals further changes near graphene than carbon nanotube surface. - Abstract: The effects of nanofiller chemistry and geometry on static and dynamic properties of an aromatic polyester, poly (trimethylene terephthalate), were addressed thanks to long-run classical molecular dynamics simulation. Two carbon nanofillers, graphene and carbon nanotube, were employed, where graphene was used in pristine and functionalized forms and carbon nanotube was used in two different diameters. The nanofiller geometry and chemistry were found to exert significant effects on conformation and dynamic behavior of PTT chain at the interface within the time scale the simulation was performed. It was found that PTT chain underwent interaction of van der Waals type with nanofiller via two subsequent phases, adsorption and orientation. The former stage, with definite characteristic time, involved translation of polymer chain toward interface while the latter was controlled by vibrational motions of chain atoms. The consequence of interaction was an increase in conformational order of polymer chain by transition to folded shape being favorable for any subsequent structural ordering (crystallization). The interaction of polymer with nanofiller gave rise to a reduction in overall mobility of polymer chain characterized by crossover from normal diffusive motion to subdiffusive mode.

  15. Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

    International Nuclear Information System (INIS)

    Asadinezhad, Ahmad; Kelich, Payam

    2017-01-01

    Highlights: • Poly (trimethylene terephthalate) (PTT) conformation adopts a folded shape near nanofiller surface. • Graphene and carbon nanotube with different size and chemistry were simulated. • Graphene functionalization induces stronger confinement on PTT chain conformation. • PTT chain motion alters in dynamics mode as it becomes adsorbed onto nanofillers. • PTT reveals further changes near graphene than carbon nanotube surface. - Abstract: The effects of nanofiller chemistry and geometry on static and dynamic properties of an aromatic polyester, poly (trimethylene terephthalate), were addressed thanks to long-run classical molecular dynamics simulation. Two carbon nanofillers, graphene and carbon nanotube, were employed, where graphene was used in pristine and functionalized forms and carbon nanotube was used in two different diameters. The nanofiller geometry and chemistry were found to exert significant effects on conformation and dynamic behavior of PTT chain at the interface within the time scale the simulation was performed. It was found that PTT chain underwent interaction of van der Waals type with nanofiller via two subsequent phases, adsorption and orientation. The former stage, with definite characteristic time, involved translation of polymer chain toward interface while the latter was controlled by vibrational motions of chain atoms. The consequence of interaction was an increase in conformational order of polymer chain by transition to folded shape being favorable for any subsequent structural ordering (crystallization). The interaction of polymer with nanofiller gave rise to a reduction in overall mobility of polymer chain characterized by crossover from normal diffusive motion to subdiffusive mode.

  16. Conformational effects in photoelectron circular dichroism

    Science.gov (United States)

    Turchini, S.

    2017-12-01

    Photoelectron circular dichroism (PECD) is a novel type of spectroscopy, which presents surprising sensitivity to conformational effects in chiral systems. While classical photoelectron spectroscopy mainly responds to conformational effects in terms of energy level shifts, PECD provides a rich and detailed response to tiny changes in electronic and structural properties by means of the intensity dispersion of the circular dichroism as a function of photoelectron kinetic energy. In this work, the basics of PECD will be outlined, emphasizing the role of interference from the l,l+/- 1 outgoing partial wave of the photoelectron in the PECD transition matrix element, which is responsible for the extreme sensitivity to conformational effects. Examples using molecular systems and interfaces will shed light on the powerful application of PECD to classical conformational effects such as group substitution, isomerism, conformer population and clustering. Moreover, the PECD results will be reported in challenging new fields where conformations play a key role, such as vibrational effects, transient chirality and time- resolved experiments. To date, PECD has mostly been based on synchrotron radiation facilities, but it also has a future as a table-top lab experiment by means of multiphoton ionization. An important application of PECD as an analytical tool will be reported. The aim of this review is to illustrate that in PECD, the presence of conformational effects is essential for understanding a wide range of effects from a new perspective, making it different from classical spectroscopy.

  17. Conformational Diffusion and Helix Formation Kinetics

    International Nuclear Information System (INIS)

    Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

    2000-01-01

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

  18. Conformational Diffusion and Helix Formation Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

    2000-09-18

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

  19. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    International Nuclear Information System (INIS)

    Forneris, Federico; Burnley, B. Tom; Gros, Piet

    2014-01-01

    Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na + and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na + ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail

  20. Phase transition of DNA-linked gold nanoparticles: Creation of a high concentration of atomic hydrogen in impurity-helium solids

    International Nuclear Information System (INIS)

    Kiselev, S.I.; Khmelenko, V.V.; Bernard, E.P.; Lee, C.Y.; Lee, D.M.

    2003-01-01

    The exchange tunneling reactions D+H 2 →HD+H and D+HD→D 2 +H were used to generate high concentrations of atomic hydrogen in impurity-helium solids. The dependence of atom concentration on the content of hydrogen in the injected gas mixture gave a maximum concentration of 7.5x10 17 cm -3 hydrogen atoms for an initial gas ratio H 2 :D 2 :He=1:4:100

  1. The effect of the electronic structure, phase transition, and localized dynamics of atoms in the formation of tiny particles of gold

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Mubarak, E-mail: mubarak74@comsats.edu.pk, E-mail: mubarak74@mail.com [COMSATS Institute of Information Technology, Department of Physics (Pakistan); Lin, I-Nan [Tamkang University, Department of Physics (China)

    2017-01-15

    In addition to self-governing properties, tiny-sized particles of metallic colloids are the building blocks of large-sized particles; thus, their study has been the subject of a large number of publications. In the present work, it has been discussed that geometry structure of tiny particle made through atom-to-atom amalgamation depends on attained dynamics of gold atoms along with protruded orientations. The localized process conditions direct two-dimensional structure of a tiny particle at atomically flat air-solution interface while heating locally dynamically approached atoms, thus, negate the role of van der Waals interactions. At electronphoton-solution interface, impinging electrons stretch or deform atoms of tiny particles depending on the mechanism of impingement. In addition, to strike regular grid of electrons ejected on split of atoms not executing excitations and de-excitations of their electrons, atoms of tiny particles also deform or stretch while occupying various sites depending on the process of synergy. Under suitable impinging electron streams, those tiny particles in monolayer two-dimensional structure electron states of their atoms are diffused in the direction of transferred energy, thus, coincide to the next adjacent atoms in each one-dimensional array dealing the same sort of behavior. Instantaneously, photons of adequate energy propagate on the surfaces of such electronic structures and modify those into smooth elements, thus, disregard the phenomenon of localized surface plasmons. This study highlights the fundamental process of formation of tiny particles where the role of localized dynamics of atoms and their electronic structure along with interaction to light are discussed. Such a tool of processing materials, in nonequilibrium pulse-based process, opens a number of possibilities to develop engineered materials with specific chemical, optical, and electronic properties.

  2. Induced quantum conformal gravity

    International Nuclear Information System (INIS)

    Novozhilov, Y.V.; Vassilevich, D.V.

    1988-11-01

    Quantum gravity is considered as induced by matter degrees of freedom and related to the symmetry breakdown in the low energy region of a non-Abelian gauge theory of fundamental fields. An effective action for quantum conformal gravity is derived where both the gravitational constant and conformal kinetic term are positive. Relation with induced classical gravity is established. (author). 15 refs

  3. Thickenings and conformal gravity

    Science.gov (United States)

    Lebrun, Claude

    1991-07-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason [B-M].

  4. Thickenings and conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    LeBrun, C. (State Univ. of New York, Stony Brook, NY (USA). Dept. of Mathematics)

    1991-07-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason (B-M). (orig.).

  5. Thickenings and conformal gravity

    International Nuclear Information System (INIS)

    LeBrun, C.

    1991-01-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason [B-M]. (orig.)

  6. Conformal transformations in superspace

    International Nuclear Information System (INIS)

    Dao Vong Duc

    1977-01-01

    The spinor extension of the conformal algebra is investigated. The transformation law of superfields under the conformal coordinate inversion R defined in the superspace is derived. Using R-technique, the superconformally covariant two-point and three-point correlation functions are found

  7. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C.S.; Trandum, C.; Larsen, N.

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

  8. Conformity index: A review

    International Nuclear Information System (INIS)

    Feuvret, Loic; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-01-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear

  9. Conformal invariance in supergravity

    International Nuclear Information System (INIS)

    Bergshoeff, E.A.

    1983-01-01

    In this thesis the author explains the role of conformal invariance in supergravity. He presents the complete structure of extended conformal supergravity for N <= 4. The outline of this work is as follows. In chapter 2 he briefly summarizes the essential properties of supersymmetry and supergravity and indicates the use of conformal invariance in supergravity. The idea that the introduction of additional symmetry transformations can make clear the structure of a field theory is not reserved to supergravity only. By means of some simple examples it is shown in chapter 3 how one can always introduce additional gauge transformations in a theory of massive vector fields. Moreover it is shown how the gauge invariant formulation sometimes explains the quantum mechanical properties of the theory. In chapter 4 the author defines the conformal transformations and summarizes their main properties. He explains how these conformal transformations can be used to analyse the structure of gravity. The supersymmetric extension of these results is discussed in chapter 5. Here he describes as an example how N=1 supergravity can be reformulated in a conformally-invariant way. He also shows that beyond N=1 the gauge fields of the superconformal symmetries do not constitute an off-shell field representation of extended conformal supergravity. Therefore, in chapter 6, a systematic method to construct the off-shell formulation of all extended conformal supergravity theories with N <= 4 is developed. As an example he uses this method to construct N=1 conformal supergravity. Finally, in chapter 7 N=4 conformal supergravity is discussed. (Auth.)

  10. Plastocyanin conformation: an analysis of its near ultraviolet absorption and circular dichroic spectra

    International Nuclear Information System (INIS)

    Draheim, J.E.; Anderson, G.P.; Duane, J.W.; Gross, E.L.

    1986-01-01

    The near-ultraviolet absorption and circular dichroic spectra of plastocyanin are dependent upon the redox state, solution pH, and ammonium sulfate concentration. This dependency was observed in plastocyanin isolated from spinach, poplar, and lettuce. Removal of the copper atom also perturbed the near-ultraviolet spectra. Upon reduction there are increases in both extinction and ellipticity at 252 nm. Further increases at 252 nm were observed upon formation of apo plastocyanin eliminating charge transfer transitions as the cause. The spectral changes in the near-ultraviolet imply a flexible tertiary conformation for plastocyanin. There are at least two charge transfer transitions at ∼295-340 nm. One of these transitions is sensitive to low pH's and is attributed to the His 87 copper ligand. The redox state dependent changes observed in the near-ultraviolet spectra of plastocyanin are attenuated either by decreasing the pH to 5 or by increasing the ammonium sulfate concentration to 2.7 M. This attenuation cannot be easily explained by simple charge screening. Hydrophobic interactions probably play an important role in this phenomenon. The pH and redox state dependent conformational changes may play an important role in regulating electron transport

  11. Dependence of the martensitic transformation and magnetic transition on the atomic order in Ni–Mn–In metamagnetic shape memory alloys

    International Nuclear Information System (INIS)

    Recarte, V.; Pérez-Landazábal, J.I.; Sánchez-Alarcos, V.; Rodríguez-Velamazán, J.A.

    2012-01-01

    The analysis of atomic order and its influence on the magnetic and structural properties of Ni–Mn–In metamagnetic shape memory alloys has been performed. The effect of the different thermal treatments on the magnetic and structural transformation temperatures, as well as on the thermodynamics of the martensitic transformation, has been made by calorimetric measurements. The evolution of the degree of long-range atomic order with temperature has been determined by neutron diffraction experiments, thus confirming the effect of thermal treatments on the atomic order. Calorimetric and structural results allow thermal treatments to be directly related to atomic order, and to allow the effect of the atomic order on the martensitic and magnetic transformations in Ni–Mn–In alloys to be quantified. The thermodynamics of the martensitic transformation depends on the atomic order as indicated out by its influence on the transformation entropy. In addition, a correlation between the transformation entropy and changes in the magnetic-field-induced transformation temperatures has been found through the evolution of the atomic order.

  12. Angular momentum coupling in atom-atom collisions

    International Nuclear Information System (INIS)

    Grosser, J.

    1986-01-01

    The coupling between the electronic angular momentum and the rotating atom-atom axis in the initial or the final phase of an atom-atom collision is discussed, making use of the concepts of radial and rotational (Coriolis) coupling between different molecular states. The description is based on a limited number of well-understood approximations, and it allows an illustrative geometric representation of the transition from the body fixed to the space fixed motion of the electrons. (orig.)

  13. Atomic inner-shell physics

    International Nuclear Information System (INIS)

    Crasemann, B.

    1985-01-01

    This book discusses: relativistic and quantum electrodynamic effects on atomic inner shells; relativistic calculation of atomic transition probabilities; many-body effects in energetic atomic transitions; Auger Electron spectrometry of core levels of atoms; experimental evaluation of inner-vacancy level energies for comparison with theory; mechanisms for energy shifts of atomic K-X rays; atomic physics research with synchrotron radiation; investigations of inner-shell states by the electron energy-loss technique at high resolution; coherence effects in electron emission by atoms; inelastic X-ray scattering including resonance phenomena; Rayleigh scattering: elastic photon scattering by bound electrons; electron-atom bremsstrahlung; X-ray and bremsstrahlung production in nuclear reactions; positron production in heavy-ion collisions, and X-ray processes in heavy-ion collisions

  14. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Ilko Bald

    2014-09-01

    Full Text Available DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.

  15. Conformal expansions and renormalons

    Energy Technology Data Exchange (ETDEWEB)

    Rathsman, J.

    2000-02-07

    The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

  16. Modern atomic physics

    CERN Document Server

    Natarajan, Vasant

    2015-01-01

    Much of our understanding of physics in the last 30-plus years has come from research on atoms, photons, and their interactions. Collecting information previously scattered throughout the literature, Modern Atomic Physics provides students with one unified guide to contemporary developments in the field. After reviewing metrology and preliminary material, the text explains core areas of atomic physics. Important topics discussed include the spontaneous emission of radiation, stimulated transitions and the properties of gas, the physics and applications of resonance fluorescence, coherence, cooling and trapping of charged and neutral particles, and atomic beam magnetic resonance experiments. Covering standards, a different way of looking at a photon, stimulated radiation, and frequency combs, the appendices avoid jargon and use historical notes and personal anecdotes to make the topics accessible to non-atomic physics students. Written by a leader in atomic and optical physics, this text gives a state-of-the...

  17. A new fundamental type of conformational isomerism

    Science.gov (United States)

    Canfield, Peter J.; Blake, Iain M.; Cai, Zheng-Li; Luck, Ian J.; Krausz, Elmars; Kobayashi, Rika; Reimers, Jeffrey R.; Crossley, Maxwell J.

    2018-06-01

    Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term `akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

  18. Conformal sequestering simplified

    International Nuclear Information System (INIS)

    Schmaltz, Martin; Sundrum, Raman

    2006-01-01

    Sequestering is important for obtaining flavor-universal soft masses in models where supersymmetry breaking is mediated at high scales. We construct a simple and robust class of hidden sector models which sequester themselves from the visible sector due to strong and conformally invariant hidden dynamics. Masses for hidden matter eventually break the conformal symmetry and lead to supersymmetry breaking by the mechanism recently discovered by Intriligator, Seiberg and Shih. We give a unified treatment of subtleties due to global symmetries of the CFT. There is enough review for the paper to constitute a self-contained account of conformal sequestering

  19. Conformally connected universes

    International Nuclear Information System (INIS)

    Cantor, M.; Piran, T.

    1983-01-01

    A well-known difficulty associated with the conformal method for the solution of the general relativistic Hamiltonian constraint is the appearance of an aphysical ''bag of gold'' singularity at the nodal surface of the conformal factor. This happens whenever the background Ricci scalar is too large. Using a simple model, it is demonstrated that some of these singular solutions do have a physical meaning, and that these can be considered as initial data for Universe containing black holes, which are connected, in a conformally nonsingular way with each other. The relation between the ADM mass and the horizon area in this solution supports the cosmic censorship conjecture. (author)

  20. Optical frequency measurements of 6s 2S1/2-6p 2P3/2 transition in a 133Cs atomic beam using a femtosecond laser frequency comb

    International Nuclear Information System (INIS)

    Gerginov, V.; Tanner, C.E.; Diddams, S.; Bartels, A.; Hollberg, L.

    2004-01-01

    Optical frequencies of the hyperfine components of the D 2 line in 133 Cs are determined using high-resolution spectroscopy and a femtosecond laser frequency comb. A narrow-linewidth probe laser excites the 6s 2 S 1/2 (F=3,4)→6p 2 P 3/2 (F=2,3,4,5) transition in a highly collimated atomic beam. Fluorescence spectra are taken by scanning the laser frequency over the excited-state hyperfine structure. The laser optical frequency is referenced to a Cs fountain clock via a reference laser and a femtosecond laser frequency comb. A retroreflected laser beam is used to estimate and minimize the Doppler shift due to misalignment between the probe laser and the atomic beam. We achieve an angular resolution on the order of 5x10 -6 rad. The final uncertainties (∼±5 kHz) in the frequencies of the optical transitions are a factor of 20 better than previous results [T. Udem et al., Phys. Rev. A 62, 031801 (2000).]. We find the centroid of the 6s 2 S 1/2 →6p 2 P 3/2 transition to be f D2 =351 725 718.4744(51) MHz

  1. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    Omer Acan

    2017-02-01

    Full Text Available In this study, we introduce the conformable variational iteration method based on new defined fractional derivative called conformable fractional derivative. This new method is applied two fractional order ordinary differential equations. To see how the solutions of this method, linear homogeneous and non-linear non-homogeneous fractional ordinary differential equations are selected. Obtained results are compared the exact solutions and their graphics are plotted to demonstrate efficiency and accuracy of the method.

  2. Delineating the conformal window

    DEFF Research Database (Denmark)

    Frandsen, Mads Toudal; Pickup, Thomas; Teper, Michael

    2011-01-01

    We identify and characterise the conformal window in gauge theories relevant for beyond the standard model building, e.g. Technicolour, using the criteria of metric confinement and causal analytic couplings, which are known to be consistent with the phase diagram of supersymmetric QCD from Seiberg...... duality. Using these criteria we find perturbation theory to be consistent throughout the predicted conformal window for several of these gauge theories and we discuss recent lattice results in the light of our findings....

  3. Essential role of conformational selection in ligand binding.

    Science.gov (United States)

    Vogt, Austin D; Pozzi, Nicola; Chen, Zhiwei; Di Cera, Enrico

    2014-02-01

    Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and

  4. Spatially resolved photoionization of ultracold atoms on an atom chip

    International Nuclear Information System (INIS)

    Kraft, S.; Guenther, A.; Fortagh, J.; Zimmermann, C.

    2007-01-01

    We report on photoionization of ultracold magnetically trapped Rb atoms on an atom chip. The atoms are trapped at 5 μK in a strongly anisotropic trap. Through a hole in the chip with a diameter of 150 μm, two laser beams are focused onto a fraction of the atomic cloud. A first laser beam with a wavelength of 778 nm excites the atoms via a two-photon transition to the 5D level. With a fiber laser at 1080 nm the excited atoms are photoionized. Ionization leads to depletion of the atomic density distribution observed by absorption imaging. The resonant ionization spectrum is reported. The setup used in this experiment is suitable not only to investigate mixtures of Bose-Einstein condensates and ions but also for single-atom detection on an atom chip

  5. Focused conformational sampling in proteins

    Science.gov (United States)

    Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

    2017-11-01

    A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

  6. Enhanced conformational sampling using enveloping distribution sampling.

    Science.gov (United States)

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2013-10-14

    To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

  7. Low energy atom-atom collisions

    International Nuclear Information System (INIS)

    Child, M.S.

    1980-01-01

    The semiclassical theory of atom-atom potential scattering and of low energy inelastic atom-atom scattering is reviewed. Particular attention is given to the origin and interpretation of rainbow structure, diffraction oscillations and exchange oscillations in the potential scattering differential cross-section, and to the glory structure and symmetry oscillations in the integral cross-section. Available methods for direct inversion of the cross-section data to recover the potential are reviewed in some detail. The theory of non-adiabatic transitions is introduced by a short discussion of interaction mechanisms and of diabetic and adiabatic representations. Analytical S matrix elements are presented for two state curve-crossing (Landau-Zener-Stuckelberg), Demkov and Nikitin models. The relation between Stuckelberg oscillations in the S matrix and in the differential cross-section is discussed in terms of interference between trajectories belonging to two different classical deflection functions. The energy dependences of the inelastic integral cross-section for curve-crossing and Demkov type transitions are also discussed. Finally the theory is reviewed in relation to a recent close-coupled study of fine structure transitions in F( 2 P) + Xe( 2 S) scattering

  8. In vivo dose estimations through transit signal measured with thimble chamber positioned along the central axis at electronic portal imaging device level in medical linear accelerator in carcinoma of the middle-third esophagus patients undergoing three-dimensional conformal radiotherapy.

    Science.gov (United States)

    Kumar, Putha Suman; Banerjee, S; Arun Kumar, E S; Srinivas, Challapalli; Vadhiraja, B M; Saxena, P U; Ravichandran, Ramamoorthy; Kasturi, Dinesh Pai

    2018-01-01

    This study presents a method to estimate midplane dose (D iso, transit ) in vivo from transit signal (S t ) measured with thimble ionization chamber in cancer of the middle-third esophagus patients treated with three-dimensional radiotherapy (RT). This detector is positioned at the level of electronic portal imaging device in the gantry of a medical linear accelerator. Efficacy of inhomogeneity corrections of three dose calculation algorithms available in XiO treatment planning system (TPS) for planned dose (for open fields) (D iso, TPS ) was studied with three heterogeneous phantoms. D iso, transit represents measured signal at transit point (S t ) far away correlating to dose at isocenter. A locally fabricated thorax phantom was used to measure the in vivo midplane dose (D iso, mid ) which was also estimated through S t . Thirteen patients with carcinoma of the middle-third esophagus treated with three-dimensional conformal RT were studied. S t was recorded (three times, with a gap of 5-6 fractions during the treatment) to estimate D iso, transit , which was compared with the doses calculated by TPS. The dose predictions by superposition algorithm were superior compared to the other algorithms. Percentage deviation of D iso, transit , D iso, mid with D iso, TPS combined all fields was 2.7 and -2.6%, respectively, with the thorax phantom. The mean percentage deviation with standard deviation of estimated D iso, transit with D iso, TPS observed in patients was within standard deviation -0.73% ±2.09% (n = 39). Midplane dose estimates in vivo using this method provide accurate determination of delivered dose in the middle-third esophagus RT treatments. This method could be useful in similar clinical circumstances for dose confirmation and documentation.

  9. Conformational Analysis of Contrast Media for X-Ray Diagnostic Radiology

    International Nuclear Information System (INIS)

    Solieman, A.H.M.

    2010-01-01

    The conformational analysis of iodinated non-ionic contrast agent, Iobitridol, was carried out using theoretical calculations to explore its conformational space, and to study different aspects connected with application of different search techniques. Monte Carlo (MC), random search (RS) and molecular dynamics (MD) based conformational search techniques were used to extract a reasonable-size sample that adequately represents and has an average behavior of the entire conformational ensemble.While MC is good for quick search for lowest energy conformer, RS is better in obtaining conformational sample that cover the whole conformational space and MD is the best for investigation of isomeric preferences inside the conformational ensemble at thermal equilibrium. Conformational analysis of the produced gas phase samples reveals that RS and MD methods could sufficiently present the 18 distinct isomeric classes that constitute the total conformational space of the Iobitridol. S samples of conformational space of Iobitridol are extensively studied, as it hypothetically cover the total conformational space. They are used to test the suitability of different methods (charge distribution methods, energy calculation methods) for Iobitridol molecular computations and internal structure forces (steric hindrance, resonance interaction), as well as dependences among the internal coordinates (dihedral angles correlations and coincidences). The atomic partial charge distribution is found to greatly affect the energy calculation for the molecular mechanics based conformational energy distributions. Further energy minimization of conformational sample by the quantum molecular orbital methods is crucial to obtain charge independent as well as energy balanced conformational sample.

  10. Conformity and statistical tolerancing

    Science.gov (United States)

    Leblond, Laurent; Pillet, Maurice

    2018-02-01

    Statistical tolerancing was first proposed by Shewhart (Economic Control of Quality of Manufactured Product, (1931) reprinted 1980 by ASQC), in spite of this long history, its use remains moderate. One of the probable reasons for this low utilization is undoubtedly the difficulty for designers to anticipate the risks of this approach. The arithmetic tolerance (worst case) allows a simple interpretation: conformity is defined by the presence of the characteristic in an interval. Statistical tolerancing is more complex in its definition. An interval is not sufficient to define the conformance. To justify the statistical tolerancing formula used by designers, a tolerance interval should be interpreted as the interval where most of the parts produced should probably be located. This tolerance is justified by considering a conformity criterion of the parts guaranteeing low offsets on the latter characteristics. Unlike traditional arithmetic tolerancing, statistical tolerancing requires a sustained exchange of information between design and manufacture to be used safely. This paper proposes a formal definition of the conformity, which we apply successively to the quadratic and arithmetic tolerancing. We introduce a concept of concavity, which helps us to demonstrate the link between tolerancing approach and conformity. We use this concept to demonstrate the various acceptable propositions of statistical tolerancing (in the space decentring, dispersion).

  11. Axiomatic conformal field theory

    International Nuclear Information System (INIS)

    Gaberdiel, M.R.; Goddard, P.

    2000-01-01

    A new rigourous approach to conformal field theory is presented. The basic objects are families of complex-valued amplitudes, which define a meromorphic conformal field theory (or chiral algebra) and which lead naturally to the definition of topological vector spaces, between which vertex operators act as continuous operators. In fact, in order to develop the theory, Moebius invariance rather than full conformal invariance is required but it is shown that every Moebius theory can be extended to a conformal theory by the construction of a Virasoro field. In this approach, a representation of a conformal field theory is naturally defined in terms of a family of amplitudes with appropriate analytic properties. It is shown that these amplitudes can also be derived from a suitable collection of states in the meromorphic theory. Zhu's algebra then appears naturally as the algebra of conditions which states defining highest weight representations must satisfy. The relationship of the representations of Zhu's algebra to the classification of highest weight representations is explained. (orig.)

  12. Entanglement analysis of a two-atom nonlinear Jaynes-Cummings model with nondegenerate two-photon transition, Kerr nonlinearity, and two-mode Stark shift

    Science.gov (United States)

    Baghshahi, H. R.; Tavassoly, M. K.; Faghihi, M. J.

    2014-12-01

    An entangled state, as an essential tool in quantum information processing, may be generated through the interaction between light and matter in cavity quantum electrodynamics. In this paper, we study the interaction between two two-level atoms and a two-mode field in an optical cavity enclosed by a medium with Kerr nonlinearity in the presence of a detuning parameter and Stark effect. It is assumed that the atom-field coupling and third-order susceptibility of the Kerr medium depend on the intensity of the light. In order to investigate the dynamics of the introduced system, we obtain the exact analytical form of the state vector of the considered atom-field system under initial conditions which may be prepared for the atoms (in a coherent superposition of their ground and upper states) and the fields (in a standard coherent state). Then, in order to evaluate the degree of entanglement between the subsystems, we investigate the dynamics of the entanglement by employing the entanglement of formation. Finally, we analyze in detail the influences of the Stark shift, the deformed Kerr medium, the intensity-dependent coupling, and also the detuning parameter on the behavior of this measure for different subsystems. The numerical results show that the amount of entanglement between the different subsystems can be controlled by choosing the evolved parameters appropriately.

  13. Current-voltage curves of atomic-sized transition metal contacts: An explanation of why Au is ohmic and Pt is not

    DEFF Research Database (Denmark)

    Nielsen, S.K.; Brandbyge, Mads; Hansen, K.

    2002-01-01

    We present an experimental study of current-voltage (I-V) curves on atomic-sized Au and Pt contacts formed under cryogenic vacuum (4.2 K). Whereas I-V curves for Au are almost Ohmic, the conductance G=I/V for Pt decreases with increasing voltage, resulting in distinct nonlinear I-V behavior...

  14. Atomic and molecular adsorption on transition-metal carbide (111) surfaces from density-functional theory: a trend study of surface electronic factors

    DEFF Research Database (Denmark)

    Vojvodic, Aleksandra; Ruberto, C.; Lundqvist, Bengt

    2010-01-01

    ) surfaces. The spatial extent and the dangling bond nature of these SRs are supported by real-space analyses of the calculated Kohn-Sham wavefunctions. Then, atomic and molecular adsorption energies, geometries, and charge transfers are presented. An analysis of the adsorbate-induced changes in surface DOSs...

  15. Confab - Systematic generation of diverse low-energy conformers

    Directory of Open Access Journals (Sweden)

    O'Boyle Noel M

    2011-03-01

    Full Text Available Abstract Background Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. Results Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 Å at a diversity level of 1.5 Å and an energy cutoff of 50 kcal/mol. Conclusions Confab is available from http://confab.googlecode.com.

  16. Extended conformal algebras

    International Nuclear Information System (INIS)

    Goddard, Peter

    1990-01-01

    The algebra of the group of conformal transformations in two dimensions consists of two commuting copies of the Virasoro algebra. In many mathematical and physical contexts, the representations of ν which are relevant satisfy two conditions: they are unitary and they have the ''positive energy'' property that L o is bounded below. In an irreducible unitary representation the central element c takes a fixed real value. In physical contexts, the value of c is a characteristic of a theory. If c < 1, it turns out that the conformal algebra is sufficient to ''solve'' the theory, in the sense of relating the calculation of the infinite set of physically interesting quantities to a finite subset which can be handled in principle. For c ≥ 1, this is no longer the case for the algebra alone and one needs some sort of extended conformal algebra, such as the superconformal algebra. It is these algebras that this paper aims at addressing. (author)

  17. Algebraic conformal field theory

    International Nuclear Information System (INIS)

    Fuchs, J.; Nationaal Inst. voor Kernfysica en Hoge-Energiefysica

    1991-11-01

    Many conformal field theory features are special versions of structures which are present in arbitrary 2-dimensional quantum field theories. So it makes sense to describe 2-dimensional conformal field theories in context of algebraic theory of superselection sectors. While most of the results of the algebraic theory are rather abstract, conformal field theories offer the possibility to work out many formulae explicitly. In particular, one can construct the full algebra A-bar of global observables and the endomorphisms of A-bar which represent the superselection sectors. Some explicit results are presented for the level 1 so(N) WZW theories; the algebra A-bar is found to be the enveloping algebra of a Lie algebra L-bar which is an extension of the chiral symmetry algebra of the WZW theory. (author). 21 refs., 6 figs

  18. Glass transition on the development of a hydrogen-bond network in nano-channel ice, and subsequent phase transitions of the ordering of hydrogen atom positions within the network in [Co(H{sub 2}bim){sub 3}](TMA){center_dot}20H{sub 2}O

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Keisuke [Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551 (Japan); Oguni, Masaharu [Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551 (Japan); Tadokoro, Makoto [Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601 (Japan); Oohata, Yuki [Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601 (Japan); Nakamura, Ryouhei [Department of Chemistry, Graduate School of Science, Osaka Municipal University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585 (Japan)

    2006-09-20

    Low-temperature thermal properties of crystalline [Co(H{sub 2}bim){sub 3}](TMA){center_dot}20H{sub 2}O were studied by adiabatic calorimetry, where H{sub 2}bim is 2,2'-biimidazole, TMA is 1,3,5-benzene tricarboxylic acid, and 20H{sub 2}O represents the water forming nano-channel in the crystal. A glass transition was observed at T{sub g} = 107 K. It was discussed as a freezing-in phenomenon of a small number of water molecules remaining partially disordered in their positional arrangement. The possibility that some defects really remain in the hydrogen-bond network of channel water was mentioned. Two subsequent phase transitions were observed at 54.8 and 59 K. These were interpreted as being of a (super-structural commensurate)-incommensurate-(normal commensurate) type in the heating direction with respect to the hydrogen-atom positions as referred to the periodicity of the hydrogen-bond network. The transition entropy was evaluated to be 0.65 J K{sup -1}(H{sub 2}O-mol){sup -1} as a total of the two, indicating that the disorder of the hydrogen atoms is present only in part of the water molecules of the channel. Based on the fact that the excess heat capacity due to the equilibrium phase transition is observed down to 35-40 K, the relaxation time for the rearrangement of the hydrogen-atom positions was assumed at the longest to be 1 ks at 35 K. This indicates that the activation energy of the rearrangement amounts to at most 13 kJ mol{sup -1} and that the transfer of Bjerrum defects is attributed to the rearrangement.

  19. Kinetics of an oxygen – iodine active medium with iodine atoms optically pumped on the {sup 2}P{sub 1/2} – {sup 2}P{sub 3/2} transition

    Energy Technology Data Exchange (ETDEWEB)

    Zagidullin, M V; Azyazov, V N [Samara Branch of the P.N. Lebedev Physical Institute, Russian Academy of Sciences, Samara (Russian Federation); Malyshev, M S [S.P. Korolev Samara State Aerospace University, Samara (Russian Federation)

    2015-08-31

    The kinetics of the processes occurring in an O{sub 2} – I{sub 2} – He – H{sub 2}O gas flow in which photodissociation of molecular iodine at a wavelength close to 500 nm and excitation of atomic iodine on the {sup 2}P{sub 1/2} – {sup 2}P{sub 3/2} transition by narrow-band radiation near 1315 nm are implemented successively has been analysed. It is shown that implementation of these processes allows one to form an oxygen – iodine medium with a high degree of dissociation of molecular iodine and a relative content of singlet oxygen O{sub 2}(a{sup 1}Δ) exceeding 10%. Having formed a supersonic gas flow with a temperature ∼100 K from this medium, one can reach a small-signal gain of about 10{sup -2} cm{sup -1} on the {sup 2}P{sub 1/2} – {sup 2}P{sub 3/2} transition in iodine atoms. The specific power per unit flow cross section in the oxygen – iodine laser with this active medium may reach ∼100 W cm{sup -2}. (active media)

  20. Killing tensors and conformal Killing tensors from conformal Killing vectors

    International Nuclear Information System (INIS)

    Rani, Raffaele; Edgar, S Brian; Barnes, Alan

    2003-01-01

    Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors

  1. Atom optics

    International Nuclear Information System (INIS)

    Balykin, V. I.; Jhe, W.

    1999-01-01

    Atom optics, in analogy to neutron and electron optics, deals with the realization of as a traditional elements, such as lenes, mirrors, beam splitters and atom interferometers, as well as a new 'dissipative' elements such as a slower and a cooler, which have no analogy in an another types of optics. Atom optics made the development of atom interferometer with high sensitivity for measurement of acceleration and rotational possible. The practical interest in atom optics lies in the opportunities to create atom microprobe with atom-size resolution and minimum damage of investigated objects. (Cho, G. S.)

  2. Single-atom lasing induced atomic self-trapping

    International Nuclear Information System (INIS)

    Salzburger, T.; Ritsch, H.

    2004-01-01

    We study atomic center of mass motion and field dynamics of a single-atom laser consisting of a single incoherently pumped free atom moving in an optical high-Q resonator. For sufficient pumping, the system starts lasing whenever the atom is close to a field antinode. If the field mode eigenfrequency is larger than the atomic transition frequency, the generated laser light attracts the atom to the field antinode and cools its motion. Using quantum Monte Carlo wave function simulations, we investigate this coupled atom-field dynamics including photon recoil and cavity decay. In the regime of strong coupling, the generated field shows strong nonclassical features like photon antibunching, and the atom is spatially confined and cooled to sub-Doppler temperatures. (author)

  3. Molecular dynamics studies of the conformation of sorbitol

    Science.gov (United States)

    Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

    2009-01-01

    Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

  4. Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy.

    KAUST Repository

    Minenkov, Yury

    2018-05-22

    A series of semiempirical PM6* and PM7 methods has been tested in reproducing of relative conformational energies of 27 realistic-size complexes of 16 different transition metals (TMs). An analysis of relative energies derived from single-point energy evaluations on density functional theory (DFT) optimized conformers revealed pronounced deviations between semiempirical and DFT methods indicating fundamental difference in potential energy surfaces (PES). To identify the origin of the deviation, we compared fully optimized PM7 and respective DFT conformers. For many complexes, differences in PM7 and DFT conformational energies have been confirmed often manifesting themselves in false coordination of some atoms (H, O) to TMs and chemical transformations/distortion of coordination center geometry in PM7 structures. Despite geometry optimization with fixed coordination center geometry leads to some improvements in conformational energies, the resulting accuracy is still too low to recommend explored semiempirical methods for out-of-the-box conformational search/sampling: careful testing is always needed.

  5. Impact of buffer gas quenching on the 1S0 → 1P1 ground-state atomic transition in nobelium

    NARCIS (Netherlands)

    Chhetri, Premaditya; Ackermann, Dieter; Backe, Hartmut; Block, Michael; Cheal, Bradley; Düllmann, Christoph Emanuel; Even, Julia; Ferrer, Rafael; Giacoppo, Francesca; Götz, Stefan; Heßberger, Fritz Peter; Kaleja, Oliver; Khuyagbaatar, Jadambaa; Kunz, Peter; Laatiaoui, Mustapha; Lautenschläger, Felix; Lauth, Werner; Ramirez, Enrique Minaya; Mistry, Andrew Kishor; Raeder, Sebastian; Wraith, Calvin; Walther, Thomas; Yakushev, Alexander

    2017-01-01

    Using the sensitive Radiation Detected Resonance Ionization Spectroscopy (RADRIS) technique an optical transition in neutral nobelium (No, Z = 102) was identified. A remnant signal when delaying the ionizing laser indicated the influence of a strong buffer gas induced de-excitation of the optically

  6. New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

    Science.gov (United States)

    Thach, Trung Thanh; Shin, Donghyuk; Han, Seungsu; Lee, Sangho

    2016-04-01

    The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

  7. Massive Conformal Gravity

    International Nuclear Information System (INIS)

    Faria, F. F.

    2014-01-01

    We construct a massive theory of gravity that is invariant under conformal transformations. The massive action of the theory depends on the metric tensor and a scalar field, which are considered the only field variables. We find the vacuum field equations of the theory and analyze its weak-field approximation and Newtonian limit.

  8. Taming the conformal zoo

    International Nuclear Information System (INIS)

    Moore, G.; Seiberg, N.

    1989-01-01

    All known rational conformal field theories may be obtained from (2+1)-dimensional Chern-Simons gauge theories by appropriate choice of gauge group. We conjecture that all rational field theories are classified by groups via (2+1)-dimensional Chern-Simons gauge theories. (orig.)

  9. Conformal special relativity

    International Nuclear Information System (INIS)

    Maia, M.D.

    2006-01-01

    It is shown that the information loss/recovery theorem based on the ADS/CFT correspondence is not consistent with the stability of the Schwarzschild or Reissner-Nordstrom black holes. Nonetheless, the conformal invariance of Yang-Mills theory points to new relativity principle compatible with quantum unitarity near those black holes

  10. Animal culture: chimpanzee conformity?

    Science.gov (United States)

    van Schaik, Carel P

    2012-05-22

    Culture-like phenomena in wild animals have received much attention, but how good is the evidence and how similar are they to human culture? New data on chimpanzees suggest their culture may even have an element of conformity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Parafermionic conformal field theory

    International Nuclear Information System (INIS)

    Kurak, V.

    1989-09-01

    Conformal parafermionic field theories are reviewed with emphasis on the computation of their OPE estructure constants. It is presented a simple computational of these for the Z(N) parafermions, unveilling their Lie algebra content. (A.C.A.S.) [pt

  12. Atom-by-atom assembly

    International Nuclear Information System (INIS)

    Hla, Saw Wai

    2014-01-01

    Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to ‘see’ individual atoms by means of imaging, but is also a tool that is used to ‘touch’ and ‘take’ the atoms, or to ‘hear’ their movements. Therefore, the STM can be considered as the ‘eyes’, ‘hands’ and ‘ears’ of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed. (review article)

  13. Transition probabilities for lines of Cr II, Na II and Sb I by laser produced plasma atomic emission spectroscopy; Probabilidades de transicion de algunos niveles de Cr II, Na II y Sb I medediante espectroscopia de plasma producidos por laser

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, A. M.; Ortiz, M.; Campos, J.

    1995-07-01

    Absolute transition probabilities for lines of CR II, Na II and Sb I were determined by emission spectroscopy of laser induced plasmas. the plasma was produced focusing the emission of a pulsed Nd-Yag laser on solid samples containing the atom in study. the light arising from the plasma region was collected by and spectrometer. the detector used was a time-resolved optical multichannel analyzer (OMA III EG and G). The wavelengths of the measured transitions range from 2000 sto 4100 A. The spectral resolution of the system was 0. 2 A. The method can be used in insulators materials as Cl Na crystals and in metallic samples as Al-Cr and Sn-Sn alloys. to avoid self-absorption effects the alloys were made with low Sb or Cr content. Relative transition probabilities have been determined from measurements of emission-line intensities and were placed on an absolute scale by using, where possible, accurate experimental lifetime values form the literature or theoretical data. From these measurements, values for plasma temperature (8000-24000 K), electron densities ({approx}{approx} 10''16 cm ''-3) and self-absorption coefficients have been obtained. (Author) 56 refs.

  14. Evolution Properties of Atomic Fidelity in the Combined Multi-Atom-Cavity Field System

    International Nuclear Information System (INIS)

    Wang Ju-Xia; Zhang Xiao-Juan; Zhang Xiu-Xing

    2015-01-01

    The atom fidelity is investigated in a system consisting of Mtwo-level atoms and M single-mode fields by use of complete quantum theory and numerical evaluation method. The influences of various system parameters on the evolution of atomic fidelity are studied. The results show that the atomic fidelity evolves in a Rabi oscillation manner. The oscillation frequency is mainly modulated by the coupling strength between atoms and light field, the atomic transition probabilities and the average photon numbers. Other factors hardly impact on the atomic fidelity. The present results may provide a useful approach to the maintenance of the atomic fidelity in the atom cavity field systems. (paper)

  15. Logarithmic conformal field theory

    Science.gov (United States)

    Gainutdinov, Azat; Ridout, David; Runkel, Ingo

    2013-12-01

    Conformal field theory (CFT) has proven to be one of the richest and deepest subjects of modern theoretical and mathematical physics research, especially as regards statistical mechanics and string theory. It has also stimulated an enormous amount of activity in mathematics, shaping and building bridges between seemingly disparate fields through the study of vertex operator algebras, a (partial) axiomatisation of a chiral CFT. One can add to this that the successes of CFT, particularly when applied to statistical lattice models, have also served as an inspiration for mathematicians to develop entirely new fields: the Schramm-Loewner evolution and Smirnov's discrete complex analysis being notable examples. When the energy operator fails to be diagonalisable on the quantum state space, the CFT is said to be logarithmic. Consequently, a logarithmic CFT is one whose quantum space of states is constructed from a collection of representations which includes reducible but indecomposable ones. This qualifier arises because of the consequence that certain correlation functions will possess logarithmic singularities, something that contrasts with the familiar case of power law singularities. While such logarithmic singularities and reducible representations were noted by Rozansky and Saleur in their study of the U (1|1) Wess-Zumino-Witten model in 1992, the link between the non-diagonalisability of the energy operator and logarithmic singularities in correlators is usually ascribed to Gurarie's 1993 article (his paper also contains the first usage of the term 'logarithmic conformal field theory'). The class of CFTs that were under control at this time was quite small. In particular, an enormous amount of work from the statistical mechanics and string theory communities had produced a fairly detailed understanding of the (so-called) rational CFTs. However, physicists from both camps were well aware that applications from many diverse fields required significantly more

  16. Stanford polarized atomic beam target

    International Nuclear Information System (INIS)

    Mavis, D.G.; Dunham, J.S.; Hugg, J.W.; Glavish, H.F.

    1976-01-01

    A polarized atomic beam source was used to produce an atomic hydrogen beam which was in turn used as a polarized proton target. A target density of 2 x 10'' atoms/cm 3 and a target polarization of 0.37 without the use of rf transitions were measured. These measurements indicate that a number of experiments are currently feasible with a variety of polarized target beams

  17. Control of the conformations of ion Coulomb crystals in a Penning trap

    Science.gov (United States)

    Mavadia, Sandeep; Goodwin, Joseph F.; Stutter, Graham; Bharadia, Shailen; Crick, Daniel R.; Segal, Daniel M.; Thompson, Richard C.

    2013-01-01

    Laser-cooled atomic ions form ordered structures in radiofrequency ion traps and in Penning traps. Here we demonstrate in a Penning trap the creation and manipulation of a wide variety of ion Coulomb crystals formed from small numbers of ions. The configuration can be changed from a linear string, through intermediate geometries, to a planar structure. The transition from a linear string to a zigzag geometry is observed for the first time in a Penning trap. The conformations of the crystals are set by the applied trap potential and the laser parameters, and agree with simulations. These simulations indicate that the rotation frequency of a small crystal is mainly determined by the laser parameters, independent of the number of ions and the axial confinement strength. This system has potential applications for quantum simulation, quantum information processing and tests of fundamental physics models from quantum field theory to cosmology. PMID:24096901

  18. Hyperfine structure of the metastable p-barHe+ atom revealed by a laser-induced (n,l) = (37,35) → (38,34) transition

    International Nuclear Information System (INIS)

    Widmann, E.; Eades, J.; Yamazaki, T.

    1996-11-01

    A precise scan of the previously discovered laser-induced transition (n,l) = (37,35) → (38,34) in p-barHe + revealed a doublet structure with a separation of Δν HF = 1.70 ± 0.05 GHz. This new type of 'hyperfine' splitting is ascribed to the interaction of the antiproton orbital angular momentum and the electron spin. (author)

  19. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    , the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows...... conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

  20. Atomic data from the IRON Project. XXXII. On the accuracy of the effective collision strength for the electron impact excitation of the quadrupole transition in AR III

    Science.gov (United States)

    Galavís, M. E.; Mendoza, C.; Zeippen, C. J.

    1998-12-01

    Since te[Burgess et al. (1997)]{bur97} have recently questioned the accuracy of the effective collision strength calculated in the IRON Project for the electron impact excitation of the 3ssp23p sp4 \\ sp1 D -sp1 S quadrupole transition in Ar iii, an extended R-matrix calculation has been performed for this transition. The original 24-state target model was maintained, but the energy regime was increased to 100 Ryd. It is shown that in order to ensure convergence of the partial wave expansion at such energies, it is necessary to take into account partial collision strengths up to L=30 and to ``top-up'' with a geometric series procedure. By comparing effective collision strengths, it is found that the differences from the original calculation are not greater than 25% around the upper end of the common temperature range and that they are much smaller than 20% over most of it. This is consistent with the accuracy rating (20%) previously assigned to transitions in this low ionisation system. Also the present high-temperature limit agrees fairly well (15%) with the Coulomb-Born limit estimated by Burgess et al., thus confirming our previous accuracy rating. It appears that Burgess et al., in their data assessment, have overextended the low-energy behaviour of our reduced effective collision strength to obtain an extrapolated high-temperature limit that appeared to be in error by a factor of 2.

  1. Empirical regularities in the excitation cross-section behavior of the lead atom (transitions from energy levels of 6pnd configurations)

    Science.gov (United States)

    Smirnov, Yu M.

    2018-03-01

    Electron-impact excitation of lead atom levels belonging to 6pnd configurations has been studied in experiment. One hundred two excitation cross-sections have been measured at an incident electron energy of 50 eV. Eleven optical excitation functions (OEFs) have been recorded in the exciting electron energy range of E = 0-200 eV. The resulting findings were used to study the excitation cross-sections dependence on the principal quantum number of upper levels for thirteen PbI spectral series.

  2. Conformally compactified homogeneous spaces (Possible Observable Consequences)

    International Nuclear Information System (INIS)

    Budinich, P.

    1995-01-01

    Some arguments based on the possible spontaneous violation of the Cosmological Principles (represented by the observed large-scale structures of galaxies), the Cartan-geometry of simple spinors and on the Fock-formulation of hydrogen-atom wave-equation in momentum-space, are presented in favour of the hypothesis that space-time and momentum-space should be both conformally compactified and represented by the two four-dimensional homogeneous spaces of the conformal group, both isomorphic to (S 3 X S 1 )/Z 2 and correlated by conformal inversion. Within this framework, the possible common origin for the S0(4) symmetry underlying the geometrical structure of the Universe, of Kepler orbits and of the H-atom is discussed. On of the consequences of the proposed hypothesis could be that any quantum field theory should be naturally free from both infrared and ultraviolet divergences. But then physical spaces defined as those where physical phenomena may be best described, could be different from those homogeneous spaces. A simple, exactly soluble, toy model, valid for a two-dimensional space-time is presented where the conjecture conformally compactified space-time and momentum-space are both isomorphic to (S 1 X S 1 )/Z 2 , while the physical spaces are two finite lattice which are dual since Fourier transforms, represented by finite, discrete, sums may be well defined on them. Furthermore, a q-deformed SU q (1,1) may be represented on them if q is a root of unity. (author). 22 refs, 3 figs

  3. Adhesion and friction in polymer films on solid substrates: conformal sites analysis and corresponding surface measurements.

    Science.gov (United States)

    An, Rong; Huang, Liangliang; Mineart, Kenneth P; Dong, Yihui; Spontak, Richard J; Gubbins, Keith E

    2017-05-21

    In this work, we present a statistical mechanical analysis to elucidate the molecular-level factors responsible for the static and dynamic properties of polymer films. This analysis, which we term conformal sites theory, establishes that three dimensionless parameters play important roles in determining differences from bulk behavior for thin polymer films near to surfaces: a microscopic wetting parameter, α wx , defined as the ratio of polymer-substrate interaction to polymer-polymer interaction; a dimensionless film thickness, H*; and dimensionless temperature, T*. The parameter α wx introduced here provides a more fundamental measure of wetting than previous metrics, since it is defined in terms of intermolecular forces and the atomic structure of the substrate, and so is valid at the nanoscale for gas, liquid or solid films. To test this theoretical analysis, we also report atomic force microscopy measurements of the friction coefficient (μ), adhesion force (F A ) and glass transition temperature (T g ) for thin films of two polymers, poly(methyl methacrylate) (PMMA) and polystyrene (PS), on two planar substrates, graphite and silica. Both the friction coefficient and the glass transition temperature are found to increase as the film thickness decreases, and this increase is more pronounced for the graphite than for the silica surface. The adhesion force is also greater for the graphite surface. The larger effects encountered for the graphite surface are attributed to the fact that the microscopic wetting parameter, α wx , is larger for graphite than for silica, indicating stronger attraction of polymer chains to the graphite surface.

  4. Entanglement analysis of a two-atom nonlinear Jaynes–Cummings model with nondegenerate two-photon transition, Kerr nonlinearity, and two-mode Stark shift

    International Nuclear Information System (INIS)

    Baghshahi, H R; Tavassoly, M K; Faghihi, M J

    2014-01-01

    An entangled state, as an essential tool in quantum information processing, may be generated through the interaction between light and matter in cavity quantum electrodynamics. In this paper, we study the interaction between two two-level atoms and a two-mode field in an optical cavity enclosed by a medium with Kerr nonlinearity in the presence of a detuning parameter and Stark effect. It is assumed that the atom–field coupling and third-order susceptibility of the Kerr medium depend on the intensity of the light. In order to investigate the dynamics of the introduced system, we obtain the exact analytical form of the state vector of the considered atom–field system under initial conditions which may be prepared for the atoms (in a coherent superposition of their ground and upper states) and the fields (in a standard coherent state). Then, in order to evaluate the degree of entanglement between the subsystems, we investigate the dynamics of the entanglement by employing the entanglement of formation. Finally, we analyze in detail the influences of the Stark shift, the deformed Kerr medium, the intensity-dependent coupling, and also the detuning parameter on the behavior of this measure for different subsystems. The numerical results show that the amount of entanglement between the different subsystems can be controlled by choosing the evolved parameters appropriately. (paper)

  5. Transportation Conformity Training and Presentations

    Science.gov (United States)

    EPA's OTAQ has provided multiple conformity training sessions in the past to assist state and local governments in implementing conformity requirements. As training information is prepared for other venues, it will be posted on this page.

  6. Src kinase conformational activation: thermodynamics, pathways, and mechanisms.

    Directory of Open Access Journals (Sweden)

    Sichun Yang

    2008-03-01

    Full Text Available Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the alphaC helix, the activation-loop, and the beta strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the alphaC helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation.

  7. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i......We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged...... in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We...

  8. Conformational flexibility of aspartame.

    Science.gov (United States)

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. © 2016 Wiley Periodicals, Inc.

  9. Conformal description of spinning particles

    International Nuclear Information System (INIS)

    Todorov, I.T.

    1986-01-01

    This book is an introduction to the application of the conformal group to quantum field theory of particles with spin. After an introduction to the twistor representations of the conformal group of a conformally flat space-time and twistor flag manifolds with Su(2,2) orbits the classical phase space of conformal spinning particles is described. Thereafter the twistor description of classical zero mass fields is considered together with the quantization. (HSI)

  10. Conformal boundaries of warped products

    DEFF Research Database (Denmark)

    Kokkendorff, Simon Lyngby

    2006-01-01

    In this note we prove a result on how to determine the conformal boundary of a type of warped product of two length spaces in terms of the individual conformal boundaries. In the situation, that we treat, the warping and conformal distortion functions are functions of distance to a base point....... The result is applied to produce examples of CAT(0)-spaces, where the conformal and ideal boundaries differ in interesting ways....

  11. Atomic collisions research with excited atomic species

    International Nuclear Information System (INIS)

    Hoogerland, M.D.; Gulley, R.J.; Colla, M.; Lu, W.; Milic, D.; Baldwin, K.G.H.; Buckman, S.J.

    1999-01-01

    Measurements and calculations of fundamental atomic collision and spectroscopic properties such as collision cross sections, reaction rates, transition probabilities etc. underpin the understanding and operation of many plasma and gas-discharge-based devices and phenomena, for example plasma processing and deposition. In almost all cases the complex series of reactions which sustains the discharge or plasma, or produces the reactive species of interest, has a precursor electron impact excitation, attachment, dissociation or ionisation event. These processes have been extensively studied in a wide range of atomic and molecular species and an impressive data base of collision cross sections and reaction rates now exists. However, most of these measurements are for collisions with stable atomic or molecular species which are initially in their ground electronic state. Relatively little information is available for scattering from excited states or for scattering from unstable molecular radicals. Examples of such species would be metastable excited rare gases, which are often used as buffer gases, or CF 2 radicals formed by electron impact dissociation in a CF 4 plasma processing discharge. We are interested in developing experimental techniques which will enable the quantitative study of such exotic atomic and molecular species. In this talk I would like to outline one such facility which is being used for studies of collisions with metastable He(2 3 S) atoms

  12. Conformal radiotherapy: a glossary

    International Nuclear Information System (INIS)

    Dubray, B.; Giraud, P.; Beaudre, A.

    1999-01-01

    Most of the concepts and terms related to conformal radiotherapy were produced by English-speaking authors and eventually validated by international groups of experts, whose working language was also English. Therefore, a significant part of this literature is poorly accessible to the French-speaking radiation oncology community. The present paper gathers the 'official' definitions already published in French, along with propositions for the remaining terms which should be submitted to a more formal and representative validation process. (author)

  13. Four-wave mixing and parametric four-wave mixing near the 4P-4S transition of the potassium atom

    International Nuclear Information System (INIS)

    Katharakis, M; Merlemis, N; Serafetinides, A; Efthimiopoulos, T

    2002-01-01

    Potassium 4S 1/2 -6S 1/2 two-photon excitation initiates the emission of several internally generated photons. For the first time two emission lines, one close to and one below the potassium 4P 3/2 level, are reported for low pumping intensity. Radiation emitted below the 4P 3/2 level is due to a parametric four-wave mixing process that uses the photons emitted at the 5P 3/2 -4S 1/2 transition and a two-step four-wave mixing process generates the line emitted close to the 4P 3/2 level

  14. Density functional calculations on the geometric structure and properties of the 3d transition metal atom doped endohedral fullerene M@C20F20 (M = Sc–Ni)

    International Nuclear Information System (INIS)

    Chun-Mei, Tang; Wei-Hua, Zhu; Kai-Ming, Deng

    2010-01-01

    This paper uses the generalised gradient approximation based on density functional theory to analyse the geometric structure and properties of the 3d transition metal atom doped endohedral fullerene M@C 20 F 20 (M = Sc–Ni). The geometric optimization shows that the cage centre is the most stable position for M, forming the structure named as M@C 20 F 20 -4. The inclusion energy, zero-point energy, and energy gap calculations tell us that N@C 20 F 20 -4 should be thermodynamically and kinetically stablest. M@C 20 F 20 -4 (M = Sc–Co) possesses high magnetic moments varied from 1 to 6 μ B , while Ni@C 20 F 20 -4 is nonmagnetic. The Ni–C bond in Ni@C 20 F 20 -4 contains both the covalent and ionic characters

  15. Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

    Science.gov (United States)

    Heshmat, Mojgan; Privalov, Timofei

    2017-07-06

    By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H 2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C 6 F 5 ) 3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H 2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H 2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H 2 splitting at the carbonyl carbon atom of (C 6 F 5 ) 3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C 6 F 5 ) 3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C 6 F 5 ) 3 B, as a catalyst, namely, 1) the step of H 2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C 6 F 5 ) 3 B-ketone adducts in which (C 6 F 5 ) 3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C 6 F 5 ) 3 B-alkoxide intermediate giving the (C 6 F 5 ) 3 B-alcohol adduct, and 3) the S N 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis.

    Science.gov (United States)

    Kamachi, Takashi; Yoshizawa, Kazunari

    2016-02-22

    A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.

  17. 3,3-Dimethylacylthioureas: "S", "-S", "U" or "W" Conformation?

    Directory of Open Access Journals (Sweden)

    M. Piris

    2000-03-01

    Full Text Available We report a study of 3,3-dimethyl substituted acylthioureas. X ray data and quantum mechanical calculations demonstrated that the "S" conformation is the most stable both for the acylthioureas and the corresponding anions. The high regioselectivity towards S-alkylation is explained on the basis of the localization of the HOMO mainly over the sulfur atom.

  18. Molecular conformation and liquid structure of 2-propanol through ...

    Indian Academy of Sciences (India)

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to ... 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky ... A Sahoo1 S Sarkar1 P S R Krishna2 R N Joarder1.

  19. Effective inclusion of polarization effects in calculations of the oscillator strengths and transition energies in atoms and molecules using the equation-of-motion method

    International Nuclear Information System (INIS)

    Glushkov, A.V.; Kol'tsova, N.Yu.

    1994-01-01

    Equations of motion were solved by a modified method in a quasi-particle representation of the density functional taking into account the most important polarization effects, including the so-called 2p-2h two-particle-two-hole interactions. Based on these calculations, spectroscopic data on energies and oscillator strengths of the helium atom (the test computation), carbon monoxide, nitrogen molecule, and ethylene are presented that refine some previously reported experimental and theoretical results. It is shown that in some cases the inclusion of polarization corrections introduced by 2p-2h effects is of basic importance because it provides up to ∼30% contribution to the energies and oscillator strengths. 23 refs., 5 tabs

  20. Atomic polarizabilities

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  1. Atomic polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-22

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

  2. Atomic physics

    CERN Document Server

    Foot, Christopher J

    2007-01-01

    This text will thoroughly update the existing literature on atomic physics. Intended to accompany an advanced undergraduate course in atomic physics, the book will lead the students up to the latest advances and the applications to Bose-Einstein Condensation of atoms, matter-wave inter-ferometry and quantum computing with trapped ions. The elementary atomic physics covered in the early chapters should be accessible to undergraduates when they are first introduced to the subject. To complement. the usual quantum mechanical treatment of atomic structure the book strongly emphasizes the experimen

  3. Tunable electronic and magnetic properties in germanene by alkali, alkaline-earth, group III and 3d transition metal atom adsorption.

    Science.gov (United States)

    Li, Sheng-shi; Zhang, Chang-wen; Ji, Wei-xiao; Li, Feng; Wang, Pei-ji; Hu, Shu-jun; Yan, Shi-shen; Liu, Yu-shen

    2014-08-14

    We performed first-principles calculations to study the adsorption characteristics of alkali, alkali-earth, group III, and 3d transition-metal (TM) adatoms on germanene. We find that the adsorption of alkali or alkali-earth adatoms on germanene has minimal effects on geometry of germanene. The significant charge transfer from alkali adatoms to germanene leads to metallization of germanene, whereas alkali-earth adatom adsorption, whose interaction is a mixture of ionic and covalent, results in semiconducting behavior with an energy gap of 17-29 meV. For group III adatoms, they also bind germanene with mixed covalent and ionic bonding character. Adsorption characteristics of the transition metals (TMs) are rather complicated, though all TM adsorptions on germanene exhibit strong covalent bonding with germanene. The main contributions to the strong bonding are from the hybridization between the TM 3d and Ge pz orbitals. Depending on the induced-TM type, the adsorbed systems can exhibit metallic, half-metallic, or semiconducting behavior. Also, the variation trends of the dipole moment and work function with the adsorption energy across the different adatoms are discussed. These findings may provide a potential avenue to design new germanene-based devices in nanoelectronics.

  4. Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations

    Science.gov (United States)

    Najbauer, Eszter E.; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

    2018-01-01

    The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, 6 conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-live of (3.7±0.5)·103 s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser induced conversions revealed that the excitation of the stretching overtone of both the side-chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations. PMID:26201050

  5. Atomic displacements in bcc dilute alloys

    Indian Academy of Sciences (India)

    We present here a systematic investigation of the atomic displacements in bcc transition metal (TM) dilute alloys. We have calculated the atomic displacements in bcc (V, Cr, Fe, Nb, Mo, Ta and W) transition metals (TMs) due to 3d, 4d and 5d TMs at the substitutional site using the Kanzaki lattice static method. Wills and ...

  6. Analysis of conformations and ESR spectra of free radicals in carbohydrates

    International Nuclear Information System (INIS)

    Abaghyan, G.V.; Abaghyan, A.G.; Apresyan, A.S.

    1998-01-01

    The conformations of free radicals arising when the unpaired electron is localized on carbon atoms in pyranose ring of carbohydrate molecule are considered. On the base of the analysis of expected conformations of radicals a possible contribution of β-protons in hyperfine structure of ESP spectra is predicted. The results of conformational analysis for different types of free radicals are in satisfactory agreement with the corresponding experimental data for the liquid phase. 17 refs

  7. Atomic physics

    International Nuclear Information System (INIS)

    Armbruster, P.; Beyer, H.; Bosch, F.; Dohmann, H.D.; Kozhuharov, C.; Liesen, D.; Mann, R.; Mokler, P.H.

    1984-01-01

    The heavy ion accelerator UNILAC is well suited to experiments in the field of atomic physics because, with the aid of high-energy heavy ions atoms can be produced in exotic states - that is, heavy atoms with only a few electrons. Also, in close collisions of heavy ions (atomic number Z 1 ) and heavy target atoms (Z 2 ) short-lived quasi-atomic 'superheavy' systems will be formed - huge 'atoms', where the inner electrons are bound in the field of the combined charge Z 1 + Z 2 , which exceeds by far the charge of the known elements (Z <= 109). Those exotic or transient superheavy atoms delivered from the heavy ion accelerator make it possible to study for the first time in a terrestrial laboratory exotic, but fundamental, processes, which occur only inside stars. Some of the basic research carried out with the UNILAC is discussed. This includes investigation of highly charged heavy atoms with the beam-foil method, the spectroscopy of highly charged slow-recoil ions, atomic collision studies with highly ionised, decelerated ions and investigations of super-heavy quasi-atoms. (U.K.)

  8. Potential Energy Surfaces for Reactions of X Metal Atoms (X = Cu, Zn, Cd, Ga, Al, Au, or Hg with YH4 Molecules (Y = C, Si, or Ge and Transition Probabilities at Avoided Crossings in Some Cases

    Directory of Open Access Journals (Sweden)

    Octavio Novaro

    2012-01-01

    Full Text Available We review ab initio studies based on quantum mechanics on the most important mechanisms of reaction leading to the C–H, Si–H, and Ge–H bond breaking of methane, silane, and germane, respectively, by a metal atom in the lowest states in Cs symmetry: X(2nd excited state, 1st excited state and ground state + YH4→ H3XYH → H + XYH3 and XH + YH3. with X = Au, Zn, Cd, Hg, Al, and G, and Y = C, Si, and Ge. Important issues considered here are (a the role that the occupation of the d-, s-, or p-shells of the metal atom plays in the interactions with a methane or silane or germane molecule, (b the role of either singlet or doublet excited states of metals on the reaction barriers, and (c the role of transition probabilities for different families of reacting metals with these gases, using the H–X–Y angle as a reaction coordinate. The breaking of the Y–H bond of YH4 is useful in the production of amorphous hydrogenated films, necessary in several fields of industry.

  9. Valence correlation in the s2d/sup n/, sd/sup n/+1, and d/sup n/+2 states of the first-row transition metal atoms

    International Nuclear Information System (INIS)

    Botch, B.H.; Dunning, T.H. Jr.; Harrison, J.F.

    1981-01-01

    The major differential valence correlation effects of the lowest lying states arising from the s 2 d/sup n/, sd/sup n/+1, and d/sup n/+2 configurations of the first-row transition metal atoms have been characterized using MCSCF and CI procedures. The important correlation effects are found to be, first, angular correlation of the 4s 2 pair arising because of the near degeneracy of the 4s and 4p orbitals and, second, radial correlation of the 3d electron pairs. This large differential radial correlation of the 3d electrons can be interpreted as being due to nonequivalent d orbitals in the sd/sup n/+1 and d/sup n/+2 excited states. Both of these effects can be incorporated into a simple MCSCF wave function that reduces the error in the excited state atomic dissociation limits (approx.0.2 eV in Sc--Cr and approx.0.5 eV in Mn--Cu for the sd/sup n/+1--s 2 d/sup n/ excitation energy), yet still is of a form which lends itself easily to molecular calculations

  10. Ultracold atoms on atom chips

    DEFF Research Database (Denmark)

    Krüger, Peter; Hofferberth, S.; Haller, E.

    2005-01-01

    Miniaturized potentials near the surface of atom chips can be used as flexible and versatile tools for the manipulation of ultracold atoms on a microscale. The full scope of possibilities is only accessible if atom-surface distances can be reduced to microns. We discuss experiments in this regime...

  11. Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.

    Science.gov (United States)

    Pancera, Marie; Majeed, Shahzad; Ban, Yih-En Andrew; Chen, Lei; Huang, Chih-chin; Kong, Leopold; Kwon, Young Do; Stuckey, Jonathan; Zhou, Tongqing; Robinson, James E; Schief, William R; Sodroski, Joseph; Wyatt, Richard; Kwong, Peter D

    2010-01-19

    The viral spike of HIV-1 is composed of three gp120 envelope glycoproteins attached noncovalently to three gp41 transmembrane molecules. Viral entry is initiated by binding to the CD4 receptor on the cell surface, which induces large conformational changes in gp120. These changes not only provide a model for receptor-triggered entry, but affect spike sensitivity to drug- and antibody-mediated neutralization. Although some of the details of the CD4-induced conformational change have been visualized by crystal structures and cryoelectron tomograms, the critical gp41-interactive region of gp120 was missing from previous atomic-level characterizations. Here we determine the crystal structure of an HIV-1 gp120 core with intact gp41-interactive region in its CD4-bound state, compare this structure to unliganded and antibody-bound forms to identify structurally invariant and plastic components, and use ligand-oriented cryoelectron tomograms to define component mobility in the viral spike context. Newly defined gp120 elements proximal to the gp41 interface complete a 7-stranded beta-sandwich, which appeared invariant in conformation. Loop excursions emanating from the sandwich form three topologically separate--and structurally plastic--layers, topped off by the highly glycosylated gp120 outer domain. Crystal structures, cryoelectron tomograms, and interlayer chemistry were consistent with a mechanism in which the layers act as a shape-changing spacer, facilitating movement between outer domain and gp41-associated beta-sandwich and providing for conformational diversity used in immune evasion. A "layered" gp120 architecture thus allows movement among alternative glycoprotein conformations required for virus entry and immune evasion, whereas a beta-sandwich clamp maintains gp120-gp41 interaction and regulates gp41 transitions.

  12. Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins.

    Science.gov (United States)

    Firman, Taylor; Ghosh, Kingshuk

    2018-03-28

    We present an analytical theory to compute conformations of heteropolymers-applicable to describe disordered proteins-as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence-while maintaining the same charge composition-can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar composition of positive and negative charges. Based on this, we provide a new diagram-of-states delineating the sequence-conformation relation for proteins in the DisProt database. Next, we study the effect of post-translational modification, e.g., phosphorylation, on IDP conformations. Modifications as little as two-site phosphorylation can significantly alter the size of an IDP with everything else being constant (temperature, salt concentration, etc.). However, not all possible modification sites have the same effect on protein conformations; there are certain "hot spots" that can cause maximal change in conformation. The location of these "hot spots" in the parent sequence can readily be identified by using a sequence charge decoration metric originally introduced by Sawle and Ghosh. The ability of our model to predict conformations (both expanded and collapsed states) of IDPs at a high

  13. Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins

    Science.gov (United States)

    Firman, Taylor; Ghosh, Kingshuk

    2018-03-01

    We present an analytical theory to compute conformations of heteropolymers—applicable to describe disordered proteins—as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence—while maintaining the same charge composition—can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar composition of positive and negative charges. Based on this, we provide a new diagram-of-states delineating the sequence-conformation relation for proteins in the DisProt database. Next, we study the effect of post-translational modification, e.g., phosphorylation, on IDP conformations. Modifications as little as two-site phosphorylation can significantly alter the size of an IDP with everything else being constant (temperature, salt concentration, etc.). However, not all possible modification sites have the same effect on protein conformations; there are certain "hot spots" that can cause maximal change in conformation. The location of these "hot spots" in the parent sequence can readily be identified by using a sequence charge decoration metric originally introduced by Sawle and Ghosh. The ability of our model to predict conformations (both expanded and collapsed states) of IDPs at

  14. Crystal structures and conformers of CyMe4-BTBP

    Directory of Open Access Journals (Sweden)

    Lyczko Krzysztof

    2015-12-01

    Full Text Available The crystal structure of new conformation of the CyMe4-BTBP ligand (ttc has been presented. The ttt conformer of this compound in a form of THF solvate has been also crystallized. The geometries of six possible conformations (ttt, ttc, tct, tcc, ctc and ccc of the CyMe4-BTBP ligand have been modeled in the gas phase and in solutions (MeOH and H2O by DFT calculations using B3LYP/6-31G(d,p method. According to the calculations, in the three different media the conformers with trans orientation of the N atoms in the bipyridyl moiety are the most stable.

  15. Conformational Study of Taurine in the Gas Phase

    Science.gov (United States)

    Cortijo, Vanessa; Sanz, M. Eugenia; López, Juan C.; Alonso, José L.

    2009-08-01

    The conformational preferences of the amino sulfonic acid taurine (NH2-CH2-CH2-SO3H) have been investigated in the gas phase by laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) in the 6-14 GHz frequency range. One conformer has been observed, and its rotational, centrifugal distortion, and hyperfine quadrupole coupling constants have been determined from the analysis of its rotational spectrum. Comparison of the experimental constants with those calculated theoretically identifies the detected conformer unambiguously. The observed conformer of taurine is stabilized by an intramolecular hydrogen bond O-H···N between the hydrogen of the sulfonic acid group and the nitrogen atom of the amino group.

  16. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

    Science.gov (United States)

    Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2017-06-05

    Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Rotational Spectrum, Conformational Composition, and Quantum Chemical Calculations of Cyanomethyl Formate (HC(O)OCH2C≡N), a Compound of Potential Astrochemical Interest.

    Science.gov (United States)

    Samdal, Svein; Møllendal, Harald; Carles, Sophie

    2015-08-27

    The rotational spectrum of cyanomethyl formate (HC(O)OCH2C≡N) has been recorded in the 12–123 GHz spectral range. The spectra of two conformers were assigned. The rotamer denoted I has a symmetry plane and two out-of plane hydrogen atoms belonging to the cyanomethyl (CH2CN) moiety. In the conformer called II, the cyanomethyl group is rotated 80.3° out of this plane. Conformer I has an energy that is 1.4(6) kJ/mol lower than the energy of II according to relative intensity measurements. A large number of rotational transitions have been assigned for the ground and vibrationally excited states of the two conformers and accurate spectroscopic constants have been obtained. These constants should predict frequencies of transitions outside the investigated spectral range with a very high degree of precision. It is suggested that cyanomethyl formate is a potential interstellar compound. This suggestion is based on the fact that its congener methyl formate (HC(O)OCH3) exists across a large variety of interstellar environments and the fact that cyanides are very prevalent in the Universe. The experimental work has been augmented by high-level quantum chemical calculations. The CCSD/cc-pVQZ calculations are found to predict structures of the two forms that are very close to the Born–Oppenheimer equilibrium structures. MP2/cc-pVTZ predictions of several vibration–rotation interaction constants were generally found to be rather inaccurate. A gas-phase reaction between methyl formate and the cyanomethyl radical CH2CN to produce a hydrogen atom and cyanomethyl formate was mimicked using MP2/cc-pVTZ calculations. It was found that this reaction is not favored thermodynamically. It is also conjectured that the possible formation of cyanomethyl formate might be catalyzed and take place on interstellar particles.

  18. Conformational analysis by intersection: CONAN.

    Science.gov (United States)

    Smellie, Andrew; Stanton, Robert; Henne, Randy; Teig, Steve

    2003-01-15

    As high throughput techniques in chemical synthesis and screening improve, more demands are placed on computer assisted design and virtual screening. Many of these computational methods require one or more three-dimensional conformations for molecules, creating a demand for a conformational analysis tool that can rapidly and robustly cover the low-energy conformational spaces of small molecules. A new algorithm of intersection is presented here, which quickly generates (on average heuristics are applied after intersection to generate a small representative collection of conformations that span the conformational space. In a study of approximately 97,000 randomly selected molecules from the MDDR, results are presented that explore these conformations and their ability to cover low-energy conformational space. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 24: 10-20, 2003

  19. Conformal superalgebras via tractor calculus

    Science.gov (United States)

    Lischewski, Andree

    2015-01-01

    We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure that has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

  20. A new method to induce transitions in muonic atoms using a high-power tunable dye laser coupled to a stopping muon beam

    CERN Document Server

    Bertin, A; Duclos, J; Gastaldi, Ugo; Gorini, G; Neri, G; Picard, J; Pitzurra, O; Placci, A; Polacco, E; Stefanini, G; Torelli, G; Vitale, A; Zavattini, E

    1974-01-01

    An apparatus is described in which a ruby-pumped dye laser is used to induce transitions from the 2S to the 2P levels of the muonic ion ( mu He)/sup +/. The dye laser supplies infra-red radiation pulses in the wavelengths (8040-8180) AA, at typical repetition rates of 1 pulse every 4 s, with an energy release per pulse of 300 mJ for 1.2 J pumping energy. A special synchronization procedure is followed to trigger the laser in close coupling with the incoming muon beam which is stopped in a helium target at pressures between 40 and 50 atm. The other performances of the device are fully discussed with reference both to the laser facility and to the special high-pressure helium target. (23 refs).

  1. The monomer-to-dimer transition and bimodal growth of Co-salen on NaCl(001): a high resolution atomic force microscopy study

    International Nuclear Information System (INIS)

    Fremy, S; Schwarz, A; Laemmle, K; Wiesendanger, R; Prosenc, M

    2009-01-01

    Molecules of Co-salen, a paramagnetic metal-organic Schiff base complex, self-assemble into two different well ordered morphologies on a NaCl(001) substrate: nanowires, which form networks, and compact nanocrystallites. Their growth can be controlled by adjusting the deposition parameters. It turns out that the nanowires are metastable. Molecular resolution images suggest that the packing in both morphologies is the same as in bulk Co-salen single crystals. Only the orientation of the c-axis with respect to the substrate is different. The origin of this intriguing bimodal growth is associated with a monomer-to-dimer transition, which probably takes place during initial nucleation at step edges.

  2. The monomer-to-dimer transition and bimodal growth of Co-salen on NaCl(001): a high resolution atomic force microscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Fremy, S; Schwarz, A; Laemmle, K; Wiesendanger, R [Institute of Applied Physics and Microstructure Research Center, University of Hamburg, Jungiusstrasse 11, 20355 Hamburg (Germany); Prosenc, M, E-mail: aschwarz@physnet.uni-hamburg.d [Institute of Inorganic and Applied Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg (Germany)

    2009-10-07

    Molecules of Co-salen, a paramagnetic metal-organic Schiff base complex, self-assemble into two different well ordered morphologies on a NaCl(001) substrate: nanowires, which form networks, and compact nanocrystallites. Their growth can be controlled by adjusting the deposition parameters. It turns out that the nanowires are metastable. Molecular resolution images suggest that the packing in both morphologies is the same as in bulk Co-salen single crystals. Only the orientation of the c-axis with respect to the substrate is different. The origin of this intriguing bimodal growth is associated with a monomer-to-dimer transition, which probably takes place during initial nucleation at step edges.

  3. Current Capability of Atomic Structure Theory

    International Nuclear Information System (INIS)

    Kim, Yong Ki

    1993-01-01

    Current capability of atomic structure theory is reviewed, and advantages, disadvantages and major features of popular atomic structure codes described. Comparisons between theoretical and experimental data on transition energies and lifetimes of excited levels are presented to illustrate the current capability of atomic structure codes.

  4. Classical extended conformal symmetries

    International Nuclear Information System (INIS)

    Viswanathan, R.

    1990-02-01

    Extensions of the Virasoro algebra are constructed as Poisson brackets of higher spin fields which appear as coefficient fields in certain covariant derivative operators of order N. These differential operators are constructed so as to be covariant under reparametrizations on fields of definite conformal dimension. Factorization of such an N-th order operator in terms of first order operators, together with the inclusion of a spin one U(1) current, is shown to lead to a two-parameter W-algebra. One of these parameters plays the role of interpolating between W-algebras based on different Lie algebras of the same rank. (author). 11 refs

  5. Atomic Layer Deposition to Enable the Production, Optimization and Protection of Spaceflight Hardware

    Data.gov (United States)

    National Aeronautics and Space Administration — Atomic Layer Deposition (ALD) a cost effective nano-manufacturing technique allows for the conformal coating of substrates with atomic control in a benign...

  6. Atomic Layer Deposition to Enable the Production, Optimization and Protection of Spaceflight Hardware Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Atomic Layer Deposition (ALD) a cost effective nano-manufacturing technique allows for the conformal coating of substrates with atomic control in a benign...

  7. Ubiquitous atom

    International Nuclear Information System (INIS)

    Spruch, G.M.; Spruch, L.

    1974-01-01

    The fundamentals of modern physics, including the basic physics and chemistry of the atom, elementary particles, cosmology, periodicity, and recent advances, are surveyed. The biology and chemistry of the life process is discussed to provide a background for considering the effects of atomic particles on living things. The uses of atomic power in space travel, merchant shipping, food preservation, desalination, and nuclear clocks are explored. (Pollut. Abstr.)

  8. Two-dimensional atom localization via probe absorption in a four-level atomic system

    International Nuclear Information System (INIS)

    Wang Zhi-Ping; Ge Qiang; Ruan Yu-Hua; Yu Ben-Li

    2013-01-01

    We have investigated the two-dimensional (2D) atom localization via probe absorption in a coherently driven four-level atomic system by means of a radio-frequency field driving a hyperfine transition. It is found that the detecting probability and precision of 2D atom localization can be significantly improved via adjusting the system parameters. As a result, our scheme may be helpful in laser cooling or the atom nano-lithography via atom localization

  9. Conformally symmetric traversable wormholes

    International Nuclear Information System (INIS)

    Boehmer, Christian G.; Harko, Tiberiu; Lobo, Francisco S. N.

    2007-01-01

    Exact solutions of traversable wormholes are found under the assumption of spherical symmetry and the existence of a nonstatic conformal symmetry, which presents a more systematic approach in searching for exact wormhole solutions. In this work, a wide variety of solutions are deduced by considering choices for the form function, a specific linear equation of state relating the energy density and the pressure anisotropy, and various phantom wormhole geometries are explored. A large class of solutions impose that the spatial distribution of the exotic matter is restricted to the throat neighborhood, with a cutoff of the stress-energy tensor at a finite junction interface, although asymptotically flat exact solutions are also found. Using the 'volume integral quantifier', it is found that the conformally symmetric phantom wormhole geometries may, in principle, be constructed by infinitesimally small amounts of averaged null energy condition violating matter. Considering the tidal acceleration traversability conditions for the phantom wormhole geometry, specific wormhole dimensions and the traversal velocity are also deduced

  10. Supergravitational conformal Galileons

    Science.gov (United States)

    Deen, Rehan; Ovrut, Burt

    2017-08-01

    The worldvolume actions of 3+1 dimensional bosonic branes embedded in a five-dimensional bulk space can lead to important effective field theories, such as the DBI conformal Galileons, and may, when the Null Energy Condition is violated, play an essential role in cosmological theories of the early universe. These include Galileon Genesis and "bouncing" cosmology, where a pre-Big Bang contracting phase bounces smoothly to the presently observed expanding universe. Perhaps the most natural arena for such branes to arise is within the context of superstring and M -theory vacua. Here, not only are branes required for the consistency of the theory, but, in many cases, the exact spectrum of particle physics occurs at low energy. However, such theories have the additional constraint that they must be N = 1 supersymmetric. This motivates us to compute the worldvolume actions of N = 1 supersymmetric three-branes, first in flat superspace and then to generalize them to N = 1 supergravitation. In this paper, for simplicity, we begin the process, not within the context of a superstring vacuum but, rather, for the conformal Galileons arising on a co-dimension one brane embedded in a maximally symmetric AdS 5 bulk space. We proceed to N = 1 supersymmetrize the associated worldvolume theory and then generalize the results to N = 1 supergravity, opening the door to possible new cosmological scenarios

  11. Atomic physics

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Research activities in atomic physics at Lawrence Berkeley Laboratory during 1976 are described. Topics covered include: experiments on stored ions; test for parity violation in neutral weak currents; energy conservation and astrophysics; atomic absorption spectroscopy, atomic and molecular detectors; theoretical studies of quantum electrodynamics and high-z ions; atomic beam magnetic resonance; radiative decay from the 2 3 Po, 2 levels of helium-like argon; quenching of the metastable 2S/sub 1/2/ state of hydrogen-like argon in an external electric field; and lifetime of the 2 3 Po level of helium-like krypton

  12. An Expression of Periodic Phenomena of Fashion on Sexual Selection Model with Conformity Genes and Memes

    Science.gov (United States)

    Mutoh, Atsuko; Tokuhara, Shinya; Kanoh, Masayoshi; Oboshi, Tamon; Kato, Shohei; Itoh, Hidenori

    It is generally thought that living things have trends in their preferences. The mechanism of occurrence of another trends in successive periods is concerned in their conformity. According to social impact theory, the minority is always exists in the group. There is a possibility that the minority make the transition to the majority by conforming agents. Because of agent's promotion of their conform actions, the majority can make the transition. We proposed an evolutionary model with both genes and memes, and elucidated the interaction between genes and memes on sexual selection. In this paper, we propose an agent model for sexual selection imported the concept of conformity. Using this model we try an environment where male agents and female agents are existed, we find that periodic phenomena of fashion are expressed. And we report the influence of conformity and differentiation on the transition of their preferences.

  13. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. In silico Exploration of the Conformational Universe of GPCRs.

    Science.gov (United States)

    Rodríguez-Espigares, Ismael; Kaczor, Agnieszka A; Selent, Jana

    2016-07-01

    The structural plasticity of G protein coupled receptors (GPCRs) leads to a conformational universe going from inactive to active receptor states with several intermediate states. Many of them have not been captured yet and their role for GPCR activation is not well understood. The study of this conformational space and the transition dynamics between different receptor populations is a major challenge in molecular biophysics. The rational design of effector molecules that target such receptor populations allows fine-tuning receptor signalling with higher specificity to produce drugs with safer therapeutic profiles. In this minireview, we outline highly conserved receptor regions which are considered determinant for the establishment of distinct receptor states. We then discuss in-silico approaches such as dimensionality reduction methods and Markov State Models to explore the GPCR conformational universe and exploit the obtained conformations through structure-based drug design. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

    Directory of Open Access Journals (Sweden)

    Jonathan Maiangwa

    2017-05-01

    Full Text Available The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent

  16. Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models.

    Science.gov (United States)

    Lindner, Benjamin; Yi, Zheng; Prinz, Jan-Hendrik; Smith, Jeremy C; Noé, Frank

    2013-11-07

    The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. Noé, S. Doose, I. Daidone, M. Löllmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. This procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.

  17. Growth of transition metal oxides in 2D layers : probing and tuning the properties of matter at the atomic-scale

    International Nuclear Information System (INIS)

    Obermüller, T.

    2015-01-01

    In surface science, accurate controlling and detailed characterization of metal supported ultrathin film growth of transition metal oxides (TMO) is a central requirement for collecting reliable empirical data which in turn can be used to improve and extend the existing theoretical models and approaches, such as density functional theory (DFT). In this work, the controlled growth of TMOs on the Ag(100) surface is investigated by means of scanning tunneling microscopy (STM) in conjunction with various other surface science techniques. In addition, a novel promising experimental approach to effectively affect and control the growth of TMOs by high electric fields is presented. The investigations concerned the TMO systems MnxOy and WOx on the Ag(100) surface. The strikingly anisotropic growth of the (2x1)-MnO/Ag(100) system is characterized by long and narrow stripes which form a complex 2D surface network of MnO islands. The growth mechanism of this system has been rationalized by first-principle DFT calculations. The (WO3)3 clusters deposited at room temperature form ramified fractal islands. Above a threshold temperature of 700 K, a fully intact 2D WOx wetting layer emerges at the surface. On top of this layer, beginning 3D growth in form of sharp needles is observed. Since the area of the wetting layer exceeds the nanometer-scale (up to 1 µm), also low energy electron microscopy (LEEM) has been employed to study the growth kinetics of the WOx/Ag(100) system. Strong electric field experiments (1-2 V/nm) have been performed on both systems by employing a custom-designed UHV apparatus. Significant field-induces surface modifications have been observed in all experiments, and have been characterized by STM and Auger electron spectroscopy. (author) [de

  18. Self-lacing atom chains

    International Nuclear Information System (INIS)

    Zandvliet, Harold J W; Van Houselt, Arie; Poelsema, Bene

    2009-01-01

    The structural and electronic properties of self-lacing atomic chains on Pt modified Ge(001) surfaces have been studied using low-temperature scanning tunnelling microscopy and spectroscopy. The self-lacing chains have a cross section of only one atom, are perfectly straight, thousands of atoms long and virtually defect free. The atomic chains are composed of dimers that have their bonds aligned in a direction parallel to the chain direction. At low temperatures the atomic chains undergo a Peierls transition: the periodicity of the chains doubles from a 2 x to a 4 x periodicity and an energy gap opens up. Furthermore, at low temperatures (T<80 K) novel quasi-one-dimensional electronic states are found. These quasi-one-dimensional electronic states originate from an electronic state of the underlying terrace that is confined between the atomic chains.

  19. Eberhard Widmann (Stefan Meyer Institute, Vienna) and Silke Federmann (Ph.D. Student from Vienna in the CERN-Austrian Ph.D. program) together with a microwave cavity developed by Silke at CERN. The cavity will be used for the first time to look for spin-flip transitions of antihydrogen atoms later this year.

    CERN Multimedia

    Maximilien Brice

    2011-01-01

    Eberhard Widmann (Stefan Meyer Institute, Vienna) and Silke Federmann (Ph.D. Student from Vienna in the CERN-Austrian Ph.D. program) together with a microwave cavity developed by Silke at CERN. The cavity will be used for the first time to look for spin-flip transitions of antihydrogen atoms later this year.

  20. Improvements to robotics-inspired conformational sampling in rosetta.

    Directory of Open Access Journals (Sweden)

    Amelie Stein

    Full Text Available To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new "next-generation KIC" method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.